kozo2 edited this page Aug 21, 2011 · 10 revisions

This is an [unconference] ( style session: a participant-driven meeting to explore problems to solve during the BioHackathon week.

Formalization of Pathway group


OpenBio* group

SADI group

  • Can any OWL Class be represented in code? Depends on the language. In languages that allow multiple inheritance (e.g. Perl) yes; in languages that don't, your code must implement all interfaces and then will not be re-inheritable, so could not be extended further. This is very hard.

  • how do we bring BioMART into SADI? First step would be to bring it into the SHARE client so that it can be queried alongside native SADI services. TASK FOR THE HACKATHON -> Do this. Making it native SADI is more complex, since SADI requires OWL Classes for all inputs and outputs, and no OWL classes have been defined for BioMART. Also difficult to make it SIO compliant because SIO has a particular structure for literals that (in this case) would utilize blank nodes; the way that BioMART exposes itself as SPARQL makes it very difficult to generate that particular SIO-compliant output data structure -> CONTINUE THINKING ABOUT THIS.

  • What is the SIO-compliant structure for BLAST? TODO AT HACKATHON: Sort this out between SADI, SIO, and UniProt teams.

  • SAWSDL: A variety of Hackathon TODOs

  • With Rutger -- TODO: build a SADI service that consumes sequence alignments + Species and creates phylogenetic tree output.

  • versus death match? or foregone conclusion? :-) is better supported so we should use them in SADI/SHARE. Could they add additional SIO-compliant metadata to their RDF to help integrate with SADI? TODO -- Discuss how to replace existing SADI dependence on LSRNs with reliance.

LinkedData group

Ontology group

Textmining group

Visualization (client software)

Support for GraphDB backend in Cytoscape

  • Sesame / Neo4j ---> RDF / SPARQL support
  • Should be implemented - independent

User Interface

Send SPARQL query

  • Get subgraph ---> Expand
  • Context menu ---> Generate Next Query

Query builder

  • For average biologists, typing SPARQL query directly is too hard!

Triple store survey

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