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17:33:39 <RRSAgent> logging to http://www.w3.org/2007/03/13-BioRDF-irc
17:33:47 <ericP> Zakim, this is BioRDF
17:33:47 <Zakim> ok, ericP; that matches SW_HCLS(BioRDF)1:00PM
17:34:24 <Don> Don has joined #biordf
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17:41:31 <alanr> alanr has joined #biordf
17:42:17 <alanr> Agenda+ Review John's current RDF
17:42:30 <jar> jar has joined #biordf
17:42:33 <alanr> Agenda+ Review NeuronDB OWL and comments about it
17:43:10 <alanr> Agenda+ Review Jonathan's NLP results. Try some queries.
17:43:29 <alanr> Agenda+ Talk about Orthology modeling (Eric, Jonathan)
17:43:42 <alanr> Agenda+ Review RGD discussion/resources there
17:44:13 <alanr> Agenda+ Review Allen Brain Atlas RDF. Devise queries we would like them to implement
17:46:26 <alanr> Agenda+ Perhaps: Lession on how to discover what's in an RDF store.
17:47:41 <alanr> Review brainmaps.org and see what we could use from it
17:48:47 <alanr> Kei has arrived.
17:49:50 <alanr> zakim, read my mind
17:49:50 <Zakim> I don't understand 'read my mind', alanr
17:51:14 <alanr> Agenda+ EricN reports on status of tox demo
17:54:28 <alanr> Agenda+ WuaJun introduce us to his system and we ask questions
17:56:55 <alanr> mesh terms about paper June is describing: MH  - Alzheimer Disease/etiology
17:56:55 <alanr> MH  - Amyloid Precursor Protein Secretases
17:56:55 <alanr> MH  - Amyloid beta-Protein/chemistry/metabolism/physiology/*secretion
17:56:55 <alanr> MH  - Animals
17:56:55 <alanr> MH  - Aspartic Endopeptidases
17:56:56 <alanr> MH  - CHO Cells
17:56:58 <alanr> MH  - Cricetinae
17:57:00 <alanr> MH  - Culture Media, Conditioned
17:57:02 <alanr> MH  - Endopeptidases/metabolism
17:57:04 <alanr> MH  - Hippocampus/*physiology
17:57:06 <alanr> MH  - Humans
17:57:08 <alanr> MH  - Insulysin/metabolism
17:57:10 <alanr> MH  - Long-Term Potentiation/*physiology
17:57:12 <alanr> MH  - Microsomes/metabolism
17:57:14 <alanr> MH  - Protease Inhibitors/pharmacology
17:57:16 <alanr> MH  - Rats
17:57:18 <alanr> MH  - Recombinant Proteins
17:57:20 <alanr> MH  - Senile Plaques/*metabolism
17:57:22 <alanr> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=Display&DB=pubmed 
17:57:24 <alanr> Also see RN lines
18:01:41 <alanr> Agenda+ How to state evidence for a fact in OWL
18:06:41 <alanr> "pathogenic narrative ontology"
18:10:33 <alanr> Action: Kei, June, Gwen, coordinate creating list of symptoms, stages, life course of the disease.
18:10:38 <Don> http://en.wikipedia.org/wiki/Diagnostic_and_Statistical_Manual_of_Mental_Disorders
18:10:49 <Don> See 2.1 Categorization
18:11:49 <alanr> Last action, Don too.
18:13:58 <ericP> alanr, i can put the orthology mapping on the wiki
18:14:09 <ericP> (or anyone else)
18:14:34 <ericP> i don't know the topology particularly well. got a recomendation for what wiki page?
18:17:11 <jar> jar has joined #biordf
18:23:16 <alanr> http://purl.org/obo/owl/MESH
18:43:37 <alanr> Action: Kei: Brainpharm OWL should have enough to do query for known contradictions, e.g. disagreement about whether something is in a particular compartment
18:48:38 <alanr> Action: Alan: Show example of curation contradiction, biology contradiction for demo, based on Kei's action
18:56:55 <alanr> agenda?
18:58:17 <ericP> Zakim, close agendum 2
18:58:17 <Zakim> agendum 2, Review NeuronDB OWL and comments about it, closed
18:58:18 <Zakim> I see 9 items remaining on the agenda; the next one is
18:58:19 <Zakim> 1. Review John's current RDF [from alanr]
18:58:54 <ericP> Zakim, take up agendum 1
18:58:54 <Zakim> agendum 1. "Review John's current RDF" taken up [from alanr]
19:01:00 <alanr> 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
19:03:51 <alanr> 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. 
19:05:11 <alanr> Action: Don will try to map these lists to MESH. Talk to Bill Bug.
19:23:46 <Zakim> -John_Barkley
19:24:40 <ericP> Zakim, close agendum 1
19:24:40 <Zakim> agendum 1, Review John's current RDF, closed
19:24:41 <Zakim> I see 8 items remaining on the agenda; the next one is
19:24:42 <Zakim> 3. Review Jonathan's NLP results. Try some queries. [from alanr]
19:25:04 <ericP> Zakim, take up agendum 4
19:25:04 <Zakim> agendum 4. "Talk about Orthology modeling (Eric, Jonathan)" taken up [from alanr]
19:25:36 <ericP> -> http://www.w3.org/2007/03/entrez-gene/ entrez-gene namespace
19:28:47 <Zakim> disconnecting the lone participant, MIT-G451, in SW_HCLS(BioRDF)1:00PM
19:28:49 <Zakim> SW_HCLS(BioRDF)1:00PM has ended
19:28:51 <Zakim> Attendees were John_Barkley, MIT-G451
19:39:41 <Don> Don has joined #biordf
20:00:36 <ericP> Zakim, please close this agendum
20:00:36 <Zakim> agendum 4 closed
20:00:37 <Zakim> I see 7 items remaining on the agenda; the next one is
20:00:38 <Zakim> 3. Review Jonathan's NLP results. Try some queries. [from alanr]
20:05:08 <ericP> Zakim, take up agendum 9
20:05:08 <Zakim> agendum 9. "WuaJun introduce us to his system and we ask questions" taken up [from alanr]
20:33:45 <ericP> q+ to ask what the mapping info looks like — can i re-use it for SPASQL?
20:37:15 <alanr> Action: Eric mapping demo using dartgrid
20:41:09 <ericP> zakim, please close this agendum
20:41:09 <Zakim> I see a speaker queue remaining and respectfully decline to close this agendum, ericP
20:41:16 <ericP> q-
20:41:17 <ericP> zakim, please close this agendum
20:41:17 <Zakim> agendum 9 closed
20:41:18 <Zakim> I see 6 items remaining on the agenda; the next one is
20:41:20 <Zakim> 3. Review Jonathan's NLP results. Try some queries. [from alanr]
20:43:04 <jar> jar has joined #biordf
20:43:49 <ericP> agenda?
20:45:26 <ericP> close agendum 8
20:53:44 <alanr> Action: Don see what's in brainmaps that would be of use for our scientific use case and demo
20:54:04 <alanr> Action: Melli will think about what image processing could be done on brainmaps images
21:22:27 <Don> prefix sc: <http://sw.neurocommons.org/2007/annotations#> 
21:22:27 <Don> SELECT distinct ?pubmed  WHERE  
21:22:27 <Don>   { ?pubmed sc:has-abstract ?abstract. 
21:22:27 <Don>     ?span sc:has-context ?abstract. 
21:22:27 <Don>     ?span sc:nc-0.0-mentions ?ggp. 
21:22:28 <Don>     ?ggp sc:if-human-identified-as ?generecord. 
21:22:30 <Don>     filter (regexp(str(?generecord),".*599?")) 
21:22:32 <Don> prefix sc: <http://sw.neurocommons.org/2007/annotations#> 
21:22:34 <Don> SELECT distinct ?pubmed  WHERE  
21:22:36 <Don>   { ?pubmed sc:has-abstract ?abstract. 
21:22:38 <Don>     ?span sc:has-context ?abstract. 
21:22:40 <Don>     ?span sc:nc-0.0-mentions ?ggp. 
21:22:42 <Don>     ?ggp sc:if-human-identified-as ?generecord. 
21:22:44 <Don>     filter (regexp(str(?generecord),".*599?")) 
21:22:46 <Don> prefix sc: <http://sw.neurocommons.org/2007/annotations#> 
21:22:48 <Don> SELECT distinct ?pubmed  WHERE  
21:22:50 <Don>   { ?pubmed sc:has-abstract ?abstract. 
21:22:52 <Don>     ?span sc:has-context ?abstract. 
21:22:54 <Don>     ?span sc:nc-0.0-mentions ?ggp. 
21:22:56 <Don>     ?ggp sc:if-human-identified-as ?generecord. 
21:22:58 <Don>     filter (regexp(str(?generecord),".*599?")) 
21:23:00 <Don> prefix sc: <http://sw.neurocommons.org/2007/annotations#> 
21:23:02 <Don> SELECT distinct ?pubmed  WHERE  
21:23:10 <Don>   { ?pubmed sc:has-abstract ?abstract. 
21:23:10 <Don>     ?span sc:has-context ?abstract. 
21:23:10 <Don>     ?span sc:nc-0.0-mentions ?ggp. 
21:23:10 <Don>     ?ggp sc:if-human-identified-as ?generecord. 
21:23:12 <Don>     filter (regexp(str(?generecord),".*599?")) 
21:23:14 <Don> }
21:23:43 <ericP> http://www.w3.org/2005/01/yacker/uploads/SPARQL?lang=perl&text=prefix+sc%3A+%3Chttp%3A%2F%2Fsw.neurocommons.org%2F2007%2Fannotations%23%3E%0D%0ASELECT+distinct+%3Fpubmed++WHERE%0D%0A++%7B+%3Fpubmed+sc%3Ahas-abstract+%3Fabstract.%0D%0A++++%3Fspan+sc%3Ahas-context+%3Fabstract.%0D%0A++++%3Fspan+sc%3Anc-0.0-mentions+%3Fggp.%0D%0A++++%3Fggp+sc%3Aif-human-identified-as+%3Fgenerecord.%0D%0A++++filter+%28regex%28str%28%3Fgenerecord%29%2C%22.*599%3F%22%29%29%0D%0A++%7D&ac
21:24:37 <ericP> http://w3.org/brief/MzQ=
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