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/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
