Ontology meeting 2012-07-18
ATTENDEES: Chris, Heiko, Kimberly, Jane, Mary, Paola, Becky, David, Tanya, Huaiyu, Paul T, Suzi
FOLLOW-UP ON CHEBI WORK
Heiko is taking Chris' hacky biochebi creating scripts and converting it to using the OPPL framework.
LEGO AND TYING IN WITH CURRENT ONTOLOGY STRUCTURE
Prototyping the LEGO model in Protege for test cases is good before diving into the project for real. This has resulted in a LEGO plugin for Protege.
Word doc for instructions on how to install plugin exists (Chris provide doc).
Basic idea: Every annotation unit is an instance of a molecular function class.
Bright shiny future: ontology and annotations are even more intertwined, esp. during annotation creation
Interim solution: use col 16, standard synonyms to reduce term length
- Q: How specific do we go with current GO processes: to the level of groups of proteins/gene product families?
- E.g is 'transcription factor catabolic process ; GO:NEW' a valid level of specificity?
Creating terms for: PMID 22017871
- SREBP signaling pathway (GO:0032933) is active (in yeast example) at low oxygen concentrations. The transcription factor SREBP (Sre1 in yeast) is cleaved, enters the nucleus, and upregulates transcription of genes required for growth at low oxygen concentrations.
- When O2 is re-introduced the pathway is shut off by rapid degradation of SREBP.
- There are members of the ubiquitin degrading pathway that catabolise SREBP (Rhp6 and Ubr1).
- Then there are upstream regulators that sense O2 (or act downstream of sensors) and regulate SREBP degradation.
- Ord1: ACCELERATES Sre1 degradation in the presence of O2.
- Nor1: PREVENTS Sre1 degradation in the presence of O2 (by binding to Ord1 to inhibit its activity).
Without mentioning what's being catabolized, the pre-composed GO terms get very long winded:
negative regulation of SREBP-mediated signaling pathway by positive regulation of proteasomal ubiquitin-dependent protein catabolic process in cellular response to hyperoxia is_a: positive regulation of proteasomal ubiquitin-dependent protein catabolic process ; GO:0032436 is_a: cellular response to hyperoxia ; GO:0071455 is_a: negative regulation of SREBP-mediated signaling pathway ; GO:2000639 (with the ID for SREBP in annotation extension column)
- having a term for 'TF catabolism' wouldn't shorten the above GO term (negative regulation of SREBP-mediated signaling pathway by positive regulation of proteasomal ubiquitin-dependent protein transcription factor catabolic process in cellular response to hyperoxia) but it would make it more informative.