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

In bold the things that differ from Karen's comments. it took me 1.5 hour to go through the paper.

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 )

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

Chris

(Only showing unique comments)

Karen already mentioned unlinking RhoGEF in "RhoGEF-2"; also "RhoGEF-1"
Should link "cell-cycle" in "cell-cycle progression" to the "cell cycle" GO Term

Kimberly

I'm seeing the same trend here as in the other papers. There are links that are correct, a few that are incorrect, and links that are in the gray area of not being wholly incorrect, but not being quite right, either.

This paper is taking longer, though. I'm up to 50 minutes and still haven't checked the Rho-GEF links....

WBPaper00038528 GO linking comments

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