HCLSIG BioRDF Subgroup/Meetings/2009-03-09

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Teleconference Minutes



IRC Transcript

(16:08:50) matthias_samwald: TOPIC -- Introductions
(16:09:12) matthias_samwald: Egon Willighagen: (Introduces himself)
(16:09:35) matthias_samwald: ... Interested in Semantic Web technologies i chemistry.
(16:09:45) matthias_samwald: ... Involved with Chemical Markup Language
(16:09:53) matthias_samwald: ... and RDF for making links between datasets.
(16:10:06) matthias_samwald: ... more details about me will follow by e-mail.
(16:11:42) matthias_samwald: TOPIC -- C-SHALS meeting update
(16:11:58) ***ericP Zakim, please dial ericP-office
(16:11:58) ***Zakim ok, ericP; the call is being made
(16:11:59) Zakim: +EricP
(16:12:03) matthias_samwald: Kei: many voiced their interests, but not everyone could be there
(16:12:11) matthias_samwald: ... I joined the HCLS tutorial section.
(16:12:20) matthias_samwald: ... I gave a presentation on BioRDF
(16:14:08) matthias_samwald: ... Mentioned the two main activities: aTags (led by Matthias, new task force), Query Federation (prototypical "receptor explorer", based on different sources...
(16:15:28) matthias_samwald: ... People seemed to be quite interested in both tasks (e.g., Tim Clark; a representative from the PDP database etc)
(16:15:42) apaschke: Zakim, unmute me
(16:15:43) Zakim: apaschke should no longer be muted
(16:15:57) matthias_samwald: TOPIC --- the HCLS Knowledge Base
(16:16:26) Martin [a03e040a@] hat den Raum betreten.
(16:16:30) kei: matthias: give update on HCLS KB at DERI
(16:16:57) kei: matthias: added functionality exposing functionality of linked data interface -- plugin for vituoso
(16:17:06) Zakim: + +1.415.425.aaaa
(16:17:18) kei: matthias: query for for selecting subclasses based on uri's
(16:18:21) kei: matthias: most of the data come from neurocommons including medline, protein databases, obo ontologies
(16:19:12) kei: matthias: can you scribe now?
(16:19:16) Zakim: + +41.61.324.aabb
(16:19:23) matthias_samwald: Adrian: We installed a LOD interface for the AllegroGraph store hosted here in Berlin.
(16:19:39) matthias_samwald: ... We loaded a dataset about traditional chinese medicine.
(16:19:48) matthias_samwald: ... Currently we are working on an extended query interface
(16:20:04) matthias_samwald: ... E.g., translation of results to JSON and other formats.
(16:20:59) matthias_samwald: ... LOD interface is still a bit buggy, but it works.
(16:21:46) apaschke: TMC endpoint
(16:21:47) apaschke: http://www.csw.inf.fu-berlin.de:4039/sesame/repositories/tcmgene
(16:22:12) matthias_samwald: Kei: I talked with Susie, they converted several knowledge bases to LOD in the Linking Open Drug Data task. We can try and see to find connections.
(16:22:22) ***mscottm says that he gets: "Unknown query language nil"
(16:22:27) egonw: same here
(16:22:29) matthias_samwald: me too
(16:23:01) matthias_samwald: a link to a linked data URI would also be interesting!
(16:23:23) matthias_samwald: Scott: I asked whether people planned to add the Sesame interface to their triplestores
(16:23:38) matthias_samwald: ... Do you know how complicated it is for AllegroGraph?
(16:23:51) matthias_samwald: Adrian: We are already using Sesame for our instance.
(16:24:58) kei: action item: scott will try to access the sesame endpoint from allegrograph
(16:24:59) apaschke hat den Raum verlassen (quit: Quit: CGI:IRC (EOF)).
(16:24:59) adrianpaschke [a02d72ec@] hat den Raum betreten.
(16:25:24) matthias_samwald: Scott: John Madden found a particular setup from Koblenz University, showing how Sesame repositories can be federated.
(16:25:29) adrianpaschke: Senselab Sesame endpoint
(16:25:41) adrianpaschke: http://www.csw.inf.fu-berlin.de:4039/sesame/repositories/senselab
(16:25:57) matthias_samwald: ... If you could put a terminology on your server, as part of the HCLS effort.
(16:26:18) matthias_samwald: ... John translated SNOMED into SKOS.
(16:26:28) adrianpaschke: you can try out here http://www.corporate-semantic-web.de/senselab.html
(16:27:42) Zakim: + +2
(16:27:43) egonw: OffTopic: is there any relation between BioRDF and Bio2RDF? (I keep wondering about that...)
(16:28:06) mscottm: No relation Egon. :)
(16:28:36) mscottm: Zakim, who is on the phone?
(16:28:36) Zakim: On the phone I see egonw, Kei_Cheung, apaschke, ??P16, Scott_Marshall, matthias_samwald, EricP, +1.415.425.aaaa, +41.61.324.aabb, +2
(16:28:44) mscottm: hi ericP. :)
(16:28:57) matthias_samwald: Kei: in reply to Egons question: they are different.
(16:29:39) matthias_samwald: ... their has been interest in collaborating with Bio2RDF. 
(16:29:59) matthias_samwald: ... I hope that we can contact them when we have concrete proposals.
(16:29:59) adrianpaschke: +q
(16:29:59) ***Zakim sees adrianpaschke on the speaker queue
(16:31:20) egonw: https://sourceforge.net/project/memberlist.php?group_id=142631
(16:32:38) matthias_samwald: Adrian: the SPARQL working group is now rechartering, and they are also looking into query federation
(16:32:49) matthias_samwald: Adrian: Axel Polleres (DERI) is leading that group.
(16:32:58) adrianpaschke: q-
(16:32:58) ***Zakim sees no one on the speaker queue
(16:33:04) matthias_samwald: Kei: This is an interesting possibility.
(16:33:11) adrianpaschke: we might form a liaison to this group
(16:33:25) matthias_samwald: ... The current SPARQL standard does not have dedicated features for federation.
(16:33:37) matthias_samwald: Adrian: we might form a liaison to this group
(16:33:56) kei: matthias: atag update
(16:34:32) kei: matthias: prototype interface -- create bookmarks
(16:34:44) mscottm: matthias - we can't hear you too well at all.
(16:35:00) adrianpaschke: quality is quite low
(16:35:01) kei: matthias: I can't hear you
(16:35:12) adrianpaschke: Zakim, mute me
(16:35:12) Zakim: sorry, adrianpaschke, I do not know which phone connection belongs to you
(16:35:21) adrianpaschke: Zakim, who is on the phone?
(16:35:22) Zakim: On the phone I see egonw, Kei_Cheung, apaschke, ??P16, Scott_Marshall, matthias_samwald, EricP, +1.415.425.aaaa, +41.61.324.aabb, +2
(16:35:27) agibson [91128399@] hat den Raum betreten.
(16:35:30) adrianpaschke: Zakim, apaschke is me
(16:35:30) Zakim: +adrianpaschke; got it
(16:35:46) mscottm: Hi Andrew!
(16:35:49) adrianpaschke: Zakim, mute me
(16:35:49) Zakim: adrianpaschke should now be muted
(16:35:53) kei: matthias: release prototype in 2-3 weeks
(16:35:58) agibson: Hi Scott
(16:36:03) matthias_samwald: days!
(16:36:06) matthias_samwald: not weeks.
(16:36:54) matthias_samwald: Kei: Can you tell us more about the BioCreative Challenge?
(16:37:45) matthias_samwald: Scott: It deals with knowledge extraction via textmining.
(16:38:00) matthias_samwald: ... This might help us in our efforts
(16:38:10) adrianpaschke: yes, biocreative is more about text mining
(16:38:44) matthias_samwald: ... Generating high-quality data directly via NLP is not currently possible, though
(16:39:14) matthias_samwald: ... The FEBS Letters experiment is also interesting in this context
(16:39:38) matthias_samwald: ... A Structured Digital Abstract is published along with the article
(16:39:43) adrianpaschke: we participated in 2007 and won the text mining competition
(16:39:46) adrianpaschke: in biocreative
(16:39:51) matthias_samwald: ... Which also facilitates textmining
(16:41:15) matthias_samwald: Kei: The principle of text mining is deriving structured information from unstructured information. Standardizing the structure of the structured information might be an interessting application of Semantic Web technology.
(16:41:26) matthias_samwald: ---- TOPIC: BioRDF publication
(16:42:01) adrianpaschke: Zakim, unmute me
(16:42:01) Zakim: adrianpaschke should no longer be muted
(16:42:02) matthias_samwald: Kei: We have explored many different possibilities and can provide an intersting summary of that.
(16:42:34) adrianpaschke: Semantic Web Applications and Tools for Life Sciences
(16:42:38) matthias_samwald: Kei: Publication in a special issue of BMC Bioinformatics is a possibilty.
(16:42:53) matthias_samwald: ... Deadline for abstract submission is March 15
(16:43:02) matthias_samwald: ... We created a Google Doc
(16:43:34) matthias_samwald: ... I created a structure for the article
(16:44:33) ***egonw does not seem subscribed to the biordf group ML yet...
(16:44:38) egonw: where can I find it?
(16:44:54) matthias_samwald: http://docs.google.com/Doc?id=dggh6vwh_48sgg85phn
(16:45:03) ***ericP tx
(16:45:11) matthias_samwald: but it is restricted to authors/editors, I think.
(16:46:11) adrianpaschke: Paper submission deadline: 6 April
(16:46:55) matthias_samwald: Scott: We should try to have a bit more implementation work (e.g., Eric's work) that we can demonstrate
(16:47:23) matthias_samwald: Eric: The code is pretty stable now.
(16:47:58) matthias_samwald: Kei: I saw it, the performance seems to be significantly improved
(16:49:25) ericP: http://swobjects.svn.sourceforge.net/viewvc/swobjects/trunk/tests/mouseToxicity/remote-all/
(16:49:41) ericP: http://swobjects.svn.sourceforge.net/viewvc/swobjects/trunk/tests/mouseToxicity/remote-all/ScreeningAssay.map?revision=472&view=markup
(16:49:50) matthias_samwald: Eric: This is a demo, it contains several mapping files.
(16:50:12) matthias_samwald: ... basically it is a SPARQL query with some additional information about how to connect to the data base
(16:50:42) matthias_samwald: ... It is a CONSTRUCT query, the top part defined the demonstration, the lower part defines how the relational database is accessed.
(16:50:51) ericP: http://swobjects.svn.sourceforge.net/viewvc/swobjects/trunk/tests/mouseToxicity/remote-all/ToxicAssoc0.rq?view=markup
(16:53:22) matthias_samwald: Kei: matthias described a way of joining DBpedia with IUPHAR data
(16:53:39) matthias_samwald: ... For example, data on the GABAA receptor can be joined.
(16:53:51) matthias_samwald: ... should we follow up on that example?
(16:54:00) matthias_samwald: Eric: Sounds good to me.
(16:54:15) Zakim: - +1.415.425.aaaa
(16:54:21) matthias_samwald: ... Give me a query and a relational database
(16:58:17) matthias_samwald: Kei: Can someone load the CSV files into a relational database?
(16:58:23) matthias_samwald: Eric: I will do that.
(16:59:51) adrianpaschke: we should also try to include the two HCLS KBs in the use case
(17:00:11) matthias_samwald: +1, Adrian.
(17:00:54) matthias_samwald: Scott: Andrew Gibson is on the call.
(17:01:15) matthias_samwald: Andrew: I am a postdoc at the University of Amsterdam
(17:01:21) matthias_samwald: ... Institute of Life Sciences
(17:01:42) matthias_samwald: ... we are using SKOS, OWL, triple stores etc. for a very specialized database.
(17:02:51) matthias_samwald: Kei: There is increasing interest in SKOS
(17:03:11) matthias_samwald: ... some scientists are complaining that understanding OWL is to complicated for them
(17:03:16) mscottm: Zakim, who is making noise?
(17:03:26) Zakim: mscottm, listening for 10 seconds I heard sound from the following: +2 (9%), egonw (14%), +41.61.324.aabb (57%), Kei_Cheung (64%)
(17:03:29) matthias_samwald: ... SKOS can be useful in these cases.
(17:03:51) matthias_samwald: ... Also, DBpedia has some SKOS components.
(17:03:55) mscottm: Zakim, mute +41.61.324.aabb
(17:03:55) Zakim: +41.61.324.aabb should now be muted
(17:04:14) matthias_samwald: Rob: SKOS is practical
(17:04:21) ***mscottm says ericP, I prob just muted you..?
(17:04:36) matthias_samwald: ... We are currently working on a project for representing various information in SKOS.
(17:04:42) ***ericP beats me, was locally muted
(17:04:56) ***mscottm I muted Andrew. :)
(17:05:03) mscottm: Zakim, unmute +41.61.324.aabb
(17:05:03) Zakim: +41.61.324.aabb should no longer be muted
(17:05:14) zhaoj [chatzilla@] hat den Raum betreten.
(17:05:49) matthias_samwald:  Scott: We could think about putting some of the RDF generated by Andrew in our knowledge base
(17:06:14) zhaoj hat den Raum verlassen (quit: Quit: ChatZilla 0.9.84 [Firefox 3.0.6/2009011913]).
(17:06:43) matthias_samwald: ... he also joined the last HCLS F2F
(17:07:07) matthias_samwald: Kei: In the next meeting, Scott will talk more about AIDA 
(17:07:14) matthias_samwald: ... the next meeting will be in two weeks.
(17:07:17) Jun [chatzilla@] hat den Raum betreten.
(17:07:28) Jun: hi, I am sorry, but I cant' dial in
(17:07:33) matthias_samwald: Bye!
(17:07:37) adrianpaschke: thanks, bye
(17:07:39) Zakim: -adrianpaschke
(17:07:41) Zakim: -??P16
(17:07:42) matthias_samwald: Jun, you fell victim to the daylight savings
(17:07:43) Zakim: -EricP
(17:07:44) matthias_samwald: in the US
(17:07:45) Zakim: - +2
(17:07:45) rfrost hat den Raum verlassen (quit: Quit: http://www.mibbit.com ajax IRC Client).
(17:07:48) Zakim: -Kei_Cheung
(17:07:49) Zakim: - +41.61.324.aabb
(17:07:52) Zakim: -egonw
(17:07:54) matthias_samwald: the call is ending right now.
(17:07:56) agibson hat den Raum verlassen.
(17:07:57) egonw: thanx all
(17:08:05) Zakim: -matthias_samwald
(17:08:16) mscottm: time diff in U.S. is only  4hours to UK now