GO Internal

Colocalizes with

GO wiki (new pages) - 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

GO wiki (new pages) - 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

GO wiki (new pages) - 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

GO wiki (new pages) - 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

GO wiki (new pages) - 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

GO wiki (new pages) - 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

GO wiki (new pages) - 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

GO wiki (new pages) - 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

GO wiki (new pages) - 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)

GO wiki (new pages) - 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)

GO wiki (new pages) - 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

GO wiki (new pages) - 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

GO wiki (new pages) - 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

GO wiki (new pages) - 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

GO wiki (new pages) - 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

GO wiki (new pages) - 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

Creating a New Ontology Term

GO wiki (new pages) - Thu, 06/07/2018 - 10:05

Pascale:

=TO BE FORMATTED=


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

To create a new term, the ‘Asserted view’ must be active (not the ‘Inferred view’).

In the Class hierarchy window, click on the ‘Add subclass’ button at the upper left of the window.

A pop-up window will appear asking you to enter the Name of the new term. When you enter the term name, you will see your ID automatically populate the IRI box. Once you have entered the term, click ‘OK’ to save the new term. You will see it appear in the class hierarchy.

Navigate to the OBO annotation window.

In the OBO annotation window add:
Namespace
Begin typing one of the three branches (autocomplete will guide you to the correct term): - biological_process - cellular _component - molecular_function
For Type, select: xsd:string
Definition
Click on the + next to the Definition box
Add the textual definition in the pop-up box.
For Type, select: Xsd:string
Click OK.
Add Definition References
Click on the circle with the ‘Ref’ in it next to add Definition References and in the resulting pop-up click on the + to add a new ref, making sure they are properly formatted with a database abbreviation followed by a colon, followed by the text string or ID. Examples: GOC:bhm, PMID:27450630.
Select Type: xsd:string
Click OK.
Add each definition reference separately by clicking on the + sign.
Add synonyms and dbxrefs following the same procedure if they are required for the term.

If you have created a logical definition for your term, you can delete the asserted is_a parent in the ‘subclass of’ section. Once you synchronize the reasoner, you will see the automated classification of your new term. If the inferred classification doesn’t make sense, then you will need to modify the logical definition.

Protege tip: If you need to create a logical definition using a GO term name that does not begin
with an alphabetic character, e.g. GO:0004534 (5'-3' exoribonuclease activity), navigate to the
View menu in Protege and select 'Render by entity IRI short name (Id). This will allow you to
enter a logical definition by entering the relations and term as IDs, e.g. RO_0002215 some GO_0004534.
Note the use of the underscore instead of the colon in the ID. You can then return to the View
menu to switch back to Render by label (rdfs:label) to see the term names.

In some cases such as part_of relations based on external partonomies, it might be necessary to assert the part_of relationships. For example: ‘heart valve development’ part_of some ‘heart development’. In those cases, it is important to browse the external ontologies to be sure that nothing is missing.

When you have finished adding the term, you can hover over it in the class window to reveal its GO_id.

Save the file and return to your terminal window. Then, type: git status. This will confirm which file has been modified.

To see how the branch was modified, type: git diff. In this case, go-edit.obo was modified. The text below is not the entire diff for this edit, but is an example. If the diff is very large, you will need to hit a space to continue to see it and then hit ‘q’ to get back to the prompt at the end of the diff file.

~/repos/go-ontology/src/ontology(issue-13390) $ git diff
diff --git a/src/ontology/go-edit.obo b/src/ontology/go-edit.obo
index 72ae7e9..8d47fa1 100644
--- a/src/ontology/go-edit.obo
+++ b/src/ontology/go-edit.obo
@@ -400751,6 +400751,85 @@ created_by: dph
creation_date: 2017-04-28T12:39:13Z

[Term]
+id: GO:0061868
+name: hepatic stellate cell migration
+namespace: biological_process
+def: "The orderly movement of a hepatic stellate cell from one site to another." [PMID:24204762]
+intersection_of: GO:0016477 ! cell migration
+intersection_of: results_in_movement_of CL:0000632 ! hepatic stellate cell
+created_by: dph
+creation_date: 2017-05-01T13:01:40Z
+
+[Term]
id: GO:0065001
name: specification of axis polarity
namespace: biological_process
~/repos/go-ontology/src/ontology(issue-13390) $

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


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

Ontology Editors Daily Workflow

GO wiki (new pages) - Thu, 06/07/2018 - 09:55

Pascale:

=TO BE FORMATTED=

Updating the local copy of the ontology with ‘git pull’

Navigate to the ontology directory of go-ontology: cd repos/go-ontology/src/ontology.

If the terminal window is not configured to display the branch name, type: git status. You will see:

On branch [master] [or the name of the branch you are on]
Your branch is up-to-date with 'origin/master'.

If you’re not in the master branch, type: git checkout master.

From the master branch, type: git pull. This will update your master branch, and all working branches, with the files that are most current on GitHub, bringing in and merging any changes that were made since you last pulled the repository using the command git pull. You will see something like this:

~/repos/go-ontology(master) $ git pull
remote: Counting objects: 26, done.
remote: Compressing objects: 100% (26/26), done.
remote: Total 26 (delta 12), reused 0 (delta 0), pack-reused 0
Unpacking objects: 100% (26/26), done.
From https://github.com/geneontology/go-ontology
580c01d..7225e89 master -> origin/master
* [new branch] issue#13029 -> origin/issue#13029
Updating 580c01d..7225e89
Fast-forward
src/ontology/go-edit.obo | 39 ++++++++++++++++++++++++---------------
1 file changed, 24 insertions(+), 15 deletions(-)
~/repos/go-ontology(master) $

Creating a New Working Branch with ‘git checkout’

When starting to work on a ticket, you should create a new branch of the repository to edit the ontology file.

Make sure you are on the master branch before creating a new branch. If the terminal window is not configured to display the branch name, type: git status to check which is the active branch. If necessary, go to master by typing git checkout master.

To create a new branch, type: git checkout -b issue-NNNNN in the terminal window. For naming branches, we recommend using the string ‘issue-‘ followed by the issue number. For instance, for this issue in the tracker: https://github.com/geneontology/go-ontology/issues/13390, you would create this branch: git checkout -b issue-13390. Typing this command will automatically put you in the new branch. You will see this message in your terminal window:

~/repos/go-ontology/src/ontology(master) $ git checkout -b issue-13390
Switched to a new branch 'issue-13390'
~/repos/go-ontology/src/ontology(issue-13390) $

Continuing work on an existing Working Branch

If you are continuing to do work on an existing branch, in addition to updating master, go to your branch by typing git checkout [branch name]. Note that you can view the existing local branches by typing git branch -l.
OPTIONAL: To update the working branch with respect to the current version of the ontology, type git pull origin master. This step is optional because it is not necessary to work on the current version of the ontology; all changes will be synchronized when git merge is performed.

Loading, navigating and saving the Ontology in Protégé

Before launching Protégé, make sure you are in the correct branch. To check the active branch, type git status.
Click on the ‘File’ pulldown. Open the file: go-edit.obo. The first time, you will have to navigate to repos/go-ontology/src/ontology. Once you have worked on the file, it will show up in the menu under ‘Open’/’Recent’.
Click on the ‘Classes’ tab.
Searching: Use the search box on the upper right to search for a term in the ontology. Wait for autocomplete to work in the pop-up window.
Viewing a term: Double-click on the term. This will reveal the term in the ‘Class hierarchy’ window after a few seconds.
Launching the reasoner: To see the term in the ‘Class hierarchy’ (inferred) window, you will need to run the ‘ELK reasoner’. ‘Reasoner’ > select ELK 0.4.3, then click ‘Start reasoner’. Close the various pop-up warnings about the ELK reasoner. You will now see the terms in the inferred hierarchy.
After modification of the ontology, synchronize the reasoner. Go to menu: ‘Reasoner’ > ‘ Synchronize reasoner’.
NOTE: The only changes that the reasoner will detect are those impacting the ontology structure: changes in equivalence axioms, subclasses, merges, obsoletions, new terms.
TIP: When adding new relations/axioms, ‘Synchronize’ the reasoner. When deleting relations/axioms, it is more reliable to ‘Stop’ and ‘Start’ the reasoner again.
Use File > Save to save your changes.

Committing, pushing and merging your changes to the repository

Review: Changes made to the ontology can be viewed by typing git diff in the terminal window. If there are changes that have already been committed, the changes in the active branch relative to master can be viewed by typing git diff master.

Commit: Changes can be committed by typing: git commit -m ‘Meaningful message Fixes #ticketnumber’ go-edit.obo.

For example:

git commit -m ‘hepatic stellate cell migration and contraction and regulation terms. Fixes #13390’ go-edit.obo

This will save the changes to the go-edit.obo file. The terminal window will show something like:

~/repos/go-ontology/src/ontology(issue-13390) $ git commit -m 'Added hepatic stellate cell migration and contraction and regulation terms. Fixes #13390' go-edit.obo
[issue-13390 dec9df0] Added hepatic stellate cell migration and contraction and regulation terms. Fixes #13390
1 file changed, 79 insertions(+)
~/repos/go-ontology/src/ontology(issue-13390) $

NOTE: The word ‘fixes’ is a magic word in GitHub; when used in combination with the ticket number, it will automatically close the ticket. In the above example, when the file is merged in GitHub, it will close issue number 13390. Learn more on this GitHub Help Documentation page about ‘Closing issues via commit messages’.

‘Fixes’ is case-insensitive.

If you don’t want to close the ticket, just refer to the ticket # without the word ‘Fixes’. The commit will be associated with the correct ticket but the ticket will remain open.

NOTE: It is also possible to type a longer message than allowed when using the ‘-m’ argument; to do this, skip the -m, and a vi window (on mac) will open in which an unlimited description may be typed.

TIP: Git needs to know who is committing changes to the repository, so the first time you commit, you may see the following message:

Committer: Kimberly Van Auken <vanauken@kimberlukensmbp.dhcp.lbnl.us>
Your name and email address were configured automatically based on your username and hostname. Please check that they are accurate.

See Configuration instructions to specify your name and email address.

Push: To incorporate the changes into the remote repository, type: git push origin mynewbranch.

Example:

git push origin issue-13390

TIP: Once you have pushed your changes to the repository, they are available for everyone to see, so at this stage you can ask for feedback.

Pull
In your browser, return to the GO Ontology repository on GitHub.
Navigate to the tab labeled as ‘Code’ geneontology/go-ontology/code. You will see your commit listed at the top of the page in a light yellow box. If you don’t see it, click on the ‘Branches’ link to reveal it in the list, and click on it.
Click the green button ‘Compare & pull request’ on the right.
You may now add comments and ask a colleague to review your pull request. If you want to have the ticket reviewed before closing it, you can select a reviewer for the ticket before you make the pull request by clicking on the ‘Reviewers’ list and entering a GitHub identifier (e.g. @superuser1). The reviewer will be notified when the pull request is submitted. Since the Pull Request is also a GitHub issue, the reviewer’s comments will show up in the dialog tab of the pull request, similarly to any other issue filed on the tracker.
The diff for your file is at the bottom of the page. Examine it as a sanity check.
Click on the green box ‘Pull request’ to generate a pull request.
Wait for the Travis checks to complete (this can take a few minutes). If the Travis checks failed, go back to your working copy and correct the reported errrors.

Merge If the Travis checks are succesful and if you are done working on that branch, merge the pull request. Confirming the merge will close the ticket if you have used the word ‘fixes’ in your commit comment. NOTE: Merge the branches only when the work is completed. If there is related work to be done as a follow up to the original request, create a new GitHub ticket and start the process from the beginning.

Delete your branch on the repository using the button on the right of the successful merge message.

You may also delete the working branch on your local copy. Note that this step is optional. However, if you wish to delete branches on your local machine, in your terminal window:
Go back to the master branch by typing git checkout master.
Update your local copy of the repository by typing git pull origin master
Delete the branch by typing git branch -d workingbranchname. Example: git branch -d issue-13390




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

Installing and Using git

GO wiki (new pages) - Thu, 06/07/2018 - 09:54

Pascale: /* Cloning the go-ontology repository from GitHub */

==Installing git==

# In order to locally edit the ontology and push changes back to the GitHub repository, you will need to have git installed on your machine.
# To check if you already have git installed, or to see what version of git you have, type either of these commands in your terminal: which git or git --version.
# To install git, follow instructions here: https://git-scm.com/

'''Note for MacOSX users:''' it is advised to install Xcode tools.

==Cloning the go-ontology repository from GitHub==

# Create a directory called repos on your local machine using this command: mkdir repos.
# Then paste this command into your terminal: git clone https://github.com/geneontology/go-ontology.git.
#* Example result:
Cloning into 'go-ontology'...
remote: Counting objects: 2541, done.
remote: Compressing objects: 100% (100/100), done.
remote: Total 2541 (delta 52), reused 0 (delta 0), pack-reused 2440
Receiving objects: 100% (2541/2541), 21.19 MiB | 5.22 MiB/s, done.
Resolving deltas: 100% (1532/1532), done.

==Editing the .profile (or .bashrc) file to indicate the branch you are working on==

It can be very helpful to know what branch you are working in on your terminal window. You can set this up to display by adding the following information to your .profile file (found by typing ls -a):

export GO_REPO=~/repos/go-ontology
. $GO_REPO/src/util/git-completion.bash
parse_git_branch() {
git branch 2> /dev/null | sed -e '/^[^*]/d' -e 's/* \(.*\)/(\1)/'
}
PS1="\w\$(parse_git_branch) $ "
export PATH=$PATH:$HOME/bin/

Note the last line is not relevant to git, but we do this now for later on when we want to run tools like robot.


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

Protégé Configuration

GO wiki (new pages) - Thu, 06/07/2018 - 09:49

Pascale: /* Configuring New Entities Metadata */

==Configuring New Entities Metadata==

# In the Protege menu, select Preferences.
# Click on: Annotate new entities with creator (user)
# Creator property: Add http://www.geneontology.org/formats/oboInOwl#created_by
# Creator value: Use username
# Check: Annotate new entities with creation date and time.
# Date property: Add http://www.geneontology.org/formats/oboInOwl#creation_date
# Check: ISO-8601

==Configuring User details==

Select 'User name', and use the supplied user name; that is, your GOC identity.

===Identifying the user for commits===

Git needs to know who is committing changes to the repository, so the first time you commit, you may see the following message:

Committer: Kimberly Van Auken <vanauken@kimberlukensmbp.dhcp.lbnl.us>
Your name and email address were configured automatically based on your username and hostname. Please check that they are accurate.

You can suppress this message by setting your name and email explicitly:

# Type git config --global user.name "Your Name"
# Type git config --global user.email you@example.com.
# You can then fix the identity used for this commit by typing: git commit --amend --reset-author.




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