View source for HCLSIG BioRDF Subgroup/DERI HCLS KB

__NOTOC__
= DERI Health Care and Life Science Knowledge Base =


<font color="red">NOTE: THIS KB HAS BEEN DEPRECATED. THE INFORMATION HERE IS FOR HISTORIC PURPOSES. 
You can access the NEW HCLS KB at http://hcls.deri.org:8080/openrdf-sesame/repositories/hclskb
We are no longer keeping this datasets updated but provided a catalogue of all linked life sciences dataset, described using the Vocabulary for Interlinked Dataset (VoiD) at http://hcls.deri.org/RoadMapEvaluation/ and queriable as a SPARQL endpoint at http://hcls.deri.org:8080/openrdf-sesame/repositories/roadmap
</font>


The knowledge base can be accessed through a SPARQL endpoint: '''http://hcls.deri.org/sparql'''
The contents of the knowledge base can also be explored through a faceted searching / browsing interface: '''http://srvgal14.deri.ie:8081/fct/'''

The HCLS Knowledge Base at DERI is a Virtuoso-based triplestore containing information relevant to life science, medicine and health care. It contains RDF/OWL data that was generated by current and previous participants of the [http://www.w3.org/2001/sw/hcls/ W3C Semantic Web for Health Care and Life Science Interest Group]. A major part of the HCLS Knowledge Base is comprised of a mirror of the [http://neurocommons.org/page/RDF_distribution Neurocommons Knowledge Base] maintained by [http://sciencecommons.org Science Commons].

The HCLS Knowledge Base contains over 400 million RDF statements.

If you have suggestions for relevant RDF/OWL data that should be added to the KB, please propose them to the mailing list public-semweb-lifesci@w3.org (requires prior registration).

== How to query named graphs contained in the knowledge base ==

The HCLS Knowledge Base is divided into subsections (named graphs) which are listed below. To query a graph such as '''`http://hcls.deri.org/resource/graph/drugbank`''' you can use a SPARQL query such as

<pre><nowiki> 
SELECT * 
FROM <http://hcls.deri.org/resource/graph/drugbank> 
WHERE {?s ?p ?o} 
LIMIT 20
</nowiki></pre>


or, alternatively:


<pre><nowiki>
SELECT * 
WHERE {
  GRAPH <http://hcls.deri.org/resource/graph/drugbank> 
    {?s ?p ?o} 
}
LIMIT 20
</nowiki></pre>


The latter syntax allows you to direct subqueries to different graphs, for example:


<pre><nowiki>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX go: <http://purl.org/obo/owl/GO#>
PREFIX obo: <http://www.geneontology.org/formats/oboInOwl#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

select  *
where {
  graph <http://purl.org/science/graph/inferred-relations> {
    ?class rdfs:subClassOf go:GO_0008150
  }
  graph <http://purl.org/science/graph/obo/GO> {
    ?class rdfs:label ?name.
    ?class obo:hasDefinition ?def.
    ?def rdfs:label ?definition .
  }
  filter(regex(str(?name),"[Dd]endrite"))
}
</nowiki></pre>


Note that clicking on the URIs of the named graphs will not necessarily lead you anywhere. They are just used inside the triplestore as names for graphs, and might not resolve via HTTP.

Please try to keep the server load of your queries low. This can easily be accomplished by 1) restricting you queries to the named graphs you need, instead of querying the entire triplestore or a multitude of graphs, 2) uinge the LIMIT clause in your queries. 

== Named graphs contained in the HCLS Knowledge Base ==

=== Neurocommons Knowledge Base ===
Named graphs derived from the Neurocommons Knowledge Base are described in more detail on [http://neurocommons.org/page/Bundles the Neurocommons RDF web page]. 

* MeSH polyhierarchy represented using SKOS: '''`http://purl.org/science/graph/mesh/mesh-skos`'''
* MeSH qualified headings - defines one URI for each valid major/minor heading: '''`http://purl.org/science/graph/mesh/qualified-headings`'''	
* Medline / NLM MeSH subject headings for all articles: '''`http://purl.org/science/graph/medline/subject-headings`'''
* Medline /  title and year of publication for each article: '''`http://purl.org/science/graph/medline/titles-years`'''
* All OBO ontologies: There is one named graph for each OBO ontology and they cannot all be listed here for space reasons. The graph names are made up of http://purl.org/science/graph/obo/ concatenated with the acronym of the OBO ontology. For example, the graph name of the Gene Ontology is: '''`http://purl.org/science/graph/obo/GO`'''     	 
* Galen ontology: '''`http://purl.org/science/graph/galen`'''
* W3C SKOS (Simple Knowledge Organization System) ontology: '''`http://purl.org/science/graph/skos`'''
* Supporting ontology for conversion of MeSH polyhierarchy to RDF: '''`http://purl.org/science/graph/mesh-eswc06`'''
* Ad hoc Science Commons ontology: '''`http://purl.org/science/graph/sciencecommons`'''
* BAMS (Brain Architecture Management System): '''`http://purl.org/science/graph/bams`'''
* Senselab: '''`http://purl.org/science/graph/senselab`'''
* PDSP Ki database of ligand-receptor interactions: '''`http://purl.org/science/graph/pdspki`'''
* NCI thesaurus: '''`http://purl.org/science/graph/nci-thesaurus`'''
* NCBI Gene Ontology annotations: '''`http://purl.org/science/graph/ncbi/goa`'''
* NCBI Homologene selection: '''`http://purl.org/science/graph/ncbi/homologene`'''
* NCBI Gene gene synonyms extraction: '''`http://purl.org/science/graph/ncbi/gene-info`'''
* Links from NCBI Gene to Medline: '''`http://purl.org/science/graph/ncbi/gene-pubmed`'''
* Addgene plasmid catalog: '''`http://purl.org/science/graph/addgene`'''
* Neurocommons text processing pilot: '''`http://purl.org/science/graph/neurocommons-text`'''
* ABA (Allen Brain Atlas): '''`http://purl.org/science/graph/aba`'''
* Reactome records (direct from RDB): '''`http://purl.org/science/graph/reactome`'''
* Transitive closure of subclass and part_of relations: '''`http://purl.org/science/graph/inferred-relations`'''

=== Linking Open Drug Data and BioRDF ===
Several [http://esw.w3.org/topic/HCLSIG/LODD/Data/ Datasets generated by the Linking Open Drug Data project] and the BioRDF group have been loaded into the knowledge base

* Dailymed: '''`http://hcls.deri.org/resource/graph/dailymed`'''
* [[DrugBank]]: '''`http://hcls.deri.org/resource/graph/drugbank`'''
* [[ClinicalTrials]].gov / LinkedCT: '''`http://hcls.deri.org/resource/graph/linkedct`'''
* Diseasome: '''`http://hcls.deri.org/resource/graph/diseasome`'''
* SIDER: '''`http://hcls.deri.org/resource/graph/sider`'''
* Traditional Chinese Medicine: '''`http://hcls.deri.org/resource/graph/tcm`'''
* Gene lists from the [http://esw.w3.org/HCLSIG_BioRDF_Subgroup/QueryFederation2 BioRDF microarray demo]: '''`http://hcls.deri.org/resource/graph/genelists`'''

=== aTags ===
See the [http://hcls.deri.org/atag/ aTag website] for background information. 

* aTag Pastebin (user-generated aTags): '''`http://hcls.deri.org/atag/data/pastebin.html`''' (triplestore is periodically and automatically updated with RDFa contained in source)
* aTags generated out of conclusion sections from [[PubMed]] abstracts:  '''`http://purl.org/concept/assertion/`''' ([http://precedings.nature.com/documents/3775/version/1 further information])
* SIDER aTags (drug side-effect data from SIDER): '''`http://hcls.deri.org/atag/data/SIDER_atags.html`'''
* aTags about pharmacological effects of plants used in TCM: '''`http://hcls.deri.org/atag/data/tcm_atags.html`'''

=== DBpedia - OBO - MeSH mapping ===
See [http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/DBpedia_to_OBO_mapping DBpedia - OBO mapping task page] for background information.

* DBpedia - OBO mapping based on xrefs contained in the OBO ontologies (a few hundred seeAlso statements): '''`http://samwald.info/res/dbpedia_obo_mapping_based_on_xrefs.ttl`'''
* DBpedia - MeSH mapping based on xrefs in DBpedia (a few hundred seeAlso statements): '''`http://samwald.info/res/dbpedia_mesh_mapping.ttl`'''

=== DBpedia ===
A subset of [http://dbpedia.org DBpedia] is contained within the HCLS Knowledge Base. This subset contains the english labels and short abstracts of all DBpedia entries, as well as the YAGO hierarchy. The rationale for including a subset of DBpedia is that it provides a huge taxonomy of entities that are relevant for the HCLS domain (among many other things).

* DBpedia subset: '''`http://hcls.deri.org/resource/graph/dbpedia`'''

=== List of all graphs ===

Below is a list of all graphs contained in the triplestore, without further description. This includes the graphs detailed above.


<pre><nowiki>
 http://www.openlinksw.com/schemas/virtrdf#
 http://srvgal14.deri.ie:8081/DAV
 http://www.w3.org/2002/07/owl#
 http://purl.org/concept/assertion/
 http://samwald.info/res/dbpedia_mesh_mapping.ttl
 http://hcls.deri.org/resource/graph/dailymed
 http://hcls.deri.org/resource/graph/drugbank
 http://samwald.info/res/dbpedia_obo_mapping_based_on_xrefs.ttl
 http://purl.org/science/graph/inferred-relations
 http://purl.org/science/graph/obo/GO
  http://hcls.deri.org/atag/data/SIDER_atags.html
 http://sw.neurocommons.org/2007/aba-20070226
 http://hcls.deri.org/resource/graph/dbpedia
 http://hcls.deri.org/resource/graph/diseasome
 http://hcls.deri.org/resource/graph/linkedct
 http://hcls.deri.org/resource/graph/medicare
 http://hcls.deri.org/resource/graph/sider
 http://purl.org/science/graph/addgene
 http://purl.org/science/graph/bams
 http://purl.org/commons/galen
 http://purl.org/science/graph/medline/subject-headings
 http://hcls.deri.org/atag/data/pastebin.html
 http://hcls.deri.org/atag/data/tcm_atags.html
 http://hcls.deri.org/atag/data/depression_atags_dumontier.ttl
 http://hcls.deri.org/resource/graph/tcm
 http://purl.org/science/graph/medline/titles-years
 http://purl.org/science/graph/mesh-eswc06
 http://purl.org/science/graph/mesh/mesh-skos
 http://purl.org/science/graph/mesh/qualified-headings
 http://purl.org/science/graph/ncbi/gene-info
 http://purl.org/science/graph/ncbi/gene-pubmed
 http://purl.org/science/graph/ncbi/goa
 http://purl.org/science/graph/ncbi/homologene
 http://purl.org/science/graph/nci-thesaurus
 http://sw.neurocommons.org/2007/2007-03-15/pubmed-annotations
 http://purl.org/science/graph/obo/AAO
 http://purl.org/science/graph/obo/BILA
 http://purl.org/science/graph/obo/BOOTStrep
 http://purl.org/science/graph/obo/BSPO
 http://purl.org/science/graph/obo/BTO
 http://purl.org/science/graph/obo/CARO
 http://purl.org/science/graph/obo/CHEBI
 http://purl.org/science/graph/obo/CL
 http://purl.org/science/graph/obo/COG2GO
 http://purl.org/science/graph/obo/DDANAT
 http://purl.org/science/graph/obo/DOID
 http://purl.org/science/graph/obo/EC2GO
 http://purl.org/science/graph/obo/ECO
 http://purl.org/science/graph/obo/EGAD2GO
 http://purl.org/science/graph/obo/EHDA
 http://purl.org/science/graph/obo/EHDAA
 http://purl.org/science/graph/obo/EMAP
 http://purl.org/science/graph/obo/ENVO
 http://purl.org/science/graph/obo/EO
 http://purl.org/science/graph/obo/EV
 http://purl.org/science/graph/obo/FAO
 http://purl.org/science/graph/obo/FBbi
 http://purl.org/science/graph/obo/FBbt
 http://purl.org/science/graph/obo/FBcv
 http://purl.org/science/graph/obo/FBdv
 http://purl.org/science/graph/obo/FBsp
 http://purl.org/science/graph/obo/FIX
 http://purl.org/science/graph/obo/FMA
 http://purl.org/science/graph/obo/GENPROTECGO
 http://purl.org/science/graph/obo/GO_XP_INTERNAL
 http://purl.org/science/graph/obo/GO_XP_REGULATION
 http://purl.org/science/graph/obo/GRO
 http://purl.org/science/graph/obo/HAMAP2GO
 http://purl.org/science/graph/obo/IDO
 http://purl.org/science/graph/obo/IEV
 http://purl.org/science/graph/obo/IMR
 http://purl.org/science/graph/obo/INTERPRO2GO
 http://purl.org/science/graph/obo/MA
 http://purl.org/science/graph/obo/METACYC2GO
 http://purl.org/science/graph/obo/MFO
 http://purl.org/science/graph/obo/MI
 http://purl.org/science/graph/obo/MIPS2GO
 http://purl.org/science/graph/obo/MIRO
 http://purl.org/science/graph/obo/MO
 http://purl.org/science/graph/obo/MP
 http://purl.org/science/graph/obo/MPATH
 http://purl.org/science/graph/obo/MP_XP
 http://purl.org/science/graph/obo/MS
 http://purl.org/science/graph/obo/MULTIFUN2GO
 http://purl.org/science/graph/obo/OBI
 http://purl.org/science/graph/obo/OBO_REL
 http://purl.org/science/graph/obo/OBO_REL_BFO_BRIDGE
 http://purl.org/science/graph/obo/PATO
 http://purl.org/science/graph/obo/PATO_BFO_BRIDGE
 http://purl.org/science/graph/obo/PFAM2GO
 http://purl.org/science/graph/obo/PLO
 http://purl.org/science/graph/obo/PO
 http://purl.org/science/graph/obo/PRINTS2GO
 http://purl.org/science/graph/obo/PRO
 http://purl.org/science/graph/obo/PRODOM2GO
 http://purl.org/science/graph/obo/PROSITE2GO
 http://purl.org/science/graph/obo/PW
 http://purl.org/science/graph/obo/ProPreO
 http://purl.org/science/graph/obo/REACTOM2GO
 http://purl.org/science/graph/obo/REX
 http://purl.org/science/graph/obo/RFAMGO
 http://purl.org/science/graph/obo/RO
 http://purl.org/science/graph/obo/SAO
 http://purl.org/science/graph/obo/SBO
 http://purl.org/science/graph/obo/SMART2GO
 http://purl.org/science/graph/obo/SO
 http://purl.org/science/graph/obo/SOPHARM
 http://purl.org/science/graph/obo/SO_XP
 http://purl.org/science/graph/obo/SPD
 http://purl.org/science/graph/obo/SPKW2GO
 http://purl.org/science/graph/obo/TADS
 http://purl.org/science/graph/obo/TAO
 http://purl.org/science/graph/obo/TGMA
 http://purl.org/science/graph/obo/TIGR2GO
 http://purl.org/science/graph/obo/TIGRFAMS2GO
 http://purl.org/science/graph/obo/TO
 http://purl.org/science/graph/obo/TO_XP
 http://purl.org/science/graph/obo/TRANS
 http://purl.org/science/graph/obo/TTO
 http://purl.org/science/graph/obo/UBERON
 http://purl.org/science/graph/obo/UMBBDENZYMEID2GO
 http://purl.org/science/graph/obo/UMBBDPATHWAYID2GO
 http://purl.org/science/graph/obo/UO
 http://purl.org/science/graph/obo/WBPhenotype
 http://purl.org/science/graph/obo/WBbt
 http://purl.org/science/graph/obo/WBls
 http://purl.org/science/graph/obo/WP_XP
 http://purl.org/science/graph/obo/XAO
 http://purl.org/science/graph/obo/YPO
 http://purl.org/science/graph/obo/ZEA
 http://purl.org/science/graph/obo/ZFA
 http://purl.org/science/graph/obo/biological_process_xp_cell
 http://purl.org/science/graph/obo/biological_process_xp_cellular_component
 http://purl.org/science/graph/obo/biological_process_xp_multi_organism_process
 http://purl.org/science/graph/obo/biological_process_xp_self
 http://purl.org/science/graph/obo/biological_process_xp_uber_anatomy
 http://purl.org/science/graph/obo/caro_to_bfo
 http://purl.org/science/graph/obo/cellular_component_xp_go
 http://purl.org/science/graph/obo/cellular_component_xp_self
 http://purl.org/science/graph/obo/go_to_chebi
 http://purl.org/science/graph/obo/habronattus_courtship
 http://purl.org/science/graph/obo/molecular_function_xp_regulators
 http://purl.org/science/graph/obo/ncbitaxon
 http://purl.org/science/graph/obo/oboInOwl
 http://purl.org/science/graph/obo/ro_proposed
 http://purl.org/science/graph/obo/ro_ucdhsc
 http://purl.org/science/graph/obo/bfo
 http://purl.org/science/graph/pdspki
 http://purl.org/science/graph/reactome
 http://purl.org/science/graph/sciencecommons
 http://purl.org/commons/hcls/senselab
 http://purl.org/science/graph/skos
 http://purl.org/science/graph/transitive-properties-direct
 http://purl.org/science/graph/transitive-properties-indirect
 http://purl.org/science/graph/temporary/original-subclassof-relations
 http://purl.org/science/graph/temporary/original-flattened-class-relations
 http://purl.org/science/graph/temporary/subclass-transitive
</nowiki></pre>


The list above was generated by the query described [http://esw.w3.org/topic/HCLS/HCLSIG_Demo_QueryScratch#head-4e3a50d139b11f595b5734de613a99e30172f047 here].

-------

== TODO ==

* Create RDF descriptions about graphs inside the triplestore, expose them via the linked data interface if possible
* Identify datasets that could be added and add them to the KB.
* Make documentation wiki page (this page) more complete.