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Ontology meeting 2018-04-16

GO wiki (new pages) - Mon, 04/16/2018 - 03:13

Pascale: 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 ==
* Who maintains the slims ? Is there any documentation anywhere about this, or should we start from scratch ?
* Should we have rules that remove slims that are taxonomically incorrect ? for eg synaptic vesicle transport (GO:0048489) was in the prok subste (https://github.com/geneontology/synapse)/issues/214


= Minutes =
*On call:



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

Directly negatively regulates

GO wiki (new pages) - Fri, 04/13/2018 - 10:50

Vanaukenk: /* Examples of Usage */

== Overview ==
=== Definition ===
Process(P1) directly negatively regulates process(P2) iff: P1 negatively 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 negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2.
=== Child Terms ===

== Examples of Usage ==
'''Example 1. Identification of ligands for DAF-12 that govern dauer formation and reproduction in C. elegans.'''

This is an example of one subfunction encoded within a gene product directly negatively regulating another subfunction encoded within the same gene product.

[https://www.ncbi.nlm.nih.gov/pubmed/16529801 PMID:16529801]

'''Summary of the paper:'''

INTRO

Nuclear receptors are a class of transcriptional regulators whose activity is modulated by ligand binding. Nuclear receptors contain DNA binding and hormone binding domains. "A hallmark of nuclear receptor agonists is their ability to diametrically regulate interactions with corepressors and coactivators." This paper investigates the ligand binding properties of the C. elegans nuclear receptor, DAF-12, and how ligand binding affects its interaction with a corepressor.

RESULTS

Figure 6. DAF-9 Metabolites of 4-Cholesten-3-One and Lathosterone Bind DAF-12 as High Affinity Ligands

Figure 5. 25(S),26-3-Keto-4-Cholestenoic Acid Functions as a Classical Nuclear-Receptor Ligand

ANNOTATIONS

[GO:1902051] (25S)-Delta(4)-dafachronate binding is enabled by DAF-12

[GO:1902051] (25S)-Delta(4)-dafachronate binding directly negatively regulates [GO:0001226] RNA polymerase II transcription corepressor binding enabled by DAF-12 that has input DIN-1S (WB:WP:CE03148)

http://noctua.berkeleybop.org/editor/graph/gomodel:5a7e68a100001875

== Quality Control Checks ==

== Relations Ontology ==

[https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0002630 directly negatively regulates]

== Review Status ==

Last reviewed: April 13, 2018

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

2018 NYU SAB Meeting Logistics

GO wiki (new pages) - Wed, 04/11/2018 - 12:34

Peterd: /* Meeting site */

=The SAB meeting will be held on May 15th.=

=Meeting site=
Translational Research Building, 227 East 30th Street, in the Murray Hill neighborhood of Manhattan. You'll need an official ID (passport, driver's license) to get into the building; Take the elevator to the 7th floor; go through the glass doors. The meeting will be in room 718, in front of you.

=Travel=
Kennedy and Newark Airports both are workable for long-distance flights; Kennedy is somewhat more convenient. LaGuardia Airport is closest to Manhattan but is accessible only by taxi or ride-sharing, or by incredibly inconvenient public transportation.
==[https://www.jfkairport.com/#/ Kennedy Airport] details==
You can get into Manhattan by taxi (up to four people can share a cab for a flat fare plus tolls and tip), or ride-sharing (Uber, Lyft, etc.), or by public transportation, which is fast (about an hour) and cheap ($7.75 per person). Here's how to do it: follow the signs in the terminal to the [https://www.jfkairport.com/#/to-from-airport/air-train AirTrain]. Take an AirTrain to Jamaica. To get off the AirTrain platform, you'll need to buy a MetroCard from a vending machine. If you'll be using the card only to travel to and from the airport, put $15.50 on the card; more if you'll be using the subway to get around New York ($2.75 per ride). Once you're off the AirTrain platform in Jamaica, follow the signs past the Jamaica Long Island Train station (overpass) to an elevator to the subway. Swipe your card again to get into the subway, and take an "E" train in the direction of Manhattan / World Trade Center. At Lexington Avenue / 53rd Street, get off the "E" train and follow the signs to transfer to a "6" train going downtown to Brooklyn Bridge / City Hall. Ride two stops to 33rd Street. Go up to the street (Park Avenue South), walk on Park Avenue South to 37th Street, turn left, walk one block to Lexington Avenue, and the Shelburne Hotel will be on your left on the far side of the street. If you're less adventurous, you can instead take the Long Island Railroad train from Jamaica to Penn Station (buy ticket from vending machine before getting on the train), and walk from Penn Station to the hotel.
==[https://www.newarkairport.com/#/ Newark Airport] details==
You can get into Manhattan by taxi or ride-sharing, or by public transportation, which takes longer and costs more than it does from Kennedy but is still reliable. Follow signs in the terminal to the [https://www.newarkairport.com/#/to-from-airport/air-train air-train]. There's only one choice; it takes you to the Newark Airport Station for Amtrak and New Jersey Transit. From a vending machine, get a combined one-way ticket that will allow you to get off the air-train platform and on to a New Jersey Transit train into New York Penn Station. (Amtrak trains are much more expensive and, for this trip, hardly faster.)

==[http://laguardiaairport.com/ LaGuardia Airport] details==
There is no good public transportation from LaGuardia Airport into Manhattan. Use a taxi (up to four people can share for the same fare) or ride-sharing service.

==By train==
Amtrak Northeast Corridor trains (Boston - New York - Washington) all stop at Penn Station as do the Long Island Railroad train from Kennedy / Jamaica or the New Jersey transit train from Newark. To get from Penn Station to the hotel, follow signs inside the station to 7th Avenue. You'll go up a long flight of stairs or escalator to leave the station and come upon a taxi queue. Take a taxi to the hotel or cross 7th Avenue and walk away from the station on 32nd Street until you get to Lexington Avenue, then turn left and walk to 37th Street to get to the hotel (0.8 mile, about 20 minutes per Google).

==By car==
Try not to. Manhattan is incredibly congested (average speed achieved by cars on weekdays is 4.7 miles per hour) and parking anywhere near the meeting site is incredibly expensive.

=Accommodations=
USC is taking care of booking rooms for the SAB members.
For information: New York is a large, busy city with many hotels but mid-May is a popular time (graduation week for many local universities). We have a block of rooms at the [[media:Shelburne Hotel Brochure.pdf | Shelburne NYC]] (a 10 minute half-mile walk from the meeting venue, comfortable, and very convenient to public transportation). They will only hold rooms until April 6, so book early. Rooms have been reserved for arrival on Friday May 11 and departure on Monday May 14 or Tuesday May 15. You can book a room online [https://gc.synxis.com/rez.aspx?Hotel=10146&Chain=5158&Dest=NYC&shell=2014GCF&group=1805NYUMEDI here] or by phone at 866-233-4642 - identify yourself as part of the GO Consortium (NYU Medical) Room Block (block code 1805NYUMEDI) to guarantee the special rate. The room rate is $289 nightly ($249 + taxes), a very good rate for a room with free WiFi and private bath.

*'''note: people should book at this hotel rather than at a separate one since we have a block booking'''

*'''note: if you have any difficulty making your hotel booking, contact megan.wiley@denihan.com with a cc to Peter D'E (deustp01@med.nyu.edu) immediately for help'''

=Attendees=
Please add your name to the table if you intend to attend the meeting, and the GOC dinner (Sunday), and the SAB dinner (Monday) so we can get a headcount estimate.

{| {{Prettytable}} class='sortable'
|-
! Name
! Organization
! Attend the GOC meeting?
! Attend the GOC dinner?
! Attend the SAB dinner?
|-
| Paul Thomas
| USC
| Yes
| Yes
| Yes
|-
| Suzanna Lewis
| GO@LBNL
| Yes
| Yes
| Yes
|-
|Judy Blake
| MGI/GOC
| Yes
| Yes
| Yes
|-
|Mike Cherry
| SGD Stanford
| Yes
| Yes
|
|-
|Chris Mungall
|LBNL
|Yes
|Yes
|
|-
| David Hill
| MGI/GOC
| Yes
| No

|-
|Kimberly Van Auken
|WormBase, Caltech
|Yes
|Yes
|
|-
| Pascale Gaudet
| USC/SIB
| Yes
| Yes
|
|-
|}


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

GO-CAM Noctua Call 2018-04-11

GO wiki (new pages) - Tue, 04/10/2018 - 15:38

Vanaukenk: /* Derived GPAD Output */

= Meeting URL =
*https://stanford.zoom.us/j/679970729

= Agenda =
== Progress Towards Noctua 1.0 Release ==
*[https://github.com/orgs/geneontology/projects/6 Review of github tickets for Noctua 1.0]

== Simple Annoton Editor ==
*Review tickets on [https://github.com/geneontology/simple-annoton-editor/issues github tracker]
*https://github.com/geneontology/simple-annoton-editor/issues/45
*https://github.com/geneontology/simple-annoton-editor/issues/37
*https://github.com/geneontology/simple-annoton-editor/issues/32
*https://github.com/geneontology/simple-annoton-editor/issues/53

== Annotation SOPs ==
*https://github.com/geneontology/noctua/issues/552

== Derived GPAD Output ==
*[https://github.com/geneontology/minerva/issues/109 Causal relations in GPAD output]
*Annotation extensions to include

== Annotation Templates ==
*We need to give curators templates of common biological processes so we can get consistent annotation
*Examples:
**Transcription
*Do we need a separate working group for this?

= Minutes =
*On call:

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

Ontology meeting 2018-04-09

GO wiki (new pages) - Mon, 04/09/2018 - 01:44

Pascale: 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 ==
* '''Checking other ontologies before obsoleting terms'''
(Pascale)
Looks like many terms are used in other ontologies, even the most unlikely ones:
http://www.ontobee.org/search?ontology=&keywords=protein+phosphorylation+involved+in+mitotic+spindle+assembly&submit=Search+terms
Can we send an email to obo foundry to ask that people monitor our tracker if changes in GO impact them ? Otherwise this involves a lot of overhead for us.


= Minutes =
*On call:






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

Experiment-Specific Annotation Guidelines

GO wiki (new pages) - Fri, 04/06/2018 - 13:58

Vanaukenk:

=== Chromatin Immunoprecipitation ===

=== Immunofluorescence ===

=== Data Not Shown ===


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

Manager Call 2018-04-19

GO wiki (new pages) - Wed, 04/04/2018 - 09:13

Suzialeksander:

[[Category:GO Managers Meetings]]

= Agenda =
== NYC Meeting Agenda ==
*Start working on the agenda in more details
**https://github.com/geneontology/go-ontology/milestone/5
**https://github.com/geneontology/go-annotation/milestone/2
**Use cases: Should we add this to the agenda? What would be a productive way of discussing this topic? https://docs.google.com/document/d/104m4jUNjPH9pCpskg8E29Zm2pLHhPFmKyIFLa9l_EOQ/edit
*SAB agenda, plans
== Working Groups/Projects ==
=== HTP Codes ===
==== RCA Evidence Code ====
*Need to work with several groups to review their annotations:
**Gramene (35815 annotations)
**As an example, 2929 RCA Molecular Function annotations
***Date: 20060831
***Reference: [http://archive.gramene.org/db/literature/pub_search?ref_id=8030 GR_REF:8030]
***Manual review of mappings; can we suggest [http://wiki.geneontology.org/index.php/Inferred_from_Sequence_Model_(ISM) ISM]?
**GeneDB
***Some annotations from reviews, but some to papers that describe a systems analysis that is probably more in line with the original intent of RCA
***RCA -> CCA (combined computational analysis)??
**EcoCyc
**AgBase
**AspGD
**PAMGO_MGG
*If we decide to keep RCA, then we'd need to remove the one-year limit; it doesn't make sense.

=== Documentation ===
=== Working Group Meetings ===
*Quarterly?
**Rotate between ontology and annotation (small, focused groups)
**Test virtual meetings, but still focused on the task

== Noctua ==
=== 1.0 Rollout ===
* Merge Tremayne's fork with Noctua-dev for further testing
* Some outstanding issues on SAE
* Single source file for MODs to consume
=== Reactome Imports ===
*David, Kimberly have looked at some imports/translations
*Ben's work looks to be potentially very useful and promising for seeding templates, models
*Will probably require significant manual input, refinement, testing
=== End User Tools ===
*What plans do we have for implementing consumption and display of GO-CAM models?
*How does the AGR GO working group fit into this task?
*https://github.com/geneontology/noctua/issues/519

== GO Helpdesk ==
Discuss this ticket: https://github.com/geneontology/go-site/issues/584

== Ontology ==
===Announcing changes to the wider user community===
* This was brought up by Birgit in the protein complex merge ticket - she was suggesting we make an announcement. However we never made annoucements before (except for obsoletions); should we start? What would be the guidelines? For example when a merge affects more than 100, 1000 annotations ? EXP only ?
* Pascale: changes to definitions of root terms: https://github.com/geneontology/go-ontology/issues/14899; isn't this a big change ? How should we notify people?
** Should we create a label in GH 'Major change', so we can easily pull out the tickets and show them at Ontology and Annotation calls ? (perhaps in annual reports as well)
* Pascale: suggestion: create a new label 'major change' and announce them either on twitter and/or on the website as user stories (or whatever it's called).


= Minutes = Suzialeksander
Categories: GO Internal

Annotation Conf. Call 2018-04-11

GO wiki (new pages) - Mon, 04/02/2018 - 14:49

Vanaukenk: Created page with "= Agenda = == GOC Meeting, NYU, New York, NY, May 12-14th == *Reminder to register, and reserve your hotel room before April 6th if staying at the Shelburne NYC *[http://wiki..."

= Agenda =
== GOC Meeting, NYU, New York, NY, May 12-14th ==
*Reminder to register, and reserve your hotel room before April 6th if staying at the Shelburne NYC
*[http://wiki.geneontology.org/index.php/2018_NYU_GOC_Meeting_Logistics Logistics]
*[http://wiki.geneontology.org/index.php/2018_NYU_GOC_Meeting_Agenda Agenda]

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

== Updates on Projects ==
*[https://github.com/geneontology/go-annotation/issues/1592 MAPK cascade- Signaling Project]
*[https://github.com/geneontology/go-ontology/projects/9 Extracellular matrix revisions]

== Evidence Codes ==
=== RCA ===
*[https://github.com/geneontology/go-annotation/issues/1801 Review RCA evidence code]
**Thank you to everyone who has reviewed their existing RCA annotations.
**Many RCA annotations were removed, but some groups are keeping annotations from papers that use methodology consistent with the definition of RCA.
**Since these annotations come from papers, the originally proposed one-year restriction does not make sense and will not be an annotation rule.
***Please send Kimberly PMIDs for papers that were kept for use as examples in our evidence code documentation.
**That said, periodic annotation review is always a good idea.
**Remaining groups will be contacted individually.

== Annotating High Throughput Experiments ==
*[https://github.com/geneontology/go-annotation/issues/1796 Proposal for curating extracellular matrix proteins from proteomics experiments]
*[https://github.com/geneontology/go-annotation/issues/1885 Review reference guidelines for GAF, GPAD]

== Annotation Survey ==
*We are putting together a survey on annotation practices across the GOC
*Should be ready very soon
*Would like results before the GOC meeting in NY

== GO-CAM/Noctua ==
*Next call tomorrow, Wednesday, March 28th at 11:00am EDT (see Google calendar)

== Protein Complexes Working Group ==
*Next call on Monday, April 23rd at 1:10pm EDT (see Google calendar)

= Minutes =
*On call: Chris, David H., Dustin, Edith, Giulia, Harold, Helen, Jim, Judy, Karen, Kevin M, Kimberly, Li, Midori, Pascale, Paul T, Penelope, Petra, Rachael, Rob, Sabrina, Sage, Stacia, Stan, Suzi A., Suzi L.

== GOC Meeting, NYU, New York, NY, May 12-14th ==
*Register and reserve your hotel room before April 6th if staying at the Shelburne NYC
*If you have any issues with reserving a room, please contact Peter D'Eustachio right away

== Updates on Projects ==
=== MAPK Signaling ===
*Some ontology updates to how MAPK signaling pathways are named in GO
*Upcoming: annotation review for potentially re-housing annotations according to the new MAPK pathway terms
*Some existing annotations to upstream genes may need to be re-housed
*The MAPK cascade is a signaling cassette or module that begins with MAP4K or MAP3K and ends with MAPK
*How a MAPK cascade relates to a larger signaling pathway or another downstream process, e.g. neurite extension, remains to be determined in both the ontology and GO-CAM models
=== Extracellular Matrix Revisions ===
*All extracellular matrices have at least some protein component
*David and Rachael working on revisions to the ontology
*Some annotation review will likely be coming
*Will be calling on people for help with top level taxonomic groupings

== Evidence Codes ==
=== RCA ===
*Most groups have reviewed their RCA annotations and removed many, but some have stayed
*Propose to remove the one-year restriction on RCA annotations that does not seem to have been enacted formally anyway
*We will work with other annotation groups to review their RCA annotations
=== Annotating High Throughput Experiments ===
*We need an evidence code for combinatorial curation using HTP results further validated by other methods
*Can work with ECO to find or create a suitable code
*Reference field will need to clearly indicate the combined curation methodology
**As a first step towards doing this, we need to determine how to indicate the combined references, e.g. a PMID plus a GO_REF that describes the subsequent analysis
**Currently, some groups include redundant, pipe-separated references in the Reference field of the GAF
**Do we need to continue doing this? Proposal is to include only one, unique ID for each reference and then, if needed, combine a paper reference with a GO_REF

== Annotation Survey ==
*We will be sending out an annotation practices survey for groups to fill in
*Survey will go out later this week or early next
*We'd like the results in time for the May GOC meeting in NYC



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

Ontology meeting 2018-04-02

GO wiki (new pages) - Mon, 04/02/2018 - 05:46

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 ==Ontology Project U..."

= Conference Line =

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

= Agenda =


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

==Ontology Project Updates==
Signaling https://github.com/geneontology/go-annotation/projects/4 <br>
ECM https://github.com/geneontology/go-ontology/projects/9 <br>
Protein Complexes https://github.com/geneontology/go-ontology/projects/8 <br>

== Editors Discussion ==
* Priorities between now and May GOC meeting in NY
** Presentation for SAB
* What's up with TermGenie? <br>


= Minutes =
Minutes should be recorded on the tickets discussed during the meeting

Attending:



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

GO QC Rules

GO wiki (new pages) - Thu, 03/29/2018 - 16:02

Cjm: Created page with "The GO Quality Control rules are numbered and are kept in github. See: https://github.com/geneontology/go-site/tree/master/metadata/rules Category:Annotation"

The GO Quality Control rules are numbered and are kept in github. See: https://github.com/geneontology/go-site/tree/master/metadata/rules

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

Release Pipeline

GO wiki (new pages) - Thu, 03/29/2018 - 15:50

Cjm:

== Release Cycle ==

The release cycle is monthly.

Additionally snapshot releases are created daily. These are intended only for internal consumption by GOC members. End-users get the monthly releases



== Per-group curator QC reports ==

Every day a dry-run of the full pipeline runs. We call this '''snapshot'''. As part of this run, we generate ''products'' and ''reports'' that are of use to db admins and curators of the various contributing groups (MODs, UniProt, etc) to the GO Consortium.

*http://snapshot.geneontology.org/reports/
** summary.txt. EXAMPLE: [http://snapshot.geneontology.org/reports/dictybase.report.md dictybase.report.md]
** prediction-report.txt EXAMPLE: [http://snapshot.geneontology.org/reports/mgi-prediction-report.txt mgi-prediction-report.txt]
** owltools-check.txt EXAMPLE: [http://snapshot.geneontology.org/reports/mgi-owltools-check.txt mgi-owltools-check.txt]
*http://snapshot.geneontology.org/products/annotations/
** GROUP-prediction.gaf EXAMPLE: [http://snapshot.geneontology.org/products/annotations/pombase-prediction.gaf pombase-prediction.gaf]

=== Summary ===

This is a basic summary of the parsing of your GAF file. It functionally replaces the old "Mike's script"

These are found in [http://snapshot.geneontology.org/reports/ reports]

Example: http://snapshot.geneontology.org/reports/dictybase.report.md

These report basic syntax errors and implement a subset of checks in the [[GO QC Rules]]

=== Prediction Report and OwlTools Checks ===

=== Predictions ===

== Technical Details ==

See the README.md in the github repo: https://github.com/geneontology/pipeline/blob/snapshot/README.md


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

2018 Berkeley GO-Dev April Hackathon

GO wiki (new pages) - Thu, 03/29/2018 - 12:36

Cjm:

== Dates ==

April 8-12

== Location ==

LBL Potter Street
http://berkeleybop.org/team_contact

== Agenda ==

== Attendees ==

* LBL GO-dev team
* Dustin (USC)
* Anushya?

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