- 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 MESH requested it be withdrawn because it has bad features: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)
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Received on Thursday, 22 March 2007 20:04:48 UTC