Version 4 (modified by markw, 16 years ago)



What metadata is required to adequately describe a service?

  • author contact
  • authority identification
  • service version
  • software title
    • nature of algorithm (likely = myGrid Task ontology)
  • software version
  • bandwidth and/or # requests per minute
  • example input
  • example output and/or REGEXP to test output
  • some description of error-handling capacity
  • sync/async
  • nature of underlying data
    • organism
    • biological nature of data
      • DNA/RNA/Protein
      • SAGE
      • Microarray
        • platform, etc.
  • input parameters and purpose of each
  • output parameters and purpose of each
  • usage/license restrictions
  • authentication (is needed or not?)
  • usage statistics (as per service provider)
  • usage statistics (as per third party commentary)
  • protocol (moby, soap, GET, POST, etc.)
  • mirrors?

What ontologies exist that could provide this metadata?

  •  myGrid Ontology - provides many of the annotation information elements we claim to need. e.g. Model Organism Databases; types/formats of flatfile records
  • myGrid ontology also provides an ontology for bioinformatics tasks
  • Moby Object - an ontology of data-types
  • Moby Service - similar to myGrid's bioinformatics_task branch of the myGrid Ontology

Do we need additional ontologies? Who should make them?

  • TBD

What would a service discovery request look like?

  • TBD


W3C HCLSWG has some recommendations

  • these are largely URL-based + various HTTP protocol redirects etc for discovery of metadata

Life Sciences Identifiers

  • LSIDs have formal spec for retrieval of both data and metadata
    • LSIDs do not support "REST" access

DOI or other redirect

  • ???

 Bio2RDF project & Banff Manifesto

  • proposed URI format: bm:namespace:id
    • for example bm:pdb:122345
  • Freebase database of data providers and their namespaces
    • Freebase is editable by end-users
    • could be automated v.v. lookup
  • Somehow map bm:pdb:122345 to its equivalent URL
  • can we convince NAR to do this, since it has a list of all databases?