View source for HCLSIG/SWANSIOC/Meetings/2009-03-20 Conference Call

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== Conference Details ==

* Date of Call: Friday March 20, 2009
* Time of Call: 11:00am Eastern Time
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Dial-In #: +33.4.89.06.34.99 (Nice, France)
* Dial-In #: +44.117.370.6152 (Bristol, UK)
* Participant Access Code: 4257 ("HCLS")
* IRC Channel: irc.w3.org port 6665 channel #HCLS (see [http://www.w3.org/Project/IRC/ W3C IRC page] for details, or see [http://cgi.w3.org/member-bin/irc/irc.cgi Web IRC])
* Duration: ~1 hour
* Convener: Tim Clark
* Scribe: Harold

== Agenda ==

* Featured John Madden, MD, Duke University will present on terminologies vs ontologies in scientific discourse.  A great opportunity to discuss SKOS vs OWL and their most appropriate use cases. [http://tinyurl.com/cssred Slides]
* Sudeshna to  give a report on the status of SCF semantic microarray repository
* Participants to review peoples' takes on the SWAN-myExperiment integration path

== Minutes ==

Attendees: Alex, Peter, Paolo, Kei, EricP, Holger, David, Ronald, Marco, Carl, Harold, Elizabeth, Scott, John, Susie

* <ericP> topic: JohnM presents on terminologies
* <ericP> Term preso http://tinyurl.com/cssred
* <ericP> ... i gave this preso at C-SHALS
* <ericP> ... timClark thought it was relevent to scientific discourse
* <ericP> ... he was trying to get scientists to formalize there knowledge in OWL
* <solbrig> Tim had issues with scientific discourse ecosystem, but found that scientists didn't speak OWL
* <ericP> ... came to the conclusion that scientists don't speak owl
* <solbrig> Terminologies don't really speak OWL either
* <solbrig> You are not crazy when you can't put terminologies in OWL - it is actually hard to do.
* <ericP> johnM: slide 2 represents the state of the art in terminologies today
* <ericP> ... e.g. lab results use LOINC...
* <solbrig> johnM: some are just term lists
* <solbrig> ... some are hierarchical
* <solbrig> ... documents will be encoded in more than one vocabulary
* <solbrig> ... what is unusual to modify CPT code w/ LOINC or SNOMED w/ HL7
* <solbrig> johnM: slide 3 - terminologies came first
* <solbrig> ... semantic web, syntax came first then content. 
* <solbrig> ... vocabularies are inherently mixable on the web
* <solbrig> ... central curation is not impossible, but you can't prevent them from using your terms in their assertions
* <solbrig> ... SNOMED is the giant among vocab - 1.25 million terms, web will probably be < 200 entries per vocabulary
* <solbrig> ... and will be very intensively modeled, highly contextualized
* <solbrig> johnM: slide 4 - 3 challenges
* <solbrig> ... common identifiers
* <solbrig> ... keeping faith with original intention of the vocabulary
* <solbrig> ... using GLUE technologies
* <solbrig> johnM: Slide5 - common identifiers
* <solbrig> ... no problem coining URL identifiers for terms.  It really isn't our place, really the place of the central curation authority
* <solbrig> ... existing software doesn't expect URL's
* <solbrig> johnM: slide 7
* <solbrig> ... identifiers for individuals.  I had a a hernia sack repaired, it is John Madden's hernia sack.
* <solbrig> ... existing terminologic systems - subject of assertion is implicit, not explicit...
* <solbrig> ... documents encoded in SNOMED - just a list at the bottom of the document.  HL7 CDA - same way, still hard to code in triples
* <solbrig> ... (rdf square brackets in slides mean "instance of")
* <solbrig> ... really trying to encode "surgeon reports a radiological history of lung mass" vs. "lung mass exists"
* <solbrig> ... existing terminologies don't worry about this because it is hard to do, but in RDF you've got to
* <solbrig> ... would like a very small, compact vocabulary of assertions (FOAF of DC for medicine)
* <solbrig> johnM: slide 8
* <solbrig> ... Slide 8, 9, 10, 11, 12 13 are use cases at varying levels of inference
* <solbrig> ... slide 17 - links.  No ontology needed, all there is is links (lhs of side).  RHS is examples of intensive inferencing
* <solbrig> ... all elements of slide are wonderful Semantic Web use cases.  We aren't failing if we don't deliver the "grand OWL ontology of medicine"
* <solbrig> johnM: slide 18
* <solbrig> ... a lot of the semantic web will links between heavily modeled, narrow ontologies...
* <solbrig> ... experts will have sw equivalent of web site - ontology of rheumenologic (sp?) diseases.  You will have to use his knowledge from the web site to do inferencing
* <solbrig> ... grab individual expert sites and apply to your problem.
* <solbrig> johnM: slide 20
* <solbrig> ... scientists will formalize tentative ideas.  Can swap ontologies in and out to perform interesting.
* <solbrig> ... it is not interesting to know that influenza is an infectuous disease.
* <solbrig> Peter Hendler: We are moving SNOMED CT into OWL, and will be presenting in IHTSDO in the first week of April.
* <solbrig> Peter Hendler:  Will be able to share it the first week of April.
* <solbrig> .... took SNOMED Tables, used Spackman's conversion script  to OWL and then added 25K negated terms.
* <solbrig> ... will be adding incrementally negation and disjunction as needed.
* <solbrig> johnM: slide 21 - from SKOS.  Notion of "features"
* <solbrig> ... using SKOS (vocabulary expressed in OWL, for describing terminologies, no assumptions about model theory)
* <solbrig> ... allows to get knowledge from terminology without forcing it into a particular model.
* <solbrig> ... "meta-inferencable" vs. "immediately inferencable"
* <solbrig> ... not what we might want it to mean, what it really means.
* <david_newman> SKOS was made a W3C candidate representation sinc 17th March
* <solbrig> ... open world principle.  If it isn't said, it isn't necessarily false.
* <solbrig> ... danger of adding your own interpretation vs. those of those who wrote the terminology.
* <solbrig> ... in OWL, if you don't make statements about disjointness, they aren't assumed to be disjoint.  UMLS Semantic Network example...
* <solbrig> ... John added disjointness axioms, but Olivier Bodenreider (curator of SN) said it wasn't what he meant.
* <solbrig> ... disjointness issues manifest on the instance level.
* <solbrig> ... relationship overloading.  "isA" is not just "isA" - could be RDFS:subclasOf, RDFS:subPropertyOf, RDF:type, equivalentClass, etc.
* <solbrig> ... might inverse of owl oneOf, owl unionOf.  Choice of meaning has consequences.
* <solbrig> johnM: slide 28 - introduction to AIDA - SKOS Semantic Aggregation Environment
* <solbrig> ... slide 29 - things you can say in SKOS
* <solbrig> ... AIDA knows about SKOS and SKOS terminologies.  Slide 30
* <solbrig> ... SNOMED is just represented as BT and NT relations - hierarchies.
* <solbrig> ... slide 32 shows grabbing RH middle pain of SNOMED hierarchy as a whole, left hand is lucene index of Medline 
* <solbrig> ... semantically enabled full text search. (Scott: index is just of Medline abstracts - not full text)
* <solbrig> johnM: slide 33 - glue technologies
* <solbrig> ... most of the artivacts of the medical world are "documents" - authorship, stewardship, atomized data, natural language
* <solbrig> ... slide 35 - have additional characteristics beyond web
* <solbrig> ... legal status, beginning and end, non-repudiation, default context.
* <solbrig> johnM: Slide 36 - Plato's ?? translated into latin by someone else, with commentaries, commentaries on commentaries, etc. purchased by vatican
* <solbrig> johnM: Slide 37 - ontologies have resemblance to forms, but more complicated.
* <solbrig> ... documents get interpreted to create semantics.  Semantics extracted using GRDDL - assigning intrepretation engine to a particular document.
* <solbrig> ... semantics change, add a different GRDDL extraction algorithm to it
* <solbrig> ... (slide 38)
* <solbrig> ... corollary in scientific discourse as well.  Significance of entities in paper isn't understood until other papers emerge.  Active of interpretation brings knowledge to document
* <solbrig> Susie: time left... questions?
* <solbrig> Peter Hendler: will you be at IHTSDO in April?
* <solbrig> johnM: no 
* <solbrig> Susie: HCLS FTF in Cambridge on April 30 and May 1.  Invited talks on where group is, breakouts
* <solbrig> johnM: won't be able to attend on Thurs, will be on Firday
* <Susie> Agenda & registration for F2F meeting -> http://esw.w3.org/topic/HCLSIG/Meetings/2009-04-30_F2F
* <solbrig> reference to Rector's paper in 2006 in model of talk? and model of meaning
* <solbrig> Alex: Space of code? and space of meaning.  This is why we picked SKOS vs. something else.
* <solbrig> ... last version of SKOS is submission (W3C) proposing SKOS / OWL version ... (unintelligable)
* <solbrig> ... why SKOS vs. OWL DL?
* <solbrig> Alex: OWL Full collapses punning, OWL DL has two classes.  
* <solbrig> Alex: in OWL 2 that isn't true anymore.