Visualization and Molecular Interactions

VisualizationAndInteraction

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

SystemsBiologySBML

Sorry for no summary. Just see our wiki page.

Text mining

• Describe briefly what we did
• BioPython? module
• Contribute to the use case