16:04:19 <RRSAgent> RRSAgent has joined #hcls
16:04:19 <RRSAgent> logging to http://www.w3.org/2010/11/29-hcls-irc
16:04:24 <matthias_samwald> indeed, eric.
16:04:47 <matthias_samwald> zakim, this is hcls
16:04:47 <Zakim> hcls matches both SW_HCLS(Disc)10:00AM and SW_HCLS(BioRDF)11:00AM, matthias_samwald
16:04:57 <matthias_samwald> zakim, this is BioRDF
16:04:57 <Zakim> ok, matthias_samwald; that matches SW_HCLS(BioRDF)11:00AM
16:06:42 <Zakim> + +44.122.383.aacc
16:06:45 <Zakim> +mscottm
16:07:03 <mscottm> mscottm has joined #hcls
16:07:07 <matthias_samwald> (Hi Scott, I will be only listening today)
16:07:10 <mscottm> Zakim, who is here?
16:07:10 <Zakim> On the phone I see +33.3.54.95.aaaa, +1.206.605.aabb, ??P21, +44.122.383.aacc, mscottm
16:07:11 <matthias_samwald> yes
16:07:13 <Zakim> On IRC I see mscottm, RRSAgent, Zakim, michael, matthias_samwald, adriencoulet, ericP
16:07:37 <matthias_samwald> zakim, ??P21 is matthias_samwald
16:07:37 <Zakim> +matthias_samwald; got it
16:07:46 <Zakim> +??P29
16:08:06 <adriencoulet> I am +33.3.54.95
16:08:12 <matthias_samwald> P29 is someone else
16:08:13 <ericP> Zakim, please dial ericP-office
16:08:13 <Zakim> ok, ericP; the call is being made
16:08:15 <Zakim> +EricP.a
16:08:17 <RobFrost> RobFrost has joined #HCLS
16:13:21 <ericP> Zakim, who is here?
16:13:21 <Zakim> On the phone I see +33.3.54.95.aaaa, +1.206.605.aabb, matthias_samwald, +44.122.383.aacc, mscottm, ??P29, EricP.a
16:13:23 <Zakim> On IRC I see RobFrost, mscottm, RRSAgent, Zakim, michael, matthias_samwald, adriencoulet, ericP
16:14:49 <mscottm> http://esw.w3.org/File:101129AdrienCouletBioRDF.PDF
16:15:29 <mscottm> http://esw.w3.org/HCLSIG_BioRDF_Subgroup/Meetings/2010/11-29_Conference_Call#Agenda
16:15:31 <ericP> http://esw.w3.org/images/d/dc/101129AdrienCouletBioRDF.PDF
16:16:54 <matthias_samwald> scribenick: matthias_samwald
16:17:18 <matthias_samwald> adrien: slide 2
16:17:37 <matthias_samwald> ... this is joint work between NCBO and PharmGKB
16:17:55 <matthias_samwald> ... goal was improving content of PharmGKB by improving relationships etc.
16:18:40 <matthias_samwald> ... three main relationships in PharmGKB : Gene – Drug; Gene – Disease; Drug– Disease
16:19:03 <matthias_samwald> ... but people at PharmGKB are concered because relations in reality are not that simple
16:19:07 <matthias_samwald> ... slide 3
16:19:42 <matthias_samwald> ... six human curators are looking at literature.
16:21:08 <matthias_samwald> ... slide 4 -- we propose to have more detailed relationships. e.g. BAK1 gene polymorphism affects doxorubicin resistance -- Resistance to Doxorubicin is influenced by BAK1 variants. -- Doxorubicin induces BAK1 activity.
16:21:32 <matthias_samwald> ... we created an ontology, asked curators for help during ontology creation
16:22:19 <matthias_samwald> ... slide 7
16:22:33 <matthias_samwald> ... co-occurence detection has some limitations
16:22:40 <matthias_samwald> ... e.g., false positives
16:23:54 <matthias_samwald> ... we don't want to only have co-occurence, but we want to know exactly what entities were involved and what relationships.
16:25:49 <matthias_samwald> ... slide 10 -- example of the parsing we are doing
16:28:19 <matthias_samwald> ... slide 11: two superficially very different sentences can contain exactly the same content (because of synonyms)
16:28:51 <matthias_samwald> ... however, there was no dedicated ontology for pharmacogenomics, so we decided to create one.
16:29:19 <matthias_samwald> ... slide 13: we created the ontology semiautomatically based on the relations we extracted
16:30:12 <matthias_samwald> ... ontology was created bottom-up, based on most frequent words used in the categoreis "relationship", "gene", "drug", "phenotype".
16:34:35 <matthias_samwald> ... slide 21: we have raw entities that were mapped to normalized entities and relations
16:36:23 <matthias_samwald> ... e.g., "influences" becomes "affects"
16:36:53 <matthias_samwald> ... normalized relationships were encoded in RDF.
16:37:53 <matthias_samwald> ... slide 23: entities related to VKORC1 shown as a graph. (thickness of edges refers to the number of statements)
16:40:26 <matthias_samwald> dietrich: some of the entities and relationships are quite complex
16:40:50 <matthias_samwald> ... i.e., you first define these concepts and that later on you try to find evidence for this concept?
16:41:57 <matthias_samwald> adrien: 75% of the entites are in the initial ontology, 25% of the entities created directly from raw text
16:43:37 <matthias_samwald> ... slide 27: the resulting knowledge base is useful for the curation and knowledge summarization at PharmGKB
16:44:01 <matthias_samwald> ... Yael Garten (PhD student at Stanford) is also using it for knowledge discovery
16:44:24 <matthias_samwald> ... the SPARQL endpoint of the KB is at http://sparql.bioontology.org/webui/
16:44:38 <matthias_samwald> ... example queries are found on http://www.loria.fr/~coulet/material/sparql_queries
16:45:06 <matthias_samwald> ... (examples about relationships beween Parkinson's and UCH-L1 gene)
16:46:42 <matthias_samwald> ... connection to the linked data cloud: IDs from Entrez Gene, DrugBank, MeSH
16:47:57 <matthias_samwald> ... not connected to the linked data URIs at the moment, but that would be interesting future work
16:48:47 <matthias_samwald> scott: is the SPARQL endpoint you gave already saving the results from  Alzheimer's disease?
16:48:57 <matthias_samwald> adrien: no, at the moment only Parkinson's
16:49:13 <matthias_samwald> ... but i can upload the one for Alzheimer's
16:51:34 <matthias_samwald> scott: how will provenance be represented?
16:55:21 <matthias_samwald> (discussion about provenance and named graphs)
16:56:57 <matthias_samwald> scott: the ConceptWiki people have the notion of cardinal assertion, i.e., assertions that are formulated differently but have the same meaning
16:57:15 <matthias_samwald> adrien: do they already have a set of triples with provenance?
16:58:01 <matthias_samwald> scott: they have some mappings to RDF now. most of the assertions were created by people visiting the people and adding data about their favourite gene. but they also include text mining results.
16:59:07 <matthias_samwald> dietrich: there are concepts, but there are also things that don't have a name / that are not concepts
16:59:35 <matthias_samwald> ... regarding provenance, there are two things: database and authorship provenance
17:00:06 <matthias_samwald> ... what we would like to see is provenance info that points to first evidence.
17:03:24 <matthias_samwald> michael: adrien, what kind of evaluation have you done?
17:03:25 <michael> michael has left #hcls
17:03:56 <Zakim> - +1.206.605.aabb
17:04:06 <matthias_samwald> adrien: we asked: what is the content of the raw relations before normalisation? evaluated the quality of normalisation.
17:04:34 <matthias_samwald> ... using wordnet i created another ontology
17:04:53 <matthias_samwald> ... (normalisation was not very good, because wordnet was too general)
17:05:07 <Zakim> -mscottm
17:05:10 <Zakim> -EricP.a
17:05:22 <Zakim> - +44.122.383.aacc
17:05:28 <matthias_samwald> zakim, make minutes world-readable
17:05:28 <Zakim> I don't understand 'make minutes world-readable', matthias_samwald
17:05:30 <Zakim> -??P29
17:05:41 <matthias_samwald> RRSagent, please draft minutes
17:05:41 <RRSAgent> I have made the request to generate http://www.w3.org/2010/11/29-hcls-minutes.html matthias_samwald
17:05:50 <matthias_samwald> RRSagent, make minutes world-visible
17:05:50 <RRSAgent> I'm logging. I don't understand 'make minutes world-visible', matthias_samwald.  Try /msg RRSAgent help
17:06:04 <Zakim> - +33.3.54.95.aaaa
17:06:04 <adriencoulet> Thanks everyone for comments and ideas
17:06:20 <Zakim> -matthias_samwald
17:06:21 <Zakim> SW_HCLS(BioRDF)11:00AM has ended
17:06:23 <Zakim> Attendees were +33.3.54.95.aaaa, +1.206.605.aabb, +44.122.383.aacc, mscottm, matthias_samwald, EricP.a
17:07:00 <matthias_samwald> RRSagent, make logs world-visible
17:07:37 <matthias_samwald1> matthias_samwald1 has joined #hcls
17:08:23 <matthias_samwald1> matthias_samwald1 has left #hcls