chromosome organization is_a children

gocentral commented 13 years ago

chromosome organzation is linked through is_a

histone H4-R3 methylation histone H3-S10 phosphorylation histone H4-K8 acetylation

which seems incorrrect. The problem may be at chromatin modification The alteration of DNA or protein in chromatin, which may result in changing the chromatin structure. which implies that it may not alter the chromatin structure...if it does not change the chromatin structure, is it organizing chromosomes?

Val

Reported by: ValWood

Original Ticket: geneontology/ontology-requests/8477

gocentral commented 13 years ago

assigned_to: aledie --> ukemi

Original comment by: ValWood

gocentral commented 13 years ago

Val and I had a brief chat this morning about this -

We think it would be nice if we could send 'chromatin modification' (GO:0016568) into a well-deserved retirement, because it doesn't use 'modification' with the same meaning -- covalent alteration -- that we've used for 'macromolecule modification' and its 'x modification' is_a descendants. Chromatin modification also has no path to macromolecule modification, and doesn't refer to the alteration of a single easily defined category of molecules (cf protein modification, DNA modification, RNA modification).

Although it has a lot of annotations, it seems like they could all be rehomed elsewhere -- everything directly annotated to GO:0016568 could be automatically moved up to 'chromatin organization', or if anyone wants to put in the effort they can see whether they can use any of the other descendants of chromatin organization instead.

Or maybe just merge 'chromatin modification' into 'chromatin organization'?? The definitions don't make the difference all that obvious to me ...

cheers, m

Original comment by: mah11

gocentral commented 13 years ago

milestone: --> PomBase

Original comment by: mah11

gocentral commented 13 years ago

Just to summarise. The current structure stands at:

chromatin organization ; GO:0006325 --[isa]chromatin modification ; GO:0016568 ----[isa]chromatin remodeling ; GO:0006338 ----[isa]covalent chromatin modification ; GO:0016569 ----[isa]non-covalent chromatin modification ; GO:0016582 ----[isa]progressive alteration of chromatin involved in cell aging ; GO:0001301

chromatin modification ; GO:0016568 The alteration of DNA, protein, or sometimes RNA, in chromatin, which may result in changing the chromatin structure.

1/ The following children can be moved directly under 'chromatin organization ; GO:0006325' chromatin remodeling ; GO:0006338 covalent chromatin modification ; GO:0016569 non-covalent chromatin modification ; GO:0016582

2/ I'll create the additional relationship: macromolecule modification ; GO:0043412 --[isa]covalent chromatin modification ; GO:0016569

(since the 'modification' terms in GO refer to COVALENT alterations).

3/ WHICH LEAVES: progressive alteration of chromatin involved in cell aging ; GO:0001301 (and its children)

Most annotations to GO:0001301 are to the child terms: -extrachromosomal circular DNA accumulation involved in cell aging -negative regulation of chromatin silencing involved in replicative cell aging -age-dependent telomere shortening

I think these can change to be 'Any chromatin organization process that …..' and change the XPs to point to GO:0006325.

Becky

Original comment by: rebeccafoulger

gocentral commented 10 years ago

assigned_to: RFoulger --> Paola Roncaglia

Original comment by: paolaroncaglia

gocentral commented 10 years ago

Marking this for discussion at the SF jamboree. I 'inherited' this ticket from Becky; I agree with her proposal which is very thorough. Can anyone think of any reason why this would NOT be the best way to go? Asking in case I missed any discussion back then. (Update: Becky confirms that there was no further discussion on this.)

Original comment by: paolaroncaglia

gocentral commented 10 years ago

labels: Term obsoletion --> Term obsoletion, jamboree

Original comment by: paolaroncaglia

gocentral commented 10 years ago

Original comment by: paolaroncaglia

gocentral commented 10 years ago

At the SF jamboree yesterday, we discussed this in detail. Resolutions:

make 'chromatin organization' is_a 'cellular component organization', part_of 'chromosome organization', results_in_organization_of 'chromatin' (rather than just is_a 'chromosome organization' as is now);
make 'chromatin' is_a 'macromolecular complex' (rather than just is_a 'chromosomal part' as is now);
add def. gloss to 'chromosome organization': "This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome";
Stemming from this discussion: 'organization' terms: many are not axiomatized and this compounds the problem. Existing 'organization' terms are of two types in GO: 1) anatomical structure organization (e.g. 'abducens nerve structural organization') 2) cellular component organization (e.g. 'actin cortical patch organization') The existing axiomatized terms are of the latter kind and have the link 'results_in_organization_of'. Can't find its full definition in RO to see if it could apply to anatomical structures too. Should we open a Jira ticket for this?
look at direct annotations to 'chromatin modification' to see if we can move those annotations elsewhere... merge with parent? see below;
merge chromatin modification into chromatin organization, and carry on the changes suggested by Becky;
add 'chromatin modification' as a (related) synonym of 'chromatin organization' (actually, it should be done automatically at merge);
look into merging 'non-covalent chromatin modification' (hasn't been used) into 'chromatin organization'.

Will update as I work on this. Paola

Original comment by: paolaroncaglia

gocentral commented 10 years ago

Done these bits:

make 'chromatin organization' is_a 'cellular component organization', part_of 'chromosome organization', results_in_organization_of 'chromatin' (rather than just is_a 'chromosome organization' as is now);
make 'chromatin' is_a 'macromolecular complex' (rather than just is_a 'chromosomal part' as is now);
add def. gloss to 'chromosome organization': "This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome".

Original comment by: paolaroncaglia

gocentral commented 10 years ago

status: pending --> open

Original comment by: paolaroncaglia

gocentral commented 10 years ago

Wrt the point below:

"Stemming from this discussion: 'organization' terms: many are not axiomatized and this compounds the problem. Existing 'organization' terms are of two types in GO: 1) anatomical structure organization (e.g. 'abducens nerve structural organization') 2) cellular component organization (e.g. 'actin cortical patch organization') The existing axiomatized terms are of the latter kind and have the link 'results_in_organization_of'. Can't find its full definition in RO to see if it could apply to anatomical structures too. Should we open a Jira ticket for this?"

We decided to punt on the anatomical structures for now - work is in progress in this area; Chris added logical defs. to cellular component organization terms; TG template for '[cellular component] organization' - added to agenda for next editors' call.

So all done for that section - need to look at the last 4 points.

Original comment by: paolaroncaglia

paolaroncaglia commented 8 years ago

@ValWood This was an old request of yours. Mentioning you as you were no longer receiving notifications after the move to GitHub.

Note for self: Some time has gone by after my last edits, so I need to check if there was any change in the meantime wrt the following points:

look at direct annotations to 'chromatin modification' to see if we can move those annotations elsewhere... merge with parent? see below;
merge chromatin modification into chromatin organization, and carry on the changes suggested by Becky;
add 'chromatin modification' as a (related) synonym of 'chromatin organization' (actually, it should be done automatically at merge);
look into merging 'non-covalent chromatin modification' (hasn't been used) into 'chromatin organization'.

ValWood commented 8 years ago

It all makes sense to me, except maybe merging 'non-covalent chromatin modification' (hasn't been used)

mainly becasue I don't know what this is...is it necessary to merge? Maybe just obsolete?

ValWood commented 8 years ago

Hi Paola, do you have any outstanding questions for this ticket before implementation?

Cheers

Val

paolaroncaglia commented 8 years ago

Following chat with Val, resolved to obsolete 'non-covalent chromatin modification' (we don't know what it was created for - has no annotations) (in the obsoletion email, may want to mention that chromatin modification will be merged into chromatin organization). Then carry on with the other plans as laid out above.

paolaroncaglia commented 8 years ago

Obsoletion email sent today.

paolaroncaglia commented 8 years ago

Obsoleted GO:0016582 'non-covalent chromatin modification' today.

paolaroncaglia commented 8 years ago

Work in progress. Done today:

progressive alteration of chromatin involved in cell aging ; GO:0001301 changed def and xp to point to chromatin organization rather than modification; placed directly under chromatin organization;
moved directly under 'chromatin organization ; GO:0006325': chromatin remodeling ; GO:0006338 and covalent chromatin modification ; GO:0016569
added link: macromolecule modification ; GO:0043412 --[isa]covalent chromatin modification ; GO:0016569

paolaroncaglia commented 8 years ago

Next: look at 'regulation of chromatin modification' branch.

paolaroncaglia commented 8 years ago

Done: descendants of ‘regulation of chromatin modification’: removed links to chromatin modification.

These terms have no direct annotations: GO:1903308 regulation of chromatin modification GO:1903309 negative regulation of chromatin modification GO:1903310 positive regulation of chromatin modification So I can now merge them with 'reg of chromatin organiz.' and pos + neg children.

paolaroncaglia commented 8 years ago

Created as they were missing:

ID: GO:1905268 Label: negative regulation of chromatin organization ID: GO:1905269 Label: positive regulation of chromatin organization

paolaroncaglia commented 8 years ago

Merged reg. terms as above.

paolaroncaglia commented 8 years ago

As of today, QuickGO shows 102 manual (all manual, not just experimental) direct annotations to 'chromatin modification', for 97 proteins. We'd need to see if they can find a better (more specific) home than 'chromatin organization'. Otherwise that's where they'll end up when we carry out the next (and last!) step i.e. merge 'chromatin modification' with 'chromatin organization'.

I'll contact the individual databases (by mentioning the relevant curators in this ticket).

paolaroncaglia commented 8 years ago

@RLovering @ukemi @hdrabkin @ValWood @tberardini @mcourtot @pfey03 @hattrill @srengel @vanaukenk @doughowe

Dear curators,

Based on earlier discussion in this ticket, I’m going to merge 'chromatin modification' into 'chromatin organization’. There are 102 manual annotations (for 97 proteins) directly to 'chromatin modification’. This is considering all manual annotations (i.e. not just experimental). Before I merge, could you please review ‘your’ annotations and see if you’d like to rehouse them under a more specific term than 'chromatin organization’. Otherwise, please be aware that that’s where they’ll end up.
For your convenience, I am attaching here a spreadsheet containing those direct annotations, as downloaded from QuickGO today. There are separate tabs for the relevant databases. I plan to do the merge in 2 weeks from today, i.e. on June 30th.

Thanks! chromatin_modification_all_manual_16062016.xlsx

ValWood commented 8 years ago

done for pombase

doughowe commented 8 years ago

In ZFIN, we also have an IEA to chromatin modification from UniProtKW2GO KW-0156. I presume that will be updated in the translation file as well?

Doug Howe, Ph.D. ZFIN Data Curation Manager Zebrafish Model Organism Database 5291 University of Oregon Eugene, OR 97403-5291 (541)346-2355

On 6/16/16 7:47 AM, paolaroncaglia wrote:

@RLovering https://github.com/RLovering @ukemi https://github.com/ukemi @hdrabkin https://github.com/hdrabkin @ValWood https://github.com/ValWood @tberardini https://github.com/tberardini @mcourtot https://github.com/mcourtot @pfey03 https://github.com/pfey03 @hattrill https://github.com/hattrill @srengel https://github.com/srengel @vanaukenk https://github.com/vanaukenk @doughowe https://github.com/doughowe

Dear curators,

Based on earlier discussion in this ticket, I’m going to merge 'chromatin modification' into 'chromatin organization’. There are 102 manual annotations (for 97 proteins) directly to 'chromatin modification’. This is considering all manual annotations (i.e. not just experimental). Before I merge, could you please review ‘your’ annotations and see if you’d like to rehouse them under a more specific term than 'chromatin organization’. Otherwise, please be aware that that’s where they’ll end up.

For your convenience, I am attaching here a spreadsheet containing those direct annotations, as downloaded from QuickGO today. There are separate tabs for the relevant databases. I plan to do the merge in 2 weeks from today, i.e. on June 30th.

Thanks! chromatin_modification_all_manual_16062016.xlsx https://github.com/geneontology/go-ontology/files/318616/chromatin_modification_all_manual_16062016.xlsx

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doughowe commented 8 years ago

Done for zebrafish

Doug Howe, Ph.D. ZFIN Data Curation Manager Zebrafish Model Organism Database 5291 University of Oregon Eugene, OR 97403-5291 (541)346-2355

On 6/16/16 7:47 AM, paolaroncaglia wrote:

@RLovering https://github.com/RLovering @ukemi https://github.com/ukemi @hdrabkin https://github.com/hdrabkin @ValWood https://github.com/ValWood @tberardini https://github.com/tberardini @mcourtot https://github.com/mcourtot @pfey03 https://github.com/pfey03 @hattrill https://github.com/hattrill @srengel https://github.com/srengel @vanaukenk https://github.com/vanaukenk @doughowe https://github.com/doughowe

Dear curators,

Based on earlier discussion in this ticket, I’m going to merge 'chromatin modification' into 'chromatin organization’. There are 102 manual annotations (for 97 proteins) directly to 'chromatin modification’. This is considering all manual annotations (i.e. not just experimental). Before I merge, could you please review ‘your’ annotations and see if you’d like to rehouse them under a more specific term than 'chromatin organization’. Otherwise, please be aware that that’s where they’ll end up.

For your convenience, I am attaching here a spreadsheet containing those direct annotations, as downloaded from QuickGO today. There are separate tabs for the relevant databases. I plan to do the merge in 2 weeks from today, i.e. on June 30th.

Thanks! chromatin_modification_all_manual_16062016.xlsx https://github.com/geneontology/go-ontology/files/318616/chromatin_modification_all_manual_16062016.xlsx

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/geneontology/go-ontology/issues/8689#issuecomment-226504727, or mute the thread https://github.com/notifications/unsubscribe/AGz6vQL8G4Npko-Qhn73dB_d7AckNv7Vks5qMWISgaJpZM4Hhuqn.

srengel commented 8 years ago

done for SGD. i edited what needed editing, and left the remainder to be rehoused under 'chromatin organization' automatically during the merge.

RLovering commented 8 years ago

BHF-UCL completed updates

hattrill commented 8 years ago

done for flybase

paolaroncaglia commented 8 years ago

Thank you all so far. Note for self: I'll have to double-check my latest edits (as above) once a current GO release/conflict issue is resolved.

paolaroncaglia commented 8 years ago

Hi @doughowe , I contacted UniProt about the mapping issue. Thanks for bringing it to attention.

pfey03 commented 8 years ago

Done for dictyBase; just a few TAF orthologs etc ISS to yeast proteins. If Stacia left them they'ill match, if not, P2G will alert later.

sylvainpoux commented 8 years ago

Sorry to interfere in the discussion but I think it is not appropriate to merge these 2 terms

I come from the chromatin field and I can say that reorganization of chromatin is not necessarily associated with modifications. You can perfectly have rearrangements of nucleosomes etc. Displacement of nucleosomes can be the consequence of ATPases, which trigger chromatin reorganization without necessarily modifying it.

In my opinion, it is correct to state that chromatin modification is a child of chromatin organization

By merging these 2 terms you would create more confusion and solve problems and I would look twice before merging these 2 terms

Thanks

Sylvain

paolaroncaglia commented 8 years ago

From @pgaudet

"I concur with Sylvain, in these case we have two very distinct concepts - the chromatin organization can be via bindings, regardless of modifications (or in addition to modifications).

Maybe the terms need to be reorganized, and the inter ontology links could need fixing, but I am in favor of keeping both concepts."

mah11 commented 8 years ago

Hi Sylvain & Pascale,

I think the "modification" you describe is covered by GO:0016569 ! covalent chromatin modification, which is and will remain a subclass of chromatin organization. The motivation for the changes proposed here is that non-covalent alterations to chromatin are better described by "organization" than "modification".

ukemi commented 8 years ago

At any rate, I have updated the mouse annotations that are not coming in through pipelines to be more specific.

ValWood commented 8 years ago

On 17/06/2016 13:27, sylvainpoux wrote:

Sorry to interfere in the discussion but I think it is not appropriate to merge these 2 terms

I come from the chromatin field and I can say that reorganization of chromatin is not necessarily associated with modifications. You can perfectly have rearrangements of nucleosomes etc. Displacement of nucleosomes can be the consequence of ATPases, which trigger chromatin reorganization without necessarily modifying it.

In my opinion, it is correct to state that chromatin modification is a child of chromatin organization

By merging these 2 terms you would create more confusion and solve problems and I would look twice before merging these 2 terms

Thanks

Sylvain

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Hi Sylvian,

The comment to read for an explanation is Midori's on 31st May. The term was defined incorrectly (there was no difference between this term and the organization term, as defined), and the covalent chromatin modificition is better defined.

Based on your comment I think it will be confusing for "chromatin organization" to have "chromatin modification" as a synonym,. Paola, could this synonym be deleted after the merge?

Val

Cambridge University PomBase http://www.pombase.org/ Cambridge Systems Biology Centre http://www.sysbiol.cam.ac.uk/Investigators/val-wood

paolaroncaglia commented 8 years ago

Yes, no problem.

paolaroncaglia commented 8 years ago

Hi @sylvainpoux and @pgaudet ,

Based on the detailed responses from Midori and Val, could you please confirm that you have no objections to merging the existing ill-defined ‘chromatin modification’ into its parent ‘chromatin organization’? The UniProtKW2GO KW-0156 should probably map to GO:0016569 ! covalent chromatin modification.

Sorry to ask, but your confirmation on this would be helpful so we know if we can go ahead with looking at rehousing the remaining existing annotations.

Many thanks,

Paola

ValWood commented 8 years ago

Also, for consistency it might make sense to call the correctly defined "covalent chromatin modification" straightforward "chromatin modification" after the merge (with "covalent chromatin modification" synonym)

tberardini commented 8 years ago

I've reviewed and updated the TAIR experimental annotations to 'chromatin organization'.

sylvainpoux commented 8 years ago

Hi Paola,

ok, I understand now. Sure you can proceed.

Sorry for the inconvenience

Sylvain

On 20.06.2016 18:47, paolaroncaglia wrote:

Hi @sylvainpoux https://github.com/sylvainpoux and @pgaudet https://github.com/pgaudet ,

Based on the detailed responses from Midori and Val, could you please confirm that you have no objections to merging the existing ill-defined ‘chromatin modification’ into its parent ‘chromatin organization’? The UniProtKW2GO KW-0156 should probably map to GO:0016569 ! covalent chromatin modification.

Sorry to ask, but your confirmation on this would be helpful so we know if we can go ahead with looking at rehousing the remaining existing annotations.

Many thanks,

Paola

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Sylvain Poux, PhD Head of annotation department Swiss-Prot group SIB Swiss Institute of Bioinformatics 1, rue Michel Servet CH-1211 Geneva 4 Switzerland

sylvain.poux@sib.swiss - www.sib.swiss

paolaroncaglia commented 8 years ago

Thanks @sylvainpoux ! No inconvenience at all. Thank you, for your feedback.

Paola

ValWood commented 8 years ago

Yes we could have made it clearer the rationale for the merge, I had forgotten myself the thread was so long! Always good to check...

paolaroncaglia commented 8 years ago

Tony S. updated the mapping.

paolaroncaglia commented 8 years ago

@mcourtot @vanaukenk

Just a friendly reminder :-) in case you haven’t had a chance to do this yet, if you’d like to look into UniProt/WormBase manual direct annotations to 'chromatin modification’ and see if they need rehousing please. Otherwise, no worries, the term will be merged into its parent 'chromatin organization’ next week, and the annotations will move too. Thanks!

paolaroncaglia commented 8 years ago

Note or self: Summing up what is left to do for this ticket, as it’s become quite long:

Double-check my latest edits (because of recent GO release issues).
On June 30th, merge 'chromatin modification' into 'chromatin organization’.
Delete the synonym ‘chromatin modification’ from 'chromatin organization’.
Rename ‘covalent chromatin modification’ as ‘chromatin modification’ (keep ‘covalent chromatin modification’ as an exact synonym).
Close ticket!

paolaroncaglia commented 8 years ago

Note for self: now verified - these went through ok: "Double-check my latest edits (because of recent GO release issues)."

geneontology / go-ontology

chromosome organization is_a children #8689