HCLSIG/SWANSIOC/Meetings/2009-09-18 Conference Call

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Conference Details

  • Date of Call: Friday Sept 18, 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: TBD

Agenda

  • OBO Relationship Ontology - Larry Hunter
  • 2009-2010 Work Plan (Contd.)
  • AOB

Useful Links

  • Final SWAN & SIOC IG Notes.
   SIOC, SIOC Types and Health Care and Life Sciences
   Semantic Web Applications in Neuromedicine (SWAN) Ontology
   SWAN/SIOC: Alignment between the SWAN and SIOC ontologies

Minutes

Attendees: Tim, Matthias, David, Joanne, Scott, Larry, Anita, Michelle, Tudor, Cartig, Susie, Jack

<Susie> Larry Hunter Presentation

<Susie> Familiar with OBO & OBO Founder

<Susie> Interested in using community curated ontologies for NLP

<Susie> Need relationships between factual assertions, and the originating text

<Susie> Need the evidence

<Susie> Participated in a Relation Ontology piece of work

<Susie> Convened a F2F meeting in Colorado

<Susie> Talked about commitments with OBO Foundary

<Susie> They want a very minimal set

<Susie> Willing to put on the pending list, 2 relations

<Susie> 1. Supports, and isSupportedBy

<Susie> 2. Contradicts, and isContradictedBy

<Susie> Barry Smith and Chris Mungall want details on epistemic relations

<Susie> Also suggested something is going to happen in this area

<Susie> Spoke with Anita about epistemic relations and community annotation

<Susie> Want to least set down a marker to say this exists

<Susie> And try to work in harmony

<Susie> At F2F, identified all sorts of relationships

<Susie> Take away from RO meeting was to keep them out of RO ontology

<Susie> But have different ontology built on GO evidence codes

<Susie> Michelle: GO uses a subset of relations from Evidence Code ontology

<Susie> Use hierarchy of relations

<Susie> And link to epistemic codes

<Susie> Information Artifact Ontology

<Susie> Could be domain for some of these relations

<Susie> URLs pointing to the pending RO, Evidence Ontology, and ...

<Susie> Want to bring stuff back from this call to these other communities

<Susie> Also happy to answer questions

<Susie> Tim: This effort is very focused on harmonization across discourse and discourse ontologies

<Susie> Tim: Last year did harmonization between SIOC and SWAN

<Susie> Tim: Jack working with Simon Buckingham Shum, Tudor (DERI), David Neumann (myExperiment), Scott (Terminology), Anita (Elsevier), etc.

<Susie> Tim: Some active in annotating documents and linking to controlled terms in ontologies

<Susie> Tim: David Shotton is missing

<Susie> Tim: Let's open up for questions

<Susie> How do you use these relationships

<Susie> Larry: Trying to do IE

<Susie> Trying: Create KB tying genes and gene products

<Susie> Larry: Try to understand what is already known that relates to the results of experiments

<Susie> Larry: Sometimes not much work done

<Susie> Larry: Sometimes (50%) lots of work but from different field

<Susie> Larry: Postdocs need to figure it all out

<Susie> Larry: First application is the Hanalyzer

<Susie> Larry: Use NLP to build networks

<Susie> Larry: Nodes are genes

<Susie> Larry: Links are existing data

<Susie> Larry: Overlay experimental and literature networks

<Susie> Larry: See what's previously known

<Susie> Larry: Cytoscape plugin used to see more information relating to the nodes or links

<Susie> Larry: Inference is used to help build the networks\

<Susie> Larry: Linkages in knowledge networks to literature is why we're intrested in epistemic relations

<Susie> Larry: Try to be a user, rather than a builder of RO

<Susie> Larry: See bunch of pending relations that have been requested

<Susie> Larry: Interested in getting these type of relations in

<Susie> Larry: Discussed with Kathy Wu at ICBO

<Susie> Larry: She's recently moved from Georgetown to Delaware

<Susie> Larry: Kathy is very focused on the protein ontology

<Susie> Tim: You have 'supports' and 'contradicts', do they have evidence codes?

<Susie> Tim: The text is just a string, the assertion is formalized in the KB?

<Susie> Larry: Correct

<Susie> Tim: Do you use reification?

<Susie> Larry: In our code, we use Protege internally, we just have a slot for it

<Susie> Larry: Likely not going to do it in a formalization

<Susie> Larry: That's what you guys are good at

<Susie> Tim: People interested in extracting info from text

<Susie> Tim: More interested in higher level models

<mscottm> Zakim, who is making noise?

<Susie> Tim: Also interest in relationships between assertions

<Susie> Tim: Are you interested in this approach

<Susie> Larry: Grad student - Elizabeth White

<Susie> Larry: Working on thesis on more tailored model for discourse, looking at what's aligned and what contradicts

<Susie> Larry: Think our approach is more abstract, rather than yours

<Susie> Larry: Don't think text is nuanced enough

<Susie> Larry: want users to be able to analyze their own data

<Susie> Larry: We can get away with less detailed models

<Susie> Larry: Would be interested in community models

<Susie> Larry: And how we can start to populate them

<Susie> Tim: Very though for an automated approach

<Susie> Tim: Have application, with 100s of users in AD community

<Susie> Tim: Have part time curator

<Susie> Tim: People also submit content

<Susie> Tim: Usually know who you are arguing with or supporting

<Susie> Larry: SWAN is awesome

<Susie> Larry: Our focus is on breadth

<Susie> Larry: Therefore have different needs

<Susie> Larry: But are complimentary

<Susie> Tim: Have you thought about when a large lab is doing an experiment

<Susie> Tim: And want to tie them to results in that way

<Susie> Larry: Not so much

<Susie> Larry: As we really focus on the literature

<Susie> Larry: Focus a little in OBI

<Susie> Larry: Have heard concerns and difficulties that people have in tying evidence to discourse

<Susie> Larry: Capture the experimental protocol, the goal of the investigation, the outcome (type of data and transformation), and conclusions

<Susie> Anita: Interesting. Close to what I'm trying to pull together

<Susie> Larry: OBI is pretty active

<Susie> Anita: Have 2 symetrical relations

<Susie> Anita: What were the ones you didn't get?

<Susie> Larry: Original proposal on RO web site

<Susie> Larry: We had a hierarchy of relations

<Susie> Larry: The foundary wanted them as a type hierarch, and wanted to keep the relations minimal

<Susie> Larry: To us this is a format difference

<Susie> Larry: We ended up with just the 2 because of their desire to have min relations, and put everything else into evidence code

<mscottm> +1

<Susie> Larry: I also wanted a superclass for 'isRelevantTo"

<Susie> Larry: Barry wasn't keen on that as he felts that evidence could be neutral

<Susie> Larry: Not a philosopher, I just want something I can use

<Susie> Larry: So can use other approaches

<Susie> Scott: That's what was trying to mention in my mail, can include in the application

<Susie> Tim: Common for people to cite relevant evidence, but then don't commit

<Susie> Larry: That's OK.

<Susie> Larry: RO always required definitions

<Susie> Larry: couldn't come up with good definition of 'neutral'

<Susie> Larry: Would be fine with a logical combination

<Susie> Scott: Where are holes in ontologies for knowledge provenance?

<Susie> Larry: Not familiar with what you are doing

<Susie> Larry: Let's make sure everyone is compatible with 2 evidence codes in the RO

<Susie> Scott: Information Artifact Ontology and evidence codes fill some gaps

<Susie> Scott: Are we missing describing knowledge with provenance, or are there other gaps?

<Susie> Larry: Don't seem gaps, but processes

<Susie> Larry: Want RO to be compatible

<Susie> Tim: Makes a lot of sense

<Susie> Tim: Where do projects overlap

<Susie> Tim: Overlap can be large or small

<Susie> Tim: Some folks are working on annotation ontologies for publications

<Susie> Tim: We could do a side call on that

<Susie> Larry: Marking up biomedical jourmal articles

<Susie> Larry: Will participate as needed

<Susie> Tim: During last, we decided next target for harmonization included the SALT ontology, myExperiment, and CITO

<Susie> Scott: BioCatalog is tied in with myExperiment

<Susie> Scott: Let people register web services

<Susie> Scott: So are making assertions about the web services

<Susie> Scott: This is Carole Goble's work, and closely connected to myExperiment

<Susie> Scott: Should also remember Matthias' aTag

<Susie> Larry: My project is called CRAFT

<Susie> Tim: Lots of common interest

<mscottm> Colorado Richly Annotated Full Text, I think.

<Susie> Larry: The other project is Hanalyzer

<Susie> Tim: Talked about order of the integration work

<Susie> Tim: We can do things in parallel if enough people are working on it

<Susie> Scott: Getting SIOC Export for various types of discourse

<Susie> Scott: Then could SPARQL across systems using the same or similar terms to gather evidence

<Susie> Tudor: Proposing using SIOC as an upper layer ontology to bridge representations

<Susie> Scott: Would shy away from calling it an upper layer ontology

<Susie> Tudor: Won't that be limited, given SIOC doesn't capture discourse

<Susie> Tim: Where just SIOC, then that's what you get

<Susie> Tim: If it's more granular, then people can use SWAN

<Susie> Tim: We have something like this for our task list for the group

<Susie> Tim: Tudor has proposal for harmonizing SWAN, SIOC and SALT, and swanalto (sp?)

<Susie> Tudor: The 4th ontology was developed in Simon's group

<Susie> Bring RO uptodate and as close to usable for Larry as possible

<Susie> Tim: Use Tudor's model as the starting point, and assign folks to work on it

<Susie> Tim: Also take Larry's requirements into consideration

<Susie> Tim: Now we just need the happy volunteers

<Susie> Tim: Will volunteer Paolo as he isn't here

<Susie> Tudor: I will volunteer

<Susie> Larry: And some of Mike's time

<Susie> Larry: And maybe Elizabeth once she's finished her PhD

<Susie> Jack: My name should be on it

<Susie> Jack: Simon will argue that I shouldn't be on it!

<Susie> Tim: This is all subject to PI approval.

<Susie> Tim: Background information on esw wiki

<Susie> http://esw.w3.org/topic/HCLSIG/SWANSIOC

<Susie> Tim: There are 3 interest groups notes which provide good background

<Susie> David: Think myExperiment is somewhat separate

<Susie> Tim: Will put scientific discourse down as a stake in the group

<Susie> Tim: Can take up the discussion during the next call

<Susie> Tim: Any other open business

<Susie> ISWC workshop on scientific discourse

<Susie> http://esw.w3.org/topic/HCLS/ISWC2009/Workshop

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