Version 8 (modified by gmicklem, 9 years ago)

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Visualization and Molecular Interactions

Possible issues to be mentioned:

  • how can uncertainty be expressed?
  • ways to describe experimental/compuational "evidence"

Semantic Data Exchange

Summary of Semantic Data Exchange for existing systems discussion

Before wholesale conversion to RDF are there things that can be done to improve existing/ legacy systems?

Members of BioMart?, CytoScape?, Galaxy, InterMine? and others met to discuss the possibilities/need for improving data exchange.

Conclusions:

  • Data exchange:
    • Current systems are arbitrary but work well.
    • A namespace for file formats would be useful.
    • A namespace for column of tabular data would be useful. Could

also be used to describe data in other formats e.g. XML, though this could be rather verbose.

  • At the moment namespaces for columns is probably more important

than URIs for each data element in a column.

  • Maybe are applicable to the above:

Ontology Lookup Service (  http://www.ebi.ac.uk/ontology-lookup) and/orLife Science Resource Name Project (  http://www.lsrn.org)

  • Agreed that worthwhile to pass URIs to describe columns for tabular data. Agreed that arbitrary human-friendly names are also good.
  • Agreed to dump all BioMart/ InterMine? column headings out, find

the common/commonly-used ones and work on naming.

  • Genome Builds:
    • Investigate whether is there a standard available for describing

genome versions/ genome annotation versions.

  • Consider whether to base naming on ensembl as planning to cover

all genomes