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Ontology meeting 2018-09-17

Thu, 09/13/2018 - 07:08

David: /* Ontology Developers' workshop */

= Conference Line =

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

= Agenda =


== Editors Discussion ==


==Meetings==

===Montreal GOC Meeting===
*Add name to attendees list if you're going

===Ontology Developers' workshop===
The meeting will be in Geneva December (8)9-13
* When to book flights and hotel?
====Topics====
* Filling in missing GO-Rhea-Reactome xrefs
** moving from reactions to biochemical pathways
** implementation of a method to keep in synch with all three resources
** GO-CAM templates for pathways??
* GH ticket work and mini-project planning
** Dealing with and migrating binding terms
** Dealing with cellular processes (https://github.com/geneontology/go-ontology/issues/12849)
** Taxon constaints- How do we handle them going forward?
* Attendees
** David H (Can make it)
** Kimberly (Can make it)
** Karen
** Harold (Can make it)
** Pascale (Can make it)
** Barbara (Maybe make it)
** Alan B (Rhea, can make any day)
** Anne (Rhea, prefers Monday or Tuesday)
** Chris
** Peter D (Can make it)
** Ben?
** Jim?
** Paul T (Can make it)

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

= Minutes =
*On call:



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

Annotation Conf. Call 2018-09-11

Fri, 09/07/2018 - 12:02

Vanaukenk: /* Pipeline */

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

= Agenda =
== 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 Biological Function
**2nd Tuesday: GO Consortium
**3rd Tuesday: Alliance Biological 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

== Pipeline ==
*Directionality of file transfer should now be GO -> Annotation group ftp (or something similar)
*Groups should no longer be submitting files to SVN
*Source URL should be indicated in the [https://github.com/geneontology/go-site/tree/master/metadata/datasets datasets.yaml files]

== Annotation Discussion ==
=== ND Annotations ===
*[https://github.com/geneontology/go-annotation/issues/2045 Automatic deletion of ND-evidenced annotations]
*ND annotations to a root node term are intended to signify that the curator looked at all available evidence and the MF, BP, or CC of a gene/gene product is not known
*GOA proposed to remove ND annotations automatically from '''their''' curation database because this was not happening manually
**Note that curators can only update or remove annotations from their respective groups in Protein2GO
**Annotation from only a select set of evidence codes would result in automatic removal of ND annotations
ECO:0000269 (EXP) and its descendants

ECO:0006056 (HTP) and its descendants

ECO:0000250 (ISS) and its descendants

ECO:0000317 (IGC) and its descendants
*Generally agreed that when there is experimental or sequence-based evidence for a more granular annotation, the ND annotation should be removed
**However, 'protein binding' MF annotations are thought of differently by different groups and we need to reach a consensus about how these MF annotations should be considered wrt automatically removing existing MF ND annotations
*Proposal: as part of QC pipeline, alert groups to genes/gene products that have an ND annotation and also an annotation to a more granular term (any evidence code?)

=== PAINT Annotations ===
*Refresher on how PAINT annotations are created
*[https://github.com/geneontology/go-annotation/issues/2042 Doubled up IBA+EXP annotations (from Karen Christie)]
*[https://github.com/geneontology/go-annotation/issues/2049 PAINT:circular transfer of annotations]

=== Annotation Review ===
*84 open annotation review tickets
*Reminder to check go-annotation tracker tickets where your group has been assigned and finish up where you can
*Questions? Please add questions/comments to the individual tickets
*We can discuss questions on future calls, if needed

= Minutes =
*On call: David, Edith, George, Harold, Helen, Karen, Kimberly, Laurent-Philippe, Li, Liz, Marie-Claire, Michele, Midori, Pascale, Paul T., Sabrina, Shur-Jen, Seth, Stacia, Suzi A, Suzi L, Tanya, Tom, Stacia, Val

== Annotation Discussion ==
=== ND Annotations ===
*We discussed the proposal to automatically remove ND annotations from the GOA database when experimental annotations from another source are available.
*Generally, removing ND annotations once a suitable, more granular term can be assigned to a gene/gene product is standard practice.
*However, not all ND annotations in Protein2GO can be edited by all groups and having an automated mechanism for dealing with ND annotations that are no longer applicable is desirable.
**One sticking point, however, has been what constitutes an appropriate Molecular Function annotation for removing NDs to the root MF node, specifically wrt child terms in the 'binding' (GO:0005488) hierarchy of MF.
**Some groups do not consider annotations to 'protein binding' (GO:0005515) sufficient to otherwise remove an ND annotation to root MF; other groups do.
***Annotations to child terms of 'protein binding' (GO:0005515) are viewed differently, however, by some groups who feel that the more granular protein binding terms provide useful information.
**Some groups also view annotations to terms like 'ATP binding' (GO:0005524) suitable for supplanting an ND annotation to root MF.
*We discussed various options around this issue, e.g. handling the potentially contradictory information at the level of display, allowing binding annotations to supplant ND annotations, moving binding out from under MF and having it as a separate ontology.
*For now, the automatic removal of ND annotations in Protein2GO is on hold.
*ACTION ITEM: Kimberly will come up with more concrete proposals for the different options and we will discuss them and pick the best option.

=== PAINT Annotations ===
*We also discussed whether it is okay to include IBA annotations derived from PAINT curation when an experimental annotation that was used to create the IBA annotation exists for that gene product.
*Are these annotations circular or do they provide an additional level of QC that should also be captured?
*Note that during PAINT curation, propagation of an annotation to a given node does not require that there is experimental evidence for more than one leaf node, i.e. annotations may be propagated based on one experimentally supported annotation and a review of the overall conservation of family members.
*If we consider propagation from one experimental annotation plus family review a good form of QC, then do other forms of QC warrant inclusion in our annotation set and if so, what would the evidence code be?
*Should we just not allow propagation of annotations using IBA when there already exists an experimental annotation?
*We didn't reach a resolution on this yet, but further discussion is on [https://github.com/geneontology/go-annotation/issues/2042 Doubled up IBA+EXP annotations (from Karen Christie)]


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

Restoring an Obsolete Ontology Term

Fri, 09/07/2018 - 08:14

Pascale:

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

# Navigate to the obsolete term
# In the annotation window:
#* Modify the term label to remove 'obsolete'
#* Modify the term definition to remove 'OBSOLETE.'
#* Update the comment to Note that this term was reinstated from obsolete.
#* Remove any replaced_by and consider tags by clicking on the (x) at the right-hand side
#* Add Subclasses as appropriate
#* Remove the owl:deprecated: true tag
# Run the reasoner
# Save.

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

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

Ontology meeting 2018-09-10

Fri, 09/07/2018 - 06:34

David:

= 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===
The meeting will focus on (Depending on who can attend):
* creating good logical definitions in both a general context and in the context of the GO-Reactome-Rhea alignment
** Filling in missing GO-Rhea xrefs
** moving from reactions to biochemical pathways
** implementation of a method to keep in synch with all three resources
** GO-CAM templates for pathways??
* potential implementation of Design Patterns and the revival of some type of TermGenie ability
* GH ticket work and mini-project planning
** Dealing with and migrating binding terms
** Dealing with cellular processes (https://github.com/geneontology/go-ontology/issues/12849)
* Attendees
** David H (Can make it)
** Kimberly (Can make it)
** Karen
** Harold (Can make it)
** Pascale (Can make it)
** Barbara (Maybe make it)
** Alan B (Rhea, can make any day)
** Anne (Rhea, prefers Monday or Tuesday)
** Chris
** Peter D?
** Ben?
** Jim?

=== Tickets ===

OBI ticket: https://github.com/obi-ontology/obi/issues/963

=== Failures due to use in other ontologies ===
Friday after much discussion, Rachael and I tried to finally obsolete lamina reticularis. When we created the pull request, the Travis check failed due to the use of the term in Uberon. Do we really want this behavior? It will make us dependent on other ontologies to proceed with our work.

https://travis-ci.org/geneontology/go-ontology/builds/425727676?utm_source=github_status&utm_medium=notification
https://github.com/geneontology/go-ontology/pull/16345


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

= Minutes =
*On call:


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

Manager Call 2018-09-06

Tue, 09/04/2018 - 07:24

Pascale: /* New Project management strategy */



=Follow up from last week=

=New Project management strategy=
* We will use 'Project level projects'

* Product owner
* Tech lead
* Lead architect




== Feedback form update (UPDATED)==
https://github.com/geneontology/go-site/issues/750

Did we figure out the payment? No, still on my plate (Seth)

What's the time line for deployment? TBD, but pretty much instantaneous when done. (Seth)

== New GAF Submissions ==
SuziA: Update on documentation

== Ontology Editors' Meeting ==
Geneva- Week of December 10th

The meeting will focus on:
* creating good logical definitions in both a general context and in the context of the GO-Reactome-Rhea alignment
** Filling in missing GO-Rhea xrefs
** moving from reactions to biochemical pathways
** implementation of a method to keep in synch with all three resources
** GO-CAM templates for pathways??
* potential implementation of Design Patterns and the revival of some type of TermGenie ability
* GH ticket work and mini-project planning
* Attendees
** David H (Can make it)
** Kimberly (Can make it)
** Karen
** Harold (Can make it)
** Pascale
** Barbara (Maybe make it)
** Alan B (Rhea, can make any day)
** Anne (Rhea, prefers Monday or Tuesday)
** Chris
** Peter D?
** Ben?
** Jim?
Pascale: needed to follow up with Paul regarding funds to hold these

=Job descriptions for each role=
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.

* Please have a look.

=Fate of pre-composed terms=
* explicit binding terms
* compound terms between two existing GO classes


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

Internal email lists

Tue, 08/28/2018 - 10:50

Pascale: Created page with "GOC communicates internally via mailing lists. These are the links to request addition to the different mailing lists: * https://mailman.stanford.edu/mailman/listinfo/go-con..."

GOC communicates internally via mailing lists. These are the links to request addition to the different mailing lists:

* https://mailman.stanford.edu/mailman/listinfo/go-consortium
* https://mailman.stanford.edu/mailman/listinfo/go-council
* https://mailman.stanford.edu/mailman/listinfo/go-curator-tracker
* https://mailman.stanford.edu/mailman/listinfo/go-directors
* https://mailman.stanford.edu/mailman/listinfo/go-discuss
* https://mailman.stanford.edu/mailman/listinfo/go-friends
* https://mailman.stanford.edu/mailman/listinfo/go-helpdesk
* https://mailman.stanford.edu/mailman/listinfo/go-managers
* https://mailman.stanford.edu/mailman/listinfo/go-obodiff
* https://mailman.stanford.edu/mailman/listinfo/go-ontology
* https://mailman.stanford.edu/mailman/listinfo/go-quality
* https://mailman.stanford.edu/mailman/listinfo/go-refgenome
* https://mailman.stanford.edu/mailman/listinfo/go-software


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

Ontology meeting 2018-08-27

Sun, 08/26/2018 - 17:33

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
* Discuss GO-relevant tickets on these calls?

===Ontology Developers' workshop possibility===
* One meeting in December; proposal to have the meeting in Geneva the week of December 10th.
* Maybe we can take a day or two to also meet with Anne and/or Alan to discuss the Rhea alignment project.
*Attendees:
**Yes:Harold, Kimberly
**Maybe: Barbara
**No:

=== Tickets ===

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

= Minutes =
*On call:


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

PAINT database update pipeline

Fri, 08/24/2018 - 09:45

Debert: /* Import ontology */

==Import EXP files==

* File location:
http://geneontology.org/gene-associations/*.gaf.gz

==Import ontology==

* File location:
http://geneontology.org/ontology/go.obo

==Integration with existing PAINT annotations==

* Managing differences:
** Missing EXP evidence
** New exp evidence
(see for ex https://github.com/pantherdb/fullgo_paint_update/issues/10)
** Handling obsolete and merged terms
- obsolete terms:
a) has a 'replaced_by' tag -> replace to the new term
b) does not have a 'replaced_by' tag -> output message xxx
** etc ?


* List of messages for automatic changed: 'Comment' ('Update comment' in PAINT interface)
** What types of messages ? obsoletes, missing EXP... what else ?
* 'View omitted annotation information' -> generated on the fly ???
** What types of messages ? tree changes information (missing nodes) - what else ?

==Managing new PTHR versions==


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

GO-CAM Working Group Call 2018-08-28

Fri, 08/24/2018 - 07:07

Vanaukenk: Created page with "= Meeting URL = https://stanford.zoom.us/j/976175422 =Agenda= == Relations between MF and Input(s) == *has_input vs has_direct_input *Proposal: replace has_direct_input with..."

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

=Agenda=

== Relations between MF and Input(s) ==
*has_input vs has_direct_input
*Proposal: replace has_direct_input with has_input; obsolete has_direct_input
*Need to review has_input annotations to remove any extensions that are inconsistent with GO-CAM usage, i.e. an indirect or unknown proximity for an input
*Seth retrieved, as of 2018-07-31, [https://drive.google.com/drive/folders/1TlwrEM2KjAzxIYiCGg0_oicMOYfhiGou all MF annotations] that use has_input in annotation extensions.
**Initial review:
***used to capture a regulatory effect, e.g. protein kinase activator activity, when it was not known whether the effect was direct or indirect (e.g. expression of protein or complex X increases the activity of Y)
***used to capture a regulatory subunit whose presence is necessary for the activity to occur (e.g. cyclin-dependent protein kinase)
***used to capture an enzymatic activity when it was not known if the effect on a substrate was direct or indirect (e.g. caspase-dependent but not known if it was the caspase mutated)
***used to capture an enzymatic substrate where there wasn't also a direct binding assay in the paper (e.g. testing possible chemical substrates for glucuronysyltransferase activity)
***used to capture metal ion-dependence of protein binding (e.g. Ca2+-dependent protein binding)
***used (correctly) to capture the physiologically relevant input in a binding reaction (i.e. cross-species experiment where with/from captures experimental binding partner and AE the relevant binding partner)
*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]

== 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

== 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]

== Missing Property Chains ==
*We still need relation chains that allow us to capture that a gene involved in process 1 that is upstream of process 2 is upstream of process 2. For example:
**In mode (activity-centric):
***part of o causally upstream of -> causally upstream of
**In annotation file (gene-centric):
*** involved in o acts upstream of -> acts upstream of

== 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: Kimberly, Tanya, Chris G, Chris M, Dave F, Dmitry, Dustin, Edith, Giulia, Harold, Helen, Jim, Jennifer, Karen, Kevin M, Laurent-Philippe, Li, Liz, Marie-Claire, Nathan, Pascale, Petra, Rob, Sabrina, Seth, Shut-Jen, Stacia, Suzi L, Suzi A, Jae

== has_input vs has_direct_input ==
*has_input has been used in MF annotation extensions in different ways and we need to be consistent both within this relation as well as with the child relation has_direct_input























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

Extensions2GO-CAM

Thu, 08/23/2018 - 11:42

Paul Thomas: /* Simple conversions */

[[Category:GO-CAM]]
=Simple conversions=
These are relations that are essentially identical in extensions and GO-CAM
*If the aspect is F (column A)
**No more than one occurs_in(CC)
**No more than one occurs_in(CL)
**No more than one occurs_in(UBERON or EMAPA)
**No more than one has_input/has_direct_input(geneID or ChEBI)
**No more than one happens_during(BP)
**No more than one part_of(BP)
**No more than one has_regulation_target(geneID)
**No more than one activated_by(ChEBI)
**No more than one inhibited_by(ChEBI)
*If the aspect is C
**No more than one occurs_in(CC)
**No more than one occurs_in(CL)
**No more than one occurs_in(UBERON or EMAPA)
*If the aspect is P
**No more than one occurs_in(CC)
**No more than one occurs_in(CL)
**No more than one occurs_in(UBERON or EMAPA)
**No more than one has_input/has_direct_input(geneID or ChEBI)
**No more than one part_of(BP)
=has_regulation_target=
*GP-A [regulation of molecular function Z] has_regulation_target GP-B
**can be expressed as [GP-A]<-enabled_by-[ GO:0003674]-regulates->[molecular function Z]-enabled_by->[GP-B]
**The variations on this are all children of the term “regulation of molecular function” (GO:0065009). Variations are “positive regulation of MF Z”, which would be expressed with the positively_regulates relation instead; “negative regulation of MF Z”. **Note that MF Z should appear in the logical definition of the term “regulation of MF Z”, so you can get the GO ID from that.
*GP-A [regulation of transcription] has_regulation_target GP-B
**can be expressed as [GP-A]<-enabled_by-[GO:0003674]-regulates->[transcription]-has_input->[GP-B]
**These are all children of “regulation of transcription, DNA templated” (GO:0006351). Similarly to above, there are positive/negative variations, and you can get the specific GO ID for [transcription] from the logical definition. Paul Thomas
Categories: GO Internal