The W3C HCLS BioRDF Task Force on Provenance

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W3C HCLS BioRDF Task force

Short description: One of the current goals of the BioRDF task force is to transform microarray gene expression results into RDF format and preserve provenance information about these gene expression results, such as what samples were used, which institutions contributed the samples, what experiment factors were used to produce the results. In the first iteration, we have created a provenance data model, that captures provenance information at four different levels:

  • the institutional level, which describes the laboratory performing an experiment and the publication reporting the results;
  • the experimental context level, which describes samples used in the experiment and the list of genes being studied;
  • the statistical and significance analysis level, which describes the statistical and significance analysis tools used in an experiment and results of the analysis;
  • the dataset description level, which provides descriptive metadata about the gene list results from each study.

In that iteration we have not reused any existing provenance vocabularies/ontologies in order to maintain an independence of our data modelling. At the moment, we are trying to refactor the model and map to some existing provenance vocabulary.

Alternative/existing provenance standard? (Or a complementary concept?) No

Domain specific? (If yes, is it only a domain specific convention for a general provenance standard? If yes, which one?) Yes

Subject specific? (Are there any restrictions on the subject of the provenance information?) Yes, metadata on microarray gene experiments and their results.

Based on existing data model? (Is the standard/concept embedded in an existing general standard or data model?) Probably, in the future

Are there bridges/crosswalks to other standards? Some, more are planned.

Are there documented use cases that should be taken into consideration for the Provenance WG? Yes, see our latest workshop paper and online demo

Known, relevant issues? ???

Website: biordf:

Contact for Provenance WG? Lena Deus, Jun Zhao and Satya Sahoo