W3C Wiki - User contributions [en]

HCLS/SWAT4LS2012/Hackathon

Ewilligh — Wed, 28 Nov 2012 06:44:14 GMT

Ewilligh: /* (Mini) Program */

The SWAT4LS Hackathon is an informal event associated with the [http://swat4ls.org/ SWAT4LS] Semantic Web Applications and Tools for Life Sciences Workshops Series.

Scope of the event is to bring together experts and enthusiasts in the application of semantic technologies in healthcare and life science for open discussion and jam coding sessions.
The Hackathon will be organized on the 28th of November 2012 at [http://lacantine.org/ La Cantine, Paris] ([https://maps.google.com/maps?q=12+Galerie+Montmartre+75002+france&hl=en&ie=UTF8&ll=48.870438,2.342089&spn=0.0013,0.001869&sll=48.87053,2.342319&sspn=0.002601,0.003739&t=h&hnear=12+Galerie+Montmartre,+75002+Paris,+%C3%8Ele-de-France,+France&z=19 map]).

street: 151 rue Montmartre, Passage des Panoramas
room: 12 Galerie Montmartre
75002 Paris

(For more information, please refer to the [http://www.swat4ls.org/workshops/paris2012/| workshop website]).
The hackathon is open to workshop participants. Registration is required and space is limited!.

== (Mini) Program ==
Hackathon starts at 9.00

* 09.00-09.30 - Welcome, registrations, informall introductions
* 09.30-10.30 - Project proposals by group leads (to be confirmed).
* 10.30-16.00 - Hack Hack Hacak (with Pizza break. There will be coffee).
* 16.00-18.00 - Presentations on what has been done, ideas, problems found, next steps

== Logistics ==
Projects and institutes attending include:
* Open PHACTS (http://www.openphacts.org)
* WikiPathways (http://www.wikipathways.org/index.php/WikiPathways)
* The Database Center for Life Sciences/BioHackathon (http://dbcls.rois.ac.jp/en/ http://www.biohackathon.org/)
* The W3C Consortium, Health Care and Life Sciences Interest Group ([[HCLS]])
* BioPAX (http://biopax.org)
* European Bioinformatics Institute (http://www.ebi.ac.uk)
* Web Science Trust Network of Labs (WSTNet) (http://webscience.org)

While the agenda will be open, we are coordinating ideas that can be developd at the network in advance, to maximize the utility of the day. Co-organizers for each community will help gathering ideas and finding point of contacts.

=== Information and registrations ===
For information, [mailto:info@swat4ls.org| info _at_ swat4ls.org]

Registrations are handled via [http://swat4ls-2012.eventbrite.com/| Eventbrite]

=== Hashtag ===
[https://twitter.com/search/realtime?q=%23swat4lshack #swat4lshack]

=== Co-Organizers ===
* Andrea Splendiani
* Andra Waagmeester
* Eric Prud'hommeaux
* M. Scott Marshall
* Toshiaki Katayama
* Ismael Navas delgado

== Open PHACTS community ==

=== Contact Point ===
* Andra Waagmeester
* Egon Willighagen

=== Proposed action points ===
# Consume [http://www.openphacts.org Open PHACTS] content in Pathway tools
# Using http://identifiers.org
# Create an example set of valuable queries
# Visualizing output
# work on further linked data integration, with possible:
## [https://ntp.niehs.nih.gov/drugmatrix/ DrugMatrix]
## [http://toxico.nibio.go.jp/open-tggates/ TG-GATEs]
## [http://thedatahub.org/nl/dataset/bio2rdf-ctd CTD] (already available as RDF, by Bio2RDF)
# shared Java client code
## for R, Bioclipse, KNIME

=== Confirmed Participants ===
* Kees Burger
* Maria Carmen Carra
* Ian Dunlop
* Chris Evelo
* Paul Groth
* Tim Harder
* Carina Haupt
* Nick Juty
* Camille Laibe
* Antonis Loizou
* Oriol Lopez
* Guillermo C. Martínez
* Nuria Queralt
* Rishi Ramgolam
* Mark Thompson
* Egon Willighagen
* Pekka Kohonen
* Ola Spjuth
* Thompson Mark (Andra)
* coulet adrien (Michel)
* Malone James (Michel)
* Dumontier Michel
* Kocbek Simon (Andrea)
* Luciano Joanne
* Jiang Guoqian (Scott)
* van Haagen Herman
* Leroux Hugo
* Garcia Leyla (Michel)
* Adamusiak Tomasz
* Jupp Simon (Michel)
* Mironov Vladimir (Andrea)
* Kamsu Foguem Bernard
* Schouwen, van Reinout (Scott)
* Yamamoto Yasunori (Andrea)
* Groth Paul (Andra)
* Helma Christoph (Egon)
* Larmande Pierre
* Whetzel Trish (Scott)
* Navas-Delgado Ismael (Andrea)
* Katayama Toshiaki (Andrea)
* Lysenko Artem (Andrea)
* Paschke Adrian (Andrea)
* Helma Christoph
* Alam Mehwish
* van dam Jesse
* Croset Samuel (Andrea)
* Helma Christoph
* Chris Evelo (Andra)
* Martina Kutmon (Andra)
* Alex Pico (Andra)

== WikiPathways community ==

=== Contact Point ===
Andra Waagmeester

=== Introduction ===
[http://www.wikipathways.org/index.php/WikiPathways WikiPathways] is a online resource for pathways. Content is provided by the audience at large. I currently contains more then 2200 pathways from 21 species [http://sparqlbin.com/#4f91f23a032a87cc46c5a526a6da673a source]. Pathways are captured in a XML-based format [http://www.pathvisio.org/wiki/EverythingGpml GPML]. Recently WikiPathways was exposed as linked open data where GPML content was exported as RDF. This data is available through a SPARQL endpoint http://sparql.wikipathways.org.

=== Proposed action points ===
==== Exploring [http://www.wikipathways.org/index.php/WikiPathways WikiPathways] RDF content, making example queries ====
==== Writing federated queries to integrate pathway content with other biological data. ====
====Using [http://code.google.com/p/pathvisiorpc/ Pathvisio RPC] to consume and visualize linked pathway data====
====Solving ID mapping in WikiPathways RDF====

=== Confirmed Participants ===
* Chris Evelo
* Martina Kutmon
* Alex Pico

== Database Center for Life Sciences Community / BioHackathon ==

=== Contact Point ===
Toshiaki Katayama

=== Proposed action points ===

* Ontology for genome annotation
** https://github.com/dbcls/bh12/wiki/Feature-annotation-locations-in-RDF
** https://github.com/dbcls/bh12/wiki/Genome-RDF
** https://gist.github.com/3704296

* Identifiers.org dataset definitions in RDF
** https://gist.github.com/3985701
** https://gist.github.com/1672112
** https://dl.dropbox.com/u/429992/20121031-miriam.ttl

* Text-mining for microbial/environmental genomics

=== Confirmed Participants ===
* Yasunori Yamamoto
* Toshiaki Katayama

== W3C HCLS Community ==

=== Contact Point ===
Eric Prud'hommeaux

=== Proposed action points ===
==== Making an online inventory of available resources (wiki) to document underlying schemas of available datasources.====
There are nice lists of active SPARQL endpoints [http://www.freebase.com/view/base/sparql/views/sparql_endpoint (example 1)] and [http://labs.mondeca.com/sparqlEndpointsStatus/index.html (example 2)]. Finding where the data actually links can still be challenging.

It would be really beneficial to create an overview with descriptions of different linked data sets describing the underlying structure. The first step would be to define a format where data providers describe their data in a predefined (wiki) format. This format could be based on [http://www.w3.org/TR/void/ VoID].
These description coulds then be used to create so called data landscapes in tools such as [http://vsdlc3.blogspot.be/ Semscape].

====Creating a review of sparql endpoints and their support for remote federated queries. ====
Within a federated query you can query different flavours of sparql endpoints. Since different endpoints have their own implementations and support for different SPARQL versions, it is essential to understand the different issues each type of endpoint might have. The community would benefit from a list mentioning each available SPARQL endpoint system (e.g. 4store, virtuoso, etc) and their support for different SPARQL versions. Also this list could mention specific features (e.g. soft limit in 4store) influencing the recall in federated queries.

== BioPAX Community ==

=== Contact Point ===
Ismael Navas Delgado

=== Proposed action points ===

=== Confirmed Participants ===
* Ismael Navas Delgado
* Andrea Splendiani

== EBI Gene Expression Atlas ==

=== Contact Point ===
Simon Jupp

James Malone

=== Introduction ===

Integration of gene expression data from the Gene Expression Atlas database (http://www.ebi.ac.uk/gxa). Schema description and SPARQL endpoint at http://wwwdev.ebi.ac.uk/fgpt/efosemweb.html
Differential gene expression annotated with Ensembl gene ids (identifiers.org URIs), includes mappings to Uniprot. Experiment assay and sample descriptions annotated with ontology terms from wide range of
bio-ontologies (anatomy, cells, disease etc).

=== Proposed action points ===

Linking gene expression to pathway data.

== Web Science Trust Network of Labs (WSTNet) (http://webscience.org) ==

=== Contact Point ===

Joanne Luciano

=== Introduction ===

Health Web Science is an new discipline emerging from Web Science aimed at understanding the impact of the web on health and wellness. The Web Observatory (http://webscience.org/web-observatory/) is a global data resource for the advancement of economic & social prosperity. Sponsored by the Web Science Trust, a global not for profit institution with a secretariat at the University of Southampton that can leverage the web science research resources of the 15 University labs affiliated with the Web Science Trust (WSTnet) including Brazil, China, Korea, Europe and US, and the existing partnerships with W3C and the Web Foundation. The Web Observatory is in early stages and we will be looking to define and construct Heath and Life Science observations for Web Science research.
=== Proposed action points ===

Creating a Health Web Observatory

=== Confirmed Participants ===
* Joanne Luciano

== Bio2RDF r2 + SIO ==

=== Contact Point ===

Michel Dumontier

=== Introduction ===
Bio2RDF (http://bio2rdf.org) is an open source project that uses Semantic Web technologies to create and provide the largest network of Linked Data for the Life Sciences. At SWAT4LS we will present the 2nd release of the Bio2RDF project in which open-source scripts were updated and consolidated with GitHub, IRIs are mapped to canonical set using a new 2100+ dataset Life Sciences Registry, datasets are described along with summary statistics and provenance, and RDF files and Virtuoso databases are available for download or query. Bio2RDF also computes dataset connectivity that is compatible with SPARQLed, thus enabling assisted SPARQL queries and faceted searches using Virtuoso's native facet browser.

The Semanticscience Integrated Ontology (SIO) is a relatively new ontology that aims to facilitate the representation and integration of biological and biomedical data in a manner that is simpler and more flexible than other upper level ontologies. SIO considers three primary kinds of things : objects, processes and their attributes. It has over 180 object properties (1/2 are inverses) to more precisly describe the nature of the relationship, and a single datatype property to capture literals. SIO has been used to integrate over 700 SADI-based semantic web services and has been recently mapped to Bio2RDF types and relations to enable querying across similar and complementary datasets.

=== Proposed action points ===

Bio2RDF
* Discuss recent developments and future plans
* Develop overview web pages for each of the datasets, drawing from the LSR, dataset provenance and statistics
* Develop simple intra and inter-dataset queries to demonstrate the potential of each dataset

SIO
* Discuss basic structures & design patterns
* Discuss user-driven use cases (gene expression, aggregation functions, gene associations, nanopublications)

=== Confirmed Participants ===
* Michel Dumontier
* Alison Callahan
* Jose Cruz Toledo

== CDA and Clinical Trial Protocols to RDF ==

=== Contact Point ===

Eric Prud'hommeaux

=== Introduction ===
The [https://github.com/projectcypress/test-deck/blob/master/patients/c32/100_George_Skeritt.xml Project Cypress corpus test patients] provides a sizable group of patients with various characteristics, some of which may line up with some [[/TrialProtocols|Trial Protocols]]. This provides a good opportunity to demonstrate the power of expression protocols in a self-describing, machine-readable format, e.g. RDF.

=== Proposed action points ===

*code inclusion/exclusion criteria in popular terminologies (e.g. SNOMED, LOINC)
*code structural information in CDA model, e.g. diagnosis vs. prescribed treatment.
*map CDA to RDF a la [http://www.w3.org/wiki/HCLS/ClinicalObservationsInteroperability/TermInfo terminfo]
*match (subsets of) clincal trial criteria to patient records.

=== Confirmed Participants ===

== Resources ==
* PathwayCommons SPARQL endpoint. Endpoint over all BioPAX representations in PathwayCommons
* Cytoscape plugin to visualize and interact with RDF knwoledge bases (new!)
* BioQueries: social site to build SPARQL queries
* Open PHACTS rdf guidelines: http://www.openphacts.org/specs/2012/WD-rdfguide-20120823/

== Data Map ==

@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix wprdf: <http://rdf.wikipathways.org/> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix wp: <http://vocabularies.wikipathways.org/wp#> .
@prefix biopax: <http://www.biopax.org/release/biopax-level3.owl#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix gpml: <http://vocabularies.wikipathways.org/gpml#> .
@prefix chembl: <http://rdf.farmbio.uu.se/chembl/onto/#> .
@prefix up: <http://purl.uniprot.org/core/> .
@prefix dbpedia: <http://dbpedia.org/page/> .
@prefix pav: <http://purl.org/pav/> .
@prefix b2rreactome: <http://bio2rdf.org/reactome:>
@prefix b2rbiopax: <http://bio2rdf.org/ns/biopax#>
@prefix b2rbiopaxresource: <http://bio2rdf.org/biopax_resource:>
@prefix up: <http://purl.uniprot.org/core/>
@prefix sio: <http://semanticscience.org/resource/>
@prefix upcitation: <http://purl.uniprot.org/citations/>
@prefix prov: <http://www.w3.org/ns/prov#>
@prefix dc: <http://purl.org/dc/elements/1.1/> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix aot: <http://purl.org/ao/types/> .
@prefix aos: <http://purl.org/ao/selectors/> .
@prefix sso: <http://nlp2rdf.lod2.eu/schema/sso/> .
@prefix void: <http://rdfs.org/ns/void#> .
@prefix pao: <http://www.scai.fraunhofer.de/prominer/vocabular/pao#> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix pav: <http://purl.org/pav/> .
@prefix ao: <http://purl.org/ao/> .
@prefix str: <http://nlp2rdf.lod2.eu/schema/string/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix base: <http://www.scai.fraunhofer.de/rdf/intern/> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix scai: <http://www.scai.fraunhofer.de/rdf/entity/> .

<http://sparql.wikipathways.org> {
# Sparql endpoint: http://sparql.wikipathways.org
# Data: http://rdf.wikipathways.org
# 
<http://identifiers.org/ncbigene/1051> rdf:type wp:GeneProduct .
<http://identifiers.org/ncbigene/1051> dcterms:isPartOf wprdf:WP3 .
<http://identifiers.org/ncbigene/1051> rdfs:label "C/EBP-beta" .
wprdf:WP3 rdf:type wp:Pathway .
wp:Pathway skos:relatedMatch biopax:Pathway .
wprdf:WP3 rdfs:label "Keap1-Nrf2 Pathway" .
wprdf:WP3 dcterms:description """Based on [http://www.nature.com/nrc/journal/v3/n10/fig_tab/nrc1189_F4.html Surh, 2003, figure 4] Nrf2 induces the expression of many
antioxidant enzymes. It is therefore thought to be involved in oxidative stress response."""^^xsd:string.
wprdf:WP3 <http://purl.org/pav/version> "48217"^^xsd:string .
wprdf:WP3 gpml:biopaxref "dba" .
wprdf:WP3 gpml:height "731.0"^^xsd:float .
wprdf:WP3 gpml:width "914.0"^^xsd:float .
wprdf:WP3 wp:category wp:CellularProcess .
wprdf:WP3 wp:organism <http://identifiers.org/taxonomy/9606> .
wprdf:WP3 wp:pathwayOntology <http://purl.obolibrary.org/obo/PW:0000378> .
wprdf:WP3 foaf:page "http://www.wikipathways.org/index.php/Pathway:WP3" .

}
<http://reactome.bio2rdf.org/sparql> {
b2rreactome:Homo_sapiens-Apoptosis rdf:type b2rbiopax:Pathway .
b2rreactome:Homo_sapiens-Apoptosis rdf:type b2rbiopaxresource:Pathway .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:name "Apoptosis" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:displayName "Apoptosis" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Reactome109581 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-REACT_578.2 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_14561771 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_4561027 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_14634621 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_15218528 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_12505355 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_12189384 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_12209154 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:comment "Apoptosis is a distinct form of cell death that is functionally and morphologically different from necrosis. Nuclear chromatin condensation, cytoplasmic shrinking, dilated endoplasmic reticulum, and membrane blebbing characterize apoptosis in general. Mitochondria remain morphologically unchanged. In 1972 Kerr et al introduced the concept of apoptosis as a distinct form of 'cell-death', and the mechanisms of various apoptotic pathways are still being revealed today. BRThe two principal pathways of apoptosis are (1) the Bcl-2 inhibitable or intrinsic pathway induced by various forms of stress like intracellular damage, developmental cues, and external stimuli and (2) the caspase 8/10 dependent or extrinsic pathway initiated by the engagement of death receptorsBR The caspase 8/10 dependent or extrinsic pathway is a death receptor mediated mechanism that results in the activation of caspase-8 and caspase-10. Activation of death receptors like Fas/CD95, TNFR1, and the TRAIL receptor is promoted by the TNF family of ligands including FASL (APO1L OR CD95L), TNF, LT-alpha, LT-beta, CD40L, LIGHT, RANKL, BLYS/BAFF, and APO2L/TRAIL. These ligands are released in response to microbial infection, or as part of the cellular, humoral immunity responses during the formation of lymphoid organs, activation of dendritic cells, stimulation or survival of T, B, and natural killer (NK) cells, cytotoxic response to viral infection or oncogenic transformation. BR The Bcl-2 inhibitable or intrinsic pathway of apoptosis is a stress-inducible process, and acts through the activation of caspase-9 via Apaf-1 and cytochrome c. The rupture of the mitochondrial membrane, a rapid process involving some of the Bcl-2 family proteins, releases these molecules into the cytoplasm. Examples of cellular processes that may induce the intrinsic pathway in response to various damage signals include: auto reactivity in lymphocytes, cytokine deprivation, calcium flux or cellular damage by cytotoxic drugs like taxol, deprivation of nutrients like glucose and growth factors like EGF, anoikis, transactivation of target genes by tumor suppressors including p53.BR In many non-immune cells, death signals initiated by the extrinsic pathway are amplified by connections to the intrinsic pathway. The connecting link appears to be the truncated BID (tBID) protein a proteolytic cleavage product mediated by caspase-8 or other enzymes." .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:comment "Edited: Gopinathrao, G, Matthews, L, Gillespie, ME, Joshi-Tope, G, 0000-00-00 00:00:00" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:comment "Authored: Alnemri, E, Hengartner, M, Tschopp, J, Tsujimoto, Y, Hardwick, JM, 2004-01-16 16:01:51" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:comment "Reviewed: Hengartner, M, Ranganathan, S, Vaux, D, 0000-00-00 00:00:00" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:dataSource b2rreactome:Homo_sapiens-ReactomeDataSource .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:organism b2rreactome:Homo_sapiens-Homo_sapiens .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayComponent b2rreactome:Homo_sapiens-Extrinsic_Pathway_for_Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayComponent b2rreactome:Homo_sapiens-Intrinsic_Pathway_for_Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayComponent b2rreactome:Homo_sapiens-Activation_of__Effector_Caspases .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayComponent b2rreactome:Homo_sapiens-Apoptotic_execution__phase .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayComponent b2rreactome:Homo_sapiens-Regulation_of_Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayOrder b2rreactome:Homo_sapiens-Apoptotic_execution__phaseStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayOrder b2rreactome:Homo_sapiens-Extrinsic_Pathway_for_ApoptosisStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayOrder b2rreactome:Homo_sapiens-Intrinsic_Pathway_for_ApoptosisStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayOrder b2rreactome:Homo_sapiens-Regulation_of_ApoptosisStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayOrder b2rreactome:Homo_sapiens-Activation_of__Effector_CaspasesStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:comment "Apoptosis is a distinct form of cell death that is functionally and morphologically different from necrosis. Nuclear chromatin condensation, cytoplasmic shrinking, dilated endoplasmic reticulum, and membrane blebbing characterize apoptosis in general. Mitochondria remain morphologically unchanged. In 1972 Kerr et al introduced the concept of apoptosis as a distinct form of 'cell-death', and the mechanisms of various apoptotic pathways are still being revealed today. BRThe two principal pathways of apoptosis are (1) the Bcl-2 inhibitable or intrinsic pathway induced by various forms of stress like intracellular damage, developmental cues, and external stimuli and (2) the caspase 8/10 dependent or extrinsic pathway initiated by the engagement of death receptorsBR The caspase 8/10 dependent or extrinsic pathway is a death receptor mediated mechanism that results in the activation of caspase-8 and caspase-10. Activation of death receptors like Fas/CD95, TNFR1, and the TRAIL receptor is promoted by the TNF family of ligands including FASL (APO1L OR CD95L), TNF, LT-alpha, LT-beta, CD40L, LIGHT, RANKL, BLYS/BAFF, and APO2L/TRAIL. These ligands are released in response to microbial infection, or as part of the cellular, humoral immunity responses during the formation of lymphoid organs, activation of dendritic cells, stimulation or survival of T, B, and natural killer (NK) cells, cytotoxic response to viral infection or oncogenic transformation. BR The Bcl-2 inhibitable or intrinsic pathway of apoptosis is a stress-inducible process, and acts through the activation of caspase-9 via Apaf-1 and cytochrome c. The rupture of the mitochondrial membrane, a rapid process involving some of the Bcl-2 family proteins, releases these molecules into the cytoplasm. Examples of cellular processes that may induce the intrinsic pathway in response to various damage signals include: auto reactivity in lymphocytes, cytokine deprivation, calcium flux or cellular damage by cytotoxic drugs like taxol, deprivation of nutrients like glucose and growth factors like EGF, anoikis, transactivation of target genes by tumor suppressors including p53.BR In many non-immune cells, death signals initiated by the extrinsic pathway are amplified by connections to the intrinsic pathway. The connecting link appears to be the truncated BID (tBID) protein a proteolytic cleavage product mediated by caspase-8 or other enzymes." .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:comment "Edited: Gopinathrao, G, Matthews, L, Gillespie, ME, Joshi-Tope, G, 0000-00-00 00:00:00" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:comment "Authored: Alnemri, E, Hengartner, M, Tschopp, J, Tsujimoto, Y, Hardwick, JM, 2004-01-16 16:01:51" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:comment "Reviewed: Hengartner, M, Ranganathan, S, Vaux, D, 0000-00-00 00:00:00" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:organism b2rreactome:Homo_sapiens-Homo_sapiens .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayComponent b2rreactome:Homo_sapiens-Extrinsic_Pathway_for_Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayComponent b2rreactome:Homo_sapiens-Intrinsic_Pathway_for_Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayComponent b2rreactome:Homo_sapiens-Activation_of__Effector_Caspases .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayComponent b2rreactome:Homo_sapiens-Apoptotic_execution__phase .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayComponent b2rreactome:Homo_sapiens-Regulation_of_Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Reactome109581 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-REACT_578.2 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_14561771 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_4561027 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_14634621 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_15218528 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_12505355 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_12189384 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_12209154 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayOrder b2rreactome:Homo_sapiens-Apoptotic_execution__phaseStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayOrder b2rreactome:Homo_sapiens-Extrinsic_Pathway_for_ApoptosisStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayOrder b2rreactome:Homo_sapiens-Intrinsic_Pathway_for_ApoptosisStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayOrder b2rreactome:Homo_sapiens-Regulation_of_ApoptosisStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayOrder b2rreactome:Homo_sapiens-Activation_of__Effector_CaspasesStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:dataSource b2rreactome:Homo_sapiens-ReactomeDataSource .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:displayName Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:name "Apoptosis" .
b2rreactome:Homo_sapiens-Apoptosis dcterms:rights <http://www.reactome.org/disclaimer.html> .
b2rreactome:Homo_sapiens-Apoptosis <http://bio2rdf.org/bio2rdf_resource:url> <http://bio2rdf.org/html/reactome:Homo_sapiens-Apoptosis> .
}
<http://rdf.farmbio.uu.se/chembl/sparql> {
<http://linkedchemistry.info/chembl/assay/a325093> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rdf.farmbio.uu.se/chembl/onto/#Assay> .
<http://linkedchemistry.info/chembl/assay/a325093> <http://www.w3.org/2000/01/rdf-schema#label> "CHEMBL860910" .
<http://linkedchemistry.info/chembl/chemblid/CHEMBL860910> <http://www.w3.org/2002/07/owl#equivalentClass> <http://linkedchemistry.info/chembl/assay/a325093> .
<http://linkedchemistry.info/chembl/assay/a325093> <http://www.w3.org/2002/07/owl#equivalentClass> <http://linkedchemistry.info/chembl/chemblid/CHEMBL860910> .
<http://linkedchemistry.info/chembl/chemblid/CHEMBL860910> <http://semanticscience.org/resource/CHEMINF_000200> <http://linkedchemistry.info/chembl/chemblid/CHEMBL860910/chemblid> .
<http://linkedchemistry.info/chembl/chemblid/CHEMBL860910/chemblid> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://semanticscience.org/resource/CHEMINF_000412> .
<http://linkedchemistry.info/chembl/chemblid/CHEMBL860910/chemblid> <http://semanticscience.org/resource/SIO_000300> "CHEMBL860910" .
<http://linkedchemistry.info/chembl/assay/a325093> <http://rdf.farmbio.uu.se/chembl/onto/#hasDescription> "Average Binding Constant for CAMK2B ; NA=Not Active at 10 uM" .
<http://linkedchemistry.info/chembl/assay/a325093> <http://purl.org/spar/cito/citesAsDataSource> <http://linkedchemistry.info/chembl/resource/r30300> .
<http://linkedchemistry.info/chembl/assay/a325093> <http://rdf.farmbio.uu.se/chembl/onto/#hasAssayType> <http://rdf.farmbio.uu.se/chembl/onto/#Binding> .
<http://linkedchemistry.info/chembl/activity/a1650154> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rdf.farmbio.uu.se/chembl/onto/#Activity> .
<http://linkedchemistry.info/chembl/activity/a1650154> <http://purl.org/spar/cito/citesAsDataSource> <http://linkedchemistry.info/chembl/resource/r30300> .
<http://linkedchemistry.info/chembl/activity/a1650154> <http://rdf.farmbio.uu.se/chembl/onto/#onAssay> <http://linkedchemistry.info/chembl/assay/a325093> .
<http://linkedchemistry.info/chembl/activity/a1650154> <http://rdf.farmbio.uu.se/chembl/onto/#forMolecule> <http://linkedchemistry.info/chembl/molecule/m604615> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <molecule> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://purl.org/spar/cito/citesAsDataSource> <http://linkedchemistry.info/chembl/resource/r13282> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://semanticscience.org/resource/CHEMINF_000000> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://purl.obolibrary.org/obo#has_role> <http://purl.org/obo/owl/CHEBI#CHEBI_23888> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.w3.org/2002/07/owl#equivalentClass> <http://bio2rdf.org/chebi:100443> .
<http://linkedchemistry.info/chembl/chemblid/CHEMBL268854> <http://www.w3.org/2002/07/owl#equivalentClass> <http://linkedchemistry.info/chembl/molecule/m443> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.w3.org/2002/07/owl#equivalentClass> <http://linkedchemistry.info/chembl/chemblid/CHEMBL268854> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.w3.org/2000/01/rdf-schema#label> "CHEMBL268854" .
<http://linkedchemistry.info/chembl/chemblid/CHEMBL268854> <http://semanticscience.org/resource/CHEMINF_000200> <http://linkedchemistry.info/chembl/chemblid/CHEMBL268854/chemblid> .
<http://linkedchemistry.info/chembl/chemblid/CHEMBL268854/chemblid> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://semanticscience.org/resource/CHEMINF_000412> .
<http://linkedchemistry.info/chembl/chemblid/CHEMBL268854/chemblid> <http://semanticscience.org/resource/SIO_000300> "CHEMBL268854" .
<http://linkedchemistry.info/chembl/molecule/m443> <http://semanticscience.org/resource/CHEMINF_000200> <http://linkedchemistry.info/chembl/molecule/m443/molform> .
<http://linkedchemistry.info/chembl/molecule/m443/molform> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://semanticscience.org/resource/CHEMINF_000042> .
<http://linkedchemistry.info/chembl/molecule/m443/molform> <http://semanticscience.org/resource/SIO_000300> "C27H23ClN4O2" .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.blueobelisk.org/chemistryblogs/smiles> "Cc1nc(O)c2cc(CN(CC#C)c3ccc(cc3)C(=O)NCc4ccc(Cl)cc4)ccc2n1" .
<http://linkedchemistry.info/chembl/molecule/m443> <http://semanticscience.org/resource/CHEMINF_000200> <http://linkedchemistry.info/chembl/molecule/m443/smiles> .
<http://linkedchemistry.info/chembl/molecule/m443/smiles> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://semanticscience.org/resource/CHEMINF_000018> .
<http://linkedchemistry.info/chembl/molecule/m443/smiles> <http://semanticscience.org/resource/SIO_000300> "Cc1nc(O)c2cc(CN(CC#C)c3ccc(cc3)C(=O)NCc4ccc(Cl)cc4)ccc2n1" .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.blueobelisk.org/chemistryblogs/inchi> "InChI=1S/C27H23ClN4O2/c1-3-14-32(17-20-6-13-25-24(15-20)27(34)31-18(2)30-25)23-11-7-21(8-12-23)26(33)29-16-19-4-9-22(28)10-5-19/h1,4-13,15H,14,16-17H2,2H3,(H,29,33)(H,30,31,34)" .
<http://linkedchemistry.info/chembl/molecule/m443> <http://semanticscience.org/resource/CHEMINF_000200> <http://linkedchemistry.info/chembl/molecule/m443/inchi> .
<http://linkedchemistry.info/chembl/molecule/m443/inchi> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://semanticscience.org/resource/CHEMINF_000113> .
<http://linkedchemistry.info/chembl/molecule/m443/inchi> <http://semanticscience.org/resource/SIO_000300> "InChI=1S/C27H23ClN4O2/c1-3-14-32(17-20-6-13-25-24(15-20)27(34)31-18(2)30-25)23-11-7-21(8-12-23)26(33)29-16-19-4-9-22(28)10-5-19/h1,4-13,15H,14,16-17H2,2H3,(H,29,33)(H,30,31,34)" .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.w3.org/2002/07/owl#equivalentClass> <http://rdf.openmolecules.net/?InChI=1S/C27H23ClN4O2/c1-3-14-32(17-20-6-13-25-24(15-20)27(34)31-18(2)30-25)23-11-7-21(8-12-23)26(33)29-16-19-4-9-22(28)10-5-19/h1,4-13,15H,14,16-17H2,2H3,(H,29,33)(H,30,31,34)> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.blueobelisk.org/chemistryblogs/inchikey> "IQCINSLNRQILLY-UHFFFAOYSA-N" .
<http://linkedchemistry.info/chembl/molecule/m443> <http://semanticscience.org/resource/CHEMINF_000200> <http://linkedchemistry.info/chembl/molecule/m443/inchikey> .
<http://linkedchemistry.info/chembl/molecule/m443/inchikey> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://semanticscience.org/resource/CHEMINF_000059> .
<http://linkedchemistry.info/chembl/molecule/m443/inchikey> <http://semanticscience.org/resource/SIO_000300> "IQCINSLNRQILLY-UHFFFAOYSA-N" .
}
<http://beta.sparql.uniprot.org/> {
<http://purl.uniprot.org/uniprot/Q6GZX4> rdf:type up:Protein .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:label "Putative transcription factor 001R" .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:citation upcitation:15165820 .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:classifiedWith <http://purl.uniprot.org/keywords/10> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:classifiedWith <http://purl.uniprot.org/go/0006351> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:classifiedWith <http://purl.uniprot.org/keywords/805> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:classifiedWith <http://purl.uniprot.org/go/0006355> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:classifiedWith <http://purl.uniprot.org/keywords/1185> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:classifiedWith <http://purl.uniprot.org/go/0046782> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:existence up:Predicted_Existence .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:organism <http://purl.uniprot.org/taxonomy/654924 .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:recommendedName <http://purl.uniprot.org/SHA-384/0777234937D8B63494C8D5F1E2AA13EA7B92452085F2FD9AA79C8DF96BF8234173E353B71AB291B114FFF71D7DB823AE> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:representativeFor <http://purl.uniprot.org/uniref/UniRef50_Q6GZX4> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:representativeFor <http://purl.uniprot.org/uniref/UniRef100_Q6GZX4> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:representativeFor <http://purl.uniprot.org/uniref/UniRef90_Q6GZX4> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:seedFor <http://purl.uniprot.org/uniref/UniRef100_Q6GZX4> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:seedFor <http://purl.uniprot.org/uniref/UniRef90_Q6GZX4> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:sequence <http://purl.uniprot.org/isoforms/Q6GZX4-1> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:created "2011-06-28" .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:mnemonic "001R_FRG3G" .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:modified "2012-04-18" .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:reviewed "true" .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:version "24" .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/embl-cds/AAT09660.1> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/refseq/YP_031579.1> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/proteinmodelportal/Q6GZX4> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/geneid/2947773> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/protclustdb/CLSP2511514> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/interpro/IPR007031> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/pfam/PF04947> .
upcitations:15165820 rdf:type up:Journal_Citation .
upcitations:15165820 rdfs:comment "Frog virus 3 (FV3) is the type species member of the genus Ranavirus (family Iridoviridae). To better understand the molecular mechanisms involved in the replication of FV3 including transcription of its highly methylated DNA genome we have determined the complete nucleotide sequence of the FV3 genome. The FV3 genome is 105903 bp long excluding the terminal redundancy. The G + C content of FV3 genome is 55% and it encodes 98 nonoverlapping potential open reading frames (ORFs) containing 50-1293 amino acids. Eighty-four ORFs have significant homology to known proteins of other iridoviruses whereas twelve of these unique FV3 proteins do not share homology to any known protein. A microsatellite containing a stretch of 34 tandemly repeated CA dinucleotide in a noncoding region was detected. To date no such sequence has been reported in any animal virus." .
upcitations:15165820 up:name "Virology" .
upcitations:15165820 up:author "Barkman T.J." .
upcitations:15165820 up:author "Essani K." .
upcitations:15165820 up:author "Tan W.G." .
upcitations:15165820 up:author "Gregory Chinchar V." .
upcitations:15165820 up:date "2004" .
upcitations:15165820 up:pages "70-84" .
upcitations:15165820 up:title "Comparative genomic analyses of frog virus 3 type species of the genus Ranavirus (family Iridoviridae)." .
upcitations:15165820 up:volume "323" .
upcitations:15165820 skos:exactMatch http://purl.uniprot.org/pubmed/15165820 .
upcitations:15165820 dcterms:identifier "doi:10.1016/j.virol.2004.02.019" .
}
# EBI gene expression atlas
<http://wwwdev.ebi.ac.uk/fgpt/gxa-sparql/sparql> {
# main linking point to the GXA data is the ensembl id and the uniprot id. 
<http://identifiers.org/ensembl/ENSG00000116962> sio:'encodes' <http://identifiers.org/ensembl/ENSP00000264187> .
<http://identifiers.org/ensembl/ENST00000264187> sio:'translatedTo' <http://identifiers.org/ensembl/ENSP00000264187> .
<http://identifiers.org/ensembl/ENST00000264187> rdfs:seeAlso ?uniprotProtein .
# differential expression value
?diffexp a sio:'differential gene expression value' .
?diffexp sio:'is attribute of' <http://identifiers.org/ensembl/ENSG00000116962> .
?diffexp sio:'has value' ?diffvalue . # e.g. UP, DOWN 
?diffexp sio'has attribute' [ a sio:p_value; sio:has-value 0.00005] .
# experiment factor from EFO 
?iv a sio:'independent variable' .
?iv sio:'represents' efo:'experimental factor' .
?iv sio:'in relation to' ?diffexp .
}
# parses up to here.
http://ops-virtuoso.scai.fraunhofer.de:8894/sparql {
<http://www.scai.fraunhofer.de/rdf/entity/CC_BY-SA_3.0>
a dcterms:LicenseDocument ;
rdfs:label "CC BY-SA 3.0"^^xsd:string ;
dcterms:references "https://creativecommons.org/licenses/by-sa/3.0/"^^xsd:string ;
dcterms:valid "2013-02-01T13:59:07.098Z"^^xsd:dateTime .
scai:Fraunhofer_SCAI
a foaf:Organization , prov:Agent ;
rdfs:label "Fraunhofer SCAI"^^xsd:string .
<http://www.scai.fraunhofer.de/rdf/intern/medline12short.xml>
a prov:Entity , pao:DocumentSet ;
dcterms:title "medline12short.xml"^^xsd:string .
<http://www.scai.fraunhofer.de/rdf/intern/Department_of_Diagnostic_Radiology__Yale_University_School_of_Medicine__New_Haven__Conn.__USA.>
a foaf:Organization ;
rdfs:label "Department of Diagnostic Radiology, Yale University School of Medicine, New Haven, Conn., USA."@en ;
foaf:member base:Charney__D_S , base:Bremner__J_D , base:Southwick__S_M , base:Staib__L_H , base:McGlashan__T , base:Narayan__M .
scai:XMLAnnotator
a prov:Activity ;
prov:endedAtTime "2012-08-06T12:59:07.1Z"^^xsd:dateTime ;
prov:startedAtTime "2012-08-06T12:59:07.1Z"^^xsd:dateTime ;
prov:used <http://www.scai.fraunhofer.de/rdf/intern/medline12short.xml> ;
prov:wasAssociatedWith
scai:chaupt .
base:Staib__L_H
a foaf:Person , dcterms:Agent ;
rdfs:label "Staib, L H"^^xsd:string .
scai:chaupt
a foaf:Person , dcterms:Agent , prov:Agent ;
rdfs:label "chaupt"^^xsd:string ;
prov:actedOnBehalfOf
scai:Fraunhofer_SCAI ;
foaf:member scai:Fraunhofer_SCAI .
<http://www.scai.fraunhofer.de/rdf/intern/medline12short.xml_XMLAnnotator>
a <http://purl.org/dc/dcmitype/Dataset> , prov:Entity , pao:DocumentSet ;
ao:item <http://www.scai.fraunhofer.de/rdf/intern/10553744> ;
dcterms:creator scai:chaupt ;
dcterms:license <http://www.scai.fraunhofer.de/rdf/entity/CC_BY-SA_3.0> ;
dcterms:rightsHolder
scai:chaupt ;
dcterms:title "medline12short.xml_XMLAnnotator"^^xsd:string ;
prov:atTime "2012-11-12T13:59:07.097Z"^^xsd:dateTime ;
prov:wasAttributedTo
scai:chaupt ;
prov:wasDerivedFrom <http://www.scai.fraunhofer.de/rdf/intern/medline12short.xml> ;
prov:wasGeneratedBy scai:XMLAnnotator .
base:Charney__D_S
a foaf:Person , dcterms:Agent ;
rdfs:label "Charney, D S"^^xsd:string .
base:Bremner__J_D
a foaf:Person , dcterms:Agent ;
rdfs:label "Bremner, J D"^^xsd:string .
base:Southwick__S_M
a foaf:Person , dcterms:Agent ;
rdfs:label "Southwick, S M"^^xsd:string .
base:The_American_journal_of_psychiatry
a dcterms:Agent ;
rdfs:label "The American journal of psychiatry"^^xsd:string .
<http://www.scai.fraunhofer.de/rdf/intern/10553744>
a str:Document ;
dcterms:creator base:Charney__D_S , base:Bremner__J_D , base:Southwick__S_M , base:Staib__L_H , base:McGlashan__T , base:Narayan__M ;
dcterms:date "1999-10-31T13:59:07.1Z"^^xsd:dateTime ;
dcterms:identifier "10553744"^^xsd:string ;
dcterms:publisher base:The_American_journal_of_psychiatry ;
dcterms:source "file://medline12short.xml"^^xsd:string ;
dcterms:title "Neural correlates of memories of childhood sexual abuse in women with and without posttraumatic stress disorder."@en .
base:McGlashan__T
a foaf:Person , dcterms:Agent ;
rdfs:label "McGlashan, T"^^xsd:string .
base:Narayan__M
a foaf:Person , dcterms:Agent ;
rdfs:label "Narayan, M"^^xsd:string .
}
:Linksets {
up:Q12345 skos:broadMatch end:000xxxxx .
}

== # VoID ==

{| style="color: black; color: #733;" width="85%" class="wikitable"
| colspan="3" | <http://sparql.wikipathways.org>
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''pav:createdOn'''
| style="width: 60%; background-color: orange;"| '''"2012-10-25"^^xsd:date ;'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''pav:createdBy'''
| style="width: 60%; background-color: orange;"| ''<https://orcid.org/0000-0001-9773-4008> ;''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''pav:createdAt'''
| style="width: 60%; background-color: orange;"| '''dbpedia:Maastricht_University ;'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''dcterms:license'''
| style="width: 60%; background-color: orange;"| ''<http://creativecommons.org/licenses/by/3.0/> .''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| ''<http://sparql.wikipathways.org> .''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:triples'''
| style="width: 60%; background-color: orange;"| '''"1794104"^^xsd:integer ;'''
|-

| colspan="3" | :ChEMBL
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''pav:createdOn'''
| style="width: 60%; background-color: orange;"| '''"2012-10-25"^^xsd:date ;'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:foo'''
| style="width: 60%; background-color: orange;"| '''void:bar .'''
|}

== Triplestore map ==

{| style="color: black; color: #733;" width="85%" class="wikitable"
| colspan="3" | WikiPathways
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''foaf:page'''
| style="width: 60%; background-color: orange;"| ''' http://www.wikipathways.org'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| '''http://sparql.wikipathways.org'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:uriLookupEndpoint'''
| style="width: 60%; background-color: orange;"| '''http://rdf.wikipathways.org '''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''prov:deployedSoftware'''
| style="width: 60%; background-color: orange;"| '''dbpedia:Virtuoso_Universal_Server '''
|-
| colspan="3" | :ChEMBL-RDF
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''foaf:page'''
| style="width: 60%; background-color: orange;"| '''https://github.com/egonw/chembl.rdf'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| ''' http://rdf.farmbio.uu.se/chembl/sparql '''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| ''' http://ragamuffin.bigcat.unimaas.nl/chembl/sparql '''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''prov:deployedSoftware'''
| style="width: 60%; background-color: orange;"| '''dbpedia:Virtuoso_Universal_Server '''
|-
| colspan="3" | :Uniprot
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''foaf:page'''
| style="width: 60%; background-color: orange;"| '''http://www.uniprot.org'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| ''' http://beta.sparql.uniprot.org '''
|-
| colspan="3" | :Gene expression atlas
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''foaf:page'''
| style="width: 60%; background-color: orange;"| '''tba'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| ''' http://wwwdev.ebi.ac.uk/fgpt/gxa-sparql/sparql '''
|-
|}

HCLS/SWAT4LS2012/Hackathon

Ewilligh — Wed, 28 Nov 2012 06:44:01 GMT

Ewilligh: /* (Mini) Program */

The SWAT4LS Hackathon is an informal event associated with the [http://swat4ls.org/ SWAT4LS] Semantic Web Applications and Tools for Life Sciences Workshops Series.

Scope of the event is to bring together experts and enthusiasts in the application of semantic technologies in healthcare and life science for open discussion and jam coding sessions.
The Hackathon will be organized on the 28th of November 2012 at [http://lacantine.org/ La Cantine, Paris] ([https://maps.google.com/maps?q=12+Galerie+Montmartre+75002+france&hl=en&ie=UTF8&ll=48.870438,2.342089&spn=0.0013,0.001869&sll=48.87053,2.342319&sspn=0.002601,0.003739&t=h&hnear=12+Galerie+Montmartre,+75002+Paris,+%C3%8Ele-de-France,+France&z=19 map]).

street: 151 rue Montmartre, Passage des Panoramas
room: 12 Galerie Montmartre
75002 Paris

(For more information, please refer to the [http://www.swat4ls.org/workshops/paris2012/| workshop website]).
The hackathon is open to workshop participants. Registration is required and space is limited!.

== (Mini) Program ==
Hackathon starts at 9.00

* 09.00-09.30 - Welcome, registrations, informall introductions
* 09.30-10.30 - Project proposals by group leads (to be confirmed). Have a proposal ? Fill our survey at (http://www.surveymonkey.com/s/8HCLTRK).
* 10.30-16.00 - Hack Hack Hacak (with Pizza break. There will be coffee).
* 16.00-18.00 - Presentations on what has been done, ideas, problems found, next steps

== Logistics ==
Projects and institutes attending include:
* Open PHACTS (http://www.openphacts.org)
* WikiPathways (http://www.wikipathways.org/index.php/WikiPathways)
* The Database Center for Life Sciences/BioHackathon (http://dbcls.rois.ac.jp/en/ http://www.biohackathon.org/)
* The W3C Consortium, Health Care and Life Sciences Interest Group ([[HCLS]])
* BioPAX (http://biopax.org)
* European Bioinformatics Institute (http://www.ebi.ac.uk)
* Web Science Trust Network of Labs (WSTNet) (http://webscience.org)

While the agenda will be open, we are coordinating ideas that can be developd at the network in advance, to maximize the utility of the day. Co-organizers for each community will help gathering ideas and finding point of contacts.

=== Information and registrations ===
For information, [mailto:info@swat4ls.org| info _at_ swat4ls.org]

Registrations are handled via [http://swat4ls-2012.eventbrite.com/| Eventbrite]

=== Hashtag ===
[https://twitter.com/search/realtime?q=%23swat4lshack #swat4lshack]

=== Co-Organizers ===
* Andrea Splendiani
* Andra Waagmeester
* Eric Prud'hommeaux
* M. Scott Marshall
* Toshiaki Katayama
* Ismael Navas delgado

== Open PHACTS community ==

=== Contact Point ===
* Andra Waagmeester
* Egon Willighagen

=== Proposed action points ===
# Consume [http://www.openphacts.org Open PHACTS] content in Pathway tools
# Using http://identifiers.org
# Create an example set of valuable queries
# Visualizing output
# work on further linked data integration, with possible:
## [https://ntp.niehs.nih.gov/drugmatrix/ DrugMatrix]
## [http://toxico.nibio.go.jp/open-tggates/ TG-GATEs]
## [http://thedatahub.org/nl/dataset/bio2rdf-ctd CTD] (already available as RDF, by Bio2RDF)
# shared Java client code
## for R, Bioclipse, KNIME

=== Confirmed Participants ===
* Kees Burger
* Maria Carmen Carra
* Ian Dunlop
* Chris Evelo
* Paul Groth
* Tim Harder
* Carina Haupt
* Nick Juty
* Camille Laibe
* Antonis Loizou
* Oriol Lopez
* Guillermo C. Martínez
* Nuria Queralt
* Rishi Ramgolam
* Mark Thompson
* Egon Willighagen
* Pekka Kohonen
* Ola Spjuth
* Thompson Mark (Andra)
* coulet adrien (Michel)
* Malone James (Michel)
* Dumontier Michel
* Kocbek Simon (Andrea)
* Luciano Joanne
* Jiang Guoqian (Scott)
* van Haagen Herman
* Leroux Hugo
* Garcia Leyla (Michel)
* Adamusiak Tomasz
* Jupp Simon (Michel)
* Mironov Vladimir (Andrea)
* Kamsu Foguem Bernard
* Schouwen, van Reinout (Scott)
* Yamamoto Yasunori (Andrea)
* Groth Paul (Andra)
* Helma Christoph (Egon)
* Larmande Pierre
* Whetzel Trish (Scott)
* Navas-Delgado Ismael (Andrea)
* Katayama Toshiaki (Andrea)
* Lysenko Artem (Andrea)
* Paschke Adrian (Andrea)
* Helma Christoph
* Alam Mehwish
* van dam Jesse
* Croset Samuel (Andrea)
* Helma Christoph
* Chris Evelo (Andra)
* Martina Kutmon (Andra)
* Alex Pico (Andra)

== WikiPathways community ==

=== Contact Point ===
Andra Waagmeester

=== Introduction ===
[http://www.wikipathways.org/index.php/WikiPathways WikiPathways] is a online resource for pathways. Content is provided by the audience at large. I currently contains more then 2200 pathways from 21 species [http://sparqlbin.com/#4f91f23a032a87cc46c5a526a6da673a source]. Pathways are captured in a XML-based format [http://www.pathvisio.org/wiki/EverythingGpml GPML]. Recently WikiPathways was exposed as linked open data where GPML content was exported as RDF. This data is available through a SPARQL endpoint http://sparql.wikipathways.org.

=== Proposed action points ===
==== Exploring [http://www.wikipathways.org/index.php/WikiPathways WikiPathways] RDF content, making example queries ====
==== Writing federated queries to integrate pathway content with other biological data. ====
====Using [http://code.google.com/p/pathvisiorpc/ Pathvisio RPC] to consume and visualize linked pathway data====
====Solving ID mapping in WikiPathways RDF====

=== Confirmed Participants ===
* Chris Evelo
* Martina Kutmon
* Alex Pico

== Database Center for Life Sciences Community / BioHackathon ==

=== Contact Point ===
Toshiaki Katayama

=== Proposed action points ===

* Ontology for genome annotation
** https://github.com/dbcls/bh12/wiki/Feature-annotation-locations-in-RDF
** https://github.com/dbcls/bh12/wiki/Genome-RDF
** https://gist.github.com/3704296

* Identifiers.org dataset definitions in RDF
** https://gist.github.com/3985701
** https://gist.github.com/1672112
** https://dl.dropbox.com/u/429992/20121031-miriam.ttl

* Text-mining for microbial/environmental genomics

=== Confirmed Participants ===
* Yasunori Yamamoto
* Toshiaki Katayama

== W3C HCLS Community ==

=== Contact Point ===
Eric Prud'hommeaux

=== Proposed action points ===
==== Making an online inventory of available resources (wiki) to document underlying schemas of available datasources.====
There are nice lists of active SPARQL endpoints [http://www.freebase.com/view/base/sparql/views/sparql_endpoint (example 1)] and [http://labs.mondeca.com/sparqlEndpointsStatus/index.html (example 2)]. Finding where the data actually links can still be challenging.

It would be really beneficial to create an overview with descriptions of different linked data sets describing the underlying structure. The first step would be to define a format where data providers describe their data in a predefined (wiki) format. This format could be based on [http://www.w3.org/TR/void/ VoID].
These description coulds then be used to create so called data landscapes in tools such as [http://vsdlc3.blogspot.be/ Semscape].

====Creating a review of sparql endpoints and their support for remote federated queries. ====
Within a federated query you can query different flavours of sparql endpoints. Since different endpoints have their own implementations and support for different SPARQL versions, it is essential to understand the different issues each type of endpoint might have. The community would benefit from a list mentioning each available SPARQL endpoint system (e.g. 4store, virtuoso, etc) and their support for different SPARQL versions. Also this list could mention specific features (e.g. soft limit in 4store) influencing the recall in federated queries.

== BioPAX Community ==

=== Contact Point ===
Ismael Navas Delgado

=== Proposed action points ===

=== Confirmed Participants ===
* Ismael Navas Delgado
* Andrea Splendiani

== EBI Gene Expression Atlas ==

=== Contact Point ===
Simon Jupp

James Malone

=== Introduction ===

Integration of gene expression data from the Gene Expression Atlas database (http://www.ebi.ac.uk/gxa). Schema description and SPARQL endpoint at http://wwwdev.ebi.ac.uk/fgpt/efosemweb.html
Differential gene expression annotated with Ensembl gene ids (identifiers.org URIs), includes mappings to Uniprot. Experiment assay and sample descriptions annotated with ontology terms from wide range of
bio-ontologies (anatomy, cells, disease etc).

=== Proposed action points ===

Linking gene expression to pathway data.

== Web Science Trust Network of Labs (WSTNet) (http://webscience.org) ==

=== Contact Point ===

Joanne Luciano

=== Introduction ===

Health Web Science is an new discipline emerging from Web Science aimed at understanding the impact of the web on health and wellness. The Web Observatory (http://webscience.org/web-observatory/) is a global data resource for the advancement of economic & social prosperity. Sponsored by the Web Science Trust, a global not for profit institution with a secretariat at the University of Southampton that can leverage the web science research resources of the 15 University labs affiliated with the Web Science Trust (WSTnet) including Brazil, China, Korea, Europe and US, and the existing partnerships with W3C and the Web Foundation. The Web Observatory is in early stages and we will be looking to define and construct Heath and Life Science observations for Web Science research.
=== Proposed action points ===

Creating a Health Web Observatory

=== Confirmed Participants ===
* Joanne Luciano

== Bio2RDF r2 + SIO ==

=== Contact Point ===

Michel Dumontier

=== Introduction ===
Bio2RDF (http://bio2rdf.org) is an open source project that uses Semantic Web technologies to create and provide the largest network of Linked Data for the Life Sciences. At SWAT4LS we will present the 2nd release of the Bio2RDF project in which open-source scripts were updated and consolidated with GitHub, IRIs are mapped to canonical set using a new 2100+ dataset Life Sciences Registry, datasets are described along with summary statistics and provenance, and RDF files and Virtuoso databases are available for download or query. Bio2RDF also computes dataset connectivity that is compatible with SPARQLed, thus enabling assisted SPARQL queries and faceted searches using Virtuoso's native facet browser.

The Semanticscience Integrated Ontology (SIO) is a relatively new ontology that aims to facilitate the representation and integration of biological and biomedical data in a manner that is simpler and more flexible than other upper level ontologies. SIO considers three primary kinds of things : objects, processes and their attributes. It has over 180 object properties (1/2 are inverses) to more precisly describe the nature of the relationship, and a single datatype property to capture literals. SIO has been used to integrate over 700 SADI-based semantic web services and has been recently mapped to Bio2RDF types and relations to enable querying across similar and complementary datasets.

=== Proposed action points ===

Bio2RDF
* Discuss recent developments and future plans
* Develop overview web pages for each of the datasets, drawing from the LSR, dataset provenance and statistics
* Develop simple intra and inter-dataset queries to demonstrate the potential of each dataset

SIO
* Discuss basic structures & design patterns
* Discuss user-driven use cases (gene expression, aggregation functions, gene associations, nanopublications)

=== Confirmed Participants ===
* Michel Dumontier
* Alison Callahan
* Jose Cruz Toledo

== CDA and Clinical Trial Protocols to RDF ==

=== Contact Point ===

Eric Prud'hommeaux

=== Introduction ===
The [https://github.com/projectcypress/test-deck/blob/master/patients/c32/100_George_Skeritt.xml Project Cypress corpus test patients] provides a sizable group of patients with various characteristics, some of which may line up with some [[/TrialProtocols|Trial Protocols]]. This provides a good opportunity to demonstrate the power of expression protocols in a self-describing, machine-readable format, e.g. RDF.

=== Proposed action points ===

*code inclusion/exclusion criteria in popular terminologies (e.g. SNOMED, LOINC)
*code structural information in CDA model, e.g. diagnosis vs. prescribed treatment.
*map CDA to RDF a la [http://www.w3.org/wiki/HCLS/ClinicalObservationsInteroperability/TermInfo terminfo]
*match (subsets of) clincal trial criteria to patient records.

=== Confirmed Participants ===

== Resources ==
* PathwayCommons SPARQL endpoint. Endpoint over all BioPAX representations in PathwayCommons
* Cytoscape plugin to visualize and interact with RDF knwoledge bases (new!)
* BioQueries: social site to build SPARQL queries
* Open PHACTS rdf guidelines: http://www.openphacts.org/specs/2012/WD-rdfguide-20120823/

== Data Map ==

@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix wprdf: <http://rdf.wikipathways.org/> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix wp: <http://vocabularies.wikipathways.org/wp#> .
@prefix biopax: <http://www.biopax.org/release/biopax-level3.owl#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix gpml: <http://vocabularies.wikipathways.org/gpml#> .
@prefix chembl: <http://rdf.farmbio.uu.se/chembl/onto/#> .
@prefix up: <http://purl.uniprot.org/core/> .
@prefix dbpedia: <http://dbpedia.org/page/> .
@prefix pav: <http://purl.org/pav/> .
@prefix b2rreactome: <http://bio2rdf.org/reactome:>
@prefix b2rbiopax: <http://bio2rdf.org/ns/biopax#>
@prefix b2rbiopaxresource: <http://bio2rdf.org/biopax_resource:>
@prefix up: <http://purl.uniprot.org/core/>
@prefix sio: <http://semanticscience.org/resource/>
@prefix upcitation: <http://purl.uniprot.org/citations/>
@prefix prov: <http://www.w3.org/ns/prov#>
@prefix dc: <http://purl.org/dc/elements/1.1/> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix aot: <http://purl.org/ao/types/> .
@prefix aos: <http://purl.org/ao/selectors/> .
@prefix sso: <http://nlp2rdf.lod2.eu/schema/sso/> .
@prefix void: <http://rdfs.org/ns/void#> .
@prefix pao: <http://www.scai.fraunhofer.de/prominer/vocabular/pao#> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix pav: <http://purl.org/pav/> .
@prefix ao: <http://purl.org/ao/> .
@prefix str: <http://nlp2rdf.lod2.eu/schema/string/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix base: <http://www.scai.fraunhofer.de/rdf/intern/> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix scai: <http://www.scai.fraunhofer.de/rdf/entity/> .

<http://sparql.wikipathways.org> {
# Sparql endpoint: http://sparql.wikipathways.org
# Data: http://rdf.wikipathways.org
# 
<http://identifiers.org/ncbigene/1051> rdf:type wp:GeneProduct .
<http://identifiers.org/ncbigene/1051> dcterms:isPartOf wprdf:WP3 .
<http://identifiers.org/ncbigene/1051> rdfs:label "C/EBP-beta" .
wprdf:WP3 rdf:type wp:Pathway .
wp:Pathway skos:relatedMatch biopax:Pathway .
wprdf:WP3 rdfs:label "Keap1-Nrf2 Pathway" .
wprdf:WP3 dcterms:description """Based on [http://www.nature.com/nrc/journal/v3/n10/fig_tab/nrc1189_F4.html Surh, 2003, figure 4] Nrf2 induces the expression of many
antioxidant enzymes. It is therefore thought to be involved in oxidative stress response."""^^xsd:string.
wprdf:WP3 <http://purl.org/pav/version> "48217"^^xsd:string .
wprdf:WP3 gpml:biopaxref "dba" .
wprdf:WP3 gpml:height "731.0"^^xsd:float .
wprdf:WP3 gpml:width "914.0"^^xsd:float .
wprdf:WP3 wp:category wp:CellularProcess .
wprdf:WP3 wp:organism <http://identifiers.org/taxonomy/9606> .
wprdf:WP3 wp:pathwayOntology <http://purl.obolibrary.org/obo/PW:0000378> .
wprdf:WP3 foaf:page "http://www.wikipathways.org/index.php/Pathway:WP3" .

}
<http://reactome.bio2rdf.org/sparql> {
b2rreactome:Homo_sapiens-Apoptosis rdf:type b2rbiopax:Pathway .
b2rreactome:Homo_sapiens-Apoptosis rdf:type b2rbiopaxresource:Pathway .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:name "Apoptosis" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:displayName "Apoptosis" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Reactome109581 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-REACT_578.2 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_14561771 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_4561027 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_14634621 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_15218528 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_12505355 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_12189384 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_12209154 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:comment "Apoptosis is a distinct form of cell death that is functionally and morphologically different from necrosis. Nuclear chromatin condensation, cytoplasmic shrinking, dilated endoplasmic reticulum, and membrane blebbing characterize apoptosis in general. Mitochondria remain morphologically unchanged. In 1972 Kerr et al introduced the concept of apoptosis as a distinct form of 'cell-death', and the mechanisms of various apoptotic pathways are still being revealed today. BRThe two principal pathways of apoptosis are (1) the Bcl-2 inhibitable or intrinsic pathway induced by various forms of stress like intracellular damage, developmental cues, and external stimuli and (2) the caspase 8/10 dependent or extrinsic pathway initiated by the engagement of death receptorsBR The caspase 8/10 dependent or extrinsic pathway is a death receptor mediated mechanism that results in the activation of caspase-8 and caspase-10. Activation of death receptors like Fas/CD95, TNFR1, and the TRAIL receptor is promoted by the TNF family of ligands including FASL (APO1L OR CD95L), TNF, LT-alpha, LT-beta, CD40L, LIGHT, RANKL, BLYS/BAFF, and APO2L/TRAIL. These ligands are released in response to microbial infection, or as part of the cellular, humoral immunity responses during the formation of lymphoid organs, activation of dendritic cells, stimulation or survival of T, B, and natural killer (NK) cells, cytotoxic response to viral infection or oncogenic transformation. BR The Bcl-2 inhibitable or intrinsic pathway of apoptosis is a stress-inducible process, and acts through the activation of caspase-9 via Apaf-1 and cytochrome c. The rupture of the mitochondrial membrane, a rapid process involving some of the Bcl-2 family proteins, releases these molecules into the cytoplasm. Examples of cellular processes that may induce the intrinsic pathway in response to various damage signals include: auto reactivity in lymphocytes, cytokine deprivation, calcium flux or cellular damage by cytotoxic drugs like taxol, deprivation of nutrients like glucose and growth factors like EGF, anoikis, transactivation of target genes by tumor suppressors including p53.BR In many non-immune cells, death signals initiated by the extrinsic pathway are amplified by connections to the intrinsic pathway. The connecting link appears to be the truncated BID (tBID) protein a proteolytic cleavage product mediated by caspase-8 or other enzymes." .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:comment "Edited: Gopinathrao, G, Matthews, L, Gillespie, ME, Joshi-Tope, G, 0000-00-00 00:00:00" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:comment "Authored: Alnemri, E, Hengartner, M, Tschopp, J, Tsujimoto, Y, Hardwick, JM, 2004-01-16 16:01:51" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:comment "Reviewed: Hengartner, M, Ranganathan, S, Vaux, D, 0000-00-00 00:00:00" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:dataSource b2rreactome:Homo_sapiens-ReactomeDataSource .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:organism b2rreactome:Homo_sapiens-Homo_sapiens .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayComponent b2rreactome:Homo_sapiens-Extrinsic_Pathway_for_Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayComponent b2rreactome:Homo_sapiens-Intrinsic_Pathway_for_Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayComponent b2rreactome:Homo_sapiens-Activation_of__Effector_Caspases .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayComponent b2rreactome:Homo_sapiens-Apoptotic_execution__phase .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayComponent b2rreactome:Homo_sapiens-Regulation_of_Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayOrder b2rreactome:Homo_sapiens-Apoptotic_execution__phaseStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayOrder b2rreactome:Homo_sapiens-Extrinsic_Pathway_for_ApoptosisStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayOrder b2rreactome:Homo_sapiens-Intrinsic_Pathway_for_ApoptosisStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayOrder b2rreactome:Homo_sapiens-Regulation_of_ApoptosisStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayOrder b2rreactome:Homo_sapiens-Activation_of__Effector_CaspasesStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:comment "Apoptosis is a distinct form of cell death that is functionally and morphologically different from necrosis. Nuclear chromatin condensation, cytoplasmic shrinking, dilated endoplasmic reticulum, and membrane blebbing characterize apoptosis in general. Mitochondria remain morphologically unchanged. In 1972 Kerr et al introduced the concept of apoptosis as a distinct form of 'cell-death', and the mechanisms of various apoptotic pathways are still being revealed today. BRThe two principal pathways of apoptosis are (1) the Bcl-2 inhibitable or intrinsic pathway induced by various forms of stress like intracellular damage, developmental cues, and external stimuli and (2) the caspase 8/10 dependent or extrinsic pathway initiated by the engagement of death receptorsBR The caspase 8/10 dependent or extrinsic pathway is a death receptor mediated mechanism that results in the activation of caspase-8 and caspase-10. Activation of death receptors like Fas/CD95, TNFR1, and the TRAIL receptor is promoted by the TNF family of ligands including FASL (APO1L OR CD95L), TNF, LT-alpha, LT-beta, CD40L, LIGHT, RANKL, BLYS/BAFF, and APO2L/TRAIL. These ligands are released in response to microbial infection, or as part of the cellular, humoral immunity responses during the formation of lymphoid organs, activation of dendritic cells, stimulation or survival of T, B, and natural killer (NK) cells, cytotoxic response to viral infection or oncogenic transformation. BR The Bcl-2 inhibitable or intrinsic pathway of apoptosis is a stress-inducible process, and acts through the activation of caspase-9 via Apaf-1 and cytochrome c. The rupture of the mitochondrial membrane, a rapid process involving some of the Bcl-2 family proteins, releases these molecules into the cytoplasm. Examples of cellular processes that may induce the intrinsic pathway in response to various damage signals include: auto reactivity in lymphocytes, cytokine deprivation, calcium flux or cellular damage by cytotoxic drugs like taxol, deprivation of nutrients like glucose and growth factors like EGF, anoikis, transactivation of target genes by tumor suppressors including p53.BR In many non-immune cells, death signals initiated by the extrinsic pathway are amplified by connections to the intrinsic pathway. The connecting link appears to be the truncated BID (tBID) protein a proteolytic cleavage product mediated by caspase-8 or other enzymes." .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:comment "Edited: Gopinathrao, G, Matthews, L, Gillespie, ME, Joshi-Tope, G, 0000-00-00 00:00:00" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:comment "Authored: Alnemri, E, Hengartner, M, Tschopp, J, Tsujimoto, Y, Hardwick, JM, 2004-01-16 16:01:51" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:comment "Reviewed: Hengartner, M, Ranganathan, S, Vaux, D, 0000-00-00 00:00:00" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:organism b2rreactome:Homo_sapiens-Homo_sapiens .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayComponent b2rreactome:Homo_sapiens-Extrinsic_Pathway_for_Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayComponent b2rreactome:Homo_sapiens-Intrinsic_Pathway_for_Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayComponent b2rreactome:Homo_sapiens-Activation_of__Effector_Caspases .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayComponent b2rreactome:Homo_sapiens-Apoptotic_execution__phase .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayComponent b2rreactome:Homo_sapiens-Regulation_of_Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Reactome109581 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-REACT_578.2 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_14561771 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_4561027 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_14634621 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_15218528 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_12505355 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_12189384 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_12209154 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayOrder b2rreactome:Homo_sapiens-Apoptotic_execution__phaseStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayOrder b2rreactome:Homo_sapiens-Extrinsic_Pathway_for_ApoptosisStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayOrder b2rreactome:Homo_sapiens-Intrinsic_Pathway_for_ApoptosisStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayOrder b2rreactome:Homo_sapiens-Regulation_of_ApoptosisStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayOrder b2rreactome:Homo_sapiens-Activation_of__Effector_CaspasesStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:dataSource b2rreactome:Homo_sapiens-ReactomeDataSource .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:displayName Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:name "Apoptosis" .
b2rreactome:Homo_sapiens-Apoptosis dcterms:rights <http://www.reactome.org/disclaimer.html> .
b2rreactome:Homo_sapiens-Apoptosis <http://bio2rdf.org/bio2rdf_resource:url> <http://bio2rdf.org/html/reactome:Homo_sapiens-Apoptosis> .
}
<http://rdf.farmbio.uu.se/chembl/sparql> {
<http://linkedchemistry.info/chembl/assay/a325093> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rdf.farmbio.uu.se/chembl/onto/#Assay> .
<http://linkedchemistry.info/chembl/assay/a325093> <http://www.w3.org/2000/01/rdf-schema#label> "CHEMBL860910" .
<http://linkedchemistry.info/chembl/chemblid/CHEMBL860910> <http://www.w3.org/2002/07/owl#equivalentClass> <http://linkedchemistry.info/chembl/assay/a325093> .
<http://linkedchemistry.info/chembl/assay/a325093> <http://www.w3.org/2002/07/owl#equivalentClass> <http://linkedchemistry.info/chembl/chemblid/CHEMBL860910> .
<http://linkedchemistry.info/chembl/chemblid/CHEMBL860910> <http://semanticscience.org/resource/CHEMINF_000200> <http://linkedchemistry.info/chembl/chemblid/CHEMBL860910/chemblid> .
<http://linkedchemistry.info/chembl/chemblid/CHEMBL860910/chemblid> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://semanticscience.org/resource/CHEMINF_000412> .
<http://linkedchemistry.info/chembl/chemblid/CHEMBL860910/chemblid> <http://semanticscience.org/resource/SIO_000300> "CHEMBL860910" .
<http://linkedchemistry.info/chembl/assay/a325093> <http://rdf.farmbio.uu.se/chembl/onto/#hasDescription> "Average Binding Constant for CAMK2B ; NA=Not Active at 10 uM" .
<http://linkedchemistry.info/chembl/assay/a325093> <http://purl.org/spar/cito/citesAsDataSource> <http://linkedchemistry.info/chembl/resource/r30300> .
<http://linkedchemistry.info/chembl/assay/a325093> <http://rdf.farmbio.uu.se/chembl/onto/#hasAssayType> <http://rdf.farmbio.uu.se/chembl/onto/#Binding> .
<http://linkedchemistry.info/chembl/activity/a1650154> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rdf.farmbio.uu.se/chembl/onto/#Activity> .
<http://linkedchemistry.info/chembl/activity/a1650154> <http://purl.org/spar/cito/citesAsDataSource> <http://linkedchemistry.info/chembl/resource/r30300> .
<http://linkedchemistry.info/chembl/activity/a1650154> <http://rdf.farmbio.uu.se/chembl/onto/#onAssay> <http://linkedchemistry.info/chembl/assay/a325093> .
<http://linkedchemistry.info/chembl/activity/a1650154> <http://rdf.farmbio.uu.se/chembl/onto/#forMolecule> <http://linkedchemistry.info/chembl/molecule/m604615> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <molecule> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://purl.org/spar/cito/citesAsDataSource> <http://linkedchemistry.info/chembl/resource/r13282> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://semanticscience.org/resource/CHEMINF_000000> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://purl.obolibrary.org/obo#has_role> <http://purl.org/obo/owl/CHEBI#CHEBI_23888> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.w3.org/2002/07/owl#equivalentClass> <http://bio2rdf.org/chebi:100443> .
<http://linkedchemistry.info/chembl/chemblid/CHEMBL268854> <http://www.w3.org/2002/07/owl#equivalentClass> <http://linkedchemistry.info/chembl/molecule/m443> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.w3.org/2002/07/owl#equivalentClass> <http://linkedchemistry.info/chembl/chemblid/CHEMBL268854> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.w3.org/2000/01/rdf-schema#label> "CHEMBL268854" .
<http://linkedchemistry.info/chembl/chemblid/CHEMBL268854> <http://semanticscience.org/resource/CHEMINF_000200> <http://linkedchemistry.info/chembl/chemblid/CHEMBL268854/chemblid> .
<http://linkedchemistry.info/chembl/chemblid/CHEMBL268854/chemblid> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://semanticscience.org/resource/CHEMINF_000412> .
<http://linkedchemistry.info/chembl/chemblid/CHEMBL268854/chemblid> <http://semanticscience.org/resource/SIO_000300> "CHEMBL268854" .
<http://linkedchemistry.info/chembl/molecule/m443> <http://semanticscience.org/resource/CHEMINF_000200> <http://linkedchemistry.info/chembl/molecule/m443/molform> .
<http://linkedchemistry.info/chembl/molecule/m443/molform> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://semanticscience.org/resource/CHEMINF_000042> .
<http://linkedchemistry.info/chembl/molecule/m443/molform> <http://semanticscience.org/resource/SIO_000300> "C27H23ClN4O2" .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.blueobelisk.org/chemistryblogs/smiles> "Cc1nc(O)c2cc(CN(CC#C)c3ccc(cc3)C(=O)NCc4ccc(Cl)cc4)ccc2n1" .
<http://linkedchemistry.info/chembl/molecule/m443> <http://semanticscience.org/resource/CHEMINF_000200> <http://linkedchemistry.info/chembl/molecule/m443/smiles> .
<http://linkedchemistry.info/chembl/molecule/m443/smiles> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://semanticscience.org/resource/CHEMINF_000018> .
<http://linkedchemistry.info/chembl/molecule/m443/smiles> <http://semanticscience.org/resource/SIO_000300> "Cc1nc(O)c2cc(CN(CC#C)c3ccc(cc3)C(=O)NCc4ccc(Cl)cc4)ccc2n1" .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.blueobelisk.org/chemistryblogs/inchi> "InChI=1S/C27H23ClN4O2/c1-3-14-32(17-20-6-13-25-24(15-20)27(34)31-18(2)30-25)23-11-7-21(8-12-23)26(33)29-16-19-4-9-22(28)10-5-19/h1,4-13,15H,14,16-17H2,2H3,(H,29,33)(H,30,31,34)" .
<http://linkedchemistry.info/chembl/molecule/m443> <http://semanticscience.org/resource/CHEMINF_000200> <http://linkedchemistry.info/chembl/molecule/m443/inchi> .
<http://linkedchemistry.info/chembl/molecule/m443/inchi> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://semanticscience.org/resource/CHEMINF_000113> .
<http://linkedchemistry.info/chembl/molecule/m443/inchi> <http://semanticscience.org/resource/SIO_000300> "InChI=1S/C27H23ClN4O2/c1-3-14-32(17-20-6-13-25-24(15-20)27(34)31-18(2)30-25)23-11-7-21(8-12-23)26(33)29-16-19-4-9-22(28)10-5-19/h1,4-13,15H,14,16-17H2,2H3,(H,29,33)(H,30,31,34)" .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.w3.org/2002/07/owl#equivalentClass> <http://rdf.openmolecules.net/?InChI=1S/C27H23ClN4O2/c1-3-14-32(17-20-6-13-25-24(15-20)27(34)31-18(2)30-25)23-11-7-21(8-12-23)26(33)29-16-19-4-9-22(28)10-5-19/h1,4-13,15H,14,16-17H2,2H3,(H,29,33)(H,30,31,34)> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.blueobelisk.org/chemistryblogs/inchikey> "IQCINSLNRQILLY-UHFFFAOYSA-N" .
<http://linkedchemistry.info/chembl/molecule/m443> <http://semanticscience.org/resource/CHEMINF_000200> <http://linkedchemistry.info/chembl/molecule/m443/inchikey> .
<http://linkedchemistry.info/chembl/molecule/m443/inchikey> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://semanticscience.org/resource/CHEMINF_000059> .
<http://linkedchemistry.info/chembl/molecule/m443/inchikey> <http://semanticscience.org/resource/SIO_000300> "IQCINSLNRQILLY-UHFFFAOYSA-N" .
}
<http://beta.sparql.uniprot.org/> {
<http://purl.uniprot.org/uniprot/Q6GZX4> rdf:type up:Protein .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:label "Putative transcription factor 001R" .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:citation upcitation:15165820 .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:classifiedWith <http://purl.uniprot.org/keywords/10> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:classifiedWith <http://purl.uniprot.org/go/0006351> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:classifiedWith <http://purl.uniprot.org/keywords/805> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:classifiedWith <http://purl.uniprot.org/go/0006355> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:classifiedWith <http://purl.uniprot.org/keywords/1185> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:classifiedWith <http://purl.uniprot.org/go/0046782> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:existence up:Predicted_Existence .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:organism <http://purl.uniprot.org/taxonomy/654924 .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:recommendedName <http://purl.uniprot.org/SHA-384/0777234937D8B63494C8D5F1E2AA13EA7B92452085F2FD9AA79C8DF96BF8234173E353B71AB291B114FFF71D7DB823AE> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:representativeFor <http://purl.uniprot.org/uniref/UniRef50_Q6GZX4> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:representativeFor <http://purl.uniprot.org/uniref/UniRef100_Q6GZX4> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:representativeFor <http://purl.uniprot.org/uniref/UniRef90_Q6GZX4> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:seedFor <http://purl.uniprot.org/uniref/UniRef100_Q6GZX4> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:seedFor <http://purl.uniprot.org/uniref/UniRef90_Q6GZX4> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:sequence <http://purl.uniprot.org/isoforms/Q6GZX4-1> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:created "2011-06-28" .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:mnemonic "001R_FRG3G" .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:modified "2012-04-18" .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:reviewed "true" .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:version "24" .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/embl-cds/AAT09660.1> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/refseq/YP_031579.1> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/proteinmodelportal/Q6GZX4> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/geneid/2947773> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/protclustdb/CLSP2511514> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/interpro/IPR007031> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/pfam/PF04947> .
upcitations:15165820 rdf:type up:Journal_Citation .
upcitations:15165820 rdfs:comment "Frog virus 3 (FV3) is the type species member of the genus Ranavirus (family Iridoviridae). To better understand the molecular mechanisms involved in the replication of FV3 including transcription of its highly methylated DNA genome we have determined the complete nucleotide sequence of the FV3 genome. The FV3 genome is 105903 bp long excluding the terminal redundancy. The G + C content of FV3 genome is 55% and it encodes 98 nonoverlapping potential open reading frames (ORFs) containing 50-1293 amino acids. Eighty-four ORFs have significant homology to known proteins of other iridoviruses whereas twelve of these unique FV3 proteins do not share homology to any known protein. A microsatellite containing a stretch of 34 tandemly repeated CA dinucleotide in a noncoding region was detected. To date no such sequence has been reported in any animal virus." .
upcitations:15165820 up:name "Virology" .
upcitations:15165820 up:author "Barkman T.J." .
upcitations:15165820 up:author "Essani K." .
upcitations:15165820 up:author "Tan W.G." .
upcitations:15165820 up:author "Gregory Chinchar V." .
upcitations:15165820 up:date "2004" .
upcitations:15165820 up:pages "70-84" .
upcitations:15165820 up:title "Comparative genomic analyses of frog virus 3 type species of the genus Ranavirus (family Iridoviridae)." .
upcitations:15165820 up:volume "323" .
upcitations:15165820 skos:exactMatch http://purl.uniprot.org/pubmed/15165820 .
upcitations:15165820 dcterms:identifier "doi:10.1016/j.virol.2004.02.019" .
}
# EBI gene expression atlas
<http://wwwdev.ebi.ac.uk/fgpt/gxa-sparql/sparql> {
# main linking point to the GXA data is the ensembl id and the uniprot id. 
<http://identifiers.org/ensembl/ENSG00000116962> sio:'encodes' <http://identifiers.org/ensembl/ENSP00000264187> .
<http://identifiers.org/ensembl/ENST00000264187> sio:'translatedTo' <http://identifiers.org/ensembl/ENSP00000264187> .
<http://identifiers.org/ensembl/ENST00000264187> rdfs:seeAlso ?uniprotProtein .
# differential expression value
?diffexp a sio:'differential gene expression value' .
?diffexp sio:'is attribute of' <http://identifiers.org/ensembl/ENSG00000116962> .
?diffexp sio:'has value' ?diffvalue . # e.g. UP, DOWN 
?diffexp sio'has attribute' [ a sio:p_value; sio:has-value 0.00005] .
# experiment factor from EFO 
?iv a sio:'independent variable' .
?iv sio:'represents' efo:'experimental factor' .
?iv sio:'in relation to' ?diffexp .
}
# parses up to here.
http://ops-virtuoso.scai.fraunhofer.de:8894/sparql {
<http://www.scai.fraunhofer.de/rdf/entity/CC_BY-SA_3.0>
a dcterms:LicenseDocument ;
rdfs:label "CC BY-SA 3.0"^^xsd:string ;
dcterms:references "https://creativecommons.org/licenses/by-sa/3.0/"^^xsd:string ;
dcterms:valid "2013-02-01T13:59:07.098Z"^^xsd:dateTime .
scai:Fraunhofer_SCAI
a foaf:Organization , prov:Agent ;
rdfs:label "Fraunhofer SCAI"^^xsd:string .
<http://www.scai.fraunhofer.de/rdf/intern/medline12short.xml>
a prov:Entity , pao:DocumentSet ;
dcterms:title "medline12short.xml"^^xsd:string .
<http://www.scai.fraunhofer.de/rdf/intern/Department_of_Diagnostic_Radiology__Yale_University_School_of_Medicine__New_Haven__Conn.__USA.>
a foaf:Organization ;
rdfs:label "Department of Diagnostic Radiology, Yale University School of Medicine, New Haven, Conn., USA."@en ;
foaf:member base:Charney__D_S , base:Bremner__J_D , base:Southwick__S_M , base:Staib__L_H , base:McGlashan__T , base:Narayan__M .
scai:XMLAnnotator
a prov:Activity ;
prov:endedAtTime "2012-08-06T12:59:07.1Z"^^xsd:dateTime ;
prov:startedAtTime "2012-08-06T12:59:07.1Z"^^xsd:dateTime ;
prov:used <http://www.scai.fraunhofer.de/rdf/intern/medline12short.xml> ;
prov:wasAssociatedWith
scai:chaupt .
base:Staib__L_H
a foaf:Person , dcterms:Agent ;
rdfs:label "Staib, L H"^^xsd:string .
scai:chaupt
a foaf:Person , dcterms:Agent , prov:Agent ;
rdfs:label "chaupt"^^xsd:string ;
prov:actedOnBehalfOf
scai:Fraunhofer_SCAI ;
foaf:member scai:Fraunhofer_SCAI .
<http://www.scai.fraunhofer.de/rdf/intern/medline12short.xml_XMLAnnotator>
a <http://purl.org/dc/dcmitype/Dataset> , prov:Entity , pao:DocumentSet ;
ao:item <http://www.scai.fraunhofer.de/rdf/intern/10553744> ;
dcterms:creator scai:chaupt ;
dcterms:license <http://www.scai.fraunhofer.de/rdf/entity/CC_BY-SA_3.0> ;
dcterms:rightsHolder
scai:chaupt ;
dcterms:title "medline12short.xml_XMLAnnotator"^^xsd:string ;
prov:atTime "2012-11-12T13:59:07.097Z"^^xsd:dateTime ;
prov:wasAttributedTo
scai:chaupt ;
prov:wasDerivedFrom <http://www.scai.fraunhofer.de/rdf/intern/medline12short.xml> ;
prov:wasGeneratedBy scai:XMLAnnotator .
base:Charney__D_S
a foaf:Person , dcterms:Agent ;
rdfs:label "Charney, D S"^^xsd:string .
base:Bremner__J_D
a foaf:Person , dcterms:Agent ;
rdfs:label "Bremner, J D"^^xsd:string .
base:Southwick__S_M
a foaf:Person , dcterms:Agent ;
rdfs:label "Southwick, S M"^^xsd:string .
base:The_American_journal_of_psychiatry
a dcterms:Agent ;
rdfs:label "The American journal of psychiatry"^^xsd:string .
<http://www.scai.fraunhofer.de/rdf/intern/10553744>
a str:Document ;
dcterms:creator base:Charney__D_S , base:Bremner__J_D , base:Southwick__S_M , base:Staib__L_H , base:McGlashan__T , base:Narayan__M ;
dcterms:date "1999-10-31T13:59:07.1Z"^^xsd:dateTime ;
dcterms:identifier "10553744"^^xsd:string ;
dcterms:publisher base:The_American_journal_of_psychiatry ;
dcterms:source "file://medline12short.xml"^^xsd:string ;
dcterms:title "Neural correlates of memories of childhood sexual abuse in women with and without posttraumatic stress disorder."@en .
base:McGlashan__T
a foaf:Person , dcterms:Agent ;
rdfs:label "McGlashan, T"^^xsd:string .
base:Narayan__M
a foaf:Person , dcterms:Agent ;
rdfs:label "Narayan, M"^^xsd:string .
}
:Linksets {
up:Q12345 skos:broadMatch end:000xxxxx .
}

== # VoID ==

{| style="color: black; color: #733;" width="85%" class="wikitable"
| colspan="3" | <http://sparql.wikipathways.org>
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''pav:createdOn'''
| style="width: 60%; background-color: orange;"| '''"2012-10-25"^^xsd:date ;'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''pav:createdBy'''
| style="width: 60%; background-color: orange;"| ''<https://orcid.org/0000-0001-9773-4008> ;''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''pav:createdAt'''
| style="width: 60%; background-color: orange;"| '''dbpedia:Maastricht_University ;'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''dcterms:license'''
| style="width: 60%; background-color: orange;"| ''<http://creativecommons.org/licenses/by/3.0/> .''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| ''<http://sparql.wikipathways.org> .''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:triples'''
| style="width: 60%; background-color: orange;"| '''"1794104"^^xsd:integer ;'''
|-

| colspan="3" | :ChEMBL
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''pav:createdOn'''
| style="width: 60%; background-color: orange;"| '''"2012-10-25"^^xsd:date ;'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:foo'''
| style="width: 60%; background-color: orange;"| '''void:bar .'''
|}

== Triplestore map ==

{| style="color: black; color: #733;" width="85%" class="wikitable"
| colspan="3" | WikiPathways
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''foaf:page'''
| style="width: 60%; background-color: orange;"| ''' http://www.wikipathways.org'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| '''http://sparql.wikipathways.org'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:uriLookupEndpoint'''
| style="width: 60%; background-color: orange;"| '''http://rdf.wikipathways.org '''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''prov:deployedSoftware'''
| style="width: 60%; background-color: orange;"| '''dbpedia:Virtuoso_Universal_Server '''
|-
| colspan="3" | :ChEMBL-RDF
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''foaf:page'''
| style="width: 60%; background-color: orange;"| '''https://github.com/egonw/chembl.rdf'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| ''' http://rdf.farmbio.uu.se/chembl/sparql '''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| ''' http://ragamuffin.bigcat.unimaas.nl/chembl/sparql '''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''prov:deployedSoftware'''
| style="width: 60%; background-color: orange;"| '''dbpedia:Virtuoso_Universal_Server '''
|-
| colspan="3" | :Uniprot
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''foaf:page'''
| style="width: 60%; background-color: orange;"| '''http://www.uniprot.org'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| ''' http://beta.sparql.uniprot.org '''
|-
| colspan="3" | :Gene expression atlas
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''foaf:page'''
| style="width: 60%; background-color: orange;"| '''tba'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| ''' http://wwwdev.ebi.ac.uk/fgpt/gxa-sparql/sparql '''
|-
|}

HCLSIG/LODD/Data

Ewilligh — Thu, 15 Nov 2012 15:04:09 GMT

Ewilligh: /* LODD-related datasets that the LODD group already made available as Linked Data */

__NOTOC__
=== LODD-related datasets that the LODD group already made available as Linked Data ===

{| border="1" cellpadding="2" cellspacing="0"
| '''Name'''
| '''Topic'''
| '''Short Description'''
| '''Size and coverage'''
| '''Status / Activity'''
| '''Example Instances'''
| '''SPARQL Endpoint'''
|-
| [http://www4.wiwiss.fu-berlin.de/drugbank/ DrugBank]
| Drugs
| [http://www.drugbank.ca/ Drugbank.ca] provides drug (i.e., chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e., sequence, structure, and pathway) information ({{doi|10.1093/nar/gkj067}})
| 766,920 triples; 4,800 drugs, 2,500 protein sequences
| updated regularly
| Varenicline [http://beckr.org/marbles?uri=http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugs/DB01273 via Marbles], [http://demo.openlinksw.com/ode/?uri=http%3A%2F%2Fwww4.wiwiss.fu-berlin.de%2Fdrugbank%2Fresource%2Fdrugs%2FDB01273 via OpenLink Data Explorer]
| http://www4.wiwiss.fu-berlin.de/drugbank/sparql
|-
| [http://linkedct.org/ LinkedCT]
| Clinical Trials
| Linked data source of trials from [http://clinicaltrials.gov ClinicalTrials.gov]
| ~25 million triples, 106,000 trials (as of April 2011)
| Updated automatically at all times, refer to [http://linkedct.org/faq/ FAQ] for more details.
| [http://data.linkedct.org/resource/condition/breast-cancer/ Breast Cancer] (Condition), a [http://data.linkedct.org/resource/trial/nct00999557/ NCT00999557] (Trial), [http://data.linkedct.org/resource/city/toronto/ Toronto] (City).
| http://data.linkedct.org/sparql
|-
| [http://www4.wiwiss.fu-berlin.de/dailymed/ DailyMed]
| Drugs
| [http://dailymed.nlm.nih.gov/dailymed/about.cfm dailymed.nlm.nih.gov] provides information about approved prescription drugs, includes FDA approved labels (package inserts)
| 164,276 triples; 4,039 drugs
| possibly subsumed by LinkedSPLs (see below)
| "Sterile Water (Irrigant)" [http://beckr.org/marbles?uri=http://www4.wiwiss.fu-berlin.de/dailymed/resource/drugs/492 via Marbles], [http://demo.openlinksw.com/ode/?uri=http%3A%2F%2Fwww4.wiwiss.fu-berlin.de%2Fdailymed%2Fresource%2Fdrugs%2F492 via OpenLink Data Explorer]
| http://www4.wiwiss.fu-berlin.de/dailymed/sparql
|-
| [http://dbpedia.org/About DBpedia]
| Drugs/ Diseases/ Proteins
| RDF data about 2.49 million things that has been extracted from Wikipedia
| 218 million RDF triples; 2,300 drugs, 2,200 proteins
| updated every 3 months
| [http://dbpedia.org/resource/Aspirin Aspirin], [http://dbpedia.org/resource/HIV HIV]
| http://dbpedia.org/sparql
|-
| [http://www4.wiwiss.fu-berlin.de/diseasome/ Diseasome]
| Diseases / Genes
| [http://www.nd.edu/~alb/Publication06/145-HumanDisease_PNAS-14My07-Proc/Suppl/ Diseasome] describes characteristics of disorders and disease genes linked by known disorder–gene associations
| 91,182 triples; 2,600 genes
| updated 2006
| Alzheimer's [http://beckr.org/marbles?uri=http://www4.wiwiss.fu-berlin.de/diseasome/resource/diseases/74 via Marbles], [http://demo.openlinksw.com/ode/?uri=http%3A%2F%2Fwww4.wiwiss.fu-berlin.de%2Fdiseasome%2Fresource%2Fdiseases%2F74 via OpenLink Data Explorer]
| http://www4.wiwiss.fu-berlin.de/diseasome/sparql
|-
| [http://code.google.com/p/junsbriefcase/wiki/TGDdataset RDF-TCM]
| Genes / Diseases / Medicine / Ingredients
| Traditional Chinese medicine, gene and disease association dataset and a linkset mapping TCM gene symbols to Extrez Gene IDs created by Neurocommons
| 117,643
| updated August 2009 (stable)
| [http://purl.org/net/tcm/tcm.lifescience.ntu.edu.tw/id/medicine/Ginkgo_biloba Ginkgo biloba]
| http://hcls.deri.org/sparql; graph name: http://hcls.deri.org/resource/graph/tcm
|-
| [http://www.nlm.nih.gov/research/umls/rxnorm/ RxNorm]
| Drugs
| A linked version of the NLM's RxNorm database that connects prescription drugs, ingredients, and NDC through RXCUI a concept unique identifier. RxNorm is a product developed by NIH’s National Library of Medicine. It currently interlinks 12 different drug vocabularies around a unique concept identifier. Due to licensing only six of the drug vocabularies are made available as part of the LODD cloud. This includes: Medical Subject Headings,, Metathesaurus FDA National Drug Code Directory, Metathesaurus FDA Structured Product Labels, National Drug File, RxNorm Vocabulary, Veterans Health Administration National Drug File
Links are provided connecting RxNorm to drug bank and to the UMLS.
|over 7.7 million triples; 165,806 RXCUI (Concept Unique Identifiers) Unique drugs and ingredients; 332,754 RXAUI (Atomic Unique Identifiers) sourced terms
| Based on 3/2010 Rxnorm Release; Last updated 5/2010
| [http://link.informatics.stonybrook.edu/rxnorm/RXAUI/2994963 Singulair from the Metathesaurus FDA Structured Product Labels]
| http://link.informatics.stonybrook.edu/sparql/
|-
| [http://www4.wiwiss.fu-berlin.de/sider/ SIDER]
| Diseases / Side Effects
| [http://sideeffects.embl.de/ SIDER] contains information on marketed drugs and their adverse effects ({{doi|10.1038/msb.2009.98}})
| 192,515 triples; 63,000 adverse effect reports, 1,737 genes
| updated 2009
| Confusion [http://beckr.org/marbles?uri=http://www4.wiwiss.fu-berlin.de/sider/resource/side_effects/C0009676 via Marbles]
| http://www4.wiwiss.fu-berlin.de/sider/sparql
|-
| [http://www4.wiwiss.fu-berlin.de/stitch/ STITCH]
| Chemicals / Proteins
| [http://stitch.embl.de/ STITCH] contains information on chemicals, proteins, and their interactions ({{doi|10.1093/nar/gkm795}})
| 7,500,000 chemicals; 500,000 proteins; 370 organisms
| updated July 2009
| Lactose [http://beckr.org/marbles?uri=http://www4.wiwiss.fu-berlin.de/stitch/resource/chemicals/CID000000294 via Marbles]
| http://www4.wiwiss.fu-berlin.de/stitch/sparql
|-
| [http://www4.wiwiss.fu-berlin.de/medicare/ Medicare]
| Medicare Formulary
| xxx
| xxx
| xxx
| xxx
| http://www4.wiwiss.fu-berlin.de/medicare/sparql
|-
| [http://www.ebi.ac.uk/chembl/ ChEMBL]
| Chemical / Assays (Proteins, Organisms) / Papers
| [http://www.ebi.ac.uk/chembl/ ChEMBL] contains information on trial drugs with information about activity against targets like but not limited to proteins. All is backed up by and linked to literature. Includes links to Bio2RDF for ChEBI and Uniprot. License: CC-BY-SA.
| ~130M triples
| Updated 2010-01
| A [http://rdf.farmbio.uu.se/chembl/snorql/?describe=http://linkedchemistry.info/chembl/activity/a2642163 IC50 activity].
| http://rdf.farmbio.uu.se/chembl/sparql
|-
| [http://apps.who.int/ghodata/ WHO's Global Health Observatory (GHO)]
| Infectious Diseases /Demography / Socioeconomic Conditions / Environmental Factors
| Data and statistics for infectious diseases at country, regional, and global levels
| ~3M triples
| Updated 2012-05
| xxx
| http://gho.aksw.org
|-
| [http://www.dbmi.pitt.edu/nlpfront University of Pittsburgh NLP Repository]
| Drugs / Procedures / Diagnoses
| A semantic index of concepts present in 800 full-text clinical notes from the University of Pittsburgh NLP Repository
| 38.664
| Proof of concept -- Updated 02/25/2011
| [http://dbmi-icode-01.dbmi.pitt.edu:8080/sparql?default-graph-uri=&query=SELECT+DISTINCT+%3Fproperty+%3FhasValue+%3FisValueOf%0D%0AWHERE+{%0D%0A++{+%3Chttp%3A%2F%2Fpurl.org%2Fnet%2Fnlprepository%2Ftest%23report_1460%3E+%3Fproperty+%3FhasValue+}%0D%0A++UNION%0D%0A++{+%3FisValueOf+%3Fproperty+%3Chttp%3A%2F%2Fpurl.org%2Fnet%2Fnlprepository%2Ftest%23report_1460%3E+}%0D%0A}%0D%0AORDER+BY+%28!BOUND%28%3FhasValue%29%29+%3Fproperty+%3FhasValue+%3FisValueOf%0D%0A&format=text%2Fhtml&debug=on&timeout= Concepts from a sample radiology report]
| [http://dbmi-icode-01.dbmi.pitt.edu:8080/sparql http://dbmi-icode-01.dbmi.pitt.edu:8080/sparql]
|-
| [http://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/front-page.html The Drug Interaction Knowledge Base]
| Drugs / Metabolic Inhibition Drug-drug Interactions (DDIs) / Claims and Evidence for drug mechanisms and DDIs
| A D2R server of more than 60 drugs currently in the DIKB
| >41K
| Updated 10/01/2012
| [http://dbmi-icode-01.dbmi.pitt.edu:2020/page/Drugs/paroxetine paroxetine], [http://dbmi-icode-01.dbmi.pitt.edu:2020/page/Drugs/atorvastatin atorvastatin]
| http://dbmi-icode-01.dbmi.pitt.edu:2020/
|-
| [http://purl.org/net/nlprepository/linkedSPLs Linked Structured Product Labels (LinkedSPLs)]
| All FDA-approved Structured Product Labels (SPLs) for currently marketed drugs enhanced with indexing to pharmacogenomics information and NDF-RT drug class assignments
| Data available via a D2R server (sample data), as an RDF dumpt (full data, ntriples), or from Virtuoso RDF Store (contact maintainer)
| 1,604,893 triples, 36,000+ product labels
| Updated every Thursday using information from the DailyMed RSS feed
| [http://thedatahub.org/dataset/linked-structured-product-labels/resource/918071ae-f570-4728-98b7-5b447ab42ab8 SPL for Venlafaxine Hydrochloride (American Health Packaging)]
| http://purl.org/net/nlprepository/linkedSPLs
|}

[[File:2010-12-04_lodd_cloud.png|600px]]

A graph of some of the LODD datasets (dark grey), related biomedical datasets (light grey), related general-purpose datasets (white) and their interconnections. Line weights correspond to the number of links. The direction of an arrow indicates the dataset that contains the links, e.g., an arrow from A to B means that dataset A contains RDF triples that use identifiers from B. Bidirectional arrows usually indicate that the links are mirrored in both datasets.
More on the interlinking methodology and statistics can be found on the [[../Interlinking|Interlinking]] page.

The LODD datasets have been crawled by the SWSE Semantic Web search engine and can be accessed via a faceted browsing interface at [http://visinav.deri.org/hcls/] ([http://visinav.deri.org/hcls/list?keyword=varenicline Example query: Varenicline]).

Most of the LODD datasets have also been integrated into the SPARQL endpoint of the HCLS Knowledge Base, see [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/DERI_HCLS_KB the wiki page of the HCLS KB] for further information.

=== Bio2RDF Data Sets ===

The [http://bio2rdf.org/ Bio2RDF project] has published 40 biology-, gene- and medical-related datasets (altogether 2.3 billion triples).
The datasets are available via SPARQL endpoints and as Linked Data. It is recommended that you use the [http://sourceforge.net/project/platformdownload.php?group_id=142631 Bio2RDF Java Servlet], and optionally [http://quebec.bio2rdf.org/download/virtuoso/indexed/ download the databases] for efficient personal use. Running your own instance of the [http://virtuoso.openlinksw.com/wiki/main/Main/VirtEC2AMIBio2rdfInstall OpenLink Virtuoso AMI for EC2] is also an option (and for basic URI resolution doesn't require the Java Servlet, although if you want advanced queries you should still download it and configure it to query your EC2 sparql endpoint).

* [http://www.freebase.com/view/user/bio2rdf/public/sparql Bio2RDF sparql endpoint list] [http://rdf.freebase.com/rdf/user/bio2rdf/public/sparql Sparql endpoint list in RDF]
* [http://linkeddata.openlinksw.com:8891/pubmed:10500064 Identification of an autoimmune enteropathy-related 75-kilodalton antigen], via an [[OpenLinkSoftware|OpenLink]] hosted edition of [[Bio2Rdf]]
* [http://linkeddata.openlinksw.com:8891/pubmed:9636670 Structure of the gene encoding the human cyclin-dependent kinase inhibitor p18 and mutational analysis in breast cancer], via an [[OpenLinkSoftware|OpenLink]] hosted edition of [[Bio2Rdf]]
* [http://beckr.org/marbles?uri=http%3A%2F%2Fbio2rdf.org%2Fpubmed%3A9626117 PubMed article] viewed using the Marbles Linked Data browser.
* [http://beckr.org/marbles?lang=en&uri=http%3A%2F%2Fbio2rdf.org%2Ffoaf%3AClemens%2C_T_L PubMed author] viewed using the Marbles Linked Data browser.
* [http://beckr.org/marbles?uri=http%3A%2F%2Fbio2rdf.org%2Fomim%3A161555 OMIM Killer Cell Lectin-Like Receptor] viewed using the Marbles Linked Data browser.
* [http://iws.seu.edu.cn/services/falcons/objectsearch/queryresult.jsp?query=%22KILLER+CELL%22 Falcons Search for KILLER CELL]. The Bio2RDF data has been crawled by the Falcons Semantic Web Search engine. This is an example on how the data is accessed by humans using the search engine. Falcons also offers an API that can by used by applications to access the data.

=== Chem2bio2RDF ===

* Information about the [http://chem2bio2rdf.org/ chem2bio2rdf] data sets

=== Data Sets for the LODD Task ===

To complement the drug-related Web of Data build by the LODD effort, the following data sets could/should also be published as Linked Data.

The LODD effort is currently gathering more information about relevant datasets. See also [[/DataSetEvaluation|Evaluation of LODD Data Sets]] for current evaluation results.

* [http://library.dialog.com/bluesheets/html/bl0107.html Adis R&D Insight]
* [http://www.ebi.ac.uk/chebi/ chEBI]
* [http://xpdb.nist.gov/pdb/chemblast.html ChemBlast]
* [http://www.chemspider.com/ ChemSpider]
* [http://ClinicalTrials.gov ClinicalTrials.gov]
* [http://www.citeline.com/trialtrove.html Citeline TrialTrove]
* [http://dailymed.nlm.nih.gov/dailymed/about.cfm DailyMed]
* [http://dbpedia.org/About DBpedia]
* [http://www.nd.edu/~alb/Publication06/145-HumanDisease_PNAS-14My07-Proc/Suppl/ Diseasome]
* [http://www.drugbank.ca/ Drug Bank]
* [http://www.virtualref.com/abs/72.htm DrugDB]
* [http://www.ncbi.nlm.nih.gov/pubmed/17921997 Drugome]
* [http://lsdis.cs.uga.edu/projects/asdoc/ Drug Ontology]
* [http://scientific.thomsonreuters.com/products/iddb/ Investigational Drug Database] - Proprietary
* [http://www.ovid.com/site/catalog/DataBase/1244.jsp?top=2&mid=3&bottom=7&subsection=10 IMS]
* [http://www.genome.jp/kegg/drug/ KEGG Drug]
* [http://Lillytrials.com LillyTrials]
* [http://www.fda.gov/medwatch/ MedWatch]
* [http://www.fda.gov/cder/ndc/ National Drug Code]
* [http://www.ncbi.nlm.nih.gov/omim/ OMIM]
* [http://www.fda.gov/cder/ob/ Orange Book]
* [http://www.pharmaprojects.com/ Pharmaprojects] - Proprietary
* [http://pubchem.ncbi.nlm.nih.gov/ PubChem]
* [http://www.nlm.nih.gov/research/umls/rxnorm/ RxNorm]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=15360858 VA NDF-RT]
* Other data sources could include blogs, discussion boards, wikis, etc.
* and....
** [http://www.who.int/globalatlas/ World Health Organization's Global Health Atlas]
** [http://www.epispider.org/ EpiSPIDER]
** [http://www.accessdata.fda.gov/Scripts/cder/DrugsatFDA/ Drugs@FDA - FDA Approved Drug Products]
** [http://www.drugdigest.org/wps/portal/ddigest DrugDigest]
** [http://humancyc.org/ HumanCyc: Encyclopedia of ''Homo sapiens'' Genes and Metabolism]
** [http://www.alzforum.org/ Alzheimer Research Forum]
** [http://wwwcf.nlm.nih.gov/umlslicense/rxtermApp/rxTerm.cfm RxTerms]
** [http://hudine.neu.edu/ HuDiNe]
** [http://wiki.medpedia.com/Cymbalta Medpedia]
** [http://tcm.lifescience.ntu.edu.tw/ TCMGeneDIT] and [[Media:HCLSIG$$LODD$$Data$TCMGeneDIT_RDF_Dataset_r1.zip|RDF dump]]
** [http://www.tuftsctsi.org/~/media/Files/CTSI/Library%20Files/FCC%20for%20CER%20Rpt%20to%20Pres%20and%20Congress_063009.ashx List of other possible data sources from page 66 onwards]

=== Alternative Herbal Medicine use case ===
* [[Data/TCMGeneDIT|TCMGeneDIT dataset]]

=== Identified Based Linkage Points ===

* INCHIs
* [[PubChem]] Compound ID (CID)
* [[PubChem]] NSC
* Chemical Abstract ID (CAS)
* New Drug Application (NDA)

=== Data Set Attributes ===

* Licensing
* Data Format
* Identifiers

HCLSIG/LODD/Data

Ewilligh — Thu, 15 Nov 2012 15:01:33 GMT

Ewilligh: Updated the example resource URI for ChEMBL.

__NOTOC__
=== LODD-related datasets that the LODD group already made available as Linked Data ===

{| border="1" cellpadding="2" cellspacing="0"
| '''Name'''
| '''Topic'''
| '''Short Description'''
| '''Size and coverage'''
| '''Status / Activity'''
| '''Example Instances'''
| '''SPARQL Endpoint'''
|-
| [http://www4.wiwiss.fu-berlin.de/drugbank/ DrugBank]
| Drugs
| [http://www.drugbank.ca/ Drugbank.ca] provides drug (i.e., chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e., sequence, structure, and pathway) information ({{doi|10.1093/nar/gkj067}})
| 766,920 triples; 4,800 drugs, 2,500 protein sequences
| updated regularly
| Varenicline [http://beckr.org/marbles?uri=http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugs/DB01273 via Marbles], [http://demo.openlinksw.com/ode/?uri=http%3A%2F%2Fwww4.wiwiss.fu-berlin.de%2Fdrugbank%2Fresource%2Fdrugs%2FDB01273 via OpenLink Data Explorer]
| http://www4.wiwiss.fu-berlin.de/drugbank/sparql
|-
| [http://linkedct.org/ LinkedCT]
| Clinical Trials
| Linked data source of trials from [http://clinicaltrials.gov ClinicalTrials.gov]
| ~25 million triples, 106,000 trials (as of April 2011)
| Updated automatically at all times, refer to [http://linkedct.org/faq/ FAQ] for more details.
| [http://data.linkedct.org/resource/condition/breast-cancer/ Breast Cancer] (Condition), a [http://data.linkedct.org/resource/trial/nct00999557/ NCT00999557] (Trial), [http://data.linkedct.org/resource/city/toronto/ Toronto] (City).
| http://data.linkedct.org/sparql
|-
| [http://www4.wiwiss.fu-berlin.de/dailymed/ DailyMed]
| Drugs
| [http://dailymed.nlm.nih.gov/dailymed/about.cfm dailymed.nlm.nih.gov] provides information about approved prescription drugs, includes FDA approved labels (package inserts)
| 164,276 triples; 4,039 drugs
| possibly subsumed by LinkedSPLs (see below)
| "Sterile Water (Irrigant)" [http://beckr.org/marbles?uri=http://www4.wiwiss.fu-berlin.de/dailymed/resource/drugs/492 via Marbles], [http://demo.openlinksw.com/ode/?uri=http%3A%2F%2Fwww4.wiwiss.fu-berlin.de%2Fdailymed%2Fresource%2Fdrugs%2F492 via OpenLink Data Explorer]
| http://www4.wiwiss.fu-berlin.de/dailymed/sparql
|-
| [http://dbpedia.org/About DBpedia]
| Drugs/ Diseases/ Proteins
| RDF data about 2.49 million things that has been extracted from Wikipedia
| 218 million RDF triples; 2,300 drugs, 2,200 proteins
| updated every 3 months
| [http://dbpedia.org/resource/Aspirin Aspirin], [http://dbpedia.org/resource/HIV HIV]
| http://dbpedia.org/sparql
|-
| [http://www4.wiwiss.fu-berlin.de/diseasome/ Diseasome]
| Diseases / Genes
| [http://www.nd.edu/~alb/Publication06/145-HumanDisease_PNAS-14My07-Proc/Suppl/ Diseasome] describes characteristics of disorders and disease genes linked by known disorder–gene associations
| 91,182 triples; 2,600 genes
| updated 2006
| Alzheimer's [http://beckr.org/marbles?uri=http://www4.wiwiss.fu-berlin.de/diseasome/resource/diseases/74 via Marbles], [http://demo.openlinksw.com/ode/?uri=http%3A%2F%2Fwww4.wiwiss.fu-berlin.de%2Fdiseasome%2Fresource%2Fdiseases%2F74 via OpenLink Data Explorer]
| http://www4.wiwiss.fu-berlin.de/diseasome/sparql
|-
| [http://code.google.com/p/junsbriefcase/wiki/TGDdataset RDF-TCM]
| Genes / Diseases / Medicine / Ingredients
| Traditional Chinese medicine, gene and disease association dataset and a linkset mapping TCM gene symbols to Extrez Gene IDs created by Neurocommons
| 117,643
| updated August 2009 (stable)
| [http://purl.org/net/tcm/tcm.lifescience.ntu.edu.tw/id/medicine/Ginkgo_biloba Ginkgo biloba]
| http://hcls.deri.org/sparql; graph name: http://hcls.deri.org/resource/graph/tcm
|-
| [http://www.nlm.nih.gov/research/umls/rxnorm/ RxNorm]
| Drugs
| A linked version of the NLM's RxNorm database that connects prescription drugs, ingredients, and NDC through RXCUI a concept unique identifier. RxNorm is a product developed by NIH’s National Library of Medicine. It currently interlinks 12 different drug vocabularies around a unique concept identifier. Due to licensing only six of the drug vocabularies are made available as part of the LODD cloud. This includes: Medical Subject Headings,, Metathesaurus FDA National Drug Code Directory, Metathesaurus FDA Structured Product Labels, National Drug File, RxNorm Vocabulary, Veterans Health Administration National Drug File
Links are provided connecting RxNorm to drug bank and to the UMLS.
|over 7.7 million triples; 165,806 RXCUI (Concept Unique Identifiers) Unique drugs and ingredients; 332,754 RXAUI (Atomic Unique Identifiers) sourced terms
| Based on 3/2010 Rxnorm Release; Last updated 5/2010
| [http://link.informatics.stonybrook.edu/rxnorm/RXAUI/2994963 Singulair from the Metathesaurus FDA Structured Product Labels]
| http://link.informatics.stonybrook.edu/sparql/
|-
| [http://www4.wiwiss.fu-berlin.de/sider/ SIDER]
| Diseases / Side Effects
| [http://sideeffects.embl.de/ SIDER] contains information on marketed drugs and their adverse effects ({{doi|10.1038/msb.2009.98}})
| 192,515 triples; 63,000 adverse effect reports, 1,737 genes
| updated 2009
| Confusion [http://beckr.org/marbles?uri=http://www4.wiwiss.fu-berlin.de/sider/resource/side_effects/C0009676 via Marbles]
| http://www4.wiwiss.fu-berlin.de/sider/sparql
|-
| [http://www4.wiwiss.fu-berlin.de/stitch/ STITCH]
| Chemicals / Proteins
| [http://stitch.embl.de/ STITCH] contains information on chemicals, proteins, and their interactions ({{doi|10.1093/nar/gkm795}})
| 7,500,000 chemicals; 500,000 proteins; 370 organisms
| updated July 2009
| Lactose [http://beckr.org/marbles?uri=http://www4.wiwiss.fu-berlin.de/stitch/resource/chemicals/CID000000294 via Marbles]
| http://www4.wiwiss.fu-berlin.de/stitch/sparql
|-
| [http://www4.wiwiss.fu-berlin.de/medicare/ Medicare]
| Medicare Formulary
| xxx
| xxx
| xxx
| xxx
| http://www4.wiwiss.fu-berlin.de/medicare/sparql
|-
| [http://www.ebi.ac.uk/chembl/ ChEMBL]
| Chemical / Assays (Proteins, Organisms) / Papers
| [http://www.ebi.ac.uk/chembl/ ChEMBL] contains information on trial drugs with information about activity against targets like but not limited to proteins. All is backed up by and linked to literature. Includes links to Bio2RDF for ChEBI and Uniprot. License: CC-BY-SA.
| ~24M triples
| Updated 2010-01
| A [http://rdf.farmbio.uu.se/chembl/snorql/?describe=http://linkedchemistry.info/chembl/activity/a2642163 IC50 activity].
| http://rdf.farmbio.uu.se/chembl/sparql
|-
| [http://apps.who.int/ghodata/ WHO's Global Health Observatory (GHO)]
| Infectious Diseases /Demography / Socioeconomic Conditions / Environmental Factors
| Data and statistics for infectious diseases at country, regional, and global levels
| ~3M triples
| Updated 2012-05
| xxx
| http://gho.aksw.org
|-
| [http://www.dbmi.pitt.edu/nlpfront University of Pittsburgh NLP Repository]
| Drugs / Procedures / Diagnoses
| A semantic index of concepts present in 800 full-text clinical notes from the University of Pittsburgh NLP Repository
| 38.664
| Proof of concept -- Updated 02/25/2011
| [http://dbmi-icode-01.dbmi.pitt.edu:8080/sparql?default-graph-uri=&query=SELECT+DISTINCT+%3Fproperty+%3FhasValue+%3FisValueOf%0D%0AWHERE+{%0D%0A++{+%3Chttp%3A%2F%2Fpurl.org%2Fnet%2Fnlprepository%2Ftest%23report_1460%3E+%3Fproperty+%3FhasValue+}%0D%0A++UNION%0D%0A++{+%3FisValueOf+%3Fproperty+%3Chttp%3A%2F%2Fpurl.org%2Fnet%2Fnlprepository%2Ftest%23report_1460%3E+}%0D%0A}%0D%0AORDER+BY+%28!BOUND%28%3FhasValue%29%29+%3Fproperty+%3FhasValue+%3FisValueOf%0D%0A&format=text%2Fhtml&debug=on&timeout= Concepts from a sample radiology report]
| [http://dbmi-icode-01.dbmi.pitt.edu:8080/sparql http://dbmi-icode-01.dbmi.pitt.edu:8080/sparql]
|-
| [http://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/front-page.html The Drug Interaction Knowledge Base]
| Drugs / Metabolic Inhibition Drug-drug Interactions (DDIs) / Claims and Evidence for drug mechanisms and DDIs
| A D2R server of more than 60 drugs currently in the DIKB
| >41K
| Updated 10/01/2012
| [http://dbmi-icode-01.dbmi.pitt.edu:2020/page/Drugs/paroxetine paroxetine], [http://dbmi-icode-01.dbmi.pitt.edu:2020/page/Drugs/atorvastatin atorvastatin]
| http://dbmi-icode-01.dbmi.pitt.edu:2020/
|-
| [http://purl.org/net/nlprepository/linkedSPLs Linked Structured Product Labels (LinkedSPLs)]
| All FDA-approved Structured Product Labels (SPLs) for currently marketed drugs enhanced with indexing to pharmacogenomics information and NDF-RT drug class assignments
| Data available via a D2R server (sample data), as an RDF dumpt (full data, ntriples), or from Virtuoso RDF Store (contact maintainer)
| 1,604,893 triples, 36,000+ product labels
| Updated every Thursday using information from the DailyMed RSS feed
| [http://thedatahub.org/dataset/linked-structured-product-labels/resource/918071ae-f570-4728-98b7-5b447ab42ab8 SPL for Venlafaxine Hydrochloride (American Health Packaging)]
| http://purl.org/net/nlprepository/linkedSPLs
|}

[[File:2010-12-04_lodd_cloud.png|600px]]

A graph of some of the LODD datasets (dark grey), related biomedical datasets (light grey), related general-purpose datasets (white) and their interconnections. Line weights correspond to the number of links. The direction of an arrow indicates the dataset that contains the links, e.g., an arrow from A to B means that dataset A contains RDF triples that use identifiers from B. Bidirectional arrows usually indicate that the links are mirrored in both datasets.
More on the interlinking methodology and statistics can be found on the [[../Interlinking|Interlinking]] page.

The LODD datasets have been crawled by the SWSE Semantic Web search engine and can be accessed via a faceted browsing interface at [http://visinav.deri.org/hcls/] ([http://visinav.deri.org/hcls/list?keyword=varenicline Example query: Varenicline]).

Most of the LODD datasets have also been integrated into the SPARQL endpoint of the HCLS Knowledge Base, see [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/DERI_HCLS_KB the wiki page of the HCLS KB] for further information.

=== Bio2RDF Data Sets ===

The [http://bio2rdf.org/ Bio2RDF project] has published 40 biology-, gene- and medical-related datasets (altogether 2.3 billion triples).
The datasets are available via SPARQL endpoints and as Linked Data. It is recommended that you use the [http://sourceforge.net/project/platformdownload.php?group_id=142631 Bio2RDF Java Servlet], and optionally [http://quebec.bio2rdf.org/download/virtuoso/indexed/ download the databases] for efficient personal use. Running your own instance of the [http://virtuoso.openlinksw.com/wiki/main/Main/VirtEC2AMIBio2rdfInstall OpenLink Virtuoso AMI for EC2] is also an option (and for basic URI resolution doesn't require the Java Servlet, although if you want advanced queries you should still download it and configure it to query your EC2 sparql endpoint).

* [http://www.freebase.com/view/user/bio2rdf/public/sparql Bio2RDF sparql endpoint list] [http://rdf.freebase.com/rdf/user/bio2rdf/public/sparql Sparql endpoint list in RDF]
* [http://linkeddata.openlinksw.com:8891/pubmed:10500064 Identification of an autoimmune enteropathy-related 75-kilodalton antigen], via an [[OpenLinkSoftware|OpenLink]] hosted edition of [[Bio2Rdf]]
* [http://linkeddata.openlinksw.com:8891/pubmed:9636670 Structure of the gene encoding the human cyclin-dependent kinase inhibitor p18 and mutational analysis in breast cancer], via an [[OpenLinkSoftware|OpenLink]] hosted edition of [[Bio2Rdf]]
* [http://beckr.org/marbles?uri=http%3A%2F%2Fbio2rdf.org%2Fpubmed%3A9626117 PubMed article] viewed using the Marbles Linked Data browser.
* [http://beckr.org/marbles?lang=en&uri=http%3A%2F%2Fbio2rdf.org%2Ffoaf%3AClemens%2C_T_L PubMed author] viewed using the Marbles Linked Data browser.
* [http://beckr.org/marbles?uri=http%3A%2F%2Fbio2rdf.org%2Fomim%3A161555 OMIM Killer Cell Lectin-Like Receptor] viewed using the Marbles Linked Data browser.
* [http://iws.seu.edu.cn/services/falcons/objectsearch/queryresult.jsp?query=%22KILLER+CELL%22 Falcons Search for KILLER CELL]. The Bio2RDF data has been crawled by the Falcons Semantic Web Search engine. This is an example on how the data is accessed by humans using the search engine. Falcons also offers an API that can by used by applications to access the data.

=== Chem2bio2RDF ===

* Information about the [http://chem2bio2rdf.org/ chem2bio2rdf] data sets

=== Data Sets for the LODD Task ===

To complement the drug-related Web of Data build by the LODD effort, the following data sets could/should also be published as Linked Data.

The LODD effort is currently gathering more information about relevant datasets. See also [[/DataSetEvaluation|Evaluation of LODD Data Sets]] for current evaluation results.

* [http://library.dialog.com/bluesheets/html/bl0107.html Adis R&D Insight]
* [http://www.ebi.ac.uk/chebi/ chEBI]
* [http://xpdb.nist.gov/pdb/chemblast.html ChemBlast]
* [http://www.chemspider.com/ ChemSpider]
* [http://ClinicalTrials.gov ClinicalTrials.gov]
* [http://www.citeline.com/trialtrove.html Citeline TrialTrove]
* [http://dailymed.nlm.nih.gov/dailymed/about.cfm DailyMed]
* [http://dbpedia.org/About DBpedia]
* [http://www.nd.edu/~alb/Publication06/145-HumanDisease_PNAS-14My07-Proc/Suppl/ Diseasome]
* [http://www.drugbank.ca/ Drug Bank]
* [http://www.virtualref.com/abs/72.htm DrugDB]
* [http://www.ncbi.nlm.nih.gov/pubmed/17921997 Drugome]
* [http://lsdis.cs.uga.edu/projects/asdoc/ Drug Ontology]
* [http://scientific.thomsonreuters.com/products/iddb/ Investigational Drug Database] - Proprietary
* [http://www.ovid.com/site/catalog/DataBase/1244.jsp?top=2&mid=3&bottom=7&subsection=10 IMS]
* [http://www.genome.jp/kegg/drug/ KEGG Drug]
* [http://Lillytrials.com LillyTrials]
* [http://www.fda.gov/medwatch/ MedWatch]
* [http://www.fda.gov/cder/ndc/ National Drug Code]
* [http://www.ncbi.nlm.nih.gov/omim/ OMIM]
* [http://www.fda.gov/cder/ob/ Orange Book]
* [http://www.pharmaprojects.com/ Pharmaprojects] - Proprietary
* [http://pubchem.ncbi.nlm.nih.gov/ PubChem]
* [http://www.nlm.nih.gov/research/umls/rxnorm/ RxNorm]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=15360858 VA NDF-RT]
* Other data sources could include blogs, discussion boards, wikis, etc.
* and....
** [http://www.who.int/globalatlas/ World Health Organization's Global Health Atlas]
** [http://www.epispider.org/ EpiSPIDER]
** [http://www.accessdata.fda.gov/Scripts/cder/DrugsatFDA/ Drugs@FDA - FDA Approved Drug Products]
** [http://www.drugdigest.org/wps/portal/ddigest DrugDigest]
** [http://humancyc.org/ HumanCyc: Encyclopedia of ''Homo sapiens'' Genes and Metabolism]
** [http://www.alzforum.org/ Alzheimer Research Forum]
** [http://wwwcf.nlm.nih.gov/umlslicense/rxtermApp/rxTerm.cfm RxTerms]
** [http://hudine.neu.edu/ HuDiNe]
** [http://wiki.medpedia.com/Cymbalta Medpedia]
** [http://tcm.lifescience.ntu.edu.tw/ TCMGeneDIT] and [[Media:HCLSIG$$LODD$$Data$TCMGeneDIT_RDF_Dataset_r1.zip|RDF dump]]
** [http://www.tuftsctsi.org/~/media/Files/CTSI/Library%20Files/FCC%20for%20CER%20Rpt%20to%20Pres%20and%20Congress_063009.ashx List of other possible data sources from page 66 onwards]

=== Alternative Herbal Medicine use case ===
* [[Data/TCMGeneDIT|TCMGeneDIT dataset]]

=== Identified Based Linkage Points ===

* INCHIs
* [[PubChem]] Compound ID (CID)
* [[PubChem]] NSC
* Chemical Abstract ID (CAS)
* New Drug Application (NDA)

=== Data Set Attributes ===

* Licensing
* Data Format
* Identifiers

HCLS/SWAT4LS2012/Hackathon

Ewilligh — Tue, 13 Nov 2012 16:26:37 GMT

Ewilligh: /* Creating a review of sparql endpoints and their support for remote federated queries. */

The SWAT4LS Hackathon is an informal event associated with the [http://swat4ls.org/ SWAT4LS] Semantic Web Applications and Tools for Life Sciences Workshops Series.

Scope of the event is to bring together experts and enthusiasts in the application of semantic technologies in healthcare and life science for open discussion and jam coding sessions.
The Hackathon will be organized on the 28th of November 2012 at [http://lacantine.org/ La Cantine, Paris] ([https://maps.google.com/maps?q=12+Galerie+Montmartre+75002+france&hl=en&ie=UTF8&ll=48.870438,2.342089&spn=0.0013,0.001869&sll=48.87053,2.342319&sspn=0.002601,0.003739&t=h&hnear=12+Galerie+Montmartre,+75002+Paris,+%C3%8Ele-de-France,+France&z=19 map]).

street: 151 rue Montmartre, Passage des Panoramas
room: 12 Galerie Montmartre
75002 Paris

(For more information, please refer to the [http://www.swat4ls.org/workshops/paris2012/| workshop website]).
The hackathon is open to workshop participants. Registration is required and space is limited!.

== Logistics ==
Projects and institutes attending include:
* OpenPhacts (http://www.openphacts.org)
* WikiPathways (http://www.wikipathways.org/index.php/WikiPathways)
* The Database Center for Life Sciences/BioHackathon (http://dbcls.rois.ac.jp/en/ http://www.biohackathon.org/)
* The W3C Consortium, Health Care and Life Sciences Interest Group ([[HCLS]])
* BioPAX (http://biopax.org)
* European Bioinformatics Institute (http://www.ebi.ac.uk)
While the agenda will be open, we are coordinating ideas that can be developd at the network in advance, to maximize the utility of the day. Co-organizers for each community will help gathering ideas and finding point of contacts.

=== Information and registrations ===
For information, [mailto:info@swat4ls.org| info _at_ swat4ls.org]

Registrations are handled via [http://swat4ls-2012.eventbrite.com/| Eventbrite]

=== Hashtag ===
[https://twitter.com/search/realtime?q=%23swat4lshack #swat4lshack]

=== Co-Organizers ===
* Andrea Splendiani
* Andra Waagmeester
* Eric Prud'hommeaux
* Toshiaki Katayama
* Ismael Navas delgado

== Open PHACTS community ==

=== Contact Point ===
* Andra Waagmeester
* Egon Willighagen

=== Proposed action points ===
# Consume [http://www.openphacts.org Open PHACTS] content in Pathway tools
# Using http://identifiers.org
# Create an example set of valuable queries
# Visualizing output
# work on further linked data integration, with possible:
## [https://ntp.niehs.nih.gov/drugmatrix/ DrugMatrix]
## [http://toxico.nibio.go.jp/open-tggates/ TG-GATEs]
## [http://thedatahub.org/nl/dataset/bio2rdf-ctd CTD] (already available as RDF, by Bio2RDF)
# shared Java client code
## for R, Bioclipse, KNIME

=== Confirmed Participants ===
* Kees Burger
* Maria Carmen Carra
* Ian Dunlop
* Chris Evelo
* Paul Groth
* Tim Harder
* Carina Haupt
* Nick Juty
* Camille Laibe
* Antonis Loizou
* Oriol Lopez
* Guillermo C. Martínez
* Nuria Queralt
* Rishi Ramgolam
* Mark Thompson
* Egon Willighagen
* Pekka Kohonen
* Ola Spjuth

== WikiPathways community ==

=== Contact Point ===
Andra Waagmeester

=== Introduction ===
[http://www.wikipathways.org/index.php/WikiPathways WikiPathways] is a online resource for pathways. Content is provided by the audience at large. I currently contains more then 2200 pathways from 21 species [http://sparqlbin.com/#4f91f23a032a87cc46c5a526a6da673a source]. Pathways are captured in a XML-based format [http://www.pathvisio.org/wiki/EverythingGpml GPML]. Recently WikiPathways was exposed as linked open data where GPML content was exported as RDF. This data is available through a SPARQL endpoint http://sparql.wikipathways.org.

=== Proposed action points ===
==== Exploring [http://www.wikipathways.org/index.php/WikiPathways WikiPathways] RDF content, making example queries ====
==== Writing federated queries to integrate pathway content with other biological data. ====
====Using [http://code.google.com/p/pathvisiorpc/ Pathvisio RPC] to consume and visualize linked pathway data====

=== Confirmed Participants ===
* Chris Evelo
* Martina Kutmon
* Alex Pico

== Database Center for Life Sciences Community / BioHackathon ==

=== Contact Point ===
Toshiaki Katayama

=== Proposed action points ===

* Ontology for genome annotation
** https://github.com/dbcls/bh12/wiki/Feature-annotation-locations-in-RDF
** https://github.com/dbcls/bh12/wiki/Genome-RDF
** https://gist.github.com/3704296

* Identifiers.org dataset definitions in RDF
** https://gist.github.com/3985701
** https://gist.github.com/1672112
** https://dl.dropbox.com/u/429992/20121031-miriam.ttl

* Text-mining for microbial/environmental genomics

=== Confirmed Participants ===
* Yasunori Yamamoto
* Toshiaki Katayama

== W3C HCLS Community ==

=== Contact Point ===
Eric Prud'hommeaux

=== Proposed action points ===
==== Making an online inventory of available resources (wiki) to document underlying schemas of available datasources.====
There are nice lists of active SPARQL endpoints [http://www.freebase.com/view/base/sparql/views/sparql_endpoint (example 1)] and [http://labs.mondeca.com/sparqlEndpointsStatus/index.html (example 2)]. Finding where the data actually links can still be challenging.

It would be really beneficial to create an overview with descriptions of different linked data sets describing the underlying structure. The first step would be to define a format where data providers describe their data in a predefined (wiki) format. This format could be based on [http://www.w3.org/TR/void/ VoID].
These description coulds then be used to create so called data landscapes in tools such as [http://vsdlc3.blogspot.be/ Semscape].

====Creating a review of sparql endpoints and their support for remote federated queries. ====
Within a federated query you can query different flavours of sparql endpoints. Since different endpoints have their own implementations and support for different SPARQL versions, it is essential to understand the different issues each type of endpoint might have. The community would benefit from a list mentioning each available SPARQL endpoint system (e.g. 4store, virtuoso, etc) and their support for different SPARQL versions. Also this list could mention specific features (e.g. soft limit in 4store) influencing the recall in federated queries.

== BioPAX Community ==

=== Contact Point ===
Ismael Navas Delgado

=== Proposed action points ===

=== Confirmed Participants ===
* Ismael Navas Delgado
* Andrea Splendiani

== EBI Gene Expression Atlas ==

=== Contact Point ===
Simon Jupp

James Malone

=== Introduction ===

Integration of gene expression data from the Gene Expression Atlas database (http://www.ebi.ac.uk/gxa). Schema description and SPARQL endpoint at http://wwwdev.ebi.ac.uk/fgpt/efosemweb.html
Differential gene expression annotated with Ensembl gene ids (identifiers.org URIs), includes mappings to Uniprot. Experiment assay and sample descriptions annotated with ontology terms from wide range of
bio-ontologies (anatomy, cells, disease etc).

=== Proposed action points ===

Linking gene expression to pathway data.

=== Confirmed Participants ===
* Simon Jupp

== Resources ==
* PathwayCommons SPARQL endpoint. Endpoint over all BioPAX representations in PathwayCommons
* Cytoscape plugin to visualize and interact with RDF knwoledge bases (new!)
* BioQueries: social site to build SPARQL queries
* Open PHACTS rdf guidelines: http://www.openphacts.org/specs/2012/WD-rdfguide-20120823/

== Data Map ==

@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix wprdf: <http://rdf.wikipathways.org/> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix wp: <http://vocabularies.wikipathways.org/wp#> .
@prefix biopax: <http://www.biopax.org/release/biopax-level3.owl#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix gpml: <http://vocabularies.wikipathways.org/gpml#> .
@prefix chembl: <http://rdf.farmbio.uu.se/chembl/onto/#> .
@prefix up: <http://purl.uniprot.org/core/> .
@prefix dbpedia: <http://dbpedia.org/page/> .
@prefix pav: <http://purl.org/pav/> .
@prefix b2rreactome: <http://bio2rdf.org/reactome:>
@prefix b2rbiopax: <http://bio2rdf.org/ns/biopax#>
@prefix b2rbiopaxresource: <http://bio2rdf.org/biopax_resource:>
@prefix up: <http://purl.uniprot.org/core/>
@prefix sio: <http://semanticscience.org/resource/>
@prefix upcitation: <http://purl.uniprot.org/citations/>
@prefix prov: <http://www.w3.org/ns/prov#>
@prefix dc: <http://purl.org/dc/elements/1.1/> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix aot: <http://purl.org/ao/types/> .
@prefix aos: <http://purl.org/ao/selectors/> .
@prefix sso: <http://nlp2rdf.lod2.eu/schema/sso/> .
@prefix void: <http://rdfs.org/ns/void#> .
@prefix pao: <http://www.scai.fraunhofer.de/prominer/vocabular/pao#> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix pav: <http://purl.org/pav/> .
@prefix ao: <http://purl.org/ao/> .
@prefix str: <http://nlp2rdf.lod2.eu/schema/string/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix base: <http://www.scai.fraunhofer.de/rdf/intern/> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix scai: <http://www.scai.fraunhofer.de/rdf/entity/> .

<http://sparql.wikipathways.org> {
# Sparql endpoint: http://sparql.wikipathways.org
# Data: http://rdf.wikipathways.org
# 
<http://identifiers.org/ncbigene/1051> rdf:type wp:GeneProduct .
<http://identifiers.org/ncbigene/1051> dcterms:isPartOf wprdf:WP3 .
<http://identifiers.org/ncbigene/1051> rdfs:label "C/EBP-beta" .
wprdf:WP3 rdf:type wp:Pathway .
wp:Pathway skos:relatedMatch biopax:Pathway .
wprdf:WP3 rdfs:label "Keap1-Nrf2 Pathway" .
wprdf:WP3 dcterms:description """Based on [http://www.nature.com/nrc/journal/v3/n10/fig_tab/nrc1189_F4.html Surh, 2003, figure 4] Nrf2 induces the expression of many
antioxidant enzymes. It is therefore thought to be involved in oxidative stress response."""^^xsd:string.
wprdf:WP3 <http://purl.org/pav/version> "48217"^^xsd:string .
wprdf:WP3 gpml:biopaxref "dba" .
wprdf:WP3 gpml:height "731.0"^^xsd:float .
wprdf:WP3 gpml:width "914.0"^^xsd:float .
wprdf:WP3 wp:category wp:CellularProcess .
wprdf:WP3 wp:organism <http://identifiers.org/taxonomy/9606> .
wprdf:WP3 wp:pathwayOntology <http://purl.obolibrary.org/obo/PW:0000378> .
wprdf:WP3 foaf:page "http://www.wikipathways.org/index.php/Pathway:WP3" .

}
<http://reactome.bio2rdf.org/sparql> {
b2rreactome:Homo_sapiens-Apoptosis rdf:type b2rbiopax:Pathway .
b2rreactome:Homo_sapiens-Apoptosis rdf:type b2rbiopaxresource:Pathway .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:name "Apoptosis" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:displayName "Apoptosis" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Reactome109581 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-REACT_578.2 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_14561771 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_4561027 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_14634621 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_15218528 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_12505355 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_12189384 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_12209154 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:comment "Apoptosis is a distinct form of cell death that is functionally and morphologically different from necrosis. Nuclear chromatin condensation, cytoplasmic shrinking, dilated endoplasmic reticulum, and membrane blebbing characterize apoptosis in general. Mitochondria remain morphologically unchanged. In 1972 Kerr et al introduced the concept of apoptosis as a distinct form of 'cell-death', and the mechanisms of various apoptotic pathways are still being revealed today. BRThe two principal pathways of apoptosis are (1) the Bcl-2 inhibitable or intrinsic pathway induced by various forms of stress like intracellular damage, developmental cues, and external stimuli and (2) the caspase 8/10 dependent or extrinsic pathway initiated by the engagement of death receptorsBR The caspase 8/10 dependent or extrinsic pathway is a death receptor mediated mechanism that results in the activation of caspase-8 and caspase-10. Activation of death receptors like Fas/CD95, TNFR1, and the TRAIL receptor is promoted by the TNF family of ligands including FASL (APO1L OR CD95L), TNF, LT-alpha, LT-beta, CD40L, LIGHT, RANKL, BLYS/BAFF, and APO2L/TRAIL. These ligands are released in response to microbial infection, or as part of the cellular, humoral immunity responses during the formation of lymphoid organs, activation of dendritic cells, stimulation or survival of T, B, and natural killer (NK) cells, cytotoxic response to viral infection or oncogenic transformation. BR The Bcl-2 inhibitable or intrinsic pathway of apoptosis is a stress-inducible process, and acts through the activation of caspase-9 via Apaf-1 and cytochrome c. The rupture of the mitochondrial membrane, a rapid process involving some of the Bcl-2 family proteins, releases these molecules into the cytoplasm. Examples of cellular processes that may induce the intrinsic pathway in response to various damage signals include: auto reactivity in lymphocytes, cytokine deprivation, calcium flux or cellular damage by cytotoxic drugs like taxol, deprivation of nutrients like glucose and growth factors like EGF, anoikis, transactivation of target genes by tumor suppressors including p53.BR In many non-immune cells, death signals initiated by the extrinsic pathway are amplified by connections to the intrinsic pathway. The connecting link appears to be the truncated BID (tBID) protein a proteolytic cleavage product mediated by caspase-8 or other enzymes." .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:comment "Edited: Gopinathrao, G, Matthews, L, Gillespie, ME, Joshi-Tope, G, 0000-00-00 00:00:00" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:comment "Authored: Alnemri, E, Hengartner, M, Tschopp, J, Tsujimoto, Y, Hardwick, JM, 2004-01-16 16:01:51" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:comment "Reviewed: Hengartner, M, Ranganathan, S, Vaux, D, 0000-00-00 00:00:00" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:dataSource b2rreactome:Homo_sapiens-ReactomeDataSource .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:organism b2rreactome:Homo_sapiens-Homo_sapiens .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayComponent b2rreactome:Homo_sapiens-Extrinsic_Pathway_for_Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayComponent b2rreactome:Homo_sapiens-Intrinsic_Pathway_for_Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayComponent b2rreactome:Homo_sapiens-Activation_of__Effector_Caspases .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayComponent b2rreactome:Homo_sapiens-Apoptotic_execution__phase .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayComponent b2rreactome:Homo_sapiens-Regulation_of_Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayOrder b2rreactome:Homo_sapiens-Apoptotic_execution__phaseStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayOrder b2rreactome:Homo_sapiens-Extrinsic_Pathway_for_ApoptosisStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayOrder b2rreactome:Homo_sapiens-Intrinsic_Pathway_for_ApoptosisStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayOrder b2rreactome:Homo_sapiens-Regulation_of_ApoptosisStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayOrder b2rreactome:Homo_sapiens-Activation_of__Effector_CaspasesStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:comment "Apoptosis is a distinct form of cell death that is functionally and morphologically different from necrosis. Nuclear chromatin condensation, cytoplasmic shrinking, dilated endoplasmic reticulum, and membrane blebbing characterize apoptosis in general. Mitochondria remain morphologically unchanged. In 1972 Kerr et al introduced the concept of apoptosis as a distinct form of 'cell-death', and the mechanisms of various apoptotic pathways are still being revealed today. BRThe two principal pathways of apoptosis are (1) the Bcl-2 inhibitable or intrinsic pathway induced by various forms of stress like intracellular damage, developmental cues, and external stimuli and (2) the caspase 8/10 dependent or extrinsic pathway initiated by the engagement of death receptorsBR The caspase 8/10 dependent or extrinsic pathway is a death receptor mediated mechanism that results in the activation of caspase-8 and caspase-10. Activation of death receptors like Fas/CD95, TNFR1, and the TRAIL receptor is promoted by the TNF family of ligands including FASL (APO1L OR CD95L), TNF, LT-alpha, LT-beta, CD40L, LIGHT, RANKL, BLYS/BAFF, and APO2L/TRAIL. These ligands are released in response to microbial infection, or as part of the cellular, humoral immunity responses during the formation of lymphoid organs, activation of dendritic cells, stimulation or survival of T, B, and natural killer (NK) cells, cytotoxic response to viral infection or oncogenic transformation. BR The Bcl-2 inhibitable or intrinsic pathway of apoptosis is a stress-inducible process, and acts through the activation of caspase-9 via Apaf-1 and cytochrome c. The rupture of the mitochondrial membrane, a rapid process involving some of the Bcl-2 family proteins, releases these molecules into the cytoplasm. Examples of cellular processes that may induce the intrinsic pathway in response to various damage signals include: auto reactivity in lymphocytes, cytokine deprivation, calcium flux or cellular damage by cytotoxic drugs like taxol, deprivation of nutrients like glucose and growth factors like EGF, anoikis, transactivation of target genes by tumor suppressors including p53.BR In many non-immune cells, death signals initiated by the extrinsic pathway are amplified by connections to the intrinsic pathway. The connecting link appears to be the truncated BID (tBID) protein a proteolytic cleavage product mediated by caspase-8 or other enzymes." .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:comment "Edited: Gopinathrao, G, Matthews, L, Gillespie, ME, Joshi-Tope, G, 0000-00-00 00:00:00" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:comment "Authored: Alnemri, E, Hengartner, M, Tschopp, J, Tsujimoto, Y, Hardwick, JM, 2004-01-16 16:01:51" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:comment "Reviewed: Hengartner, M, Ranganathan, S, Vaux, D, 0000-00-00 00:00:00" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:organism b2rreactome:Homo_sapiens-Homo_sapiens .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayComponent b2rreactome:Homo_sapiens-Extrinsic_Pathway_for_Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayComponent b2rreactome:Homo_sapiens-Intrinsic_Pathway_for_Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayComponent b2rreactome:Homo_sapiens-Activation_of__Effector_Caspases .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayComponent b2rreactome:Homo_sapiens-Apoptotic_execution__phase .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayComponent b2rreactome:Homo_sapiens-Regulation_of_Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Reactome109581 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-REACT_578.2 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_14561771 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_4561027 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_14634621 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_15218528 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_12505355 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_12189384 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_12209154 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayOrder b2rreactome:Homo_sapiens-Apoptotic_execution__phaseStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayOrder b2rreactome:Homo_sapiens-Extrinsic_Pathway_for_ApoptosisStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayOrder b2rreactome:Homo_sapiens-Intrinsic_Pathway_for_ApoptosisStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayOrder b2rreactome:Homo_sapiens-Regulation_of_ApoptosisStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayOrder b2rreactome:Homo_sapiens-Activation_of__Effector_CaspasesStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:dataSource b2rreactome:Homo_sapiens-ReactomeDataSource .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:displayName Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:name "Apoptosis" .
b2rreactome:Homo_sapiens-Apoptosis dcterms:rights <http://www.reactome.org/disclaimer.html> .
b2rreactome:Homo_sapiens-Apoptosis <http://bio2rdf.org/bio2rdf_resource:url> <http://bio2rdf.org/html/reactome:Homo_sapiens-Apoptosis> .
}
<http://rdf.farmbio.uu.se/chembl/sparql> {
<http://linkedchemistry.info/chembl/assay/a325093> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rdf.farmbio.uu.se/chembl/onto/#Assay> .
<http://linkedchemistry.info/chembl/assay/a325093> <http://www.w3.org/2000/01/rdf-schema#label> "CHEMBL860910" .
<http://linkedchemistry.info/chembl/chemblid/CHEMBL860910> <http://www.w3.org/2002/07/owl#equivalentClass> <http://linkedchemistry.info/chembl/assay/a325093> .
<http://linkedchemistry.info/chembl/assay/a325093> <http://www.w3.org/2002/07/owl#equivalentClass> <http://linkedchemistry.info/chembl/chemblid/CHEMBL860910> .
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<http://linkedchemistry.info/chembl/chemblid/CHEMBL860910/chemblid> <http://semanticscience.org/resource/SIO_000300> "CHEMBL860910" .
<http://linkedchemistry.info/chembl/assay/a325093> <http://rdf.farmbio.uu.se/chembl/onto/#hasDescription> "Average Binding Constant for CAMK2B ; NA=Not Active at 10 uM" .
<http://linkedchemistry.info/chembl/assay/a325093> <http://purl.org/spar/cito/citesAsDataSource> <http://linkedchemistry.info/chembl/resource/r30300> .
<http://linkedchemistry.info/chembl/assay/a325093> <http://rdf.farmbio.uu.se/chembl/onto/#hasAssayType> <http://rdf.farmbio.uu.se/chembl/onto/#Binding> .
<http://linkedchemistry.info/chembl/activity/a1650154> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rdf.farmbio.uu.se/chembl/onto/#Activity> .
<http://linkedchemistry.info/chembl/activity/a1650154> <http://purl.org/spar/cito/citesAsDataSource> <http://linkedchemistry.info/chembl/resource/r30300> .
<http://linkedchemistry.info/chembl/activity/a1650154> <http://rdf.farmbio.uu.se/chembl/onto/#onAssay> <http://linkedchemistry.info/chembl/assay/a325093> .
<http://linkedchemistry.info/chembl/activity/a1650154> <http://rdf.farmbio.uu.se/chembl/onto/#forMolecule> <http://linkedchemistry.info/chembl/molecule/m604615> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <molecule> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://purl.org/spar/cito/citesAsDataSource> <http://linkedchemistry.info/chembl/resource/r13282> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://semanticscience.org/resource/CHEMINF_000000> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://purl.obolibrary.org/obo#has_role> <http://purl.org/obo/owl/CHEBI#CHEBI_23888> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.w3.org/2002/07/owl#equivalentClass> <http://bio2rdf.org/chebi:100443> .
<http://linkedchemistry.info/chembl/chemblid/CHEMBL268854> <http://www.w3.org/2002/07/owl#equivalentClass> <http://linkedchemistry.info/chembl/molecule/m443> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.w3.org/2002/07/owl#equivalentClass> <http://linkedchemistry.info/chembl/chemblid/CHEMBL268854> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.w3.org/2000/01/rdf-schema#label> "CHEMBL268854" .
<http://linkedchemistry.info/chembl/chemblid/CHEMBL268854> <http://semanticscience.org/resource/CHEMINF_000200> <http://linkedchemistry.info/chembl/chemblid/CHEMBL268854/chemblid> .
<http://linkedchemistry.info/chembl/chemblid/CHEMBL268854/chemblid> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://semanticscience.org/resource/CHEMINF_000412> .
<http://linkedchemistry.info/chembl/chemblid/CHEMBL268854/chemblid> <http://semanticscience.org/resource/SIO_000300> "CHEMBL268854" .
<http://linkedchemistry.info/chembl/molecule/m443> <http://semanticscience.org/resource/CHEMINF_000200> <http://linkedchemistry.info/chembl/molecule/m443/molform> .
<http://linkedchemistry.info/chembl/molecule/m443/molform> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://semanticscience.org/resource/CHEMINF_000042> .
<http://linkedchemistry.info/chembl/molecule/m443/molform> <http://semanticscience.org/resource/SIO_000300> "C27H23ClN4O2" .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.blueobelisk.org/chemistryblogs/smiles> "Cc1nc(O)c2cc(CN(CC#C)c3ccc(cc3)C(=O)NCc4ccc(Cl)cc4)ccc2n1" .
<http://linkedchemistry.info/chembl/molecule/m443> <http://semanticscience.org/resource/CHEMINF_000200> <http://linkedchemistry.info/chembl/molecule/m443/smiles> .
<http://linkedchemistry.info/chembl/molecule/m443/smiles> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://semanticscience.org/resource/CHEMINF_000018> .
<http://linkedchemistry.info/chembl/molecule/m443/smiles> <http://semanticscience.org/resource/SIO_000300> "Cc1nc(O)c2cc(CN(CC#C)c3ccc(cc3)C(=O)NCc4ccc(Cl)cc4)ccc2n1" .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.blueobelisk.org/chemistryblogs/inchi> "InChI=1S/C27H23ClN4O2/c1-3-14-32(17-20-6-13-25-24(15-20)27(34)31-18(2)30-25)23-11-7-21(8-12-23)26(33)29-16-19-4-9-22(28)10-5-19/h1,4-13,15H,14,16-17H2,2H3,(H,29,33)(H,30,31,34)" .
<http://linkedchemistry.info/chembl/molecule/m443> <http://semanticscience.org/resource/CHEMINF_000200> <http://linkedchemistry.info/chembl/molecule/m443/inchi> .
<http://linkedchemistry.info/chembl/molecule/m443/inchi> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://semanticscience.org/resource/CHEMINF_000113> .
<http://linkedchemistry.info/chembl/molecule/m443/inchi> <http://semanticscience.org/resource/SIO_000300> "InChI=1S/C27H23ClN4O2/c1-3-14-32(17-20-6-13-25-24(15-20)27(34)31-18(2)30-25)23-11-7-21(8-12-23)26(33)29-16-19-4-9-22(28)10-5-19/h1,4-13,15H,14,16-17H2,2H3,(H,29,33)(H,30,31,34)" .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.w3.org/2002/07/owl#equivalentClass> <http://rdf.openmolecules.net/?InChI=1S/C27H23ClN4O2/c1-3-14-32(17-20-6-13-25-24(15-20)27(34)31-18(2)30-25)23-11-7-21(8-12-23)26(33)29-16-19-4-9-22(28)10-5-19/h1,4-13,15H,14,16-17H2,2H3,(H,29,33)(H,30,31,34)> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.blueobelisk.org/chemistryblogs/inchikey> "IQCINSLNRQILLY-UHFFFAOYSA-N" .
<http://linkedchemistry.info/chembl/molecule/m443> <http://semanticscience.org/resource/CHEMINF_000200> <http://linkedchemistry.info/chembl/molecule/m443/inchikey> .
<http://linkedchemistry.info/chembl/molecule/m443/inchikey> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://semanticscience.org/resource/CHEMINF_000059> .
<http://linkedchemistry.info/chembl/molecule/m443/inchikey> <http://semanticscience.org/resource/SIO_000300> "IQCINSLNRQILLY-UHFFFAOYSA-N" .
}
<http://beta.sparql.uniprot.org/> {
<http://purl.uniprot.org/uniprot/Q6GZX4> rdf:type up:Protein .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:label "Putative transcription factor 001R" .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:citation upcitation:15165820 .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:classifiedWith <http://purl.uniprot.org/keywords/10> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:classifiedWith <http://purl.uniprot.org/go/0006351> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:classifiedWith <http://purl.uniprot.org/keywords/805> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:classifiedWith <http://purl.uniprot.org/go/0006355> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:classifiedWith <http://purl.uniprot.org/keywords/1185> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:classifiedWith <http://purl.uniprot.org/go/0046782> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:existence up:Predicted_Existence .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:organism <http://purl.uniprot.org/taxonomy/654924 .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:recommendedName <http://purl.uniprot.org/SHA-384/0777234937D8B63494C8D5F1E2AA13EA7B92452085F2FD9AA79C8DF96BF8234173E353B71AB291B114FFF71D7DB823AE> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:representativeFor <http://purl.uniprot.org/uniref/UniRef50_Q6GZX4> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:representativeFor <http://purl.uniprot.org/uniref/UniRef100_Q6GZX4> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:representativeFor <http://purl.uniprot.org/uniref/UniRef90_Q6GZX4> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:seedFor <http://purl.uniprot.org/uniref/UniRef100_Q6GZX4> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:seedFor <http://purl.uniprot.org/uniref/UniRef90_Q6GZX4> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:sequence <http://purl.uniprot.org/isoforms/Q6GZX4-1> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:created "2011-06-28" .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:mnemonic "001R_FRG3G" .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:modified "2012-04-18" .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:reviewed "true" .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:version "24" .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/embl-cds/AAT09660.1> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/refseq/YP_031579.1> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/proteinmodelportal/Q6GZX4> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/geneid/2947773> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/protclustdb/CLSP2511514> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/interpro/IPR007031> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/pfam/PF04947> .
upcitations:15165820 rdf:type up:Journal_Citation .
upcitations:15165820 rdfs:comment "Frog virus 3 (FV3) is the type species member of the genus Ranavirus (family Iridoviridae). To better understand the molecular mechanisms involved in the replication of FV3 including transcription of its highly methylated DNA genome we have determined the complete nucleotide sequence of the FV3 genome. The FV3 genome is 105903 bp long excluding the terminal redundancy. The G + C content of FV3 genome is 55% and it encodes 98 nonoverlapping potential open reading frames (ORFs) containing 50-1293 amino acids. Eighty-four ORFs have significant homology to known proteins of other iridoviruses whereas twelve of these unique FV3 proteins do not share homology to any known protein. A microsatellite containing a stretch of 34 tandemly repeated CA dinucleotide in a noncoding region was detected. To date no such sequence has been reported in any animal virus." .
upcitations:15165820 up:name "Virology" .
upcitations:15165820 up:author "Barkman T.J." .
upcitations:15165820 up:author "Essani K." .
upcitations:15165820 up:author "Tan W.G." .
upcitations:15165820 up:author "Gregory Chinchar V." .
upcitations:15165820 up:date "2004" .
upcitations:15165820 up:pages "70-84" .
upcitations:15165820 up:title "Comparative genomic analyses of frog virus 3 type species of the genus Ranavirus (family Iridoviridae)." .
upcitations:15165820 up:volume "323" .
upcitations:15165820 skos:exactMatch http://purl.uniprot.org/pubmed/15165820 .
upcitations:15165820 dcterms:identifier "doi:10.1016/j.virol.2004.02.019" .
}
# EBI gene expression atlas
<http://wwwdev.ebi.ac.uk/fgpt/gxa-sparql/sparql> {
# main linking point to the GXA data is the ensembl id and the uniprot id. 
<http://identifiers.org/ensembl/ENSG00000116962> sio:'encodes' <http://purl.uniprot.org/uniprot/P14543> .
# differential expression value
?diffexp a sio:'differential gene expression value' .
?diffexp sio:'is attribute of' <http://identifiers.org/ensembl/ENSG00000116962> .
?diffexp sio:'has value' ?diffvalue . # e.g. UP, DOWN 
?diffexp sio'has attribute' [ a sio:p_value; sio:has-value 0.00005] .
# experiment factor from EFO 
?iv a sio:'independent variable' .
?iv sio:'represents' efo:'experimental factor' .
?iv sio:'in relation to' ?diffexp .
}
# parses up to here.
http://ops-virtuoso.scai.fraunhofer.de:8894/sparql {
<http://www.scai.fraunhofer.de/rdf/entity/CC_BY-SA_3.0>
a dcterms:LicenseDocument ;
rdfs:label "CC BY-SA 3.0"^^xsd:string ;
dcterms:references "https://creativecommons.org/licenses/by-sa/3.0/"^^xsd:string ;
dcterms:valid "2013-02-01T13:59:07.098Z"^^xsd:dateTime .
scai:Fraunhofer_SCAI
a foaf:Organization , prov:Agent ;
rdfs:label "Fraunhofer SCAI"^^xsd:string .
<http://www.scai.fraunhofer.de/rdf/intern/medline12short.xml>
a prov:Entity , pao:DocumentSet ;
dcterms:title "medline12short.xml"^^xsd:string .
<http://www.scai.fraunhofer.de/rdf/intern/Department_of_Diagnostic_Radiology__Yale_University_School_of_Medicine__New_Haven__Conn.__USA.>
a foaf:Organization ;
rdfs:label "Department of Diagnostic Radiology, Yale University School of Medicine, New Haven, Conn., USA."@en ;
foaf:member base:Charney__D_S , base:Bremner__J_D , base:Southwick__S_M , base:Staib__L_H , base:McGlashan__T , base:Narayan__M .
scai:XMLAnnotator
a prov:Activity ;
prov:endedAtTime "2012-08-06T12:59:07.1Z"^^xsd:dateTime ;
prov:startedAtTime "2012-08-06T12:59:07.1Z"^^xsd:dateTime ;
prov:used <http://www.scai.fraunhofer.de/rdf/intern/medline12short.xml> ;
prov:wasAssociatedWith
scai:chaupt .
base:Staib__L_H
a foaf:Person , dcterms:Agent ;
rdfs:label "Staib, L H"^^xsd:string .
scai:chaupt
a foaf:Person , dcterms:Agent , prov:Agent ;
rdfs:label "chaupt"^^xsd:string ;
prov:actedOnBehalfOf
scai:Fraunhofer_SCAI ;
foaf:member scai:Fraunhofer_SCAI .
<http://www.scai.fraunhofer.de/rdf/intern/medline12short.xml_XMLAnnotator>
a <http://purl.org/dc/dcmitype/Dataset> , prov:Entity , pao:DocumentSet ;
ao:item <http://www.scai.fraunhofer.de/rdf/intern/10553744> ;
dcterms:creator scai:chaupt ;
dcterms:license <http://www.scai.fraunhofer.de/rdf/entity/CC_BY-SA_3.0> ;
dcterms:rightsHolder
scai:chaupt ;
dcterms:title "medline12short.xml_XMLAnnotator"^^xsd:string ;
prov:atTime "2012-11-12T13:59:07.097Z"^^xsd:dateTime ;
prov:wasAttributedTo
scai:chaupt ;
prov:wasDerivedFrom <http://www.scai.fraunhofer.de/rdf/intern/medline12short.xml> ;
prov:wasGeneratedBy scai:XMLAnnotator .
base:Charney__D_S
a foaf:Person , dcterms:Agent ;
rdfs:label "Charney, D S"^^xsd:string .
base:Bremner__J_D
a foaf:Person , dcterms:Agent ;
rdfs:label "Bremner, J D"^^xsd:string .
base:Southwick__S_M
a foaf:Person , dcterms:Agent ;
rdfs:label "Southwick, S M"^^xsd:string .
base:The_American_journal_of_psychiatry
a dcterms:Agent ;
rdfs:label "The American journal of psychiatry"^^xsd:string .
<http://www.scai.fraunhofer.de/rdf/intern/10553744>
a str:Document ;
dcterms:creator base:Charney__D_S , base:Bremner__J_D , base:Southwick__S_M , base:Staib__L_H , base:McGlashan__T , base:Narayan__M ;
dcterms:date "1999-10-31T13:59:07.1Z"^^xsd:dateTime ;
dcterms:identifier "10553744"^^xsd:string ;
dcterms:publisher base:The_American_journal_of_psychiatry ;
dcterms:source "file://medline12short.xml"^^xsd:string ;
dcterms:title "Neural correlates of memories of childhood sexual abuse in women with and without posttraumatic stress disorder."@en .
base:McGlashan__T
a foaf:Person , dcterms:Agent ;
rdfs:label "McGlashan, T"^^xsd:string .
base:Narayan__M
a foaf:Person , dcterms:Agent ;
rdfs:label "Narayan, M"^^xsd:string .
}
:Linksets {
up:Q12345 skos:broadMatch end:000xxxxx .
}

== # VoID ==

{| style="color: black; color: #733;" width="85%" class="wikitable"
| colspan="3" | <http://sparql.wikipathways.org>
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''pav:createdOn'''
| style="width: 60%; background-color: orange;"| '''"2012-10-25"^^xsd:date ;'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''pav:createdBy'''
| style="width: 60%; background-color: orange;"| ''<https://orcid.org/0000-0001-9773-4008> ;''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''pav:createdAt'''
| style="width: 60%; background-color: orange;"| '''dbpedia:Maastricht_University ;'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''dcterms:license'''
| style="width: 60%; background-color: orange;"| ''<http://creativecommons.org/licenses/by/3.0/> .''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| ''<http://sparql.wikipathways.org> .''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:triples'''
| style="width: 60%; background-color: orange;"| '''"1794104"^^xsd:integer ;'''
|-

| colspan="3" | :ChEMBL
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''pav:createdOn'''
| style="width: 60%; background-color: orange;"| '''"2012-10-25"^^xsd:date ;'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:foo'''
| style="width: 60%; background-color: orange;"| '''void:bar .'''
|}

== Triplestore map ==

{| style="color: black; color: #733;" width="85%" class="wikitable"
| colspan="3" | WikiPathways
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''foaf:page'''
| style="width: 60%; background-color: orange;"| ''' http://www.wikipathways.org'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| '''http://sparql.wikipathways.org'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:uriLookupEndpoint'''
| style="width: 60%; background-color: orange;"| '''http://rdf.wikipathways.org '''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''prov:deployedSoftware'''
| style="width: 60%; background-color: orange;"| '''dbpedia:Virtuoso_Universal_Server '''
|-
| colspan="3" | :ChEMBL-RDF
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''foaf:page'''
| style="width: 60%; background-color: orange;"| '''https://github.com/egonw/chembl.rdf'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| ''' http://rdf.farmbio.uu.se/chembl/sparql '''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| ''' http://ragamuffin.bigcat.unimaas.nl/chembl/sparql '''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''prov:deployedSoftware'''
| style="width: 60%; background-color: orange;"| '''dbpedia:Virtuoso_Universal_Server '''
|-
| colspan="3" | :Uniprot
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''foaf:page'''
| style="width: 60%; background-color: orange;"| '''http://www.uniprot.org'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| ''' http://beta.sparql.uniprot.org '''
|-
| colspan="3" | :Gene expression atlas
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''foaf:page'''
| style="width: 60%; background-color: orange;"| '''tba'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| ''' http://wwwdev.ebi.ac.uk/fgpt/gxa-sparql/sparql '''
|-
|}

HCLS/BridgeDB

Ewilligh — Thu, 08 Nov 2012 21:35:03 GMT

Ewilligh: Created page with "There are several options to make BridgeDB available in SPARQL. BridgeDB is an identifier mapping service (http://www.biomedcentral.com/1471-2105/11/5) and currently being exten…"

There are several options to make BridgeDB available in SPARQL.

BridgeDB is an identifier mapping service (http://www.biomedcentral.com/1471-2105/11/5) and currently being extended in the Open PHACTS project. It can map both URIs between databases (with different identifiers) as between databases with the same identifier (URL rewrites).

This page is to discuss options, and outline the issues. Involved as me, [[User:Eric]], and Andra.

= Option X =

This option uses BridgeDB as an interactive intermediate.

GRAPH <g1> { ?x <p1> ?g1_v } GRAPH <BridgeDB> { ?m <foo> ?g1_v ; <bar> ?g2_v } GRAPH <g2> { ?foo <p2> ?g2_v }

HCLS/SWAT4LS2012/Hackathon

Ewilligh — Mon, 05 Nov 2012 17:07:22 GMT

Ewilligh: /* Triplestore map */

The SWAT4LS Hackathon is an informal event associated with the [http://swat4ls.org/ SWAT4LS] Semantic Web Applications and Tools for Life Sciences Workshops Series.

Scope of the event is to bring together experts and enthusiasts in the application of semantic technologies in healthcare and life science for open discussion and jam coding sessions.
The Hackathon will be organized on the 28th of November 2012 at [http://lacantine.org/ La Cantine, Paris] ([https://maps.google.com/maps?q=12+Galerie+Montmartre+75002+france&hl=en&ie=UTF8&ll=48.870438,2.342089&spn=0.0013,0.001869&sll=48.87053,2.342319&sspn=0.002601,0.003739&t=h&hnear=12+Galerie+Montmartre,+75002+Paris,+%C3%8Ele-de-France,+France&z=19 map]).

street: 151 rue Montmartre, Passage des Panoramas
room: 12 Galerie Montmartre
75002 Paris

(For more information, please refer to the [http://www.swat4ls.org/workshops/paris2012/| workshop website]).
The hackathon is open to workshop participants. Registration is required and space is limited!.

== Logistics ==
Projects and institutes attending include:
* OpenPhacts (http://www.openphacts.org)
* WikiPathways (http://www.wikipathways.org/index.php/WikiPathways)
* The Database Center for Life Sciences/BioHackathon (http://dbcls.rois.ac.jp/en/ http://www.biohackathon.org/)
* The W3C Consortium, Health Care and Life Sciences Interest Group ([[HCLS]])
* BioPAX (http://biopax.org)
* European Bioinformatics Institute (http://www.ebi.ac.uk)
While the agenda will be open, we are coordinating ideas that can be developd at the network in advance, to maximize the utility of the day. Co-organizers for each community will help gathering ideas and finding point of contacts.

=== Information and registrations ===
For information, [mailto:info@swat4ls.org| info _at_ swat4ls.org]

Registrations are handled via [http://swat4ls-2012.eventbrite.com/| Eventbrite]

=== Hashtag ===
[https://twitter.com/search/realtime?q=%23swat4lshack #swat4lshack]

=== Co-Organizers ===
* Andrea Splendiani
* Andra Waagmeester
* Eric Prud'hommeaux
* Toshiaki Katayama
* Ismael Navas delgado

== Open PHACTS community ==

=== Contact Point ===
* Andra Waagmeester
* Egon Willighagen

=== Proposed action points ===
# Consume [http://www.openphacts.org Open PHACTS] content in Pathway tools
# Using http://identifiers.org
# Create an example set of valuable queries
# Visualizing output
# work on further linked data integration, with possible:
## [https://ntp.niehs.nih.gov/drugmatrix/ DrugMatrix]
## [http://toxico.nibio.go.jp/open-tggates/ TG-GATEs]
## [http://thedatahub.org/nl/dataset/bio2rdf-ctd CTD] (already available as RDF, by Bio2RDF)
# shared Java client code
## for R, Bioclipse, KNIME

=== Confirmed Participants ===
* Kees Burger
* Maria Carmen Carra
* Ian Dunlop
* Chris Evelo
* Paul Groth
* Tim Harder
* Carina Haupt
* Nick Juty
* Camille Laibe
* Antonis Loizou
* Oriol Lopez
* Guillermo C. Martínez
* Nuria Queralt
* Rishi Ramgolam
* Mark Thompson
* Egon Willighagen
* Pekka Kohonen
* Ola Spjuth

== WikiPathways community ==

=== Contact Point ===
Andra Waagmeester

=== Introduction ===
[http://www.wikipathways.org/index.php/WikiPathways WikiPathways] is a online resource for pathways. Content is provided by the audience at large. I currently contains more then 2200 pathways from 21 species [http://sparqlbin.com/#4f91f23a032a87cc46c5a526a6da673a source]. Pathways are captured in a XML-based format [http://www.pathvisio.org/wiki/EverythingGpml GPML]. Recently WikiPathways was exposed as linked open data where GPML content was exported as RDF. This data is available through a SPARQL endpoint http://sparql.wikipathways.org.

=== Proposed action points ===
==== Exploring [http://www.wikipathways.org/index.php/WikiPathways WikiPathways] RDF content, making example queries ====
==== Writing federated queries to integrate pathway content with other biological data. ====
====Using [http://code.google.com/p/pathvisiorpc/ Pathvisio RPC] to consume and visualize linked pathway data====

=== Confirmed Participants ===
* Chris Evelo
* Martina Kutmon
* Alex Pico

== Database Center for Life Sciences Community / BioHackathon ==

=== Contact Point ===
Toshiaki Katayama

=== Proposed action points ===

== W3C HCLS Community ==

=== Contact Point ===
Eric Prud'hommeaux

=== Proposed action points ===
==== Making an online inventory of available resources (wiki) to document underlying schemas of available datasources.====
There are nice lists of active SPARQL endpoints [http://www.freebase.com/view/base/sparql/views/sparql_endpoint (example 1)] and [http://labs.mondeca.com/sparqlEndpointsStatus/index.html (example 2)]. Finding where the data actually links can still be challenging.

It would be really beneficial to create an overview with descriptions of different linked data sets describing the underlying structure. The first step would be to define a format where data providers describe their data in a predefined (wiki) format. This format could be based on [http://www.w3.org/TR/void/ VoID].
These description coulds then be used to create so called data landscapes in tools such as [http://vsdlc3.blogspot.be/ Semscape].

====Creating a review of sparql endpoints and their support for remote federated queries. ====
Within a federated query you can query different flavours of sparql endpoints. SInce different endpoints have their own implementations and support for different SPARQL versions, it is essential to understand the different issues each type of endpoint might have. The community would benefit from a list mentioning each available SPARQL endpoint system (e.g. 4store, virtuoso, etc) and their support for different SPARQL versions. Also this list could mention specific features (e.g. soft limit in 4store) influencing the recall in federated queries.

== BioPAX Community ==

=== Contact Point ===
Ismael Navas Delgado

=== Proposed action points ===

=== Confirmed Participants ===
* Ismael Navas Delgado
* Andrea Splendiani

== EBI Gene Expression Atlas ==

=== Contact Point ===
Simon Jupp

James Malone

=== Introduction ===

Integration of gene expression data from the Gene Expression Atlas database (http://www.ebi.ac.uk/gxa). Schema description and SPARQL endpoint at http://wwwdev.ebi.ac.uk/fgpt/efosemweb.html
Differential gene expression annotated with Ensembl gene ids (identifiers.org URIs), includes mappings to Uniprot. Experiment assay and sample descriptions annotated with ontology terms from wide range of
bio-ontologies (anatomy, cells, disease etc).

=== Proposed action points ===

Linking gene expression to pathway data.

=== Confirmed Participants ===
* Simon Jupp

== Resources ==
* PathwayCommons SPARQL endpoint. Endpoint over all BioPAX representations in PathwayCommons
* Cytoscape plugin to visualize and interact with RDF knwoledge bases (new!)
* BioQueries: social site to build SPARQL queries
* Open PHACTS rdf guidelines: http://www.openphacts.org/specs/2012/WD-rdfguide-20120823/

== Data Map ==

@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix wprdf: <http://rdf.wikipathways.org/> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix wp: <http://vocabularies.wikipathways.org/wp#> .
@prefix biopax: <http://www.biopax.org/release/biopax-level3.owl#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix gpml: <http://vocabularies.wikipathways.org/gpml#> .
@prefix chembl: <http://rdf.farmbio.uu.se/chembl/onto/#> .
@prefix up: <http://purl.uniprot.org/core/> .
@prefix dbpedia: <http://dbpedia.org/page/> .
@prefix pav: <http://purl.org/pav/> .
@prefix b2rreactome: <http://bio2rdf.org/reactome:>
@prefix b2rbiopax: <http://bio2rdf.org/ns/biopax#>
@prefix b2rbiopaxresource: <http://bio2rdf.org/biopax_resource:>
@prefix up: <http://purl.uniprot.org/core/>
@prefix sio: <http://semanticscience.org/resource/>
@prefix upcitation: <http://purl.uniprot.org/citations/>
@prefix prov: <http://www.w3.org/ns/prov#>

<http://sparql.wikipathways.org> {
# Sparql endpoint: http://sparql.wikipathways.org
# Data: http://rdf.wikipathways.org
# 
<http://identifiers.org/ncbigene/1051> rdf:type wp:GeneProduct .
<http://identifiers.org/ncbigene/1051> dcterms:isPartOf wprdf:WP3 .
<http://identifiers.org/ncbigene/1051> rdfs:label "C/EBP-beta" .
wprdf:WP3 rdf:type wp:Pathway .
wp:Pathway skos:relatedMatch biopax:Pathway .
wprdf:WP3 rdfs:label "Keap1-Nrf2 Pathway" .
wprdf:WP3 dcterms:description """Based on [http://www.nature.com/nrc/journal/v3/n10/fig_tab/nrc1189_F4.html Surh, 2003, figure 4] Nrf2 induces the expression of many
antioxidant enzymes. It is therefore thought to be involved in oxidative stress response."""^^xsd:string.
wprdf:WP3 <http://purl.org/pav/version> "48217"^^xsd:string .
wprdf:WP3 gpml:biopaxref "dba" .
wprdf:WP3 gpml:height "731.0"^^xsd:float .
wprdf:WP3 gpml:width "914.0"^^xsd:float .
wprdf:WP3 wp:category wp:CellularProcess .
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wprdf:WP3 wp:pathwayOntology <http://purl.obolibrary.org/obo/PW:0000378> .
wprdf:WP3 foaf:page "http://www.wikipathways.org/index.php/Pathway:WP3" .

}
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b2rreactome:Homo_sapiens-Apoptosis rdf:type b2rbiopaxresource:Pathway .
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b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Reactome109581 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-REACT_578.2 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_14561771 .
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b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_12209154 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:comment "Apoptosis is a distinct form of cell death that is functionally and morphologically different from necrosis. Nuclear chromatin condensation, cytoplasmic shrinking, dilated endoplasmic reticulum, and membrane blebbing characterize apoptosis in general. Mitochondria remain morphologically unchanged. In 1972 Kerr et al introduced the concept of apoptosis as a distinct form of 'cell-death', and the mechanisms of various apoptotic pathways are still being revealed today. BRThe two principal pathways of apoptosis are (1) the Bcl-2 inhibitable or intrinsic pathway induced by various forms of stress like intracellular damage, developmental cues, and external stimuli and (2) the caspase 8/10 dependent or extrinsic pathway initiated by the engagement of death receptorsBR The caspase 8/10 dependent or extrinsic pathway is a death receptor mediated mechanism that results in the activation of caspase-8 and caspase-10. Activation of death receptors like Fas/CD95, TNFR1, and the TRAIL receptor is promoted by the TNF family of ligands including FASL (APO1L OR CD95L), TNF, LT-alpha, LT-beta, CD40L, LIGHT, RANKL, BLYS/BAFF, and APO2L/TRAIL. These ligands are released in response to microbial infection, or as part of the cellular, humoral immunity responses during the formation of lymphoid organs, activation of dendritic cells, stimulation or survival of T, B, and natural killer (NK) cells, cytotoxic response to viral infection or oncogenic transformation. BR The Bcl-2 inhibitable or intrinsic pathway of apoptosis is a stress-inducible process, and acts through the activation of caspase-9 via Apaf-1 and cytochrome c. The rupture of the mitochondrial membrane, a rapid process involving some of the Bcl-2 family proteins, releases these molecules into the cytoplasm. Examples of cellular processes that may induce the intrinsic pathway in response to various damage signals include: auto reactivity in lymphocytes, cytokine deprivation, calcium flux or cellular damage by cytotoxic drugs like taxol, deprivation of nutrients like glucose and growth factors like EGF, anoikis, transactivation of target genes by tumor suppressors including p53.BR In many non-immune cells, death signals initiated by the extrinsic pathway are amplified by connections to the intrinsic pathway. The connecting link appears to be the truncated BID (tBID) protein a proteolytic cleavage product mediated by caspase-8 or other enzymes." .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:comment "Edited: Gopinathrao, G, Matthews, L, Gillespie, ME, Joshi-Tope, G, 0000-00-00 00:00:00" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:comment "Authored: Alnemri, E, Hengartner, M, Tschopp, J, Tsujimoto, Y, Hardwick, JM, 2004-01-16 16:01:51" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:comment "Reviewed: Hengartner, M, Ranganathan, S, Vaux, D, 0000-00-00 00:00:00" .
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b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:comment "Apoptosis is a distinct form of cell death that is functionally and morphologically different from necrosis. Nuclear chromatin condensation, cytoplasmic shrinking, dilated endoplasmic reticulum, and membrane blebbing characterize apoptosis in general. Mitochondria remain morphologically unchanged. In 1972 Kerr et al introduced the concept of apoptosis as a distinct form of 'cell-death', and the mechanisms of various apoptotic pathways are still being revealed today. BRThe two principal pathways of apoptosis are (1) the Bcl-2 inhibitable or intrinsic pathway induced by various forms of stress like intracellular damage, developmental cues, and external stimuli and (2) the caspase 8/10 dependent or extrinsic pathway initiated by the engagement of death receptorsBR The caspase 8/10 dependent or extrinsic pathway is a death receptor mediated mechanism that results in the activation of caspase-8 and caspase-10. Activation of death receptors like Fas/CD95, TNFR1, and the TRAIL receptor is promoted by the TNF family of ligands including FASL (APO1L OR CD95L), TNF, LT-alpha, LT-beta, CD40L, LIGHT, RANKL, BLYS/BAFF, and APO2L/TRAIL. These ligands are released in response to microbial infection, or as part of the cellular, humoral immunity responses during the formation of lymphoid organs, activation of dendritic cells, stimulation or survival of T, B, and natural killer (NK) cells, cytotoxic response to viral infection or oncogenic transformation. BR The Bcl-2 inhibitable or intrinsic pathway of apoptosis is a stress-inducible process, and acts through the activation of caspase-9 via Apaf-1 and cytochrome c. The rupture of the mitochondrial membrane, a rapid process involving some of the Bcl-2 family proteins, releases these molecules into the cytoplasm. Examples of cellular processes that may induce the intrinsic pathway in response to various damage signals include: auto reactivity in lymphocytes, cytokine deprivation, calcium flux or cellular damage by cytotoxic drugs like taxol, deprivation of nutrients like glucose and growth factors like EGF, anoikis, transactivation of target genes by tumor suppressors including p53.BR In many non-immune cells, death signals initiated by the extrinsic pathway are amplified by connections to the intrinsic pathway. The connecting link appears to be the truncated BID (tBID) protein a proteolytic cleavage product mediated by caspase-8 or other enzymes." .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:comment "Edited: Gopinathrao, G, Matthews, L, Gillespie, ME, Joshi-Tope, G, 0000-00-00 00:00:00" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:comment "Authored: Alnemri, E, Hengartner, M, Tschopp, J, Tsujimoto, Y, Hardwick, JM, 2004-01-16 16:01:51" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:comment "Reviewed: Hengartner, M, Ranganathan, S, Vaux, D, 0000-00-00 00:00:00" .
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b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_14561771 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_4561027 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_14634621 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_15218528 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_12505355 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_12189384 .
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<http://purl.uniprot.org/uniprot/Q6GZX4> up:seedFor <http://purl.uniprot.org/uniref/UniRef90_Q6GZX4> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:sequence <http://purl.uniprot.org/isoforms/Q6GZX4-1> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:created "2011-06-28" .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:mnemonic "001R_FRG3G" .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:modified "2012-04-18" .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:reviewed "true" .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:version "24" .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/embl-cds/AAT09660.1> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/refseq/YP_031579.1> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/proteinmodelportal/Q6GZX4> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/geneid/2947773> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/protclustdb/CLSP2511514> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/interpro/IPR007031> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/pfam/PF04947> .
upcitations:15165820 rdf:type up:Journal_Citation .
upcitations:15165820 rdfs:comment "Frog virus 3 (FV3) is the type species member of the genus Ranavirus (family Iridoviridae). To better understand the molecular mechanisms involved in the replication of FV3 including transcription of its highly methylated DNA genome we have determined the complete nucleotide sequence of the FV3 genome. The FV3 genome is 105903 bp long excluding the terminal redundancy. The G + C content of FV3 genome is 55% and it encodes 98 nonoverlapping potential open reading frames (ORFs) containing 50-1293 amino acids. Eighty-four ORFs have significant homology to known proteins of other iridoviruses whereas twelve of these unique FV3 proteins do not share homology to any known protein. A microsatellite containing a stretch of 34 tandemly repeated CA dinucleotide in a noncoding region was detected. To date no such sequence has been reported in any animal virus." .
upcitations:15165820 up:name "Virology" .
upcitations:15165820 up:author "Barkman T.J." .
upcitations:15165820 up:author "Essani K." .
upcitations:15165820 up:author "Tan W.G." .
upcitations:15165820 up:author "Gregory Chinchar V." .
upcitations:15165820 up:date "2004" .
upcitations:15165820 up:pages "70-84" .
upcitations:15165820 up:title "Comparative genomic analyses of frog virus 3 type species of the genus Ranavirus (family Iridoviridae)." .
upcitations:15165820 up:volume "323" .
upcitations:15165820 skos:exactMatch http://purl.uniprot.org/pubmed/15165820 .
upcitations:15165820 dcterms:identifier "doi:10.1016/j.virol.2004.02.019" .
}
# EBI gene expression atlas
<http://wwwdev.ebi.ac.uk/fgpt/gxa-sparql/sparql> {
# main linking point to the GXA data is the ensembl id and the uniprot id. 
<http://identifiers.org/ensembl/ENSG00000116962> sio:'encodes' <http://purl.uniprot.org/uniprot/P14543> .
# differential expression value
?diffexp a sio:'differential gene expression value' .
?diffexp sio:'is attribute of' <http://identifiers.org/ensembl/ENSG00000116962> .
?diffexp sio:'has value' ?diffvalue . # e.g. UP, DOWN 
?diffexp sio'has attribute' [ a sio:p_value; sio:has-value 0.00005] .
# experiment factor from EFO 
?iv a sio:'independent variable' .
?iv sio:'represents' efo:'experimental factor' .
?iv sio:'in relation to' ?diffexp .
}
# parses up to here.
:Textmining {
:hit ao:fdgr "blabla"
}
:Linksets {
up:Q12345 skos:broadMatch end:000xxxxx .
}

== # VoID ==

{| style="color: black; color: #733;" width="85%" class="wikitable"
| colspan="3" | <http://sparql.wikipathways.org>
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''pav:createdOn'''
| style="width: 60%; background-color: orange;"| '''"2012-10-25"^^xsd:date ;'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''pav:createdBy'''
| style="width: 60%; background-color: orange;"| ''<https://orcid.org/0000-0001-9773-4008> ;''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''pav:createdAt'''
| style="width: 60%; background-color: orange;"| '''dbpedia:Maastricht_University ;'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''dcterms:license'''
| style="width: 60%; background-color: orange;"| ''<http://creativecommons.org/licenses/by/3.0/> .''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| ''<http://sparql.wikipathways.org> .''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:triples'''
| style="width: 60%; background-color: orange;"| '''"1794104"^^xsd:integer ;'''
|-

| colspan="3" | :ChEMBL
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''pav:createdOn'''
| style="width: 60%; background-color: orange;"| '''"2012-10-25"^^xsd:date ;'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:foo'''
| style="width: 60%; background-color: orange;"| '''void:bar .'''
|}

== Triplestore map ==

{| style="color: black; color: #733;" width="85%" class="wikitable"
| colspan="3" | WikiPathways
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''foaf:page'''
| style="width: 60%; background-color: orange;"| ''' http://www.wikipathways.org'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| '''http://sparql.wikipathways.org'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:uriLookupEndpoint'''
| style="width: 60%; background-color: orange;"| '''http://rdf.wikipathways.org '''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''prov:deployedSoftware'''
| style="width: 60%; background-color: orange;"| '''dbpedia:Virtuoso_Universal_Server '''
|-
| colspan="3" | :ChEMBL-RDF
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''foaf:page'''
| style="width: 60%; background-color: orange;"| '''https://github.com/egonw/chembl.rdf'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| ''' http://rdf.farmbio.uu.se/chembl/sparql '''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| ''' http://ragamuffin.bigcat.unimaas.nl/chembl/sparql '''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''prov:deployedSoftware'''
| style="width: 60%; background-color: orange;"| '''dbpedia:Virtuoso_Universal_Server '''
|-
| colspan="3" | :Uniprot
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''foaf:page'''
| style="width: 60%; background-color: orange;"| '''http://www.uniprot.org'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| ''' http://beta.sparql.uniprot.org '''
|-
| colspan="3" | :Gene expression atlas
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''foaf:page'''
| style="width: 60%; background-color: orange;"| '''tba'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| ''' http://wwwdev.ebi.ac.uk/fgpt/gxa-sparql/sparql '''
|-
|}

HCLS/SWAT4LS2012/Hackathon

Ewilligh — Mon, 05 Nov 2012 17:05:18 GMT

Ewilligh: /* Data Map */

The SWAT4LS Hackathon is an informal event associated with the [http://swat4ls.org/ SWAT4LS] Semantic Web Applications and Tools for Life Sciences Workshops Series.

Scope of the event is to bring together experts and enthusiasts in the application of semantic technologies in healthcare and life science for open discussion and jam coding sessions.
The Hackathon will be organized on the 28th of November 2012 at [http://lacantine.org/ La Cantine, Paris] ([https://maps.google.com/maps?q=12+Galerie+Montmartre+75002+france&hl=en&ie=UTF8&ll=48.870438,2.342089&spn=0.0013,0.001869&sll=48.87053,2.342319&sspn=0.002601,0.003739&t=h&hnear=12+Galerie+Montmartre,+75002+Paris,+%C3%8Ele-de-France,+France&z=19 map]).

street: 151 rue Montmartre, Passage des Panoramas
room: 12 Galerie Montmartre
75002 Paris

(For more information, please refer to the [http://www.swat4ls.org/workshops/paris2012/| workshop website]).
The hackathon is open to workshop participants. Registration is required and space is limited!.

== Logistics ==
Projects and institutes attending include:
* OpenPhacts (http://www.openphacts.org)
* WikiPathways (http://www.wikipathways.org/index.php/WikiPathways)
* The Database Center for Life Sciences/BioHackathon (http://dbcls.rois.ac.jp/en/ http://www.biohackathon.org/)
* The W3C Consortium, Health Care and Life Sciences Interest Group ([[HCLS]])
* BioPAX (http://biopax.org)
* European Bioinformatics Institute (http://www.ebi.ac.uk)
While the agenda will be open, we are coordinating ideas that can be developd at the network in advance, to maximize the utility of the day. Co-organizers for each community will help gathering ideas and finding point of contacts.

=== Information and registrations ===
For information, [mailto:info@swat4ls.org| info _at_ swat4ls.org]

Registrations are handled via [http://swat4ls-2012.eventbrite.com/| Eventbrite]

=== Hashtag ===
[https://twitter.com/search/realtime?q=%23swat4lshack #swat4lshack]

=== Co-Organizers ===
* Andrea Splendiani
* Andra Waagmeester
* Eric Prud'hommeaux
* Toshiaki Katayama
* Ismael Navas delgado

== Open PHACTS community ==

=== Contact Point ===
* Andra Waagmeester
* Egon Willighagen

=== Proposed action points ===
# Consume [http://www.openphacts.org Open PHACTS] content in Pathway tools
# Using http://identifiers.org
# Create an example set of valuable queries
# Visualizing output
# work on further linked data integration, with possible:
## [https://ntp.niehs.nih.gov/drugmatrix/ DrugMatrix]
## [http://toxico.nibio.go.jp/open-tggates/ TG-GATEs]
## [http://thedatahub.org/nl/dataset/bio2rdf-ctd CTD] (already available as RDF, by Bio2RDF)
# shared Java client code
## for R, Bioclipse, KNIME

=== Confirmed Participants ===
* Kees Burger
* Maria Carmen Carra
* Ian Dunlop
* Chris Evelo
* Paul Groth
* Tim Harder
* Carina Haupt
* Nick Juty
* Camille Laibe
* Antonis Loizou
* Oriol Lopez
* Guillermo C. Martínez
* Nuria Queralt
* Rishi Ramgolam
* Mark Thompson
* Egon Willighagen
* Pekka Kohonen
* Ola Spjuth

== WikiPathways community ==

=== Contact Point ===
Andra Waagmeester

=== Introduction ===
[http://www.wikipathways.org/index.php/WikiPathways WikiPathways] is a online resource for pathways. Content is provided by the audience at large. I currently contains more then 2200 pathways from 21 species [http://sparqlbin.com/#4f91f23a032a87cc46c5a526a6da673a source]. Pathways are captured in a XML-based format [http://www.pathvisio.org/wiki/EverythingGpml GPML]. Recently WikiPathways was exposed as linked open data where GPML content was exported as RDF. This data is available through a SPARQL endpoint http://sparql.wikipathways.org.

=== Proposed action points ===
==== Exploring [http://www.wikipathways.org/index.php/WikiPathways WikiPathways] RDF content, making example queries ====
==== Writing federated queries to integrate pathway content with other biological data. ====
====Using [http://code.google.com/p/pathvisiorpc/ Pathvisio RPC] to consume and visualize linked pathway data====

=== Confirmed Participants ===
* Chris Evelo
* Martina Kutmon
* Alex Pico

== Database Center for Life Sciences Community / BioHackathon ==

=== Contact Point ===
Toshiaki Katayama

=== Proposed action points ===

== W3C HCLS Community ==

=== Contact Point ===
Eric Prud'hommeaux

=== Proposed action points ===
==== Making an online inventory of available resources (wiki) to document underlying schemas of available datasources.====
There are nice lists of active SPARQL endpoints [http://www.freebase.com/view/base/sparql/views/sparql_endpoint (example 1)] and [http://labs.mondeca.com/sparqlEndpointsStatus/index.html (example 2)]. Finding where the data actually links can still be challenging.

It would be really beneficial to create an overview with descriptions of different linked data sets describing the underlying structure. The first step would be to define a format where data providers describe their data in a predefined (wiki) format. This format could be based on [http://www.w3.org/TR/void/ VoID].
These description coulds then be used to create so called data landscapes in tools such as [http://vsdlc3.blogspot.be/ Semscape].

====Creating a review of sparql endpoints and their support for remote federated queries. ====
Within a federated query you can query different flavours of sparql endpoints. SInce different endpoints have their own implementations and support for different SPARQL versions, it is essential to understand the different issues each type of endpoint might have. The community would benefit from a list mentioning each available SPARQL endpoint system (e.g. 4store, virtuoso, etc) and their support for different SPARQL versions. Also this list could mention specific features (e.g. soft limit in 4store) influencing the recall in federated queries.

== BioPAX Community ==

=== Contact Point ===
Ismael Navas Delgado

=== Proposed action points ===

=== Confirmed Participants ===
* Ismael Navas Delgado
* Andrea Splendiani

== EBI Gene Expression Atlas ==

=== Contact Point ===
Simon Jupp

James Malone

=== Introduction ===

Integration of gene expression data from the Gene Expression Atlas database (http://www.ebi.ac.uk/gxa). Schema description and SPARQL endpoint at http://wwwdev.ebi.ac.uk/fgpt/efosemweb.html
Differential gene expression annotated with Ensembl gene ids (identifiers.org URIs), includes mappings to Uniprot. Experiment assay and sample descriptions annotated with ontology terms from wide range of
bio-ontologies (anatomy, cells, disease etc).

=== Proposed action points ===

Linking gene expression to pathway data.

=== Confirmed Participants ===
* Simon Jupp

== Resources ==
* PathwayCommons SPARQL endpoint. Endpoint over all BioPAX representations in PathwayCommons
* Cytoscape plugin to visualize and interact with RDF knwoledge bases (new!)
* BioQueries: social site to build SPARQL queries
* Open PHACTS rdf guidelines: http://www.openphacts.org/specs/2012/WD-rdfguide-20120823/

== Data Map ==

@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix wprdf: <http://rdf.wikipathways.org/> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix wp: <http://vocabularies.wikipathways.org/wp#> .
@prefix biopax: <http://www.biopax.org/release/biopax-level3.owl#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix gpml: <http://vocabularies.wikipathways.org/gpml#> .
@prefix chembl: <http://rdf.farmbio.uu.se/chembl/onto/#> .
@prefix up: <http://purl.uniprot.org/core/> .
@prefix dbpedia: <http://dbpedia.org/page/> .
@prefix pav: <http://purl.org/pav/> .
@prefix b2rreactome: <http://bio2rdf.org/reactome:>
@prefix b2rbiopax: <http://bio2rdf.org/ns/biopax#>
@prefix b2rbiopaxresource: <http://bio2rdf.org/biopax_resource:>
@prefix up: <http://purl.uniprot.org/core/>
@prefix sio: <http://semanticscience.org/resource/>
@prefix upcitation: <http://purl.uniprot.org/citations/>
@prefix prov: <http://www.w3.org/ns/prov#>

<http://sparql.wikipathways.org> {
# Sparql endpoint: http://sparql.wikipathways.org
# Data: http://rdf.wikipathways.org
# 
<http://identifiers.org/ncbigene/1051> rdf:type wp:GeneProduct .
<http://identifiers.org/ncbigene/1051> dcterms:isPartOf wprdf:WP3 .
<http://identifiers.org/ncbigene/1051> rdfs:label "C/EBP-beta" .
wprdf:WP3 rdf:type wp:Pathway .
wp:Pathway skos:relatedMatch biopax:Pathway .
wprdf:WP3 rdfs:label "Keap1-Nrf2 Pathway" .
wprdf:WP3 dcterms:description """Based on [http://www.nature.com/nrc/journal/v3/n10/fig_tab/nrc1189_F4.html Surh, 2003, figure 4] Nrf2 induces the expression of many
antioxidant enzymes. It is therefore thought to be involved in oxidative stress response."""^^xsd:string.
wprdf:WP3 <http://purl.org/pav/version> "48217"^^xsd:string .
wprdf:WP3 gpml:biopaxref "dba" .
wprdf:WP3 gpml:height "731.0"^^xsd:float .
wprdf:WP3 gpml:width "914.0"^^xsd:float .
wprdf:WP3 wp:category wp:CellularProcess .
wprdf:WP3 wp:organism <http://identifiers.org/taxonomy/9606> .
wprdf:WP3 wp:pathwayOntology <http://purl.obolibrary.org/obo/PW:0000378> .
wprdf:WP3 foaf:page "http://www.wikipathways.org/index.php/Pathway:WP3" .

}
<http://reactome.bio2rdf.org/sparql> {
b2rreactome:Homo_sapiens-Apoptosis rdf:type b2rbiopax:Pathway .
b2rreactome:Homo_sapiens-Apoptosis rdf:type b2rbiopaxresource:Pathway .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:name "Apoptosis" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:displayName "Apoptosis" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Reactome109581 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-REACT_578.2 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_14561771 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_4561027 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_14634621 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_15218528 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_12505355 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_12189384 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_12209154 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:comment "Apoptosis is a distinct form of cell death that is functionally and morphologically different from necrosis. Nuclear chromatin condensation, cytoplasmic shrinking, dilated endoplasmic reticulum, and membrane blebbing characterize apoptosis in general. Mitochondria remain morphologically unchanged. In 1972 Kerr et al introduced the concept of apoptosis as a distinct form of 'cell-death', and the mechanisms of various apoptotic pathways are still being revealed today. BRThe two principal pathways of apoptosis are (1) the Bcl-2 inhibitable or intrinsic pathway induced by various forms of stress like intracellular damage, developmental cues, and external stimuli and (2) the caspase 8/10 dependent or extrinsic pathway initiated by the engagement of death receptorsBR The caspase 8/10 dependent or extrinsic pathway is a death receptor mediated mechanism that results in the activation of caspase-8 and caspase-10. Activation of death receptors like Fas/CD95, TNFR1, and the TRAIL receptor is promoted by the TNF family of ligands including FASL (APO1L OR CD95L), TNF, LT-alpha, LT-beta, CD40L, LIGHT, RANKL, BLYS/BAFF, and APO2L/TRAIL. These ligands are released in response to microbial infection, or as part of the cellular, humoral immunity responses during the formation of lymphoid organs, activation of dendritic cells, stimulation or survival of T, B, and natural killer (NK) cells, cytotoxic response to viral infection or oncogenic transformation. BR The Bcl-2 inhibitable or intrinsic pathway of apoptosis is a stress-inducible process, and acts through the activation of caspase-9 via Apaf-1 and cytochrome c. The rupture of the mitochondrial membrane, a rapid process involving some of the Bcl-2 family proteins, releases these molecules into the cytoplasm. Examples of cellular processes that may induce the intrinsic pathway in response to various damage signals include: auto reactivity in lymphocytes, cytokine deprivation, calcium flux or cellular damage by cytotoxic drugs like taxol, deprivation of nutrients like glucose and growth factors like EGF, anoikis, transactivation of target genes by tumor suppressors including p53.BR In many non-immune cells, death signals initiated by the extrinsic pathway are amplified by connections to the intrinsic pathway. The connecting link appears to be the truncated BID (tBID) protein a proteolytic cleavage product mediated by caspase-8 or other enzymes." .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:comment "Edited: Gopinathrao, G, Matthews, L, Gillespie, ME, Joshi-Tope, G, 0000-00-00 00:00:00" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:comment "Authored: Alnemri, E, Hengartner, M, Tschopp, J, Tsujimoto, Y, Hardwick, JM, 2004-01-16 16:01:51" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:comment "Reviewed: Hengartner, M, Ranganathan, S, Vaux, D, 0000-00-00 00:00:00" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:dataSource b2rreactome:Homo_sapiens-ReactomeDataSource .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:organism b2rreactome:Homo_sapiens-Homo_sapiens .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayComponent b2rreactome:Homo_sapiens-Extrinsic_Pathway_for_Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayComponent b2rreactome:Homo_sapiens-Intrinsic_Pathway_for_Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayComponent b2rreactome:Homo_sapiens-Activation_of__Effector_Caspases .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayComponent b2rreactome:Homo_sapiens-Apoptotic_execution__phase .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayComponent b2rreactome:Homo_sapiens-Regulation_of_Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayOrder b2rreactome:Homo_sapiens-Apoptotic_execution__phaseStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayOrder b2rreactome:Homo_sapiens-Extrinsic_Pathway_for_ApoptosisStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayOrder b2rreactome:Homo_sapiens-Intrinsic_Pathway_for_ApoptosisStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayOrder b2rreactome:Homo_sapiens-Regulation_of_ApoptosisStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayOrder b2rreactome:Homo_sapiens-Activation_of__Effector_CaspasesStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:comment "Apoptosis is a distinct form of cell death that is functionally and morphologically different from necrosis. Nuclear chromatin condensation, cytoplasmic shrinking, dilated endoplasmic reticulum, and membrane blebbing characterize apoptosis in general. Mitochondria remain morphologically unchanged. In 1972 Kerr et al introduced the concept of apoptosis as a distinct form of 'cell-death', and the mechanisms of various apoptotic pathways are still being revealed today. BRThe two principal pathways of apoptosis are (1) the Bcl-2 inhibitable or intrinsic pathway induced by various forms of stress like intracellular damage, developmental cues, and external stimuli and (2) the caspase 8/10 dependent or extrinsic pathway initiated by the engagement of death receptorsBR The caspase 8/10 dependent or extrinsic pathway is a death receptor mediated mechanism that results in the activation of caspase-8 and caspase-10. Activation of death receptors like Fas/CD95, TNFR1, and the TRAIL receptor is promoted by the TNF family of ligands including FASL (APO1L OR CD95L), TNF, LT-alpha, LT-beta, CD40L, LIGHT, RANKL, BLYS/BAFF, and APO2L/TRAIL. These ligands are released in response to microbial infection, or as part of the cellular, humoral immunity responses during the formation of lymphoid organs, activation of dendritic cells, stimulation or survival of T, B, and natural killer (NK) cells, cytotoxic response to viral infection or oncogenic transformation. BR The Bcl-2 inhibitable or intrinsic pathway of apoptosis is a stress-inducible process, and acts through the activation of caspase-9 via Apaf-1 and cytochrome c. The rupture of the mitochondrial membrane, a rapid process involving some of the Bcl-2 family proteins, releases these molecules into the cytoplasm. Examples of cellular processes that may induce the intrinsic pathway in response to various damage signals include: auto reactivity in lymphocytes, cytokine deprivation, calcium flux or cellular damage by cytotoxic drugs like taxol, deprivation of nutrients like glucose and growth factors like EGF, anoikis, transactivation of target genes by tumor suppressors including p53.BR In many non-immune cells, death signals initiated by the extrinsic pathway are amplified by connections to the intrinsic pathway. The connecting link appears to be the truncated BID (tBID) protein a proteolytic cleavage product mediated by caspase-8 or other enzymes." .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:comment "Edited: Gopinathrao, G, Matthews, L, Gillespie, ME, Joshi-Tope, G, 0000-00-00 00:00:00" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:comment "Authored: Alnemri, E, Hengartner, M, Tschopp, J, Tsujimoto, Y, Hardwick, JM, 2004-01-16 16:01:51" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:comment "Reviewed: Hengartner, M, Ranganathan, S, Vaux, D, 0000-00-00 00:00:00" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:organism b2rreactome:Homo_sapiens-Homo_sapiens .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayComponent b2rreactome:Homo_sapiens-Extrinsic_Pathway_for_Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayComponent b2rreactome:Homo_sapiens-Intrinsic_Pathway_for_Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayComponent b2rreactome:Homo_sapiens-Activation_of__Effector_Caspases .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayComponent b2rreactome:Homo_sapiens-Apoptotic_execution__phase .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayComponent b2rreactome:Homo_sapiens-Regulation_of_Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Reactome109581 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-REACT_578.2 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_14561771 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_4561027 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_14634621 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_15218528 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_12505355 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_12189384 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_12209154 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayOrder b2rreactome:Homo_sapiens-Apoptotic_execution__phaseStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayOrder b2rreactome:Homo_sapiens-Extrinsic_Pathway_for_ApoptosisStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayOrder b2rreactome:Homo_sapiens-Intrinsic_Pathway_for_ApoptosisStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayOrder b2rreactome:Homo_sapiens-Regulation_of_ApoptosisStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayOrder b2rreactome:Homo_sapiens-Activation_of__Effector_CaspasesStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:dataSource b2rreactome:Homo_sapiens-ReactomeDataSource .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:displayName Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:name "Apoptosis" .
b2rreactome:Homo_sapiens-Apoptosis dcterms:rights <http://www.reactome.org/disclaimer.html> .
b2rreactome:Homo_sapiens-Apoptosis <http://bio2rdf.org/bio2rdf_resource:url> <http://bio2rdf.org/html/reactome:Homo_sapiens-Apoptosis> .
}
<http://rdf.farmbio.uu.se/chembl/sparql> {
<http://linkedchemistry.info/chembl/assay/a325093> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rdf.farmbio.uu.se/chembl/onto/#Assay> .
<http://linkedchemistry.info/chembl/assay/a325093> <http://www.w3.org/2000/01/rdf-schema#label> "CHEMBL860910" .
<http://linkedchemistry.info/chembl/chemblid/CHEMBL860910> <http://www.w3.org/2002/07/owl#equivalentClass> <http://linkedchemistry.info/chembl/assay/a325093> .
<http://linkedchemistry.info/chembl/assay/a325093> <http://www.w3.org/2002/07/owl#equivalentClass> <http://linkedchemistry.info/chembl/chemblid/CHEMBL860910> .
<http://linkedchemistry.info/chembl/chemblid/CHEMBL860910> <http://semanticscience.org/resource/CHEMINF_000200> <http://linkedchemistry.info/chembl/chemblid/CHEMBL860910/chemblid> .
<http://linkedchemistry.info/chembl/chemblid/CHEMBL860910/chemblid> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://semanticscience.org/resource/CHEMINF_000412> .
<http://linkedchemistry.info/chembl/chemblid/CHEMBL860910/chemblid> <http://semanticscience.org/resource/SIO_000300> "CHEMBL860910" .
<http://linkedchemistry.info/chembl/assay/a325093> <http://rdf.farmbio.uu.se/chembl/onto/#hasDescription> "Average Binding Constant for CAMK2B ; NA=Not Active at 10 uM" .
<http://linkedchemistry.info/chembl/assay/a325093> <http://purl.org/spar/cito/citesAsDataSource> <http://linkedchemistry.info/chembl/resource/r30300> .
<http://linkedchemistry.info/chembl/assay/a325093> <http://rdf.farmbio.uu.se/chembl/onto/#hasAssayType> <http://rdf.farmbio.uu.se/chembl/onto/#Binding> .
<http://linkedchemistry.info/chembl/activity/a1650154> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rdf.farmbio.uu.se/chembl/onto/#Activity> .
<http://linkedchemistry.info/chembl/activity/a1650154> <http://purl.org/spar/cito/citesAsDataSource> <http://linkedchemistry.info/chembl/resource/r30300> .
<http://linkedchemistry.info/chembl/activity/a1650154> <http://rdf.farmbio.uu.se/chembl/onto/#onAssay> <http://linkedchemistry.info/chembl/assay/a325093> .
<http://linkedchemistry.info/chembl/activity/a1650154> <http://rdf.farmbio.uu.se/chembl/onto/#forMolecule> <http://linkedchemistry.info/chembl/molecule/m604615> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <molecule> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://purl.org/spar/cito/citesAsDataSource> <http://linkedchemistry.info/chembl/resource/r13282> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://semanticscience.org/resource/CHEMINF_000000> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://purl.obolibrary.org/obo#has_role> <http://purl.org/obo/owl/CHEBI#CHEBI_23888> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.w3.org/2002/07/owl#equivalentClass> <http://bio2rdf.org/chebi:100443> .
<http://linkedchemistry.info/chembl/chemblid/CHEMBL268854> <http://www.w3.org/2002/07/owl#equivalentClass> <http://linkedchemistry.info/chembl/molecule/m443> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.w3.org/2002/07/owl#equivalentClass> <http://linkedchemistry.info/chembl/chemblid/CHEMBL268854> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.w3.org/2000/01/rdf-schema#label> "CHEMBL268854" .
<http://linkedchemistry.info/chembl/chemblid/CHEMBL268854> <http://semanticscience.org/resource/CHEMINF_000200> <http://linkedchemistry.info/chembl/chemblid/CHEMBL268854/chemblid> .
<http://linkedchemistry.info/chembl/chemblid/CHEMBL268854/chemblid> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://semanticscience.org/resource/CHEMINF_000412> .
<http://linkedchemistry.info/chembl/chemblid/CHEMBL268854/chemblid> <http://semanticscience.org/resource/SIO_000300> "CHEMBL268854" .
<http://linkedchemistry.info/chembl/molecule/m443> <http://semanticscience.org/resource/CHEMINF_000200> <http://linkedchemistry.info/chembl/molecule/m443/molform> .
<http://linkedchemistry.info/chembl/molecule/m443/molform> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://semanticscience.org/resource/CHEMINF_000042> .
<http://linkedchemistry.info/chembl/molecule/m443/molform> <http://semanticscience.org/resource/SIO_000300> "C27H23ClN4O2" .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.blueobelisk.org/chemistryblogs/smiles> "Cc1nc(O)c2cc(CN(CC#C)c3ccc(cc3)C(=O)NCc4ccc(Cl)cc4)ccc2n1" .
<http://linkedchemistry.info/chembl/molecule/m443> <http://semanticscience.org/resource/CHEMINF_000200> <http://linkedchemistry.info/chembl/molecule/m443/smiles> .
<http://linkedchemistry.info/chembl/molecule/m443/smiles> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://semanticscience.org/resource/CHEMINF_000018> .
<http://linkedchemistry.info/chembl/molecule/m443/smiles> <http://semanticscience.org/resource/SIO_000300> "Cc1nc(O)c2cc(CN(CC#C)c3ccc(cc3)C(=O)NCc4ccc(Cl)cc4)ccc2n1" .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.blueobelisk.org/chemistryblogs/inchi> "InChI=1S/C27H23ClN4O2/c1-3-14-32(17-20-6-13-25-24(15-20)27(34)31-18(2)30-25)23-11-7-21(8-12-23)26(33)29-16-19-4-9-22(28)10-5-19/h1,4-13,15H,14,16-17H2,2H3,(H,29,33)(H,30,31,34)" .
<http://linkedchemistry.info/chembl/molecule/m443> <http://semanticscience.org/resource/CHEMINF_000200> <http://linkedchemistry.info/chembl/molecule/m443/inchi> .
<http://linkedchemistry.info/chembl/molecule/m443/inchi> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://semanticscience.org/resource/CHEMINF_000113> .
<http://linkedchemistry.info/chembl/molecule/m443/inchi> <http://semanticscience.org/resource/SIO_000300> "InChI=1S/C27H23ClN4O2/c1-3-14-32(17-20-6-13-25-24(15-20)27(34)31-18(2)30-25)23-11-7-21(8-12-23)26(33)29-16-19-4-9-22(28)10-5-19/h1,4-13,15H,14,16-17H2,2H3,(H,29,33)(H,30,31,34)" .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.w3.org/2002/07/owl#equivalentClass> <http://rdf.openmolecules.net/?InChI=1S/C27H23ClN4O2/c1-3-14-32(17-20-6-13-25-24(15-20)27(34)31-18(2)30-25)23-11-7-21(8-12-23)26(33)29-16-19-4-9-22(28)10-5-19/h1,4-13,15H,14,16-17H2,2H3,(H,29,33)(H,30,31,34)> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.blueobelisk.org/chemistryblogs/inchikey> "IQCINSLNRQILLY-UHFFFAOYSA-N" .
<http://linkedchemistry.info/chembl/molecule/m443> <http://semanticscience.org/resource/CHEMINF_000200> <http://linkedchemistry.info/chembl/molecule/m443/inchikey> .
<http://linkedchemistry.info/chembl/molecule/m443/inchikey> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://semanticscience.org/resource/CHEMINF_000059> .
<http://linkedchemistry.info/chembl/molecule/m443/inchikey> <http://semanticscience.org/resource/SIO_000300> "IQCINSLNRQILLY-UHFFFAOYSA-N" .
}
<http://beta.sparql.uniprot.org/> {
<http://purl.uniprot.org/uniprot/Q6GZX4> rdf:type up:Protein .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:label "Putative transcription factor 001R" .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:citation upcitation:15165820 .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:classifiedWith <http://purl.uniprot.org/keywords/10> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:classifiedWith <http://purl.uniprot.org/go/0006351> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:classifiedWith <http://purl.uniprot.org/keywords/805> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:classifiedWith <http://purl.uniprot.org/go/0006355> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:classifiedWith <http://purl.uniprot.org/keywords/1185> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:classifiedWith <http://purl.uniprot.org/go/0046782> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:existence up:Predicted_Existence .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:organism <http://purl.uniprot.org/taxonomy/654924 .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:recommendedName <http://purl.uniprot.org/SHA-384/0777234937D8B63494C8D5F1E2AA13EA7B92452085F2FD9AA79C8DF96BF8234173E353B71AB291B114FFF71D7DB823AE> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:representativeFor <http://purl.uniprot.org/uniref/UniRef50_Q6GZX4> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:representativeFor <http://purl.uniprot.org/uniref/UniRef100_Q6GZX4> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:representativeFor <http://purl.uniprot.org/uniref/UniRef90_Q6GZX4> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:seedFor <http://purl.uniprot.org/uniref/UniRef100_Q6GZX4> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:seedFor <http://purl.uniprot.org/uniref/UniRef90_Q6GZX4> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:sequence <http://purl.uniprot.org/isoforms/Q6GZX4-1> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:created "2011-06-28" .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:mnemonic "001R_FRG3G" .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:modified "2012-04-18" .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:reviewed "true" .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:version "24" .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/embl-cds/AAT09660.1> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/refseq/YP_031579.1> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/proteinmodelportal/Q6GZX4> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/geneid/2947773> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/protclustdb/CLSP2511514> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/interpro/IPR007031> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/pfam/PF04947> .
upcitations:15165820 rdf:type up:Journal_Citation .
upcitations:15165820 rdfs:comment "Frog virus 3 (FV3) is the type species member of the genus Ranavirus (family Iridoviridae). To better understand the molecular mechanisms involved in the replication of FV3 including transcription of its highly methylated DNA genome we have determined the complete nucleotide sequence of the FV3 genome. The FV3 genome is 105903 bp long excluding the terminal redundancy. The G + C content of FV3 genome is 55% and it encodes 98 nonoverlapping potential open reading frames (ORFs) containing 50-1293 amino acids. Eighty-four ORFs have significant homology to known proteins of other iridoviruses whereas twelve of these unique FV3 proteins do not share homology to any known protein. A microsatellite containing a stretch of 34 tandemly repeated CA dinucleotide in a noncoding region was detected. To date no such sequence has been reported in any animal virus." .
upcitations:15165820 up:name "Virology" .
upcitations:15165820 up:author "Barkman T.J." .
upcitations:15165820 up:author "Essani K." .
upcitations:15165820 up:author "Tan W.G." .
upcitations:15165820 up:author "Gregory Chinchar V." .
upcitations:15165820 up:date "2004" .
upcitations:15165820 up:pages "70-84" .
upcitations:15165820 up:title "Comparative genomic analyses of frog virus 3 type species of the genus Ranavirus (family Iridoviridae)." .
upcitations:15165820 up:volume "323" .
upcitations:15165820 skos:exactMatch http://purl.uniprot.org/pubmed/15165820 .
upcitations:15165820 dcterms:identifier "doi:10.1016/j.virol.2004.02.019" .
}
# EBI gene expression atlas
<http://wwwdev.ebi.ac.uk/fgpt/gxa-sparql/sparql> {
# main linking point to the GXA data is the ensembl id and the uniprot id. 
<http://identifiers.org/ensembl/ENSG00000116962> sio:'encodes' <http://purl.uniprot.org/uniprot/P14543> .
# differential expression value
?diffexp a sio:'differential gene expression value' .
?diffexp sio:'is attribute of' <http://identifiers.org/ensembl/ENSG00000116962> .
?diffexp sio:'has value' ?diffvalue . # e.g. UP, DOWN 
?diffexp sio'has attribute' [ a sio:p_value; sio:has-value 0.00005] .
# experiment factor from EFO 
?iv a sio:'independent variable' .
?iv sio:'represents' efo:'experimental factor' .
?iv sio:'in relation to' ?diffexp .
}
# parses up to here.
:Textmining {
:hit ao:fdgr "blabla"
}
:Linksets {
up:Q12345 skos:broadMatch end:000xxxxx .
}

== # VoID ==

{| style="color: black; color: #733;" width="85%" class="wikitable"
| colspan="3" | <http://sparql.wikipathways.org>
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''pav:createdOn'''
| style="width: 60%; background-color: orange;"| '''"2012-10-25"^^xsd:date ;'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''pav:createdBy'''
| style="width: 60%; background-color: orange;"| ''<https://orcid.org/0000-0001-9773-4008> ;''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''pav:createdAt'''
| style="width: 60%; background-color: orange;"| '''dbpedia:Maastricht_University ;'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''dcterms:license'''
| style="width: 60%; background-color: orange;"| ''<http://creativecommons.org/licenses/by/3.0/> .''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| ''<http://sparql.wikipathways.org> .''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:triples'''
| style="width: 60%; background-color: orange;"| '''"1794104"^^xsd:integer ;'''
|-

| colspan="3" | :ChEMBL
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''pav:createdOn'''
| style="width: 60%; background-color: orange;"| '''"2012-10-25"^^xsd:date ;'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:foo'''
| style="width: 60%; background-color: orange;"| '''void:bar .'''
|}

== Triplestore map ==

{| style="color: black; color: #733;" width="85%" class="wikitable"
| colspan="3" | WikiPathways
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''foaf:page'''
| style="width: 60%; background-color: orange;"| ''' http://www.wikipathways.org'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| '''http://sparql.wikipathways.org'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:uriLookupEndpoint'''
| style="width: 60%; background-color: orange;"| '''http://rdf.wikipathways.org '''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''prov:deployedSoftware'''
| style="width: 60%; background-color: orange;"| '''dbpedia:Virtuoso_Universal_Server '''
|-
| colspan="3" | :ChEMBL
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''foaf:page'''
| style="width: 60%; background-color: orange;"| '''"tba'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| ''' http://rdf.farmbio.uu.se/chembl/sparql '''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| ''' http://ragamuffin.bigcat.unimaas.nl/chembl/sparql '''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''prov:deployedSoftware'''
| style="width: 60%; background-color: orange;"| '''dbpedia:Virtuoso_Universal_Server '''
|-
| colspan="3" | :Uniprot
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''foaf:page'''
| style="width: 60%; background-color: orange;"| '''http://www.uniprot.org'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| ''' http://beta.sparql.uniprot.org '''
|-
| colspan="3" | :Gene expression atlas
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''foaf:page'''
| style="width: 60%; background-color: orange;"| '''tba'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| ''' http://wwwdev.ebi.ac.uk/fgpt/gxa-sparql/sparql '''
|-
|}

HCLS/SWAT4LS2012/Hackathon

Ewilligh — Mon, 05 Nov 2012 17:03:16 GMT

Ewilligh: /* Data Map */

The SWAT4LS Hackathon is an informal event associated with the [http://swat4ls.org/ SWAT4LS] Semantic Web Applications and Tools for Life Sciences Workshops Series.

Scope of the event is to bring together experts and enthusiasts in the application of semantic technologies in healthcare and life science for open discussion and jam coding sessions.
The Hackathon will be organized on the 28th of November 2012 at [http://lacantine.org/ La Cantine, Paris] ([https://maps.google.com/maps?q=12+Galerie+Montmartre+75002+france&hl=en&ie=UTF8&ll=48.870438,2.342089&spn=0.0013,0.001869&sll=48.87053,2.342319&sspn=0.002601,0.003739&t=h&hnear=12+Galerie+Montmartre,+75002+Paris,+%C3%8Ele-de-France,+France&z=19 map]).

street: 151 rue Montmartre, Passage des Panoramas
room: 12 Galerie Montmartre
75002 Paris

(For more information, please refer to the [http://www.swat4ls.org/workshops/paris2012/| workshop website]).
The hackathon is open to workshop participants. Registration is required and space is limited!.

== Logistics ==
Projects and institutes attending include:
* OpenPhacts (http://www.openphacts.org)
* WikiPathways (http://www.wikipathways.org/index.php/WikiPathways)
* The Database Center for Life Sciences/BioHackathon (http://dbcls.rois.ac.jp/en/ http://www.biohackathon.org/)
* The W3C Consortium, Health Care and Life Sciences Interest Group ([[HCLS]])
* BioPAX (http://biopax.org)
* European Bioinformatics Institute (http://www.ebi.ac.uk)
While the agenda will be open, we are coordinating ideas that can be developd at the network in advance, to maximize the utility of the day. Co-organizers for each community will help gathering ideas and finding point of contacts.

=== Information and registrations ===
For information, [mailto:info@swat4ls.org| info _at_ swat4ls.org]

Registrations are handled via [http://swat4ls-2012.eventbrite.com/| Eventbrite]

=== Hashtag ===
[https://twitter.com/search/realtime?q=%23swat4lshack #swat4lshack]

=== Co-Organizers ===
* Andrea Splendiani
* Andra Waagmeester
* Eric Prud'hommeaux
* Toshiaki Katayama
* Ismael Navas delgado

== Open PHACTS community ==

=== Contact Point ===
* Andra Waagmeester
* Egon Willighagen

=== Proposed action points ===
# Consume [http://www.openphacts.org Open PHACTS] content in Pathway tools
# Using http://identifiers.org
# Create an example set of valuable queries
# Visualizing output
# work on further linked data integration, with possible:
## [https://ntp.niehs.nih.gov/drugmatrix/ DrugMatrix]
## [http://toxico.nibio.go.jp/open-tggates/ TG-GATEs]
## [http://thedatahub.org/nl/dataset/bio2rdf-ctd CTD] (already available as RDF, by Bio2RDF)
# shared Java client code
## for R, Bioclipse, KNIME

=== Confirmed Participants ===
* Kees Burger
* Maria Carmen Carra
* Ian Dunlop
* Chris Evelo
* Paul Groth
* Tim Harder
* Carina Haupt
* Nick Juty
* Camille Laibe
* Antonis Loizou
* Oriol Lopez
* Guillermo C. Martínez
* Nuria Queralt
* Rishi Ramgolam
* Mark Thompson
* Egon Willighagen
* Pekka Kohonen
* Ola Spjuth

== WikiPathways community ==

=== Contact Point ===
Andra Waagmeester

=== Introduction ===
[http://www.wikipathways.org/index.php/WikiPathways WikiPathways] is a online resource for pathways. Content is provided by the audience at large. I currently contains more then 2200 pathways from 21 species [http://sparqlbin.com/#4f91f23a032a87cc46c5a526a6da673a source]. Pathways are captured in a XML-based format [http://www.pathvisio.org/wiki/EverythingGpml GPML]. Recently WikiPathways was exposed as linked open data where GPML content was exported as RDF. This data is available through a SPARQL endpoint http://sparql.wikipathways.org.

=== Proposed action points ===
==== Exploring [http://www.wikipathways.org/index.php/WikiPathways WikiPathways] RDF content, making example queries ====
==== Writing federated queries to integrate pathway content with other biological data. ====
====Using [http://code.google.com/p/pathvisiorpc/ Pathvisio RPC] to consume and visualize linked pathway data====

=== Confirmed Participants ===
* Chris Evelo
* Martina Kutmon
* Alex Pico

== Database Center for Life Sciences Community / BioHackathon ==

=== Contact Point ===
Toshiaki Katayama

=== Proposed action points ===

== W3C HCLS Community ==

=== Contact Point ===
Eric Prud'hommeaux

=== Proposed action points ===
==== Making an online inventory of available resources (wiki) to document underlying schemas of available datasources.====
There are nice lists of active SPARQL endpoints [http://www.freebase.com/view/base/sparql/views/sparql_endpoint (example 1)] and [http://labs.mondeca.com/sparqlEndpointsStatus/index.html (example 2)]. Finding where the data actually links can still be challenging.

It would be really beneficial to create an overview with descriptions of different linked data sets describing the underlying structure. The first step would be to define a format where data providers describe their data in a predefined (wiki) format. This format could be based on [http://www.w3.org/TR/void/ VoID].
These description coulds then be used to create so called data landscapes in tools such as [http://vsdlc3.blogspot.be/ Semscape].

====Creating a review of sparql endpoints and their support for remote federated queries. ====
Within a federated query you can query different flavours of sparql endpoints. SInce different endpoints have their own implementations and support for different SPARQL versions, it is essential to understand the different issues each type of endpoint might have. The community would benefit from a list mentioning each available SPARQL endpoint system (e.g. 4store, virtuoso, etc) and their support for different SPARQL versions. Also this list could mention specific features (e.g. soft limit in 4store) influencing the recall in federated queries.

== BioPAX Community ==

=== Contact Point ===
Ismael Navas Delgado

=== Proposed action points ===

=== Confirmed Participants ===
* Ismael Navas Delgado
* Andrea Splendiani

== EBI Gene Expression Atlas ==

=== Contact Point ===
Simon Jupp

James Malone

=== Introduction ===

Integration of gene expression data from the Gene Expression Atlas database (http://www.ebi.ac.uk/gxa). Schema description and SPARQL endpoint at http://wwwdev.ebi.ac.uk/fgpt/efosemweb.html
Differential gene expression annotated with Ensembl gene ids (identifiers.org URIs), includes mappings to Uniprot. Experiment assay and sample descriptions annotated with ontology terms from wide range of
bio-ontologies (anatomy, cells, disease etc).

=== Proposed action points ===

Linking gene expression to pathway data.

=== Confirmed Participants ===
* Simon Jupp

== Resources ==
* PathwayCommons SPARQL endpoint. Endpoint over all BioPAX representations in PathwayCommons
* Cytoscape plugin to visualize and interact with RDF knwoledge bases (new!)
* BioQueries: social site to build SPARQL queries
* Open PHACTS rdf guidelines: http://www.openphacts.org/specs/2012/WD-rdfguide-20120823/

== Data Map ==

@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix wprdf: <http://rdf.wikipathways.org/> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix wp: <http://vocabularies.wikipathways.org/wp#> .
@prefix biopax: <http://www.biopax.org/release/biopax-level3.owl#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix gpml: <http://vocabularies.wikipathways.org/gpml#> .
@prefix chembl: <http://rdf.farmbio.uu.se/chembl/onto/#> .
@prefix up: <http://purl.uniprot.org/core/> .
@prefix dbpedia: <http://dbpedia.org/page/> .
@prefix pav: <http://purl.org/pav/> .
@prefix b2rreactome: <http://bio2rdf.org/reactome:>
@prefix b2rbiopax: <http://bio2rdf.org/ns/biopax#>
@prefix b2rbiopaxresource: <http://bio2rdf.org/biopax_resource:>
@prefix up: <http://purl.uniprot.org/core/>
@prefix sio: <http://semanticscience.org/resource/>
@prefix upcitation: <http://purl.uniprot.org/citations/>
@prefix prov: <http://www.w3.org/ns/prov#>

<http://sparql.wikipathways.org> {
# Sparql endpoint: http://sparql.wikipathways.org
# Data: http://rdf.wikipathways.org
# 
<http://identifiers.org/ncbigene/1051> rdf:type wp:GeneProduct .
<http://identifiers.org/ncbigene/1051> dcterms:isPartOf wprdf:WP3 .
<http://identifiers.org/ncbigene/1051> rdfs:label "C/EBP-beta" .
wprdf:WP3 rdf:type wp:Pathway .
wp:Pathway skos:relatedMatch biopax:Pathway .
wprdf:WP3 rdfs:label "Keap1-Nrf2 Pathway" .
wprdf:WP3 dcterms:description """Based on [http://www.nature.com/nrc/journal/v3/n10/fig_tab/nrc1189_F4.html Surh, 2003, figure 4] Nrf2 induces the expression of many
antioxidant enzymes. It is therefore thought to be involved in oxidative stress response."""^^xsd:string.
wprdf:WP3 <http://purl.org/pav/version> "48217"^^xsd:string .
wprdf:WP3 gpml:biopaxref "dba" .
wprdf:WP3 gpml:height "731.0"^^xsd:float .
wprdf:WP3 gpml:width "914.0"^^xsd:float .
wprdf:WP3 wp:category wp:CellularProcess .
wprdf:WP3 wp:organism <http://identifiers.org/taxonomy/9606> .
wprdf:WP3 wp:pathwayOntology <http://purl.obolibrary.org/obo/PW:0000378> .
wprdf:WP3 foaf:page "http://www.wikipathways.org/index.php/Pathway:WP3" .

}
<http://reactome.bio2rdf.org/sparql> {
b2rreactome:Homo_sapiens-Apoptosis rdf:type b2rbiopax:Pathway .
b2rreactome:Homo_sapiens-Apoptosis rdf:type b2rbiopaxresource:Pathway .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:name "Apoptosis" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:displayName "Apoptosis" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Reactome109581 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-REACT_578.2 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_14561771 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_4561027 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_14634621 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_15218528 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_12505355 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_12189384 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_12209154 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:comment "Apoptosis is a distinct form of cell death that is functionally and morphologically different from necrosis. Nuclear chromatin condensation, cytoplasmic shrinking, dilated endoplasmic reticulum, and membrane blebbing characterize apoptosis in general. Mitochondria remain morphologically unchanged. In 1972 Kerr et al introduced the concept of apoptosis as a distinct form of 'cell-death', and the mechanisms of various apoptotic pathways are still being revealed today. BRThe two principal pathways of apoptosis are (1) the Bcl-2 inhibitable or intrinsic pathway induced by various forms of stress like intracellular damage, developmental cues, and external stimuli and (2) the caspase 8/10 dependent or extrinsic pathway initiated by the engagement of death receptorsBR The caspase 8/10 dependent or extrinsic pathway is a death receptor mediated mechanism that results in the activation of caspase-8 and caspase-10. Activation of death receptors like Fas/CD95, TNFR1, and the TRAIL receptor is promoted by the TNF family of ligands including FASL (APO1L OR CD95L), TNF, LT-alpha, LT-beta, CD40L, LIGHT, RANKL, BLYS/BAFF, and APO2L/TRAIL. These ligands are released in response to microbial infection, or as part of the cellular, humoral immunity responses during the formation of lymphoid organs, activation of dendritic cells, stimulation or survival of T, B, and natural killer (NK) cells, cytotoxic response to viral infection or oncogenic transformation. BR The Bcl-2 inhibitable or intrinsic pathway of apoptosis is a stress-inducible process, and acts through the activation of caspase-9 via Apaf-1 and cytochrome c. The rupture of the mitochondrial membrane, a rapid process involving some of the Bcl-2 family proteins, releases these molecules into the cytoplasm. Examples of cellular processes that may induce the intrinsic pathway in response to various damage signals include: auto reactivity in lymphocytes, cytokine deprivation, calcium flux or cellular damage by cytotoxic drugs like taxol, deprivation of nutrients like glucose and growth factors like EGF, anoikis, transactivation of target genes by tumor suppressors including p53.BR In many non-immune cells, death signals initiated by the extrinsic pathway are amplified by connections to the intrinsic pathway. The connecting link appears to be the truncated BID (tBID) protein a proteolytic cleavage product mediated by caspase-8 or other enzymes." .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:comment "Edited: Gopinathrao, G, Matthews, L, Gillespie, ME, Joshi-Tope, G, 0000-00-00 00:00:00" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:comment "Authored: Alnemri, E, Hengartner, M, Tschopp, J, Tsujimoto, Y, Hardwick, JM, 2004-01-16 16:01:51" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:comment "Reviewed: Hengartner, M, Ranganathan, S, Vaux, D, 0000-00-00 00:00:00" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:dataSource b2rreactome:Homo_sapiens-ReactomeDataSource .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:organism b2rreactome:Homo_sapiens-Homo_sapiens .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayComponent b2rreactome:Homo_sapiens-Extrinsic_Pathway_for_Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayComponent b2rreactome:Homo_sapiens-Intrinsic_Pathway_for_Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayComponent b2rreactome:Homo_sapiens-Activation_of__Effector_Caspases .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayComponent b2rreactome:Homo_sapiens-Apoptotic_execution__phase .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayComponent b2rreactome:Homo_sapiens-Regulation_of_Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayOrder b2rreactome:Homo_sapiens-Apoptotic_execution__phaseStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayOrder b2rreactome:Homo_sapiens-Extrinsic_Pathway_for_ApoptosisStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayOrder b2rreactome:Homo_sapiens-Intrinsic_Pathway_for_ApoptosisStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayOrder b2rreactome:Homo_sapiens-Regulation_of_ApoptosisStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayOrder b2rreactome:Homo_sapiens-Activation_of__Effector_CaspasesStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:comment "Apoptosis is a distinct form of cell death that is functionally and morphologically different from necrosis. Nuclear chromatin condensation, cytoplasmic shrinking, dilated endoplasmic reticulum, and membrane blebbing characterize apoptosis in general. Mitochondria remain morphologically unchanged. In 1972 Kerr et al introduced the concept of apoptosis as a distinct form of 'cell-death', and the mechanisms of various apoptotic pathways are still being revealed today. BRThe two principal pathways of apoptosis are (1) the Bcl-2 inhibitable or intrinsic pathway induced by various forms of stress like intracellular damage, developmental cues, and external stimuli and (2) the caspase 8/10 dependent or extrinsic pathway initiated by the engagement of death receptorsBR The caspase 8/10 dependent or extrinsic pathway is a death receptor mediated mechanism that results in the activation of caspase-8 and caspase-10. Activation of death receptors like Fas/CD95, TNFR1, and the TRAIL receptor is promoted by the TNF family of ligands including FASL (APO1L OR CD95L), TNF, LT-alpha, LT-beta, CD40L, LIGHT, RANKL, BLYS/BAFF, and APO2L/TRAIL. These ligands are released in response to microbial infection, or as part of the cellular, humoral immunity responses during the formation of lymphoid organs, activation of dendritic cells, stimulation or survival of T, B, and natural killer (NK) cells, cytotoxic response to viral infection or oncogenic transformation. BR The Bcl-2 inhibitable or intrinsic pathway of apoptosis is a stress-inducible process, and acts through the activation of caspase-9 via Apaf-1 and cytochrome c. The rupture of the mitochondrial membrane, a rapid process involving some of the Bcl-2 family proteins, releases these molecules into the cytoplasm. Examples of cellular processes that may induce the intrinsic pathway in response to various damage signals include: auto reactivity in lymphocytes, cytokine deprivation, calcium flux or cellular damage by cytotoxic drugs like taxol, deprivation of nutrients like glucose and growth factors like EGF, anoikis, transactivation of target genes by tumor suppressors including p53.BR In many non-immune cells, death signals initiated by the extrinsic pathway are amplified by connections to the intrinsic pathway. The connecting link appears to be the truncated BID (tBID) protein a proteolytic cleavage product mediated by caspase-8 or other enzymes." .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:comment "Edited: Gopinathrao, G, Matthews, L, Gillespie, ME, Joshi-Tope, G, 0000-00-00 00:00:00" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:comment "Authored: Alnemri, E, Hengartner, M, Tschopp, J, Tsujimoto, Y, Hardwick, JM, 2004-01-16 16:01:51" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:comment "Reviewed: Hengartner, M, Ranganathan, S, Vaux, D, 0000-00-00 00:00:00" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:organism b2rreactome:Homo_sapiens-Homo_sapiens .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayComponent b2rreactome:Homo_sapiens-Extrinsic_Pathway_for_Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayComponent b2rreactome:Homo_sapiens-Intrinsic_Pathway_for_Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayComponent b2rreactome:Homo_sapiens-Activation_of__Effector_Caspases .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayComponent b2rreactome:Homo_sapiens-Apoptotic_execution__phase .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayComponent b2rreactome:Homo_sapiens-Regulation_of_Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Reactome109581 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-REACT_578.2 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_14561771 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_4561027 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_14634621 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_15218528 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_12505355 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_12189384 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_12209154 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayOrder b2rreactome:Homo_sapiens-Apoptotic_execution__phaseStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayOrder b2rreactome:Homo_sapiens-Extrinsic_Pathway_for_ApoptosisStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayOrder b2rreactome:Homo_sapiens-Intrinsic_Pathway_for_ApoptosisStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayOrder b2rreactome:Homo_sapiens-Regulation_of_ApoptosisStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayOrder b2rreactome:Homo_sapiens-Activation_of__Effector_CaspasesStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:dataSource b2rreactome:Homo_sapiens-ReactomeDataSource .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:displayName Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:name "Apoptosis" .
b2rreactome:Homo_sapiens-Apoptosis dcterms:rights <http://www.reactome.org/disclaimer.html> .
b2rreactome:Homo_sapiens-Apoptosis <http://bio2rdf.org/bio2rdf_resource:url> <http://bio2rdf.org/html/reactome:Homo_sapiens-Apoptosis> .
}
<http://rdf.farmbio.uu.se/chembl/sparql> {
<http://linkedchemistry.info/chembl/activity/a1650154> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rdf.farmbio.uu.se/chembl/onto/#Activity> .
<http://linkedchemistry.info/chembl/activity/a1650154> <http://purl.org/spar/cito/citesAsDataSource> <http://linkedchemistry.info/chembl/resource/r30300> .
<http://linkedchemistry.info/chembl/activity/a1650154> <http://rdf.farmbio.uu.se/chembl/onto/#onAssay> <http://linkedchemistry.info/chembl/assay/a325093> .
<http://linkedchemistry.info/chembl/activity/a1650154> <http://rdf.farmbio.uu.se/chembl/onto/#forMolecule> <http://linkedchemistry.info/chembl/molecule/m604615> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <molecule> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://purl.org/spar/cito/citesAsDataSource> <http://linkedchemistry.info/chembl/resource/r13282> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://semanticscience.org/resource/CHEMINF_000000> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://purl.obolibrary.org/obo#has_role> <http://purl.org/obo/owl/CHEBI#CHEBI_23888> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.w3.org/2002/07/owl#equivalentClass> <http://bio2rdf.org/chebi:100443> .
<http://linkedchemistry.info/chembl/chemblid/CHEMBL268854> <http://www.w3.org/2002/07/owl#equivalentClass> <http://linkedchemistry.info/chembl/molecule/m443> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.w3.org/2002/07/owl#equivalentClass> <http://linkedchemistry.info/chembl/chemblid/CHEMBL268854> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.w3.org/2000/01/rdf-schema#label> "CHEMBL268854" .
<http://linkedchemistry.info/chembl/chemblid/CHEMBL268854> <http://semanticscience.org/resource/CHEMINF_000200> <http://linkedchemistry.info/chembl/chemblid/CHEMBL268854/chemblid> .
<http://linkedchemistry.info/chembl/chemblid/CHEMBL268854/chemblid> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://semanticscience.org/resource/CHEMINF_000412> .
<http://linkedchemistry.info/chembl/chemblid/CHEMBL268854/chemblid> <http://semanticscience.org/resource/SIO_000300> "CHEMBL268854" .
<http://linkedchemistry.info/chembl/molecule/m443> <http://semanticscience.org/resource/CHEMINF_000200> <http://linkedchemistry.info/chembl/molecule/m443/molform> .
<http://linkedchemistry.info/chembl/molecule/m443/molform> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://semanticscience.org/resource/CHEMINF_000042> .
<http://linkedchemistry.info/chembl/molecule/m443/molform> <http://semanticscience.org/resource/SIO_000300> "C27H23ClN4O2" .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.blueobelisk.org/chemistryblogs/smiles> "Cc1nc(O)c2cc(CN(CC#C)c3ccc(cc3)C(=O)NCc4ccc(Cl)cc4)ccc2n1" .
<http://linkedchemistry.info/chembl/molecule/m443> <http://semanticscience.org/resource/CHEMINF_000200> <http://linkedchemistry.info/chembl/molecule/m443/smiles> .
<http://linkedchemistry.info/chembl/molecule/m443/smiles> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://semanticscience.org/resource/CHEMINF_000018> .
<http://linkedchemistry.info/chembl/molecule/m443/smiles> <http://semanticscience.org/resource/SIO_000300> "Cc1nc(O)c2cc(CN(CC#C)c3ccc(cc3)C(=O)NCc4ccc(Cl)cc4)ccc2n1" .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.blueobelisk.org/chemistryblogs/inchi> "InChI=1S/C27H23ClN4O2/c1-3-14-32(17-20-6-13-25-24(15-20)27(34)31-18(2)30-25)23-11-7-21(8-12-23)26(33)29-16-19-4-9-22(28)10-5-19/h1,4-13,15H,14,16-17H2,2H3,(H,29,33)(H,30,31,34)" .
<http://linkedchemistry.info/chembl/molecule/m443> <http://semanticscience.org/resource/CHEMINF_000200> <http://linkedchemistry.info/chembl/molecule/m443/inchi> .
<http://linkedchemistry.info/chembl/molecule/m443/inchi> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://semanticscience.org/resource/CHEMINF_000113> .
<http://linkedchemistry.info/chembl/molecule/m443/inchi> <http://semanticscience.org/resource/SIO_000300> "InChI=1S/C27H23ClN4O2/c1-3-14-32(17-20-6-13-25-24(15-20)27(34)31-18(2)30-25)23-11-7-21(8-12-23)26(33)29-16-19-4-9-22(28)10-5-19/h1,4-13,15H,14,16-17H2,2H3,(H,29,33)(H,30,31,34)" .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.w3.org/2002/07/owl#equivalentClass> <http://rdf.openmolecules.net/?InChI=1S/C27H23ClN4O2/c1-3-14-32(17-20-6-13-25-24(15-20)27(34)31-18(2)30-25)23-11-7-21(8-12-23)26(33)29-16-19-4-9-22(28)10-5-19/h1,4-13,15H,14,16-17H2,2H3,(H,29,33)(H,30,31,34)> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.blueobelisk.org/chemistryblogs/inchikey> "IQCINSLNRQILLY-UHFFFAOYSA-N" .
<http://linkedchemistry.info/chembl/molecule/m443> <http://semanticscience.org/resource/CHEMINF_000200> <http://linkedchemistry.info/chembl/molecule/m443/inchikey> .
<http://linkedchemistry.info/chembl/molecule/m443/inchikey> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://semanticscience.org/resource/CHEMINF_000059> .
<http://linkedchemistry.info/chembl/molecule/m443/inchikey> <http://semanticscience.org/resource/SIO_000300> "IQCINSLNRQILLY-UHFFFAOYSA-N" .
}
<http://beta.sparql.uniprot.org/> {
<http://purl.uniprot.org/uniprot/Q6GZX4> rdf:type up:Protein .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:label "Putative transcription factor 001R" .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:citation upcitation:15165820 .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:classifiedWith <http://purl.uniprot.org/keywords/10> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:classifiedWith <http://purl.uniprot.org/go/0006351> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:classifiedWith <http://purl.uniprot.org/keywords/805> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:classifiedWith <http://purl.uniprot.org/go/0006355> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:classifiedWith <http://purl.uniprot.org/keywords/1185> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:classifiedWith <http://purl.uniprot.org/go/0046782> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:existence up:Predicted_Existence .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:organism <http://purl.uniprot.org/taxonomy/654924 .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:recommendedName <http://purl.uniprot.org/SHA-384/0777234937D8B63494C8D5F1E2AA13EA7B92452085F2FD9AA79C8DF96BF8234173E353B71AB291B114FFF71D7DB823AE> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:representativeFor <http://purl.uniprot.org/uniref/UniRef50_Q6GZX4> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:representativeFor <http://purl.uniprot.org/uniref/UniRef100_Q6GZX4> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:representativeFor <http://purl.uniprot.org/uniref/UniRef90_Q6GZX4> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:seedFor <http://purl.uniprot.org/uniref/UniRef100_Q6GZX4> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:seedFor <http://purl.uniprot.org/uniref/UniRef90_Q6GZX4> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:sequence <http://purl.uniprot.org/isoforms/Q6GZX4-1> .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:created "2011-06-28" .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:mnemonic "001R_FRG3G" .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:modified "2012-04-18" .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:reviewed "true" .
<http://purl.uniprot.org/uniprot/Q6GZX4> up:version "24" .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/embl-cds/AAT09660.1> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/refseq/YP_031579.1> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/proteinmodelportal/Q6GZX4> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/geneid/2947773> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/protclustdb/CLSP2511514> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/interpro/IPR007031> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/pfam/PF04947> .
upcitations:15165820 rdf:type up:Journal_Citation .
upcitations:15165820 rdfs:comment "Frog virus 3 (FV3) is the type species member of the genus Ranavirus (family Iridoviridae). To better understand the molecular mechanisms involved in the replication of FV3 including transcription of its highly methylated DNA genome we have determined the complete nucleotide sequence of the FV3 genome. The FV3 genome is 105903 bp long excluding the terminal redundancy. The G + C content of FV3 genome is 55% and it encodes 98 nonoverlapping potential open reading frames (ORFs) containing 50-1293 amino acids. Eighty-four ORFs have significant homology to known proteins of other iridoviruses whereas twelve of these unique FV3 proteins do not share homology to any known protein. A microsatellite containing a stretch of 34 tandemly repeated CA dinucleotide in a noncoding region was detected. To date no such sequence has been reported in any animal virus." .
upcitations:15165820 up:name "Virology" .
upcitations:15165820 up:author "Barkman T.J." .
upcitations:15165820 up:author "Essani K." .
upcitations:15165820 up:author "Tan W.G." .
upcitations:15165820 up:author "Gregory Chinchar V." .
upcitations:15165820 up:date "2004" .
upcitations:15165820 up:pages "70-84" .
upcitations:15165820 up:title "Comparative genomic analyses of frog virus 3 type species of the genus Ranavirus (family Iridoviridae)." .
upcitations:15165820 up:volume "323" .
upcitations:15165820 skos:exactMatch http://purl.uniprot.org/pubmed/15165820 .
upcitations:15165820 dcterms:identifier "doi:10.1016/j.virol.2004.02.019" .
}
# EBI gene expression atlas
<http://wwwdev.ebi.ac.uk/fgpt/gxa-sparql/sparql> {
# main linking point to the GXA data is the ensembl id and the uniprot id. 
<http://identifiers.org/ensembl/ENSG00000116962> sio:'encodes' <http://purl.uniprot.org/uniprot/P14543> .
# differential expression value
?diffexp a sio:'differential gene expression value' .
?diffexp sio:'is attribute of' <http://identifiers.org/ensembl/ENSG00000116962> .
?diffexp sio:'has value' ?diffvalue . # e.g. UP, DOWN 
?diffexp sio'has attribute' [ a sio:p_value; sio:has-value 0.00005] .
# experiment factor from EFO 
?iv a sio:'independent variable' .
?iv sio:'represents' efo:'experimental factor' .
?iv sio:'in relation to' ?diffexp .
}
# parses up to here.
:Textmining {
:hit ao:fdgr "blabla"
}
:Linksets {
up:Q12345 skos:broadMatch end:000xxxxx .
}

== # VoID ==

{| style="color: black; color: #733;" width="85%" class="wikitable"
| colspan="3" | <http://sparql.wikipathways.org>
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''pav:createdOn'''
| style="width: 60%; background-color: orange;"| '''"2012-10-25"^^xsd:date ;'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''pav:createdBy'''
| style="width: 60%; background-color: orange;"| ''<https://orcid.org/0000-0001-9773-4008> ;''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''pav:createdAt'''
| style="width: 60%; background-color: orange;"| '''dbpedia:Maastricht_University ;'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''dcterms:license'''
| style="width: 60%; background-color: orange;"| ''<http://creativecommons.org/licenses/by/3.0/> .''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| ''<http://sparql.wikipathways.org> .''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:triples'''
| style="width: 60%; background-color: orange;"| '''"1794104"^^xsd:integer ;'''
|-

| colspan="3" | :ChEMBL
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''pav:createdOn'''
| style="width: 60%; background-color: orange;"| '''"2012-10-25"^^xsd:date ;'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:foo'''
| style="width: 60%; background-color: orange;"| '''void:bar .'''
|}

== Triplestore map ==

{| style="color: black; color: #733;" width="85%" class="wikitable"
| colspan="3" | WikiPathways
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''foaf:page'''
| style="width: 60%; background-color: orange;"| ''' http://www.wikipathways.org'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| '''http://sparql.wikipathways.org'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:uriLookupEndpoint'''
| style="width: 60%; background-color: orange;"| '''http://rdf.wikipathways.org '''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''prov:deployedSoftware'''
| style="width: 60%; background-color: orange;"| '''dbpedia:Virtuoso_Universal_Server '''
|-
| colspan="3" | :ChEMBL
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''foaf:page'''
| style="width: 60%; background-color: orange;"| '''"tba'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| ''' http://rdf.farmbio.uu.se/chembl/sparql '''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| ''' http://ragamuffin.bigcat.unimaas.nl/chembl/sparql '''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''prov:deployedSoftware'''
| style="width: 60%; background-color: orange;"| '''dbpedia:Virtuoso_Universal_Server '''
|-
| colspan="3" | :Uniprot
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''foaf:page'''
| style="width: 60%; background-color: orange;"| '''http://www.uniprot.org'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| ''' http://beta.sparql.uniprot.org '''
|-
| colspan="3" | :Gene expression atlas
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''foaf:page'''
| style="width: 60%; background-color: orange;"| '''tba'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| ''' http://wwwdev.ebi.ac.uk/fgpt/gxa-sparql/sparql '''
|-
|}

HCLS/SWAT4LS2012/Hackathon

Ewilligh — Mon, 05 Nov 2012 17:02:17 GMT

Ewilligh: /* Data Map */

The SWAT4LS Hackathon is an informal event associated with the [http://swat4ls.org/ SWAT4LS] Semantic Web Applications and Tools for Life Sciences Workshops Series.

Scope of the event is to bring together experts and enthusiasts in the application of semantic technologies in healthcare and life science for open discussion and jam coding sessions.
The Hackathon will be organized on the 28th of November 2012 at [http://lacantine.org/ La Cantine, Paris] ([https://maps.google.com/maps?q=12+Galerie+Montmartre+75002+france&hl=en&ie=UTF8&ll=48.870438,2.342089&spn=0.0013,0.001869&sll=48.87053,2.342319&sspn=0.002601,0.003739&t=h&hnear=12+Galerie+Montmartre,+75002+Paris,+%C3%8Ele-de-France,+France&z=19 map]).

street: 151 rue Montmartre, Passage des Panoramas
room: 12 Galerie Montmartre
75002 Paris

(For more information, please refer to the [http://www.swat4ls.org/workshops/paris2012/| workshop website]).
The hackathon is open to workshop participants. Registration is required and space is limited!.

== Logistics ==
Projects and institutes attending include:
* OpenPhacts (http://www.openphacts.org)
* WikiPathways (http://www.wikipathways.org/index.php/WikiPathways)
* The Database Center for Life Sciences/BioHackathon (http://dbcls.rois.ac.jp/en/ http://www.biohackathon.org/)
* The W3C Consortium, Health Care and Life Sciences Interest Group ([[HCLS]])
* BioPAX (http://biopax.org)
* European Bioinformatics Institute (http://www.ebi.ac.uk)
While the agenda will be open, we are coordinating ideas that can be developd at the network in advance, to maximize the utility of the day. Co-organizers for each community will help gathering ideas and finding point of contacts.

=== Information and registrations ===
For information, [mailto:info@swat4ls.org| info _at_ swat4ls.org]

Registrations are handled via [http://swat4ls-2012.eventbrite.com/| Eventbrite]

=== Hashtag ===
[https://twitter.com/search/realtime?q=%23swat4lshack #swat4lshack]

=== Co-Organizers ===
* Andrea Splendiani
* Andra Waagmeester
* Eric Prud'hommeaux
* Toshiaki Katayama
* Ismael Navas delgado

== Open PHACTS community ==

=== Contact Point ===
* Andra Waagmeester
* Egon Willighagen

=== Proposed action points ===
# Consume [http://www.openphacts.org Open PHACTS] content in Pathway tools
# Using http://identifiers.org
# Create an example set of valuable queries
# Visualizing output
# work on further linked data integration, with possible:
## [https://ntp.niehs.nih.gov/drugmatrix/ DrugMatrix]
## [http://toxico.nibio.go.jp/open-tggates/ TG-GATEs]
## [http://thedatahub.org/nl/dataset/bio2rdf-ctd CTD] (already available as RDF, by Bio2RDF)
# shared Java client code
## for R, Bioclipse, KNIME

=== Confirmed Participants ===
* Kees Burger
* Maria Carmen Carra
* Ian Dunlop
* Chris Evelo
* Paul Groth
* Tim Harder
* Carina Haupt
* Nick Juty
* Camille Laibe
* Antonis Loizou
* Oriol Lopez
* Guillermo C. Martínez
* Nuria Queralt
* Rishi Ramgolam
* Mark Thompson
* Egon Willighagen
* Pekka Kohonen
* Ola Spjuth

== WikiPathways community ==

=== Contact Point ===
Andra Waagmeester

=== Introduction ===
[http://www.wikipathways.org/index.php/WikiPathways WikiPathways] is a online resource for pathways. Content is provided by the audience at large. I currently contains more then 2200 pathways from 21 species [http://sparqlbin.com/#4f91f23a032a87cc46c5a526a6da673a source]. Pathways are captured in a XML-based format [http://www.pathvisio.org/wiki/EverythingGpml GPML]. Recently WikiPathways was exposed as linked open data where GPML content was exported as RDF. This data is available through a SPARQL endpoint http://sparql.wikipathways.org.

=== Proposed action points ===
==== Exploring [http://www.wikipathways.org/index.php/WikiPathways WikiPathways] RDF content, making example queries ====
==== Writing federated queries to integrate pathway content with other biological data. ====
====Using [http://code.google.com/p/pathvisiorpc/ Pathvisio RPC] to consume and visualize linked pathway data====

=== Confirmed Participants ===
* Chris Evelo
* Martina Kutmon
* Alex Pico

== Database Center for Life Sciences Community / BioHackathon ==

=== Contact Point ===
Toshiaki Katayama

=== Proposed action points ===

== W3C HCLS Community ==

=== Contact Point ===
Eric Prud'hommeaux

=== Proposed action points ===
==== Making an online inventory of available resources (wiki) to document underlying schemas of available datasources.====
There are nice lists of active SPARQL endpoints [http://www.freebase.com/view/base/sparql/views/sparql_endpoint (example 1)] and [http://labs.mondeca.com/sparqlEndpointsStatus/index.html (example 2)]. Finding where the data actually links can still be challenging.

It would be really beneficial to create an overview with descriptions of different linked data sets describing the underlying structure. The first step would be to define a format where data providers describe their data in a predefined (wiki) format. This format could be based on [http://www.w3.org/TR/void/ VoID].
These description coulds then be used to create so called data landscapes in tools such as [http://vsdlc3.blogspot.be/ Semscape].

====Creating a review of sparql endpoints and their support for remote federated queries. ====
Within a federated query you can query different flavours of sparql endpoints. SInce different endpoints have their own implementations and support for different SPARQL versions, it is essential to understand the different issues each type of endpoint might have. The community would benefit from a list mentioning each available SPARQL endpoint system (e.g. 4store, virtuoso, etc) and their support for different SPARQL versions. Also this list could mention specific features (e.g. soft limit in 4store) influencing the recall in federated queries.

== BioPAX Community ==

=== Contact Point ===
Ismael Navas Delgado

=== Proposed action points ===

=== Confirmed Participants ===
* Ismael Navas Delgado
* Andrea Splendiani

== EBI Gene Expression Atlas ==

=== Contact Point ===
Simon Jupp

James Malone

=== Introduction ===

Integration of gene expression data from the Gene Expression Atlas database (http://www.ebi.ac.uk/gxa). Schema description and SPARQL endpoint at http://wwwdev.ebi.ac.uk/fgpt/efosemweb.html
Differential gene expression annotated with Ensembl gene ids (identifiers.org URIs), includes mappings to Uniprot. Experiment assay and sample descriptions annotated with ontology terms from wide range of
bio-ontologies (anatomy, cells, disease etc).

=== Proposed action points ===

Linking gene expression to pathway data.

=== Confirmed Participants ===
* Simon Jupp

== Resources ==
* PathwayCommons SPARQL endpoint. Endpoint over all BioPAX representations in PathwayCommons
* Cytoscape plugin to visualize and interact with RDF knwoledge bases (new!)
* BioQueries: social site to build SPARQL queries
* Open PHACTS rdf guidelines: http://www.openphacts.org/specs/2012/WD-rdfguide-20120823/

== Data Map ==

@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix wprdf: <http://rdf.wikipathways.org/> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix wp: <http://vocabularies.wikipathways.org/wp#> .
@prefix biopax: <http://www.biopax.org/release/biopax-level3.owl#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix gpml: <http://vocabularies.wikipathways.org/gpml#> .
@prefix chembl: <http://rdf.farmbio.uu.se/chembl/onto/#> .
@prefix up: <http://purl.uniprot.org/core/> .
@prefix dbpedia: <http://dbpedia.org/page/> .
@prefix pav: <http://purl.org/pav/> .
@prefix b2rreactome: <http://bio2rdf.org/reactome:>
@prefix b2rbiopax: <http://bio2rdf.org/ns/biopax#>
@prefix b2rbiopaxresource: <http://bio2rdf.org/biopax_resource:>
@prefix up: <http://purl.uniprot.org/core/>
@prefix sio: <http://semanticscience.org/resource/>
@prefix upcitation: <http://purl.uniprot.org/citations/>
@prefix prov: <http://www.w3.org/ns/prov#>

<http://sparql.wikipathways.org> {
# Sparql endpoint: http://sparql.wikipathways.org
# Data: http://rdf.wikipathways.org
# 
<http://identifiers.org/ncbigene/1051> rdf:type wp:GeneProduct .
<http://identifiers.org/ncbigene/1051> dcterms:isPartOf wprdf:WP3 .
<http://identifiers.org/ncbigene/1051> rdfs:label "C/EBP-beta" .
wprdf:WP3 rdf:type wp:Pathway .
wp:Pathway skos:relatedMatch biopax:Pathway .
wprdf:WP3 rdfs:label "Keap1-Nrf2 Pathway" .
wprdf:WP3 dcterms:description """Based on [http://www.nature.com/nrc/journal/v3/n10/fig_tab/nrc1189_F4.html Surh, 2003, figure 4] Nrf2 induces the expression of many
antioxidant enzymes. It is therefore thought to be involved in oxidative stress response."""^^xsd:string.
wprdf:WP3 <http://purl.org/pav/version> "48217"^^xsd:string .
wprdf:WP3 gpml:biopaxref "dba" .
wprdf:WP3 gpml:height "731.0"^^xsd:float .
wprdf:WP3 gpml:width "914.0"^^xsd:float .
wprdf:WP3 wp:category wp:CellularProcess .
wprdf:WP3 wp:organism <http://identifiers.org/taxonomy/9606> .
wprdf:WP3 wp:pathwayOntology <http://purl.obolibrary.org/obo/PW:0000378> .
wprdf:WP3 foaf:page "http://www.wikipathways.org/index.php/Pathway:WP3" .

}
<http://reactome.bio2rdf.org/sparql> {
b2rreactome:Homo_sapiens-Apoptosis rdf:type b2rbiopax:Pathway .
b2rreactome:Homo_sapiens-Apoptosis rdf:type b2rbiopaxresource:Pathway .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:name "Apoptosis" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:displayName "Apoptosis" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Reactome109581 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-REACT_578.2 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_14561771 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_4561027 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_14634621 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_15218528 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_12505355 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_12189384 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:xref b2rreactome:Homo_sapiens-Pubmed_12209154 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:comment "Apoptosis is a distinct form of cell death that is functionally and morphologically different from necrosis. Nuclear chromatin condensation, cytoplasmic shrinking, dilated endoplasmic reticulum, and membrane blebbing characterize apoptosis in general. Mitochondria remain morphologically unchanged. In 1972 Kerr et al introduced the concept of apoptosis as a distinct form of 'cell-death', and the mechanisms of various apoptotic pathways are still being revealed today. BRThe two principal pathways of apoptosis are (1) the Bcl-2 inhibitable or intrinsic pathway induced by various forms of stress like intracellular damage, developmental cues, and external stimuli and (2) the caspase 8/10 dependent or extrinsic pathway initiated by the engagement of death receptorsBR The caspase 8/10 dependent or extrinsic pathway is a death receptor mediated mechanism that results in the activation of caspase-8 and caspase-10. Activation of death receptors like Fas/CD95, TNFR1, and the TRAIL receptor is promoted by the TNF family of ligands including FASL (APO1L OR CD95L), TNF, LT-alpha, LT-beta, CD40L, LIGHT, RANKL, BLYS/BAFF, and APO2L/TRAIL. These ligands are released in response to microbial infection, or as part of the cellular, humoral immunity responses during the formation of lymphoid organs, activation of dendritic cells, stimulation or survival of T, B, and natural killer (NK) cells, cytotoxic response to viral infection or oncogenic transformation. BR The Bcl-2 inhibitable or intrinsic pathway of apoptosis is a stress-inducible process, and acts through the activation of caspase-9 via Apaf-1 and cytochrome c. The rupture of the mitochondrial membrane, a rapid process involving some of the Bcl-2 family proteins, releases these molecules into the cytoplasm. Examples of cellular processes that may induce the intrinsic pathway in response to various damage signals include: auto reactivity in lymphocytes, cytokine deprivation, calcium flux or cellular damage by cytotoxic drugs like taxol, deprivation of nutrients like glucose and growth factors like EGF, anoikis, transactivation of target genes by tumor suppressors including p53.BR In many non-immune cells, death signals initiated by the extrinsic pathway are amplified by connections to the intrinsic pathway. The connecting link appears to be the truncated BID (tBID) protein a proteolytic cleavage product mediated by caspase-8 or other enzymes." .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:comment "Edited: Gopinathrao, G, Matthews, L, Gillespie, ME, Joshi-Tope, G, 0000-00-00 00:00:00" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:comment "Authored: Alnemri, E, Hengartner, M, Tschopp, J, Tsujimoto, Y, Hardwick, JM, 2004-01-16 16:01:51" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:comment "Reviewed: Hengartner, M, Ranganathan, S, Vaux, D, 0000-00-00 00:00:00" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:dataSource b2rreactome:Homo_sapiens-ReactomeDataSource .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:organism b2rreactome:Homo_sapiens-Homo_sapiens .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayComponent b2rreactome:Homo_sapiens-Extrinsic_Pathway_for_Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayComponent b2rreactome:Homo_sapiens-Intrinsic_Pathway_for_Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayComponent b2rreactome:Homo_sapiens-Activation_of__Effector_Caspases .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayComponent b2rreactome:Homo_sapiens-Apoptotic_execution__phase .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayComponent b2rreactome:Homo_sapiens-Regulation_of_Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayOrder b2rreactome:Homo_sapiens-Apoptotic_execution__phaseStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayOrder b2rreactome:Homo_sapiens-Extrinsic_Pathway_for_ApoptosisStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayOrder b2rreactome:Homo_sapiens-Intrinsic_Pathway_for_ApoptosisStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayOrder b2rreactome:Homo_sapiens-Regulation_of_ApoptosisStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopax:pathwayOrder b2rreactome:Homo_sapiens-Activation_of__Effector_CaspasesStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:comment "Apoptosis is a distinct form of cell death that is functionally and morphologically different from necrosis. Nuclear chromatin condensation, cytoplasmic shrinking, dilated endoplasmic reticulum, and membrane blebbing characterize apoptosis in general. Mitochondria remain morphologically unchanged. In 1972 Kerr et al introduced the concept of apoptosis as a distinct form of 'cell-death', and the mechanisms of various apoptotic pathways are still being revealed today. BRThe two principal pathways of apoptosis are (1) the Bcl-2 inhibitable or intrinsic pathway induced by various forms of stress like intracellular damage, developmental cues, and external stimuli and (2) the caspase 8/10 dependent or extrinsic pathway initiated by the engagement of death receptorsBR The caspase 8/10 dependent or extrinsic pathway is a death receptor mediated mechanism that results in the activation of caspase-8 and caspase-10. Activation of death receptors like Fas/CD95, TNFR1, and the TRAIL receptor is promoted by the TNF family of ligands including FASL (APO1L OR CD95L), TNF, LT-alpha, LT-beta, CD40L, LIGHT, RANKL, BLYS/BAFF, and APO2L/TRAIL. These ligands are released in response to microbial infection, or as part of the cellular, humoral immunity responses during the formation of lymphoid organs, activation of dendritic cells, stimulation or survival of T, B, and natural killer (NK) cells, cytotoxic response to viral infection or oncogenic transformation. BR The Bcl-2 inhibitable or intrinsic pathway of apoptosis is a stress-inducible process, and acts through the activation of caspase-9 via Apaf-1 and cytochrome c. The rupture of the mitochondrial membrane, a rapid process involving some of the Bcl-2 family proteins, releases these molecules into the cytoplasm. Examples of cellular processes that may induce the intrinsic pathway in response to various damage signals include: auto reactivity in lymphocytes, cytokine deprivation, calcium flux or cellular damage by cytotoxic drugs like taxol, deprivation of nutrients like glucose and growth factors like EGF, anoikis, transactivation of target genes by tumor suppressors including p53.BR In many non-immune cells, death signals initiated by the extrinsic pathway are amplified by connections to the intrinsic pathway. The connecting link appears to be the truncated BID (tBID) protein a proteolytic cleavage product mediated by caspase-8 or other enzymes." .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:comment "Edited: Gopinathrao, G, Matthews, L, Gillespie, ME, Joshi-Tope, G, 0000-00-00 00:00:00" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:comment "Authored: Alnemri, E, Hengartner, M, Tschopp, J, Tsujimoto, Y, Hardwick, JM, 2004-01-16 16:01:51" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:comment "Reviewed: Hengartner, M, Ranganathan, S, Vaux, D, 0000-00-00 00:00:00" .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:organism b2rreactome:Homo_sapiens-Homo_sapiens .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayComponent b2rreactome:Homo_sapiens-Extrinsic_Pathway_for_Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayComponent b2rreactome:Homo_sapiens-Intrinsic_Pathway_for_Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayComponent b2rreactome:Homo_sapiens-Activation_of__Effector_Caspases .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayComponent b2rreactome:Homo_sapiens-Apoptotic_execution__phase .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayComponent b2rreactome:Homo_sapiens-Regulation_of_Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Reactome109581 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-REACT_578.2 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_14561771 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_4561027 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_14634621 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_15218528 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_12505355 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_12189384 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:xref b2rreactome:Homo_sapiens-Pubmed_12209154 .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayOrder b2rreactome:Homo_sapiens-Apoptotic_execution__phaseStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayOrder b2rreactome:Homo_sapiens-Extrinsic_Pathway_for_ApoptosisStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayOrder b2rreactome:Homo_sapiens-Intrinsic_Pathway_for_ApoptosisStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayOrder b2rreactome:Homo_sapiens-Regulation_of_ApoptosisStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:pathwayOrder b2rreactome:Homo_sapiens-Activation_of__Effector_CaspasesStep .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:dataSource b2rreactome:Homo_sapiens-ReactomeDataSource .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:displayName Apoptosis .
b2rreactome:Homo_sapiens-Apoptosis b2rbiopaxresource:name "Apoptosis" .
b2rreactome:Homo_sapiens-Apoptosis dcterms:rights <http://www.reactome.org/disclaimer.html> .
b2rreactome:Homo_sapiens-Apoptosis <http://bio2rdf.org/bio2rdf_resource:url> <http://bio2rdf.org/html/reactome:Homo_sapiens-Apoptosis> .
}
<http://rdf.farmbio.uu.se/chembl/sparql> {
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <molecule> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://purl.org/spar/cito/citesAsDataSource> <http://linkedchemistry.info/chembl/resource/r13282> .
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<http://linkedchemistry.info/chembl/molecule/m443> <http://www.w3.org/2002/07/owl#equivalentClass> <http://bio2rdf.org/chebi:100443> .
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<http://linkedchemistry.info/chembl/molecule/m443> <http://www.w3.org/2002/07/owl#equivalentClass> <http://linkedchemistry.info/chembl/chemblid/CHEMBL268854> .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.w3.org/2000/01/rdf-schema#label> "CHEMBL268854" .
<http://linkedchemistry.info/chembl/chemblid/CHEMBL268854> <http://semanticscience.org/resource/CHEMINF_000200> <http://linkedchemistry.info/chembl/chemblid/CHEMBL268854/chemblid> .
<http://linkedchemistry.info/chembl/chemblid/CHEMBL268854/chemblid> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://semanticscience.org/resource/CHEMINF_000412> .
<http://linkedchemistry.info/chembl/chemblid/CHEMBL268854/chemblid> <http://semanticscience.org/resource/SIO_000300> "CHEMBL268854" .
<http://linkedchemistry.info/chembl/molecule/m443> <http://semanticscience.org/resource/CHEMINF_000200> <http://linkedchemistry.info/chembl/molecule/m443/molform> .
<http://linkedchemistry.info/chembl/molecule/m443/molform> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://semanticscience.org/resource/CHEMINF_000042> .
<http://linkedchemistry.info/chembl/molecule/m443/molform> <http://semanticscience.org/resource/SIO_000300> "C27H23ClN4O2" .
<http://linkedchemistry.info/chembl/molecule/m443> <http://www.blueobelisk.org/chemistryblogs/smiles> "Cc1nc(O)c2cc(CN(CC#C)c3ccc(cc3)C(=O)NCc4ccc(Cl)cc4)ccc2n1" .
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<http://linkedchemistry.info/chembl/molecule/m443/smiles> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://semanticscience.org/resource/CHEMINF_000018> .
<http://linkedchemistry.info/chembl/molecule/m443/smiles> <http://semanticscience.org/resource/SIO_000300> "Cc1nc(O)c2cc(CN(CC#C)c3ccc(cc3)C(=O)NCc4ccc(Cl)cc4)ccc2n1" .
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<http://linkedchemistry.info/chembl/molecule/m443> <http://semanticscience.org/resource/CHEMINF_000200> <http://linkedchemistry.info/chembl/molecule/m443/inchi> .
<http://linkedchemistry.info/chembl/molecule/m443/inchi> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://semanticscience.org/resource/CHEMINF_000113> .
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<http://linkedchemistry.info/chembl/molecule/m443> <http://www.w3.org/2002/07/owl#equivalentClass> <http://rdf.openmolecules.net/?InChI=1S/C27H23ClN4O2/c1-3-14-32(17-20-6-13-25-24(15-20)27(34)31-18(2)30-25)23-11-7-21(8-12-23)26(33)29-16-19-4-9-22(28)10-5-19/h1,4-13,15H,14,16-17H2,2H3,(H,29,33)(H,30,31,34)> .
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<http://linkedchemistry.info/chembl/molecule/m443/inchikey> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://semanticscience.org/resource/CHEMINF_000059> .
<http://linkedchemistry.info/chembl/molecule/m443/inchikey> <http://semanticscience.org/resource/SIO_000300> "IQCINSLNRQILLY-UHFFFAOYSA-N" .
}
<http://beta.sparql.uniprot.org/> {
<http://purl.uniprot.org/uniprot/Q6GZX4> rdf:type up:Protein .
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<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/proteinmodelportal/Q6GZX4> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/geneid/2947773> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/protclustdb/CLSP2511514> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/interpro/IPR007031> .
<http://purl.uniprot.org/uniprot/Q6GZX4> rdfs:seeAlso <http://purl.uniprot.org/pfam/PF04947> .
upcitations:15165820 rdf:type up:Journal_Citation .
upcitations:15165820 rdfs:comment "Frog virus 3 (FV3) is the type species member of the genus Ranavirus (family Iridoviridae). To better understand the molecular mechanisms involved in the replication of FV3 including transcription of its highly methylated DNA genome we have determined the complete nucleotide sequence of the FV3 genome. The FV3 genome is 105903 bp long excluding the terminal redundancy. The G + C content of FV3 genome is 55% and it encodes 98 nonoverlapping potential open reading frames (ORFs) containing 50-1293 amino acids. Eighty-four ORFs have significant homology to known proteins of other iridoviruses whereas twelve of these unique FV3 proteins do not share homology to any known protein. A microsatellite containing a stretch of 34 tandemly repeated CA dinucleotide in a noncoding region was detected. To date no such sequence has been reported in any animal virus." .
upcitations:15165820 up:name "Virology" .
upcitations:15165820 up:author "Barkman T.J." .
upcitations:15165820 up:author "Essani K." .
upcitations:15165820 up:author "Tan W.G." .
upcitations:15165820 up:author "Gregory Chinchar V." .
upcitations:15165820 up:date "2004" .
upcitations:15165820 up:pages "70-84" .
upcitations:15165820 up:title "Comparative genomic analyses of frog virus 3 type species of the genus Ranavirus (family Iridoviridae)." .
upcitations:15165820 up:volume "323" .
upcitations:15165820 skos:exactMatch http://purl.uniprot.org/pubmed/15165820 .
upcitations:15165820 dcterms:identifier "doi:10.1016/j.virol.2004.02.019" .
}
# EBI gene expression atlas
<http://wwwdev.ebi.ac.uk/fgpt/gxa-sparql/sparql> {
# main linking point to the GXA data is the ensembl id and the uniprot id. 
<http://identifiers.org/ensembl/ENSG00000116962> sio:'encodes' <http://purl.uniprot.org/uniprot/P14543> .
# differential expression value
?diffexp a sio:'differential gene expression value' .
?diffexp sio:'is attribute of' <http://identifiers.org/ensembl/ENSG00000116962> .
?diffexp sio:'has value' ?diffvalue . # e.g. UP, DOWN 
?diffexp sio'has attribute' [ a sio:p_value; sio:has-value 0.00005] .
# experiment factor from EFO 
?iv a sio:'independent variable' .
?iv sio:'represents' efo:'experimental factor' .
?iv sio:'in relation to' ?diffexp .
}
# parses up to here.
:Textmining {
:hit ao:fdgr "blabla"
}
:Linksets {
up:Q12345 skos:broadMatch end:000xxxxx .
}

== # VoID ==

{| style="color: black; color: #733;" width="85%" class="wikitable"
| colspan="3" | <http://sparql.wikipathways.org>
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''pav:createdOn'''
| style="width: 60%; background-color: orange;"| '''"2012-10-25"^^xsd:date ;'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''pav:createdBy'''
| style="width: 60%; background-color: orange;"| ''<https://orcid.org/0000-0001-9773-4008> ;''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''pav:createdAt'''
| style="width: 60%; background-color: orange;"| '''dbpedia:Maastricht_University ;'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''dcterms:license'''
| style="width: 60%; background-color: orange;"| ''<http://creativecommons.org/licenses/by/3.0/> .''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| ''<http://sparql.wikipathways.org> .''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:triples'''
| style="width: 60%; background-color: orange;"| '''"1794104"^^xsd:integer ;'''
|-

| colspan="3" | :ChEMBL
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''pav:createdOn'''
| style="width: 60%; background-color: orange;"| '''"2012-10-25"^^xsd:date ;'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:foo'''
| style="width: 60%; background-color: orange;"| '''void:bar .'''
|}

== Triplestore map ==

{| style="color: black; color: #733;" width="85%" class="wikitable"
| colspan="3" | WikiPathways
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''foaf:page'''
| style="width: 60%; background-color: orange;"| ''' http://www.wikipathways.org'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| '''http://sparql.wikipathways.org'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:uriLookupEndpoint'''
| style="width: 60%; background-color: orange;"| '''http://rdf.wikipathways.org '''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''prov:deployedSoftware'''
| style="width: 60%; background-color: orange;"| '''dbpedia:Virtuoso_Universal_Server '''
|-
| colspan="3" | :ChEMBL
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''foaf:page'''
| style="width: 60%; background-color: orange;"| '''"tba'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| ''' http://rdf.farmbio.uu.se/chembl/sparql '''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| ''' http://ragamuffin.bigcat.unimaas.nl/chembl/sparql '''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''prov:deployedSoftware'''
| style="width: 60%; background-color: orange;"| '''dbpedia:Virtuoso_Universal_Server '''
|-
| colspan="3" | :Uniprot
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''foaf:page'''
| style="width: 60%; background-color: orange;"| '''http://www.uniprot.org'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| ''' http://beta.sparql.uniprot.org '''
|-
| colspan="3" | :Gene expression atlas
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''foaf:page'''
| style="width: 60%; background-color: orange;"| '''tba'''
|-
| style="width: 10%;"|
| style="width: 30%; color: #733;"| '''void:sparqlEndpoint'''
| style="width: 60%; background-color: orange;"| ''' http://wwwdev.ebi.ac.uk/fgpt/gxa-sparql/sparql '''
|-
|}

HCLS/SWAT4LS2012/Hackathon

Ewilligh — Fri, 26 Oct 2012 10:21:31 GMT

Ewilligh: /* Confirmed Participants */

HCLS/SWAT4LS2012/Hackathon

Ewilligh — Thu, 25 Oct 2012 13:52:24 GMT

Ewilligh: /* Proposed action points */

HCLS/SWAT4LS2012/Hackathon

Ewilligh — Thu, 18 Oct 2012 20:09:41 GMT

Ewilligh:

== Introduction ==

=== Co-Organizers ===
* Andrea Splendiani
* Andra Waagmeester
* Eric Prud'hommeaux
* Toshiaki Katayama
* Ismael Navas delgado

=== Description ===
The SWAT4LS Hackathon is an informal event associated with the [http://swat4ls.org/ SWAT4LS] Semantic Web Applications and Tools for Life Sciences Workshops Series.

Scope of the event is to bring together experts and enthusiasts in the application of semantic technologies in healthcare and life science for open discussion and jam coding sessions.
The Hackathon will be organized on the 28th of November 2012 at La Cantine, Paris (for more information, please refer to the [http://www.swat4ls.org/workshops/paris2012/| workshop website]) and it is open to workshop participants and not (registration is required and space is limited!).

Projects and institutes that have already expressed their interest in attending include:
* OpenPhacts (http://www.openphacts.org)
* WikiPathways (http://www.wikipathways.org/index.php/WikiPathways)
* The Database Center for Life Sciences/BioHackathon (http://dbcls.rois.ac.jp/en/ http://www.biohackathon.org/)
* The W3C Consortium, Health Care and Life Sciences Interest Group ([[HCLS]])
* BioPAX (http://biopax.org)
While the agenda will be open, we are coordinating ideas that can be developd at the network in advance, to maximize the utility of the day. Co-organizers for each community will help gathering ideas and finding point of contacts.

=== Information and registrations ===
For information, [mailto:info@swat4ls.org| info _at_ swat4ls.org]

Registrations are handled via [http://swat4ls-2012.eventbrite.com/| Eventbrite]

=== Hashtag ===
[https://twitter.com/search/realtime?q=%23swat4lshack #swat4lshack]

== Open PHACTS community ==

=== Contact Point ===
* Andra Waagmeester
* Egon Willighagen

=== Proposed action points ===
# Consume [http://www.openphacts.org Open PHACTS] content in Pathway tools
# Using http://identifiers.org
# Create an example set of valuable queries
# Visualizing output
# work on further linked data integration, with possible:
## [https://ntp.niehs.nih.gov/drugmatrix/ DrugMatrix]
## [http://toxico.nibio.go.jp/open-tggates/ TG-GATEs]
## [http://thedatahub.org/nl/dataset/bio2rdf-ctd CTD] (already available as RDF, by Bio2RDF)

=== Confirmed Participants ===
* Kees Burger
* Maria Carmen Carra
* Ian Dunlop
* Chris Evelo
* Paul Groth
* Tim Harder
* Carina Haupt
* Nick Juty
* Camille Laibe
* Antonis Loizou
* Oriol Lopez
* Guillermo C. Martínez
* Nuria Queralt
* Rishi Ramgolam
* Mark Thompson
* Egon Willighagen
* Pekka Kohonen

== WikiPathways community ==

=== Contact Point ===
Andra Waagmeester

=== Proposed action points ===
# Exploring [http://www.wikipathways.org/index.php/WikiPathways WikiPathways] RDF content, making default queries
# Using [http://code.google.com/p/pathvisiorpc/ Pathvisio RPC].
# Creating a pathway oriented Linked Data Cloud
## [https://github.com/egonw/chembl.rdf/blob/master/README.markdown ChEMBL]
## Uniprot

=== Confirmed Participants ===
* Chris Evelo
* Martina Kutmon
* Alex Pico

== Database Center for Life Sciences Community / BioHackathon ==

=== Contact Point ===
Toshiaki Katayama

=== Proposed action points ===

== W3C HCLS Community ==

=== Contact Point ===
Eric Prud'hommeaux

=== Proposed action points ===

== BioPAX Community ==

=== Contact Point ===
Ismael Navas Delgado

=== Proposed action points ===

=== Confirmed Participants ===
* Ismael Navas Delgado
* Andrea Splendiani

=== Resources ===
* PathwayCommons SPARQL endpoint. Endpoint over all BioPAX representations in PathwayCommons
* Cytoscape plugin to visualize and interact with RDF knwoledge bases (new!)
* BioQueries: social site to build SPARQL queries
* Open PHACTS rdf guidelines: http://www.openphacts.org/specs/2012/WD-rdfguide-20120823/

HCLS/SWAT4LS2012/Hackathon

Ewilligh — Thu, 18 Oct 2012 17:36:28 GMT

Ewilligh: /* Confirmed Participants */

== Introduction ==

=== Co-Organizers ===
* Andrea Splendiani
* Andra Waagmeester
* Eric Prud'hommeaux
* Toshiaki Katayama
* Ismael Navas delgado

=== Description ===
The SWAT4LS Hackathon is an informal event associated with the [http://swat4ls.org/ SWAT4LS] Semantic Web Applications and Tools for Life Sciences Workshops Series.

Scope of the event is to bring together experts and enthusiasts in the application of semantic technologies in healthcare and life science for open discussion and jam coding sessions.
The Hackathon will be organized on the 28th of November 2012 at La Cantine, Paris (for more information, please refer to the [http://www.swat4ls.org/workshops/paris2012/| workshop website]) and it is open to workshop participants and not (registration is required and space is limited!).

Projects and institutes that have already expressed their interest in attending include:
* OpenPhacts (http://www.openphacts.org)
* WikiPathways (http://www.wikipathways.org/index.php/WikiPathways)
* The Database Center for Life Sciences/BioHackathon (http://dbcls.rois.ac.jp/en/ http://www.biohackathon.org/)
* The W3C Consortium, Health Care and Life Sciences Interest Group ([[HCLS]])
* BioPAX (http://biopax.org)
While the agenda will be open, we are coordinating ideas that can be developd at the network in advance, to maximize the utility of the day. Co-organizers for each community will help gathering ideas and finding point of contacts.

=== Information and registrations ===
For information, [mailto:info@swat4ls.org| info _at_ swat4ls.org]

Registrations are handled via [http://swat4ls-2012.eventbrite.com/| Eventbrite]

=== Hashtag ===
[https://twitter.com/search/realtime?q=%23swat4lshack #swat4lshack]

== Open PHACTS community ==

=== Contact Point ===
* Andra Waagmeester
* Egon Willighagen

=== Proposed action points ===
# Consume [http://www.openphacts.org Open PHACTS] content in Pathway tools
# Using http://identifiers.org
# Create an example set of valuable queries
# Visualizing output
# work on further linked data integration, with possible:
## [https://ntp.niehs.nih.gov/drugmatrix/ DrugMatrix]
## [http://toxico.nibio.go.jp/open-tggates/ TG-GATEs]
## [http://thedatahub.org/nl/dataset/bio2rdf-ctd CTD] (already available as RDF, by Bio2RDF)

=== Confirmed Participants ===
* Kees Burger
* Maria Carmen Carra
* Ian Dunlop
* Chris Evelo
* Paul Groth
* Tim Harder
* Carina Haupt
* Nick Juty
* Camille Laibe
* Antonis Loizou
* Oriol Lopez
* Guillermo C. Martínez
* Nuria Queralt
* Rishi Ramgolam
* Mark Thompson
* Egon Willighagen
* Pekka Kohonen wants to join; non-Open PHACTS

== WikiPathways community ==

=== Contact Point ===
Andra Waagmeester

=== Proposed action points ===
# Exploring [http://www.wikipathways.org/index.php/WikiPathways WikiPathways] RDF content, making default queries
# Using [http://code.google.com/p/pathvisiorpc/ Pathvisio RPC].
# Creating a pathway oriented Linked Data Cloud
## [https://github.com/egonw/chembl.rdf/blob/master/README.markdown ChEMBL]
## Uniprot

=== Confirmed Participants ===
* Chris Evelo
* Martina Kutmon
* Alex Pico

== Database Center for Life Sciences Community / BioHackathon ==

=== Contact Point ===
Toshiaki Katayama

=== Proposed action points ===

== W3C HCLS Community ==

=== Contact Point ===
Eric Prud'hommeaux

=== Proposed action points ===

== BioPAX Community ==

=== Contact Point ===
Ismael Navas Delgado

=== Proposed action points ===

=== Confirmed Participants ===
* Ismael Navas Delgado
* Andrea Splendiani

=== Resources ===
* PathwayCommons SPARQL endpoint. Endpoint over all BioPAX representations in PathwayCommons
* Cytoscape plugin to visualize and interact with RDF knwoledge bases (new!)
* BioQueries: social site to build SPARQL queries
* Open PHACTS rdf guidelines: http://www.openphacts.org/specs/2012/WD-rdfguide-20120823/

HCLS/SWAT4LS2012/Hackathon

Ewilligh — Wed, 17 Oct 2012 14:20:47 GMT

Ewilligh:

== Introduction ==

=== Co-Organizers ===
* Andrea Splendiani
* Andra Waagmeester
* Eric Prud'hommeaux
* Toshiaki Katayama
* Ismael Navas delgado

=== Description ===
The SWAT4LS Hackathon is an informal event associated with the [http://swat4ls.org/ SWAT4LS] Semantic Web Applications and Tools for Life Sciences Workshops Series.

Scope of the event is to bring together experts and enthusiasts in the application of semantic technologies in healthcare and life science for open discussion and jam coding sessions.
The Hackathon will be organized on the 28th of November 2012 at La Cantine, Paris (for more information, please refer to the [http://www.swat4ls.org/workshops/paris2012/| workshop website]) and it is open to workshop participants and not (registration is required and space is limited!).

Projects and institutes that have already expressed their interest in attending include:
* OpenPhacts (http://www.openphacts.org)
* WikiPathways (http://www.wikipathways.org/index.php/WikiPathways)
* The Database Center for Life Sciences/BioHackathon (http://dbcls.rois.ac.jp/en/ http://www.biohackathon.org/)
* The W3C Consortium, Health Care and Life Sciences Interest Group ([[HCLS]])
* BioPAX (http://biopax.org)
While the agenda will be open, we are coordinating ideas that can be developd at the network in advance, to maximize the utility of the day. Co-organizers for each community will help gathering ideas and finding point of contacts.

=== Information and registrations ===
For information, [mailto:info@swat4ls.org| info _at_ swat4ls.org]

Registrations are handled via [http://swat4ls-2012.eventbrite.com/| Eventbrite]

=== Hashtag ===
[https://twitter.com/search/realtime?q=%23swat4lshack #swat4lshack]

== Open PHACTS community ==

=== Contact Point ===
* Andra Waagmeester
* Egon Willighagen

=== Proposed action points ===
# Consume [http://www.openphacts.org Open PHACTS] content in Pathway tools
# Using http://identifiers.org
# Create an example set of valuable queries
# Visualizing output
# work on further linked data integration, with possible:
## [https://ntp.niehs.nih.gov/drugmatrix/ DrugMatrix]
## [http://toxico.nibio.go.jp/open-tggates/ TG-GATEs]
## [http://thedatahub.org/nl/dataset/bio2rdf-ctd CTD] (already available as RDF, by Bio2RDF)

=== Confirmed Participants ===
* Kees Burger
* Maria Carmen Carra
* Ian Dunlop
* Chris Evelo
* Paul Groth
* Tim Harder
* Carina Haupt
* Nick Juty
* Camille Laibe
* Antonis Loizou
* Oriol Lopez
* Guillermo C. Martínez
* Nuria Queralt
* Rishi Ramgolam
* Mark Thompson
* Egon Willighagen

== WikiPathways community ==

=== Contact Point ===
Andra Waagmeester

=== Proposed action points ===
# Exploring [http://www.wikipathways.org/index.php/WikiPathways WikiPathways] RDF content, making default queries
# Using [http://code.google.com/p/pathvisiorpc/ Pathvisio RPC].
# Creating a pathway oriented Linked Data Cloud
## [https://github.com/egonw/chembl.rdf/blob/master/README.markdown ChEMBL]
## Uniprot

=== Confirmed Participants ===
* Chris Evelo
* Martina Kutmon
* Alex Pico

== Database Center for Life Sciences Community / BioHackathon ==

=== Contact Point ===
Toshiaki Katayama

=== Proposed action points ===

== W3C HCLS Community ==

=== Contact Point ===
Eric Prud'hommeaux

=== Proposed action points ===

== BioPAX Community ==

=== Contact Point ===
Ismael Navas Delgado

=== Proposed action points ===

=== Confirmed Participants ===
* Ismael Navas Delgado
* Andrea Splendiani

=== Resources ===
* PathwayCommons SPARQL endpoint. Endpoint over all BioPAX representations in PathwayCommons
* Cytoscape plugin to visualize and interact with RDF knwoledge bases (new!)
* BioQueries: social site to build SPARQL queries
* Open PHACTS rdf guidelines: http://www.openphacts.org/specs/2012/WD-rdfguide-20120823/

HCLS/SWAT4LS2012/Hackathon

Ewilligh — Wed, 17 Oct 2012 14:20:21 GMT

Ewilligh: /* Contact Point */

== Introduction ==

=== Co-Organizers ===
* Andrea Splendiani
* Andra Waagmeester
* Eric Prud'hommeaux
* Toshiaki Katayama
* Ismael Navas delgado

=== Description ===
The SWAT4LS Hackathon is an informal event associated with the [http://swat4ls.org/ SWAT4LS] Semantic Web Applications and Tools for Life Sciences Workshops Series.

Scope of the event is to bring together experts and enthusiasts in the application of semantic technologies in healthcare and life science for open discussion and jam coding sessions.
The Hackathon will be organized on the 28th of November 2012 at La Cantine, Paris (for more information, please refer to the [http://www.swat4ls.org/workshops/paris2012/| workshop website]) and it is open to workshop participants and not (registration is required and space is limited!).

Projects and institutes that have already expressed their interest in attending include:
* OpenPhacts (http://www.openphacts.org)
* WikiPathways (http://www.wikipathways.org/index.php/WikiPathways)
* The Database Center for Life Sciences/BioHackathon (http://dbcls.rois.ac.jp/en/ http://www.biohackathon.org/)
* The W3C Consortium, Health Care and Life Sciences Interest Group ([[HCLS]])
* BioPAX (http://biopax.org)
While the agenda will be open, we are coordinating ideas that can be developd at the network in advance, to maximize the utility of the day. Co-organizers for each community will help gathering ideas and finding point of contacts.

=== Information and registrations ===
For information, [mailto:info@swat4ls.org| info _at_ swat4ls.org]

Registrations are handled via [http://swat4ls-2012.eventbrite.com/| Eventbrite]

=== Hashtag ===
[https://twitter.com/search/realtime?q=%23swat4lshack #swat4lshack]

== Open PHACTS community ==

=== Contact Point ===
Andra Waagmeester
Egon Willighagen

=== Proposed action points ===
# Consume [http://www.openphacts.org Open PHACTS] content in Pathway tools
# Using http://identifiers.org
# Create an example set of valuable queries
# Visualizing output
# work on further linked data integration, with possible:
## [https://ntp.niehs.nih.gov/drugmatrix/ DrugMatrix]
## [http://toxico.nibio.go.jp/open-tggates/ TG-GATEs]
## [http://thedatahub.org/nl/dataset/bio2rdf-ctd CTD] (already available as RDF, by Bio2RDF)

=== Confirmed Participants ===
* Kees Burger
* Maria Carmen Carra
* Ian Dunlop
* Chris Evelo
* Paul Groth
* Tim Harder
* Carina Haupt
* Nick Juty
* Camille Laibe
* Antonis Loizou
* Oriol Lopez
* Guillermo C. Martínez
* Nuria Queralt
* Rishi Ramgolam
* Mark Thompson
* Egon Willighagen

== WikiPathways community ==

=== Contact Point ===
Andra Waagmeester

=== Proposed action points ===
# Exploring [http://www.wikipathways.org/index.php/WikiPathways WikiPathways] RDF content, making default queries
# Using [http://code.google.com/p/pathvisiorpc/ Pathvisio RPC].
# Creating a pathway oriented Linked Data Cloud
## [https://github.com/egonw/chembl.rdf/blob/master/README.markdown ChEMBL]
## Uniprot

=== Confirmed Participants ===
* Chris Evelo
* Martina Kutmon
* Alex Pico

== Database Center for Life Sciences Community / BioHackathon ==

=== Contact Point ===
Toshiaki Katayama

=== Proposed action points ===

== W3C HCLS Community ==

=== Contact Point ===
Eric Prud'hommeaux

=== Proposed action points ===

== BioPAX Community ==

=== Contact Point ===
Ismael Navas Delgado

=== Proposed action points ===

=== Confirmed Participants ===
* Ismael Navas Delgado
* Andrea Splendiani

=== Resources ===
* PathwayCommons SPARQL endpoint. Endpoint over all BioPAX representations in PathwayCommons
* Cytoscape plugin to visualize and interact with RDF knwoledge bases (new!)
* BioQueries: social site to build SPARQL queries
* Open PHACTS rdf guidelines: http://www.openphacts.org/specs/2012/WD-rdfguide-20120823/

HCLS/SWAT4LS2012/Hackathon

Ewilligh — Wed, 17 Oct 2012 14:20:04 GMT

Ewilligh: /* Proposed action points */

== Introduction ==

=== Co-Organizers ===
* Andrea Splendiani
* Andra Waagmeester
* Eric Prud'hommeaux
* Toshiaki Katayama
* Ismael Navas delgado

=== Description ===
The SWAT4LS Hackathon is an informal event associated with the [http://swat4ls.org/ SWAT4LS] Semantic Web Applications and Tools for Life Sciences Workshops Series.

Scope of the event is to bring together experts and enthusiasts in the application of semantic technologies in healthcare and life science for open discussion and jam coding sessions.
The Hackathon will be organized on the 28th of November 2012 at La Cantine, Paris (for more information, please refer to the [http://www.swat4ls.org/workshops/paris2012/| workshop website]) and it is open to workshop participants and not (registration is required and space is limited!).

Projects and institutes that have already expressed their interest in attending include:
* OpenPhacts (http://www.openphacts.org)
* WikiPathways (http://www.wikipathways.org/index.php/WikiPathways)
* The Database Center for Life Sciences/BioHackathon (http://dbcls.rois.ac.jp/en/ http://www.biohackathon.org/)
* The W3C Consortium, Health Care and Life Sciences Interest Group ([[HCLS]])
* BioPAX (http://biopax.org)
While the agenda will be open, we are coordinating ideas that can be developd at the network in advance, to maximize the utility of the day. Co-organizers for each community will help gathering ideas and finding point of contacts.

=== Information and registrations ===
For information, [mailto:info@swat4ls.org| info _at_ swat4ls.org]

Registrations are handled via [http://swat4ls-2012.eventbrite.com/| Eventbrite]

=== Hashtag ===
[https://twitter.com/search/realtime?q=%23swat4lshack #swat4lshack]

== Open PHACTS community ==

=== Contact Point ===
Andra Waagmeester

=== Proposed action points ===
# Consume [http://www.openphacts.org Open PHACTS] content in Pathway tools
# Using http://identifiers.org
# Create an example set of valuable queries
# Visualizing output
# work on further linked data integration, with possible:
## [https://ntp.niehs.nih.gov/drugmatrix/ DrugMatrix]
## [http://toxico.nibio.go.jp/open-tggates/ TG-GATEs]
## [http://thedatahub.org/nl/dataset/bio2rdf-ctd CTD] (already available as RDF, by Bio2RDF)

=== Confirmed Participants ===
* Kees Burger
* Maria Carmen Carra
* Ian Dunlop
* Chris Evelo
* Paul Groth
* Tim Harder
* Carina Haupt
* Nick Juty
* Camille Laibe
* Antonis Loizou
* Oriol Lopez
* Guillermo C. Martínez
* Nuria Queralt
* Rishi Ramgolam
* Mark Thompson
* Egon Willighagen

== WikiPathways community ==

=== Contact Point ===
Andra Waagmeester

=== Proposed action points ===
# Exploring [http://www.wikipathways.org/index.php/WikiPathways WikiPathways] RDF content, making default queries
# Using [http://code.google.com/p/pathvisiorpc/ Pathvisio RPC].
# Creating a pathway oriented Linked Data Cloud
## [https://github.com/egonw/chembl.rdf/blob/master/README.markdown ChEMBL]
## Uniprot

=== Confirmed Participants ===
* Chris Evelo
* Martina Kutmon
* Alex Pico

== Database Center for Life Sciences Community / BioHackathon ==

=== Contact Point ===
Toshiaki Katayama

=== Proposed action points ===

== W3C HCLS Community ==

=== Contact Point ===
Eric Prud'hommeaux

=== Proposed action points ===

== BioPAX Community ==

=== Contact Point ===
Ismael Navas Delgado

=== Proposed action points ===

=== Confirmed Participants ===
* Ismael Navas Delgado
* Andrea Splendiani

=== Resources ===
* PathwayCommons SPARQL endpoint. Endpoint over all BioPAX representations in PathwayCommons
* Cytoscape plugin to visualize and interact with RDF knwoledge bases (new!)
* BioQueries: social site to build SPARQL queries
* Open PHACTS rdf guidelines: http://www.openphacts.org/specs/2012/WD-rdfguide-20120823/

HCLS/SWAT4LS2012/Hackathon

Ewilligh — Wed, 17 Oct 2012 14:19:00 GMT

Ewilligh: /* Proposed action points */

== Introduction ==

=== Co-Organizers ===
* Andrea Splendiani
* Andra Waagmeester
* Eric Prud'hommeaux
* Toshiaki Katayama
* Ismael Navas delgado

=== Description ===
The SWAT4LS Hackathon is an informal event associated with the [http://swat4ls.org/ SWAT4LS] Semantic Web Applications and Tools for Life Sciences Workshops Series.

Scope of the event is to bring together experts and enthusiasts in the application of semantic technologies in healthcare and life science for open discussion and jam coding sessions.
The Hackathon will be organized on the 28th of November 2012 at La Cantine, Paris (for more information, please refer to the [http://www.swat4ls.org/workshops/paris2012/| workshop website]) and it is open to workshop participants and not (registration is required and space is limited!).

Projects and institutes that have already expressed their interest in attending include:
* OpenPhacts (http://www.openphacts.org)
* WikiPathways (http://www.wikipathways.org/index.php/WikiPathways)
* The Database Center for Life Sciences/BioHackathon (http://dbcls.rois.ac.jp/en/ http://www.biohackathon.org/)
* The W3C Consortium, Health Care and Life Sciences Interest Group ([[HCLS]])
* BioPAX (http://biopax.org)
While the agenda will be open, we are coordinating ideas that can be developd at the network in advance, to maximize the utility of the day. Co-organizers for each community will help gathering ideas and finding point of contacts.

=== Information and registrations ===
For information, [mailto:info@swat4ls.org| info _at_ swat4ls.org]

Registrations are handled via [http://swat4ls-2012.eventbrite.com/| Eventbrite]

=== Hashtag ===
[https://twitter.com/search/realtime?q=%23swat4lshack #swat4lshack]

== Open PHACTS community ==

=== Contact Point ===
Andra Waagmeester

=== Proposed action points ===
# Consume [http://www.openphacts.org Open PHACTS] content in Pathway tools
# Using http://identifiers.org
# Create an example set of valuable queries
# Visualizing output
# work on further linked data integration, with possible:
## [https://ntp.niehs.nih.gov/drugmatrix/ DrugMatrix]
## [http://toxico.nibio.go.jp/open-tggates/ TG-GATEs]

=== Confirmed Participants ===
* Kees Burger
* Maria Carmen Carra
* Ian Dunlop
* Chris Evelo
* Paul Groth
* Tim Harder
* Carina Haupt
* Nick Juty
* Camille Laibe
* Antonis Loizou
* Oriol Lopez
* Guillermo C. Martínez
* Nuria Queralt
* Rishi Ramgolam
* Mark Thompson
* Egon Willighagen

== WikiPathways community ==

=== Contact Point ===
Andra Waagmeester

=== Proposed action points ===
# Exploring [http://www.wikipathways.org/index.php/WikiPathways WikiPathways] RDF content, making default queries
# Using [http://code.google.com/p/pathvisiorpc/ Pathvisio RPC].
# Creating a pathway oriented Linked Data Cloud
## [https://github.com/egonw/chembl.rdf/blob/master/README.markdown ChEMBL]
## Uniprot

=== Confirmed Participants ===
* Chris Evelo
* Martina Kutmon
* Alex Pico

== Database Center for Life Sciences Community / BioHackathon ==

=== Contact Point ===
Toshiaki Katayama

=== Proposed action points ===

== W3C HCLS Community ==

=== Contact Point ===
Eric Prud'hommeaux

=== Proposed action points ===

== BioPAX Community ==

=== Contact Point ===
Ismael Navas Delgado

=== Proposed action points ===

=== Confirmed Participants ===
* Ismael Navas Delgado
* Andrea Splendiani

=== Resources ===
* PathwayCommons SPARQL endpoint. Endpoint over all BioPAX representations in PathwayCommons
* Cytoscape plugin to visualize and interact with RDF knwoledge bases (new!)
* BioQueries: social site to build SPARQL queries
* Open PHACTS rdf guidelines: http://www.openphacts.org/specs/2012/WD-rdfguide-20120823/

HCLS/SWAT4LS2012/Hackathon

Ewilligh — Tue, 16 Oct 2012 10:01:32 GMT

Ewilligh: /* Proposed action points */

== Introduction ==

=== Co-Organizers ===
* Andrea Splendiani
* Andra Waagmeester
* Eric Prud'hommeaux
* Toshiaki Katayama
* Ismael Navas delgado

=== Description ===
The SWAT4LS Hackathon is an informal event associated with the [http://swat4ls.org/ SWAT4LS] Semantic Web Applications and Tools for Life Sciences Workshops Series.

Scope of the event is to bring together experts and enthusiasts in the application of semantic technologies in healthcare and life science for open discussion and jam coding sessions.
The Hackathon will be organized on the 28th of November 2012 at La Cantine, Paris (for more information, please refer to the [http://www.swat4ls.org/workshops/paris2012/| workshop website]) and it is open to workshop participants and not (registration is required and space is limited!).

Projects and institutes that have already expressed their interest in attending include:
* OpenPhacts (http://www.openphacts.org)
* WikiPathways (http://www.wikipathways.org/index.php/WikiPathways)
* The Database Center for Life Sciences/BioHackathon (http://dbcls.rois.ac.jp/en/ http://www.biohackathon.org/)
* The W3C Consortium, Health Care and Life Sciences Interest Group ([[HCLS]])
* BioPAX (http://biopax.org)
While the agenda will be open, we are coordinating ideas that can be developd at the network in advance, to maximize the utility of the day. Co-organizers for each community will help gathering ideas and finding point of contacts.

=== Information and registrations ===
For information, [mailto:info@swat4ls.org| info _at_ swat4ls.org]

Registrations are handled via [http://swat4ls-2012.eventbrite.com/| Eventbrite]

=== Hashtag ===
[https://twitter.com/search/realtime?q=%23swat4lshack #swat4lshack]

== Open PHACTS community ==

=== Contact Point ===
Andra Waagmeester

=== Proposed action points ===
# Consume [http://www.openphacts.org Open PHACTS] content in Pathway tools
# Using http://identifiers.org
# Create an example set of valuable queries
# Visualizing output

=== Confirmed Participants ===
* Kees Burger
* Maria Carmen Carra
* Ian Dunlop
* Chris Evelo
* Paul Goth
* Tim Harder
* Carina Haupt
* Nick Juty
* Camille Laibe
* Antonis Loizou
* Oriol Lopez
* Guillermo C. Martínez
* Nuria Queralt
* Rishi Ramgolam
* Mark Thompson
* Egon Willighagen

== WikiPathways community ==

=== Contact Point ===
Andra Waagmeester

=== Proposed action points ===
# Exploring [http://www.wikipathways.org/index.php/WikiPathways WikiPathways] RDF content, making default queries
# Using [http://code.google.com/p/pathvisiorpc/ Pathvisio RPC].
# Creating a pathway oriented Linked Data Cloud
## [https://github.com/egonw/chembl.rdf/blob/master/README.markdown ChEMBL]
## Uniprot

=== Confirmed Participants ===
* Chris Evelo
* Martina Kutmon
* Alex Pico

== Database Center for Life Sciences Community / BioHackathon ==

=== Contact Point ===
Toshiaki Katayama

=== Proposed action points ===

== W3C HCLS Community ==

=== Contact Point ===
Eric Prud'hommeaux

=== Proposed action points ===

== BioPAX Community ==

=== Contact Point ===
Ismael Navas Delgado

=== Proposed action points ===

=== Confirmed Participants ===
* Ismael Navas Delgado
* Andrea Splendiani

=== Resources ===
* PathwayCommons SPARQL endpoint. Endpoint over all BioPAX representations in PathwayCommons
* Cytoscape plugin to visualize and interact with RDF knwoledge bases (new!)
* BioQueries: social site to build SPARQL queries
* Open PHACTS rdf guidelines: http://www.openphacts.org/specs/2012/WD-rdfguide-20120823/

HCLS/SWAT4LS2012/Hackathon

Ewilligh — Mon, 15 Oct 2012 10:21:33 GMT

Ewilligh: /* Description */

== Introduction ==

=== Co-Organizers ===
* Andrea Splendiani
* Andra Waagmeester
* Eric Prud'hommeaux
* Toshiaki Katayama
* Ismael Navas delgado

=== Description ===
The SWAT4LS Hackathon is an informal event associated with the [http://swat4ls.org/ SWAT4LS] Semantic Web Applications and Tools for Life Sciences Workshops Series.

Scope of the event is to bring together experts and enthusiasts in the application of semantic technologies in healthcare and life science for open discussion and jam coding sessions.
The Hackathon will be organized on the 28th of November 2012 at La Cantine, Paris (for more information, please refer to the [http://www.swat4ls.org/workshops/paris2012/| workshop website]) and it is open to workshop participants and not (registration is required and space is limited!).

Projects and institutes that have already expressed their interest in attending include:
* OpenPhacts (http://www.openphacts.org)
* WikiPathways (http://www.wikipathways.org/index.php/WikiPathways)
* The Database Center for Life Sciences/BioHackathon (http://dbcls.rois.ac.jp/en/ http://www.biohackathon.org/)
* The W3C Consortium, Health Care and Life Sciences Interest Group ([[HCLS]])
* BioPAX (http://biopax.org)
While the agenda will be open, we are coordinating ideas that can be developd at the network in advance, to maximize the utility of the day. Co-organizers for each community will help gathering ideas and finding point of contacts.

=== Information and registrations ===
For information, [mailto:info@swat4ls.org| info _at_ swat4ls.org]

Registrations are handled via [http://swat4ls-2012.eventbrite.com/| Eventbrite]

=== Hashtag ===
[https://twitter.com/search/realtime?q=%23swat4lshack #swat4lshack]

== Open PHACTS community ==

=== Contact Point ===
Andra Waagmeester

=== Proposed action points ===
# Consume [http://www.openphacts.org Open PHACTS] content in Pathway tools
# Using http://identifiers.org
# Create an example set of valuable queries
# Visualizing output

=== Confirmed Participants ===
* Kees Burger
* Maria Carmen Carra
* Ian Dunlop
* Chris Evelo
* Paul Goth
* Tim Harder
* Carina Haupt
* Nick Juty
* Camille Laibe
* Antonis Loizou
* Oriol Lopez
* Guillermo C. Martínez
* Nuria Queralt
* Rishi Ramgolam
* Mark Thompson
* Egon Willighagen

== WikiPathways community ==

=== Contact Point ===
Andra Waagmeester

=== Proposed action points ===
# Exploring [http://www.wikipathways.org/index.php/WikiPathways WikiPathways] RDF content, making default queries
# Using [http://code.google.com/p/pathvisiorpc/ Pathvisio RPC].

=== Confirmed Participants ===
* Chris Evelo
* Martina Kutmon
* Alex Pico

== Database Center for Life Sciences Community / BioHackathon ==

=== Contact Point ===
Toshiaki Katayama

=== Proposed action points ===

== W3C HCLS Community ==

=== Contact Point ===
Eric Prud'hommeaux

=== Proposed action points ===

== BioPAX Community ==

=== Contact Point ===
Ismael Navas Delgado

=== Proposed action points ===

=== Confirmed Participants ===
* Ismael Navas Delgado
* Andrea Splendiani

=== Resources ===
* PathwayCommons SPARQL endpoint. Endpoint over all BioPAX representations in PathwayCommons
* Cytoscape plugin to visualize and interact with RDF knwoledge bases (new!)
* BioQueries: social site to build SPARQL queries
* Open PHACTS rdf guidelines: http://www.openphacts.org/specs/2012/WD-rdfguide-20120823/

HCLS/SWAT4LS2012/Hackathon

Ewilligh — Mon, 15 Oct 2012 09:49:19 GMT

Ewilligh: /* Proposed action points */

== Introduction ==

=== Co-Organizers ===
* Andrea Splendiani
* Andra Waagmeester
* Eric Prud'hommeaux
* Toshiaki Katayama
* Ismael Navas delgado

=== Description ===
The SWAT4LS Hackathon is an informal event associated with the [http://swat4ls.org/| SWAT4LS] Semantic Web Applications and Tools for Life Sciences Workshops Series.

Scope of the event is to bring together experts and enthusiasts in the application of semantic technologies in healthcare and life science for open discussion and jam coding sessions.
The Hackathon will be organized on the 28th of November 2012 at La Cantine, Paris (for more information, please refer to the [http://www.swat4ls.org/workshops/paris2012/| workshop website]) and it is open to workshop participants and not (registration is required and space is limited!).

Projects and institutes that have already expressed their interest in attending include:
* OpenPhacts (http://www.openphacts.org)
* WikiPathways (http://www.wikipathways.org/index.php/WikiPathways)
* The Database Center for Life Sciences/BioHackathon (http://dbcls.rois.ac.jp/en/ http://www.biohackathon.org/)
* The W3C Consortium, Health Care and Life Sciences Interest Group ([[HCLS]])
* BioPAX (http://biopax.org)
While the agenda will be open, we are coordinating ideas that can be developd at the network in advance, to maximize the utility of the day. Co-organizers for each community will help gathering ideas and finding point of contacts.

=== Information and registrations ===
For information, [mailto:info@swat4ls.org| info _at_ swat4ls.org]

Registrations are handled via [http://swat4ls-2012.eventbrite.com/| Eventbrite]

=== Hashtag ===
[https://twitter.com/search/realtime?q=%23swat4lshack #swat4lshack]

== Open PHACTS community ==

=== Contact Point ===
Andra Waagmeester

=== Proposed action points ===
# Consume [http://www.openphacts.org Open PHACTS] content in Pathway tools
# Using http://identifiers.org
# Create an example set of valuable queries
# Visualizing output

=== Confirmed Participants ===
* Kees Burger
* Maria Carmen Carra
* Ian Dunlop
* Chris Evelo
* Paul Goth
* Tim Harder
* Carina Haupt
* Nick Juty
* Camille Laibe
* Antonis Loizou
* Oriol Lopez
* Guillermo C. Martínez
* Nuria Queralt
* Rishi Ramgolam
* Mark Thompson
* Egon Willighagen

== WikiPathways community ==

=== Contact Point ===
Andra Waagmeester

=== Proposed action points ===
# Exploring [http://www.wikipathways.org/index.php/WikiPathways WikiPathways] RDF content, making default queries
# Using [http://code.google.com/p/pathvisiorpc/ Pathvisio RPC].

=== Confirmed Participants ===
* Chris Evelo
* Martina Kutmon
* Alex Pico

== Database Center for Life Sciences Community / BioHackathon ==

=== Contact Point ===
Toshiaki Katayama

=== Proposed action points ===

== W3C HCLS Community ==

=== Contact Point ===
Eric Prud'hommeaux

=== Proposed action points ===

== BioPAX Community ==

=== Contact Point ===
Ismael Navas Delgado

=== Proposed action points ===

=== Confirmed Participants ===
* Ismael Navas Delgado
* Andrea Splendiani

=== Resources ===
* PathwayCommons SPARQL endpoint. Endpoint over all BioPAX representations in PathwayCommons
* Cytoscape plugin to visualize and interact with RDF knwoledge bases (new!)
* BioQueries: social site to build SPARQL queries
* Open PHACTS rdf guidelines: http://www.openphacts.org/specs/2012/WD-rdfguide-20120823/

HCLS/SWAT4LS2012/Hackathon

Ewilligh — Mon, 15 Oct 2012 09:48:58 GMT

Ewilligh: /* OpenPhacts community */

== Introduction ==

=== Co-Organizers ===
* Andrea Splendiani
* Andra Waagmeester
* Eric Prud'hommeaux
* Toshiaki Katayama
* Ismael Navas delgado

=== Description ===
The SWAT4LS Hackathon is an informal event associated with the [http://swat4ls.org/| SWAT4LS] Semantic Web Applications and Tools for Life Sciences Workshops Series.

Scope of the event is to bring together experts and enthusiasts in the application of semantic technologies in healthcare and life science for open discussion and jam coding sessions.
The Hackathon will be organized on the 28th of November 2012 at La Cantine, Paris (for more information, please refer to the [http://www.swat4ls.org/workshops/paris2012/| workshop website]) and it is open to workshop participants and not (registration is required and space is limited!).

Projects and institutes that have already expressed their interest in attending include:
* OpenPhacts (http://www.openphacts.org)
* WikiPathways (http://www.wikipathways.org/index.php/WikiPathways)
* The Database Center for Life Sciences/BioHackathon (http://dbcls.rois.ac.jp/en/ http://www.biohackathon.org/)
* The W3C Consortium, Health Care and Life Sciences Interest Group ([[HCLS]])
* BioPAX (http://biopax.org)
While the agenda will be open, we are coordinating ideas that can be developd at the network in advance, to maximize the utility of the day. Co-organizers for each community will help gathering ideas and finding point of contacts.

=== Information and registrations ===
For information, [mailto:info@swat4ls.org| info _at_ swat4ls.org]

Registrations are handled via [http://swat4ls-2012.eventbrite.com/| Eventbrite]

=== Hashtag ===
[https://twitter.com/search/realtime?q=%23swat4lshack #swat4lshack]

== Open PHACTS community ==

=== Contact Point ===
Andra Waagmeester

=== Proposed action points ===
# Consume [http://www.openphacts.org Open PHACTS] content in Pathway tools
# Using Identifiers.org
# Create an example set of valuable queries
# Visualizing output

=== Confirmed Participants ===
* Kees Burger
* Maria Carmen Carra
* Ian Dunlop
* Chris Evelo
* Paul Goth
* Tim Harder
* Carina Haupt
* Nick Juty
* Camille Laibe
* Antonis Loizou
* Oriol Lopez
* Guillermo C. Martínez
* Nuria Queralt
* Rishi Ramgolam
* Mark Thompson
* Egon Willighagen

== WikiPathways community ==

=== Contact Point ===
Andra Waagmeester

=== Proposed action points ===
# Exploring [http://www.wikipathways.org/index.php/WikiPathways WikiPathways] RDF content, making default queries
# Using [http://code.google.com/p/pathvisiorpc/ Pathvisio RPC].

=== Confirmed Participants ===
* Chris Evelo
* Martina Kutmon
* Alex Pico

== Database Center for Life Sciences Community / BioHackathon ==

=== Contact Point ===
Toshiaki Katayama

=== Proposed action points ===

== W3C HCLS Community ==

=== Contact Point ===
Eric Prud'hommeaux

=== Proposed action points ===

== BioPAX Community ==

=== Contact Point ===
Ismael Navas Delgado

=== Proposed action points ===

=== Confirmed Participants ===
* Ismael Navas Delgado
* Andrea Splendiani

=== Resources ===
* PathwayCommons SPARQL endpoint. Endpoint over all BioPAX representations in PathwayCommons
* Cytoscape plugin to visualize and interact with RDF knwoledge bases (new!)
* BioQueries: social site to build SPARQL queries
* Open PHACTS rdf guidelines: http://www.openphacts.org/specs/2012/WD-rdfguide-20120823/

HCLS/SWAT4LS2012/Hackathon

Ewilligh — Thu, 11 Oct 2012 19:35:45 GMT

Ewilligh: /* Hashtag */

== Introduction ==

=== Co-Organizers ===
* Andrea Splendiani
* Andra Waagmeester
* Eric Prud'hommeaux
* Toshiaki Katayama
* Ismael Navas delgado

=== Description ===
The SWAT4LS Hackathon is an informal event associated with the [http://swat4ls.org/| SWAT4LS] Semantic Web Applications and Tools for Life Sciences Workshops Series.

Scope of the event is to bring together experts and enthusiasts in the application of semantic technologies in healthcare and life science for open discussion and jam coding sessions.
The Hackathon will be organized on the 28th of November 2012 at La Cantine, Paris (for more information, please refer to the [http://www.swat4ls.org/workshops/paris2012/| workshop website]) and it is open to workshop participants and not (registration is required and space is limited!).

Projects and institutes that have already expressed their interest in attending include:
* OpenPhacts (http://www.openphacts.org)
* WikiPathways (http://www.wikipathways.org/index.php/WikiPathways)
* The Database Center for Life Sciences/BioHackathon (http://dbcls.rois.ac.jp/en/ http://www.biohackathon.org/)
* The W3C Consortium, Health Care and Life Sciences Interest Group ([[HCLS]])
* BioPAX (http://biopax.org)
While the agenda will be open, we are coordinating ideas that can be developd at the network in advance, to maximize the utility of the day. Co-organizers for each community will help gathering ideas and finding point of contacts.

=== Information and registrations ===
For information, [mailto:info@swat4ls.org| info _at_ swat4ls.org]

Registrations are handled via [http://swat4ls-2012.eventbrite.com/| Eventbrite]

=== Hashtag ===
[https://twitter.com/search/realtime?q=%23swat4lshack #swat4lshack]

== OpenPhacts community ==

=== Contact Point ===
Andra Waagmeester

=== Proposed action points ===
# Consume [http://www.openphacts.org Open PHACTS] content in Pathway tools
# Using Identifiers.org
# Visualizing RDF output in Pathvision

=== Confirmed Participants ===
* Kees Burger
* Maria Carmen Carra
* Ian Dunlop
* Chris Evelo
* Paul Goth
* Tim Harder
* Carina Haupt
* Nick Juty
* Camille Laibe
* Antonis Loizou
* Oriol Lopez
* Guillermo C. Martínez
* Nuria Queralt
* Rishi Ramgolam
* Mark Thompson
* Egon Willighagen

== WikiPathways community ==

=== Contact Point ===
Andra Waagmeester

=== Proposed action points ===
# Exploring [http://www.wikipathways.org/index.php/WikiPathways WikiPathways] RDF content, making default queries
# Using [http://code.google.com/p/pathvisiorpc/ Pathvisio RPC].

=== Confirmed Participants ===
* Chris Evelo
* Martina Kutmon
* Alex Pico

== Database Center for Life Sciences Community / BioHackathon ==

=== Contact Point ===
Toshiaki Katayama

=== Proposed action points ===

== W3C HCLS Community ==

=== Contact Point ===
Eric Prud'hommeaux

=== Proposed action points ===

== BioPAX Community ==

=== Contact Point ===
Ismael Navas Delgado

=== Proposed action points ===

=== Confirmed Participants ===
* Ismael Navas Delgado
* Andrea Splendiani

=== Resources ===
* PathwayCommons SPARQL endpoint. Endpoint over all BioPAX representations in PathwayCommons
* Cytoscape plugin to visualize and interact with RDF knwoledge bases (new!)
* BioQueries: social site to build SPARQL queries
* Open PHACTS rdf guidelines: http://www.openphacts.org/specs/2012/WD-rdfguide-20120823/

HCLS/SWAT4LS2012/Hackathon

Ewilligh — Thu, 11 Oct 2012 19:33:13 GMT

Ewilligh: typo fixed

== Introduction ==

=== Co-Organizers ===
* Andrea Splendiani
* Andra Waagmeester
* Eric Prud'hommeaux
* Toshiaki Katayama
* Ismael Navas delgado

=== Description ===
The SWAT4LS Hackathon is an informal event associated with the [http://swat4ls.org/| SWAT4LS] Semantic Web Applications and Tools for Life Sciences Workshops Series.

Scope of the event is to bring together experts and enthusiasts in the application of semantic technologies in healthcare and life science for open discussion and jam coding sessions.
The Hackathon will be organized on the 28th of November 2012 at La Cantine, Paris (for more information, please refer to the [http://www.swat4ls.org/workshops/paris2012/| workshop website]) and it is open to workshop participants and not (registration is required and space is limited!).

Projects and institutes that have already expressed their interest in attending include:
* OpenPhacts (http://www.openphacts.org)
* WikiPathways (http://www.wikipathways.org/index.php/WikiPathways)
* The Database Center for Life Sciences/BioHackathon (http://dbcls.rois.ac.jp/en/ http://www.biohackathon.org/)
* The W3C Consortium, Health Care and Life Sciences Interest Group ([[HCLS]])
* BioPAX (http://biopax.org)
While the agenda will be open, we are coordinating ideas that can be developd at the network in advance, to maximize the utility of the day. Co-organizers for each community will help gathering ideas and finding point of contacts.

=== Information and registrations ===
For information, [mailto:info@swat4ls.org| info _at_ swat4ls.org]

Registrations are handled via [http://swat4ls-2012.eventbrite.com/| Eventbrite]

=== Hashtag ===
swat4lshack

== OpenPhacts community ==

=== Contact Point ===
Andra Waagmeester

=== Proposed action points ===
# Consume [http://www.openphacts.org Open PHACTS] content in Pathway tools
# Using Identifiers.org
# Visualizing RDF output in Pathvision

=== Confirmed Participants ===
* Kees Burger
* Maria Carmen Carra
* Ian Dunlop
* Chris Evelo
* Paul Goth
* Tim Harder
* Carina Haupt
* Nick Juty
* Camille Laibe
* Antonis Loizou
* Oriol Lopez
* Guillermo C. Martínez
* Nuria Queralt
* Rishi Ramgolam
* Mark Thompson
* Egon Willighagen

== WikiPathways community ==

=== Contact Point ===
Andra Waagmeester

=== Proposed action points ===
# Exploring [http://www.wikipathways.org/index.php/WikiPathways WikiPathways] RDF content, making default queries
# Using [http://code.google.com/p/pathvisiorpc/ Pathvisio RPC].

=== Confirmed Participants ===
* Chris Evelo
* Martina Kutmon
* Alex Pico

== Database Center for Life Sciences Community / BioHackathon ==

=== Contact Point ===
Toshiaki Katayama

=== Proposed action points ===

== W3C HCLS Community ==

=== Contact Point ===
Eric Prud'hommeaux

=== Proposed action points ===

== BioPAX Community ==

=== Contact Point ===
Ismael Navas Delgado

=== Proposed action points ===

=== Confirmed Participants ===
* Ismael Navas Delgado
* Andrea Splendiani

=== Resources ===
* PathwayCommons SPARQL endpoint. Endpoint over all BioPAX representations in PathwayCommons
* Cytoscape plugin to visualize and interact with RDF knwoledge bases (new!)
* BioQueries: social site to build SPARQL queries
* Open PHACTS rdf guidelines: http://www.openphacts.org/specs/2012/WD-rdfguide-20120823/

HCLSIG/LLD

Ewilligh — Thu, 03 May 2012 08:07:58 GMT

Ewilligh: /* Publications */

__NOTOC__
== Linked Life Data ==
''Best practices in creating, publishing, linking, querying and visualizing linked life data''

With the advent of high-throughput experimentation, there has been an explosion of biomedical data on the Internet. While most of the data is available in Web accessible formats (e.g. HTML), many biomedical researchers rely on the use of Web browsers (e.g., Firefox and Internet Explorer) and search engines like Google to browse and search data on the Internet. Such manual browsing and keyword searching approaches are inadequate for large-scale integration of data on the Web. The Semantic Web transforms the Web into a global database or knowledge base that can be accessed by computer programs/agents through a standard data/ontology format. The Resource Description Framework (RDF) and the Web Ontology Language (OWL) are the W3C standards for encoding data/knowledge. This task group explores how to use RDF and OWL (as well as their enabling technologies) to better enable the computer to represent, identify, publish, query and integrate data/knowledge in the health care and life science domain.

=== Coordinator ===
The task coordinator is [[MScottMarshall]] (marshall@science.uva.nl)

=== Objectives ===

* Create a network of linked life data.
* Develop methods to keep resources up to date.
* Develop human-friendly user interfaces
* Produce how-to W3C notes

===Products===
Currently there are two HCLS KBs: [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/DERI_HCLS_KB HCLS KB hosted by DERI] and [http://www.corporate-semantic-web.de/hcls.html HCLS KB hosted by Free University Berlin].

===Publications===

Helena Deus, Jun Zhao, Satya Sahoo, Matthias Samwald, Eric Prud'hommeaux, Michael Miller, M.Scott Marshall and Kei-Hoi Cheung. Provenance of Microarray Experiments for a Better Understanding of Experiment Results ([http://wiki.knoesis.org/index.php/SWPM-2010 SWPM2010 Workshop wiki page], [http://people.csail.mit.edu/pcm/tempISWC/workshops/SWPM2010/InvitedPaper_6.pdf pdf])

Samwald, M.; Jentzsch, A.; Bouton, C.; Kallesoe, C.; Willighagen, E.; Hajagos, J.; Marshall, M.; Prud'hommeaux, E.; Hassanzadeh, O.; Pichler, E.; Stephens, S. Journal of Cheminformatics 2011, 3, 19 ([http://www.jcheminf.com/content/3/1/19 HTML]).

Cheung KH, Frost HR, Marshall MS, Prud'hommeaux E, Samwald M, Zhao J, Paschke A. (2009). A Journey to Semantic Web Query Federation in Life Sciences. BMC Bioinformatics, 10(Suppl 10):S10 ([http://www.biomedcentral.com/1471-2105/10/S10/S10 HTML]).

Zhao J, Jentzsch A, Samwald M, Cheung KH. Linked Data for Connnecting Traditional Chinese Medicine and Western Medicine. Data Integration in the Life Sciences Workshops ([http://www.cs.manchester.ac.uk/DILS09/ DILS 09]), University of Manchester, UK ([http://www.cs.manchester.ac.uk/DILS09/PosterDemoProceedings.pdf poster presentation]) -- this work is in collaboration with the LoDD task force.

=== Meetings ===
* [[/Meetings/2012-05-07_Conference_Call|Next Meeting May 07, 2012]]
* [[/Meetings|Past Meetings]]

=== Current Tasks ===
* Query Federation
** [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation Use case 1 -- receptors]
** [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2 Use case 2 -- microarrays]
** [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/MinimalInformationAboutAGraph Minimal Information About a Graph (MIAG)]
* [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/aTags BioSIOC / aTags]
* [http://esw.w3.org/topic/Data/TCMGeneDIT Linking TCM with LoDD Datasets]
* [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/MicroarrayExperimentContext Provenance]
* [[/DeepCapture|Deep Knowledge Representation Challenge]]

=== Participants ===
* Kei Cheung (Yale University)
* Matthias Samwald (Medical University of Vienna)
* Rob Frost (Vector C)
* Adrian Paschke (Freie Universitat Berlin)
* Eric Prud'hommeaux (W3C)
* Don Doherty (Brainstage)
* Susie Stephens (Johnson & Johnson Pharmaceutical Research & Development)
* Scott Marshall (University of Amsterdam)
* TN Bhat (NIST)
* Huajun Chen (Zhejiang University)
* Jun Zhao (Oxford University)
* [[KingsleyIdehen|Kingsley Idehen]] ([[OpenLinkSoftware|OpenLink Software]])
* Helena Deus (University of Texas)
* Satya Sahoo (Wright State University)
* Egon Willighagen (Maastricht University)

We welcome new participants.

=== Resources/References ===
* [http://www.eswc2008.org/final-pdfs-for-web-site/qpII-1.pdf SemWIQ]
* [http://www.eswc2008.org/final-pdfs-for-web-site/qpII-2.pdf Querying Distributed RDF Data Sources with SPARQL]
* [http://agraph.franz.com/support/documentation/current/agraph-introduction.html#intro-federation AllegroGraph documentation]
* [http://darq.sourceforge.net/ DARQ]
* [http://www.faviki.com/ Faviki]
* [http://www.corporate-semantic-web.de/tl_files/pub/RuleResponder_HCLS_eScience.pdf SPARQL Service Bus middleware]
* [http://users.ox.ac.uk/~zool0770/presentations/HCLS-BioRDF-Feb-09.pdf Vocabulary of Interlinked Dataset]
* [[Media:HCLSIG_BioRDF_Subgroup$TCMGeneDIT_RDF_Dataset_r1.zip|The RDF dump of the TCMGeneDIT Database]]
* [[Media:HCLSIG_BioRDF_Subgroup$TCMGeneDIT_RDF_Dataset_r2.tar.gz|The new release of RDF dump of the TCMGeneDIT Database]]
* [[VirtuosoUniversalServer|OpenLink Virtuoso]] - Quad Store and Linked Data Deployment
* [http://lod.openlinksw.com/fct/facet.vsp Live Virtuoso Instance] - [[NeuroCommons]], [[Bio2Rdf]], Uniprot, Yago, and other data sets from the Linked Data Cloud (note: [http://lod.openlinksw.com/sparql Live SPARQL endpoint])
* [http://www.iscb.org/cms_addon/conferences/cshals2009/ C-SHALS 2009]
* [http://www.cs.manchester.ac.uk/DILS09/ DILS 2009]
* [[Media:HCLSIG_BioRDF_Subgroup$biordf_f2f_2009.pdf|BioRDF update F2F 2009]]
* [[Media:HCLSIG_BioRDF_Subgroup$biordf_f2f_breakout_2009.pdf|BioRDF breakout session F2F 2009]]
=== Old Archives ===
* [[HCLSIG/LODD]]
* [[HCLSIG BioRDF Subgroup]]

Categories: [[Category:Hclsig]]

HCLSIG/LLD

Ewilligh — Thu, 03 May 2012 08:05:42 GMT

Ewilligh: /* Publications */

__NOTOC__
== Linked Life Data ==
''Best practices in creating, publishing, linking, querying and visualizing linked life data''

With the advent of high-throughput experimentation, there has been an explosion of biomedical data on the Internet. While most of the data is available in Web accessible formats (e.g. HTML), many biomedical researchers rely on the use of Web browsers (e.g., Firefox and Internet Explorer) and search engines like Google to browse and search data on the Internet. Such manual browsing and keyword searching approaches are inadequate for large-scale integration of data on the Web. The Semantic Web transforms the Web into a global database or knowledge base that can be accessed by computer programs/agents through a standard data/ontology format. The Resource Description Framework (RDF) and the Web Ontology Language (OWL) are the W3C standards for encoding data/knowledge. This task group explores how to use RDF and OWL (as well as their enabling technologies) to better enable the computer to represent, identify, publish, query and integrate data/knowledge in the health care and life science domain.

=== Coordinator ===
The task coordinator is [[MScottMarshall]] (marshall@science.uva.nl)

=== Objectives ===

* Create a network of linked life data.
* Develop methods to keep resources up to date.
* Develop human-friendly user interfaces
* Produce how-to W3C notes

===Products===
Currently there are two HCLS KBs: [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/DERI_HCLS_KB HCLS KB hosted by DERI] and [http://www.corporate-semantic-web.de/hcls.html HCLS KB hosted by Free University Berlin].

===Publications===

Helena Deus, Jun Zhao, Satya Sahoo, Matthias Samwald, Eric Prud'hommeaux, Michael Miller, M.Scott Marshall and Kei-Hoi Cheung. Provenance of Microarray Experiments for a Better Understanding of Experiment Results ([http://wiki.knoesis.org/index.php/SWPM-2010 SWPM2010 Workshop wiki page], [http://people.csail.mit.edu/pcm/tempISWC/workshops/SWPM2010/InvitedPaper_6.pdf pdf])

Cheung KH, Frost HR, Marshall MS, Prud'hommeaux E, Samwald M, Zhao J, Paschke A. (2009). A Journey to Semantic Web Query Federation in Life Sciences. BMC Bioinformatics, 10(Suppl 10):S10 ([http://www.biomedcentral.com/1471-2105/10/S10/S10 HTML]).

Zhao J, Jentzsch A, Samwald M, Cheung KH. Linked Data for Connnecting Traditional Chinese Medicine and Western Medicine. Data Integration in the Life Sciences Workshops ([http://www.cs.manchester.ac.uk/DILS09/ DILS 09]), University of Manchester, UK ([http://www.cs.manchester.ac.uk/DILS09/PosterDemoProceedings.pdf poster presentation]) -- this work is in collaboration with the LoDD task force.

=== Meetings ===
* [[/Meetings/2012-05-07_Conference_Call|Next Meeting May 07, 2012]]
* [[/Meetings|Past Meetings]]

=== Current Tasks ===
* Query Federation
** [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation Use case 1 -- receptors]
** [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2 Use case 2 -- microarrays]
** [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/MinimalInformationAboutAGraph Minimal Information About a Graph (MIAG)]
* [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/aTags BioSIOC / aTags]
* [http://esw.w3.org/topic/Data/TCMGeneDIT Linking TCM with LoDD Datasets]
* [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/MicroarrayExperimentContext Provenance]
* [[/DeepCapture|Deep Knowledge Representation Challenge]]

=== Participants ===
* Kei Cheung (Yale University)
* Matthias Samwald (Medical University of Vienna)
* Rob Frost (Vector C)
* Adrian Paschke (Freie Universitat Berlin)
* Eric Prud'hommeaux (W3C)
* Don Doherty (Brainstage)
* Susie Stephens (Johnson & Johnson Pharmaceutical Research & Development)
* Scott Marshall (University of Amsterdam)
* TN Bhat (NIST)
* Huajun Chen (Zhejiang University)
* Jun Zhao (Oxford University)
* [[KingsleyIdehen|Kingsley Idehen]] ([[OpenLinkSoftware|OpenLink Software]])
* Helena Deus (University of Texas)
* Satya Sahoo (Wright State University)
* Egon Willighagen (Maastricht University)

We welcome new participants.

=== Resources/References ===
* [http://www.eswc2008.org/final-pdfs-for-web-site/qpII-1.pdf SemWIQ]
* [http://www.eswc2008.org/final-pdfs-for-web-site/qpII-2.pdf Querying Distributed RDF Data Sources with SPARQL]
* [http://agraph.franz.com/support/documentation/current/agraph-introduction.html#intro-federation AllegroGraph documentation]
* [http://darq.sourceforge.net/ DARQ]
* [http://www.faviki.com/ Faviki]
* [http://www.corporate-semantic-web.de/tl_files/pub/RuleResponder_HCLS_eScience.pdf SPARQL Service Bus middleware]
* [http://users.ox.ac.uk/~zool0770/presentations/HCLS-BioRDF-Feb-09.pdf Vocabulary of Interlinked Dataset]
* [[Media:HCLSIG_BioRDF_Subgroup$TCMGeneDIT_RDF_Dataset_r1.zip|The RDF dump of the TCMGeneDIT Database]]
* [[Media:HCLSIG_BioRDF_Subgroup$TCMGeneDIT_RDF_Dataset_r2.tar.gz|The new release of RDF dump of the TCMGeneDIT Database]]
* [[VirtuosoUniversalServer|OpenLink Virtuoso]] - Quad Store and Linked Data Deployment
* [http://lod.openlinksw.com/fct/facet.vsp Live Virtuoso Instance] - [[NeuroCommons]], [[Bio2Rdf]], Uniprot, Yago, and other data sets from the Linked Data Cloud (note: [http://lod.openlinksw.com/sparql Live SPARQL endpoint])
* [http://www.iscb.org/cms_addon/conferences/cshals2009/ C-SHALS 2009]
* [http://www.cs.manchester.ac.uk/DILS09/ DILS 2009]
* [[Media:HCLSIG_BioRDF_Subgroup$biordf_f2f_2009.pdf|BioRDF update F2F 2009]]
* [[Media:HCLSIG_BioRDF_Subgroup$biordf_f2f_breakout_2009.pdf|BioRDF breakout session F2F 2009]]
=== Old Archives ===
* [[HCLSIG/LODD]]
* [[HCLSIG BioRDF Subgroup]]

Categories: [[Category:Hclsig]]

HCLSIG/LLD/Meetings/2012-05-07 Conference Call

Ewilligh — Tue, 01 May 2012 16:27:56 GMT

Ewilligh:

== Conference Details ==
* Date of Call: Monday, May 07, 2012
* Time of Call: 17:00 CEST
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Participant Access Code: 4257 ("HCLS")
* VOIP: To be added
* IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls for IRC access.
* Duration: ~1 hour
* Convener: Scott Marshall
* Scribe: TBD

==Agenda==
TBD

HCLSIG/LLD/Meetings/2012-04-23 Conference Call

Ewilligh — Tue, 01 May 2012 16:27:21 GMT

Ewilligh:

== Conference Details ==
* Date of Call: Monday, April 23, 2012
* Time of Call: 17:00 CEST
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Participant Access Code: 4257 ("HCLS")
* VOIP: To be added
* IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls for IRC access.
* Duration: ~1 hour
* Convener: Scott Marshall
* Scribe: [[User:Ewilligh]]

== IRC Transcript ==

<pre>
[Monday, April 23, 2012] [03:38:40 PM] Join MacTed has joined this channel (Thud@63.119.36.36).
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[Monday, April 23, 2012] [05:00:55 PM] Join Helena has joined this channel (qw3birc@128.30.52.28).
[Monday, April 23, 2012] [05:01:00 PM] Join JanosHajagos has joined this channel (8131f99d@78.129.202.38).
[Monday, April 23, 2012] [05:01:33 PM] * Helena can't join audio due to overlapping meeting but happy to read the minutes :)
[Monday, April 23, 2012] [05:01:50 PM] * egonw notices he is late once again
[Monday, April 23, 2012] [05:03:01 PM] Join mscottm has joined this channel (mscottm@81.69.36.208).
[Monday, April 23, 2012] [05:04:29 PM] Join Zakim has joined this channel (rrs-bridgg@128.30.52.169).
[Monday, April 23, 2012] [05:04:44 PM] Join JimMcCusker has joined this channel (8024285a@109.169.29.95).
[Monday, April 23, 2012] [05:04:48 PM] Join RRSAgent has joined this channel (rrs-loggee@128.30.52.169).
[Monday, April 23, 2012] [05:04:48 PM] <RRSAgent> logging to http://www.w3.org/2012/04/23-HCLS-irc
[Monday, April 23, 2012] [05:07:38 PM] <egonw> hi all
[Monday, April 23, 2012] [05:07:55 PM] * egonw will scribe
[Monday, April 23, 2012] [05:08:24 PM] <egonw> mscottm: today start discussing remaining issues for expression rdf document
[Monday, April 23, 2012] [05:08:32 PM] <egonw> there has been a publication already
[Monday, April 23, 2012] [05:08:41 PM] <egonw> link follows:
[Monday, April 23, 2012] [05:09:01 PM] <mscottm> https://plus.google.com/u/0/114642613065018821852/posts/XYJuMDFfkK6
[Monday, April 23, 2012] [05:09:29 PM] <egonw> (michael joined)
[Monday, April 23, 2012] [05:09:42 PM] Join michael has joined this channel (d17cbd27@78.129.202.38).
[Monday, April 23, 2012] [05:10:23 PM] <mscottm> https://plus.google.com/u/0/114642613065018821852/posts/XYJuMDFfkK6
[Monday, April 23, 2012] [05:10:40 PM] <egonw> paper uses swobjects
[Monday, April 23, 2012] [05:10:56 PM] <egonw> http://sourceforge.net/projects/swobjects/
[Monday, April 23, 2012] [05:12:34 PM] <mscottm> https://docs.google.com/document/d/1A5-3tOsifPWPpETBKU-ZA9d7O7wK_nBzTFUBEe-0Bzo/edit?authkey=CK-y8Y8C
[Monday, April 23, 2012] [05:12:54 PM] <egonw> that GDoc discusses using RDF for gene expression
[Monday, April 23, 2012] [05:13:14 PM] <egonw> biggest missing pieces
[Monday, April 23, 2012] [05:13:27 PM] <egonw> a general tool that converts MageTab into RDF
[Monday, April 23, 2012] [05:13:52 PM] <egonw> take interesting gene list and convert into RDF, including exp details, etc
[Monday, April 23, 2012] [05:13:58 PM] <ericP> hi all, i'm pushing to get some stuff presentable for an hl7 meeting.
[Monday, April 23, 2012] [05:14:08 PM] * ericP can you ping me here if you need me for a short moment?
[Monday, April 23, 2012] [05:14:30 PM] <ericP> s/hi all, i'm pushing to get some stuff presentable for an hl7 meeting.//
[Monday, April 23, 2012] [05:14:40 PM] * ericP doesn't want to leave crap in the log
[Monday, April 23, 2012] [05:15:42 PM] <egonw> mscottm: I did not full get that last major point
[Monday, April 23, 2012] [05:17:37 PM] <JimMcCusker> http://code.google.com/p/magetab2rdf/source/browse/trunk/magetab2magerdf/mapping.ttl
[Monday, April 23, 2012] [05:17:56 PM] <egonw> jim: general framework for converting MageTAB into RDF...
[Monday, April 23, 2012] [05:20:57 PM] <JimMcCusker> http://aquarius.tw.rpi.edu/projects/lobi/virtuoso/sparql
[Monday, April 23, 2012] [05:21:22 PM] <JimMcCusker> http://aquarius.tw.rpi.edu/projects/lobi/
[Monday, April 23, 2012] [05:21:35 PM] <JimMcCusker> http://purl.org/twc/arrayexpress/
[Monday, April 23, 2012] [05:22:15 PM] <JimMcCusker> http://purl.org/twc/arrayexpress/E-GEOD-17089
[Monday, April 23, 2012] [05:25:21 PM] <egonw> .ttl did not work for me either
[Monday, April 23, 2012] [05:26:18 PM] <pekkoh> Hello. I know i am a bit new at this (Pekka Kohonen from Karolinska Institutet) but are you aware of the ISA-TAB and the ISA2RDF tools?
[Monday, April 23, 2012] [05:27:24 PM] <pekkoh> This is a ToxBank/SEURAT-1 consortium project (Egon knows). Can convert automatically mage2ISA and then ISA2RDF.
[Monday, April 23, 2012] [05:27:44 PM] <mscottm> Pekka - Jim mentioned "ISA" a few minutes ago as a way to reference assays, IIR
[Monday, April 23, 2012] [05:27:54 PM] <michael> hi pekkoh, yes we are, but we've started with MAGE-TAB, ISA-TAB would be similar
[Monday, April 23, 2012] [05:29:15 PM] <pekkoh> OK.
[Monday, April 23, 2012] [05:29:36 PM] <JimMcCusker> http://aquarius.tw.rpi.edu/projects/lobi/P-GSE17089-4.html
[Monday, April 23, 2012] [05:29:47 PM] <egonw> JimMcCusker talks the telcon through some of the patterns
[Monday, April 23, 2012] [05:30:04 PM] <egonw> mscottm noted that the .ttl link did not work, may have been misrepresented, said JimMcCusker
[Monday, April 23, 2012] [05:33:39 PM] <mscottm> bnode used to represent implicit input to the activity in the provenance for the protocol
[Monday, April 23, 2012] [05:35:05 PM] <egonw> OBI is used to refer to general processes...
[Monday, April 23, 2012] [05:35:22 PM] <JimMcCusker> http://aquarius.tw.rpi.edu/projects/lobi/E-GEOD-17089.html
[Monday, April 23, 2012] [05:35:28 PM] <egonw> protocols realize some process (more than one?), e.g. http://aquarius.tw.rpi.edu/projects/lobi/P-GSE17089-4.html
[Monday, April 23, 2012] [05:36:24 PM] <egonw> and investigation (:investigation, prov:Activity) has protocol realizations as parts (has_part)
[Monday, April 23, 2012] [05:37:08 PM] <egonw> study designs are represented using EFO: http://aquarius.tw.rpi.edu/projects/lobi/E-GEOD-17089/studyDesign.html
[Monday, April 23, 2012] [05:38:39 PM] <egonw> egonw: is there an ordering of has_part linked protocols...
[Monday, April 23, 2012] [05:38:53 PM] <egonw> JimMcCusker: that order is implied by input and output of protocols
[Monday, April 23, 2012] [05:39:05 PM] <egonw> ok, thanx :)
[Monday, April 23, 2012] [05:41:08 PM] <egonw> JimMcCusker: prov:used is used to refer to the samples, materials, etc... e.g. http://purl.org/twc/arrayexpress/E-GEOD-17089/sourcename/GSM427343_1
[Monday, April 23, 2012] [05:41:21 PM] <egonw> this happens to be a cell line, A375P
[Monday, April 23, 2012] [05:41:51 PM] <egonw> here modeled as a "material entity" (BFO_0000040)
[Monday, April 23, 2012] [05:43:18 PM] <JimMcCusker> http://aquarius.tw.rpi.edu/projects/lobi/P-GSE17089-1.html
[Monday, April 23, 2012] [05:45:47 PM] <egonw> primary use case: discoverability, reuseability of results
[Monday, April 23, 2012] [05:46:07 PM] <egonw> JimMcCusker has visualizations, e.g. showing how methods changed over time
[Monday, April 23, 2012] [05:47:43 PM] <egonw> ? suggests the example of a refuted cancer study...
[Monday, April 23, 2012] [05:47:55 PM] <egonw> which could be looked up in microarray dbs
[Monday, April 23, 2012] [05:52:28 PM] <egonw> practical problems in the data analysis which may have been tracked with a systematic approach
[Monday, April 23, 2012] [05:52:49 PM] <egonw> mscottm asks what is missing in JimMcCusker's work
[Monday, April 23, 2012] [05:53:33 PM] <egonw> JimMcCusker: one problem is samples from human, which are not instantiations of humans
[Monday, April 23, 2012] [05:53:45 PM] <egonw> so, tricky to pick the right OBI/... predicate
[Monday, April 23, 2012] [05:54:03 PM] <michael> reanalisis of duke gene expression experiment: http://www.economist.com/node/21528593
[Monday, April 23, 2012] [05:54:10 PM] <mscottm> Scott confirms understanding of use case application: Find studies that make use of same assay, protocol, enzyme, analysis, etc.
[Monday, April 23, 2012] [05:55:08 PM] <egonw> that is: how to encode "is a sample originating from human"
[Monday, April 23, 2012] [05:55:45 PM] <egonw> closest now is "has characteristic"
[Monday, April 23, 2012] [05:56:11 PM] <egonw> btw, I need to leave in 4 minutes...
[Monday, April 23, 2012] [05:56:22 PM] <mscottm> tx for the warning
[Monday, April 23, 2012] [05:56:23 PM] <egonw> if we are not done by then, can someone scribe the remaining few minutes?
[Monday, April 23, 2012] [05:56:26 PM] <mscottm> sure
[Monday, April 23, 2012] [05:57:00 PM] * egonw wonderes how the proteomics does this with "human protein"
[Monday, April 23, 2012] [05:57:38 PM] <Helena> <michael> reanalisis of duke gene expression experiment: http://www.economist.com/node/21528593 -> michael: I know Keith Baggerly and Kevin Coombes (the statistians who uncovered the fraud) - they spent at least 3 years attempting to reanalize the data
[Monday, April 23, 2012] [05:59:09 PM] <JimMcCusker> http://aquarius.tw.rpi.edu/projects/lobi/E-GEOD-17275/sourcename/GSM429727_2.html
[Monday, April 23, 2012] [05:59:47 PM] <egonw> ok, I have to leave
[Monday, April 23, 2012] [05:59:54 PM] <egonw> I note that our group does this pipeline:
[Monday, April 23, 2012] [06:00:00 PM] <egonw> http://arrayanalysis.org/
[Monday, April 23, 2012] [06:00:18 PM] <egonw> and will see if people here can be interested in magetab2rdf
[Monday, April 23, 2012] [06:00:21 PM] <egonw> cheers!
</pre>

HCLSIG/LLD/Meetings/2012-04-23 Conference Call

Ewilligh — Tue, 01 May 2012 16:26:42 GMT

Ewilligh: Created page with "== Conference Details == * Date of Call: Monday, April 23, 2012 * Time of Call: 16:00 CEST * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Participant Access Code: 4257 ("HCLS") *…"

== Conference Details ==
* Date of Call: Monday, April 23, 2012
* Time of Call: 16:00 CEST
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Participant Access Code: 4257 ("HCLS")
* VOIP: To be added
* IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls for IRC access.
* Duration: ~1 hour
* Convener: Scott Marshall
* Scribe: [[User:Ewilligh]]

== IRC Transcript ==

<pre>
[Monday, April 23, 2012] [03:38:40 PM] Join MacTed has joined this channel (Thud@63.119.36.36).
[Monday, April 23, 2012] [04:00:28 PM] Join pekkoh has joined this channel (82ed85a6@109.169.29.95).
[Monday, April 23, 2012] [04:17:33 PM] Join JoanneLuciano has joined this channel (4a68ac2f@207.192.75.252).
[Monday, April 23, 2012] [05:00:22 PM] Join egombocz has joined this channel (42758fa2@64.62.228.82).
[Monday, April 23, 2012] [05:00:55 PM] Join Helena has joined this channel (qw3birc@128.30.52.28).
[Monday, April 23, 2012] [05:01:00 PM] Join JanosHajagos has joined this channel (8131f99d@78.129.202.38).
[Monday, April 23, 2012] [05:01:33 PM] * Helena can't join audio due to overlapping meeting but happy to read the minutes :)
[Monday, April 23, 2012] [05:01:50 PM] * egonw notices he is late once again
[Monday, April 23, 2012] [05:03:01 PM] Join mscottm has joined this channel (mscottm@81.69.36.208).
[Monday, April 23, 2012] [05:04:29 PM] Join Zakim has joined this channel (rrs-bridgg@128.30.52.169).
[Monday, April 23, 2012] [05:04:44 PM] Join JimMcCusker has joined this channel (8024285a@109.169.29.95).
[Monday, April 23, 2012] [05:04:48 PM] Join RRSAgent has joined this channel (rrs-loggee@128.30.52.169).
[Monday, April 23, 2012] [05:04:48 PM] <RRSAgent> logging to http://www.w3.org/2012/04/23-HCLS-irc
[Monday, April 23, 2012] [05:07:38 PM] <egonw> hi all
[Monday, April 23, 2012] [05:07:55 PM] * egonw will scribe
[Monday, April 23, 2012] [05:08:24 PM] <egonw> mscottm: today start discussing remaining issues for expression rdf document
[Monday, April 23, 2012] [05:08:32 PM] <egonw> there has been a publication already
[Monday, April 23, 2012] [05:08:41 PM] <egonw> link follows:
[Monday, April 23, 2012] [05:09:01 PM] <mscottm> https://plus.google.com/u/0/114642613065018821852/posts/XYJuMDFfkK6
[Monday, April 23, 2012] [05:09:29 PM] <egonw> (michael joined)
[Monday, April 23, 2012] [05:09:42 PM] Join michael has joined this channel (d17cbd27@78.129.202.38).
[Monday, April 23, 2012] [05:10:23 PM] <mscottm> https://plus.google.com/u/0/114642613065018821852/posts/XYJuMDFfkK6
[Monday, April 23, 2012] [05:10:40 PM] <egonw> paper uses swobjects
[Monday, April 23, 2012] [05:10:56 PM] <egonw> http://sourceforge.net/projects/swobjects/
[Monday, April 23, 2012] [05:12:34 PM] <mscottm> https://docs.google.com/document/d/1A5-3tOsifPWPpETBKU-ZA9d7O7wK_nBzTFUBEe-0Bzo/edit?authkey=CK-y8Y8C
[Monday, April 23, 2012] [05:12:54 PM] <egonw> that GDoc discusses using RDF for gene expression
[Monday, April 23, 2012] [05:13:14 PM] <egonw> biggest missing pieces
[Monday, April 23, 2012] [05:13:27 PM] <egonw> a general tool that converts MageTab into RDF
[Monday, April 23, 2012] [05:13:52 PM] <egonw> take interesting gene list and convert into RDF, including exp details, etc
[Monday, April 23, 2012] [05:13:58 PM] <ericP> hi all, i'm pushing to get some stuff presentable for an hl7 meeting.
[Monday, April 23, 2012] [05:14:08 PM] * ericP can you ping me here if you need me for a short moment?
[Monday, April 23, 2012] [05:14:30 PM] <ericP> s/hi all, i'm pushing to get some stuff presentable for an hl7 meeting.//
[Monday, April 23, 2012] [05:14:40 PM] * ericP doesn't want to leave crap in the log
[Monday, April 23, 2012] [05:15:42 PM] <egonw> mscottm: I did not full get that last major point
[Monday, April 23, 2012] [05:17:37 PM] <JimMcCusker> http://code.google.com/p/magetab2rdf/source/browse/trunk/magetab2magerdf/mapping.ttl
[Monday, April 23, 2012] [05:17:56 PM] <egonw> jim: general framework for converting MageTAB into RDF...
[Monday, April 23, 2012] [05:20:57 PM] <JimMcCusker> http://aquarius.tw.rpi.edu/projects/lobi/virtuoso/sparql
[Monday, April 23, 2012] [05:21:22 PM] <JimMcCusker> http://aquarius.tw.rpi.edu/projects/lobi/
[Monday, April 23, 2012] [05:21:35 PM] <JimMcCusker> http://purl.org/twc/arrayexpress/
[Monday, April 23, 2012] [05:22:15 PM] <JimMcCusker> http://purl.org/twc/arrayexpress/E-GEOD-17089
[Monday, April 23, 2012] [05:25:21 PM] <egonw> .ttl did not work for me either
[Monday, April 23, 2012] [05:26:18 PM] <pekkoh> Hello. I know i am a bit new at this (Pekka Kohonen from Karolinska Institutet) but are you aware of the ISA-TAB and the ISA2RDF tools?
[Monday, April 23, 2012] [05:27:24 PM] <pekkoh> This is a ToxBank/SEURAT-1 consortium project (Egon knows). Can convert automatically mage2ISA and then ISA2RDF.
[Monday, April 23, 2012] [05:27:44 PM] <mscottm> Pekka - Jim mentioned "ISA" a few minutes ago as a way to reference assays, IIR
[Monday, April 23, 2012] [05:27:54 PM] <michael> hi pekkoh, yes we are, but we've started with MAGE-TAB, ISA-TAB would be similar
[Monday, April 23, 2012] [05:29:15 PM] <pekkoh> OK.
[Monday, April 23, 2012] [05:29:36 PM] <JimMcCusker> http://aquarius.tw.rpi.edu/projects/lobi/P-GSE17089-4.html
[Monday, April 23, 2012] [05:29:47 PM] <egonw> JimMcCusker talks the telcon through some of the patterns
[Monday, April 23, 2012] [05:30:04 PM] <egonw> mscottm noted that the .ttl link did not work, may have been misrepresented, said JimMcCusker
[Monday, April 23, 2012] [05:33:39 PM] <mscottm> bnode used to represent implicit input to the activity in the provenance for the protocol
[Monday, April 23, 2012] [05:35:05 PM] <egonw> OBI is used to refer to general processes...
[Monday, April 23, 2012] [05:35:22 PM] <JimMcCusker> http://aquarius.tw.rpi.edu/projects/lobi/E-GEOD-17089.html
[Monday, April 23, 2012] [05:35:28 PM] <egonw> protocols realize some process (more than one?), e.g. http://aquarius.tw.rpi.edu/projects/lobi/P-GSE17089-4.html
[Monday, April 23, 2012] [05:36:24 PM] <egonw> and investigation (:investigation, prov:Activity) has protocol realizations as parts (has_part)
[Monday, April 23, 2012] [05:37:08 PM] <egonw> study designs are represented using EFO: http://aquarius.tw.rpi.edu/projects/lobi/E-GEOD-17089/studyDesign.html
[Monday, April 23, 2012] [05:38:39 PM] <egonw> egonw: is there an ordering of has_part linked protocols...
[Monday, April 23, 2012] [05:38:53 PM] <egonw> JimMcCusker: that order is implied by input and output of protocols
[Monday, April 23, 2012] [05:39:05 PM] <egonw> ok, thanx :)
[Monday, April 23, 2012] [05:41:08 PM] <egonw> JimMcCusker: prov:used is used to refer to the samples, materials, etc... e.g. http://purl.org/twc/arrayexpress/E-GEOD-17089/sourcename/GSM427343_1
[Monday, April 23, 2012] [05:41:21 PM] <egonw> this happens to be a cell line, A375P
[Monday, April 23, 2012] [05:41:51 PM] <egonw> here modeled as a "material entity" (BFO_0000040)
[Monday, April 23, 2012] [05:43:18 PM] <JimMcCusker> http://aquarius.tw.rpi.edu/projects/lobi/P-GSE17089-1.html
[Monday, April 23, 2012] [05:45:47 PM] <egonw> primary use case: discoverability, reuseability of results
[Monday, April 23, 2012] [05:46:07 PM] <egonw> JimMcCusker has visualizations, e.g. showing how methods changed over time
[Monday, April 23, 2012] [05:47:43 PM] <egonw> ? suggests the example of a refuted cancer study...
[Monday, April 23, 2012] [05:47:55 PM] <egonw> which could be looked up in microarray dbs
[Monday, April 23, 2012] [05:52:28 PM] <egonw> practical problems in the data analysis which may have been tracked with a systematic approach
[Monday, April 23, 2012] [05:52:49 PM] <egonw> mscottm asks what is missing in JimMcCusker's work
[Monday, April 23, 2012] [05:53:33 PM] <egonw> JimMcCusker: one problem is samples from human, which are not instantiations of humans
[Monday, April 23, 2012] [05:53:45 PM] <egonw> so, tricky to pick the right OBI/... predicate
[Monday, April 23, 2012] [05:54:03 PM] <michael> reanalisis of duke gene expression experiment: http://www.economist.com/node/21528593
[Monday, April 23, 2012] [05:54:10 PM] <mscottm> Scott confirms understanding of use case application: Find studies that make use of same assay, protocol, enzyme, analysis, etc.
[Monday, April 23, 2012] [05:55:08 PM] <egonw> that is: how to encode "is a sample originating from human"
[Monday, April 23, 2012] [05:55:45 PM] <egonw> closest now is "has characteristic"
[Monday, April 23, 2012] [05:56:11 PM] <egonw> btw, I need to leave in 4 minutes...
[Monday, April 23, 2012] [05:56:22 PM] <mscottm> tx for the warning
[Monday, April 23, 2012] [05:56:23 PM] <egonw> if we are not done by then, can someone scribe the remaining few minutes?
[Monday, April 23, 2012] [05:56:26 PM] <mscottm> sure
[Monday, April 23, 2012] [05:57:00 PM] * egonw wonderes how the proteomics does this with "human protein"
[Monday, April 23, 2012] [05:57:38 PM] <Helena> <michael> reanalisis of duke gene expression experiment: http://www.economist.com/node/21528593 -> michael: I know Keith Baggerly and Kevin Coombes (the statistians who uncovered the fraud) - they spent at least 3 years attempting to reanalize the data
[Monday, April 23, 2012] [05:59:09 PM] <JimMcCusker> http://aquarius.tw.rpi.edu/projects/lobi/E-GEOD-17275/sourcename/GSM429727_2.html
[Monday, April 23, 2012] [05:59:47 PM] <egonw> ok, I have to leave
[Monday, April 23, 2012] [05:59:54 PM] <egonw> I note that our group does this pipeline:
[Monday, April 23, 2012] [06:00:00 PM] <egonw> http://arrayanalysis.org/
[Monday, April 23, 2012] [06:00:18 PM] <egonw> and will see if people here can be interested in magetab2rdf
[Monday, April 23, 2012] [06:00:21 PM] <egonw> cheers!
</pre>

User:Ewilligh

Ewilligh — Tue, 01 May 2012 16:26:29 GMT

Ewilligh:

Egon Willighagen

Blog: http://chem-bla-ics.blogspot.com/

HCLSIG/LLD/Meetings/2012-05-07 Conference Call

Ewilligh — Tue, 01 May 2012 16:23:34 GMT

Ewilligh: Created page with "== Conference Details == * Date of Call: Monday, May 07, 2012 * Time of Call: 16:00 CEST * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Participant Access Code: 4257 ("HCLS") * V…"

== Conference Details ==
* Date of Call: Monday, May 07, 2012
* Time of Call: 16:00 CEST
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Participant Access Code: 4257 ("HCLS")
* VOIP: To be added
* IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls for IRC access.
* Duration: ~1 hour
* Convener: Scott Marshall
* Scribe: TBD

==Agenda==
TBD

HCLSIG/LLD

Ewilligh — Tue, 01 May 2012 16:21:33 GMT

Ewilligh: /* Meetings */

__NOTOC__
== Linked Life Data ==
''Best practices in creating, publishing, linking, querying and visualizing linked life data''

With the advent of high-throughput experimentation, there has been an explosion of biomedical data on the Internet. While most of the data is available in Web accessible formats (e.g. HTML), many biomedical researchers rely on the use of Web browsers (e.g., Firefox and Internet Explorer) and search engines like Google to browse and search data on the Internet. Such manual browsing and keyword searching approaches are inadequate for large-scale integration of data on the Web. The Semantic Web transforms the Web into a global database or knowledge base that can be accessed by computer programs/agents through a standard data/ontology format. The Resource Description Framework (RDF) and the Web Ontology Language (OWL) are the W3C standards for encoding data/knowledge. This task group explores how to use RDF and OWL (as well as their enabling technologies) to better enable the computer to represent, identify, publish, query and integrate data/knowledge in the health care and life science domain.

=== Coordinator ===
The task coordinator is [[MScottMarshall]] (marshall@science.uva.nl)

=== Objectives ===

* Create a network of linked life data.
* Develop methods to keep resources up to date.
* Develop human-friendly user interfaces
* Produce how-to W3C notes

===Products===
Currently there are two HCLS KBs: [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/DERI_HCLS_KB HCLS KB hosted by DERI] and [http://www.corporate-semantic-web.de/hcls.html HCLS KB hosted by Free University Berlin].

===Publications===

Helena Deus, Jun Zhao, Satya Sahoo, Matthias Samwald, Eric Prud'hommeaux, Michael Miller, M.Scott Marshall and Kei-Hoi Cheung. Provenance of Microarray Experiments for a Better Understanding of Experiment Results ([http://wiki.knoesis.org/index.php/SWPM-2010 SWPM2010 Workshop wiki page], [http://people.csail.mit.edu/pcm/tempISWC/workshops/SWPM2010/InvitedPaper_6.pdf pdf])

Cheung KH, Frost HR, Marshall MS, Prud'hommeaux E, Samwald M, Zhao J, Paschke A. (2009). A Journey to Semantic Web Query Federation in Life Sciences. BMC Bioinformatics, 10(Suppl 10):S10.

Zhao J, Jentzsch A, Samwald M, Cheung KH. Linked Data for Connnecting Traditional Chinese Medicine and Western Medicine. Data Integration in the Life Sciences Workshops ([http://www.cs.manchester.ac.uk/DILS09/ DILS 09]), University of Manchester, UK ([http://www.cs.manchester.ac.uk/DILS09/PosterDemoProceedings.pdf poster presentation]) -- this work is in collaboration with the LoDD task force.

=== Meetings ===
* [[/Meetings/2012-05-07_Conference_Call|Next Meeting May 07, 2012]]
* [[/Meetings|Past Meetings]]

=== Current Tasks ===
* Query Federation
** [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation Use case 1 -- receptors]
** [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2 Use case 2 -- microarrays]
** [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/MinimalInformationAboutAGraph Minimal Information About a Graph (MIAG)]
* [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/aTags BioSIOC / aTags]
* [http://esw.w3.org/topic/Data/TCMGeneDIT Linking TCM with LoDD Datasets]
* [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/MicroarrayExperimentContext Provenance]
* [[/DeepCapture|Deep Knowledge Representation Challenge]]

=== Participants ===
* Kei Cheung (Yale University)
* Matthias Samwald (Medical University of Vienna)
* Rob Frost (Vector C)
* Adrian Paschke (Freie Universitat Berlin)
* Eric Prud'hommeaux (W3C)
* Don Doherty (Brainstage)
* Susie Stephens (Johnson & Johnson Pharmaceutical Research & Development)
* Scott Marshall (University of Amsterdam)
* TN Bhat (NIST)
* Huajun Chen (Zhejiang University)
* Jun Zhao (Oxford University)
* [[KingsleyIdehen|Kingsley Idehen]] ([[OpenLinkSoftware|OpenLink Software]])
* Helena Deus (University of Texas)
* Satya Sahoo (Wright State University)
* Egon Willighagen (Maastricht University)

We welcome new participants.

=== Resources/References ===
* [http://www.eswc2008.org/final-pdfs-for-web-site/qpII-1.pdf SemWIQ]
* [http://www.eswc2008.org/final-pdfs-for-web-site/qpII-2.pdf Querying Distributed RDF Data Sources with SPARQL]
* [http://agraph.franz.com/support/documentation/current/agraph-introduction.html#intro-federation AllegroGraph documentation]
* [http://darq.sourceforge.net/ DARQ]
* [http://www.faviki.com/ Faviki]
* [http://www.corporate-semantic-web.de/tl_files/pub/RuleResponder_HCLS_eScience.pdf SPARQL Service Bus middleware]
* [http://users.ox.ac.uk/~zool0770/presentations/HCLS-BioRDF-Feb-09.pdf Vocabulary of Interlinked Dataset]
* [[Media:HCLSIG_BioRDF_Subgroup$TCMGeneDIT_RDF_Dataset_r1.zip|The RDF dump of the TCMGeneDIT Database]]
* [[Media:HCLSIG_BioRDF_Subgroup$TCMGeneDIT_RDF_Dataset_r2.tar.gz|The new release of RDF dump of the TCMGeneDIT Database]]
* [[VirtuosoUniversalServer|OpenLink Virtuoso]] - Quad Store and Linked Data Deployment
* [http://lod.openlinksw.com/fct/facet.vsp Live Virtuoso Instance] - [[NeuroCommons]], [[Bio2Rdf]], Uniprot, Yago, and other data sets from the Linked Data Cloud (note: [http://lod.openlinksw.com/sparql Live SPARQL endpoint])
* [http://www.iscb.org/cms_addon/conferences/cshals2009/ C-SHALS 2009]
* [http://www.cs.manchester.ac.uk/DILS09/ DILS 2009]
* [[Media:HCLSIG_BioRDF_Subgroup$biordf_f2f_2009.pdf|BioRDF update F2F 2009]]
* [[Media:HCLSIG_BioRDF_Subgroup$biordf_f2f_breakout_2009.pdf|BioRDF breakout session F2F 2009]]
=== Old Archives ===
* [[HCLSIG/LODD]]
* [[HCLSIG BioRDF Subgroup]]

Categories: [[Category:Hclsig]]

HCLSIG/LLD

Ewilligh — Tue, 01 May 2012 16:21:22 GMT

Ewilligh: /* Meetings */

__NOTOC__
== Linked Life Data ==
''Best practices in creating, publishing, linking, querying and visualizing linked life data''

With the advent of high-throughput experimentation, there has been an explosion of biomedical data on the Internet. While most of the data is available in Web accessible formats (e.g. HTML), many biomedical researchers rely on the use of Web browsers (e.g., Firefox and Internet Explorer) and search engines like Google to browse and search data on the Internet. Such manual browsing and keyword searching approaches are inadequate for large-scale integration of data on the Web. The Semantic Web transforms the Web into a global database or knowledge base that can be accessed by computer programs/agents through a standard data/ontology format. The Resource Description Framework (RDF) and the Web Ontology Language (OWL) are the W3C standards for encoding data/knowledge. This task group explores how to use RDF and OWL (as well as their enabling technologies) to better enable the computer to represent, identify, publish, query and integrate data/knowledge in the health care and life science domain.

=== Coordinator ===
The task coordinator is [[MScottMarshall]] (marshall@science.uva.nl)

=== Objectives ===

* Create a network of linked life data.
* Develop methods to keep resources up to date.
* Develop human-friendly user interfaces
* Produce how-to W3C notes

===Products===
Currently there are two HCLS KBs: [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/DERI_HCLS_KB HCLS KB hosted by DERI] and [http://www.corporate-semantic-web.de/hcls.html HCLS KB hosted by Free University Berlin].

===Publications===

Helena Deus, Jun Zhao, Satya Sahoo, Matthias Samwald, Eric Prud'hommeaux, Michael Miller, M.Scott Marshall and Kei-Hoi Cheung. Provenance of Microarray Experiments for a Better Understanding of Experiment Results ([http://wiki.knoesis.org/index.php/SWPM-2010 SWPM2010 Workshop wiki page], [http://people.csail.mit.edu/pcm/tempISWC/workshops/SWPM2010/InvitedPaper_6.pdf pdf])

Cheung KH, Frost HR, Marshall MS, Prud'hommeaux E, Samwald M, Zhao J, Paschke A. (2009). A Journey to Semantic Web Query Federation in Life Sciences. BMC Bioinformatics, 10(Suppl 10):S10.

Zhao J, Jentzsch A, Samwald M, Cheung KH. Linked Data for Connnecting Traditional Chinese Medicine and Western Medicine. Data Integration in the Life Sciences Workshops ([http://www.cs.manchester.ac.uk/DILS09/ DILS 09]), University of Manchester, UK ([http://www.cs.manchester.ac.uk/DILS09/PosterDemoProceedings.pdf poster presentation]) -- this work is in collaboration with the LoDD task force.

=== Meetings ===
* [[/Meetings/2012-05-07_Conference_Call Next Meeting May 07, 2012]]
* [[/Meetings|Past Meetings]]

=== Current Tasks ===
* Query Federation
** [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation Use case 1 -- receptors]
** [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2 Use case 2 -- microarrays]
** [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/MinimalInformationAboutAGraph Minimal Information About a Graph (MIAG)]
* [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/aTags BioSIOC / aTags]
* [http://esw.w3.org/topic/Data/TCMGeneDIT Linking TCM with LoDD Datasets]
* [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/MicroarrayExperimentContext Provenance]
* [[/DeepCapture|Deep Knowledge Representation Challenge]]

=== Participants ===
* Kei Cheung (Yale University)
* Matthias Samwald (Medical University of Vienna)
* Rob Frost (Vector C)
* Adrian Paschke (Freie Universitat Berlin)
* Eric Prud'hommeaux (W3C)
* Don Doherty (Brainstage)
* Susie Stephens (Johnson & Johnson Pharmaceutical Research & Development)
* Scott Marshall (University of Amsterdam)
* TN Bhat (NIST)
* Huajun Chen (Zhejiang University)
* Jun Zhao (Oxford University)
* [[KingsleyIdehen|Kingsley Idehen]] ([[OpenLinkSoftware|OpenLink Software]])
* Helena Deus (University of Texas)
* Satya Sahoo (Wright State University)
* Egon Willighagen (Maastricht University)

We welcome new participants.

=== Resources/References ===
* [http://www.eswc2008.org/final-pdfs-for-web-site/qpII-1.pdf SemWIQ]
* [http://www.eswc2008.org/final-pdfs-for-web-site/qpII-2.pdf Querying Distributed RDF Data Sources with SPARQL]
* [http://agraph.franz.com/support/documentation/current/agraph-introduction.html#intro-federation AllegroGraph documentation]
* [http://darq.sourceforge.net/ DARQ]
* [http://www.faviki.com/ Faviki]
* [http://www.corporate-semantic-web.de/tl_files/pub/RuleResponder_HCLS_eScience.pdf SPARQL Service Bus middleware]
* [http://users.ox.ac.uk/~zool0770/presentations/HCLS-BioRDF-Feb-09.pdf Vocabulary of Interlinked Dataset]
* [[Media:HCLSIG_BioRDF_Subgroup$TCMGeneDIT_RDF_Dataset_r1.zip|The RDF dump of the TCMGeneDIT Database]]
* [[Media:HCLSIG_BioRDF_Subgroup$TCMGeneDIT_RDF_Dataset_r2.tar.gz|The new release of RDF dump of the TCMGeneDIT Database]]
* [[VirtuosoUniversalServer|OpenLink Virtuoso]] - Quad Store and Linked Data Deployment
* [http://lod.openlinksw.com/fct/facet.vsp Live Virtuoso Instance] - [[NeuroCommons]], [[Bio2Rdf]], Uniprot, Yago, and other data sets from the Linked Data Cloud (note: [http://lod.openlinksw.com/sparql Live SPARQL endpoint])
* [http://www.iscb.org/cms_addon/conferences/cshals2009/ C-SHALS 2009]
* [http://www.cs.manchester.ac.uk/DILS09/ DILS 2009]
* [[Media:HCLSIG_BioRDF_Subgroup$biordf_f2f_2009.pdf|BioRDF update F2F 2009]]
* [[Media:HCLSIG_BioRDF_Subgroup$biordf_f2f_breakout_2009.pdf|BioRDF breakout session F2F 2009]]
=== Old Archives ===
* [[HCLSIG/LODD]]
* [[HCLSIG BioRDF Subgroup]]

Categories: [[Category:Hclsig]]

HCLSIG/LLD

Ewilligh — Tue, 01 May 2012 16:21:11 GMT

Ewilligh: /* Meetings */

__NOTOC__
== Linked Life Data ==
''Best practices in creating, publishing, linking, querying and visualizing linked life data''

With the advent of high-throughput experimentation, there has been an explosion of biomedical data on the Internet. While most of the data is available in Web accessible formats (e.g. HTML), many biomedical researchers rely on the use of Web browsers (e.g., Firefox and Internet Explorer) and search engines like Google to browse and search data on the Internet. Such manual browsing and keyword searching approaches are inadequate for large-scale integration of data on the Web. The Semantic Web transforms the Web into a global database or knowledge base that can be accessed by computer programs/agents through a standard data/ontology format. The Resource Description Framework (RDF) and the Web Ontology Language (OWL) are the W3C standards for encoding data/knowledge. This task group explores how to use RDF and OWL (as well as their enabling technologies) to better enable the computer to represent, identify, publish, query and integrate data/knowledge in the health care and life science domain.

=== Coordinator ===
The task coordinator is [[MScottMarshall]] (marshall@science.uva.nl)

=== Objectives ===

* Create a network of linked life data.
* Develop methods to keep resources up to date.
* Develop human-friendly user interfaces
* Produce how-to W3C notes

===Products===
Currently there are two HCLS KBs: [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/DERI_HCLS_KB HCLS KB hosted by DERI] and [http://www.corporate-semantic-web.de/hcls.html HCLS KB hosted by Free University Berlin].

===Publications===

Helena Deus, Jun Zhao, Satya Sahoo, Matthias Samwald, Eric Prud'hommeaux, Michael Miller, M.Scott Marshall and Kei-Hoi Cheung. Provenance of Microarray Experiments for a Better Understanding of Experiment Results ([http://wiki.knoesis.org/index.php/SWPM-2010 SWPM2010 Workshop wiki page], [http://people.csail.mit.edu/pcm/tempISWC/workshops/SWPM2010/InvitedPaper_6.pdf pdf])

Cheung KH, Frost HR, Marshall MS, Prud'hommeaux E, Samwald M, Zhao J, Paschke A. (2009). A Journey to Semantic Web Query Federation in Life Sciences. BMC Bioinformatics, 10(Suppl 10):S10.

Zhao J, Jentzsch A, Samwald M, Cheung KH. Linked Data for Connnecting Traditional Chinese Medicine and Western Medicine. Data Integration in the Life Sciences Workshops ([http://www.cs.manchester.ac.uk/DILS09/ DILS 09]), University of Manchester, UK ([http://www.cs.manchester.ac.uk/DILS09/PosterDemoProceedings.pdf poster presentation]) -- this work is in collaboration with the LoDD task force.

=== Meetings ===
* [[/Meetings/2012-05-07_Conference_Call Next Meeting May 07, 2012]
* [[/Meetings|Past Meetings]]

=== Current Tasks ===
* Query Federation
** [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation Use case 1 -- receptors]
** [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2 Use case 2 -- microarrays]
** [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/MinimalInformationAboutAGraph Minimal Information About a Graph (MIAG)]
* [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/aTags BioSIOC / aTags]
* [http://esw.w3.org/topic/Data/TCMGeneDIT Linking TCM with LoDD Datasets]
* [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/MicroarrayExperimentContext Provenance]
* [[/DeepCapture|Deep Knowledge Representation Challenge]]

=== Participants ===
* Kei Cheung (Yale University)
* Matthias Samwald (Medical University of Vienna)
* Rob Frost (Vector C)
* Adrian Paschke (Freie Universitat Berlin)
* Eric Prud'hommeaux (W3C)
* Don Doherty (Brainstage)
* Susie Stephens (Johnson & Johnson Pharmaceutical Research & Development)
* Scott Marshall (University of Amsterdam)
* TN Bhat (NIST)
* Huajun Chen (Zhejiang University)
* Jun Zhao (Oxford University)
* [[KingsleyIdehen|Kingsley Idehen]] ([[OpenLinkSoftware|OpenLink Software]])
* Helena Deus (University of Texas)
* Satya Sahoo (Wright State University)
* Egon Willighagen (Maastricht University)

We welcome new participants.

=== Resources/References ===
* [http://www.eswc2008.org/final-pdfs-for-web-site/qpII-1.pdf SemWIQ]
* [http://www.eswc2008.org/final-pdfs-for-web-site/qpII-2.pdf Querying Distributed RDF Data Sources with SPARQL]
* [http://agraph.franz.com/support/documentation/current/agraph-introduction.html#intro-federation AllegroGraph documentation]
* [http://darq.sourceforge.net/ DARQ]
* [http://www.faviki.com/ Faviki]
* [http://www.corporate-semantic-web.de/tl_files/pub/RuleResponder_HCLS_eScience.pdf SPARQL Service Bus middleware]
* [http://users.ox.ac.uk/~zool0770/presentations/HCLS-BioRDF-Feb-09.pdf Vocabulary of Interlinked Dataset]
* [[Media:HCLSIG_BioRDF_Subgroup$TCMGeneDIT_RDF_Dataset_r1.zip|The RDF dump of the TCMGeneDIT Database]]
* [[Media:HCLSIG_BioRDF_Subgroup$TCMGeneDIT_RDF_Dataset_r2.tar.gz|The new release of RDF dump of the TCMGeneDIT Database]]
* [[VirtuosoUniversalServer|OpenLink Virtuoso]] - Quad Store and Linked Data Deployment
* [http://lod.openlinksw.com/fct/facet.vsp Live Virtuoso Instance] - [[NeuroCommons]], [[Bio2Rdf]], Uniprot, Yago, and other data sets from the Linked Data Cloud (note: [http://lod.openlinksw.com/sparql Live SPARQL endpoint])
* [http://www.iscb.org/cms_addon/conferences/cshals2009/ C-SHALS 2009]
* [http://www.cs.manchester.ac.uk/DILS09/ DILS 2009]
* [[Media:HCLSIG_BioRDF_Subgroup$biordf_f2f_2009.pdf|BioRDF update F2F 2009]]
* [[Media:HCLSIG_BioRDF_Subgroup$biordf_f2f_breakout_2009.pdf|BioRDF breakout session F2F 2009]]
=== Old Archives ===
* [[HCLSIG/LODD]]
* [[HCLSIG BioRDF Subgroup]]

Categories: [[Category:Hclsig]]

HCLSIG/LLD/Meetings

Ewilligh — Tue, 01 May 2012 16:18:21 GMT

Ewilligh: Created page with "__NOTOC__ Meeting notes for previous meetings. * /2012-04-23 Conference Call"

__NOTOC__
Meeting notes for previous meetings.
 
* [[/2012-04-23 Conference Call]]

HCLSIG/LLD

Ewilligh — Tue, 01 May 2012 16:14:47 GMT

Ewilligh: /* Old Archives */

__NOTOC__
== Linked Life Data ==
''Best practices in creating, publishing, linking, querying and visualizing linked life data''

With the advent of high-throughput experimentation, there has been an explosion of biomedical data on the Internet. While most of the data is available in Web accessible formats (e.g. HTML), many biomedical researchers rely on the use of Web browsers (e.g., Firefox and Internet Explorer) and search engines like Google to browse and search data on the Internet. Such manual browsing and keyword searching approaches are inadequate for large-scale integration of data on the Web. The Semantic Web transforms the Web into a global database or knowledge base that can be accessed by computer programs/agents through a standard data/ontology format. The Resource Description Framework (RDF) and the Web Ontology Language (OWL) are the W3C standards for encoding data/knowledge. This task group explores how to use RDF and OWL (as well as their enabling technologies) to better enable the computer to represent, identify, publish, query and integrate data/knowledge in the health care and life science domain.

=== Coordinator ===
The task coordinator is [[MScottMarshall]] (marshall@science.uva.nl)

=== Objectives ===

* Create a network of linked life data.
* Develop methods to keep resources up to date.
* Develop human-friendly user interfaces
* Produce how-to W3C notes

===Products===
Currently there are two HCLS KBs: [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/DERI_HCLS_KB HCLS KB hosted by DERI] and [http://www.corporate-semantic-web.de/hcls.html HCLS KB hosted by Free University Berlin].

===Publications===

Helena Deus, Jun Zhao, Satya Sahoo, Matthias Samwald, Eric Prud'hommeaux, Michael Miller, M.Scott Marshall and Kei-Hoi Cheung. Provenance of Microarray Experiments for a Better Understanding of Experiment Results ([http://wiki.knoesis.org/index.php/SWPM-2010 SWPM2010 Workshop wiki page], [http://people.csail.mit.edu/pcm/tempISWC/workshops/SWPM2010/InvitedPaper_6.pdf pdf])

Cheung KH, Frost HR, Marshall MS, Prud'hommeaux E, Samwald M, Zhao J, Paschke A. (2009). A Journey to Semantic Web Query Federation in Life Sciences. BMC Bioinformatics, 10(Suppl 10):S10.

Zhao J, Jentzsch A, Samwald M, Cheung KH. Linked Data for Connnecting Traditional Chinese Medicine and Western Medicine. Data Integration in the Life Sciences Workshops ([http://www.cs.manchester.ac.uk/DILS09/ DILS 09]), University of Manchester, UK ([http://www.cs.manchester.ac.uk/DILS09/PosterDemoProceedings.pdf poster presentation]) -- this work is in collaboration with the LoDD task force.

=== Meetings ===
* [http://www.w3.org/wiki/HCLSIG_BioRDF_Subgroup/Meetings/2011/09-26_Conference_Call Next Meeting September 26, 2011]
* [[/Meetings|Past Meetings]]

=== Current Tasks ===
* Query Federation
** [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation Use case 1 -- receptors]
** [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2 Use case 2 -- microarrays]
** [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/MinimalInformationAboutAGraph Minimal Information About a Graph (MIAG)]
* [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/aTags BioSIOC / aTags]
* [http://esw.w3.org/topic/Data/TCMGeneDIT Linking TCM with LoDD Datasets]
* [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/MicroarrayExperimentContext Provenance]
* [[/DeepCapture|Deep Knowledge Representation Challenge]]

=== Participants ===
* Kei Cheung (Yale University)
* Matthias Samwald (Medical University of Vienna)
* Rob Frost (Vector C)
* Adrian Paschke (Freie Universitat Berlin)
* Eric Prud'hommeaux (W3C)
* Don Doherty (Brainstage)
* Susie Stephens (Johnson & Johnson Pharmaceutical Research & Development)
* Scott Marshall (University of Amsterdam)
* TN Bhat (NIST)
* Huajun Chen (Zhejiang University)
* Jun Zhao (Oxford University)
* [[KingsleyIdehen|Kingsley Idehen]] ([[OpenLinkSoftware|OpenLink Software]])
* Helena Deus (University of Texas)
* Satya Sahoo (Wright State University)
* Egon Willighagen (Maastricht University)

We welcome new participants.

=== Resources/References ===
* [http://www.eswc2008.org/final-pdfs-for-web-site/qpII-1.pdf SemWIQ]
* [http://www.eswc2008.org/final-pdfs-for-web-site/qpII-2.pdf Querying Distributed RDF Data Sources with SPARQL]
* [http://agraph.franz.com/support/documentation/current/agraph-introduction.html#intro-federation AllegroGraph documentation]
* [http://darq.sourceforge.net/ DARQ]
* [http://www.faviki.com/ Faviki]
* [http://www.corporate-semantic-web.de/tl_files/pub/RuleResponder_HCLS_eScience.pdf SPARQL Service Bus middleware]
* [http://users.ox.ac.uk/~zool0770/presentations/HCLS-BioRDF-Feb-09.pdf Vocabulary of Interlinked Dataset]
* [[Media:HCLSIG_BioRDF_Subgroup$TCMGeneDIT_RDF_Dataset_r1.zip|The RDF dump of the TCMGeneDIT Database]]
* [[Media:HCLSIG_BioRDF_Subgroup$TCMGeneDIT_RDF_Dataset_r2.tar.gz|The new release of RDF dump of the TCMGeneDIT Database]]
* [[VirtuosoUniversalServer|OpenLink Virtuoso]] - Quad Store and Linked Data Deployment
* [http://lod.openlinksw.com/fct/facet.vsp Live Virtuoso Instance] - [[NeuroCommons]], [[Bio2Rdf]], Uniprot, Yago, and other data sets from the Linked Data Cloud (note: [http://lod.openlinksw.com/sparql Live SPARQL endpoint])
* [http://www.iscb.org/cms_addon/conferences/cshals2009/ C-SHALS 2009]
* [http://www.cs.manchester.ac.uk/DILS09/ DILS 2009]
* [[Media:HCLSIG_BioRDF_Subgroup$biordf_f2f_2009.pdf|BioRDF update F2F 2009]]
* [[Media:HCLSIG_BioRDF_Subgroup$biordf_f2f_breakout_2009.pdf|BioRDF breakout session F2F 2009]]
=== Old Archives ===
* [[HCLSIG/LODD]]
* [[HCLSIG BioRDF Subgroup]]

Categories: [[Category:Hclsig]]

HCLSIG

Ewilligh — Tue, 01 May 2012 16:10:18 GMT

Ewilligh: Added frequency.

__NOTOC__
== Semantic Web for Health Care and Life Sciences Interest Group ==

[[#groups|Groups]] | [[#who|Participants]] | [[#deliverables|Deliverables]] | [[#outreach|Outreach]]

----

This is the public wiki for the Semantic Web for Health Care and Life Sciences Interest Group (HCLSIG).
 See the [http://www.w3.org/2001/sw/hcls/ W3C Web site for the HCLSIG] for more information.

=== Groups ===

Groups meet via regularly scheduled [http://esw.w3.org/topic/HTML/Teleconferences conference calls]. Below are a list of the groups and their meeting schedules. A [http://www.google.com/calendar/embed?src=w3.hcls%40gmail.com HCLS Google calendar] is also available.

'''HCLSIG'''
 ''New developments and fostering interaction with experts worldwide.''
 1st Tuesday of the month at 11am EST. Next call [[/Meetings/2012-04-03_Conference_Call|May 1, 2012]].
 
 
'''Life Sciences'''
 ''Maximizing the utility of linked life science data, ontologies and services.''
 2nd Tuesday at 11am EST. Next call [[/Meetings/2012-05-08_Conference_Call|May 8, 2012]].
* [[/LLD|Linked Life Data]]: ''Best practices in creating, publishing, linking, querying and visualizing linked life data''. Weekly, Tuesday at 12pm EST.
* [[/SWANSIOC|Scientific Discourse]] ''Digital scientific communication and web-based research collaboratories''. Weekly, Monday at 10am EST.
 
'''Pharmaceutical and Clinical Research'''
 ''Enabling drug discovery, drug development and clinical research''.
 3rd Tuesday at 11am EST. Next call : [[/Meetings/2012-02-21_Conference_Call|Feb 21, 2012]]
* [[/SysBio|Systems Biology for Drug Discovery]]. Building and mining protein-drug networks for targets. Wednesday 11am EST.
* [[/Pharmacogenomics|Pharmacogenomics for Clinical Research]]. Building and mining pharmacogenomic data for drug-gene-disease associations. 1st and 3rd Thursday at 11am.
 
'''Health Care'''
 ''Clinical standards, electronic health records, clinical decision support, patient care, health economics, health policy''.
 4th Tuesday at 11am EST - next call : [[/Meetings/2012-02-28_Conference_Call|Feb 28, 2012]]
* [[/Terminology|Clinical Terminology]]. Friday 11am.
* [[/CDS|Clinical Decision Support]]. 2nd and 4th Thursday 10am EST.
* [[/CDI|Clinical Data Interoperability]].



=== Participants ===
* [[Introductions|Introductions 2008-2011]]
* [[SemanticWebForLifeSciencesPeople|Introductions 2005-2008]]


=== Deliverables ===
* [[/Project Ideas|Ideas]]
* [[PotentialDataSources|Potential data sources]]
* [[/UseCases|Use cases]]
* [[/Tools|Tools and Resources]]


=== Outreach ===
* [[/Presentation_Archive|Presentations]]
* [[/Conferences|Conferences]]
* [[/Media|Media]]
* [[/Recruitment|Recruitment]]
* [[/StandardsOrganizations|Standards Organizations]]
* [http://esw.w3.org/topic/HCLSIG/Authorship Authorship Guidelines]

=== Organization ===
The HCLS is divided into three broad areas: Life Sciences, Pharmaceutical and Clinical Research, Health Care.
Within each group are several task forces which focus on particular tasks.
These task forces usualy have a regular meeting time and organizer.
Please try to keep the [http://www.google.com/calendar/embed?src=w3.hcls%40gmail.com HCLS Google calendar] up to date and send invitations/reminders for task force calls.

* [[/Teleconference_Invitation|template for telecon invitation]]

If you have any questions about the group, please email the co-chairs (Michel Dumontier, Vijay Bulusu and Charlie Mead) and W3C Staff Contact (Eric Prud'hommeaux) at team-hcls-chairs@w3.org

----
[[Category:Hclsig]]

HCLSIG/LLD

Ewilligh — Mon, 23 Apr 2012 15:31:43 GMT

Ewilligh: /* Participants */

__NOTOC__
== Linked Life Data ==
''Best practices in creating, publishing, linking, querying and visualizing linked life data''

With the advent of high-throughput experimentation, there has been an explosion of biomedical data on the Internet. While most of the data is available in Web accessible formats (e.g. HTML), many biomedical researchers rely on the use of Web browsers (e.g., Firefox and Internet Explorer) and search engines like Google to browse and search data on the Internet. Such manual browsing and keyword searching approaches are inadequate for large-scale integration of data on the Web. The Semantic Web transforms the Web into a global database or knowledge base that can be accessed by computer programs/agents through a standard data/ontology format. The Resource Description Framework (RDF) and the Web Ontology Language (OWL) are the W3C standards for encoding data/knowledge. This task group explores how to use RDF and OWL (as well as their enabling technologies) to better enable the computer to represent, identify, publish, query and integrate data/knowledge in the health care and life science domain.

=== Coordinator ===
The task coordinator is [[MScottMarshall]] (marshall@science.uva.nl)

=== Objectives ===

* Create a network of linked life data.
* Develop methods to keep resources up to date.
* Develop human-friendly user interfaces
* Produce how-to W3C notes

===Products===
Currently there are two HCLS KBs: [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/DERI_HCLS_KB HCLS KB hosted by DERI] and [http://www.corporate-semantic-web.de/hcls.html HCLS KB hosted by Free University Berlin].

===Publications===

Helena Deus, Jun Zhao, Satya Sahoo, Matthias Samwald, Eric Prud'hommeaux, Michael Miller, M.Scott Marshall and Kei-Hoi Cheung. Provenance of Microarray Experiments for a Better Understanding of Experiment Results ([http://wiki.knoesis.org/index.php/SWPM-2010 SWPM2010 Workshop wiki page], [http://people.csail.mit.edu/pcm/tempISWC/workshops/SWPM2010/InvitedPaper_6.pdf pdf])

Cheung KH, Frost HR, Marshall MS, Prud'hommeaux E, Samwald M, Zhao J, Paschke A. (2009). A Journey to Semantic Web Query Federation in Life Sciences. BMC Bioinformatics, 10(Suppl 10):S10.

Zhao J, Jentzsch A, Samwald M, Cheung KH. Linked Data for Connnecting Traditional Chinese Medicine and Western Medicine. Data Integration in the Life Sciences Workshops ([http://www.cs.manchester.ac.uk/DILS09/ DILS 09]), University of Manchester, UK ([http://www.cs.manchester.ac.uk/DILS09/PosterDemoProceedings.pdf poster presentation]) -- this work is in collaboration with the LoDD task force.

=== Meetings ===
* [http://www.w3.org/wiki/HCLSIG_BioRDF_Subgroup/Meetings/2011/09-26_Conference_Call Next Meeting September 26, 2011]
* [[/Meetings|Past Meetings]]

=== Current Tasks ===
* Query Federation
** [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation Use case 1 -- receptors]
** [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2 Use case 2 -- microarrays]
** [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/MinimalInformationAboutAGraph Minimal Information About a Graph (MIAG)]
* [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/aTags BioSIOC / aTags]
* [http://esw.w3.org/topic/Data/TCMGeneDIT Linking TCM with LoDD Datasets]
* [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/MicroarrayExperimentContext Provenance]
* [[/DeepCapture|Deep Knowledge Representation Challenge]]

=== Participants ===
* Kei Cheung (Yale University)
* Matthias Samwald (Medical University of Vienna)
* Rob Frost (Vector C)
* Adrian Paschke (Freie Universitat Berlin)
* Eric Prud'hommeaux (W3C)
* Don Doherty (Brainstage)
* Susie Stephens (Johnson & Johnson Pharmaceutical Research & Development)
* Scott Marshall (University of Amsterdam)
* TN Bhat (NIST)
* Huajun Chen (Zhejiang University)
* Jun Zhao (Oxford University)
* [[KingsleyIdehen|Kingsley Idehen]] ([[OpenLinkSoftware|OpenLink Software]])
* Helena Deus (University of Texas)
* Satya Sahoo (Wright State University)
* Egon Willighagen (Maastricht University)

We welcome new participants.

=== Resources/References ===
* [http://www.eswc2008.org/final-pdfs-for-web-site/qpII-1.pdf SemWIQ]
* [http://www.eswc2008.org/final-pdfs-for-web-site/qpII-2.pdf Querying Distributed RDF Data Sources with SPARQL]
* [http://agraph.franz.com/support/documentation/current/agraph-introduction.html#intro-federation AllegroGraph documentation]
* [http://darq.sourceforge.net/ DARQ]
* [http://www.faviki.com/ Faviki]
* [http://www.corporate-semantic-web.de/tl_files/pub/RuleResponder_HCLS_eScience.pdf SPARQL Service Bus middleware]
* [http://users.ox.ac.uk/~zool0770/presentations/HCLS-BioRDF-Feb-09.pdf Vocabulary of Interlinked Dataset]
* [[Media:HCLSIG_BioRDF_Subgroup$TCMGeneDIT_RDF_Dataset_r1.zip|The RDF dump of the TCMGeneDIT Database]]
* [[Media:HCLSIG_BioRDF_Subgroup$TCMGeneDIT_RDF_Dataset_r2.tar.gz|The new release of RDF dump of the TCMGeneDIT Database]]
* [[VirtuosoUniversalServer|OpenLink Virtuoso]] - Quad Store and Linked Data Deployment
* [http://lod.openlinksw.com/fct/facet.vsp Live Virtuoso Instance] - [[NeuroCommons]], [[Bio2Rdf]], Uniprot, Yago, and other data sets from the Linked Data Cloud (note: [http://lod.openlinksw.com/sparql Live SPARQL endpoint])
* [http://www.iscb.org/cms_addon/conferences/cshals2009/ C-SHALS 2009]
* [http://www.cs.manchester.ac.uk/DILS09/ DILS 2009]
* [[Media:HCLSIG_BioRDF_Subgroup$biordf_f2f_2009.pdf|BioRDF update F2F 2009]]
* [[Media:HCLSIG_BioRDF_Subgroup$biordf_f2f_breakout_2009.pdf|BioRDF breakout session F2F 2009]]
=== Old Archives ===
* [[/BioRDF archive]]

Categories: [[Category:Hclsig]]

HCLSIG/Products

Ewilligh — Tue, 14 Jun 2011 19:11:28 GMT

Ewilligh: /* HCLS Documents */

== Semantic Web for Health Care and Life Sciences Interest Group ==

[[HCLSIG|Home]] | [[#outreachs|Outreach]] | [[#docs|Documents]] | [[#demos|Demonstrations]] | [[HCLSIG/Products/TranslationalMedicine|Translational Medicine perspective]]

----

This list of HCLSIG products serves as an index for the community and attests to the productivity and impact of the group.
Presentations are on their [[../Presentation_Archive|own page]].

 

=== Summary of Deliverables ===
We would like to acknowledge the health care and life sciences community for meeting the [http://www.w3.org/2008/05/HCLSIGCharter#deliverables goals of the last charter].
Over the course of the charter, the IG has developed a set of data and demonstrators enabling life science and health care practitioners to consume and reason over domain data.
Here are some highlights:

* Linked Open Drug Data (LODD) and winning the iTriplification Challenge 2009
* Light-weight CDISC – HL7 bridge for patient eligibility studies
* SPARQL Federation and RDF to SQL through SWObjects
* Semantic integration of LODD, patient data via the Translational Medicine Ontology (TMO)
* non-proliferation of ontologies and interoperability with other standards and conventions
* HCLS Knowledge Base

More follow in the sections below.

 


=== Recent/Upcoming Outreach Activities ===
* [http://www.ebi.ac.uk/industry/Workshops/previous-workshops.html EBI Semantic Web Industry Workshop] HCLS sent three speakers May 16 - 18, 2011
* [http://www.prismforum.org/ PRISME meeting] M. Scott Marshall invited to present W3C perspective, Wellcome Trust, Hinxton, UK May 2011
* [http://s-web.sfc.keio.ac.jp/conference2011/ Japanese Semantic Web conference] M. Scott Marshall gave HCLS Keynote at March 2011
* [http://www.b2pm.org/B2PM_Conference/Agenda.html Best Practices in Personalized Medicine Workshop] HCLS Presentation, March 2011
* [http://www.vanbug.org/calendar/ Vancouver Bioinformatics Users Group] M. Scott Marshall, HCLS presentation, March 2011
* [http://www.iscb.org/cshals2011-program C-SHALS 2011] HCLS members gave tutorials and presentations
* [http://www.swat4ls.org/2010/index.php Semantic Web Applications and Tools for the Life Sciences (SWAT4LS) in Berlin Dec 2010]
* [http://www.pharmatechnology-summit.com/ Pharmaceutical Technology IT Summit] M. Scott Marshall invited speaker, London, Sept 2010
* [http://semtech2010.semanticuniverse.com/sessionPop.cfm?confid=42&proposalid=3271 Semantic Technology Conference] M. Scott Marshall co-organized HCLS session with Christine Golbreich June 2010
* [http://esw.w3.org/topic/HCLS/WWW2010/Workshop The Future of the Web for Collaborative Science 2010]
* [http://esw.w3.org/topic/HCLS/CSHALS2010/Tutorial HCLS Tutorial at CSHALS 2010]
* [[../Archive|Meeting Archive]]

 


=== HCLS Documents ===
* [http://www.w3.org/2001/sw/hcls/notes/orb/ Ontology of Rhetorical Blocks (ORB)] W3C Note 2011
* [http://www.jbiomedsem.com/content/2/S2/S1/ The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside]
* [http://www.jcheminf.com/content/3/1/19 Linked open drug data for pharmaceutical research and development] Journal of Cheminformatics Thematic Series around the "ACS RDF 2010" meeting 2011
* [http://precedings.nature.com/documents/5538/ Tutorial: Query Federation with SWObjects at SWAT4LS 2010]
* [http://people.csail.mit.edu/pcm/tempISWC/workshops/SWPM2010/InvitedPaper_6.pdf Provenance of Microarray Experiments for a Better Understanding of Experiment Results]
* [http://www.w3.org/TR/hcls-swan/ Semantic Web Applications in Neuromedicine (SWAN) Ontology] - W3C Note 2009
* [http://www.w3.org/TR/hcls-sioc/ SIOC, SIOC Types and Health Care and Life Sciences] - W3C Note 2009
* [http://www.w3.org/TR/hcls-swansioc/ SWAN/SIOC: Alignment Between the SWAN and SIOC Ontologies] - W3C Note 2009
* [http://www.biomedcentral.com/1471-2105/10/S10/S10 A journey to Semantic Web query federation in the life sciences] - BMC Bioinformatics Special Issue: "Semantic Web Applications and Tools for Life Sciences" 2009
* [[Media:HCLSIG$2009%20Triplification%20Challenge%20-%20LODD.pdf|Linking Open Drug Data]] - iTriplification Challenge 2009
* [[Media:HCLSIG$dils09poster|Linked Data for Connecting Traditional Chinese Medicine and Western Medicine]] - Abstract for poster at DILS 2009
* [[Media:HCLSIG$PharmaOntology_ICBO_09.pdf|Pharma Ontology: Creating a Patient-centric Ontology for Translational Medicine]] - Abstract for poster at ICBO 2009
* [[Media:HCLSIG$Final_ldow2009.pdf|Enabling Tailored Therapeutics with Linked Data]] - LDOW Workshop, WWW 2009
* [http://www.w3.org/TR/2008/NOTE-hcls-kb-20080604/ A Prototype Knowledge Base for the Life Sciences] - W3C Note 2008
* [http://www.w3.org/TR/2008/NOTE-hcls-senselab-20080604/ Experiences with the Conversion of SenseLab Databases to RDF/OWL] - W3C Note 2008

 


=== HCLS Demonstrations ===
* [http://purl.org/net/biordfmicroarray/demo BioRDF Microarray RDF Demo]
* [http://hcls.deri.org/coi/demo/ Clinical Observations Interoperability Demonstration]
* [http://www.w3.org/2009/08/7tmdemo 7 Translational Membrane federated query]
* [http://hcls.deri.org/hcls_demo.html HCLS Knowledge Base]

HCLSIG/LODD/Data

Ewilligh — Thu, 02 Dec 2010 13:21:53 GMT

Ewilligh: Added some more details on the data sets.

__NOTOC__
=== LODD-related datasets that the LODD group already made available as Linked Data ===

{| border="1" cellpadding="2" cellspacing="0"
| '''Name'''
| '''Topic'''
| '''Short Description'''
| '''Size'''
| '''Status/ Activity'''
| '''Example Instances'''
| '''SPARQL Endpoint'''
|-
| [http://www4.wiwiss.fu-berlin.de/drugbank/ DrugBank]
| Drugs
| [http://www.drugbank.ca/ Drugbank.ca] provides drug (i.e., chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e., sequence, structure, and pathway) information ({{doi|10.1093/nar/gkj067}})
| 766,920 triples; 4,800 drugs, 2,500 protein sequences
| updated regularly
| Varenicline [http://beckr.org/marbles?uri=http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugs/DB01273 via Marbles], [http://demo.openlinksw.com/ode/?uri=http%3A%2F%2Fwww4.wiwiss.fu-berlin.de%2Fdrugbank%2Fresource%2Fdrugs%2FDB01273 via OpenLink Data Explorer]
| http://www4.wiwiss.fu-berlin.de/drugbank/sparql
|-
| [http://linkedct.org/ LinkedCT]
| Clinical Trials
| Linked data source of trials from [http://clinicaltrials.gov ClinicalTrials.gov]
| 7 million triples, 62000 trials
| preview release
| [http://data.linkedct.org/resource/intervention/7322 Influenza] (Intervention), A [http://data.linkedct.org/resource/trials/NCT00001872 Trial], [http://data.linkedct.org/resource/condition/52 AIDS] (condition), A [http://data.linkedct.org/resource/reference/12201 reference], A [http://data.linkedct.org/resource/location/162398 location]
| http://data.linkedct.org/sparql
|-
| [http://www4.wiwiss.fu-berlin.de/dailymed/ DailyMed]
| Drugs
| [http://dailymed.nlm.nih.gov/dailymed/about.cfm dailymed.nlm.nih.gov] provides information about approved prescription drugs, includes FDA approved labels (package inserts)
| 164,276 triples; 4,039 drugs
| updated regularly
| "Sterile Water (Irrigant)" [http://beckr.org/marbles?uri=http://www4.wiwiss.fu-berlin.de/dailymed/resource/drugs/492 via Marbles], [http://demo.openlinksw.com/ode/?uri=http%3A%2F%2Fwww4.wiwiss.fu-berlin.de%2Fdailymed%2Fresource%2Fdrugs%2F492 via OpenLink Data Explorer]
| http://www4.wiwiss.fu-berlin.de/dailymed/sparql
|-
| [http://dbpedia.org/About DBpedia]
| Drugs/ Diseases/ Proteins
| RDF data about 2.49 million things that has been extracted from Wikipedia
| 218 million RDF triples; 2,300 drugs, 2,200 proteins
| updated every 3 months
| [http://dbpedia.org/resource/Aspirin Aspirin], [http://dbpedia.org/resource/HIV HIV]
| http://dbpedia.org/sparql
|-
| [http://www4.wiwiss.fu-berlin.de/diseasome/ Diseasome]
| Diseases / Genes
| [http://www.nd.edu/~alb/Publication06/145-HumanDisease_PNAS-14My07-Proc/Suppl/ Diseasome] describes characteristics of disorders and disease genes linked by known disorder–gene associations
| 91,182 triples; 2,600 genes
| updated 2006
| Alzheimer's [http://beckr.org/marbles?uri=http://www4.wiwiss.fu-berlin.de/diseasome/resource/diseases/74 via Marbles], [http://demo.openlinksw.com/ode/?uri=http%3A%2F%2Fwww4.wiwiss.fu-berlin.de%2Fdiseasome%2Fresource%2Fdiseases%2F74 via OpenLink Data Explorer]
| http://www4.wiwiss.fu-berlin.de/diseasome/sparql
|-
| [http://code.google.com/p/junsbriefcase/wiki/TGDdataset RDF-TCM]
| Genes / Diseases / Medicine / Ingredients
| Traditional Chinese medicine, gene and disease association dataset and a linkset mapping TCM gene symbols to Extrez Gene IDs created by Neurocommons
| 117,643
| updated August 2009 (stable)
| [http://purl.org/net/tcm/tcm.lifescience.ntu.edu.tw/id/medicine/Ginkgo_biloba Ginkgo biloba]
| http://hcls.deri.org/sparql; graph name: http://hcls.deri.org/resource/graph/tcm
|-
| [http://www.nlm.nih.gov/research/umls/rxnorm/ RxNorm]
| Drugs
| A linked version of the NLM's RxNorm database that connects prescription drugs, ingredients, and NDC through RXCUI a concept unique identifier. RxNorm is a product developed by NIH’s National Library of Medicine. It currently interlinks 12 different drug vocabularies around a unique concept identifier. Due to licensing only six of the drug vocabularies are made available as part of the LODD cloud. This includes: Medical Subject Headings,, Metathesaurus FDA National Drug Code Directory, Metathesaurus FDA Structured Product Labels, National Drug File, RxNorm Vocabulary, Veterans Health Administration National Drug File
Links are provided connecting RxNorm to drug bank and to the UMLS.
|over 7.7 million triples; 165,806 RXCUI (Concept Unique Identifiers) Unique drugs and ingredients; 332,754 RXAUI (Atomic Unique Identifiers) sourced terms
| Based on 3/2010 Rxnorm Release; Last updated 5/2010
| [http://link.informatics.stonybrook.edu/rxnorm/RXAUI/2994963 Singulair from the Metathesaurus FDA Structured Product Labels]
| http://link.informatics.stonybrook.edu/sparql/
|-
| [http://www4.wiwiss.fu-berlin.de/sider/ SIDER]
| Diseases / Side Effects
| [http://sideeffects.embl.de/ SIDER] contains information on marketed drugs and their adverse effects ({{doi|10.1038/msb.2009.98}})
| 192,515 triples; 1,737 genes
| updated 2009
| Confusion [http://beckr.org/marbles?uri=http://www4.wiwiss.fu-berlin.de/sider/resource/side_effects/C0009676 via Marbles]
| http://www4.wiwiss.fu-berlin.de/sider/sparql
|-
| [http://www4.wiwiss.fu-berlin.de/stitch/ STITCH]
| Chemicals / Proteins
| [http://stitch.embl.de/ STITCH] contains information on chemicals, proteins, and their interactions ({{doi|10.1093/nar/gkm795}})
| 7,500,000 chemicals; 500,000 proteins; 370 organisms
| updated July 2009
| Lactose [http://beckr.org/marbles?uri=http://www4.wiwiss.fu-berlin.de/stitch/resource/chemicals/CID000000294 via Marbles]
| http://www4.wiwiss.fu-berlin.de/stitch/sparql
|-
| [http://www4.wiwiss.fu-berlin.de/medicare/ Medicare]
| Medicare Formulary
| xxx
| xxx
| xxx
| xxx
| http://www4.wiwiss.fu-berlin.de/medicare/sparql
|-
| [http://www.ebi.ac.uk/chembl/ ChEMBL]
| Chemical / Assays (Proteins, Organisms) / Papers
| [http://www.ebi.ac.uk/chembl/ ChEMBL]] contains information on trial drugs with information about activity against targets like but not limited to proteins. All is backed up by and linked to literature. Includes links to Bio2RDF for ChEBI and Uniprot. License: CC-BY-SA.
| ~24M triples
| Updated 2010-01
| A [http://rdf.farmbio.uu.se/chembl/snorql/?describe=http://rdf.farmbio.uu.se/chembl/activity/a2642163 IC50 activity].
| http://rdf.farmbio.uu.se/chembl/sparql
|-
| [http://www.who.int/gho/en/index.html WHO Global Health Observatory]
| Infectious Diseases /Demography / Socioeconomic Conditions / Environmental Factors
| Data and statistics for infectious diseases at country, regional, and global levels
| 354300
| Updated 2010-09
| xxx
| http://aksw.org/Projects/GHO2SCOVO?v=wmb
|}

http://www4.wiwiss.fu-berlin.de/lodd/lodd-datasets_2009-08-06.png

This figure shows the incorporation of LinkedCT, [[DailyMed]], [[DrugBank]], Diseasome, RDF-TCM, and SIDER into the Linked Data cloud. These data sets are represented in dark gray, while light gray represents other Linked Data from the life sciences, and white indicates interlinked datasets covering geographic, person-related and conceptual data.
More on the interlinking methodology and statistics can be found on the [[../Interlinking|Interlinking]] page.

The LODD datasets have been crawled by the SWSE Semantic Web search engine and can be accessed via a faceted browsing interface at [http://visinav.deri.org/hcls/] ([http://visinav.deri.org/hcls/list?keyword=varenicline Example query: Varenicline]).

Most of the LODD datasets have also been integrated into the SPARQL endpoint of the HCLS Knowledge Base, see [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/DERI_HCLS_KB the wiki page of the HCLS KB] for further information.

=== Bio2RDF Data Sets ===

The [http://bio2rdf.org/ Bio2RDF project] has published 40 biology-, gene- and medical-related datasets (altogether 2.3 billion triples).
The datasets are available via SPARQL endpoints and as Linked Data. It is recommended that you use the [http://sourceforge.net/project/platformdownload.php?group_id=142631 Bio2RDF Java Servlet], and optionally [http://quebec.bio2rdf.org/download/virtuoso/indexed/ download the databases] for efficient personal use. Running your own instance of the [http://virtuoso.openlinksw.com/wiki/main/Main/VirtEC2AMIBio2rdfInstall OpenLink Virtuoso AMI for EC2] is also an option (and for basic URI resolution doesn't require the Java Servlet, although if you want advanced queries you should still download it and configure it to query your EC2 sparql endpoint).

* [http://www.freebase.com/view/user/bio2rdf/public/sparql Bio2RDF sparql endpoint list] [http://rdf.freebase.com/rdf/user/bio2rdf/public/sparql Sparql endpoint list in RDF]
* [http://linkeddata.openlinksw.com:8891/pubmed:10500064 Identification of an autoimmune enteropathy-related 75-kilodalton antigen], via an [[OpenLinkSoftware|OpenLink]] hosted edition of [[Bio2Rdf]]
* [http://linkeddata.openlinksw.com:8891/pubmed:9636670 Structure of the gene encoding the human cyclin-dependent kinase inhibitor p18 and mutational analysis in breast cancer], via an [[OpenLinkSoftware|OpenLink]] hosted edition of [[Bio2Rdf]]
* [http://beckr.org/marbles?uri=http%3A%2F%2Fbio2rdf.org%2Fpubmed%3A9626117 PubMed article] viewed using the Marbles Linked Data browser.
* [http://beckr.org/marbles?lang=en&uri=http%3A%2F%2Fbio2rdf.org%2Ffoaf%3AClemens%2C_T_L PubMed author] viewed using the Marbles Linked Data browser.
* [http://beckr.org/marbles?uri=http%3A%2F%2Fbio2rdf.org%2Fomim%3A161555 OMIM Killer Cell Lectin-Like Receptor] viewed using the Marbles Linked Data browser.
* [http://iws.seu.edu.cn/services/falcons/objectsearch/queryresult.jsp?query=%22KILLER+CELL%22 Falcons Search for KILLER CELL]. The Bio2RDF data has been crawled by the Falcons Semantic Web Search engine. This is an example on how the data is accessed by humans using the search engine. Falcons also offers an API that can by used by applications to access the data.

=== Chem2bio2RDF ===

* Information about the [http://chem2bio2rdf.org/ chem2bio2rdf] data sets

=== Data Sets for the LODD Task ===

To complement the drug-related Web of Data build by the LODD effort, the following data sets could/should also be published as Linked Data.

The LODD effort is currently gathering more information about relevant datasets. See also [[/DataSetEvaluation|Evaluation of LODD Data Sets]] for current evaluation results.

* [http://library.dialog.com/bluesheets/html/bl0107.html Adis R&D Insight]
* [http://www.ebi.ac.uk/chebi/ chEBI]
* [http://xpdb.nist.gov/pdb/chemblast.html ChemBlast]
* [http://www.chemspider.com/ ChemSpider]
* [http://ClinicalTrials.gov ClinicalTrials.gov]
* [http://www.citeline.com/trialtrove.html Citeline TrialTrove]
* [http://dailymed.nlm.nih.gov/dailymed/about.cfm DailyMed]
* [http://dbpedia.org/About DBpedia]
* [http://www.nd.edu/~alb/Publication06/145-HumanDisease_PNAS-14My07-Proc/Suppl/ Diseasome]
* [http://www.drugbank.ca/ Drug Bank]
* [http://www.virtualref.com/abs/72.htm DrugDB]
* [http://www.ncbi.nlm.nih.gov/pubmed/17921997 Drugome]
* [http://lsdis.cs.uga.edu/projects/asdoc/ Drug Ontology]
* [http://scientific.thomsonreuters.com/products/iddb/ Investigational Drug Database] - Proprietary
* [http://www.ovid.com/site/catalog/DataBase/1244.jsp?top=2&mid=3&bottom=7&subsection=10 IMS]
* [http://www.genome.jp/kegg/drug/ KEGG Drug]
* [http://Lillytrials.com LillyTrials]
* [http://www.fda.gov/medwatch/ MedWatch]
* [http://www.fda.gov/cder/ndc/ National Drug Code]
* [http://www.ncbi.nlm.nih.gov/omim/ OMIM]
* [http://www.fda.gov/cder/ob/ Orange Book]
* [http://www.pharmaprojects.com/ Pharmaprojects] - Proprietary
* [http://pubchem.ncbi.nlm.nih.gov/ PubChem]
* [http://www.nlm.nih.gov/research/umls/rxnorm/ RxNorm]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=15360858 VA NDF-RT]
* Other data sources could include blogs, discussion boards, wikis, etc.
* and....
** [http://www.who.int/globalatlas/ World Health Organization's Global Health Atlas]
** [http://www.epispider.org/ EpiSPIDER]
** [http://www.accessdata.fda.gov/Scripts/cder/DrugsatFDA/ Drugs@FDA - FDA Approved Drug Products]
** [http://www.drugdigest.org/wps/portal/ddigest DrugDigest]
** [http://humancyc.org/ HumanCyc: Encyclopedia of ''Homo sapiens'' Genes and Metabolism]
** [http://www.alzforum.org/ Alzheimer Research Forum]
** [http://wwwcf.nlm.nih.gov/umlslicense/rxtermApp/rxTerm.cfm RxTerms]
** [http://hudine.neu.edu/ HuDiNe]
** [http://wiki.medpedia.com/Cymbalta Medpedia]
** [http://tcm.lifescience.ntu.edu.tw/ TCMGeneDIT] and [[Media:HCLSIG$$LODD$$Data$TCMGeneDIT_RDF_Dataset_r1.zip|RDF dump]]
** [http://www.tuftsctsi.org/~/media/Files/CTSI/Library%20Files/FCC%20for%20CER%20Rpt%20to%20Pres%20and%20Congress_063009.ashx List of other possible data sources from page 66 onwards]

=== Alternative Herbal Medicine use case ===
* [[Data/TCMGeneDIT|TCMGeneDIT dataset]]

=== Identified Based Linkage Points ===

* INCHIs
* [[PubChem]] Compound ID (CID)
* [[PubChem]] NSC
* Chemical Abstract ID (CAS)
* New Drug Application (NDA)

=== Data Set Attributes ===

* Licensing
* Data Format
* Identifiers

Digital object identifier

Ewilligh — Thu, 02 Dec 2010 13:17:20 GMT

Ewilligh: Created page with "A [http://en.wikipedia.org/wiki/Digital_object_identifier Digital Object Identifier] is a unique identifier used by many publishers to label articles, papers, etc."

A [http://en.wikipedia.org/wiki/Digital_object_identifier Digital Object Identifier] is a unique identifier used by many publishers to label articles, papers, etc.

Template:Doi

Ewilligh — Thu, 02 Dec 2010 13:16:31 GMT

Ewilligh: Undo revision 46450 by Ewilligh (Talk)

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Ewilligh — Thu, 02 Dec 2010 13:16:01 GMT

Ewilligh:

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Ewilligh:

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User:Ewilligh

Ewilligh — Thu, 02 Dec 2010 13:12:54 GMT

Ewilligh: Created page with "Egon Willighagen {{doi|10.1016/j.coi.2004.08.001}}"

Egon Willighagen

{{doi|10.1016/j.coi.2004.08.001}}

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TaskForces/CommunityProjects/LinkingOpenData/DataLicensing

Ewilligh — Sun, 19 Sep 2010 10:53:06 GMT

Ewilligh: /* People Interested in the Area */

__NOTOC__
== Linking Open Data Community Effort ==

= Data Licensing =

In order to enable people to use the data that you are publishing on the Web on a secure legal basis, you need to explicitly state which license applies to your data. If no license is specified, people cannot use your data within any serious applications.

Thus, this page collects information about
* data licenses that you can use for your data.
* best practices on how to annotate your data with licensing meta-information.

The page is part of the community project [[SweoIG/TaskForces/CommunityProjects/LinkingOpenData|SweoIG/TaskForces/CommunityProjects/LinkingOpenData]]

=== Licenses ===

* [http://www.opendatacommons.org/licenses/by/ Open Data Commons Attribution License] Attribution for Data/Databases.
* [http://www.opendatacommons.org/licenses/odbl/ Open Database License (ODbL)] Attribution and Share-Alike for Data/Databases.
* [http://www.opendatacommons.org/licenses/pddl/ Public Domain Dedication and License (PDDL)] The PDDL places the data(base) in the public domain (waiving all rights).
* [http://creativecommons.org/publicdomain/zero/1.0/ Creative Commons CC0 1.0 Universal] Waiver for placing the data(base) in the public domain (waiving all rights). Please note that other Creative Commons licenses should not be used for data as data is not considered creative works in many legal frameworks.

=== Best practices for annotating data with licensing information ===

* [http://www.talis.com/nodalities/pdf/nodalities_issue9.pdf Applying Licenses and Waivers to Linked Data]. Article by Tom Heath in Nodalities, Issue 10, 2009.
* [http://www4.wiwiss.fu-berlin.de/bizer/pub/LinkedDataTutorial/#deref How to publish Linked Data Tutorial] Section: What should I return as RDF description for a URI?

=== Websites about Data Licensing ===

* [http://www.opendatacommons.org/ OpenDataCommons]

=== Papers and articles about Data Licensing ===

* Open Knowledge Foundation: [http://www.opendefinition.org/guide/data/ Guide to Open Data Licensing]
* Paul Miller, Rob Styles, Tom Heath: [http://data.semanticweb.org/workshop/LDOW/2008/paper/8 Open Data Commons, a license for open data], LDOW workshop 2008.
* Kaitlin Thaney: [http://blogs.talis.com/nodalities/2010/02/sharing-data-on-the-web.php Sharing Data on the Web]

=== People Interested in the Area ===

* Tom Heath
* Chris Bizer
* Egon Willighagen

EgonWillighagen

Ewilligh — Sat, 21 Aug 2010 19:22:03 GMT

Ewilligh:

__NOTOC__


== Egon Willighagen ==

* Homepage: http://egonw.github.com/ (XHTML+RDFa, with FOAF and more)
* Blog: http://chem-bla-ics.blogspot.com/
* Email: [[MailTo(egon DOT willighagen AT gmail SPAMFREE DOT com)]]

Participates in [[../HCLSIG/LODD|LODD]].

----
[[Category:Homepage]]

HCLSIG/LODD/Meetings/2010-06-23 Conference Call

Ewilligh — Wed, 23 Jun 2010 15:53:22 GMT

Ewilligh: /* Minutes */

== Conference Details ==
* Date of Call: Wednesday June 23, 2010
* Time of Call: 11:00am Eastern Daylight Time (EDT), 16:00 British Summer Time (BST), 17:00 Central European Time (CET)
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Dial-In #: +33.4.89.06.34.99 (Nice, France)
* Dial-In #: +44.117.370.6152 (Bristol, UK)
* Participant Access Code: 4257 ("HCLS").
* IRC Channel: irc.w3.org port 6665 channel #HCLS (see [http://www.w3.org/Project/IRC/ W3C IRC page] for details, or see [http://cgi.w3.org/member-bin/irc/irc.cgi Web IRC])
* Duration: ~1h
* Convener: Susie

== Agenda ==
* Data Interlinking Track, Ontology Alignment Evalutation Initiative Follow Up - Susie
* Other Data updates - Egon, Matthias, Anja, Oktie
* Mapping experimental data - All
* Outreach (TCM, ACS) - All
* AOB

== Minutes ==

[06/23/10 17:09] <rboyce> susie: recap of previous meeting
[06/23/10 17:10] <Susie> [http://www.instancematching.org/oaei/imei2010.html]
[06/23/10 17:10] <rboyce> scribenick: rboyce
[06/23/10 17:10] <Susie> [http://www.scharffe.fr/events/oaei2010/]
[06/23/10 17:11] <rboyce> topic: ontology alignment initiative
[06/23/10 17:11] <rboyce> Francois Scharffe et al have selected LODD nodes of interest
[06/23/10 17:12] <rboyce> from group perspective -- wait for feedback
[06/23/10 17:12] <rboyce> agenda other data updates:
[06/23/10 17:13] <rboyce> rxnorm --
[06/23/10 17:13] <janos> [http://link.informatics.stonybrook.edu/rxnorm/RXAUI/3051391]
[06/23/10 17:14] <rboyce> added ~35K links to dailymed using OWL "same-as"
[06/23/10 17:15] <rboyce> links from drug product in rxnorm to dailymed label
[06/23/10 17:15] <rboyce> why not link to RDF version?
[06/23/10 17:16] <janos> [http://dailymed.nlm.nih.gov/dailymed/lookup.cfm?setid=8c166755-7711-4df9-d689-8836a1a70885]
[06/23/10 17:17] <rboyce> using ID a document ID
[06/23/10 17:17] <rboyce> not present in RDF
[06/23/10 17:18] <rboyce> will this document id change when dailymed labels change?
[06/23/10 17:19] <rboyce> how could we avoid dead links
[06/23/10 17:19] <rboyce> might be able to link on active-moiety or chemical id
[06/23/10 17:20] <Susie> exploring using lodd
[06/23/10 17:20] <Susie> especially dailymed, and to some extent drugbank
[06/23/10 17:20] <Susie> want to pull out labels
[06/23/10 17:20] <Susie> using nlp to see information about pharmacokinetics
[06/23/10 17:21] <Susie> see if other information that supplements the product label
[06/23/10 17:21] <Susie> the poc exposed some issues in those data sources
[06/23/10 17:21] <Susie> been trying to contact Anja
[06/23/10 17:22] * egonw is booting the computer for Skype to call in
[06/23/10 17:23] <rboyce> offering to mirror LODD at U of Pitt
[06/23/10 17:23] <rboyce> maintain DailyMed and DrugBank note
[06/23/10 17:25] <rboyce> todo: Rich -- try to get fixes working with Anja and then discuss how to mirror or maintain nodes
[06/23/10 17:25] <rboyce> would possibly need to get a persistent URL
[06/23/10 17:26] <rboyce> would make sense to generate persistent URLs for new data sources moving forward (where possible)
[06/23/10 17:27] <rboyce> Susie suggests being opportunistic about the use of persistant URLs
[06/23/10 17:27] <rboyce> no other updates
[06/23/10 17:27] <rboyce> agenda item: outreach
[06/23/10 17:27] <rboyce> paper on traditional chinese medicine will be published
[06/23/10 17:28] <rboyce> Egon -- hosting a session on linked data at ACS in the fall (Boston)
[06/23/10 17:28] <rboyce> Eric will present on LODD at same conference
[06/23/10 17:28] <rboyce> agenda item: mapping experimental data to RDF
[06/23/10 17:29] <rboyce> not much progress to date -- is this aligned with interest of group?
[06/23/10 17:30] <rboyce> there is a paper on mapping some experimental data to RDF
[06/23/10 17:30] <rboyce> how about taking that paper and extending it to create some guidelines for W3C?
[06/23/10 17:31] <Susie> [http://esw.w3.org/HCLSIG/LODD/Mapping_Experimental_Data]
[06/23/10 17:32] <rboyce> Rich is interested for drug safety / post-market reasons
[06/23/10 17:33] <rboyce> most agree that the mapping effort would be of interest to several in the group
[06/23/10 17:33] <rboyce> Susie will share copy of the accepted paper with group -- give feedback if we could build on this work.
[06/23/10 17:34] <rboyce> Proposed team goal: commit to reading by next phone call
[06/23/10 17:34] * egonw managed to get skyped in
[06/23/10 17:35] <rboyce> discuss at the next call -- what is useful?
[06/23/10 17:36] <rboyce> Also -- read content of Wiki page ([http://esw.w3.org/HCLSIG/LODD/Mapping_Experimental_Data])
[06/23/10 17:36] <rboyce> Edits -- make directly on the Wiki page -- more controversial issues; please discuss at next meeting.
[06/23/10 17:36] <rboyce> Action 1) Susie will post paper
[06/23/10 17:37] <rboyce> Action 2) group -- read the paper
[06/23/10 17:37] <rboyce> Action 3) assess if the content on the wiki page makes sense and if the components in the paper will address the isseus that have been raised
[06/23/10 17:38] <rboyce> potential grant opportunities?
[06/23/10 17:38] <rboyce> Susie - seed grants from pharma
[06/23/10 17:39] <rboyce> now apply more to informatics
[06/23/10 17:41] <rboyce> grant proposals should probably have a strong applications focus
[06/23/10 17:41] <rboyce> Susie will post information on next call