Function-Process Links
Archive: Function-process Pilot Studies
Personnel:
- Chris Mungall
- Tanya Berardini
- David Hill
- Jane Lomax
Implementation plan:
- Use part_of as described in Eugene ppt presentation slides
- We will work on the live file, gene_ontology_write.obo
- Chris' script will filter out all inter-ontology links.
- Begin working on the 1:1 function-process part-of links. We will work in both directions, looking at functions to see if they correspond to processes and looking at processes to see if they contain a certain type of function.
- First round:
- Jane: metabolism
- Tanya and David: enzyme regulator activity, structural molecule activity, transporter activity and children
- We will start from the top down, splitting up the categories as we go.
- While doing the transporters/transport, we noticed that it is easier to work from the bottom up. This way a renderer can be set in OBO-Edit to easily identify MF terms that do not have a direct part_of relationship to BP.
- Once we make a first pass, we (Chris) will create a new 'gene_association file' to prove to the world that this is a good thing.
- After 'easy' metabolic processes are done, move on to mining metabolic pathway databases for links (face to face meeting for finalization of method/implementation?). Possibly involve Peter D'Eustacio at this point to deal with issues involving Reactome and GO. Resources will be:
- KEGG
- Reactome
- Metacyc
Mining links from pathway databases
Display of links:
See also: