Web feeds

Inferred from Physical Interaction (IPI)

GO wiki (new pages) - 8 hours 24 min ago

Vanaukenk:

'''IPI: Inferred from Physical Interaction'''

*2-hybrid interactions
*Co-purification
*Co-immunoprecipitation
*Ion/protein binding experiments

Covers physical interactions between the entity of interest and another molecule (such as a protein, ion or complex). IPI can be thought of as a type of IDA, where the actual binding partner or target can be specified, using "with" in the with/from field.

Often it is difficult to tell from the evidence presented in a paper whether an interaction is direct or not. Any in vivo/cell lysate method always has the possibility of a third 'bridge' protein - there are many examples of this happening in, for example, yeast 2-hybrid experiments when yeast proteins have proven essential for interactions between two human proteins to occur. The only methods that show direct evidence of two proteins binding are when the two proteins have been isolated and pre-purified. Ideally, curators should only capture direct interactions however, it is acceptable to curate interactions even if it is not known whether they are direct or not.

Examples where the IPI evidence code should be used:

*Binding assays where it is possible to put an ID corresponding to the specific binding partner that was shown to interact with the entity being annotated should be annotated with the IPI code, not with IDA.
*Annotations to the GO term ‘binding’ (GO:0005488) or ‘protein complex' (GO:0043234), or their child terms, which are supported by the isolation of a complex by co-immunoprecipitation or pull-down assays may use IPI with the ID corresponding to the ‘antibody target' or ‘tagged' subunit in the with/from column.
*The GO term ‘protein binding’ (GO:0005515) should only be used with the evidence code IPI and an identifier in the ‘with’ field. A reciprocal annotation must also be made to indicate the interaction in the opposite direction.
*Annotations to Molecular Functions (except ‘catalytic activity’ GO:0003824 or its child terms, see below) or Biological Processes may be made using IPI and an entry in the ‘with/from’ field in order to indicate the inference that the annotated entity is involved in the process or function because it interacts with another entity that was shown experimentally to be involved in that process or function.

Examples where the IPI evidence code should not be used:

*The GO term ‘protein binding’ (GO:0005515) should not be used to describe an antibody binding to another protein. However, an effect of an antibody on an activity or process can support a function or process annotation, using the IMP code.
*Annotations to the GO term ‘binding’ (GO:0005488), or its child terms, which are supported by binding assays where it is NOT possible to put an ID corresponding to the specific binding partner that was shown to interact with the gene product being annotated should be annotated with the IDA code, not with IPI (see table 1).
*Annotations to the GO term ‘catalytic activity’ (GO:0003824), or its child terms, should not use the IPI evidence code. It is unlikely that enough information can be obtained from a binding interaction to support such an annotation.


'''Table 1. Example annotation where it is not possible to add the interacting partner.'''
{| class="wikitable" style="text-align:center"
{| border="1" cellpading="2"
|-
! DB Object ID !! DB Object Symbol !! GO ID !! DB:Reference !! Evidence Code !! With (or) From
|-
| MGI:2137706 || Actn1 || GO:0051015 (actin filament binding) || PMID:15465019 || IDA || -
|}

[http://wiki.geneontology.org/index.php/Guide_to_GO_Evidence_Codes Guide_to_GO_Evidence_Codes]

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

Inferred from Direct Assay (IDA)

GO wiki (new pages) - 8 hours 27 min ago

Vanaukenk: Created page with "'''IDA: Inferred from Direct Assay''' *Enzyme assays *In vitro reconstitution (e.g. transcription) *Immunofluorescence (for cellular component) *Cell fractionation (for cellu..."

'''IDA: Inferred from Direct Assay'''

*Enzyme assays
*In vitro reconstitution (e.g. transcription)
*Immunofluorescence (for cellular component)
*Cell fractionation (for cellular component)
*Physical interaction/binding assay (sometimes appropriate for cellular component or molecular function)

The IDA evidence code is used to indicate a direct assay was carried out to determine the function, process, or component indicated by the GO term. Curators therefore need to be careful, because an experiment considered as a direct assay for a term from one ontology may be a different kind of evidence for a term from another of the ontologies. In particular, there are more kinds of direct assays for cellular component than for function or process. For example, a fractionation experiment might provide "direct assay" evidence that a gene product is in the nucleus, but "protein interaction" (IPI) evidence for its function or process.

For transfection experiments or other experiments where a gene from one organism or tissue is put into a system that is not its normal environment, the annotator should use the author's intent and interpretation of the experiment as a guide as to whether IMP or IDA is appropriate. When the author is comparing differences between alleles, regardless of the simplicity or complexity of the assay, IMP is appropriate. When the author is using an expression system as a way to investigate the normal function of a gene product, IDA is appropriate.

Examples where the IDA evidence code should be used:

*Binding assays can provide direct assay evidence for annotating to the xxx binding molecular function terms. (Use IDA only when no identifier can be placed in the with/from column; when there is an appropriate ID for the with/from column, use IPI).
*Assays describing the isolation of a complex by immunoprecipitation of a tagged subunit should use IDA, not IPI. Thus this type of assay can provide IDA for annotation to a component term for the specific complex because it is a direct assay for a complex.
*Transfections into a cell line, overexpression, or ectopic expression of a gene when the expression system used is considered to be an assay system to address basic, normal functions of gene product even if it would not normally be expressed in that cell type or location. If the experiments were conducted to assess the normal function of the gene and the assay system is believed to reproduce this function, i.e., the authors would consider their experiment to be a direct assay, and not a comparison between various alleles of a gene, then the IDA code should be used. This is in contrast with a situation where overexpression affects the function or expression of the gene and that difference from normal is used to make an inference about the normal function; in this case use the IMP evidence code.

Examples where the IDA evidence code should not be used:

*Binding assays where it is possible to put an ID corresponding to the specific binding partner that was shown to interact directly the gene product being annotated should be annotated with the IPI code, not with IDA.
*Transfection into a cell line, overexpression, or ectopic expression of a gene where the effects of various alleles of a gene are compared to each other or to wild-type. For this type of experiment, annotate using IMP.

[http://wiki.geneontology.org/index.php/Guide_to_GO_Evidence_Codes Guide_to_GO_Evidence_Codes]

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

Inferred from Experiment (EXP)

GO wiki (new pages) - 8 hours 34 min ago

Vanaukenk:

'''EXP: Inferred from Experiment'''

This code is used in an annotation to indicate that an experimental assay has been located in the cited reference, whose results indicate a gene product's function, process involvement, or subcellular location (indicated by the GO term). The EXP code is the parent code for the IDA, IPI, IMP, IGI and IEP experimental codes.

The EXP evidence code can be used where any of the assays described for the IDA, IPI, IMP, IGI, or IEP evidence codes is reported. However it is highly encouraged that groups should annotate to one of the more specific experimental codes (IDA, IPI, IMP, IGI, or IEP) instead of EXP, and all curators directly involved in the GO Reference Genome annotation effort are obliged to use these and not EXP.

The EXP code exists for groups who would like to contribute high-quality GO annotations that are produced from directly associating GO terms to gene products by citing experimental published results, but where the group is unable to fit the appropriate specific experimental GO evidence code to each annotation.

A published reference should always be cited in the reference column, and no value should be entered into the with/from column of EXP annotations.

[http://wiki.geneontology.org/index.php/Guide_to_GO_Evidence_Codes Guide_to_GO_Evidence_Codes]


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

Guide to GO Evidence Codes

GO wiki (new pages) - 8 hours 53 min ago

Vanaukenk:

*These guidelines are a guide to standard usage of the GO evidence codes.
*Annotators may also find the evidence code decision tree useful in selecting the correct evidence code for an annotation.

= Introduction =
A GO annotation consists of a GO term associated with a specific reference that describes the work or analysis upon which the association between a specific GO term and gene product is based. Each annotation must also include an evidence code to indicate how the annotation to a particular term is supported. Although evidence codes do reflect the type of work or analysis described in the cited reference which supports the GO term to gene product association, they are not necessarily a classification of types of experiments/analyses. Note that these evidence codes are intended for use in conjunction with GO terms, and should not be considered in isolation from the terms. If a reference describes multiple methods that each provide evidence to make a GO annotation to a particular term, then multiple annotations with identical GO identifiers and reference identifiers but different evidence codes may be made.

Out of all the evidence codes available, only Inferred from Electronic Annotation (IEA) is not assigned by a curator. Manually-assigned evidence codes fall into four general categories: experimental, computational analysis, author statements, and curatorial statements.

Use of an experimental evidence code in a GO annotation indicates that the cited paper displayed results from a physical characterization of a gene or gene product that has supported the association of a GO term. The Experimental Evidence codes are:

*[[Inferred from Experiment (EXP)]]
*[[Inferred from Direct Assay (IDA)]]
*[[Inferred from Physical Interaction (IPI)]]
*[[Inferred from Mutant Phenotype (IMP)]]
*[[Inferred from Genetic Interaction (IGI)]]
*[[Inferred from Expression Pattern (IEP)]]

High throughput (HTP) evidence codes may be used to make annotations based upon high throughput methodologies. Use of HTP evidence codes should be carefully considered and follow the GOC's guidelines for their use.

*Add list of HTP evidence codes here

Use of the computational analysis evidence codes indicates that the annotation is based on an in silico analysis of the gene sequence and/or other data as described in the cited reference. The evidence codes in this category also indicate a varying degree of curatorial input. The Computational Analysis evidence codes are:

*[[Inferred from Sequence or structural Similarity (ISS)]]
*[[Inferred from Sequence Orthology (ISO)]]
*[[Inferred from Sequence Alignment (ISA)]]
*[[Inferred from Sequence Model (ISM)]]
*[[Inferred from Genomic Context (IGC)]]
*[[Inferred from Biological aspect of Ancestor (IBA)]]
*[[Inferred from Biological aspect of Descendant (IBD)]]
*[[Inferred from Key Residues (IKR)]]
*[[Inferred from Rapid Divergence(IRD)]]
*[[Inferred from Reviewed Computational Analysis (RCA)]]

Author statement codes indicate that the annotation was made on the basis of a statement made by the author(s) in the reference cited. The Author Statement evidence codes used by GO are:

*[[Traceable Author Statement (TAS)]]
*[[Non-traceable Author Statement (NAS)]]

Use of the curatorial statement evidence codes indicates an annotation made on the basis of a curatorial judgement that does not fit into one of the other evidence code classifications. The Curatorial Statement codes are:

*[[Inferred by Curator (IC)]]
*[[No biological Data available (ND) evidence code]]

All of the above evidence codes are assigned by curators. However, GO also used one evidence code that is assigned by automated methods, without curatorial judgement. The Automatically-Assigned evidence code is:

*[[Inferred from Electronic Annotation (IEA)]]

Evidence codes are '''not''' statements of the quality of the annotation. Within each evidence code classification, some methods produce annotations of higher confidence or greater specificity than other methods, in addition the way in which a technique has been applied or interpreted in a paper will also affect the quality of the resulting annotation. Thus evidence codes '''cannot''' be used as a measure of the quality of the annotation.



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

GO-CAM November 22, 2017

GO wiki (new pages) - Mon, 11/20/2017 - 08:52

Vanaukenk: Created page with "= Zoom URL = = Agenda = = Minutes = *On call: Category: Annotation Working Group"

= Zoom URL =

= Agenda =

= Minutes =
*On call:



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

Ontology meeting 2017-11-20

GO wiki (new pages) - Fri, 11/17/2017 - 10:41

Vanaukenk: /* Editors Discussion */

= Conference Line =

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

= Agenda =
== Documentation on Asserted Parents ==
*Deleting asserted parents was already included in the section on [https://github.com/geneontology/go-ontology/blob/master/docs/CreateNewTerm.md CreateNewTerm].
*Does it need to be somewhere else?
*Is it not clear enough?
==GH project link==
https://github.com/geneontology/go-ontology/projects/1

== Editors Discussion ==
*[https://github.com/geneontology/go-ontology/issues/14579 GO:0043683 type IV pilus biogenesis parentage]
**cellular component assembly vs biogenesis vs morphogenesis - any guidelines for deciding when to instantiate which terms?

= Minutes =
*On call:





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

Publications, Talks, Posters 2017

GO wiki (new pages) - Fri, 11/17/2017 - 07:45

Hdrabkin: Publications

Roncaglia P, van Dam TJP, Christie KR, Nacheva L, Toedt G, Huynen MA, Huntley RP, Gibson TJ, Lomax J. The Gene Ontology of eukaryotic cilia and flagella. Cilia. 2017 6:10. https://doi.org/10.1186/s13630-017-0054-8 Hdrabkin
Categories: GO Internal

Grant Progress reports 2017

GO wiki (new pages) - Fri, 11/17/2017 - 07:26

Hdrabkin: Catagory:Reports

== Subcontract Projects ==
===Infrastructure===

[[Berkely Software Infrastructure]] This is linked to 2015; rename to begin new


===MOD Annotation Groups===
[http://wiki.geneontology.org/images/3/39/MODProgressReportTemplate_2008.doc MOD template]

[[MGI December 2017]

[[WormBase December 2017]]

[[EcoliWiki December 2017]]

[[RGD December 2017]]

[[dictyBase December 2017]]

[[FlyBase December 2017]]

[[TAIR December 2017]]

[[GOA December 2017]]

[[PomBase_December 2017]]

[[SGD_December 2017]]

[[UCL_December 2017]]

[[ZFIN_December 2017]] Hdrabkin
Categories: GO Internal

Annotation Conf. Call 2017-11-28

GO wiki (new pages) - Wed, 11/15/2017 - 12:42

Vanaukenk: Created page with "= Meeting URL = *https://stanford.zoom.us/j/976175422 = Agenda = == Guidelines for Annotation Display == == Signaling Project == *Review of cAMP-related signaling and biosynt..."

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

= Agenda =
== Guidelines for Annotation Display ==
== Signaling Project ==
*Review of cAMP-related signaling and biosynthesis terms



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

Manager Call 2017-11-15

GO wiki (new pages) - Mon, 11/13/2017 - 02:18

Pascale: Created page with " PanTree IDs in 'with' column https://github.com/geneontology/go-annotation/issues/1673 Category: GO Managers Meetings"





PanTree IDs in 'with' column
https://github.com/geneontology/go-annotation/issues/1673



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

Ontology meeting 2017-11-13

GO wiki (new pages) - Fri, 11/10/2017 - 08:35

Vanaukenk: Created page with "= Conference Line = *Zoom: https://stanford.zoom.us/j/828418143 = Agenda = * Logical definition vs. asserted terms (Pascale): I have been removing SubClasses when they are..."

= Conference Line =

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

= Agenda =

* Logical definition vs. asserted terms
(Pascale): I have been removing SubClasses when they are redundant with the logical definition. But in some releases of the ontology they are not added back. Would it be safer to always assert both?
See for example: GO:0015603 - I would have removed the SubClasses.

==GH project link==

https://github.com/geneontology/go-ontology/projects/1


==Discussion==
*On call:



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

2017-11-08

GO wiki (new pages) - Wed, 11/08/2017 - 11:54

David:

= Agenda =

== Ontology ==
*Managing tickets, training, editors' calls for November
*Reviewing minimal information for new term requests
**https://github.com/geneontology/go-ontology/blob/master/CONTRIBUTING.md

== Annotation ==
*transport do not annotate
**[https://github.com/geneontology/go-annotation/issues/1648 improving specificity by banning high level terms]
*HTP data
**[https://github.com/geneontology/go-annotation/issues/1655 Review HTP annotations]
*signaling workshop follow-up
*Noctua/GO-CAM
**groups in users.yaml



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

GO-CAM November 8th, 2017

GO wiki (new pages) - Tue, 11/07/2017 - 12:46

Vanaukenk: /* Minutes */

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

= Agenda =

== Noctua GitHub Organization ==
*Using projects to organize tickets
*Using milestones for ticket prioritization

== Requirements/Roadmap ==
[[https://docs.google.com/document/d/1dfPnt8fHtO3gP9Xr76SUF90aiDtT3K_2KqhanMFfsXo/edit Noctua Requirements/Roadmap]]

== GPAD Outputs ==
*[https://github.com/geneontology/noctua/issues/500 GPAD missing annotations via 'causally upstream of'?]
*[http://noctua.berkeleybop.org/editor/graph/gomodel:59bee34700000110 TEST: causally upstream of - KRC]
*With Chris, Jim, and Karen out for today's call, I suggest that we take up these issues again on the next GO-CAM call on November 8th

*ACTION ITEM: on a future GO-CAM call, review the Inference Explanations for some models

== Attribution ==
[https://github.com/geneontology/noctua/issues/458 Attribution with GO-CAM exports to GOC annotation files]

== Simple Annoton Editor ==

[https://github.com/geneontology/noctua/issues/492 dealing with blank MF in the simple annoton editor]

[https://github.com/geneontology/simple-annoton-editor/issues/12 Extend form to include standard GO-CAM model fields]

[https://github.com/geneontology/simple-annoton-editor/issues/10 Bare MF annotation should generate part-of triples]

*Editor enhancements to come:
**Ability to add basic set of annotation extensions, e.g. has_input for an MF
**Ability to just add a CC annotation and get the resulting part_of annotation in the graphical interface

= Minutes =
*On call:




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

2017 November Berkeley Noctua Developers Meeting

GO wiki (new pages) - Mon, 11/06/2017 - 12:49

Cjm: Created page with " = Agenda (Draft) = = Logistics = == Accommodations == You can get the lab rate and any of these hotels: * http://travel.lbl.gov/air_car_hotel/preferred_hotels.html * Clos..."


= Agenda (Draft) =

= Logistics =

== Accommodations ==

You can get the lab rate and any of these hotels:

* http://travel.lbl.gov/air_car_hotel/preferred_hotels.html
* Closest hotel: http://www.fourpointssanfranciscobaybridge.com/ -- However, it is still 30 mins walk away
* The most pleasant option is to stay in downtown berkeley and get the lab shuttle in the morning. Others may be staying here: http://www.senshotelberkeley.com
* Non-lab employees may want to look on airbnb

== Parking ==

Park temporarily and grab a parking pass from the person at the gate, you can then park in the garage:

* http://biosciopsatberkeley.lbl.gov/location/aquatic-park-office/

== Meeting Location ==

[http://biosciopsatberkeley.lbl.gov/location/aquatic-park-office/ Berkeley Lab, Aquatic Park Offices]

Lawrence Berkeley National Laboratory (LBNL), Aquatic Park office of Biosciences Operations at Berkeley
Physical address: 717 Potter Street, Berkeley, CA 94710

Meeting room: room 181

=== Travel between hotel and meeting ===

* [https://www.google.com/maps/dir/Four+Points+by+Sheraton+San+Francisco+Bay+Bridge,+Powell+Street,+Emeryville,+CA/717+Potter+St,+Berkeley,+CA+94710/@37.8448697,-122.3011831,15z/data=!3m1!4b1!4m14!4m13!1m5!1m1!1s0x80857e44a03ff3e3:0xc502416c1c31eb3a!2m2!1d-122.2939195!2d37.8381923!1m5!1m1!1s0x80857ef68fea8821:0xeaa3c4e92d0ec6a9!2m2!1d-122.294537!2d37.85145!3e2 Walk, 1.3 miles]
* [https://www.google.com/maps/dir/Four+Points+by+Sheraton+San+Francisco+Bay+Bridge,+Powell+Street,+Emeryville,+CA/717+Potter+St,+Berkeley,+CA+94710/@37.8450306,-122.3024045,15z/am=t/data=!4m14!4m13!1m5!1m1!1s0x80857e44a03ff3e3:0xc502416c1c31eb3a!2m2!1d-122.2939195!2d37.8381923!1m5!1m1!1s0x80857ef68fea8821:0xeaa3c4e92d0ec6a9!2m2!1d-122.294537!2d37.85145!3e3 Free Hollis Shuttle ]
* Taxi/Lyft/Uber

Aim to be at the lab for 9.30am



== Participants ==

USC:

*Tremayne Mushayahama
*Anushya?

LBL:

* Chris Mungall
* Eric Douglass
* Seth Carbon
* HyeongSik Kim
* Suzi Lewis


[[Category:Meetings]]
[[Category:Protege]] Cjm
Categories: GO Internal

Annotation Conf. Call 2017-11-14

GO wiki (new pages) - Mon, 11/06/2017 - 09:25

Vanaukenk: Created page with "= Meeting URL = *https://stanford.zoom.us/j/976175422 = Agenda = == Ontology Term Requests == *Refresher on information required for term requests: **Term name **Parents **Te..."

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

= Agenda =
== Ontology Term Requests ==
*Refresher on information required for term requests:
**Term name
**Parents
**Term definition
**Reference(s)
*If you need help with parentage or definitions, the ontology editors can help with this, but please make a first-pass at parentage and defs to help expedite the ticket.
== Annotation QC ==
* Manual annotation to uninformative high-level terms is strongly discouraged
** See: [https://github.com/geneontology/go-annotation/issues/1648 improving specificity by banning high level terms #1648]
** For example: direct annotation to 'transport' (GO:0006810) is one case where a more specific annotation can likely be made
** In AmiGO, there are 53 experimentally supported annotations to 'transport'.
** Can groups check these annotations to see if a more granular term is appropriate?
** Annotations according to group:
(8) EcoCyc
(7) EcoliWiki
(7) MGI
(7) PseudoCAP
(6) SGD
(5) UniProt
(4) BHF-UCL
(3) RGD
(3) TAIR
(2) GR
(1) SynGO
* PomBase has a list of >1300 high-level terms that have a 'do not manually annotate' flag
* The proposal is to work through this list so annotations are consistent amongst all GOC members

== Ontology Updates ==
*Pascale:
** [https://github.com/geneontology/go-ontology/projects/7 Transcription factor activity refactor]
** Molecular Function terms describing 'transcription factors'
** See: [https://github.com/geneontology/go-ontology/issues/13588 Make parent term for transcription factor activity]
** See: [https://github.com/geneontology/go-annotation/issues/1668 Transcription factor branch refactoring: overview of annotations of TFIIIC and TFIIB complexes]

== GOC Meetings Cambridge ==
*Review key action items from signaling workshop and GOC meeting
**[https://docs.google.com/document/d/1Y9_Mvqes3op36TPHgfaS7K5FHnGZLgUApghIFYyUKR8/edit GOC Cambridge 2017 Meeting Minutes]
** Focus on annotation to signaling pathways
*** [https://drive.google.com/drive/u/0/folders/0B7bEr6HANSlGQmlCYm5VRHNMNW8 Folder on Google drive for signaling pathways working group]
*** [https://docs.google.com/document/d/1wCzCkPL9ft20ZP5XnTn8IQAcxoFEduaBmzVWKN0hbU0/edit Signaling Workshop Meeting Minutes]
*** [https://github.com/geneontology/go-annotation/issues/1597 How to name specific MAPK pathways]
*** [https://github.com/geneontology/go-ontology/issues/14275 NTR: “receptor ligand agonist activity” and “receptor ligand antagonist activity”]
*** [https://github.com/geneontology/go-ontology/issues/13912 MP cell surface receptor signaling pathway]
** Adoption of expanded set of BP relations
** Review use of contributes_to and colocalizes_with
** Noctua into full production mode
*** Meetings on second and fourth Wednesdays at 8am PST to discuss issues
** Representation of protein complexes, and their constituent members, in GO and GO-CAM models
*** [https://drive.google.com/drive/u/0/folders/0B7bEr6HANSlGTTJfbXY4OUxUU1k Folder on Google drive for protein complexes working group]
*** [https://github.com/geneontology/go-annotation/issues/1662 inferring MFs from annotations to complex portal IDs to individual complex participants]
***[https://github.com/geneontology/go-annotation/issues/1661 Protein complex representation in Noctua]
** Review HTP annotations
*** [https://github.com/geneontology/go-annotation/issues/1655 Review HTP annotations]
***[https://docs.google.com/document/d/1ScIeclAzUXMe-tU6n0lVfsSwMHpOeNb7uK8On9-iKXc/edit Draft of HTP guidelines]
*** [https://docs.google.com/spreadsheets/d/11xExGJfj_39xPQUGkam3Xvtd6dtZ5DfANXhM2ZtDYB0/edit#gid=0 HTP data currently in GO]

= Minutes =
*On call:

== Annotation QC ==
* Action Item: Need curators to review experimental annotations to 'transport'
* Report back on any annotations that can't reasonably be transferred to a more granular term
* We will continue to look at the PomBase list and prioritize additional flags and error checks

== Ontology Updates ==
* Will merge DNA binding transcription factor activity into nucleic acid binding transcription factor activity
* Goal: trying to more easily distinguish 'general' transcription factors (generally only described wrt pol II TFs) from specific, regulatory TFs
* Pascale will tag groups/people if annotations need review
* Pascale, Karen, Paul T. will discuss further

== GOC Cambridge Meetings ==
=== Signaling Pathways ===
* Will follow-up on signaling workshop with items using the go-annotation tracker
=== HTP Evidence Codes ===
* Helen will finish updating guidelines
* How doe the HTP evidence codes map up to existing GO evidence codes?
** They are in a separate branch, although still experimental.



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

Ontology meeting 2017-11-06

GO wiki (new pages) - Fri, 11/03/2017 - 06:32

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 ==Discussion==..."

= Conference Line =

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

= Agenda =



==GH project link==

https://github.com/geneontology/go-ontology/projects/1


==Discussion==




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

Ontology meeting 2017-11-03

GO wiki (new pages) - Wed, 11/01/2017 - 09:39

Pascale:

= Conference Line =

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

= Agenda =



==GH project link==

https://github.com/geneontology/go-ontology/projects/1


==Discussion==

===DOS patterns - what are the next steps?===
https://github.com/geneontology/go-ontology/issues/14473
* What's already implemented ? For eg, if you change a DOS pattern, will it propagate in the ontology?
* How will we keep track of changes ? Will the DOS patterns get an identifier ?



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

2018 NYU GOC Meeting Agenda

GO wiki (new pages) - Wed, 11/01/2017 - 09:04

Pascale: Created page with " == Suggestions for topics== 'Response to' workshop (similar to the signaling WS) Category:Meetings"


== Suggestions for topics==
'Response to' workshop
(similar to the signaling WS)


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

Biological Process

GO wiki (new pages) - Wed, 10/25/2017 - 11:48

Vanaukenk:

= Biological Process Annotation Guidelines =

== Do I annotate to the process or regulation of the process? ==


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

Ontology meeting 2017-10-27

GO wiki (new pages) - Wed, 10/25/2017 - 11:37

Vanaukenk: Created page with "= Conference Line = *Zoom: https://stanford.zoom.us/j/828418143 = Agenda = == Should we pick a different time for this meeting? == == Feedback from Barbara == == Compound..."

= Conference Line =

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

= Agenda =

== Should we pick a different time for this meeting? ==

== Feedback from Barbara ==

== Compound Functions and Multiple Parentage ==

https://github.com/geneontology/go-ontology/issues/14161

==GH project link==

https://github.com/geneontology/go-ontology/projects/1


==Discussion==
*On call:



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