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?