HCLSIG/SWANSIOC/Meetings/2010-09-13 Conference Call

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SciDisc Minutes 9.13.10

In attendance:

  • Paolo Ciccarese (Harvard)
  • Tim Clark (Harvard)
  • Sudeshna Das (Harvard)
  • Michel Dumontier (Carleton)
  • Rob Frost (Harvard)
  • Bob Futrelle (Northeastern)
  • Matt Gamble (Manchester)
  • Scott Marshall (Leiden), HCLS co-chair
  • David Newman (Southampton)
  • Matthias Samwald (DERI)
  • Susanna Sansone (Oxford)
  • Jack Park (Open University)
  • Eric Prud'hommeaux (W3C)
  • Jodi Schneider (DERI)
  • David Shotton (Oxford)

Scribe: Scott Marshall

A. Current Task Description

  • Provide a Semantic Web platform for biomedical discourse which can be evolved over time into a more general facility for many types of scientific discourse, and which is linked to key biological categories specified by ontologies.
  • Discourse categories should include research questions, scientific assertions or claims, hypotheses, comments and discussion, experiments, data, publications, citations, and evidence.

B. Current Objectives

1. Scientific Discourse formalization: Prepare SWAN IG Note. (Ciccarese et al.) Completed.

2. Scientific Discourse in Online Communities: Integrate SWAN and SIOC ontologies. (Passant et al.) Completed

3. Rhetorical Document Model: Integrate SWAN, SALT & ABCDE for coarse-grained rhetorical structure. (Anita DeWaard et al.)

Tim: [Explains goal of course-grained rhetorical structure] Want to have names of the different parts of document structure and their synonyms

Paolo: Annotation ontology enables us to describe different types of annotations for online documents. See Annotation Ontology (AO) website at http://code.google.com/p/annotation-ontology/ ...AO includes a way to refer to images within those documents.

Tim: I think that both Annotation Ontology and course-grained rhetorical structure both deserve IG notes

4. Discourse, Data & Experiment: Integrate SWAN, myExperiment, MO and OBI ontologies. (Sudeshna Das et al.)

Sudeshna: Representing metadata about experiments of all kinds, including next gen sequencing, mass spec, *any* type.

5. Bibliographic Ontologies: Integrate SWAN Citations with PRISM & CiTO to enable widely interoperable bibliographic ontologies. (Shotton, Ciccarese et al.)

DavidShotton [on integrating SWAN and PRISM and CITO]: We are almost there. Some details such as restrictions on classes need to be worked out. I think that we will be ready with the work in the next few weeks,

6. Biomedical Article of the Future: Orchestrate tasks 1-5 to support "BAF"Discussion: (Anita DeWaard et al.)

Scott: Asks about the context of Current Task Description. Checks <description> of goal. Quick description: Overall Goal of accessing textual and human discourse resources in order to link with other types of linked data such as ontologies and data.

Tim: Agree. Would like it up front in the text. …[Re: Harmonization]: Maybe we should have a teleconf with Anita to check harmonization with coarse grained.

Futrelle: Am looking for fine grained representation of claims and support in the graph. ...I'm unsure about precisely how it relates to the SciDisc work..

Tim: Yes, we've been working on representing the relations between assertions in different articles. ... I hope that we can learn more about each other's work in the calls to come. … Anita and I have set up a Dagstuhl Seminar for next summer on the last topic, Biomedical Article of the Future (BAF).

DavidShotton: We've developed a suite of ontologies including CITO and FABIO Further Aligned Bibliographic Ontology. There are 6 others in the suite. I would like to see these released to the public.

Jodi: I think that would be a very good idea.

DavidShotton: FaBiO: FRBR-aligned Bibliographic Ontology. FRBR is a bibliographic data model involving Works, Expressions, Manifestations and Items.

Scott: Mined terms in PharmaGKB and created a graph structure of relationships between them. Proposal - task about organizing a RDF resource of assertions and claims from biomedical literature

MichelDumontier: adrien coulet presented the pharmgkb data mining at bio-ontologies 2010

Rob: scott can we chat after the call

Scott: Mentioned a Silver Corpus Standard from Collaborative Annotation of Large Biomedical Corpora (CALBC) Euro Project in XML. Would be interesting to apply SciDisc ontologies to these types of resources in order to make it possible to use them in linked data. ...CALBC is coordinated by Dietrich Rebholz.

Jack: DARPA project on Machine Reading …https://www.fbo.gov/index?s=opportunity&mode=form&id=e63eb15a220ae3a7b626ade7dccafa74&tab=core&_cview=1

Tim: Thanks all.

Jack: Regrets for next week.

Tim: Intersection of text mining and biomedical ontologies in next call