Ontology meeting 2020-11-02

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Present

David, Peter, Harold, Jim, Karen, Tanya, Kimberly, Chris

Regrets:

Group members

Pascale, Karen, Harold, Peter, Jim, Tanya, Kimberly, David, Chris, Paul

Agenda

Standardize MF definitions

and in design patterns - for eg


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.

Relations ontology

Val suggest an ancestor of "regulates quantity of", "NTR regulates availability of" https://github.com/oborel/obo-relations/issues/393

Other Business

https://github.com/geneontology/go-ontology/projects/1


Minutes should be recorded on individual tickets and in individual projects