W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > March 2007

minutes BioRDF 19 Mar 2007

From: Eric Prud'hommeaux <eric@w3.org>
Date: Thu, 22 Mar 2007 16:03:50 -0400
To: public-semweb-lifesci@w3.org
Message-ID: <20070322200350.GS4098@w3.org>
http://www.w3.org/2007/03/19-BioRDF-minutes



   [1]W3C 

                                    BioRDF

19 Mar 2007

   See also: [2]IRC log

Attendees

   Present
          Scott_Marshall, Vipul_Kashyap, Elizabeth, John_Barkley,
          Olivier_Bodenreider, Helen_Chen, Alan_Ruttenberg, EricP,
          Don_Doherty, Kei_Cheung, MIT308, Michael Heuer (heuermh)

   Regrets
   Chair
          Vipul, AlanR

   Scribe
          ericP

Contents

     * [3]Topics
         1. [4]Action items review
         2. [5]MESH terms
         3. [6]update on use case (ericP)
         4. [7]introduce Michael Heuer
     * [8]Summary of Action Items
     _________________________________________________________________

   [9]13 March F2F minutes

Action items review

   ACTION: Alan asks Olivier about MeSH terms [recorded in
   [10]http://www.w3.org/2007/03/19-BioRDF-minutes.html#action01]

   <vipul> Don update on mapping of BAM names

   ACTION: Elizabeth to ask June about states of Alz [recorded in
   [11]http://www.w3.org/2007/03/19-BioRDF-minutes.html#action02]

   ACTION: Alan to show example of curation contradiction, biology
   contradiction for demo, based on Kei's action [CONTINUES] [recorded in
   [12]http://www.w3.org/2007/03/19-BioRDF-minutes.html#action03]

   AlanR: two types of contradiction
   ... statement -- two people say X said something different
   ... biology -- brain has 3, no 4 (latent discovery), receptors
   ... demonstrated as little snippets
   ... in how OWL reasoning helps us

   AlanR: general issue is mapping (sameAs or equivClass)
   ... Don looking at this for MESH terms

   ACTION: Kei look at
   [13]http://hissa.nist.gov/jb/biordf-demo/bams_cell_names.txt too. Alan
   send list to Cell ontology people for maps as well. [CONTINUES]
   [recorded in
   [14]http://www.w3.org/2007/03/19-BioRDF-minutes.html#action05]

   ACTION: Don will try to map these lists to MESH. Talk to Bill Bug.
   [CONTINUES] [recorded in
   [15]http://www.w3.org/2007/03/19-BioRDF-minutes.html#action06]

   Olivier: OWL version of MESH is unoffical and unsupported
   ... MESH requested it be withdrawn because it has bad features:
   ... wrond IDs
   ... oversimplifies MESH
   ... leads to inaccurate relations
   ... (liver is a kind of abdomen)

   AlanR: were planning to use it because they had URIs for MESH terms

   Olivier: they are the wrong URIs -- used tree number, which simply
   indicates the position in the MESH tree
   ... should use MESH id (starts with D for main headings), and not
   numbers with '.'s in them
   ... a main heading have several tree numbers
   ... not unique

   AlanR: we need URIs for MESH terms

   Olvier: point well taken
   ... for this purpose, make up a URI: NLM + "mesh" + MESH id

   Matthias: did this. will send URL after meeting

   Olivier: probably much to use Matthias's version
   ... Gus Shriber also translated MESH to SKOS last summer
   ...have mapped every UMLs concept to MESH

   ACTION: ScottM to get a URL from Gus Shriber for MESH work [recorded
   in [16]http://www.w3.org/2007/03/19-BioRDF-minutes.html#action07]

   ACTION: Olivier to provide guidance to Don Doherty for finding
   mappings between BAM and MeSH [recorded in
   [17]http://www.w3.org/2007/03/19-BioRDF-minutes.html#action08]

   <samwaldmatthias> Here is the URL for my newer SKOS version of MeSH
   2007, based on the unique MeSH IDs:
   [18]http://neuroscientific.net/ont/bio-zen-MESH-new.zip

   Kei: we have example inconsistent data in NeuronDB

   ACTION: Kei to identify URL for terms in
   [19]http://hissa.nist.gov/jb/biordf-demo/bams_part_names.txt that are
   already in neurondb etc [WITHDRAWN] [recorded in
   [20]http://www.w3.org/2007/03/19-BioRDF-minutes.html#action09]

   ACTION: Kei, Bill to identify URL for terms in
   [21]http://hissa.nist.gov/jb/biordf-demo/bams_part_names.txt that are
   already in neurondb etc [recorded in
   [22]http://www.w3.org/2007/03/19-BioRDF-minutes.html#action10]

   <mscottm> The Guus Schreiber student that I think was involved with
   the MESH SKOS work is Willem van Hage
   [23]http://www.few.vu.nl/~wrvhage/index_work.html

   ACTION: Don see what's in brainmaps that would be of use for our
   scientific use case and demo [CONTINUES] [recorded in
   [24]http://www.w3.org/2007/03/19-BioRDF-minutes.html#action12]

   Don: just looking to see if we can use [25]http://brainmaps.org/

   ACTION: Melli will think about what image processing could be done on
   brainmaps images [CONTINUES] [recorded in
   [26]http://www.w3.org/2007/03/19-BioRDF-minutes.html#action13]

MESH terms

   AlanR: want MESH to PubMed mapping
   ... what do MESH descriptions of pubmed terms mean?

   Olivier: '*'s reprepsent main topic in medline paper
   ... subheadings give facets of the main heading
   ... main headings identify single MESH term

   Note: main medline headings identify a single MESH term

   AlanR: first things is MESH term, and each '/' is a facet, and '*'
   someone signifies special lines

   ACTION: Olivier to send (to list) pointer to MESH curation manual
   [recorded in
   [27]http://www.w3.org/2007/03/19-BioRDF-minutes.html#action14]

   ACTION: Olivier to send pointer to a pubmedID to MESHid mapping
   [recorded in
   [28]http://www.w3.org/2007/03/19-BioRDF-minutes.html#action15]

update on use case

   ericP: am importing JAX data into
   [29]http://www.w3.org/2007/03/entrez-gene/snapshots/

   AlanR: start with accurate set of MESH terms

   <mscottm> Mark van Assem.

   <mscottm> [30]http://thesauri.cs.vu.nl/

   AlanR: our demo keeps us on track
   ... but our real compelling demo will come from things that people
   like June discover as we assemble this

   Kei: in senselab, we export in RDF and OWL
   ... which should we focus on?

   AlanR: prefer OWL -- just a focused sublanguage of RDF

   <samwaldmatthias> [31]http://3ba.se/

   <samwaldmatthias> [32]http://3ba.se/

   -> [33]http://3ba.se/ OntoWiki

   matthias: on left, see KBs

   -> [34]http://3ba.se/instance.php?model=http://3ba.se/conferences/

   scribe: classes on left
   ... classes and individuals rendered differently
   ... clicking on a class gives a list of individuals

   [35]http://3ba.se/index.php?instance=AIMSA2006

   scribe: can click on Edit, or in-line in the actions box
   ... would like to use OntoWiki to show that RDF is not something the
   scientists use in the labs and they export data, but instead something
   that we can use
   ... OntoWiki not tailored to a particular ontology, just upload
   RDFS/OWL and you can visualize the data

   vipul: can you edit classes, or just instances?

   matthias: can add classes, but this is not the main use case

   vipul: could import all our demo data into wiki

   matthias: shouldn't be an afterthought

   vipul: also considering faceted browser
   ... also AlanR's prefuse

   <samwaldmatthias> prefuse

   scott: faceted browser of OntoWiki are handy for browsing data
   ... the faceted browser incorporates selected facets into a query
   ... faceted browser shows thumbnails and "..." for plentiful data for
   further refinement

   <alanr> times up

   <alanr> got to go...

   matthias: yes, can SPARQL OntoWiki

   <alanr> Welcome Michael!

   vipul: would like scott amd matthias to recommend UI

introduce Michael Heuer

   <vipul> Gotta go...

   <mscottm> Mark van Assem.

   <mscottm> [36]http://thesauri.cs.vu.nl/

   UNKNOWN_SPEAKER: have a couple weeks slack and volunteering to Alzgene
   to OWL

   Elizabeth: you have contacts at Alzforum?

   AlanR: working me right now

   <mscottm> Mark van Assem.

   <mscottm> [37]http://thesauri.cs.vu.nl/

   -> [38]http://thesauri.cs.vu.nl/ MESH mapping

   ACTION: Kei, June, Gwen, coordinate creating list of symptoms, stages,
   life course of the disease [CONTINUES] [recorded in
   [39]http://www.w3.org/2007/03/19-BioRDF-minutes.html#action16]

   ACTION: Kei: Brainpharm OWL should have enough to do query for known
   contradictions, e.g. disagreement about whether something is in a
   particular compartment [CONTINUES] [recorded in
   [40]http://www.w3.org/2007/03/19-BioRDF-minutes.html#action17]

   ACTION: Eric mapping demo using dartgrid [DROPPED] [recorded in
   [41]http://www.w3.org/2007/03/19-BioRDF-minutes.html#action21]

   <heuermh> For the record, +1.612.821.aaaa is me, Michael Heuer

Summary of Action Items

   [NEW] ACTION: Alan asks Olivier about MeSH terms [recorded in
   [42]http://www.w3.org/2007/03/19-BioRDF-minutes.html#action01]
   [NEW] ACTION: Don see what's in brainmaps that would be of use for our
   scientific use case and demo [recorded in
   [43]http://www.w3.org/2007/03/19-BioRDF-minutes.html#action12]
   [NEW] ACTION: Elizabeth to ask June about states of Alz [recorded in
   [44]http://www.w3.org/2007/03/19-BioRDF-minutes.html#action02]
   [NEW] ACTION: Kei to identify URL for terms in
   [45]http://hissa.nist.gov/jb/biordf-demo/bams_part_names.txt that are
   already in neurondb etc [recorded in
   [46]http://www.w3.org/2007/03/19-BioRDF-minutes.html#action04]
   [NEW] ACTION: Kei, Bill to identify URL for terms in
   [47]http://hissa.nist.gov/jb/biordf-demo/bams_part_names.txt that are
   already in neurondb etc [recorded in
   [48]http://www.w3.org/2007/03/19-BioRDF-minutes.html#action10]
   [NEW] ACTION: Olivier to provide guidance to Don Doherty for finding
   mappings between BAM and MeSH [recorded in
   [49]http://www.w3.org/2007/03/19-BioRDF-minutes.html#action08]
   [NEW] ACTION: Olivier to send (to list) pointer to MESH curation
   manual [recorded in
   [50]http://www.w3.org/2007/03/19-BioRDF-minutes.html#action14]
   [NEW] ACTION: Olivier to send pointer to a pubmedID to MESHid mapping
   [recorded in
   [51]http://www.w3.org/2007/03/19-BioRDF-minutes.html#action15]
   [NEW] ACTION: ScottM to get a URL from Gus Shriber for MESH work
   [recorded in
   [52]http://www.w3.org/2007/03/19-BioRDF-minutes.html#action07]

   [PENDING] ACTION: Alan to show example of curation contradiction,
   biology contradiction for demo, based on Kei's action [recorded in
   [53]http://www.w3.org/2007/03/19-BioRDF-minutes.html#action03]
   [PENDING] ACTION: Don will try to map these lists to MESH. Talk to
   Bill Bug. [recorded in
   [54]http://www.w3.org/2007/03/19-BioRDF-minutes.html#action06]
   [PENDING] ACTION: Kei look at
   [55]http://hissa.nist.gov/jb/biordf-demo/bams_cell_names.txt too. Alan
   send list to Cell ontology people for maps as well. [recorded in
   [56]http://www.w3.org/2007/03/19-BioRDF-minutes.html#action05]
   [PENDING] ACTION: Kei, June, Gwen, coordinate creating list of
   symptoms, stages, life course of the disease [recorded in
   [57]http://www.w3.org/2007/03/19-BioRDF-minutes.html#action16]
   [PENDING] ACTION: Kei: Brainpharm OWL should have enough to do query
   for known contradictions, e.g. disagreement about whether something is
   in a particular compartment [recorded in
   [58]http://www.w3.org/2007/03/19-BioRDF-minutes.html#action17]
   [PENDING] ACTION: Melli will think about what image processing could
   be done on brainmaps images [recorded in
   [59]http://www.w3.org/2007/03/19-BioRDF-minutes.html#action13]

   [DROPPED] ACTION: Eric mapping demo using dartgrid [recorded in
   [60]http://www.w3.org/2007/03/19-BioRDF-minutes.html#action21]

   [DROPPED] ACTION: Kei to identify URL for terms in
   [61]http://hissa.nist.gov/jb/biordf-demo/bams_part_names.txt that are
   already in neurondb etc [recorded in
   [62]http://www.w3.org/2007/03/19-BioRDF-minutes.html#action09]

   [End of minutes]
     _________________________________________________________________


    Minutes formatted by David Booth's [63]scribe.perl version 1.128
    ([64]CVS log)
    $Date: 2007/03/22 19:54:40 $

References

   1. http://www.w3.org/
   2. http://www.w3.org/2007/03/19-BioRDF-irc
   3. http://www.w3.org/2007/03/19-BioRDF-minutes#agenda
   4. http://www.w3.org/2007/03/19-BioRDF-minutes#item00
   5. http://www.w3.org/2007/03/19-BioRDF-minutes#item01
   6. http://www.w3.org/2007/03/19-BioRDF-minutes#item02
   7. http://www.w3.org/2007/03/19-BioRDF-minutes#item03
   8. http://www.w3.org/2007/03/19-BioRDF-minutes#ActionSummary
   9. http://www.w3.org/2007/03/13-BioRDF-irc
  10. http://www.w3.org/2007/03/19-BioRDF-minutes.html#action01
  11. http://www.w3.org/2007/03/19-BioRDF-minutes.html#action02
  12. http://www.w3.org/2007/03/19-BioRDF-minutes.html#action03
  13. http://hissa.nist.gov/jb/biordf-demo/bams_cell_names.txt
  14. http://www.w3.org/2007/03/19-BioRDF-minutes.html#action05
  15. http://www.w3.org/2007/03/19-BioRDF-minutes.html#action06
  16. http://www.w3.org/2007/03/19-BioRDF-minutes.html#action07
  17. http://www.w3.org/2007/03/19-BioRDF-minutes.html#action08
  18. http://neuroscientific.net/ont/bio-zen-MESH-new.zip
  19. http://hissa.nist.gov/jb/biordf-demo/bams_part_names.txt
  20. http://www.w3.org/2007/03/19-BioRDF-minutes.html#action09
  21. http://hissa.nist.gov/jb/biordf-demo/bams_part_names.txt
  22. http://www.w3.org/2007/03/19-BioRDF-minutes.html#action10
  23. http://www.few.vu.nl/~wrvhage/index_work.html
  24. http://www.w3.org/2007/03/19-BioRDF-minutes.html#action12
  25. http://brainmaps.org/
  26. http://www.w3.org/2007/03/19-BioRDF-minutes.html#action13
  27. http://www.w3.org/2007/03/19-BioRDF-minutes.html#action14
  28. http://www.w3.org/2007/03/19-BioRDF-minutes.html#action15
  29. http://www.w3.org/2007/03/entrez-gene/snapshots/
  30. http://thesauri.cs.vu.nl/
  31. http://3ba.se/
  32. http://3ba.se/
  33. http://3ba.se/
  34. http://3ba.se/instance.php?model=http://3ba.se/conferences/
  35. http://3ba.se/index.php?instance=AIMSA2006
  36. http://thesauri.cs.vu.nl/
  37. http://thesauri.cs.vu.nl/
  38. http://thesauri.cs.vu.nl/
  39. http://www.w3.org/2007/03/19-BioRDF-minutes.html#action16
  40. http://www.w3.org/2007/03/19-BioRDF-minutes.html#action17
  41. http://www.w3.org/2007/03/19-BioRDF-minutes.html#action21
  42. http://www.w3.org/2007/03/19-BioRDF-minutes.html#action01
  43. http://www.w3.org/2007/03/19-BioRDF-minutes.html#action12
  44. http://www.w3.org/2007/03/19-BioRDF-minutes.html#action02
  45. http://hissa.nist.gov/jb/biordf-demo/bams_part_names.txt
  46. http://www.w3.org/2007/03/19-BioRDF-minutes.html#action04
  47. http://hissa.nist.gov/jb/biordf-demo/bams_part_names.txt
  48. http://www.w3.org/2007/03/19-BioRDF-minutes.html#action10
  49. http://www.w3.org/2007/03/19-BioRDF-minutes.html#action08
  50. http://www.w3.org/2007/03/19-BioRDF-minutes.html#action14
  51. http://www.w3.org/2007/03/19-BioRDF-minutes.html#action15
  52. http://www.w3.org/2007/03/19-BioRDF-minutes.html#action07
  53. http://www.w3.org/2007/03/19-BioRDF-minutes.html#action03
  54. http://www.w3.org/2007/03/19-BioRDF-minutes.html#action06
  55. http://hissa.nist.gov/jb/biordf-demo/bams_cell_names.txt
  56. http://www.w3.org/2007/03/19-BioRDF-minutes.html#action05
  57. http://www.w3.org/2007/03/19-BioRDF-minutes.html#action16
  58. http://www.w3.org/2007/03/19-BioRDF-minutes.html#action17
  59. http://www.w3.org/2007/03/19-BioRDF-minutes.html#action13
  60. http://www.w3.org/2007/03/19-BioRDF-minutes.html#action21
  61. http://hissa.nist.gov/jb/biordf-demo/bams_part_names.txt
  62. http://www.w3.org/2007/03/19-BioRDF-minutes.html#action09
  63. http://dev.w3.org/cvsweb/~checkout~/2002/scribe/scribedoc.htm
  64. http://dev.w3.org/cvsweb/2002/scribe/

-- 
-eric

office: +1.617.258.5741 NE43-344, MIT, Cambridge, MA 02144 USA

(eric@w3.org)
Feel free to forward this message to any list for any purpose other than
email address distribution.

Received on Thursday, 22 March 2007 20:04:48 UTC

This archive was generated by hypermail 2.3.1 : Wednesday, 7 January 2015 14:52:30 UTC