Ontology meeting 2020-11-02
David, Peter, Harold, Jim, Karen, Tanya, Kimberly, Chris
Pascale, Karen, Harold, Peter, Jim, Tanya, Kimberly, David, Chris, Paul
Standardize MF definitions
- We have little documentation - http://wiki.geneontology.org/index.php/Guidelines_for_new_Molecular_Functions#Standard_Definitions
and in design patterns - for eg
- https://github.com/geneontology/go-ontology/blob/master/src/design_patterns/activator_activity.yaml: Direct interaction with a gene product or complex that has %s, resulting in positive regulation of its %s. Direct interaction in this case includes binding and interactions leading to covalent modification.
but it's not consistent with more recent guidelines from Chris and others, see https://douroucouli.wordpress.com/2019/07/08/ontotip-write-simple-concise-clear-operational-textual-definitions/ and https://philpapers.org/archive/SEPGFW.pdf, that state we should make definition of the form "an X that Y" - so, starting with a verb should not be correct ?
- Examples of what we have in the ontology:
- Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
- Interacting selectively and non-covalently with a specific double-stranded genomic DNA sequence in order to activate or increase the frequency, rate or extent of transcription by a RNA polymerase.
- Enables the directed movement of electrons from the cytochrome b6/f complex of photosystem II.
- Interacting selectively and non-covalently with zinc (Zn) ions.
- Catalysis of two successive methyl transfer reactions from AdoMet to the N-2 atom of guanosine, thereby converting 7-methylguanosine in an RNA cap to 2,2,7 trimethylguanosine.
- A catalytic activity that contributes to the degradation of peptidoglycan.
Val suggest an ancestor of "regulates quantity of", "NTR regulates availability of" https://github.com/oborel/obo-relations/issues/393