Visualization and Molecular Interactions

VisualizationAndInteraction

Possible issues to be mentioned:

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

Semantic Data Exchange

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/or Life 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

See TextMiningReport for more details