Feed aggregator

Initial Setup

GO wiki (new pages) - Thu, 06/07/2018 - 09:30

Pascale:

==Installing Protege==

# Follow the instructions on the GO wiki page: [http://wiki.geneontology.org/index.php Protege_setup_for_GO_Eds] '''CHECK THAT INFORMATION IS NOT REDUNDANT WITH INFORMATION HERE'''
# ''Need to add more here about the different Views and Tabs needed for working.''

==ID Ranges==

# Curators and projects are assigned specific GO term ID ranges.
# These ID ranges are stored in the file: [https://github.com/geneontology/go-ontology/blob/master/src/ontology/go-idranges.owl go-idranges.owl]
# '''NOTE:''' You should only use IDs within your range.
# If you have only just set up this repository, modify the idranges file and add yourself or other editors.

==Setting ID ranges in Protege==
# Once you have your assigned ID range, you need to configure Protege so that your ID range is recorded in the Preferences menu. Protege does not read the go-idranges.owl file.
# In the Protege menu, select Preferences.
# In the resulting pop-up window, click on the New Entities tab and set the values as follows.
# In the Entity IRI box: #* '''Start with:''' Specified IRI: [http://purl.obolibrary.org/obo http://purl.obolibrary.org/obo]
#* '''Followed by:''' /
#* '''End with:''' Auto-generated ID
# In the Entity Label section:
#* '''Same as label renderer:'''IRI: [http://www.w3.org/2000/01/rdf-schema#label http://www.w3.org/2000/01/rdf-schema#label]
# In the Auto-generated ID section:
#* Numeric
#* Prefix: "GO"
#* Suffix: ''leave this blank''
#* Digit Count "7"
#* '''Start:''' see [go-idranges.owl](https://github.com/geneontology/go-ontology/blob/master/src/ontology/go-idranges.owl). Only paste the number after the '''GO:''' prefix. Also, note that when you paste in your GO ID range, the number will automatically be converted to a standard number, e.g. pasting 0110001 will be converted to 110,001.)
#* '''End:''' see [go-idranges.owl](https://github.com/geneontology/go-ontology/blob/master/src/ontology/go-idranges.owl)
#* Remember last ID between Protege sessions: ALWAYS CHECK THIS
#* ('''Note:''' You want the ID to be remembered to prevent clashes when working in parallel on branches.)


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

Editor Guide 2018

GO wiki (new pages) - Thu, 06/07/2018 - 09:19

Pascale: /* This guide was developed following the Protégé meeting in November 2017. Last updated: June 2018 */

=This guide was developed following the Protégé meeting in November 2017. Last updated: June 2018=


[[Initial Setup]]

Configuration

Installing and Using git

Daily Workflow

Creating a New Ontology Term
Creating Regulation Terms
Deleting Asserted Subclasses
Obsoleting an Existing Ontology Term
Merging Ontology Terms
Term Comments

Adding a term to a GO Subset (Slim)
Adding a new GO Subset (Slim)
Adding taxon restrictions
Adding Terms to the Import Files




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

Annotation Conf. Call 2018-06-12

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

Vanaukenk: /* GO Annotation Meetings */

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

= Agenda =
== Annotation File Pipeline ==
*Presentation on the new annotation file production pipeline
**How to submit annotation files
**Where to retrieve annotation files
**Annotation file reports

== GO Annotation Meetings ==
*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

= Minutes =



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

PAINT GAF production

GO wiki (new pages) - Wed, 06/06/2018 - 12:55

Pascale: /* PAINT GAF export */

[[Category:Reference Genome]]

=PAINT GAF Format=
By Huaiyu Mi

This document is to define the data used in each column of the PAINT GAF file. The file follows the GO Annotation File (GAF) format 2.1. See http://geneontology.org/page/go-annotation-file-gaf-format-21 for more details.

==Some history==

The legacy PAINT GAF files were created and stored on SVN at:
http://viewvc.geneontology.org/viewvc/GO-SVN/trunk/gene-associations/submission/paint/pre-submission/?sortby=date

In March 2017, a modified PAINT tool was released to retrieve and store all PAINT data through a database. A new process was created to generate PAINT GAF from the database The format of these GAF files were strictly based on the legacy PAINT GAFs. In Feb. 2018, during the transition of GO data release, a number of issues were raised with regard to the data in the GAF files, especially what type of data that should be captured in each column.

This document will serve as a guideline to create and use the PAINT GAF.


==PAINT GAF export==
* Monthly release (not yet implemented; currently ad hoc)
* Load current GO file (date of the GO.obo download got in the GAF file header)(not yet implemented?)
* Run touchup: (?)
* Remove annotations to obsolete terms: If there is a replaced_by tag, annotation is updated; otherwise it is just removed (?)
* Remove annotations for which experimental evidence is no longer available (?)
* During the annual Panther release: all the PTNs, all IBDs are forwardly tracked. PTN can change families,
* Remove annotations to ‘do not annotate’ and ‘do not manually annotate’ term (?)
* Run taxon constraints checks (?)
* All these actions are recorded in the ‘comments’ file (mostly; some notes were not yet populated
* If a, b or c happens, the family curation status will be changed to ‘REQUIRE PAINT REVIEW’
* Generate GAF as described below
* GAF are stored on the Panther db: ftp://ftp.pantherdb.org/downloads/paint/presubmission
* GO loads the yaml file from https://github.com/geneontology/go-site/blob/master/metadata/datasets/paint.yaml

==PAINT GAF Files==
File Header
All gene association files must start with a single line denoting the file format, followed by the date of creation, PANTHER and GO versions, as below, for example:

!gaf-version: 2.1
!Created on Thu Apr 5 23:42:21 2018.
!PANTHER version: v.13.1.
!GO version: 2017-12-27.

===Annotation Fields and Data Contents===
====DB (column 1)====
refers to the database from which the identifier in DB object ID (column 2) is drawn.
According to the GAF document, it must be one of the values from the set of GO database cross-references.
Below is the DB used for the GAF of each genome. The ones in red are the ones that are not in the GO database cross-references.

gene_association.paint_cgd.gaf
CGD
UniProtKB

gene_association.paint_chicken.gaf
UniProtKB

gene_association.paint_dictyBase.gaf
UniProtKB
dictyBase → DictyBase

gene_association.paint_ecocyc.gaf
EcoGene
UniProtKB

gene_association.paint_fb.gaf
FB
UniProtKB

gene_association.paint_human.gaf
UniProtKB
!!! Please note that UniProtKB IDs, NOT HGNC IDs, are used for human genes.

gene_association.paint_mgi.gaf
MGI
UniProtKB

gene_association.paint_pombase.gaf
PomBase
UniProtKB

gene_association.paint_rgd.gaf
RGD
UniProtKB

gene_association.paint_sgd.gaf
SGD

gene_association.paint_tair.gaf
Araport
TAIR
UniProtKB

gene_association.paint_wb.gaf
UniProtKB
WB

gene_association.paint_zfin.gaf
UniProtKB

gene_association.paint_other.gaf
UniProtKB
WB (some CAEBR genes)
Xenbase
ZFIN (???)

====DB Object ID (column 2)====
Primary identifier of the gene from the DB specified in column 1.
Example:
MGI:1921966
SPCC895.04c
Q13217

====DB Object Symbol (column 3)====
A gene symbol or gene name is used here. This is usually from the Reference Proteome dataset, from the GN file of their fasta file header.

====Qualifier (column 4)====
Enter qualifier such as NOT, contributes_to and colocalizes_with.

====GO ID (column 5)====
The GO identifier that is annotated to the gene in column 2, e.g., GO:0060070.

====DB:Reference (column 6)====

PMID:21873635

====Evidence Code (column 7)====
Should always be IBA

====With [or] From (column 8)====
The column contains the ancestral node PTN id that the annotation inherits from, as well as all the leaf sequence IDs with experimental annotations that are used as evidence for the IBD annotation to the ancestral node. They are in the following format:

PANTHER:PTNxxxxx|[seq1]|[seq 2]

Example:
PANTHER:PTN001527784|UniProtKB:Q14833|UniProtKB:Q14831

====Aspect (column 9)====
refers to the namespace or ontology to which the GO ID (column 5) belongs.
P (biological process)
F (molecular function)
C (cellular component)

====DB Object Name (column 10)====
Name of gene or gene product obtained from the UniProt Reference Proteomes.
All annotated genomes should be in the UniProt Reference Proteomes to have the correct names.

====DB Object Synonym (column 11)====
It is the UniProtKB ID and the leaf PTN ID separated by a pipe. If the DB (column 1) is already UniProtKB, then it is not included.
Example:
UniProtKB:Q8R4E4|PTN000409177

====DB Object Type (column 12)====
It is always ‘protein’.

====Taxon (column 13)====
This is the taxon ID in the format as below:
taxon:10090

====Date (column 14)====
Currently it is the date the update is done, but we will change to the date the original curation was done.

====Assigned By (column 15)====
‘GO_Central’.

====Annotation Extension (column 16)====
Blank now.

====Gene Product Form ID (column 17)====
Blank now. Pascale
Categories: GO Internal

Manager Call 2018-06-21

GO wiki (new pages) - Wed, 06/06/2018 - 10:42

Pascale: Created page with "Category:GO Managers Meetings ==From PI call== Managers should help define the tasks of the helpdesk group Proposal: (Pascale) * monitor helpdesk repo * monitor Biostar..."

[[Category:GO Managers Meetings]]

==From PI call==
Managers should help define the tasks of the helpdesk group

Proposal: (Pascale)
* monitor helpdesk repo
* monitor Biostars for GO-related questions





== Topics not discussed at last meeting ==

* create a simple challenge form? (see noctua new user form)
* licensing and "remix" for upstream sources (e.g. Reactome)
* licensing sign-over or statement (annotation input)
* zenodo and user metadata; proposal: "active" users and cull users.yaml (possibly a small sub-group from there, about half an hour)
* Laurent-Philippe: collect information / links / contacts about the GO user communities (e.g. R/bioconductor and ?)
* (Pascale) Rules, especially taxon checks: can we have this for the July release? https://github.com/geneontology/go-annotation/issues/1928


==Minutes== Pascale
Categories: GO Internal

Guidelines for equivalence axioms

GO wiki (new pages) - Tue, 06/05/2018 - 12:49

Pascale: /* In progress */

=In progress=


==Molecular function==
Equivalent axioms for MF that include 'binding': use 'has_part' some binding (see https://github.com/geneontology/go-ontology/issues/14266)


==Children of transcription regulator activity==

For example: DNA-binding transcription factor activity

transcription regulator activity
'part of' some 'regulation of transcription, DNA-templated'
'has necessary component activity' some 'transcription regulatory region sequence-specific DNA binding'



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

Ontology meeting 2018-06-04

GO wiki (new pages) - Fri, 06/01/2018 - 11:54

David: Created page with "= Conference Line = *Zoom: https://stanford.zoom.us/j/828418143 = Agenda = ==GH project link== https://github.com/geneontology/go-ontology/projects/1 == Editors Discussio..."

= Conference Line =

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

= Agenda =


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

== Editors Discussion ==

===Ontology Developers' workshop possibility- Geneva in late August (or maybe September)?===
* Topics
** GH Jamboree
** Creating necessary and sufficient logical definitions (We never got around to this in Berkeley)
** Updating Documentation
** GO-Rhea-Reactome alignment
** Dealing with GH conflicts

=== Outstanding Pull Requests ===
There are now 26 open requests. We are getting better.

=== Regenerate Imports File ===
What is the status of Docker and do we have documentation on its use?

=== 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?

=== DBxrefs ===
There was a recent thread about the scope of dbxrefs in the ontology. If we are going to use the dbxrefs to seed an alignment between GO Rhea and Reactome, at least for MF, they should be 1:1.

Did this get covered last week?

= Minutes =
*On call:


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

QCQA next call

GO wiki (new pages) - Wed, 05/30/2018 - 01:45

Pascale:

* Which annotation validation rules are currently implemented ? https://github.com/geneontology/go-annotation/issues/1928
* Taxon checks should be a hard check: https://github.com/geneontology/go-site/issues/660
* 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.


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

Manager Call 2018-06-07

GO wiki (new pages) - Thu, 05/24/2018 - 09:16

Pascale:

[[Category:GO Managers Meetings]]


==Review action points from NYC meeting==

==Communicating with users==

How about creating a repo that people can sign up for, or just as they want ?
This would include
* changes in file format
* obsoletion and merge notices
* Other important ontology changes
* releases
* QC annoucements
* GO meting announcements
* etc Pascale
Categories: GO Internal

Fall 2018 ontology editors meeting - potential agenda topics

GO wiki (new pages) - Wed, 05/23/2018 - 07:36

Pascale:


* Define, wherever possible, the start and end of biological processes, e.g. signaling pathways.


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

Why isn't interleukin in GO?

GO wiki (new pages) - Wed, 05/23/2018 - 01:36

Pascale: Created page with " Category:Ontology"





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

Notes on specific terms

GO wiki (new pages) - Wed, 05/23/2018 - 01:36

Pascale: Created page with " ===Guidelines on 'protein complex' terms=== ===Why isn't interleukin in GO?=== Category:Ontology"


===[[Guidelines on 'protein complex' terms]]===
===[[Why isn't interleukin in GO?]]===


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

GO-CAM Noctua Call 2018-05-23

GO wiki (new pages) - Tue, 05/22/2018 - 12:45

Vanaukenk: /* GO-CAM Modeling Working Group */

= Meeting URL =
https://stanford.zoom.us/j/679970729
= Discuss Development Priorities =
== Annotation ==
*Editing ('conventional' and GO-CAM)
*Model cloning
== Error checks ==
*Incorporating annotation rules into Noctua
== Evidence codes ==
*Working with ECO to create manual/automatic assertion children
== GPAD Outputs ==
*Protein complexes
*Annotation extension relations white list
== Landing Page ==
*Model searching
== Model Seeding ==
*From GAFs
*From Reactome
== Relations ==
*Reconcile CC annotation relations with CC ontology relations
*Use of has_input vs has_participant for binding annotations
== Templates ==
*Create and use templates for curation
== Text Mining ==
*TPC integration into form

= GO-CAM Modeling Working Group =
*Engage at least one curator from each annotation group in GOC
*Discuss specific modeling issues
*Add to GO-CAM curation documentation

= Onboarding Additional Curation Groups =
*Next groups to bring onboard

= Minutes =
*On call:
[[Category: Annotation Working Group]] Vanaukenk
Categories: GO Internal

Annotation Conf. Call 2018-05-22

GO wiki (new pages) - Mon, 05/21/2018 - 12:02

Vanaukenk: /* Canonical Wnt Signaling */

= Agenda =
== 20th Anniversary GO Meeting, Montreal, Canada ==
*Dates set for Oct 17-19

== Annotation Review ==
=== Cyclic nucleotide metabolic process (and child terms) ===
*[https://github.com/geneontology/go-annotation/issues/1979 Review annotations to GO:0009190 cyclic nucleotide biosynthetic process]
*[https://github.com/geneontology/go-annotation/issues/1978 Review annotations to GO:0009187 cyclic nucleotide metabolic process]
*[https://github.com/geneontology/go-annotation/issues/1977 Review annotations to GO:0006182 cGMP biosynthetic process]
*[https://github.com/geneontology/go-annotation/issues/1974 Review annotations to cAMP catabolic process]
*[https://github.com/geneontology/go-annotation/issues/1971 Review annotations to GO:0030820 regulation of cAMP catabolic process and children]

=== Growth ===
*[https://github.com/geneontology/go-annotation/issues/1973 Review annotations to 'growth']

=== Canonical Wnt Signaling ===
*[https://github.com/geneontology/go-annotation/issues/1967 Review annotations wrt GO:0090090 'negative regulation of canonical Wnt signaling pathway']
**Refer to first tab in sheet titled, ALL-CHECK

== GOC Meeting - NYC ==
=== Minutes ===
*[https://docs.google.com/document/d/1Px8AgghIABKaGP174Av2XYXQ8NfUrkMRT1yJ8kwCgx4/edit Agenda and Minutes]
=== Presentations/Slides ===
*Presentations and slides are available in the GO's [https://drive.google.com/drive/folders/1wxi52dercOofm6cCg1jr6eCvU2py6wtI Google drive]
**If you presented and your slides are not here, please add them.
=== Action Items ===
=== Curation Decisions ===

== Annotation Survey Results ==
*We are conducting a [https://goo.gl/forms/rLovY736aX1gxqHe2 survey] on annotation practices across the GOC
*Thank you to everyone who responded
*Compiling all of the responses

== Ontology Development and Annotation Review ==
=== Transcription factor refactoring ===
*Any updates?

== Updates on Projects ==
=== MAPK Cascade ===
*[https://github.com/geneontology/go-annotation/issues/1592 MAPK cascade- Signaling Project]
=== Extracellular Matrix ===
*[https://github.com/geneontology/go-ontology/projects/9 Extracellular matrix revisions]
**[https://github.com/geneontology/go-ontology/issues/15294 proposal]
=== Canonical Wnt Signaling Pathway ===
*Have compiled annotations to review
**[https://github.com/geneontology/go-annotation/issues/1966 Review annotations wrt GO:0060070 'canonical Wnt signaling pathway']
**[https://github.com/geneontology/go-annotation/issues/1967 Review annotations wrt GO:0090090 'negative regulation of canonical Wnt signaling pathway']
*Note: each Google spreadsheet has multiple sheets; please be sure to check each sheet
*Main issues:
**Distinguishing gene products that are involved in canonical Wnt signaling vs +/- regulation of canonical Wnt signaling
**Annotating to more granular child of Wnt signaling pathway when appropriate
**Annotation of downstream targets to the canonical Wnt signaling pathway

== GO-CAM/Noctua ==
*Next call tomorrow, Wednesday, May 23rd at 11:00am EDT (see Google calendar)

= Minutes =
*On call:



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

Ontology meeting 2018-05-21

GO wiki (new pages) - Thu, 05/17/2018 - 04:56

David: Created page with "= Conference Line = *Zoom: https://stanford.zoom.us/j/828418143 = Agenda = ==GH project link== https://github.com/geneontology/go-ontology/projects/1 == Editors Discussio..."

= Conference Line =

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

= Agenda =


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

== Editors Discussion ==

*Ontology Developers' workshop possibility- Geneva in late August?
** Topics
*** GH Jamboree
*** Creating necessary and sufficient logical definitions (We never got around to this in Berkeley)
*** Updating Documentation
*** GO-Rhea-Reactome alignment
*** Dealing with GH conflicts

=== Outstanding Pull Requests ===
There are still 33 open pull requests in the repository.

=== Regenerate Imports File ===
Could one of the software folks please regenerate the imports? There have been some import requests that have been outstanding for months and it is limiting our ability to close tickets.


= Minutes =
*On call:



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

Ontology meeting 2018-02-19

GO wiki (new pages) - Thu, 05/17/2018 - 04:46

David: Created page with "No Call"

No Call David
Categories: GO Internal

Causally upstream of or within, negative effect

GO wiki (new pages) - Fri, 05/11/2018 - 14:05

Vanaukenk: /* Examples of Usage */

== Overview ==
The 'causally upstream of or within, negative effect' relation is used to relate two GO Biological Processes.
=== Definition ===


=== Child Terms ===

== Examples of Usage ==
*[https://www.ncbi.nlm.nih.gov/pubmed/?term=26265472 The zebrafish miR-462/miR-731 cluster is induced under hypoxic stress via hypoxia-inducible factor 1α and functions in cellular adaptations.]
**Overexpression of miR-462 and miR-731 represses cell proliferation through blocking cell cycle progress of DNA replication, and induces apoptosis.
**Exemplar: http://noctua.berkeleybop.org/editor/graph/gomodel:5a7e68a100001507

== Quality Control Checks ==

== Relations Ontology ==
[http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0004046 causally upstream of or within, negative effect]

== Review Status ==

Last reviewed: May 11, 2018

[http://wiki.geneontology.org/index.php/Annotation_Relations Back to: Annotation Relations]

[[Category: Annotation]]
[[Category: Relations]]
[[Category: GO-CAM Relations]] Vanaukenk
Categories: GO Internal

Causally upstream of or within, positive effect

GO wiki (new pages) - Fri, 05/11/2018 - 13:58

Vanaukenk: /* Examples of Usage */

== Overview ==
The 'causally upstream of or within, positive effect' relation is used to relate two GO Biological Processes.
=== Definition ===


=== Child Terms ===

== Examples of Usage ==
Exemplar:http://noctua.berkeleybop.org/editor/graph/gomodel:57c82fad00000847

== Quality Control Checks ==

== Relations Ontology ==
[http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0004047 causally upstream of or within, positive effect]

== Review Status ==

Last reviewed: May 11, 2018

[http://wiki.geneontology.org/index.php/Annotation_Relations Back to: Annotation Relations]

[[Category: Annotation]]
[[Category: Relations]]
[[Category: GO-CAM Relations]] Vanaukenk
Categories: GO Internal

Directly positively regulates

GO wiki (new pages) - Fri, 05/11/2018 - 12:30

Vanaukenk: /* Examples of Usage */

== Overview ==
The 'directly positively regulates' relation is used to relate two GO Molecular Functions whenever two Molecular Functions succeed one another directly, and the first provides regulates the activity of the second via a direct physical interactions. The 'directly positively regulates' relation is used to describe a relation, for example, between a ligand and the receptor that it activates.
=== Definition ===
Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2.

=== Child Terms ===

== Examples of Usage ==
*In GO-CAM models, the 'directly positively regulates' relation is used for associations between two Molecular Functions.

*In canonical Wnt signaling, a Wnt ligand 'directly positively regulates' the activity of a Frizzled receptor.
* Examplar: http://noctua.berkeleybop.org/editor/graph/gomodel:56d1143000003025

== Quality Control Checks ==

== Relations Ontology ==
[http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0002413 directly provides input for]

== Review Status ==

Last reviewed: May 11, 2018

[http://wiki.geneontology.org/index.php/Annotation_Relations Back to: Annotation Relations]

[[Category: Annotation]]
[[Category: Relations]]
[[Category: GO-CAM Relations]] Vanaukenk
Categories: GO Internal

Directly provides input for

GO wiki (new pages) - Fri, 05/11/2018 - 11:30

Vanaukenk: /* Examples of Usage */

== Overview ==
The 'directly provides input for' relation is used to relate two GO Molecular Functions whenever two Molecular Functions succeed one another directly, and the first provides an input for the Molecular Function of the second. The 'directly provides input for' relation is used to describe a relations, for example, between the Molecular Functions that are part of metabolic pathways.

=== Definition ===
P1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c

=== Child Terms ===

== Examples of Usage ==
*In GO-CAM models, the 'directly provides input' relation is used for associations between two Molecular Functions.

*In glycolysis, triose phosphate isomerase activity 'directly provides input for' glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity.
* Examplar: http://noctua.berkeleybop.org/editor/graph/gomodel:55c3ef4c00000001
** Inferred GPAD: http://noctua.berkeleybop.org/workbench/annpreview/?model_id=gomodel:5323da1800000002

== Quality Control Checks ==

== Relations Ontology ==
[http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0002413 directly provides input for]

== Review Status ==

Last reviewed: May 11, 2018

[http://wiki.geneontology.org/index.php/Annotation_Relations Back to: Annotation Relations]

[[Category: Annotation]]
[[Category: Relations]]
[[Category: GO-CAM Relations]] Vanaukenk
Categories: GO Internal