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geneontology / annotation_extensions

Documentation, tickets & usage reports for annotation extension relations.
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in_presence_of - if we obsolete, what should we do with current annotations? #18

Open dosumis opened 9 years ago

dosumis commented 9 years ago

in_presence_of

Has been used in 2600 annotations It has been proposed that this relationship is depreciated

Suggestions need to be made to:

I have just extracted a selection of GOC annotations for examples

Examples

ChEBI ID

926 annotations

SOURCE ANNOTATED GO_ID GO_NAME ANNOTATION EXTENSIONS EVIDENCE PUB TYPE PUB ACC
WB Q9U3C6 GO:0008355 olfactory learning in_presence_of(CHEBI:28398) IGI PMID 23993094
SGD P53599 GO:2000251 positive regulation of actin cytoskeleton reorganization in_presence_of(CHEBI:26710) IGI PMID 12857882
SGD Q02521 GO:0001671 ATPase activator activity in_presence_of(CHEBI:8758) IDA PMID 25561498
SGD Q05789 GO:0000407 pre-autophagosomal structure in_presence_of(CHEBI:9168) IDA PMID 24165940

wide range of BP and MFs with ChEBI IDs. Possible activated_by, has_input?

GO ID

30 annotations the majority represented by the annotations listed below

SOURCE ANNOTATED GO_ID GO_NAME ANNOTATION EXTENSIONS EVIDENCE PUB TYPE PUB ACC
SWIS P49757 GO:0030335 positive regulation of cell migration in_presence_of(GO:0005587) collagen type IV trimer IGI PMID 19581412
SWIS P13020 GO:0005925 focal adhesion in_presence_of(GO:0005584 collagen type I trimer IDA PMID 23325791
AB P07812 GO:0044877 macromolecular complex binding in_presence_of(GO:0000790) nuclear chromatin IDA PMID 2021645
SWIS Q96J84 GO:0005886 plasma membrane in_presence_of(GO:0031941) filamentous actin IDA PMID 21402783

no idea about what to suggest here

Protein IDs

1500 annotations to some sort of protein ID

SOURCE ANNOTATED GO_ID GO_NAME ANNOTATION EXTENSIONS EVIDENCE PUB TYPE PUB ACC
SWIS Q6UX65 GO:0010506 regulation of autophagy in_presence_of(UniProtKB:Q8N682) IDA PMID 19895784
SWIS P61019 GO:0003924 GTPase activity in_presence_of(UniProtKB:Q96BZ9) IDA PMID 17684057
SGD P41800 GO:0032865 ERMES complex in_presence_of(UniProtKB:Q92328 IDA PMID 17410204

no idea about what to suggest here

(Converted from md doc generated by @RLovering & Rachael Huntley)

dosumis commented 9 years ago

Comments please @cmungall @ukemi (Should also get comment from Paul Thomas (Github name = ??)

Not clear to me how this is meant to be different from dependent_on - so should probably be considered together with #17

dosumis commented 9 years ago

Notes from editor's meeting:

More defensible than 'dependent_on', but only if strictly defined. Usage should exclude substrates and general experimental conditions, but could be useful to record where the presence of some chemical is necessary for an activity.

pfey03 commented 9 years ago

should be considered with in_absence_of - these can be used together, in two separate annotations from the same paper