Add lexical checks for naming conventions in MF

[cmungall]

See #15322

We should enforce stylistic conventions.

If T in MF
and T not subClassOf* binding
and T not deprecated
THEN T.label MUST endWith " activity"

[pgaudet]

are we sure there are no exception ?

[ukemi]

Easy enough to check. I think all the exceptions are in binding as indicated above.

[ValWood]

from https://github.com/geneontology/go-ontology/issues/18840

I made a spreadsheet of all types of 'activities' that are NOT under the 'catalytic activity branch:

https://docs.google.com/spreadsheets/d/1t4Oene3WmUIFaAAH2S37k-Pa81qdU2V5IKVq8eYYSL8/edit#gid=0

My plan would be to fix branch by branch, removing 'activity' as appropriate.

To be approved by the ontology group.

Thanks, Pascale

[pgaudet]

• Note that 'binding' must also be allowed
• There seems to be a few terms failing, in particular x involved in some bp. Are we good to obsolete all these ?

[pgaudet]

Terms that wold be obsoleted include:

'3\'-5\'-exoribonuclease activity involved in mature miRNA 3\'-end processing' http://purl.obolibrary.org/obo/GO_0044748 'activin receptor antagonist activity involved in negative regulation of nodal signaling pathway' http://purl.obolibrary.org/obo/GO_0038103 'aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process' http://purl.obolibrary.org/obo/GO_1902944 'ATPase coupled ion transmembrane transporter activity involved in regulation of postsynaptic membrane potential' http://purl.obolibrary.org/obo/GO_0099581 'ATPase coupled ion transmembrane transporter activity involved in regulation of presynaptic membrane potential' http://purl.obolibrary.org/obo/GO_0099521 'calcium-induced calcium release activity involved in regulation of postsynaptic cytosolic calcium ion concentration' http://purl.obolibrary.org/obo/GO_1905058 'calcium-induced calcium release activity involved in regulation of presynaptic cytosolic calcium ion concentration' http://purl.obolibrary.org/obo/GO_1905054 'calcium:monoatomic cation antiporter activity involved in regulation of postsynaptic cytosolic calcium ion concentration' http://purl.obolibrary.org/obo/GO_1905060 'calcium:monoatomic cation antiporter activity involved in regulation of presynaptic cytosolic calcium ion concentration' http://purl.obolibrary.org/obo/GO_1905055 'calcium:sodium antiporter activity involved in regulation of cardiac muscle cell membrane potential' http://purl.obolibrary.org/obo/GO_0086038 'chemoattractant activity involved in axon guidance' http://purl.obolibrary.org/obo/GO_1902379 'coreceptor activity involved in canonical Wnt signaling pathway' http://purl.obolibrary.org/obo/GO_1904928 'coreceptor activity involved in epidermal growth factor receptor signaling pathway' http://purl.obolibrary.org/obo/GO_0060724 'coreceptor activity involved in Wnt signaling pathway, planar cell polarity pathway' http://purl.obolibrary.org/obo/GO_1904929 'coreceptor activity involved in Wnt signaling pathway' http://purl.obolibrary.org/obo/GO_0071936 'cysteine-type endopeptidase activator activity involved in apoptotic process' http://purl.obolibrary.org/obo/GO_0008656 'cysteine-type endopeptidase activity involved in apoptotic process' http://purl.obolibrary.org/obo/GO_0097153 'cysteine-type endopeptidase activity involved in apoptotic signaling pathway' http://purl.obolibrary.org/obo/GO_0097199 'cysteine-type endopeptidase activity involved in execution phase of apoptosis' http://purl.obolibrary.org/obo/GO_0097200 'cysteine-type endopeptidase inhibitor activity involved in apoptotic process' http://purl.obolibrary.org/obo/GO_0043027 'cysteine-type endopeptidase regulator activity involved in apoptotic process' http://purl.obolibrary.org/obo/GO_0043028 'endoribonuclease activity involved in viral induction of host mRNA catabolic process' http://purl.obolibrary.org/obo/GO_0039594 'G protein-coupled neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration' http://purl.obolibrary.org/obo/GO_0098872 'G protein-coupled neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential' http://purl.obolibrary.org/obo/GO_0099579 'G protein-coupled neurotransmitter receptor activity involved in regulation of presynaptic membrane potential' http://purl.obolibrary.org/obo/GO_0150047 'G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential' http://purl.obolibrary.org/obo/GO_0099530 'G-protein gated potassium channel activity involved in regulation of postsynaptic membrane potential' http://purl.obolibrary.org/obo/GO_0099102 'gap junction channel activity involved in atrial cardiac muscle cell-AV node cell electrical coupling' http://purl.obolibrary.org/obo/GO_0086076 'gap junction channel activity involved in AV node cell-bundle of His cell electrical coupling' http://purl.obolibrary.org/obo/GO_0086077 'gap junction channel activity involved in bundle of His cell-Purkinje myocyte electrical coupling' http://purl.obolibrary.org/obo/GO_0086078 'gap junction channel activity involved in cardiac conduction electrical coupling' http://purl.obolibrary.org/obo/GO_0086075 'gap junction channel activity involved in cell communication by electrical coupling' http://purl.obolibrary.org/obo/GO_1903763 'gap junction channel activity involved in Purkinje myocyte-ventricular cardiac muscle cell electrical coupling' http://purl.obolibrary.org/obo/GO_0086079 'gap junction channel activity involved in SA node cell-atrial cardiac muscle cell electrical coupling' http://purl.obolibrary.org/obo/GO_0086020 'inhibition of cysteine-type endopeptidase activity involved in apoptotic process' http://purl.obolibrary.org/obo/GO_1990001 'inositol 1,4,5-trisphosphate receptor activity involved in regulation of postsynaptic cytosolic calcium levels' http://purl.obolibrary.org/obo/GO_0098695 'intracellular cAMP-activated cation channel activity involved in regulation of postsynaptic membrane potential' http://purl.obolibrary.org/obo/GO_0140233 'intracellular cAMP-activated cation channel activity involved in regulation of presynaptic membrane potential' http://purl.obolibrary.org/obo/GO_0140232 'ion channel regulator activity involved in G protein-coupled receptor signaling pathway' http://purl.obolibrary.org/obo/GO_0099107 'ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential' http://purl.obolibrary.org/obo/GO_0099507 'metalloendopeptidase activity involved in amyloid precursor protein catabolic process' http://purl.obolibrary.org/obo/GO_1902945 'monoatomic ion antiporter activity involved in regulation of postsynaptic membrane potential' http://purl.obolibrary.org/obo/GO_0099580 'monoatomic ion antiporter activity involved in regulation of presynaptic membrane potential' http://purl.obolibrary.org/obo/GO_0099520 'netrin receptor activity involved in chemoattraction' http://purl.obolibrary.org/obo/GO_0038006 'netrin receptor activity involved in chemorepulsion' http://purl.obolibrary.org/obo/GO_0005043 'neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration' http://purl.obolibrary.org/obo/GO_0099583 'neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential' http://purl.obolibrary.org/obo/GO_0099529 'neurotransmitter receptor activity involved in regulation of presynaptic cytosolic calcium ion concentration' http://purl.obolibrary.org/obo/GO_0099582 'nitrate reductase activity involved in anaerobic electron transport chain' http://purl.obolibrary.org/obo/GO_1903264 'P-type calcium transporter activity involved in regulation of cardiac muscle cell membrane potential' http://purl.obolibrary.org/obo/GO_0086039 'P-type calcium transporter activity involved in regulation of postsynaptic cytosolic calcium ion concentration' http://purl.obolibrary.org/obo/GO_1905059 'P-type calcium transporter activity involved in regulation of presynaptic cytosolic calcium ion concentration' http://purl.obolibrary.org/obo/GO_1905056 'P-type sodium:potassium-exchanging transporter activity involved in regulation of cardiac muscle cell membrane potential' http://purl.obolibrary.org/obo/GO_0086037 'peptidase activator activity involved in apoptotic process' http://purl.obolibrary.org/obo/GO_0016505 'potassium channel activator activity involved in G protein-coupled receptor signaling pathway' http://purl.obolibrary.org/obo/GO_0099108 'ryanodine-sensitive calcium-release channel activity involved in regulation of postsynaptic cytosolic calcium levels' http://purl.obolibrary.org/obo/GO_0098697 'sodium:proton antiporter activity involved in regulation of cardiac muscle cell membrane potential' http://purl.obolibrary.org/obo/GO_0086040 'stretch-activated, monoatomic cation-selective, calcium channel activity involved in regulation of action potential' http://purl.obolibrary.org/obo/GO_0097364 'stretch-activated, monoatomic cation-selective, calcium channel activity involved in regulation of cardiac muscle cell action potential' http://purl.obolibrary.org/obo/GO_0097365 'transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential' http://purl.obolibrary.org/obo/GO_1904315 'voltage-gated calcium channel activity involved in AV node cell action potential' http://purl.obolibrary.org/obo/GO_0086056 'voltage-gated calcium channel activity involved in bundle of His cell action potential' http://purl.obolibrary.org/obo/GO_0086057 'voltage-gated calcium channel activity involved in cardiac muscle cell action potential' http://purl.obolibrary.org/obo/GO_0086007 'voltage-gated calcium channel activity involved in positive regulation of presynaptic cytosolic calcium levels' http://purl.obolibrary.org/obo/GO_0099635 'voltage-gated calcium channel activity involved in Purkinje myocyte cell action potential' http://purl.obolibrary.org/obo/GO_0086058 'voltage-gated calcium channel activity involved in regulation of cytosolic calcium levels' http://purl.obolibrary.org/obo/GO_0099511 'voltage-gated calcium channel activity involved in regulation of postsynaptic cytosolic calcium levels' http://purl.obolibrary.org/obo/GO_1905057 'voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels' http://purl.obolibrary.org/obo/GO_0099626 'voltage-gated calcium channel activity involved SA node cell action potential' http://purl.obolibrary.org/obo/GO_0086059 'voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential' http://purl.obolibrary.org/obo/GO_1905030 'voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential' http://purl.obolibrary.org/obo/GO_0099508 'voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization' http://purl.obolibrary.org/obo/GO_0086089 'voltage-gated potassium channel activity involved in AV node cell action potential repolarization' http://purl.obolibrary.org/obo/GO_0086086 'voltage-gated potassium channel activity involved in bundle of His cell action potential repolarization' http://purl.obolibrary.org/obo/GO_0086087 'voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization' http://purl.obolibrary.org/obo/GO_0086008 'voltage-gated potassium channel activity involved in Purkinje myocyte action potential repolarization' http://purl.obolibrary.org/obo/GO_0086088 'voltage-gated potassium channel activity involved in SA node cell action potential depolarization' http://purl.obolibrary.org/obo/GO_0086041 'voltage-gated potassium channel activity involved in SA node cell action potential repolarization' http://purl.obolibrary.org/obo/GO_0086090 'voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization' http://purl.obolibrary.org/obo/GO_1902282 'voltage-gated sodium channel activity involved in AV node cell action potential' http://purl.obolibrary.org/obo/GO_0086060 'voltage-gated sodium channel activity involved in bundle of His cell action potential' http://purl.obolibrary.org/obo/GO_0086061 'voltage-gated sodium channel activity involved in cardiac muscle cell action potential' http://purl.obolibrary.org/obo/GO_0086006 'voltage-gated sodium channel activity involved in Purkinje myocyte action potential' http://purl.obolibrary.org/obo/GO_0086062 'voltage-gated sodium channel activity involved in SA node cell action potential' http://purl.obolibrary.org/obo/GO_0086063