in_presence_of - if we obsolete, what should we do with current annotations?

[dosumis]

in_presence_of

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

Suggestions need to be made to:

• 1. explain how to capture the current annotations to this term in GO AE field
• 2. document whether or not the information should be in GO at all

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]

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]

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]

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