HCLSIG/SWANSIOC/Meetings/2010-5-3 Conference Call

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Attending:

Tim Clark: MIND 
Paolo Ciccarese: MIND
Sudeshna Das: MIND
Scott Marshall
David R Newman
Alex Garcia
Satya Sahoo

Minutes: Preliminary Discussion

  • Discussion on http://esw.w3.org/HCLSIG/SWANSIOC/Actions/SWANmyExpArray#Ontology
  • Need semantic annotation of services as well their description. Satya has looked into extending Taverna workflow model to add semantic annotation and also extending Provenir [[1]]
  • BioRDF micro-array use case: Jun and Satya created a schema taking concepts from OBI and other concepts at NCBO; Lena has integrated with the DiseaseOme [[2]] Possible overlap with this task - Could use Research Statements, Claims & Hypothesis
  • Discussion on where the computational studies fit into the model

Action Items:

  • Work to define one particular use case to capture details of computation & work flow for next call
  • David will provide more details of myExp services and services provenance and how to align with the SWAN ontology.



Full discussion notes can be found here.[[3]]


David R Newman's Note following call:
During yesterday's concall I was asked to flesh out some detail surrounding the myExperiment classes defined in [[4]]that are to be aligned with the SWAN Ontology.

I mentioned how one of the modules of the myExperiment Ontology (http://rdf.myexperiment.org/ontologies/components/) allows the inner workings of a workflow to be defined, including which processors (e.g. web services) it uses and how these are arranged. [[5]] is a basic diagram summarizing how these inner workings are organised. The metadata to describe these processors is fairly basic, limited to what can be extracted from the workflow specification itself.

It is the goal of myExperiment to integrate with a similar project called BioCatalogue (http://www.biocatalogue.org/). This project provides a web-based system to allow users to submit, annotate, monitor, curate and discover web services, particularly those in the life sciences domain. At present this project is in the process producing an ontology so that it can provide RDF for representing both the services and metadata gathered from the community about these services. This will contain a lot more information about the actually biological entities involved with a web service. I had a brief chat with one of the people working on this and he said that he was hoping to use the myGrid (http://www.mygrid.org.uk/tools/service-management/mygrid-ontology/) and EDAM (http://edamontology.sourceforge.net/) ontologies as a basis for defining the service and biological aspects of the ontology.

The intention is to use a Linked Data approach to facilitate this integration, so that a web service described as part of a workflow on myExperiment can be associated with one that is described by BioCatalogue through an owl:sameAs relationship. This would allow myExperiment to take advantage of this extra information. This information could be used in a scientific discourse context to better understand in a biologicial sense what is being analysed when a workflow is enacted. The community annotation of these services may also be useful.

I hope this information clarifies some of the questions raised by the discussion yesterday.

Regards

David R Newman