15:00:11 <RRSAgent> RRSAgent has joined #BioRDF
15:00:11 <RRSAgent> logging to http://www.w3.org/2007/03/19-BioRDF-irc
15:00:25 <vipul> rrsagent, make logs world-visible
15:01:21 <vipul> Zakim, who's on the call?
15:01:21 <Zakim> sorry, vipul, I don't know what conference this is
15:01:23 <Zakim> On IRC I see RRSAgent, samwaldmatthias, Zakim, vipul, ericP
15:01:36 <vipul> Zakim, this is BIORDF
15:01:37 <Zakim> ok, vipul; that matches SW_HCLS(BioRDF)11:00AM
15:01:43 <Zakim> +John_Barkley
15:02:03 <vipul> zakim, who's on the call?
15:02:03 <Zakim> On the phone I see Scott_Marshall, Vipul_Kashyap, Elizabeth, John_Barkley
15:02:14 <Zakim> +Olivier_Bodenreider
15:02:55 <vipul> ericP are you in Zakim, yet?
15:02:59 <Zakim> +??P21
15:03:08 <mscottm> mscottm has joined #biordf
15:03:28 <vipul> Zakim, +??P21 is Matthias
15:03:28 <Zakim> sorry, vipul, I do not recognize a party named '+??P21'
15:04:14 <Zakim> +Helen_Chen
15:05:22 <helen> helen has joined #BioRDF
15:05:28 <Zakim> +Alan_Ruttenberg
15:05:58 <vipul> Zakim, who's on the call 
15:05:58 <Zakim> I don't understand 'who's on the call', vipul
15:06:10 <vipul> Zakim, who's on the call?
15:06:10 <Zakim> On the phone I see Scott_Marshall, Vipul_Kashyap, Elizabeth, John_Barkley, Olivier_Bodenreider, ??P21, Helen_Chen, Alan_Ruttenberg
15:06:18 <Zakim> +EricP
15:08:02 <vipul> http://www.w3.org/2007/03/13-BioRDF-irc
15:08:45 <ericP> all now accessible according to http://www.w3.org/2007/03/13-BioRDF-*,access*
15:08:50 <vipul> ACTION: Alan asks Olivier about MeSH terms
15:09:28 <vipul> Agenda:
15:09:32 <vipul> Hardware
15:09:35 <ericP> agenda + hardware
15:09:39 <vipul> John Barkley update
15:09:40 <ericP> agenda + JohnB update
15:09:43 <vipul> Eric P update
15:09:43 <ericP> agenda + ericP update
15:09:56 <vipul> Don update on mapping of BAM names
15:10:01 <ericP> agenda + Don update of BAM names
15:10:54 <ericP> ACTION: Elizabeth to ask June about states of Alz
15:12:06 <Zakim> +Don_Doherty
15:12:13 <ericP> Action: Alan: Show example of curation contradiction, biology contradiction for demo, based on Kei's action
15:12:18 <ericP> CONTINUES
15:12:21 <Don> Don has joined #biordf
15:12:41 <ericP> AlanR: two types of contradiction
15:12:54 <ewu> ewu has joined #BIORDF
15:13:11 <ericP> ...  statement -- two people say X said something different
15:13:44 <ericP> ...  biology -- brain has 3, no 4 (latent discovery), receptors
15:14:05 <ericP> ... demonstrated as little snippets
15:14:18 <ericP> ... in how OWL reasoning helps us
15:15:27 <ericP> Action: Kei to identify URL for terms in http://hissa.nist.gov/jb/biordf-demo/bams_part_names.txt that are already in neurondb etc
15:16:35 <ericP> AlanR: general issue is mapping (sameAs or equivClass)
15:16:51 <ericP> ... Don looking at this for MESH terms
15:17:03 <ericP> CONTINUES
15:17:15 <ericP> Action: Kei look at http://hissa.nist.gov/jb/biordf-demo/bams_cell_names.txt too. Alan send list to Cell ontology people for maps as well.
15:17:18 <ericP> CONTINUES
15:17:29 <ericP> Action: Don will try to map these lists to MESH. Talk to Bill Bug.
15:17:43 <ericP> CONTINUES
15:18:28 <Zakim> +Kei_Cheung
15:18:38 <ericP> Olivier: OWL version of MESH is unoffical and unsupported
15:19:05 <ericP> ... MESH requested it be withdrawn because it has bad features:
15:19:13 <ericP> ...   wrond IDs
15:19:24 <ericP> ...   oversimplifies MESH
15:19:25 <samwaldmatthias> q+
15:19:37 <ericP> ...   leads to inaccurate relations
15:19:51 <ericP> ...     (liver is a kind of abdomen)
15:20:08 <ericP> AlanR: were planning to use it because they had URIs for MESH terms
15:20:47 <ericP> Olivier: they are the wrong URIs -- used tree number, which simply indicates the position in the MESH tree
15:21:14 <ericP> ... should use MESH id (starts with D for main headings), and not numbers with '.'s in them
15:21:27 <ericP> ... a main heading have several tree numbers
15:21:33 <ericP> ... not unique
15:21:55 <ericP> AlanR: we need URIs for MESH terms
15:22:02 <ericP> Olvier: point well taken
15:22:42 <ericP> ... for this purpose, make up a URI: NLM + "mesh" + MESH id
15:22:53 <vipul> q
15:23:01 <vipul> q?
15:23:25 <Zakim> +MIT308
15:23:29 <Zakim> -Alan_Ruttenberg
15:23:32 <ericP> Zakim, who is here?
15:23:32 <Zakim> On the phone I see Scott_Marshall, Vipul_Kashyap, Elizabeth, John_Barkley, Olivier_Bodenreider, ??P21, Helen_Chen, EricP, Don_Doherty, Kei_Cheung, MIT308
15:23:35 <Zakim> On IRC I see ewu, Don, helen, mscottm, RRSAgent, samwaldmatthias, Zakim, vipul, ericP
15:24:03 <ericP> Matthias: did this. will send URL after meeting
15:24:30 <ericP> Olivier: probably much to use Matthias's version
15:24:52 <ericP> ... Gus Shriber also translated MESH to SKOS last summer
15:25:32 <heuermh> heuermh has joined #BioRDF
15:26:17 <ericP> ACTION: ScottM to get a URL from Gus Shriber for MESH work
15:26:58 <vipul> ACTION: Olivier to provide guidance to Don Doherty for finding mappings between BAM and MeSH
15:28:49 <samwaldmatthias> Here is the URL for my newer SKOS version of MeSH 2007, based on the unique MeSH IDs: http://neuroscientific.net/ont/bio-zen-MESH-new.zip
15:28:53 <ericP> have mapped every UMLs concept to MESH
15:28:55 <vipul> q?
15:30:01 <ericP> Kei: we have example inconsistent data in NeuronDB
15:32:03 <ericP> Action: Kei to identify URL for terms in http://hissa.nist.gov/jb/biordf-demo/bams_part_names.txt that are already in neurondb etc
15:32:08 <ericP> WITHDRAWN
15:32:16 <ericP> Action: Kei, Bill to identify URL for terms in http://hissa.nist.gov/jb/biordf-demo/bams_part_names.txt that are already in neurondb etc
15:32:19 <mscottm> The Guus Schreiber student that I think was involved with the MESH SKOS work is Willem van Hage http://www.few.vu.nl/~wrvhage/index_work.html
15:32:42 <ericP> Action: Eric mapping demo using dartgrid
15:32:46 <ericP> CONTINUES
15:34:58 <ericP> Action: Don see what's in brainmaps that would be of use for our scientific use case and demo
15:36:13 <ericP> Don: just looking to see if we can use http://brainmaps.org/
15:36:15 <ericP> CONTINUES
15:36:39 <ericP> Action: Melli will think about what image processing could be done on brainmaps images
15:36:42 <ericP> CONTINUES
15:36:56 <ericP> topic: MESH terms
15:37:24 <ericP> AlanR: want MESH to PubMed mapping
15:37:41 <ericP> ... what do MESH descriptions of pubmed terms mean?
15:38:17 <ericP> Olivier: '*'s reprepsent main topic in medline paper
15:38:59 <ericP> ... subheadings give facets of the main heading
15:39:20 <ericP> ... main headings identify single MESH term
15:39:51 <ericP> Note: main medline headings identify a single MESH term
15:41:09 <ericP> AlanR: first things is MESH term, and each '/' is a facet, and '*' someone signifies special lines 
15:41:39 <ericP> ACTION: Olivier to send (to list) pointer to MESH curation manual
15:44:38 <ericP> ACTION: Olivier to send pointer to a pubmedID to MESHid 
15:44:58 <ericP> (mapping)
15:45:40 <ericP> Topic: update on use case
15:47:03 <ericP> ericP: am importing JAX data into http://www.w3.org/2007/03/entrez-gene/snapshots/
15:47:58 <ericP> AlanR: start with accurate set of MESH terms
15:48:33 <mscottm> Mark van Assem.
15:48:33 <mscottm> http://thesauri.cs.vu.nl/ 
15:48:48 <ericP> ... our demo keeps us on track
15:49:10 <ericP> ... but our real compelling demo will come from things that people like June discover as we assemble this
15:49:49 <ericP> Kei: in senselab, we export in RDF and OWL
15:49:56 <ericP> ... which should we focus on?
15:50:25 <ericP> AlanR: prefer OWL -- just a focused sublanguage of RDF
15:50:47 <samwaldmatthias> http://3ba.se/
15:51:03 <alanr> alanr has joined #biordf
15:51:10 <samwaldmatthias> http://3ba.se/
15:51:34 <ericP> -> http://3ba.se/ OntoWiki
15:51:43 <ericP> matthias: on left, see KBs
15:52:08 <ericP> -> http://3ba.se/instance.php?model=http://3ba.se/conferences/
15:52:31 <ericP> ... classes on left
15:53:06 <ericP> ... classes and individuals rendered differently
15:53:15 <ericP> ... clicking on a class gives a list of individuals
15:53:39 <ericP> http://3ba.se/index.php?instance=AIMSA2006
15:54:07 <ericP> ... can click on Edit, or in-line in the actions box
15:55:10 <ericP> ... 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
15:56:52 <ericP> ... OntoWiki not tailored to a particular ontology, just upload RDFS/OWL and you can visualize the data
15:57:17 <ericP> vipul: can you edit classes, or just instances?
15:57:36 <ericP> matthias: can add classes, but this is not the main use case
15:57:54 <ericP> q+ can we SPARQL it?
15:58:09 <Zakim> + +1.612.821.aaaa
15:59:23 <ericP> vipul: could import all our demo data into wiki
15:59:34 <ericP> matthias: shouldn't be an afterthought
15:59:51 <ericP> vipul: also considering faceted browser
16:00:15 <ericP> ... also AlanR's treeviews
16:00:26 <samwaldmatthias> prefuse
16:00:36 <ericP> s/treeviews/prefuse/
16:01:03 <ericP> scott: faceted browser of OntoWiki are handy for browsing data
16:01:52 <ericP> ... the faceted browser incorporates selected facets into a query
16:02:08 <ericP> q+ to ask if we can SPARQL OntoWiki
16:03:18 <ericP> scott: faceted browser shows thumbnails and "..." for plentiful data for further refinement
16:03:33 <alanr> times up
16:03:37 <alanr> got to go...
16:03:50 <ericP> matthias: yes, can SPARQL OntoWiki
16:04:00 <alanr> Welcome Michael!
16:04:56 <ericP> vipul: would like scott amd matthias to recommend UI
16:05:25 <ericP> topic: introduce Michael Heuer
16:05:26 <vipul> Gotta go...
16:05:50 <Zakim> -Vipul_Kashyap
16:05:51 <mscottm> Mark van Assem.
16:05:51 <mscottm> http://thesauri.cs.vu.nl/ 
16:06:06 <ericP> ... have a couple weeks slack and volunteering to Alzgene to OWL
16:06:59 <ericP> Elizabeth: you have contacts at Alzforum?
16:07:13 <ericP> AlanR: working me right now
16:07:21 <mscottm> Mark van Assem.
16:07:21 <mscottm> http://thesauri.cs.vu.nl/ 
16:07:24 <Zakim> -Helen_Chen
16:07:45 <Zakim> -Kei_Cheung
16:07:47 <Zakim> -MIT308
16:07:48 <ericP> -> http://thesauri.cs.vu.nl/ MESH mapping
16:07:49 <Zakim> -Scott_Marshall
16:07:50 <Zakim> - +1.612.821.aaaa
16:07:51 <Zakim> -John_Barkley
16:07:53 <Zakim> -Olivier_Bodenreider
16:07:54 <Zakim> -Elizabeth
16:07:55 <Zakim> -Don_Doherty
16:07:55 <Zakim> -??P21
16:07:57 <Zakim> -EricP
16:07:59 <Zakim> SW_HCLS(BioRDF)11:00AM has ended
16:08:01 <Zakim> Attendees were Scott_Marshall, Vipul_Kashyap, Elizabeth, John_Barkley, Olivier_Bodenreider, Helen_Chen, Alan_Ruttenberg, EricP, Don_Doherty, Kei_Cheung, MIT308, +1.612.821.aaaa
16:08:31 <ericP> Action: Kei, June, Gwen, coordinate creating list of symptoms, stages, life course of the disease
16:08:35 <ericP> CONTINUES
16:08:54 <ericP> Action: Kei: Brainpharm OWL should have enough to do query for known contradictions, e.g. disagreement about whether something is in a particular compartment
16:08:57 <ericP> CONTINUES
16:09:05 <ericP> Action: Alan: Show example of curation contradiction, biology contradiction for demo, based on Kei's action
16:09:08 <ericP> CONTINUES
16:09:32 <ericP> Action: Kei look at http://hissa.nist.gov/jb/biordf-demo/bams_cell_names.txt too. Alan send list to Cell ontology people for maps as well.
16:09:35 <ericP> CONTINUES
16:09:45 <ericP> Action: Don will try to map these lists to MESH. Talk to Bill Bug.
16:09:47 <ericP> CONTINUES
16:10:20 <ericP> Action: Eric mapping demo using dartgrid
16:10:21 <ericP> DONE
16:11:20 <heuermh> For the record, +1.612.821.aaaa is me, Michael Heuer
16:11:47 <ericP> Zakim, +1.612.821.aaaa was MichaelHeuer
16:11:47 <Zakim> I don't understand '+1.612.821.aaaa was MichaelHeuer', ericP
16:11:50 <ericP> Zakim, +1.612.821.aaaa is MichaelHeuer
16:11:50 <Zakim> sorry, ericP, I do not recognize a party named '+1.612.821.aaaa'
16:12:01 <ericP> RRSAgent, please draft minutes
16:12:01 <RRSAgent> I have made the request to generate http://www.w3.org/2007/03/19-BioRDF-minutes.html ericP
16:12:10 <ericP> RRSAgent, please make log world-visible
16:12:40 <ericP> heuermh, tx. looks like i'll have to patch that in the text file
16:12:57 <heuermh> no prob, thanks.
16:13:35 <heuermh> /bye
16:13:41 <heuermh> heuermh has left #BioRDF
17:09:07 <samwaldmatthias> samwaldmatthias has left #biordf