Difference between revisions of "WBPaper00038528 GO linking comments"
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* '''synaptic vesicle release -> could be added as a synonym of synaptic vesicle exocytosis ( GO:0016079 )? ''' | * '''synaptic vesicle release -> could be added as a synonym of synaptic vesicle exocytosis ( GO:0016079 )? ''' | ||
− | * secretory pathway not linked -> ( GO:0045045 ) | + | * '''secretory pathway not linked -> ( GO:0045045 )''' |
* peptidylglycine-amidating monooxygenase linked to monooxygenase could be linked to peptidylglycine monooxygenase activity GO:0004504 | * peptidylglycine-amidating monooxygenase linked to monooxygenase could be linked to peptidylglycine monooxygenase activity GO:0004504 |
Revision as of 17:58, 27 July 2011
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 )
- 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