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
#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