HCLSIG/LODD/Meetings/2009-09-02 Conference Call

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Conference Details

  • Date of Call: Wednesday September 2, 2009
  • 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 #: + (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 W3C IRC page for details, or see Web IRC)
  • Duration: ~1h
  • Convener: Susie
  • Attendee Live Meeting - https://www.livemeeting.com/cc/jnjamericas/join?id=W6D6JD&role=attend&pw=x%60%236X%22w


  • Application demo - Jun
  • Brainstage demo - Don
  • Web questions demo - Anja
  • Paper/conference opportunities (iTriplify, WWW, TCM paper) - all
  • Data update - Anja, Jun, Matthias
  • AOB


Attendees: Oktie, Anja, Tim, Rudi, Susie, Scott, Julia, Bosse, Don, Eric

Apologies: Jun

<kei> Anja: Jun is away ...

<kei> Susie: see how the software can be related to HCLS

<kei> Susie: data updates ...

<kei> Susie: Anja has good news about the iTriplification paper -- made it to the top 3 nominations

<mscottm> Excellent!

<kei> Anja: expensive trip for a 5 minutes talk -- do screen cast instead ...

<kei> Anja: thanks to everybody for contributing to the paper

<Susie> https://www.livemeeting.com/cc/jnjamericas/join?id=W6D6JD&role=attend&pw=x%60%236X%22w

<kei> Anja: update on data update

<kei> Anja: not much has been happening in the last two weeks

<kei> Susie: paper, conference opportunities

<kei> Susie: potential journal paper

<mscottm> DILS = Data Integration for the Life Sciences

<mscottm> Kei: Thinking about submitting a journal article about similar work to that described in the DILS poster

<mscottm> Kei: have had contact with open access journal about possibility of special issue

<kei> Susie: other ideas ...

<kei> possible journal paper submission (http://www.cmjournal.org/)

<kei> Anja: workshop paper opportunities

<kei> Susie: ISMB?

<kei> Anja: a conference in Stockholm ...

<kei> Anja: Semantic Web challenge (Oct 1 deadline?)

<AnjaJentzsch> http://challenge.semanticweb.org/

<kei> Susie: ISWC is past, but WWW conference is another option, ISMB is another option, wiki page can be created for listing these options

<kei> Anja: go for a main paper?

<kei> Susie: yes

<kei> Anja: emphasize link data results (using linker?) and do some comparisons

<kei> Oktie: may be more important to develop use cases

<kei> Oktie: based on the use cases, we can discuss the links (e.g., quality of the links) in the context of use cases

<kei> Susie: quality of the links is an interesting issue and show some contents/examples for this discussion

<kei> Susie: the main thrust may not be on comparison

<kei> Anja: not exactly the comparison

<kei> Susie: people should think about what to include in the paper

<kei> Oktie: based on community feedback, use case is important (any real scenarios for demonstrating the use of these links)

<kei> Oktie: evaluation of the quality of links would become easier to do once use cases are created

<kei> Susie: Don's demonstration may be relevant

<kei> Don: some compatibility issue with FireFox, work well with IE

<kei> Don: work well on Safari

<kei> Don: Brainstage platform --information retrieval search engine, knowledge base - oracle RDF repository, transformation

<kei> Don: dynamic web interface invoking services and javascripts on the fly ...

<kei> Don: use case -- interested in memory in AD and protein targets (e.g.,neurotransmitters)

<kei> Don: start with a brain region (e.g., Hippocampus)

<kei> Don: next go into neuron types (e.g., pyramidal neurons)

<kei> Don: retrieve papers, genes, proteins, cells ...

<kei> Don: thousand cells focused on the central nervous system

<kei> Don: can be extended to clinical domain

<kei> Don: start search at the cellular level

<kei> Don: listing the cells that matched the search criteria

<kei> Don: cell types and brain regions -- select one for detail (e.g., morphology)

<kei> Don: 3D reconstruction of the raw data (dynamically created)

<kei> Don: access raw data

<kei> Don: access to publications as well

<kei> Don: view a particular paper (e.g., abstract)

<kei> Don: semantics -- neurons (morphology) -- links to ontology

<kei> Don: targets (e.g., neurotransmitters) -- apical dendrites

<kei> Don: find targets in different parts of the neurons

<kei> Don: visualization is scalable

<kei> Don: personal workspace and team workspace are available

<kei> Don: ontology exposed, terminology presented by the Brainstage platform

<kei> Don: in the workspace, one can select a concept with the data and add it to the knowledge in the workspace

<kei> Don: Such annotated knowledge can be shared at different levels

<kei> Don: in this example: gaba is the returned target

<kei> Don: for proteins, the system can find what genes encoding the proteins

<kei> Don: no ligands yet

<kei> Don: drug information is available

<kei> Don: give a list of proteins that the drug binds to

<kei> Don: the system is visual allowing scientists to work with a intuitive interface

<kei> Don: go back to paper -- can be added to the library (personal or team)

<kei> Don: annotate papers -- accumulating semantics

<kei> Don: web-based applications on top of a semantic layer

<kei> Don: the semantic knowledge can grow dynamically

<kei> Don: any questions?

<kei> Susie: were any specific ontologies used?

<kei> Don: many ontologies were used and integrated ...

<kei> Don: neuro and protein ontologies

<kei> Don: Is NIF ontology there?

<kei> Don: SOM is used instead

<kei> Susie: will brain images (e.g., ADNI) be incorporated?

<kei> Don: possible (e.g., hippocampus) ... with a focus on a particular disease

<kei> Don: Alzheimer's disease for example,

<kei> Don: based on papers, genes, proteins, links can be made to other types of data

<kei> Susie: links to derived data (e.g., images)

<kei> Don: can bring in large images (large size) and other types of data

<kei> Susie: Can LoDD data sets be incorporated?

<kei> Don: Yes

<kei> Kei: how about gene expression data (e.g., microarray, atlas)

<kei> Don: Yes, the next level.

<kei> Don: also needs to deal with images

<kei> Don: for microarrays, which genes are over-expressed or under-expressed under what conditions

<kei> Don: breast cancer group is using microarray data

<kei> Julia: efficiency -- data size -- how to address

<kei> Don: depending how much data is being looked at at once? visualization can become an issue

<kei> Don: image data can be a challenge in terms of size and efficiency

<kei> Scott: is any components of the system open source?

<kei> Don: the platform is a large collections of components -- a freely available version is available on the web

<kei> Don: the next plan is the availability of open API

<kei> Don: services that can help generate revenue

<kei> Don: private data are not available to the community

<kei> Scott: what about RDF data / linked data -- can they be available?

<kei> Don: published data can be available to the public domain in RDF format

<kei> Scott: is the systemm currently supporting RDF export

<kei> Don: yes

<kei> Scott: can some researchers working in the hospital contact you?

<kei> Don: yes

<kei> Don: it's still in beta version, early stage ...

<kei> Don: academic contracts (lower costs)?

<kei> Don: yes

<kei> Don: public version, lab (academic version), enterprise version

<kei> Susie: is paper submission/collaboration possible?

<kei> Don: possible

<kei> Oktie: conflict resolution supported?

<kei> Don: there are challenges, but this is addressed to a certain extent

<kei> Don: e.g., gene name resolution