HCLSIG/SWANSIOC/Meetings/2009-04-17 Conference Call

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Conference Details

  • Date of Call: Friday April 17, 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 W3C IRC page for details, or see Web IRC)
  • Duration: ~1 hour
  • Convener: Tim Clark
  • Scribe: Susie

Agenda

Minutes

Attendees: Matthias, Tim, Susie, Kei, David, Scott, EricP

<Susie> topic: chart out F2F breakout

<Susie> Tim: plot roadmap for aligning with output of terminology and BioRDF

<Susie> Tim: I've drafted a document that describes the integration

<Tim> http://esw.w3.org/topic/HCLSIG/SWANSIOC/Meetings/2009-04-17_Conference_Call

<Susie> Tim: Pleased if people come up with missing pieces

<Susie> Tim: walks us through the document

<Susie> Tim: Integrating Scientific Discourse ontologies with BioRDF and Terminology

<Susie> Tim: Understand landscape, opportunities, and challenges

<Susie> Tim: Outlined phrases representing use cases

<Susie> Tim: A couple of the issues

<Susie> Tim: Ontologies versus terminologies

<Susie> Tim: There are methodology implications of that

<Susie> Tim: When would you want to use things from very controlled

<Susie> Tim: How can you provide a scaffold

<Susie> Tim: How can people work with legacy terminology

<Susie> Tim: Legacy for us includes mesh and snomed

<Susie> Eric: Will Peter Hendler be at the F2F? He's done lots of stuff in OWL

<Susie> Eric: I'd be interested in hearing his views

<Susie> Kei: SKOS isn't OWL based

<Susie> Kei: Boundaries between representations is blurred for many people

<Susie> Kei: Paolo's paper addresses some of these issues

<Susie> EricP: To me it seems like we need use cases

<ericP> Susie: components of your proposal overlap Pharma Ontology

<ericP> ... pharmaOntology is working on a high-level ontology to bridge data sources which are required for translational medicine

<ericP> ... some folks would call it a scaffold or template ontology

<ericP> ... want to use it to enable domain-specific ontologies to be bridged together

<ericP> ... work today involves id'ing 15 common roles in trans med, e.g. primary care phys, chemists, payers...

<ericP> ... id'd key questions these players would ask, as well as what parts of an ont they would depend on

<ericP> ... madden has done word-freq analysis to see which words come up in the roles

<ericP> ... at f2f, expect to look for core entities to go in the core ont

<ericP> ... to restrain size, expect to build something:

<ericP> ... .. write up 3 use cases which involve more than one role

<ericP> ... .. then build out the ont (to meet the use case)

<ericP> ... LODD folks are looking for well-designed onts to map to RDF

<ericP> ... LODD folks are thus customers of pharma ont

<ericP> ... if our template doesn't meet needs of scientific discourse, we've failed

<ericP> ... you'd be a use case for pharma ont

<ericP> ... have a poster at BioMed Ont conference

<ericP> mscottm: work freq analysis sounds like language models: a histogram of words associated with terms

<ericP> RDF gives you "and" for free

<ericP> it's innate to the data model

<Susie> word frequencies http://esw.w3.org/topic/HCLSIG/PharmaOntology/Ontology

<ericP> Susie: did nothing super-clever; just looked for most common words in the pages describing the tasks

<ericP> ... "and" at the top, but see page for relevent top words

<Susie> roles and questions http://esw.w3.org/topic/HCLSIG/PharmaOntology/Roles

<Susie> ericP: Alignment between SciDiscourse and PharmaOntology requires that alignment between terms

<Susie> scott: need to characterize what's in the named graph

<Susie> scott: trying to do coupling between resources

<kei> void link: http://users.ox.ac.uk/~zool0770/presentations/HCLS-BioRDF-Feb-09.pdf

<Susie> Tim: one thing that tends to be missing from bridging ontologies is actions

<Susie> Tim: integration is a practical question

<mscottm> http://rdfs.org/ns/void-guide

<Susie> Tim: integration occurs through the activities in companies

<mscottm> http://rdfs.org/ns/void/html

<Susie> Tim: For example, an experiment is an activity in science

<Susie> Tim: Still don't have an entity that describes what an experiment is

<Susie> Tim: I think this is a problem

<Susie> Tim: SWAN maps into more classic ontology by using 'research statement' connects to a 'reagent', 'entity', etc.

<Susie> Tim: But that isn't really enough

<Susie> Tim: Want to say what the results of work were

<Susie> David: Explain work Manchester and Southampton are doing

<Susie> David: myExperiment and BioCatalogue are similar for example

<Susie> David: Started an architecture overview board

<Susie> David: Have a project focused on Research Objects

<Susie> David: Goal to share objects across repositories

<Susie> David: Results in a aggregation

<Susie> David: Based on ORE

<Susie> Tim: Are you familiar with 'Life Sciences Entity' in SWAN?

<Susie> David: No I haven't.

<Susie> David - ORE - Object Reuse and Exchange

<ericP> Susie: lilly is also using information objects

<ericP> ... working with manchester

<Susie> Tim: Sounds like it deserves its own piece in this structure

<Susie> Scott: Thought I heard a use case relating to defining experiments

<Susie> Scott: And machine processable results

<Susie> EricP: Tim, are you talking about sentences?

<david_newman> http://openarchives.org/ore

<Susie> Tim: We are trying to create ability to have structured representations and sentences

<Susie> EricP: By sentence I meant a triple

<Susie> EricP: Do you mean triples or single key words?

<Susie> Tim: Hypotheses, research questions, and claims have to be lightweight and very flexible

<Susie> Tim: Too many things that you want to represent

<david_newman> http://rdf.myexperiment.org/example/ExperimentResourceMap <- example ore resource map for an experiment in myExperiment (this currently only includes enactment of workflows, i.e. jobs but could be extended)

<Susie> Tim: Want English sentences that are related to formal data

<Susie> Tim: Document in pharma company about a research plan

<Susie> Tim: Want to relate things to the document for improved precision and recall

<Susie> Tim: Controlled terms could just be terms, or terms in a well defined ontology

<david_newman> http://rdf.myexperiment.org/example/PackResourceMap <- example of a pack which has a more heterogenous content, ultimately a Research Object would be a more structured version of this

<Susie> EricP: Was wondering if use of a few predicates would help

<Susie> Tim: Would need examples, and work it through

<Susie> Tim: If very structured experiment (e.g. microarray) then question whether could prescribe for an experiment in general, but open to discussion

<Susie> Tim: Might want to start with the statistical approach for designing the experiment

<Susie> Tim: Nice to say upfront with predicates what you are planning to do for the analysis

<Susie> Tim: Often people do the experiment and then change the hypothesis

<Susie> David: Not working at the level of a research statement in an object

<Susie> EricP: Thinking of doing something lightweight

<Susie> David: Would have though part of defining a research object, would be to define more than rich keywords, so maybe also relationships

<Susie> EricP: Relationships could help you to identify a subset of things of interest, rather than everything about an entity

<Susie> Tim: Would be interesting to discuss our approaches at the F2F

<Susie> Tim: Should we add it to the roadmap agenda

<Susie> David: Dave de Roure will be at the F2F

<Susie> David: Would you be prepared to take the document, and talk about integrating with ORE

<Susie> David: Thinking about how best to describe ORE other than what's on the web site

<Susie> David: Some content in paper we submitted - but don't know if it has been accepted yet or not

<Susie> David: Maybe can share a copy with a handful of people

<Susie> Tim: Do people think it makes sense to discuss the Southampton and Manchester approach at the F2F

<Susie> EricP: Yep

<Susie> Tim: Need some action points

<Susie> David: I can add a couple of bullet points to Tim's document

<Susie> Tim: Could you take document and do a critical re-write of the BioRDF section

<Susie> Kei: Sure I can give it a go - will provide feedback early next week

<Susie> EricP: Is this for general consumption

<Susie> Tim: Sure, it's for everyone to provide feedback on

<Susie> Tim: Will ask Scott to provide content

<Susie> Tim: Will you write some text on alignment with Pharma Ontology

<Susie> Susie: Sure

<Susie> Tim: It'd be excellent if we could get feedback by the end of next week

<Susie> Tim: Then ask for feedback from everyone after that

<Susie> Tim: Matthias it'd be great if you could also contribute

<Susie> Tim: The SWAN IG Note is about half done, so it's getting there

<Susie> Tim: Thanks for being on the call

<Susie> Tim: Looking forward to seeing everyone at the F2F

<Susie> Tim: Next telcon on May 8

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