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GO-CAM Working Group Call 2018-06-26

Mon, 06/25/2018 - 12:04

Vanaukenk: /* Noctua */

= Meeting URL =
https://stanford.zoom.us/j/976175422

=Agenda=
== Logistics ==
*User accounts
**Follow-up from last week: Sandy L
**https://github.com/geneontology/noctua/issues/563
***Closed - all okay
*Groups
**https://github.com/geneontology/noctua-models/issues/96
***Should this be discussed on Wednesday's technical call?

== Noctua ==
*[http://geneontology.org/gocam Landing Page (under development)]
**Browsing GO-CAMs
**User and Group Pages
**Curators should look around the landing page, provide feedback

== Documentation ==
*[http://wiki.geneontology.org/index.php/Noctua Noctua tool]
*[http://wiki.geneontology.org/index.php/Annotation_Relations Annotation relations]

== Proposal for this group ==
*Focus on specific, commonly used curation modules
**For example, transcription, signaling pathways, metabolic pathways
*Groups will annotate papers of their own choosing
*We will discuss representation of the data in GO-CAMs, and any questions or issues that arise
**Choosing the appropriate relation
**Assigning evidence
*Give feedback to tool developers, ontology editors based on our discussions
**Github trackers
***[https://github.com/geneontology/noctua noctua]
***[https://github.com/geneontology/simple-annoton-editor simple annoton editor]
***[https://github.com/geneontology/go-ontology go-ontology]
*Develop additional documentation

=Minutes=
*On call: Dustin, Giulia, Jim, Kimberly, Laurent-Philippe, Penelope, Rob, Sabrina, Sandy L, Stacia, Suzi A, Suzi L

== Noctua ==
*Current landing page provides links to form and graph editors
*Landing page under development provides additional model search functionality, links to curator reports, information about GO terms in models
**Could be used to help identify related curation and experts who can review models on specific areas of biology

*Sabrina asked about what happens to group affiliation on older models if a curator is no longer with that group?
**Check with Seth, but the group affiliation at the time of model curation will likely remain unless the curator specifically requests that it be changed - use the noctua-models tracker to do this
**Removing an affiliation from a users.yaml entry should not affect affiliations in existing models

== QA/QC ==
*Noctua does not yet have taxon restrictions for annotation
**Will be added in the future
*gp2term relations for legacy annotations
**High priority for this summer is to address existing BP annotations and develop as many rules-based approaches for applying new relations as possible
**Whatever annotations are left will need to be manually reviewed by curators

== Curation Projects for this Group ==
*Will try creating models for papers that describe transcriptional regulation
*A caveat to this is that right now the MF branch for transcription factors is still under review, so we may have to make some changes to annotations in the future
**However, it would still be good to work out the relations between the MFs and the BPs wrt transcription and upstream and downstream activities and processes
*[https://docs.google.com/document/d/1icc1pb3mRFb4kK_ELVY1rjqxEjXNehrQzelWTqM-ZD4/edit# Google doc for entering papers and curation questions]





















[[Category: Annotation Working Group]] Vanaukenk
Categories: GO Internal

2018 Montreal GOC Meeting Logistics

Mon, 06/25/2018 - 08:32

Pascale:


=Start and end of meeting=


=Registration fee=


=Meeting site=


=Call-in information=


=Travel=



=Accommodations=




=Food=


=Bicycling and walking / running=


=Attendees=
Please add your name to the table if you intend to attend the meeting, and the dinner, so we can get a headcount estimate.
{| {{Prettytable}} class='sortable'
|-
! Name
! Organization
! Attend the GOC dinner?
|-
| Pascale Gaudet
| SIB/GO Central
| Yes
|-
|}

=Remote attendees=
If you plan to attend remotely, please sign up here and indicate the sessions you are likely to attend:
{| {{Prettytable}} class='sortable'
|-
! Name
! Organization
|-
|}

[[Category: GO Consortium Meetings]] Pascale
Categories: GO Internal

2018 Montreal GOC Meeting Agenda

Mon, 06/25/2018 - 08:24

Pascale: /* New topics */

= AGENDA=




== Suggestions for topics Fall 2018==
===Carried over from May 2018===
*'Response to' workshop (similar to the signaling WS)
* Documentation of rules: Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928
* Use cases: Should we add this to the agenda? What would be a productive way of discussing this topic? https://docs.google.com/document/d/104m4jUNjPH9pCpskg8E29Zm2pLHhPFmKyIFLa9l_EOQ/edit


===New topics===
* Which organisms other than cerevisiae and pombe have looked at all protein coding genes for the availability/possibility of GO annotation? If anyone is interested, there is a very quick/easy way to establish the difference between: (1) "not in the GO database (not found); (2) "unknown" (ND), and (3) "unannotated" (no ND, and no annotation in Aspect of interest) for your organisms proteins using the complete known protein ID set for your organism and the GO term mapper tool https://go.princeton.edu/cgi-bin/GOTermMapper
(GOTermMapper provides these numbers as part of the output so that the slim set results can be interpreted correctly).
(Val)

[[Category: GO Consortium Meetings]] Pascale
Categories: GO Internal

Ontology meeting 2018-06-25

Mon, 06/25/2018 - 06:01

David: Created page with "= Conference Line = *Zoom: https://stanford.zoom.us/j/828418143 = Agenda = == Editors Discussion == ===Project Update=== Rhea-Reactome_GO alignment--- https://github.com/g..."

= Conference Line =

*Zoom: https://stanford.zoom.us/j/828418143

= Agenda =

== Editors Discussion ==

===Project Update===
Rhea-Reactome_GO alignment--- https://github.com/geneontology/go-ontology/projects/10


=== Regenerate Imports File ===
We continue to have issues with imported files. Although we can modify the import files, this isn't really a solution.

=== Obsoletion plugin for Protege ===
Please add you Protege versions and the plugin you have here.


=== Ontology Documentation ===
Pascale, David and Kimberly have been working on standardizing the ontology documentation to make it align with the documentation work that Kimberly and Pascal have been doing for other areas of GO. Specifically, we have moved the official documentation to the wiki and have arranged the wiki in a way that is similar to the annotation section. We are now going through the documentation to check it for accuracy and to be sure it is up to date.


===Ontology Developers' workshop possibility- Geneva in September?===
* David, Pascale and Kimberly will discuss possible dates and make a doodle poll.


==GH project link==
https://github.com/geneontology/go-ontology/projects/1

= Minutes =
*On call:





[[Category: Ontology]]
[[Category: Meetings]] David
Categories: GO Internal

Colocalizes with

Tue, 06/19/2018 - 06:55

Vanaukenk:

== Overview ==
*The 'colocalizes with' relation has traditionally been used with Cellular Component annotations to describe cases "where the resolution of an assay is not accurate enough to say that the gene product is a bona fide component member."
*Note that this relation has been interpreted differently by curators, and thus its use is currently under review.

=== Definition ===
A colocalizes_with b if and only if a is transiently or peripherally associated with b[GO].

=== Child Terms ===
None

== Examples of Usage ==
*Under review

== Quality Control Checks ==

== Relations Ontology ==
[http://purl.obolibrary.org/obo/RO_0002325 colocalizes with]

== Review Status ==

Last reviewed: June 19, 2018

[[Category: Annotation]]
[[Category: Relations]]
[[Category: Gene Product to Term Relations]] Vanaukenk
Categories: GO Internal

GO-CAM Working Group Call 2018-06-19

Mon, 06/18/2018 - 13:53

Vanaukenk: /* Proposal for this group */

= Meeting URL =
https://stanford.zoom.us/j/976175422

== Logistics ==
*User accounts
*Groups

== Noctua ==
*Review of the curation tool
**Form editor
**Graph editor

== Documentation ==
*[http://wiki.geneontology.org/index.php/Noctua Noctua tool]
*Annotation relations

== Proposal for this group ==
*Focus on specific, commonly used curation modules
**For example, transcription, signaling pathways, metabolic pathways
*Groups will annotate papers of their own choosing
*We will discuss representation of the data in GO-CAMs, and any questions or issues that arise
**Choosing the appropriate relation
**Assigning evidence
*Give feedback to tool developers, ontology editors based on our discussions
**Github trackers
***[https://github.com/geneontology/noctua noctua]
***[https://github.com/geneontology/simple-annoton-editor simple annoton editor]
***[https://github.com/geneontology/go-ontology go-ontology]
*Develop additional documentation





















[[Category: Annotation Working Group]] Vanaukenk
Categories: GO Internal

Ontology meeting 2018-06-18

Mon, 06/18/2018 - 06:25

David: Created page with "= Conference Line = *Zoom: https://stanford.zoom.us/j/828418143 = Agenda = == Editors Discussion == === Issue with SVN release === The SVN Release is successful again. =..."

= Conference Line =

*Zoom: https://stanford.zoom.us/j/828418143

= Agenda =

== Editors Discussion ==

=== Issue with SVN release ===

The SVN Release is successful again.

=== Regenerate Imports File ===
We continue to have issues with imported files. Although we can modify the import files, this isn't really a solution.

=== Obsoletion plugin for Protege ===
Does everyone have Jim's plugin? If not we should all install it and I will update the documentation.

What is the status of the merge plugin?

What is the best way to determine if a term is used in another ontology?

Is it okay to resurrect obsoleted terms?

=== Ontology Documentation ===
Pascale, David and Kimberly have been working on standardizing the ontology documentation to make it align with the documentation work that Kimberly and Pascal have been doing for other areas of GO. Specifically, we have moved the official documentation to the wiki and have arranged the wiki in a way that is similar to the annotation section. We are now going through the documentation to check it for accuracy and to be sure it is up to date.


===Ontology Developers' workshop possibility- Geneva in September?===
* David, Pascale and Kimberly will discuss possible dates and make a doodle poll.


==GH project link==
https://github.com/geneontology/go-ontology/projects/1

= Minutes =
*On call:



[[Category: Ontology]]
[[Category: Meetings]] David
Categories: GO Internal

GO-CAM Noctua Call 2018-06-13

Tue, 06/12/2018 - 12:06

Vanaukenk:

= Meeting URL =
https://stanford.zoom.us/j/679970729

= Agenda =

= Minutes =
*On call:

[[Category: Annotation Working Group]] Vanaukenk
Categories: GO Internal

Ontology meeting 2018-06-11

Sun, 06/10/2018 - 22:33

David: Created page with "= Conference Line = *Zoom: https://stanford.zoom.us/j/828418143 = Agenda = == Editors Discussion == ===Ontology Developers' workshop possibility- Geneva in September?=== *..."

= Conference Line =

*Zoom: https://stanford.zoom.us/j/828418143

= Agenda =

== Editors Discussion ==

===Ontology Developers' workshop possibility- Geneva in September?===
* David, Pascale and Kimberly will discuss possible dates and make a doodle poll.

=== Issue with SVN release ===

The SVN Release is failing, but in the live editors file, but the error that is being reported doesn't appear in the editors' version of the ontology.

=== Regenerate Imports File ===
We continue to have issues with imported files. Although we can modify the import files, this isn't really a solution.

=== Obsoletion plugin for Protege ===
Does everyone have Jim's plugin? If not we should all install it and I will update the documentation.
What is the status of the merge plugin?

Is it okay to resurrect obsoleted terms?

=== Ontology Documentation ===
Pascale, David and Kimberly have been working on standardizing the ontology documentation to make it align with the documentation work that Kimberly and Pascal have been doing for other areas of GO. Specifically, we have moved the official documentation to the wiki and have arranged the wiki in a way that is similar to the annotation section. We are now going through the documentation to check it for accuracy and to be sure it is up to date.


==GH project link==
https://github.com/geneontology/go-ontology/projects/1

= Minutes =
*On call:



[[Category: Ontology]]
[[Category: Meetings]] David
Categories: GO Internal

General Gene Ontology Principles

Fri, 06/08/2018 - 06:57

Pascale: Created page with " In progress For in depth background on principles of the Gene Ontology, see the following publication: * Paul's chapter in the GO handbook == Review Status == Last rev..."

In progress

For in depth background on principles of the Gene Ontology, see the following publication:
* Paul's chapter in the GO handbook




== Review Status ==
Last reviewed:

[http://wiki.geneontology.org/index.php/Ontology_Development Back to: Ontology Development]

[[Category:GO Editors]][[Category:Ontology]][[Category:Editor_Guide_2018]] Pascale
Categories: GO Internal

Requesting a New Complex ID from IntAct

Thu, 06/07/2018 - 18:17

Pascale:

Users can request complex IDs from IntAct by filling the Complex submission template and emailing it to intact-help@ebi.ac.uk or bmeldal@ebi.ac.uk with as much detail as possible.

==[https://www.ebi.ac.uk/intact/ IntAct] Complex submission template==

* Please supply as much information as possible to allow us to make your term.
* Find definition at: http://www.ebi.ac.uk/complexportal/documentation/data_content and http://wiki.geneontology.org/index.php/Guidelines_on_%27protein_complex%27_terms

===Complex names===
* Most commonly known name (recommended name):
* Synonyms (could be any and many!):

===Participants===
* [http://www.uniprot.org/ UniProt] IDs for proteins (and their binding regions and stoichiometry - if available)
* [https://www.ebi.ac.uk/chebi/ ChEBI] IDs for small molecules (and stoichiometry - if available)
* [http://rnacentral.org/ RNAcentral] IDs for ncRNAs (and stoichiometry - if available)

===Evidence===
* PMID for papers showing that the complex exists (if you are familiar with IntAct please add the IntAct interaction AC if applicable)
* '''Note:''' It should be evidence for all or most of the participants, not lots of binaries and not from high throughput experiments.

===Additional information===
PMIDs that show what the complex does and where (so we can add MF & BP GO terms, see below).

===Description===
A nice, concise description would help, similar to that required for GO term submissions :)

===Properties===
Any additional information such as molecular weight of the COMPLEX, size, buried surface area, stokes radius, binding regions…

===GO annotations===
Any terms that apply to the COMPLEX:
CC for the complex class and the cellular location (e.g. nucleus, plasma membrane…)
MFs & BPs: as many as applicable
Please supply PMIDs if possible

===Xrefs (if applicable)===
* [https://www.wwpdb.org/ wwPDB]
* [https://enzyme.expasy.org/ EC number] (for enzymes)

----

==Using Intact Helpdesk for new complex requests==
Alternatively, new complexes can now also be requested directly from the yellow tile on the new CP homepage (www.ebi.ac.uk/complexportal) but that's just a helpdesk message until we get round to create a form behind that tile.

== Review Status ==

Last reviewed: July 5, 2017

[[Category:GO Editors]][[Category:Ontology]] Pascale
Categories: GO Internal

Adding Terms to the Import Files

Thu, 06/07/2018 - 11:29

Pascale:

=TO BE FORMATTED=



''See [[Ontology_Editors_Daily_Workflow]] for creating branches and basic Protégé instructions.''

Terms are imported to GO from other ontologies, but not all terms from external ontologies are imported. Occasionally, you will find that a valid identifier exists in an external ontology, but the identifier is not available in Protege because that term is not yet imported. To import a term from an external ontology:

Navigate to the imports folder on GitHub, located at https://github.com/geneontology/go-ontology/tree/master/src/ontology/imports.
Look in the list of ontologies for the ontology that contains the term you wish to import.
Identify the ontology_terms.txt file for the target ontology. For example, for the addition of a new taxon, the file can be found at https://github.com/geneontology/go-ontology/blob/master/src/ontology/imports/ncbitaxon_terms.txt.
Click on the icon of a pencil in the upper right corner of the window to edit the file.
Add the new term on the next available line at the bottom of the file.
Click preview changes.
You can now either commit the file directly to master or create a branch and a pull request as described before.


''See [[Ontology_Editors_Daily_Workflow]] for commit, push and merge instructions.''

[[Category:GO Editors]][[Category:Ontology]][[Category:Editor_Guide_2018]] Pascale
Categories: GO Internal

Adding taxon restrictions

Thu, 06/07/2018 - 11:28

Pascale:

=TO BE FORMATTED=


''See [[Ontology_Editors_Daily_Workflow]] for creating branches and basic Protégé instructions.''

Only in taxon relations are added as Subclasses.
Navigate to the term for which you want to add the only in taxon restriction.
In the Description window click on the +.
In the pop-up window type a new relationship (e.g. 'only in taxon' some Viridiplantae).
The taxa available are imported ontology terms and can be browsed just like any other ontology term.
Never in taxon relations added as Annotations.
Navigate to the term for which you want to add the never in taxon restriction.
In the class annotations window, click on the +.
In the left-hand panel, select never_in_taxon.
In the right-hand panel, in the Entity IRI tab, navigate to the correct taxon. The full path is: thing/continuant/independent continuant/material entity/object/organism.
Select the appropriate taxon.
Click OK to save your changes.

''See [[Ontology_Editors_Daily_Workflow]] for commit, push and merge instructions.''

[[Category:GO Editors]][[Category:Ontology]][[Category:Editor_Guide_2018]] Pascale
Categories: GO Internal

Adding a new GO Subset (Slim)

Thu, 06/07/2018 - 11:27

Pascale:

=TO BE FORMATTED=

''See [[Ontology_Editors_Daily_Workflow]] for creating branches and basic Protégé instructions.''

In the main Protege window, click on the Annotation Properties tab.
Navigate to the subset_property and select it.
Click on the top left-hand button of the window to add a new subset property.
In the pop-up window add the name of the new slim. The identifier will fill in according to your preferences and will be the next GO identifier in your set. Click on Refactor in the menu. Select rename entities.
Replace the GO_ identifier with the name of your new slim. It is standard to use the same string as when you created the term.
In the annotations tab, click on the +.
In the pop up window, select rdfs:comment.
In the right hand window, type a small descriptor statement for the slim. Select xsd:string as the type.
Click OK to save the changes. You should now see the comment field in the annotations tab.


''See [[Ontology_Editors_Daily_Workflow]] for commit, push and merge instructions.''




[[Category:GO Editors]][[Category:Ontology]][[Category:Editor_Guide_2018]] Pascale
Categories: GO Internal

Adding a term to a GO Subset (Slim)

Thu, 06/07/2018 - 11:27

Pascale:

=TO BE FORMATTED=

''See [[Ontology_Editors_Daily_Workflow]] for creating branches and basic Protégé instructions.''

In Protege, navigate to the term you wish to add to a GO subset.
With the term selected, click on the Entities tab.
In the Annotation window on the right, click on the + to the right of ‘Annotations’ at the very top of the window.
In the pop-up window that appears, click on in_subset on the left-hand panel.
In the right-hand panel click on the ‘Entity IRI’ tab.
Navigate to the ‘Annotation Properties’ sub-tab.
Navigate to the subtypes of subset_property and select the appropriate slim.
Click on OK to save your edits.

''See [[Ontology_Editors_Daily_Workflow]] for commit, push and merge instructions.''


[[Category:GO Editors]][[Category:Ontology]][[Category:Editor_Guide_2018]] Pascale
Categories: GO Internal

Adding Term Comments

Thu, 06/07/2018 - 11:25

Pascale:

=TO BE FORMATTED=

''See [[Ontology_Editors_Daily_Workflow]] for creating branches and basic Protégé instructions.''

Adding Comments to Terms

Comments may be added to ontology terms to further explain their intended usage.

Wherever possible, we strive to use standard language for similar types of comments and suggest alternative terms to use.

Some examples of comments, and standard language for their usage, are:
Do Not Annotate

This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term.

Example: GO:0006810 transport

Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. transmembrane transport, microtubule-based transport, vesicle-mediated transport, etc.
Do Not Manually Annotate

This term should not be used for direct manual annotation. It should be possible to make a more specific manual annotation to one of the children of this term.

Example: GO:0000910 cytokinesis

Note that this term should not be used for direct annotation. When annotating eukaryotic species, mitotic or meiotic cytokinesis should always be specified for manual annotation and for prokaryotic species use ‘FtsZ-dependent cytokinesis; GO:0043093’ or ‘Cdv-dependent cytokinesis; GO:0061639’. Also, note that cytokinesis does not necessarily result in physical separation and detachment of the two daughter cells from each other.


''See [[Ontology_Editors_Daily_Workflow]] for commit, push and merge instructions.''

[[Category:GO Editors]][[Category:Ontology]][[Category:Editor_Guide_2018]] Pascale
Categories: GO Internal

Merging Ontology Terms

Thu, 06/07/2018 - 11:23

Pascale:

=TO BE FORMATTED=

''See [[Ontology_Editors_Daily_Workflow]] for creating branches and basic Protégé instructions.''

Note Before performing a merge, make sure that you know all of the consequences that the merge will cause. In particular, be sure to look at child terms and any other terms that refer to the ‘deprecated’ term. In many cases a simple merge of two terms is not sufficient because it will result in equivalent classes for child terms. For example if deprecated term X is going to be merged into target term Y and ‘regulation of X’ and ‘regulation of Y’ terms exist, then you will need to merge the regulation terms in addition to the primary terms. You will also need to edit any terms that refer to the deprecated term to be sure that the names and definitions are consistent.

Find the ID of the term in which the deprecated term will be merged
Navigate to ‘winning’ term using the Search box. Copy the ID of the winning term somewhere.
Remove annotations from the deprecated terms
Navigate to the term to be deprecated.
Remove the logical definition by clicking on the x on the right.
Remove all subclasses by clicking on the x on the right.
Look at the definition; if it does not seem relevant, remove it by clicking on the x on the right; otherwise copy/paste it somewhere to refer to when reviewing the definition for the winning term.
Note down the created_by and created_date (there can only be one value per term for each of these fields; this will be useful if you need to pick one after the merge is done).
Check existing list of synonyms to see if they need to be moved to the new term, otherwise delete them by clicking on the x on the right.
Change the ID of the term to be deprecated to the winning term’s ID
In the term to be deprecated, click on Refactor > Rename entity’ in the Protege menu (shortcut: command-U)
Copy the ID of the winning term (obtained in Step 1).
Be sure to use the underscore _ in the identifier instead of the colon :, for example: GO_1234567. Make sure that the ‘change all entities with this URI’ box is checked.
Make the deprecated ID an ‘alternative ID’
Navigate to the winning term. In the Annotations box, locate the ID of the deprecated term. Click the o to change the ID type.
In the resulting pop-up window, making sure the ‘Literal’ tab is selected in the top right side box, select has_alternative_id from the list on the left side. Double check that the entry corresponds to the GO ID of the deprecated term.
Click ‘OK’. The deprecated term identifier should now have the label has_alternative_id instead of id.
Change deprecated term label to a synonym
In the annotations box of the winning term there are now two terms with labels ‘rdfs:label’. Click the o to change the label of the deprecated term.
In the resulting pop-up window, select the appropriate synonym label from the list on the left:
has_broad_synonym
has_exact_synonym
has_narrow_synonym
has_related_synonym (if unsure, this is the safest choice)
Fix synonyms
In the annotations box of the winning term, check the list of synonyms to see if they are all still make appropriate.
If needed, fix the definition, using information from the deprecated term as appropriate.
Synchronize the reasoner and make sure there are no terms that have identical definitions as a result of the merge. These are displayed with an ‘equivalent’ sign ≡ in the class hierarchy view on the left hand panel.
Save changes.

See Daily Workflow section for commit, push and merge instructions.

TROUBLESHOOTING: Travis/Jenkins errors

Merging a term that is used as ‘replaced by’ for an obsolete term

:: ERROR: ID-mentioned-twice:: GO:0048126
GO:0030722 :: ERROR: has-definition: missing definition for id

The cause of this error is that Term A (GO:0048126) was obsoleted and had replace by Term B (GO:0030722). The GO editor tried to merge Term B into a third term term C (GO:0007312). The Jenkins checkk failed because ‘Term A replaced by’ was an alternative_id rather than by a main_id. Solution: In the ontology, go to the obsolete term A and replace the Term B by term C to have a primary ID as the replace_by.

''See [[Ontology_Editors_Daily_Workflow]] for commit, push and merge instructions.''

[[Category:GO Editors]][[Category:Ontology]][[Category:Editor_Guide_2018]] Pascale
Categories: GO Internal

Obsoleting an Existing Ontology Term

Thu, 06/07/2018 - 11:22

Pascale:

=TO BE FORMATTED=

''See [[Ontology_Editors_Daily_Workflow]] for creating branches and basic Protégé instructions.''

Check if the term (or any of its children) is being used for annotation:
Go to AmiGO, search for the term, either by label or ID
Use filters on the left to look at direct annotations, EXP annotation, InterPro2GO annotations
Notify affected groups
Check if the term is used elsewhere in the ontology
In Protégé, go to the ‘Usage’ tab to see if that ID is used elsewhere. Search for the term name or the term IRI (ie with underscore between GO and the numerical part of the ID, for example: ‘’‘GO_0030722’‘’
If the term is a parent to other terms or is used in logical definitions, make sure that another term replaces the obsolete term
Send a notification email. Template:
SUBJECT: Proposal to obsolete [GO:ID] [GO term name]
BODY: Dear all, The proposal has been made to obsolete: [GO:ID] [GO term name]. The reason for obsoletion is [SPECIFY]. There are X experimental annotations to this term. There are X InterPro2GO mappings to this term. Any comments can be added to the issue: [link to GitHub ticket]. We are opening a comment period for this proposed obsoletion. We’d like to proceed and obsolete this term on [7 days after the message; unless it involves a lot of reannotation, in this case it can be longer] *** Unless objections are received by [DATE] , we will assume that you agree to this change. ***

Remember to list the databases affected by the obsoletion and tag people in the GH ticket Check go-slims

Possible reasons for obsoletions:

The reason for obsoletion is that there is no evidence that this function/process/component exists. (eg: GO:0019562 L-phenylalanine catabolic process to phosphoenolpyruvate; GO:0097605 regulation of nuclear envelope permeability’; GO:0015993 molecular hydrogen transport)
The reason for obsoletion is that the term is not clearly defined and usage has been inconsistent (eg: GO:0030818 negative regulation of cAMP biosynthetic process)
The reason for obsoletion is that this term represent a GO-CAM model. (eg: GO:0072317 glucan endo-1,3-beta-D-glucosidase activity involved in ascospore release from ascus; GO:0100060 negative regulation of SREBP signaling pathway by DNA binding)
The reason for obsoletion is that this term represent an assay and not a real process. (eg: GO:0035826 rubidium ion transport)
The reason for obsoletion is that the data from the paper for which the term was requested can be accurately described using [appropriate GO term]. (eg: GO:0015032 storage protein import into fat body)
etc

OBSOLETION PROCESS

Navigate to the term to be obsoleted.
Make the status of the term obsolete:
In the ‘Annotations’ window, click on the + sign next to ‘Annotations’.
In the resulting pop-up window, select owl:deprecated from the left-hand menu.
Make sure the ‘Literal’ tab view is selected from the right-hand tab list. Type true in the text box.
In the ‘Type’ drop-down menu underneath the text box, select xsd:boolean
Click OK. You should now see the term crossed out in the Class hierarchy view.
Remove equivalence axiom: In the ‘Description’ window, under the ‘Equivalent To’, click the x on the right-hand side to delete the logical definition.
Remove ‘SubClass Of’ relations: In the ‘Description’ window, under the ‘SubClass Of’ entry, click the x on the right-hand side to delete the SubClass Relation.
Add ‘obsolete’ to the term name: In the ‘Annotations’ window, click on the o on the right-hand side of the rdfs:label entry to edit the term string. In the resulting window, in the Literal tab, in front of the term name, type: obsolete For example: obsolete gamma-glutamyltransferase activity Note the case-sensitivity. Make sure to have a space (and no other character) between ‘obsolete’ and the term label.
Add ‘OBSOLETE’ to the term definition: In the ‘Description’ window, click on the o on the right-hand side of the definition entry. In the resulting window, in the Literal tab, at the beginning of the definition, type: OBSOLETE. For example: OBSOLETE. Catalysis of the reaction: (5-L-glutamyl)-peptide + an amino acid = peptide + 5-L-glutamyl-amino acid. Note the case-sensitivity.
Add a statement about why the term was made obsolete: In the ‘Annotations’ window, select + to add an annotation. In the resulting menu, select rdfs:comment and select Type: Xsd:string. Consult the wiki documentation for suggestions on standard comments:
http://wiki.geneontology.org/index.php/Curator_Guide:_Obsoletion
http://wiki.geneontology.org/index.php/Obsoleting_GO_Terms
http://wiki.geneontology.org/index.php/Editor_Guide
If the obsoleted term was replaced by another term in the ontology: In the ‘Annotations’ window, select + to add an annotation. In the resulting menu, select term replaced by and enter the ID of the replacement term.
If the obsoleted term was not replaced by another term in the ontology, but there are existing terms that might be appropriate for annotation, add those term IDs in the ‘consider’ tag: In the ‘Annotations’ window, select + to add an annotation. In the resulting menu, select consider and enter the ID of the replacement term.
Save changes.

''See [[Ontology_Editors_Daily_Workflow]] for commit, push and merge instructions.''


[[Category:GO Editors]][[Category:Ontology]][[Category:Editor_Guide_2018]] Pascale
Categories: GO Internal

Deleting Asserted Subclasses

Thu, 06/07/2018 - 11:19

Pascale:


* Asserted '''is_a parents''' do not need to be retained as entries in the '''SubClass of''' section of the Description window in Protege if the logical definition for a term results in their inference.

* If you have created a logical definition for your term, you can delete the asserted is_a parent by clicking on the X to the right term.

* Once you synchronize the Reasoner, you will see the reasoned classification of your new term, including the inferred is_a parent(s).

* If the inferred classification does not contain the correct parentage, or doesn’t make sense, then you will need to modify the logical definition.
* If an existing term contains a logical definition and still shows an asserted is_a parent in the ‘SubClass of’ section, you may delete that asserted parent, as well.

* Make sure to run the Reasoner to check that the asserted parent is now replaced with the correct reasoned parent(s).

[[Category:GO Editors]][[Category:Ontology]][[Category:Editor_Guide_2018]] Pascale
Categories: GO Internal

Creating a Regulation Term

Thu, 06/07/2018 - 11:18

Pascale:

=TO BE FORMATTED=
''See [[Ontology_Editors_Daily_Workflow]] for creating branches and basic Protégé instructions.''






To create a ‘positive regulation of x’ or ‘negative regulation of x’ term, the parent ‘regulation of x’ term must first be created. To create a parent regulation term:

Make sure the ‘Asserted view’ is active (not the ‘Inferred view’).

In the Protege classes view navigate to ‘biological regulation’

Click on the add subclass button at the top left corner.

In the pop-up window add the name of the new regulation term ‘regulation of target process’. The identifier should auto-populate. Click the button to add the term.

Enter the appropriate information for namespace, definition, synonyms, etc. in the obo editing view as decribed in the ‘Creating a New Ontology Term’ Section.

Standard definitions for regulation terms:
Regulation Any process that modulates the frequency, rate or extent of [process]
Positive regulation: Any process that activates or increases the frequency, rate or extent of [process]
Negative regulation: Any process that stops, prevents or reduces the frequency, rate or extent of [process]

Create a logical definition for the term: biological regulation and regulates some target process.

Remove the asserted ‘biological regulation’ parent.

Run the reasoner to be sure that reasoning results in the correct inferred parents.

Save changes.

''See [[Ontology_Editors_Daily_Workflow]] for commit, push and merge instructions.''


[[Category:GO Editors]][[Category:Ontology]][[Category:Editor_Guide_2018]] Pascale
Categories: GO Internal