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Ontology Development-v2

GO wiki (new pages) - 18 hours 58 min ago

Pascale: /* Editing the Ontology */

= Documentation=
==[[Protege_setup_for_GO_Eds|Setting up Protege for GO editors]]==
==[[Installing and Using git]]==
==[[Ontology Editors Daily Workflow]]==
==Editing the Ontology==


{| class="wikitable"
!colspan="2" | Creating a GO term
|-
|rowspan="2"|[[Principles for creating a GO term]] (being reviewed)
|[[Guidelines for creating a GO term]]
|-
|[[Guidelines for creating a Regulation Term]]
|-
!colspan="2" |Modifying an Existing Ontology Term
|-
|rowspan="4"|[[Principles for Modifying an Existing Ontology Term]] (To be reviewed)
|-
|[[Deleting Asserted Subclasses]]
|-
|[[Adding Term Comments]]
|-
|[[Adding a Term to a GO Subset (Slim)]]
|-
|[[Adding Taxon Restrictions]]
!colspan="2" |Obsoleting an Existing Ontology Term
|
|-
|[[Obsoleting an Existing Ontology Term]]
|-
!colspan="2" |Merging Ontology Terms
|[[Principles for merging terms]]
|-
|[[Merging Ontology Terms]]
|-
|}




====[[Adding and Removing GO Subsets (Slims)]]====


===[[Adding Terms and Regenerating the Import Files]]===

==[[General Gene Ontology Principles]]==
====[[Guidelines for GO term definitions]] Being reviewed====

===[[Editor Guide to has part]] To be reviewed===
===[[Editor Guide to Regulates]] To be reviewed===
===[[Guidelines for equivalence axioms]] To be reviewed===
===[[Curator_Guide:_Merge]] To be reviewed===
===[[Curator Guide: Obsoletion]] To be reviewed===
===[[Curator Guide: Enzymes and Reactions]] To be reviewed===
===[[Notes on specific terms]] To be reviewed===

==[[Requesting a New Complex ID from IntAct]]==
==[[Editor file guide]] To be reviewed==
==[[Ontology Documentation Drafts]] To be reviewed==
for working on documentation of ontology content that will become part of the web-based documentation
==[[Ontology Editing Examples|Ontology Editing Examples: Regulation of a pathway by regulation of enzyme activity]] To be reviewed==

==[[New Ontology Editor Training]] To be reviewed==
==Website - to be moved to the wiki?==
*[[Editorial-type sections copied over from the GO website ontology documentation: MF]]
* [[http://www.geneontology.org/page/biological-process-ontology-guidelines Biological-process-ontology-guidelines]]

=[[Identifiers]] To be reviewed=

=[[Content Meeting Documentation|Guidance for organizing content meetings]]=
(old doc, but basic principles still apply)


=Content Development =
==Projects==
===High Priority/Ongoing===
*[[Transcription 2018]] (Pascale, Ruth, Astrid, Marcio, Paul T)
*[[Cell Cycle]] (Val, Pombe experts, GOEds)
*[[Enzymes and EC mappings]]
*[https://github.com/geneontology/synapse Synapse project] (Synapse experts, DavidOS, Becky Foulger)
*Extracellular RNA-containing vesicles (Paola, Aleks and community experts)
*Ciliary components and processes (Paola, Karen Christie, SYSCILIA experts)
*Autophagy (Paul D, Marc F, David H, Ruth, Paola and community experts)

===Medium Priority===
*[[Non-symbiotic multi-organism processes]] (Jane, David OS)

===Low priority===
*[[Neuro Behaviour Ontology (NBO)-GO alignment]] (Jane, George Gkoutos, Chris, DavidOS)
*[[microbial ontology development and annotation]]

===Recently completed projects===
*[[Uberon alignment]] (DavidH)
*Addition of cross-products - see [[:Category:Cross_Products]] and [[Cross_Product_Guide]]
**[[Cell cross-products]], [[Cell-type specific GO terms]] (Jane, Paola, Alex, Chris, DavidOS)
**[[Adding missing CHEBI xps]]
*[[Signaling |Signaling overhaul]] (Becky, signaling WG)
*[[Virus terms|Virus-related term overhaul]], [[Virus_ontology_devt_July_2012|Phage Terms]] (Jane Lomax, Brenley McIntosh, Rebecca Foulger & others)
*[[Neurobiology Project]] (David, Tanya, Jane, Paola, DavidOS)
*[[Apoptosis]] (Emily, Becky, Paola, Pablo and community experts) - Feb 2013
*[[Transcription |Transcription & transcription factor activity overhaul]] (Karen, David) - 2012
*[[Kidney Physiology]] (David, Yasmin, Doug, Tanya, Becky, Edinburgh GUDMAP group)
*[[Cardiac conduction]] (David, Ruth, Doug, Tanya, Becky, Paola, Stan)
*Rework disjoint terms as [http://gocwiki.geneontology.org/index.php/Are_multi-organism_process_and_cellular_process_disjoint%3F#Conclusion concluded in discussion on GO list] (Jane).
*[[:Category:Content MENGO|MENGO collaboration]] (Jane)

===Proposed content work===
A list of topics that we propose to address, but for which a timeline has not been set

*Peripheral nervous system development
*Revamp embryonic and post-embryonic terms to be logically defined with cross products to stage ontology.
*Overhaul [[translation]], similar to what's being done for transcription. [https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1891512&group_id=36855| SF 1891512] is closed, but notes some issues for consideration. (midori 2010-10-04)
* [[Recombination and DNA repair]]
* [[RNA processes]]
* [[Bile formation and secretion processes]]
* [[protein and peptidyl amino acid modification / protein processing]]
* [[Response to drug]]
* [[Polyketide synthases]]
* [[cell growth/proliferation/division]]
* [[oxidoreductases]]

===[[Completed ontology content work]]===

=Quality Control=
==SPARQL checks on the ontology==
[[https://github.com/rctauber/robot/tree/reporting/robot-core/src/main/resources/queries |SPARQL checks on the ontology]]

==Ontology release pipeline==
http://wiki.geneontology.org/index.php/Release_Pipeline
Errors: http://current.geneontology.org/ontology/reports/index.html

'''TO BE REPLACED'''
*Ongoing work on Quality control reports; see [[Ontology_Quality_Control]] (David, Jane, Chris, Tanya)

=Other Ontology Development Group Activities=

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

GO-CAM Working Group Call 2018-08-21

GO wiki (new pages) - Mon, 08/20/2018 - 06:55

Vanaukenk: Created page with "= Meeting URL = https://stanford.zoom.us/j/976175422 =Agenda= == GO Annotation Meetings == *Tuesdays at 8am PDT *Meeting schedule: **1st Tuesday: Alliance Gene Function **2n..."

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

=Agenda=

== GO Annotation Meetings ==
*Tuesdays at 8am PDT
*Meeting schedule:
**1st Tuesday: Alliance Gene Function
**2nd Tuesday: GO Consortium
**3rd Tuesday: Alliance Gene Function/GO-CAM Working Group
**4th Tuesday: GO-CAM Working Group
**5th Tuesday: ad hoc, as needed
*One Zoom URL for all - https://stanford.zoom.us/j/976175422

== Modeling Transcription in GO-CAM ==
*Sabrina - [http://noctua.berkeleybop.org/editor/graph/gomodel:5a5fc23a00000137 PMID:28687631 'Clock1a affects mesoderm development and primitive hematopoiesis by regulating Nodal-Smad3 signaling in the zebrafish embryo.']

=== Relations between Transcription Factor MFs and Regulation of Transcription BPs ===
*Transcription factor activity is 'part_of' regulation of transcription
*This is consistent with the relations in the ontology and produces the correct annotations in the GPAD output file
*A consequence of this is that any regulation terms needed for annotation will have to be instantiated in the ontology
*This principle will be applied more broadly, i.e. if an entity plays a regulatory role in a process, its MF is 'part_of' some regulation of BP

== Relations between MF and Input(s) ==
*has_input vs has_direct_input
*Is there a meaningful distinction between these two relations for MF? What are we really trying to capture with MF inputs?
*Proposal: review MF annotations using has_input
**Relations Ontology working group (broader than just GO) that is also considering [https://github.com/oborel/obo-relations/issues/244 how to model participants in an MF] and [https://github.com/oborel/obo-relations/issues/171 documentation of has_input and child relations]
*Right now, no changes to GO-CAM models (will continue to use has_input)

== Direct vs Unknown Mechanism of Regulation ==
=== Capturing Unknown Mechanism of Regulation ===
*If it is not known if the TF directly regulates the expression of a gene, then the input for the TF activity is left blank.
**In this case, however, it is okay to use evidence from another experiment that might have shown different context (i.e. a different gene was regulated) as supporting evidence for the TF activity.
*The curator can model the unknown mechanism of regulation by saying that the TF is part_of regulation of transcription that is causally_upstream_of_or_within the positive or negative regulation of transcription that ultimately controls the expression of the gene. The gene is then added as 'has input' to the most distal transcriptional regulatory process.

== Relations between BP and input(s) ==
*Duplicating has_input for MF and BP results in multiple entries in the AE field of the BP annotation in the GPAD

== Relations between BP and MF of transcriptional target ==
*[https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0002304 causally upstream of, positive effect]
*[https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0002305 causally upstream of, negative effect]

== Root Node vs Existing Molecular Functions ==
*Curators should always try to construct models using the known MF of a gene product, even if that MF was not specifically demonstrated in the paper they are annotating.
*Associated evidence for that MF will always point back to the paper in which the MF was interrogated.
*Creating models in this way will allow us to build on existing knowledge to create the most comprehensive and up-to-date model for a given BP.
*Proposal: if a gene product has more than one MF, curators should use either: 1) experimental data that supports the selection of one function vs another, 2) the common parent of the two functions, or 3) the biological context of the annotated process to select the most appropriate function(s) for that gene product.
**Examples: beta-catenin and PDIA6

=Minutes=
*On call: Bob, Chris, David, Dustin, Giulia, Harold, Jim, Karen, Kevin M, Kimberly, Laurent-Philippe, Marie-Claire, Pascale, Penelope, Ruth, Sabrina, Seth, Stacia, Suzi A, Suzi L,























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

QCQA call 2018-08-21

GO wiki (new pages) - Thu, 08/16/2018 - 10:58

Vanaukenk: Created page with "* What should the QC priorities be ? * Which annotation validation rules are currently implemented ? https://github.com/geneontology/go-annotation/issues/1928 * Protein2GO c..."

* What should the QC priorities be ?

* Which annotation validation rules are currently implemented ? https://github.com/geneontology/go-annotation/issues/1928
* Protein2GO checks

* Should Taxon checks be a hard check:
https://github.com/geneontology/go-site/issues/660
https://github.com/geneontology/go-site/issues/758

* Unmaintained annotation sets:
https://github.com/geneontology/go-annotation/issues/1724#issuecomment-390136730

TIGR, JCVI, PAMGO ISS annotations: Michelle:
The ISS annotations from at least TIGR (and should be also JCVI and PAMGO) were all manual. They were either matches to HMMs or based on pairwise alignments. We used IEA for any annotations that were automatic from our pipeline and not reviewed. I assume JCVI continued that process after I left - at least until they stopped using their pipeline and shifted completely to using the NCBI PGAP tool (prokaryotic genome annotation pipeline).
I think we (and hopefully PAMGO) were pretty good about using the GO_REFs to indicate whether it was HMM or pairwise. The problem with replacing our HMM annotations with InterPro2GO mappings is that we made much more specific annotations based on HMMs than what the InterPro mappings often do. I'd hate to lose those but I understand your desire to keep the annotations current.

* SPKW hierarchy - at odds with transitivity as found in GO ontology?
**https://github.com/geneontology/go-annotation/issues/2036
**emailed Chris, Seth about help with querying the GO database for non-redundant SPKW-based annotations (2018-08-16)

*Annotation redundancy - non-experimental annotations
**Can we come up with a proposal for the Montreal meeting?
**http://wiki.geneontology.org/index.php/2018_Montreal_GOC_Meeting_Agenda#Handling_redundant_information

* GO-CAM QC plan
** including SynGO, > 90 % of the production models



[[Category:Quality Control]] Vanaukenk
Categories: GO Internal

Ontology meeting 2018-08-20

GO wiki (new pages) - Wed, 08/15/2018 - 10:28

Vanaukenk: Created page with "= Conference Line = *Zoom: https://stanford.zoom.us/j/828418143 = Agenda = == Editors Discussion == ===Project Update=== * RO meeting to take place in Colorado in October..."

= Conference Line =

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

= Agenda =

== Editors Discussion ==

===Project Update===
* RO meeting to take place in Colorado in October

===Ontology Developers' workshop possibility===
* One meeting in December; proposal to have the meeting in Geneva.
* Maybe we can take a day or two to also meet with Anne and/or Alan to discuss the Rhea alignment project.
*Attendees:


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

= Minutes =
*On call:


[[Category: Ontology]]
[[Category: Meetings]]

Barbara's new term request (child terms of 'cell-cell signalling') was discussed: https://github.com/geneontology/go-ontology/issues/16216
A decision was made to continue the discussion on 20/08/2018 during the next Ontology call. Vanaukenk
Categories: GO Internal

QCQA call 2018-08-14

GO wiki (new pages) - Tue, 08/14/2018 - 06:17

Pascale:

* What should the QC priorities be ?

* Which annotation validation rules are currently implemented ? https://github.com/geneontology/go-annotation/issues/1928

* Should Taxon checks be a hard check:
https://github.com/geneontology/go-site/issues/660
https://github.com/geneontology/go-site/issues/758

* Unmaintained annotation sets:
https://github.com/geneontology/go-annotation/issues/1724#issuecomment-390136730

TIGR, JCVI, PAMGO ISS annotations: Michelle:
The ISS annotations from at least TIGR (and should be also JCVI and PAMGO) were all manual. They were either matches to HMMs or based on pairwise alignments. We used IEA for any annotations that were automatic from our pipeline and not reviewed. I assume JCVI continued that process after I left - at least until they stopped using their pipeline and shifted completely to using the NCBI PGAP tool (prokaryotic genome annotation pipeline).
I think we (and hopefully PAMGO) were pretty good about using the GO_REFs to indicate whether it was HMM or pairwise. The problem with replacing our HMM annotations with InterPro2GO mappings is that we made much more specific annotations based on HMMs than what the InterPro mappings often do. I'd hate to lose those but I understand your desire to keep the annotations current.

* SPKW hierarchy - at odds with transitivity as found in GO ontology?
**https://github.com/geneontology/go-annotation/issues/2036

* Protein2GO checks

[[Category:Quality Control]] Pascale
Categories: GO Internal

Annotation Conf. Call 2018-08-14

GO wiki (new pages) - Mon, 08/13/2018 - 07:08

Vanaukenk: /* Transcription Overhaul */

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

== Montreal Meeting, October Wednesday, 17th - Friday, 19th ==
*[http://wiki.geneontology.org/index.php/2018_Montreal_GOC_Meeting_Logistics Logistics]
*[http://wiki.geneontology.org/index.php/2018_Montreal_GOC_Meeting_Agenda Agenda]

== GO Conference Calls ==
=== Tuesdays ===
*Still will be Tuesdays at 8am PDT
*Proposed meeting schedule:
**1st Tuesday: Alliance Gene Function
**2nd Tuesday: GO Consortium
**3rd Tuesday: Alliance Gene Function/GO-CAM Working Group
**4th Tuesday: GO-CAM Working Group
**5th Tuesday: ad hoc, as needed
*One Zoom URL for all - https://stanford.zoom.us/j/976175422

== Annotation Discussion ==
=== ND Annotations ===

=== PAINT Annotations ===
*[https://github.com/geneontology/go-annotation/issues/2049 PAINT:circular transfer of annotations]

=== Transcription Overhaul ===
[https://github.com/geneontology/go-annotation/issues/2024 Review annotations to 'GO:0000988 transcription factor activity, protein binding' and similar children]



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

Ontology meeting 2018-08-13

GO wiki (new pages) - Mon, 08/13/2018 - 05:43

David: /* Editors Discussion */

= Conference Line =

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

= Agenda =

DavidH will not be here for the next two meetings. Can we get a volunteer to chair them and take notes?

== Editors Discussion ==

===Project Update===
* RO meeting to take place in Colorado in October

* Ontology Editors' Daily Workflow Documentation is complete: http://wiki.geneontology.org/index.php/Ontology_Editors_Daily_Workflow


===Ontology Developers' workshop possibility===
* December in Geneva? One meeting or 2? Maybe we can take a day or two to also meet with Anne and/or Alan to discuss the Rhea alignment project.

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

= Minutes =
*On call:


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

Modifying an Existing Ontology Term

GO wiki (new pages) - Wed, 08/08/2018 - 08:05

Pascale: Created page with " ==Moving terms== Terms can be moved as long as the term's new position correctly reflects its relationships to other terms and moving the term does not imply a significant..."



==Moving terms==

Terms can be moved as long as the term's new position correctly reflects its relationships to other terms and moving the term does not imply a significant change in the meaning of the term. Terms should not, however, be moved between ontologies; only within the same ontology. If you need to move a term to a different ontology, first obsolete it and then create a new term in the other ontology.


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

Merge Split Move v2 2018-08-06

GO wiki (new pages) - Mon, 08/06/2018 - 09:02

Pascale: Created page with "Term Merges, Splits and Movements Merge Split Move v2 2018-08-06 ==What is a GO term merge?== Term merges results from two or more terms being subsumed by a single term...."

Term Merges, Splits and Movements

[[Merge Split Move v2 2018-08-06]]

==What is a GO term merge?==
Term merges results from two or more terms being subsumed by a single term.

==When are GO terms merged?==
Terms are merged in cases where two terms have exactly the same meaning or when the meaning is too close to support consistent, distinct annotations. (Usually this situation arises when one term exists, and another wording of the same concept is added as a new term instead of as a synonym, either because a curator didn't find the old term or didn't know it meant the same thing.

When two terms are merged, e.g. term A and term B are merged into term A, the GO ID of term B is made an alternative (secondary) GO ID, and the term string is made a synonym. Secondary GO IDs remain in GO with the 'alt_id' tag.

==Term splits==

A term can be split if curators decide that it combines two or more concepts that should be represented by separate terms.

The standard procedure for splitting a term is to obsolete the original term and add to add 'consider' tags for the old term ID to all new terms. It's also good practice to add a comment explaining why the term was split, e.g.:

id: GO:0004327
name: formaldehyde dehydrogenase (glutathione) activity
namespace: molecular_function
def: "OBSOLETE. Catalysis of the reaction: formaldehyde + glutathione + NAD+ = S-formylglutathione + NADH + H+." [EC:1.2.1.1]
comment: This term was made obsolete because it was derived from an EC entry (1.2.1.1) that has since been split into two entries.
subset: gosubset_prok
xref: UM-BBD_enzymeID:e0028
is_obsolete: true
consider: GO:0051903
consider: GO:0051907

==Moving terms==

Terms can be moved as long as the term's new position correctly reflects its relationships to other terms and moving the term does not imply a significant change in the meaning of the term. Terms should not, however, be moved between ontologies; only within the same ontology. If you need to move a term to a different ontology, first obsolete it and then create a new term in the other ontology.


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

Guide to obsoletion -v2 2018-08-06

GO wiki (new pages) - Mon, 08/06/2018 - 06:52

Pascale: /* What is obsolete? */

==What is obsolete?==
* Terms removed from the ontology are not deleted, but tagged '''obsolete'''. In the obsoletion process, GO IDs remain in the ontology.
* Obsolete terms looses their relationships to other terms.
* Obsolete terms are identified in the OBO format flat file by the 'is_obsolete: true' tag.

==When is a term made obsolete?==
* A term can become obsolete when it is redefined in a way that invalidates existing annotations, or when ontology term creation guidelines change (for example, the development of GO-CAM models may result in a GO term being obsoleted in favor of producing annotations using GO-CAM that represent the same concept).
* Changes in term label or definition that do not alter the meaning of the term do not usually lead to obsoletion. On the other hand, when a term's definition changes meaning, the term should be obsoleted and a new term created instead. In this case, ontology editors usually add a tag 'consider: new term ID', or 'replaced by: new term ID'.
* The fact that a term is has incorrect annotations associated does not usually lead to term obsoletion; ideally the database that submitted the annotations should be informed of the error instead.

==Term Obsoletion Protocol==


The following [[Obsoleting_an_Existing_Ontology_Term]] should be used by ontology editors when emailing the GO lists regarding obsoletion notifications.

==Comments for Obsolete Terms==

When you make a term obsolete, insert the word 'OBSOLETE.' at the beginning of the term definition and add a comment that explains why the term has become obsolete and suggests alternative terms for annotators to use.

Use the following syntax for the reason for obsoletion:

comment: This term was made obsolete because [reason].

E.g.
comment: This term was made obsolete because it represents a gene product.
comment: This term was made obsolete because it refers to a class of proteins.
comment: This term was made obsolete because it was added in error; it does not refer to a normal subcellular structure.
comment: This term was made obsolete because more specific terms were created.
comment: This term was made obsolete because it was an unnecessary grouping term.
comment: This term was made obsolete because the meaning of the term is ambiguous.



==Alternatives for Obsolete Terms==

To suggest alternative terms, use the replaced_by and consider tags.

===Exact replacement(s)===

If exact replacement is possible (i.e. it is safe to move all existing annotations, keyword mappings, etc. to a suggested term), use the '''replaced_by''' tag:

example:

[Term]
id: GO:0005563
name: transfer RNA
namespace: molecular_function
def: "OBSOLETE (was not defined before being made obsolete)." [GOC:mah]
comment: This term was made obsolete because it represents a gene product.
is_obsolete: true
replaced_by: GO:0030533

===No exact replacement(s)===

In cases where all existing annotations and mappings can't necessarily be transferred to one term, use the '''consider''' tag:

example:

[Term]
id: GO:0030464
name: ginger dependent sterility (sensu Fungi)
namespace: biological_process
def: "OBSOLETE (was not defined before being made obsolete)." [GOC:sgd_curators]
comment: This term was made obsolete because it reflected a trait or phenotype.
is_obsolete: true
consider: GO:0030466

===Using multiple tags===

It is possible to use more than one replaced_by or consider tags, or to combine them. Suggested terms may be chosen from more than one ontology. Examples:

====More than one replaced_by tag====

[Term]
id: GO:0016733
name: iron-iron nitrogenase activity
namespace: molecular_function
def: "OBSOLETE. Catalysis of the reaction: iron + iron = nitrogenase." [EC:1.18.6.1]
comment: This term was made obsolete because it represents a cellular component.
is_obsolete: true
replaced_by: GO:0016163
replaced_by: GO:0016611

====More than one consider tag====
(also shows use of terms from two ontologies)

[Term]
id: GO:0016910
name: SAP kinase 3 activity
namespace: molecular_function
def: "OBSOLETE (was not defined before being made obsolete)." [GOC:mah]
comment: This term was made obsolete because it describes a gene product.
synonym: "SAPK3" EXACT []
is_obsolete: true
consider: GO:0004674
consider: GO:0004871
consider: GO:0007254

====Consider and replaced_by tags both used====

[Term]
id: GO:0004207
name: effector caspase activity
namespace: molecular_function
def: "OBSOLETE (was not defined before being made obsolete)." [GOC:mah]
comment: This term was made obsolete because it includes biological process information.
is_obsolete: true
replaced_by: GO:0004197
consider: GO:0006915

Note: the consider and replaced_by tags are used in the OBO format version 1.2 files. In the OBO format 1.0 files, these tags are converted to text comments.

Note: to add consider or replaced_by tags in OBO-Edit, drag the suggested term, drop it onto an obsolete term, and choose 'set consider term' or 'set replacement term' from the popup menu; repeat as needed to add multiple terms.

==Restoring obsolete terms==

If you need to reinstate an obsolete term back into the ontologies, use the following:

comment: Note that this term was reinstated from obsolete.


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

2018 August USC Developers Meeting

GO wiki (new pages) - Fri, 08/03/2018 - 09:30

Vanaukenk: /* Agenda */

== Venue ==
* USC Health Sciences Campus
** Campus Map: http://web-app.usc.edu/maps/#hsc (search for NRT)

== Hotel ==

== Agenda ==

*[https://docs.google.com/document/d/1n8BB3amKiYJAJayEotTjDr0sJcIS8292VGaZQpIdzIs/edit#heading=h.kjcvqles13j8 August agenda and notes]
*[https://docs.google.com/document/d/1u3UZs8zrjTWwpca3rgpaqhlo7V7iLnT8JIMNV1ZUM2M/edit February agenda and notes]

=== Monday ===
*Overview of meeting objectives

=== Tuesday ===

=== Wednesday ===

=== Software Overviews ===

=== Hacking ===

=== Parking Lot ===

== Participants ==

LBL

* Chris Mungall LBL
* Eric Douglass LBL
* Nathan Dunn LBL
* Ben Good LBL
* Suzi Lewis LBL

USC

*Laurent-Philippe Albou
*Anushya Muruganujan
*Tremayne Mushayahama
*Dustin Ebert
*Pascale Gaudet
*Paul Thomas

Caltech

*Valerio Arnobaldi
*Hans-Michael Mueller
*Kimberly Van Auken


[[Category:Meetings]] Vanaukenk
Categories: GO Internal

Ontology meeting 2018-08-06

GO wiki (new pages) - Fri, 08/03/2018 - 08:03

David: Created page with "= Conference Line = *Zoom: https://stanford.zoom.us/j/828418143 = Agenda = == Editors Discussion == ===Project Update=== ====MF Refactor Transcription Factor Branch-- http..."

= Conference Line =

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

= Agenda =

== Editors Discussion ==

===Project Update===
====MF Refactor Transcription Factor Branch-- https://github.com/geneontology/go-ontology/projects/7====

===Ontology Developers' workshop possibility===
* December in Geneva? One meeting or 2? Maybe we can take a day or two to also meet with Anne and/or Alan to discuss the Rhea alignment project.


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

= Minutes =
*On call:


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

Release Pipeline v2

GO wiki (new pages) - Fri, 08/03/2018 - 02:47

Pascale: /* Annotations files */

'''August 2018: Pascale - trying to clarify the document- This documentation is currently a work in progress.'''



= Overview =
The information below is meant to provide an overall summary and basic instructions for submitting and consuming GO data. For a more detailed discussion of the technical details, please see the


[https://github.com/geneontology/pipeline README.md file]
THIS PAGE JUST HAS:
pipeline
Declarative pipeline for the Gene Ontology.


in the pipeline repository on GitHub.

==Release schedule and content overview==
The GO Consortium (GOC) is now publicly releasing data on a monthly basis. These monthly releases contain:
* Annotation files (including GO-CAM models and PAINT-generated annotations)
* Ontology files
* Error reports
* Predictions

The pipeline runs daily starting at midnight (12am) PDT, and the 1st of each month (or as close as can be obtained if there are failures) for the official monthly release.

==Versioning==
* '''Official monthly releases''': versioned and archived so that analyses performed with these data can be reproduced at any point in the future. Note that all files generated as part of the monthly release will have a permanent, stable release identifier.
* '''Daily snapshot releases''': intended for internal use by GOC members. Daily snapshots are not versioned and not archived, therefore not citable. Note that the ''daily snapshot release'' is not generated on the day of the ''official monthly release''.
Note also that all files generated as part of the snapshot release will NOT have permanent, stable release identifiers.

==Data access==
Data associated with each release can be accessed at the URLs below:
*http://current.geneontology.org: Current official monthly release
*http://release.geneontology.org: Monthly releases, including archived releases
*http://snapshot.geneontology.org: Daily snapshot release

==Release Contents==

=== Annotations files===
Annotation files are retrieved from each participating consortium member by GO Central, '''merged with additional annotation files???''', run through annotation QA/QC checks (https://github.com/geneontology/go-site/blob/master/metadata/rules/README.md) and then released as daily snapshot and monthly public releases.

=== What Happens to Annotations During a Release Cycle ===
*For both the monthly public releases and the daily snapshot releases, the same set of QA/QC checks and '''annotation file merges (PAINT, GO-CAM, predictions, other external groups, e.g. UniProt)''' are performed. Resulting annotation files and reports are then made accessible via the release URLs listed above.
*When GO Central retrieves an annotation file from a contributing group, the pipeline will run checks on the file and repair any auto-repairable issues (for example, migrating annotations to merged terms). It will then publish the processed GAFs, GPADs, GPIs, etc. to a public site, available for download.
*'''Need to link to the GO rules on github and/or articulate all of the checks that annotation files undergo after submission.'''

=== Annotation Files and Reports ===
*The annotation release pipeline generates ''products'', e.g. annotation and gpi files, and ''reports'' e.g. error reports, inferred annotations, etc., that provide feedback to GOC contributing groups (MODs, UniProt, etc).
*Below is more detailed information about what files are generated during a release, '''using the snapshot URLs as an example'''.

==== Annotation and GPI Files ====
*Annotation (gaf and gpad) and gpi files are available here:
**http://snapshot.geneontology.org/annotations/index.html
*Currently, annotation (gaf and gpad) and gpi files are sorted according to contributing group.
*'''In the future, annotation files will be sorted according to species.'''
*Note that the file names now conform to a new naming schema that indicates the file type in the extension:
**mgi.gaf.gz
**mgi.gpad.gz
**mgi.gpi.gz
*'''There are also annotation files under the products directory. What are the intended use cases for each of these files?'''
**http://snapshot.geneontology.org/products/annotations/
***[http://snapshot.geneontology.org/products/annotations/wb-prediction.gaf wb-prediction.gaf]
***[http://snapshot.geneontology.org/products/annotations/index.html/wb-src.gaf.gz wb-src.gaf.gz]
***[http://snapshot.geneontology.org/products/annotations/index.htmlwb_noiea.gaf.gz wb_noiea.gaf.gz]
***[http://snapshot.geneontology.org/products/annotations/index.html/wb_valid.gaf.gz wb_valid.gaf.gz]

==== Annotation Reports ====
*Annotation reports are available here:
**http://snapshot.geneontology.org/reports/
*Each contributing group currently has a consolidated report rendered as HTML for easier viewing in the form:
http://snapshot.geneontology.org/reports/dictybase-report.html

=== Ontology ===


=== Data integrated in the release ===
====Data sources====
* Primary annotations by GOC contributing groups
* PAINT annotations
* +++?

====Original data location====
* Annotation files produced by GOC members are accessed via the URL or address provided by each group's [https://github.com/geneontology/go-site/tree/master/metadata/datasets datasets metadata file], in the ''Source'' field. The files most be stored on a publicly accessible site (such as an FTP site, an Amazon S3 bucket, an HTTP server, etc.) to be accessible by GO. Important note: the Source address must resolve to the latest annotation file produced by the submitting group, since that link is used directly in the script fetching the data.

**More information about the format of the datasets metadata file can be found in the [https://github.com/geneontology/go-site/blob/master/metadata/datasets/README.md datasets README.md file] under the Schema heading.
404 PAGE NOT FOUND

== Consuming and Displaying GO Data ==
=== GO Consortium Members ===
*While GOC members may consume snapshot release files for internal purposes, we strongly encourage members to only display data from the monthly releases.
*GOC members may filter GO annotations before display on their local sites.
*GO annotations should not be changed in any way from their original content.



== GO Consortium Dataflow ==

https://github.com/geneontology/go-site/blob/master/docs/go-consortium-dataflow.png




[[Category:Annotation]] Pascale
Categories: GO Internal

PAINT GAF QC-examples

GO wiki (new pages) - Thu, 08/02/2018 - 11:25

Pascale:

1. Nested IKR/IRD annotations
PTN000167322 (PTHR22778) ->
https://github.com/geneontology/go-annotation/issues/2043

2. Qualifiers: annotations with both 'contributes to' and direct annotation
Anushya says that its not possible to do this in PAINT - Pascale asks whether family merges could be responsible?
https://github.com/geneontology/go-annotation/issues/2019



[[Category:Reference Genome]] Pascale
Categories: GO Internal

Manager Call 2018-08-16

GO wiki (new pages) - Thu, 08/02/2018 - 06:46

Pascale:



=Follow up from last week=

== Feedback form update==
Did we figure out the payment ? What's the time line for deployment?

== New GO-announcement repo==
Twitter/facebook: SuziA is this done ?


== New GAF Submissions ==
Did we make any progress on documentation?

== Ontology Editors' Meeting ==
David: Who would attend each meeting ?
Pascale: needed to follow up with Paul regarding funds to hold these

== GO Site Migration ==
Status update

=Job descriptions for each manager=
Pascale and Kimberly stared to create job descriptions for all managers roles:

https://drive.google.com/drive/folders/1F7e2D7T4hleIq8VaH7YW60D9wxQnRFRV

Every manager should add what they believe are their tasks. And then we discuss it here.

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

GO-CAM Working Group Call 2018-07-31

GO wiki (new pages) - Mon, 07/30/2018 - 14:56

Vanaukenk: Created page with "= Meeting URL = https://stanford.zoom.us/j/976175422 =Agenda= == Re-cap of Last Week's Call == === Modeling Transcription in GO-CAM === *Sabrina - PMID:28687631 'Clock1a a..."

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

=Agenda=

== Re-cap of Last Week's Call ==

=== Modeling Transcription in GO-CAM ===
*Sabrina - PMID:28687631 'Clock1a affects mesoderm development and primitive hematopoiesis by regulating Nodal-Smad3 signaling in the zebrafish embryo.'

=== Relations between Transcription Factor MFs and Regulation of Transcription BPs ===
*Transcription factor activity is 'part_of' regulation of transcription
*This is consistent with the relations in the ontology and produces the correct annotations in the GPAD output file

=== General Rule for MFs and Regulation of BPs ===
*MFs and BPs are linked by part_of (or other relations, e.g. acts upstream of, acts upstream of or within) but NOT by regulates relations

== Relations between MF and Input(s) ==
*has_input vs has_direct_input
*[https://github.com/oborel/obo-relations/issues/171 Improve documentation on 'has input' and subproperties, deprecating unnecessary terms]
*[https://github.com/oborel/obo-relations/issues/187 obsolete 'has direct input' ?]
*has_direct_input has been used much more widely in conventional annotation for MF extensions
*has_input has been used less widely, but how is it used?
**select participants in catalytic activities
**metal ions (e.g. calcium-dependent protein binding)
**drug binding
*Is there a meaningful distinction between these two relations for MF? What are we really trying to capture with MF inputs?
*Proposal: review MF annotations using has_input
**This would be good information to have in light of the Relations Ontology work that is currently being done
=== Relations between BP and input(s) ===
*Duplicating has_input for MF and BP results in multiple entries in the AE field of the BP annotation in the GPAD
=== Relations between MF and Inputs (from previous call) ===
*We discussed the relation to use when capturing the input of the transcription factor.
*Even in conventional annotations, groups have differed on how they do this.
**To illustrate, groups have used: has_input, has_direct_input, has_regulation_target
*For MFs, is there any real difference in meaning between has_input and has_direct_input?
**No, an input to an MF is, by necessity, a direct input to the activity.
*For BP, the use of has_input may mean something different, though.
**For BP, curators have used has_input to indicate the entity that is affected by a process but for which the precise MF that directly mediates that effect is not known.
**As an example, Rob described how SGD has annotated IDA vs IMP for protein kinase activity and phosphorylation.
*The curation task of indicating inputs for MFs vs BPs needs to be clear for GO-CAM models.
*Rob was asked to create a GO-CAM model for the phosphorylation example.
*Sabrina's paper from last month also touches on this; in one case, the evidence for direct regulation of transcription was supported by several different pieces of evidence, whereas in the other cases, there wasn't sufficient evidence to assert the direct regulation. We need to re-visit this model to make sure we have a satisfactory way of distinguishing between these two cases. This will likely be a common occurrence during curation of transcription papers.
=== Relations between BP and MF of transcriptional target ===
*[https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0002304 causally upstream of, positive effect]
*[https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0002305 causally upstream of, negative effect]

=Minutes=
*On call: Bob, Dave F, David H, Dmitry, Edith, Giulia, Harold, Kimberly, Laurent-Philippe, Pascale, Paul T, Petra, Sabrina, Seth, Stan, Suzi A, Suzi L (others -please add your name to the list if you joined later)

== Transcription Models - Decisions Made ==

=== Relations between MFs and Regulatory BPs ===
**Transcription factor activities are related to regulation of transcription BP terms using the 'part_of' relation
***This is consistent with the use of relations in the ontology and produces the desired annotations in the GPAD output
**Note that this is a general guideline that will apply to any MF that is 'part_of' a regulatory process
**A consequence of this is that any regulation terms needed for annotation will have to be instantiated in the ontology

=== Capturing Direct Regulation ===
*Direct regulation of a TF on the expression of a gene may be captured by adding the gene as input to the TF activity, e.g. has_input 'gene x'
=== Capturing Unknown Mechanism of Regulation ===
*If it is not known if the TF directly regulates the expression of a gene, then the input for the TF activity is left blank.
**In this case, however, it is okay to use evidence from another experiment that might have shown different context (i.e. a different gene was regulated) as supporting evidence for the TF activity.
*The curator can model the unknown mechanism of regulation by saying that the TF is part_of regulation of transcription that is causally_upstream_of_or_within the positive or negative regulation of transcription that ultimately controls the expression of the gene. The gene is then added as 'has input' to the most distal transcriptional regulatory process.

=== Root Node vs Existing Molecular Functions ===
*Curators should always try to construct models using the known MF of a gene product, even if that MF was not specifically demonstrated in the paper they are annotating.
*Associated evidence for that MF will always point back to the paper in which the MF was interrogated.
*Creating models in this way will allow us to build on existing knowledge to create the most comprehensive and up-to-date model for a given BP.
*If a gene product has more than one MF, curators should use the biological context of the annotated process to select the most appropriate function(s) for that gene product.

== Transcription Models - Decisions Outstanding ==
*has_input vs has_direct_input
*Most, but not all, conventional MF annotations have used 'has_direct_input' for contextual information
*GO-CAM models, and the form editor, however, use has_input
*We need to converge on a consistent way to capture MF context
*Note that the ongoing RO work in which this topic is being discussed may have a significant impact on what we ultimately decide to do here
*In the meantime, what should we do?
*One thing we could do is review MF annotations that used 'has_input' to determine what curators were really trying to capture with 'has_input' for MFs

== Screenshot of Model used for Discussion ==
[[File:Sabrina model 2017-07-24.png|800px|thumb|left]]
*The top part of the model shows alternative representations of the relation between the TF and transcription.
*The part_of relation is the agreed upon correct way to model the relationship between the TF and regulation of transcription.
*Note that this model is still under discussion and not the final version; this screenshot represented the model as of 2018-07-24.
























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

Ontology meeting 2018-07-30

GO wiki (new pages) - Fri, 07/27/2018 - 05:28

David: /* Project Update */

= Conference Line =

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

= Agenda =

== Editors Discussion ==

===Project Update===
====Reactome-Rhea-GO Alignment----https://github.com/geneontology/go-ontology/projects/10====
====ECM----https://github.com/geneontology/go-ontology/projects/9====

=== Regenerate Imports File ===
David will show how to regenerate an import file using docker.

===Ontology Developers' workshop possibility===
* December in Geneva. Maybe we can take a day or two to also meet with Anne and/or Alan to discuss the Rhea alignment project.

===New Repository for Announcements===
* New GO-announcement repo: https://github.com/geneontology/go-announcements
* Documentation. We can also discuss if we need more SOPs that what’s currently in the README (https://github.com/geneontology/go-announcements/blob/master/README.md) - admittedly very succinct.
* http://wiki.geneontology.org/index.php/Manager_Call_2018-07-19

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

= Minutes =
*On call:


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

Manager Call 2018-08-02

GO wiki (new pages) - Tue, 07/24/2018 - 07:55

Pascale:

[[Category:GO Consortium]] [[Category:GO Managers Meetings ]]


* Check topics from last call: http://wiki.geneontology.org/index.php/Manager_Call_2018-07-19

== New GO-announcememt repo==
'''Action point''': Chris was to write to go-friends and obo-discuss to announce it - was this done ?

== Plasmodium annotations==
See mail thread related to https://github.com/geneontology/helpdesk/issues/143

== Outreach coordinator role ==
MGD outreach job description:
* Responsible for assisting users with questions regarding biological/scientific aspects of MGD
* triage and tracks requests using the ServiceNow Helpdesk system,
* answer or forward user queries, as appropriate, and tracks responses.
* work closely with the MGD software team as new software is implemented to ensure that new users help documents are written, and existing documents updated.
* develop online turorials and FAQs, including pictorial step-by-step instructions, and animated videos.
* organize training sessions at conferences and meetings and at road shows given at other institutions.
* responsible for developing problem sets and tutorials for training sessions, as well as tutorials for the MGD website.
* maintains the listserve system for our Email scientific community forum and technical forum, monitors email flow, responds to MGD-relevant listserve postings, and updates the Lists as needed.
* maintains the Facebook and Twitter accounts Pascale
Categories: GO Internal

GO-CAM Working Group Call 2018-07-24

GO wiki (new pages) - Mon, 07/23/2018 - 08:13

Vanaukenk: /* Modeling Transcription in GO-CAM */

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

=Agenda=

== 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
***Can now search using a PMID
***Green paper icons beneath model titles; mouse over shows paper data
***One question about presentation of author name(s) - first? last?
*https://github.com/geneontology/web-gocam/issues

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


== Modeling Transcription in GO-CAM ==
*Sabrina - PMID:28687631 'Clock1a affects mesoderm development and primitive hematopoiesis by regulating Nodal-Smad3 signaling in the zebrafish embryo.'
*Kimberly - PMID: 28578929 'Morphological Diversity of C. elegans Sensory Cilia Instructed by the Differential Expression of an Immunoglobulin Domain Protein.'
*Kimberly - [http://noctua.berkeleybop.org/editor/graph/gomodel:5b318d0900000602 unc-86 regulates transcription of mec-3]
=== Relations between MF and BP ===
*Transcription factor activity is 'part_of' regulation of transcription
*This is consistent with the ontology
**[http://amigo.geneontology.org/amigo/term/GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding]

=== Relations between MF and BP (from previous call) ===
*We discussed models of transcription factors and their relation to transcription BP terms
*Transcription factor activities are modeled as 'part of' a regulation of transcription process
**Why? In the ontology, regulation is modeled is a biological process, and so functions need to be part of biological processes that regulate other processes.
**This can be captured succinctly in models by stating that a transcription factor activity is part_of '(+/-) regulation of transcription'.
**This will also produce the correct annotations in the GPAD output file.
**If a transcription factor activity is connected to the process of transcription with a regulates relation, the reasoner cannot then use the logical definitions of the process terms to infer that the transcription factor activity is 'part_of' a regulatory process.
[[File:Ontology TF BP.png|thumb|left|'''Figure 1. Transcription Factor Relation to BP'''|500px]]



== Relations between MF and Input(s) ==
*has_input vs has_direct_input
*[https://github.com/oborel/obo-relations/issues/171 Improve documentation on 'has input' and subproperties, deprecating unnecessary terms]
*[https://github.com/oborel/obo-relations/issues/187 obsolete 'has direct input' ?]
=== Relations between BP and input(s) ===
*Duplicating has_input for MF and BP results in multiple entries in the AE field of the BP annotation in the GPAD
=== Relations between MF and Inputs (from previous call) ===
*We discussed the relation to use when capturing the input of the transcription factor.
*Even in conventional annotations, groups have differed on how they do this.
**To illustrate, groups have used: has_input, has_direct_input, has_regulation_target
*For MFs, is there any real difference in meaning between has_input and has_direct_input?
**No, an input to an MF is, by necessity, a direct input to the activity.
*For BP, the use of has_input may mean something different, though.
**For BP, curators have used has_input to indicate the entity that is affected by a process but for which the precise MF that directly mediates that effect is not known.
**As an example, Rob described how SGD has annotated IDA vs IMP for protein kinase activity and phosphorylation.
*The curation task of indicating inputs for MFs vs BPs needs to be clear for GO-CAM models.
*Rob was asked to create a GO-CAM model for the phosphorylation example.
*Sabrina's paper from last month also touches on this; in one case, the evidence for direct regulation of transcription was supported by several different pieces of evidence, whereas in the other cases, there wasn't sufficient evidence to assert the direct regulation. We need to re-visit this model to make sure we have a satisfactory way of distinguishing between these two cases. This will likely be a common occurrence during curation of transcription papers.
=== Relations between BP and MF of transcriptional target ===
*[https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0002304 causally upstream of, positive effect]
*[https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0002305 causally upstream of, negative effect]

=Minutes=
*On call:

== Documentation ==





















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

Ontology meeting 2018-07-23

GO wiki (new pages) - Mon, 07/23/2018 - 06:12

David: Created page with "= Conference Line = *Zoom: https://stanford.zoom.us/j/828418143 = Agenda = == Editors Discussion == ===Project Update=== ====Reactome-Rhea-GO Alignment----https://github.c..."

= Conference Line =

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

= Agenda =

== Editors Discussion ==

===Project Update===
====Reactome-Rhea-GO Alignment----https://github.com/geneontology/go-ontology/projects/10====

=== Regenerate Imports File ===
Docker has worked successfully for regenerating the CL import and appears to have worked for the ChEBI import.
Should we push and merge the large chebi_import file?

===Ontology Developers' workshop possibility===
* December in Geneva?

===New Repository for Announcements===
* New GO-announcement repo: https://github.com/geneontology/go-announcements
* Documentation. We can also discuss if we need more SOPs that what’s currently in the README (https://github.com/geneontology/go-announcements/blob/master/README.md) - admittedly very succinct.
* http://wiki.geneontology.org/index.php/Manager_Call_2018-07-19

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

= Minutes =
*On call:


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