dependent on - if we obsolete, what should we do with the current annotations?

[dosumis]

Dependent_on

This has been used in 1800 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

Examples

Many of these look like the extension information cannot be covered using the AE current relationships, and may be out of the scope of GO. Considerable guidance is required in order to ensure edits follow consistent approach, ie improved documentation

ChEBI ID

SOURCE	ANNOTATED	GO_ID	GO_NAME	ANNOTATION EXTENSIONS	EVIDENCE	PUB TYPE	PUB ACC
SGD	P25632	GO:0015616	DNA translocase activity	dependent_on(CHEBI:15422: ATP	IDA	PMID	17918861

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

Also note that this example is a substrate and that this is recorded in the ontology:

GO:0015616
DNA translocase activity
Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive movement along a single- or double-stranded DNA molecule.

GO ID

SOURCE	ANNOTATED	GO_ID	GO_NAME	ANNOTATION EXTENSIONS	EVIDENCE	PUB TYPE	PUB ACC
PARL	O75460	GO:0006379	mRNA cleavage	dependent_on(GO:0042803 protein homodimerization activity	IDA	PMID	21317875
PARL	Q02948	GO:0000045	autophagic vacuole assembly	dependent_on(GO:0031667) response to nutrient levels	IGI	PMID	23878393
SWIS	Q7TS55	GO:0045785	positive regulation of cell adhesion	dependent_on(GO:0032496 response to lipopolysaccharide	IMP	PMID	23892569
SWIS	P07108	GO:0046983	protein dimerization activity	dependent_on(GO:0036042) long-chain fatty acyl-CoA binding	IDA	PMID	21079819
BHFL	O43474	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	dependent_on(GO:0000165 MAPK cascade	IGI	PMID	20551324

all BP and MF annotations C16 dependent_on GO IDs, consider changing to part_of, or reversing extension and using causally_upstream_of

SOURCE	ANNOTATED	GO_ID	GO_NAME	ANNOTATION EXTENSIONS	EVIDENCE	PUB TYPE	PUB ACC
SWIS	Q60855	GO:0097527	necroptotic signaling pathway	dependent_on(GO:0004672) protein kinase activity	IMP	PMID	21876153

would this one work in reverse, stating protein kinase activity part of necroptotic signaling pathway?

SOURCE	ANNOTATED	GO_ID	GO_NAME	ANNOTATION EXTENSIONS	EVIDENCE	PUB TYPE	PUB ACC
SWIS	Q15485	GO:0001867	complement activation, lectin pathway	dependent_on(GO:0003823 antigen binding	IDA	PMID	14707097

would this one work in reverse, stating antigen binding part of complement activation, lectin pathway?

SOURCE	ANNOTATED	GO_ID	GO_NAME	ANNOTATION EXTENSIONS	EVIDENCE	PUB TYPE	PUB ACC
SGD	P04147	GO:0010494	cytoplasmic stress granule	dependent_on(GO:0034605) cellular response to heat	IDA	PMID	24291094
SWIS	P07737	GO:0005938	cell cortex	dependent_on(GO:0006939) smooth muscle contraction	IDA	PMID	24700464
SWIS	D4ABB2	GO:0005783	endoplasmic reticulum	dependent_on(GO:0000226 microtubule cytoskeleton organization	IDA	PMID	19931615

all CC annotations C16 dependent_on GO IDs, consider changing to exists_during

SOURCE	ANNOTATED	GO_ID	GO_NAME	ANNOTATION EXTENSIONS	EVIDENCE	PUB TYPE	PUB ACC
SGD	P38144	GO:0016887	ATPase activity	dependent_on(GO:0000786) nucleosome	IDA	PMID	12482963
SPOM	U3H042	GO:0000778	condensed nuclear chromosome kinetochore	dependent_on(GO:0000818) nuclear MIS12/MIND complex	IDA	PMID	22711988
SWIS	Q99829	GO:0016020	membrane	dependent_on(GO:0005509) calcium ion binding	IDA	PMID	25450385

No idea what to suggest with these

[RH] For the nucleosome example, I've looked at the paper and think there are better ways of capturing the data; see suggestions here http://wiki.geneontology.org/index.php/Annotation_Conf._Call,_July_28,_2015#i.29_PMID:_12482963

Pfam IDs

SOURCE	ANNOTATED	GO_ID	GO_NAME	ANNOTATION EXTENSIONS	EVIDENCE	PUB TYPE	PUB ACC
SPOM	O60132	GO:0005515	protein binding	dependent_on(Pfam:PF00018) SH3 domain	IPI	PMID	24554432

this hasn't been annotated to SH3 domain binding, so presumably this means that the protein annotated needs to have the SH3 domain to bind the target, is it necessary to state this? Is the the reciprocal annotation to SH3 binding

Protein IDs

SOURCE	ANNOTATED	GO_ID	GO_NAME	ANNOTATION EXTENSIONS	EVIDENCE	PUB TYPE	PUB ACC
SPOM	Q9US03	GO:0036449	microtubule minus-end	dependent_on(PomBase:SPAC18G6.15) mal3	IDA	PMID	24039245
PARL	Q9C0C7	GO:0043552	positive regulation of phosphatidylinositol 3-kinase activity	dependent_on(UniProtKB:O60260)	IDA	PMID	21753002

is this suggesting that we list all proteins involved in a process in C16?

SOURCE	ANNOTATED	GO_ID	GO_NAME	ANNOTATION EXTENSIONS	EVIDENCE	PUB TYPE	PUB ACC
SWIS	Q9ESD1	GO:0005615	extracellular space	dependent_on(UniProtKB:O70362)	IDA	PMID	16822939

annotate the reverse ie O70362 protein localization to extracellular space C16 transports Q9ESD1

SO IDs

SOURCE	ANNOTATED	GO_ID	GO_NAME	ANNOTATION EXTENSIONS	EVIDENCE	PUB TYPE	PUB ACC
WB	G5EDK8	GO:0042826	histone deacetylase binding	dependent_on(SO:0000170 RNApol_II_promoter	IPI	PMID	23437011
WB	O17695	GO:0001103	RNA polymerase II repressing transcription factor binding	dependent_on(SO:0000170 RNApol_II_promoter	IPI	PMID	23437011

could this be Occurs_at?
[RH] Looking at the paper, Fos-1 and Hda-1 associate on the promoter of kreg-1 , so I think the correct way to represent this is with occurs_at, however you are not capturing the fact that it is the kreg-1 promoter. Is there a better ID that can be used to indicate this?

Converted from md report page created by @RLovering

[dosumis]

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

Is there a case for keeping this for chemicals?

[dosumis]

General conclusions:

1. dependent_on is not in the ontology. Many use cases here actually substitute for patterns that are used in the ontology and so instead this usage of dependent_on prevents folding/integration with ontology.
2. May be a use case for use with chemicals, but would in_presence_of be better for this?

[dosumis]

CC @rbalakri

[rachhuntley]

I think we need to be careful with capturing chemicals regardless of whether it is with dependent_on or in_presence_of. We need to consider if the chemical is physiologically relevant and not just an assay condition, for example using a chemical to induce a physiological response: if an author uses hydrogen peroxide to induce oxidative stress I would annotate to the relevant oxidative stress term rather than putting H2O2 in the extension.

In the case of the ATP example above, we decided it shouldn't be added to the extension as ATP is actually mentioned in the reaction in the definition.

In other cases we should consider creating new GO terms, e.g. ATP-dependent 'process/function'.

Bottom line, the curator needs to start thinking a bit more about what physiological process is being demonstrated and not just blindly copy down what the author says.

I'm still not sure we should keep this relation at all, I don't think I've yet come across a good example to justify keeping it.

[rbalakri]

I agree with Rachael. Curators need to think about what the authors are saying. I would like to hold a workshop or tutorial at the GOC meeting (turns out the Symposium day is not packed after all) to highlight these issues.

Rama

[RLovering]

Hi Rama

An AE workshop would be brilliant, hopefully this would give us a chance to really work through examples

Best

Ruth

From: rbalakri <[email protected]mailto:[email protected]>
Reply-To: geneontology/annotation_extensions <[email protected]mailto:[email protected]>
Date: Wednesday, 29 July 2015 18:40
To: geneontology/annotation_extensions <[email protected]mailto:[email protected]>
Cc: Ruth Lovering <[email protected]mailto:[email protected]>
Subject: Re: [annotation_extensions] dependent on - if we obsolete, what should we do with the current annotations? (#17)

I agree with Rachael. Curators need to think about what the authors are saying. I would like to hold a workshop or tutorial at the GOC meeting (turns out the Symposium day is not packed after all) to highlight these issues.

Rama

Reply to this email directly or view it on GitHubhttps://github.com//issues/17#issuecomment-126031331.

[pfey03]

Hi All,

So sorry I missed the call on Tue and because of our Dicty2015 meeting, I'll also miss Aug. 11. Thanks a lot for the notes, will go through when I get a chance. And yes, I’ll be in for an AE workshop on the symposium day!

Best,
Petra

On 30 Jul 2015, at 00:22, Ruth Lovering <[email protected]mailto:[email protected]> wrote:

Hi Rama

An AE workshop would be brilliant, hopefully this would give us a chance to really work through examples

Best

Ruth

From: rbalakri <[email protected]mailto:[email protected]mailto:[email protected]>
Reply-To: geneontology/annotation_extensions <[email protected]mailto:[email protected]mailto:[email protected]>
Date: Wednesday, 29 July 2015 18:40
To: geneontology/annotation_extensions <[email protected]mailto:[email protected]mailto:[email protected]>
Cc: Ruth Lovering <[email protected]mailto:[email protected]mailto:[email protected]>
Subject: Re: [annotation_extensions] dependent on - if we obsolete, what should we do with the current annotations? (#17)

I agree with Rachael. Curators need to think about what the authors are saying. I would like to hold a workshop or tutorial at the GOC meeting (turns out the Symposium day is not packed after all) to highlight these issues.

Rama

Reply to this email directly or view it on GitHubhttps://github.com//issues/17#issuecomment-126031331.

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/17#issuecomment-126114235.