WBPaper00038528 GO linking comments

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WBPaper00038528

doi10.1534/genetics.111.131227 00038528
GO_linked_html
GO_entity_list

karen

From the entity list

• signaling doesn't have a page in wormbase although there is a page in AmiGo; regardless, in most of the cases to make a link to signaling is not as informative as it would be to make a link to the larger phrase e.g., 'DCV-mediated signaling', 'acetylcholine neurotransmitter signaling'
• synaptic membrane doesn't have a page in WB although it does in AmiGo

Links to consider removing:

• acetylcholine receptor is linked- a better link would be to 'acetylcholine receptor agonist' or even to 'receptor agonist'
• RhoGEF should be unlinked in instances of 'RhoGEF-2'
• motor should not be linked - this will be taken care of if WB entities are linked first
• phospholipase C shouldn't be linked in the phrase 'phospholipase C beta', which is the complete phrase
• growth in the phrase nematode growth media
• carrier different term from that defined by GO
• ER -refers to a camera mount in the paper, not the GO term
• cell in instances of cell nonautonomous
• hypersensitivity - the GO definition is specific to an immune response. in the paper, it is referring to a response to drug.
• antibody -the definition of the GO antibody term is not informative to its use here.
• hormone? -the GO definition describes these as hormone activity, the paper talk more of horomone entities
• RNAi in instances of nlp-21 RNAi
• neurotrophin -not sure the GO term reflects the meaning of the term used here.
• transcription in the instance of transcription factor, instead perhaps map it to transcription factor activity?

Possible links that could have been made:

• dense core vesicles and DCVs are not linked-- add plural form to the entity list?
• presynaptic -> linked to presynaptic membrane?
• depolarization -> linked to membrane depolarization?
• postsynaptic -> linked to postsynaptic membrane?
• synaptic vesicles ->synaptic vesicle --add plural form to entity list?
• heterotrimeric G-protein -> linked??
• Coelomocyte -> add case insensitivity?
• growth factor ->growth factor activity?
• neuropeptide ->neuropeptide hormone activity?
• catecholamin uptake ->catecholamine uptake in synaptic transmission?
• cell bodies ->cell body (add plural)?
• peptidylglycine-amidating monooxygenase -add as synonym to peptidylglycine monooxygenase activity?
• dauer formation -> regulation of dauer larval development, dauer larval development, or dauer entry?

daniela

• signaling -> broken link to WB term present in obo file

• Dense core vesicle not linked everywhere -> plural issue? Add DVC too

• motor neuron -> 'motor' linked to 'motor activity', not correct but when adding GO linking to the normal pipeline it will not be a problem since the term 'motor neuron' will be linked to the Anatomy Ontology

• cellular process ( GO:0009987 ) not linked -> singular/plural issue?

• cell-cycle progression could be linked to regulation of cell cycle GO:0051726 (could not find exact match). If not linking cell-cycle progression I would remove the link to cell

• synaptic membrane -> broken link to WB term present in obo file

• remove link in RhoGEF-2

• acetylcholine release -> could we add a synonym to acetylcholine secretion ( GO:0014055 )?

• link to heterotrimeric G-protein ( GO:0005065 ) could be added

• did not link to neurotransmission because of capital N in the sentence 'Neurotransmission involves two separate mechanisms of neurotransmitter release (Sudhof 2008).'

• Add 'presynaptic site' as synonym of presynaptic active zone ( GO:0048786 ) ?

• growth media -> link to growth should be removed manually by a curator

• cell-specific -> I would remove the link to cell

• Locomotion not linked when capitalized

• ethanol carrier -> link to carrier should be removed manually by a curator

• ORCA-ER camera -> link to ER should be removed manually by a curator

• cell bodies -> only cell is linked, if we add plural we could link it to cell body ( GO:0044297 )

• could we add 'cholinergic signaling' as synonym of 'synaptic transmission, cholinergic' ( GO:0007271 )?

• hypersensitivity -> link pointing to 'An inflammatory response to an exogenous environmental antigen or an endogenous antigen initiated by the adaptive immune system.'. Different context, I will remove the link

• synapse not linked -> synapse ( GO:0045202 )

• synaptic vesicle not linked -> synaptic vesicle ( GO:0008021 )

• growth factors -> remove link to growth

• hormone linked to hormone activity -> not quite right but I think we were stripping activity to increase the match rate. If this is the case I would just remove the link manually. the same is true for 'calcium channel', link points to calcium channel activity.

• I cannot find a GO term for neuropeptide release. Why? They have neuropeptide binding, neuropeptide catabolic process ….

• catecholamine uptake -> add this synonym to 'catecholamine uptake involved in synaptic transmission' ( GO:0051934 ) ?

• synaptic vesicle release -> could be added as a synonym of synaptic vesicle exocytosis ( GO:0016079 )?

• secretory pathway not linked -> ( GO:0045045 )

• peptidylglycine-amidating monooxygenase linked to monooxygenase could be linked to peptidylglycine monooxygenase activity GO:0004504

• endosomes -. could be linked to endosome ( GO:0005768 )

• dauer formation -> I would remove the link to formation. Would it be ok to add the link to 'dauer entry' ( GO:0043053 )?

• neurotrophin linked to neurotrophin receptor binding -> I would remove the link