HCLSIG BioRDF Subgroup/Meetings/2008-09-08 Conference Call

Conference Details

• Date of Call: Monday September 8, 2008
• Time of Call: 11:00am Eastern Time
• 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: 246733 ("BIORDF")
• IRC Channel: irc.w3.org port 6665 channel #BioRDF (see W3C IRC page for details, or see Web IRC)
• Duration: ~1 hour
• Frequency: bi-weekly
• Convener: Kei Cheung
• Scribe: Matthias Samwald

Agenda

• Introduction - Kei Cheung
• UMLS discussion (All)
• HCLS KB hosting (Matthias Samwald, Adrian Paschke)
• ideas of future work (All)
• Publication of HCLS workshop papers - Susie

Minutes

• <RRSAgent> logging to http://www.w3.org/2008/09/08-BioRDF-irc
• <kei> agenda+ roll call [Kei]
• Zakim notes agendum 1 added
• <kei> agenda+ introduction [Kei]
• Zakim notes agendum 2 added
• <kei> agenda+ UMLS discussion [Kei]
• Zakim notes agendum 3 added
• <kei> agenda+ HCLS hosting [Matthias, Adrian]
• Zakim notes agendum 4 added
• <kei> agenda+ ideas of future work [All]
• Zakim notes agendum 5 added
• <matthiassamwald> eric, i will be scribe.
• <matthiassamwald> How do I capture multiple lines for one speaker without re-typing the name for each line?
• <matthiassamwald> I think there was a trick.
• <@ericP> matthiassamwald: I'd loved to scribe
• <@ericP> ... but how do i capture multiple lines
• <@ericP> ericP: like that ^
• <kei> Zakim, this is the biordf call
• <Zakim> sorry, kei, I do not see a conference named 'the biordf call' in progress or scheduled at this time
• <matthiassamwald> understood.
• Huajun (huajunsir@125.120.180.44) has joined #BioRDF
• <kei> Zakim, this is biordf
• <Zakim> kei, SW_HCLS()11:00AM is already associated with an irc channel; use 'move biordf to here' if you mean to reassociate the channel
• cgolbrei (5a234034@128.30.52.43) has joined #BioRDF
• @ericP Zakim, code?
• Zakim the conference code is 246733 (tel:+1.617.761.6200 tel:+33.4.89.06.34.99 tel:+44.117.370.6152), ericP
• <@ericP> Zakim, move BioRDF to here
• <Zakim> ok, ericP; that matches SW_HCLS()11:00AM
• <Zakim> +??P4
• <Zakim> +??P7
• holger_stenzhorn (hstenzho@132.230.10.94) has joined #biordf
• <kei> zakim, who is here
• <Zakim> kei, you need to end that query with '?'
• <kei> zakim, where is here?
• <Zakim> sorry, kei, I do not understand your question
• <@ericP> Zakim, who is here?
• <Zakim> On the phone I see Kei_Cheung, ??P16, ??P17, ??P4, ??P7
• <Zakim> On IRC I see holger_stenzhorn, cgolbrei, Huajun, RRSAgent, Zakim, matthiassamwald, kei, ericP
• <kei> zakim who is here?
• <Zakim> -??P7
• <kei> matthias, did you call in?
• <matthiassamwald> technical diff
• <Zakim> +??P12
• <cgolbrei> christine
• <matthiassamwald> is the passcode HCLS or BIORDF?
• Donald_Doherty (Donald_Doh@151.201.29.168) has joined #biordf
• <holger_stenzhorn> BIORDF
• <Zakim> +EricP
• <Huajun> the pass code is biordf
• <kei> the passcode is BIORDF
• <@ericP> Zakim, who is speaking?
• <Zakim> ericP, listening for 10 seconds I heard sound from the following: Kei_Cheung (33%), EricP (14%), ??P16 (59%)
• <@ericP> Zakim, please mute ??P16
• <Zakim> ??P16 should now be muted
• <Zakim> +Don_Doherty
• <@ericP> Zakim, who is here?
• <Zakim> On the phone I see Kei_Cheung, ??P16 (muted), ??P17, ??P4, ??P12, EricP, Don_Doherty
• <Zakim> On IRC I see Donald_Doherty, holger_stenzhorn, cgolbrei, Huajun, RRSAgent, Zakim, matthiassamwald, kei, ericP
• <Zakim> +??P24
• AdrianPa (8d1ec108@128.30.52.43) has joined #BioRDF
• <matthiassamwald> give me one minute.
• <Zakim> + +0493516aaaa
• Zakim hears ??P4's hand up
• Zakim sees ??P4 on the speaker queue
• <AdrianPa> Zakim, aaaa is me
• <Zakim> +AdrianPa; got it
• <AdrianPa> Zakim, mute me
• <Zakim> AdrianPa should now be muted
• <holger_stenzhorn> Zakim, ??P4 is holger_stenzhorn
• <Zakim> +holger_stenzhorn; got it
• <kei> rrsagent, make minutes
• <RRSAgent> I have made the request to generate http://www.w3.org/2008/09/08-BioRDF-minutes.html kei
• Huajun (huajunsir@125.120.180.44) Quit (Ping timeout )
• Zakim hears ??P24's hand up
• Zakim sees ??P4, ??P24 on the speaker queue
• <Zakim> +??P25
• <@ericP> Zakim, ??P24 is DanielRueben
• <Zakim> +DanielRueben; got it
• <matthiassamwald> Zakim ??P25 is matthiassamwald
• <AdrianPa> I can not see the link to the slides on the webpage
• <AdrianPa> me neither
• <holger_stenzhorn> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2008-09-08
• <matthiassamwald> Kei: Olivier sent his regrets.
• <matthiassamwald> Kei: He will hold his presentation in the next BioRDF call, in two weeks.
• <matthiassamwald> Kei: First, let me introduce myself
• <matthiassamwald> ... I have been involved in Semantic Web developments for more than 3 years, before the HCLSIG started.
• holger_stenzhorn (hstenzho@132.230.10.94) Quit (Ping timeout )
• <matthiassamwald> ... My main interests are bioinformatics and database integration
• holger_stenzhorn (hstenzho@132.230.10.94) has joined #biordf
• Huajun (huajunsir@125.120.180.44) has joined #BioRDF
• <matthiassamwald> ... Let's start with the agenda. Please open the slides that are attached to http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2008-09-08
• <matthiassamwald> ... First I would like to thank Susie for coordinating the last charter of the task force. She did a very good job.
• <matthiassamwald> ... I will talk about the near-term goals of the task force.
• <@ericP> -> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2008-09-08?action=AttachFile&do=view&target=biordf_intro.pdf slides
• <matthiassamwald> ... I listed four near-term goals
• <matthiassamwald> ... "Enhance the HCLS KB. As part of the enhancement, we would like to incorporate new data sets that help the KB span from bench to bedside."
• <matthiassamwald> ... "Broaden the community of users who have skills to add data to the KB."
• <matthiassamwald> ... "Increase the value and use of the HCLS KB by identifying scientific use cases"
• <matthiassamwald> ... "Work on a human-friendly UI, explore
• <matthiassamwald> mechanisms for updating the data sources, and
• <matthiassamwald> adding new data sets.
• <matthiassamwald> ... "
• <@ericP> -> http://www.w3.org/TR/2008/NOTE-hcls-kb-20080604/#rdfbundles HCLS KB sources
• <matthiassamwald> ... a list of datasets in the Neurocommons KB can be found at http://www.w3.org/TR/hcls-kb/
• <matthiassamwald> ... The datasets were available in a variety of formats, some of them already were provided as RDF/OWL
• <matthiassamwald> ... But in most cases we needed to convert to RDF/OWL
• <matthiassamwald> ... During this process, we also created semantic links between datasets.
• <matthiassamwald> ... Once we have these ontologies loaded into these triplestores, applications can be developed.
• <@ericP> q+ to mention query federation
• Zakim sees ??P4, ??P24, ericP on the speaker queue
• <@ericP> Zakim, ??P4 is holger_stenzhorn
• <Zakim> I already had ??P4 as holger_stenzhorn, ericP
• <@ericP> Zakim, ack holger_stenzhorn
• <Zakim> I see ??P4, ??P24, ericP on the speaker queue
• <matthiassamwald> ... The datasets we include will be driven by the needs of the scientists.
• @ericP sees an update failure in zakim
• <AdrianPa> q+
• Zakim sees ??P4, ??P24, ericP, AdrianPa on the speaker queue
• <AdrianPa> Zakim, unmute me
• <Zakim> AdrianPa should no longer be muted
• [11:24] <matthiassamwald> EricP: A federation approach would be better than an aggregation approach, which is not THAT different from warehousing.
• <matthiassamwald> Kei: (agrees)
• <@ericP> q=
• Zakim ericP, if you meant to query the queue, please say 'q?'; if you meant to replace the queue, please say 'queue= ...'
• @ericP Zakim queue=
• <matthiassamwald> Adrian: Would it be a static or a dynamic integration?
• <matthiassamwald> Kei: In the warehouse approach, the datasources would be converted periodically and loaded into the triplestore from time to time. This might be associated with better performance for query.
• <matthiassamwald> ... In the federated approach, queries must be mapped to distributed sub-queries.
• @ericP Zakim q?
• <AdrianPa> Zakim, mute me
• <Zakim> AdrianPa should now be muted
• <@ericP> Zakim, who is muted?
• <Zakim> I see ??P16, AdrianPa muted
• <Huajun> can u hear me?
• <@ericP> ack ??P16
• Zakim unmutes ??P16
• Zakim sees ??P4, ??P24, ericP, AdrianPa on the speaker queue
• <matthiassamwald> Huajun: As more datasets will be loaded, will there be a performance issue?
• <@ericP> queue=
• Zakim sees no one on the speaker queue
• <matthiassamwald> Kei: I cannot answer that accurately now. It depends on the queries.
• <@ericP> Zakim, please mute ??P16
• <Zakim> ??P16 should now be muted
• <@ericP> Zakim, ??P16 is Huajun
• <Zakim> +Huajun; got it
• <matthiassamwald> ... On with the agenda... Olivier will talk about the conversion of UMLS into RDF in the next telecon.
• <matthiassamwald> ... The reason for inlcuding the work on UMLS was motivated by the interest of many participants, e.g., interest in SNOMED, interest from the COI group...
• <matthiassamwald> ... UMLS is also important for bioinformatics, e.g., for network analysis and data mining.
• <matthiassamwald> Kei: Of course, there is an issue with licensing.
• <matthiassamwald> ... It is open-access within the US if you sign an agreement with NLM.
• <matthiassamwald> ... It might be a problem.
• <matthiassamwald> ... What are the licensing issues with SNOMED?
• <matthiassamwald> Holger: We are currently working with SNOMED, it is a problem here in Germany.
• <matthiassamwald> ... John Madden wanted to ask the people at SNOMED. We can give you an update when we find out more.
• <matthiassamwald> EricP: It might make it easier if we just require parts of SNOMED for certain projects.
• <matthiassamwald> Kei: Exploring those licensing issues could be an agenda item for someone in this group.
• <matthiassamwald> (Who is talking?)
• <AdrianPa> Zakim, unmute me
• <Zakim> AdrianPa should no longer be muted
• <matthiassamwald> Kei: Let's talk about hosting of the KB
• <matthiassamwald> ... The first was at Science Commons, the other at DERI. They were not exact mirrors, but close.
• <matthiassamwald> ... How do we migrate the data from the current to the new KB?
• <AdrianPa> Zakim, mute me
• <Zakim> AdrianPa should now be muted
• <holger_stenzhorn> Matthais: finished my PhD on SW and biomedical research and neurological research
• <holger_stenzhorn> M.. now working for DERI Ireleand
• <matthiassamwald> http://hcls.deri.ie
• <holger_stenzhorn> ....DERI agreed on hosting the knowledgebase at their site
• <holger_stenzhorn> ...DERI still has still this commitment
• <holger_stenzhorn> ...and to start projects in the HCLS area
• <holger_stenzhorn> ...cureently, quite good situation: we can probably use the DERI server for the next 2 years in our developments
• <holger_stenzhorn> Kei: what support can be given by DERI for the hosting?
• <holger_stenzhorn> Matthias: inofficial agreement, that we can use the DERI servers for the next 2 years
• <holger_stenzhorn> ...but it needs to get official agreement for that
• <holger_stenzhorn> ...but everybody gives me thumbs up
• <holger_stenzhorn> ...I have personally set up the current HCLS server at DERI and would continue that
• <holger_stenzhorn> ...the machine that the Virtuoso server is running on is quite good, a quad core with large memory
• <holger_stenzhorn> ...should be sufficient for supporting the data over the next 2 years
• <holger_stenzhorn> ...so that server can be the main hub for the data over the next 2 years
• <holger_stenzhorn> Kei: could relay that to the request to the HCLS chairs and get back to you
• <holger_stenzhorn> Matthias: that makes sense
• <holger_stenzhorn> Kei: so I will do that request
• <AdrianPa> Zakim, unmute me
• <Zakim> AdrianPa should no longer be muted
• <matthiassamwald> thanks, holger. will scribe again.
• <matthiassamwald> Kei: Adrian, could you describe your situation now.
• <matthiassamwald> Adrian: I will move to Berlin soon and be part of a new working group.
• <matthiassamwald> ... I keep on working on Rule Responder and Semantic Web for e-science.
• <matthiassamwald> ... So this would still be of interest.
• Huajun (huajunsir@125.120.180.44) Quit (Ping timeout )
• <matthiassamwald> ... But I am still negotiating with the institution in Berlin.
• <matthiassamwald> ... So I cannot commit anything at the moment.
• <matthiassamwald> ... I will try to get more details soon.
• <AdrianPa> Zakim, mute me
• <Zakim> AdrianPa should now be muted
• <@ericP> matthiassamwald: re KB development, how will the HCLS KB sync with the Science Commons KB
• <@ericP> ?
• <matthiassamwald> Kei: Unfortunately, I still don't know the official status of Science Commons in this charter.
• <matthiassamwald> ... We need to talk to Neurocommons and the HCLS chairs to build some consensus.
• <matthiassamwald> Kei: Last agenda item -- ideas for future work.
• <matthiassamwald> ... There is a wiki page about project ideas.
• <matthiassamwald> ... We should also define how we can interact with other task forces (e.g. clinical).
• Huajun (huajunsir@125.120.180.44) has joined #BioRDF
• <kei> http://esw.w3.org/topic/HCLSIG/Project_Ideas/
• <matthiassamwald> eric: i am most interested in projects that build on what we currently have.
• <matthiassamwald> ... and also 'bench to bedside' work.
• <matthiassamwald> ... we have some gaps in the KB that hinder interesting use cases.
• <matthiassamwald> kei: huajun proposed an integration of traditional chinese medicine data with western medicine.
• <matthiassamwald> ... i proposed 'wiki neuron'.
• <Zakim> -DanielRueben
• <matthiassamwald> matthias: i plan to focus on semantic web technologies for (neuro-)cognitive science.
• <matthiassamwald> Kei: the next call will be in two weeks.
• <AdrianPa> bye
• <Zakim> -holger_stenzhorn
• <Zakim> -Don_Doherty
• <Zakim> -AdrianPa
• <Zakim> -??P25
• <Zakim> -EricP
• <Zakim> -??P17
• Donald_Doherty (Donald_Doh@151.201.29.168) Quit (Quit: Donald_Doherty )
• <Zakim> -Huajun
• <cgolbrei> bye
• Huajun (huajunsir@125.120.180.44) Quit (Quit: Huajun )
• <Zakim> -??P12
• <kei> eric, are you still there?
• <@ericP> on irc, yes
• <matthiassamwald> eric, you take care about rrsagent, right?
• <@ericP> RRSAgent, please draft minutes
• <RRSAgent> I have made the request to generate http://www.w3.org/2008/09/08-BioRDF-minutes.html ericP
• <matthiassamwald> thanks. bye!
• <@ericP> RRSAgent, bye