HCLSIG/Meetings/2009-09-03 Conference Call

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Conference Details

  • Date of Call: Thursday September 3, 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: Scott, Susie
  • Scribe: TBD



Session Start: Thu Sep 03 17:00:38 2009
Session Ident: #hcls
[17:00] * Now talking in #hcls
[17:00] * Topic is 'HCLSIG semi-weekly telecon. agenda: http://esw.w3.org/topic/HCLSIG/Meetings/2009-09-03_Conference_Call'
[17:00] * Set by sandro on Thu Sep 03 16:58:54
[17:02] <ericP> Zakim, please dial ericP-office
[17:02] <Zakim> sorry, ericP, I don't know what conference this is
[17:02] <ericP> Zakim, this is hcls
[17:02] <Zakim> ok, ericP; that matches SW_HCLS()11:00AM
[17:02] <ericP> Zakim, please dial ericP-office
[17:02] <Zakim> ok, ericP; the call is being made
[17:02] <Zakim> +EricP
[17:02] * RRSAgent has joined #hcls
[17:02] <RRSAgent> logging to http://www.w3.org/2009/09/03-hcls-irc
[17:03] <mscottm> Zakim, who is on the phone?
[17:03] <Zakim> On the phone I see +1.410.720.aaaa, Susie, jkangash, +49.308.385.aabb, EricP
[17:03] <Zakim> +Julia
[17:03] <Zakim> +Sandro
[17:03] <Zakim> +Kei_Cheung
[17:03] * kei has joined #HCLS
[17:03] <mscottm> Zakim, +1.410.720.aaaa is Joshua
[17:03] <Zakim> +Joshua; got it
[17:04] <Zakim> + +
[17:04] <mscottm> Zakim, who is on the phone?
[17:04] <Zakim> On the phone I see Joshua, Susie, jkangash, +49.308.385.aabb, EricP, Julia, Sandro, Kei_Cheung, +
[17:04] <Zakim> - +
[17:05] <Zakim> -Sandro
[17:05] * AnjaJentzsch has joined #hcls
[17:05] <Zakim> + +
[17:06] <mscottm> Zakim, + is Bosse
[17:06] <Zakim> +Bosse; got it
[17:06] <mscottm> Zakim, +49.308.385.aabb is AnjaJentzsc
[17:06] <Zakim> +AnjaJentzsc; got it
[17:06] <Zakim> +Joanne_Luciano
[17:06] <mscottm> Zakim, pick a victim
[17:06] <Zakim> Not knowing who is chairing or who scribed recently, I propose Kei_Cheung
[17:07] <AnjaJentzsch> Zakim, +49.308.385.aabb is AnjaJentzsch
[17:07] <Zakim> sorry, AnjaJentzsch, I do not recognize a party named '+49.308.385.aabb'
[17:07] * jluciano has joined #hcls
[17:08] <mscottm> Kei (BioRDF): Most active is the microarray query federation.
[17:09] <mscottm> ..Working with Helen Parkinson (EBI, ArrayExpress) and Maryanne Martone (NIF - Neuroinformatics Framework, Neurolex).
[17:11] <mscottm> ..They are working together to annotate microarrays with neuroscience-related ontological concepts, with an emphasis on NIFSTD, available from the NCBO Bioportal.
[17:12] <kei> COI update
[17:13] <mscottm> Helen Parkinson (EBI) and Sudeshna Das from Harvard/MGH gave presentations at the last BioRDF call.
[17:13] * Julia_Kozlovsky has joined #HCLS
[17:13] <kei> Eric: activities: grad. student in Italy work on that,but not directly related to the task force, need more follow up to make it relate to the task force
[17:14] <kei> Scott: no call since last update?
[17:14] <kei> Eric: need to motivate people ...
[17:14] <kei> Eric: should touch base with Helen, Vipul ...
[17:15] <kei> Scott: SparQL endpoint and other use cases for FeDeRate
[17:16] <kei> Eric: some talk will be given in a meeting in November?
[17:16] <kei> Scott: LoDD update
[17:16] <kei> Anja: the paper made it to the top 3 nominations
[17:16] <AnjaJentzsch> http://www.anjajentzsch.de/lodd/2009%20Triplification%20Challenge%20-%20LODD.pdf
[17:16] <kei> Anja: the datasets include links to TCM data and drug data ...
[17:17] <AnjaJentzsch> http://www4.wiwiss.fu-berlin.de/lodd/topquestions/
[17:17] <kei> Anja: work with the translational medicine ontology group on coming up with questions
[17:17] <kei> Anja: data browsing, querying, linking, other feetures
[17:17] <mscottm> http://hcls.deri.org/coi/demo/
[17:18] <kei> Anja: data clean up, linking method evaluation, ...
[17:18] <kei> Anja: search based on company name, drug name, herb name , ..
[17:18] <kei> Anja: that's the current focus
[17:19] <kei> Scott: in terms of the Triplification Challenge, is the a web page people can go to look at the demo ...
[17:19] <AnjaJentzsch> http://esw.w3.org/topic/HCLSIG/LODD/
[17:19] <kei> Anja: datasets are available, and browsable using browsers like Marble
[17:20] <kei> Scott: it'd be helpful to make these links available to the community
[17:21] <kei> Anja: did you mean creating an HCLS web page
[17:21] <AnjaJentzsch> http://triplify.org/Challenge/2009
[17:21] <kei> Susie: we should promote this, HCLS main page is based on blog ...
[17:22] <kei> Susie: In addition, aggregate information obtained from different task forces
[17:22] <kei> Scott: e.g., HCLS, W3C note, running applications, demos, etc
[17:23] <kei> Scott: translation medicine ontology update
[17:23] <kei> Susie: nice progress
[17:23] <Susie> http://esw.w3.org/topic/HCLSIG/PharmaOntology
[17:23] <kei> Susie: currently we're working on what should be included in the ontology
[17:24] <kei> Susie: the group is working on a paper submitted to the JBI special issue -- ontology related
[17:24] <kei> Susie: 150 terms might be included in the ontology
[17:25] <kei> Susie: narrow down to ~80
[17:25] <kei> Susie: examples include drugs, active ingredients, compounds, etc for describing drugs
[17:26] <kei> Susie: need to continue and accelerate the effort to make the deadline
[17:26] <kei> Scott: long session (4 hours) for the last call -- generating good momentum
[17:26] <kei> Susie: F2F meeting will also help
[17:27] <kei> Scott: We will cover the F2F meeting shortly
[17:27] <kei> Scott: Terminology update
[17:27] <kei> Scott: one recent development -- Andrew Gibson joined the call
[17:28] <kei> Scott: Andrew make the OBO-SKOS translation work
[17:28] <kei> Scott: working on SNOMED and MeSH currently
[17:28] <kei> Scott: John Madden has access to some hospital data
[17:29] <kei> Scott: it may be possible to use Eric secure SPARQL approach ...
[17:29] <kei> Scott: SKOS lens code ?
[17:30] <kei> Scott: facilitate concept transversal, seach across multiple repositories, ...
[17:31] <kei> Scott: automatic detection of repositories, which may be relevant to the query federation in BioRDF 
[17:31] <kei> Who is asking the question?
[17:32] <kei> Joanne: what is the scope of the ontology
[17:32] <jluciano> terminology
[17:32] <kei> Kei: thanks, Joanne
[17:32] <kei> Scott: make SNOMED into SKOS format
[17:33] <kei> Kei: use SNOMED terminology for searching in a facetted way
[17:33] <kei> Scott: how can one use the terminology such as MeSH, GO, ...
[17:34] <kei> Joanne: how to use it to integrate task forces such as the translational medicine ontology
[17:35] <kei> Scott: when the translational medicine ontology is more developed, these terminology tools may be explored
[17:35] <kei> Scott: Sci Discourse update
[17:36] <kei> Scott: three IG notes were released
[17:36] <kei> Scott: feedback/suggestions are welcome and can be relayed to Paolo and Alex
[17:36] <ericP> q+ a propos de review
[17:36] * Zakim ericP, you typed too many words without commas; I suspect you forgot to start with 'to ...'
[17:36] <ericP> q+
[17:36] * Zakim sees ericP on the speaker queue
[17:37] <mscottm> ack ericP
[17:37] * Zakim sees no one on the speaker queue
[17:37] <kei> Eric: review process -- whether agree and/or disagree with part of it
[17:38] <Susie> Next F2F meeting
[17:38] <kei> Scott: F2F meeting
[17:38] <Susie> http://esw.w3.org/topic/HCLSIG/Meetings/2009-11-02_F2F
[17:38] <kei> Scott: ideas for F2F meeting
[17:38] <kei> Scott: Alex sent out the IG note announcement
[17:39] <kei> Susie: is there an outline?
[17:39] <kei> Who is asking the question?
[17:39] <mscottm> Julia
[17:39] <kei> thanks, scott
[17:39] <kei> Julia: is there a summary of the last F2F
[17:40] <ericP> documents for review:
[17:40] <ericP> -> http://www.w3.org/2001/sw/hcls/notes/sioc/ SIOC, SIOC Types and Health Care and Life Sciences
[17:40] <ericP> -> http://www.w3.org/2001/sw/hcls/notes/swan/ Semantic Web Applications in Neuromedicine (SWAN) Ontology
[17:40] <ericP> -> http://www.w3.org/2001/sw/hcls/notes/swansioc/> SWAN/SIOC: Alignment Between the SWAN and SIOC Ontologies
[17:40] <kei> Susie: each task force lead is holding focused discussion/meeting to discuss issues and identify next steps ../
[17:40] <mscottm> http://esw.w3.org/topic/HCLSIG/Project_Ideas
[17:41] <mscottm> distilled from http://www.w3.org/2009/05/28-hcls-minutes
[17:41] <kei> Julia: are there any lingering issues from the last F2F, which need to be issued
[17:41] <kei> Susie: one issue is how to HCLS calls feasible/practical to people
[17:41] * sandro has left #hcls (Leaving)
[17:42] <kei> Susie: invite presenters to cover relevant topics 
[17:42] <kei> Susie: next F2F -- 2nd of Nov in California
[17:42] <kei> Susie: a modest registration fee is $50
[17:43] <kei> Susie: register as soon as possible
[17:43] <kei> Susie: what each task force group look to accomplish
[17:43] <kei> Susie: may be too early to provide concrete answer, but think may be in terms of content and outcome
[17:44] <kei> Susie: wiki page was created for people to indicate their attendence
[17:44] <ericP> q+ to mention overlap with SPARQL
[17:44] * Zakim sees ericP on the speaker queue
[17:44] <kei> Susie: special time slots may be created if needed
[17:45] <kei> Susie: if people can suggest more things, it'd be great
[17:45] <mscottm> ack ericP
[17:45] <Zakim> ericP, you wanted to mention overlap with SPARQL
[17:45] * Zakim sees no one on the speaker queue
[17:45] <kei> Eric: use cases for SPARQL are welcome
[17:46] <kei> Susie: it's important to interact SPARQL
[17:46] * bbalsa has joined #HCLS
[17:47] <kei> Eric: before we schedule, it'd be useful to collect people's wish lists for SPARQL in preparation
[17:47] <kei> Scott: AD demo, for example, might be useful
[17:48] <kei> Eric: find resources to implement tasks
[17:48] <kei> Scott: look into the SPARQL charter 
[17:48] <ericP> -> http://www.w3.org/2009/05/sparql-phase-II-charter SPARQL phase II charter
[17:48] <kei> Scott: some task forces might identify SPARQL features they need
[17:49] <kei> Eric: good point
[17:49] <mscottm> http://www.w3.org/2009/sparql/wiki/Feature:PropertyPaths
[17:49] <kei> Eric: encourage task forces to look at it and provide comments
[17:52] <kei> Kei: for BioRDF, the F2F may help the current microarray data federation use case
[17:53] <kei> Anja: will try her best to attend
[17:53] <kei> Susie: tanslational medicine ontology will do something for the 
[17:54] <kei> Susie: any other suggestions ..
[17:54] <kei> Joanne: how long is the f2f meeting?
[17:54] <kei> Susie: 2 days
[17:54] <kei> What group?
[17:54] <Susie> eGov
[17:55] <kei> Eric: eGov may intersect with HCLS
[17:55] <kei> Susie: good idea
[17:55] <mscottm> http://esw.w3.org/topic/HCLSIG/Authorship
[17:55] <kei> Susie: authorship issue
[17:55] <kei> Susie: clear guideline needs to be established
[17:56] <kei> susie people should look at it and provide feedback
[17:58] <kei> Kei: how publication costs can be shared among authors for open-access journals
[17:59] <kei> Susie: HCLS workshop on Sci. Discourse in ISWC
[17:59] <kei> Susie: paper presentation, panel discussion, ...
[18:00] <kei> Susie: panelists have been identified, keynote speakers are being confirmed
[18:00] <kei> Susie: HCLS invited to give a tutorial at C-SHALS 2010 in Boston
[18:01] <Zakim> -Joshua
[18:01] <ericP> -> http://www.iscb.org/cshals2010 C-SHALS home page
[18:01] <mscottm> http://www.swat4ls.org/2009/index.php
[18:01] * Susie has quit IRC (Quit: CGI:IRC)
[18:02] * Julia_Kozlovsky has quit IRC (Quit: http://www.mibbit.com ajax IRC Client)
[18:02] <kei> Scott: SWATLS workshop paper submission open soon, workshop in Nov
[18:02] <Zakim> -Bosse
[18:02] <Zakim> -Julia
[18:02] <kei> Scott: possible publication biomedical semantics journal
[18:03] <kei> Scott: linking data workshop AAAI in march in Stanford
[18:03] <Zakim> -Susie
[18:03] <kei> bye