View source for 2015 Washington DC GOC Meeting Agenda

Please plan to join us this fall on August 30th through September 2nd for the next meeting of the Gene Ontology Consortium. We will host the meeting at the [http://virtualtour.gwu.edu/#UMAP_2013090592962%7CBLD_2013101747929%7B%22mediaArea%22:%22Photos%22%7D Marvin Conference Center, George Washington University], at the heart of Washington, DC. The Marvin Conference Center is located at [https://www.google.com/maps/place/The+Marvin+Center/@38.899938,-77.047167,17z/data=!3m1!4b1!4m2!3m1!1s0x89b7b7b0f084314b:0x90983f7d137cf222 800 21st St NW Washington, DC 20052]. 

The 2015 GO meeting will include an all-day symposium + workshops day, open to the research community. During the GO Symposium + Workshops day we will host two talks about research projects that highlight the use of our resources, and offer workshops on annotation and term enrichment using the GO. More details are available on the [http://wiki.geneontology.org/index.php/Consortium_Meetings#2015 Agenda Pages for the GOC2015 Meeting]. We will also count with the participation of our Scientific Advisory Board. 

==Planned Schedule for the Week of the Meeting== 

* '''Sunday August 30 and Monday August 31 - GOC Meeting''': 
:* On the first day of the GOC Meeting, Sunday 30-August-2015, please meet us in '''Room 310'''.
:* On Monday 31-August-2015 - the GOC Meeting will take place in '''Room 311'''.
:* [http://wiki.geneontology.org/index.php/2015_Washington_DC_GOC_Meeting_Agenda The agenda for the GOC2015 Meeting can be found here].

*'''Tuesday September 1 - GO Symposium + Workshops''': 
:* On Tuesday 01-Sept-2015 the GO Symposium & Workshops Day will take place in '''Room 309'''.
:* [http://wiki.geneontology.org/index.php/2015_Washington_DC_GOC_Symposium_Agenda The agenda for the Symposium + Workshops Day can be found here]. 

*'''Wednesday September 2 - Scientific Advisory Board Meeting''': 
:* On Wednesday 02-Sept-2015 the GO Scientific Advisory Board (SAB) will meet in '''Room 407'''.
:* [http://wiki.geneontology.org/index.php/2015_Washington_DC_GOC_Scientific_Advisory_Board_Meeting_Agenda The agenda for the SAB Meeting can be found here].


==Daily Schedule for the GOC Meeting==
* Plan to arrive on Sunday and Monday morning at 8:30AM.
:* Breakfast will be served from 8:30AM - 9:00 AM
* Morning coffee break: 10:30AM
* Lunch: 12:30 - 1:30 PM
* Afternoon session: 1:30 PM
* Afternoon coffee break: 3:30 PM
* Close of day: 4:30 PM


== Minutes ==
The Minutes of the GOC2015 Meeting are recorded in this [https://docs.google.com/document/d/1HjFgya5d5vL63GoU4k_M0CkOBPIe7xjzOL5_WGtUcPM/edit# Google Document].


=Agenda=

Please ensure that all outstanding items from the Trello board are covered here and under the appropriate heading.


==Breakout Groups - Fit in however possible==
# Annotation transition to Noctua- Getting Ready
#* Rama, David H, Chris, Kimberly, Seth
# Shedding server services from Stanford (move to Amazon)
#* Chris, Seth, Mike, Rama
#GO Hand Book Chapters - coordination and reconciliation of contents. (Paul T, Suzi, Chris, Claire, Rachael, Ruth, Pascale, moni). 
[[Category: GO Consortium Meetings]]
# UniProt & Ensembl: how to remedy the change in PAINT files format (we expect uniprot accessions in column 2 and those have been replaced by ensembl IDs) - Tony S, Paul T, Suzi. [https://github.com/geneontology/touchup/issues/14 - See GitHub Issue here].
# Review SAB slides
# Revise GO user survey - Paola, PIs

=Day 1=

==Operations Update==
* GitHub update (Chris) 
** This should come first as it pertains to other business on agenda
** A brief introduction to GitHub, with a focus on ontology requests
*** getting accounts
*** submitting and updating tickets etc.
*** permissions and pull requests (editing metadata, and the general github workflow)
** https://docs.google.com/document/d/1iyVY8kDBJIEydoWFLG9j5BoO4VmdIXES95fVhIkFXfk/edit#
** How to be more effective in organizing and prioritizing issues
** Proposed migration of ontologies from SVN
* New architecture (Chris)

==Usability: are we delivering?==
* AmiGO [https://github.com/geneontology/amigo/milestones/2.3 2.3] (Seth)
* GO survey and user experience (Paola)
* GO website, FAQs, mailing lists - (moni, Seth, Chris): Statistics, update, cleanup. 
* GO HelpDesk - (moni, Rama) Rota checkup, Stats on open/closed topics, efficiency.
* GO Facebook page - (moni)
* GO on Wikipedia/Wikidata (melanie, davidOS, chris)
* GO tools registry (Paola)
* GO for non-GOC members: how can non-MODs most effectively use GO? (suggested by moni). Related: displaying all PANTHER species in GO website enrichment tool (see http://jira.geneontology.org/browse/GO-888) (suggested by Paola).
* Contributing to GO
:* Documentation (moni)
:* Deposit GAF2.0 on GitHub (Seth)
:* [http://wiki.geneontology.org/index.php/2015_Washington_DC_GOC_Meeting_Agenda#GAF.2FGPAD Updated naming conventions (Kimberly)]. 
:* Improving the assistance we provide to external groups offering to annotate (Moni, Melanie, Rama)

==Common Curation Environment and LEGO annotations==
* Noctua update (Seth, Chris)
* Refresher on LEGO concepts (Paul, Chris)
* Walkthrough (TBA: we will send a paper out in advance of the meeting)
* Combined GO/Phenotype annotation (Chris)
* Scaling up and next steps (Chris)
** [https://github.com/geneontology/noctua/milestones/2015-12-push 2015-12 milestone]
** Bootcamp/Jamboree? Where?

==Ontology==

===Molecular Function refactoring===

David OS/Paul T?

===Deepening annotations - develop ontology patterns e.g. protein binding===
(David H/Chris/Paul T) https://trello.com/c/J9jFm8Ex/95-deepening-annotations-develop-ontology-patterns-e-g-protein-binding

===Standardizing protein production classes===
See: https://github.com/geneontology/go-ontology/issues/10787
(Pascale)

==Annotation==

===GAF/GPAD===
*Standardizing GAF/GPAD Names and Versions (Tony S)
**Proposal to standardize GAF names - 5-10 min. proposal + discussion time (Kimberly)
***Generic file name: lower case submitting group abbreviation from GO.xrf_abbs_NCBI taxon id_NCBI taxon id name.gaf.gz
***NCBI taxon id name would be the corresponding taxonomic name or lower case genus species name abbreviated as: gspecies
**Examples:
***wb_6239_celegans.gaf.gz
***wb_6157_platyhelminthes.gaf.gz
**Does this work for everyone?
**Other information currently in file names, such as 'ref' and 'noieas'.  Will this information stay?
**Related issue: How many varieties of GAF files should GO offer for download, i.e. gene-centric, transcript-centric, proteome-centric?

===Evidence codes===
* Set timelines for deprecation of the 3 letters codes in GPAD and replacing with ECO identifiers
* Is it possible to compose evidence codes and is it appropriate? An example of this would be capturing the evidence when a direct enzymatic assay is used to test the loss of function in a mutant enzyme (IDA or IMP) - Rama?
* Continuing discussion of IGI example from [http://wiki.geneontology.org/index.php/Annotation_Conf._Call,_May_26,_2015 May annotation call]  - Rama

===Annotating complexes to GO===
(Claire will be chairing the discussion)
* Annotation guidance (Rama)
* Ontology issues (David OS)
* ID co-ordination between GO, Intact, and PRO (Sandra)
** Contacts: Darren Natale (dan5@georgetown.edu), Ceci Arighi (arighi@dbi.udel.edu), KRC, HJD

=Day 2=

==Annotation (Continued)==

===Guidelines for curators: Lessons from PAINTing===
* PAINT curation progress update (Huaiyu)
* Guidelines for annotation to x-catabolism to capture the product of a reaction rather than the end product of a pathway (Pascale)
* Guidelines for annotation of ligands (Pascale) - see email exchange dates Aug 7, 2015

===gp2protein Files & Proteome sets===
* Update on what the ref_proteome is, what a gene centric proteome reference proteome is, TrEMBL, SwissProt etc. See [https://docs.google.com/document/d/1l4hZw_ZTor8RoTjYTNS4FtGAba4HZrewmjccrSXJ9Hs/edit UniProt-in-GO Glossary document here] and the [http://jira.geneontology.org/browse/GO-820 related JIRA ticket here].

* 5-10 min. + discussion (Kimberly)
** How are they currently used?
** Are they still needed?
** What other options are available, and currently used, for mapping IDs across databases?
** How should responsibility/workflow for ID synchronization be managed?
** If we continue to provide them, standardize file names, as well, e.g. wb_gp2protein_6239_celegans.tab.gz?

===Update on focused projects===
* PSIQUIC GO annotations (5 min) - Ruth
* Synapse and Roche projects (David OS, Huaiyu)
* Strategies and templates for independent funding of targeted projects ? (e.g. eye, Ruth)
* Internal: Vesicles (Paola), Biochemical pathways (David H), Autophagy (David H), Cilia (Paola/Karen)

=== Making use of annotation extensions ===
* Usefulness of annotation extensions, intelligent querying (5 min) - David OS?
* Survey how many groups who are actively annotating are using or are capable of using annotation extensions (5 min) - Rama?
* Dealing with annotation extension inconsistencies (30 min) - Ruth/Rachael (e.g. dependent_on https://github.com/geneontology/annotation_extensions/issues/17)
* Downstream, very few tools can consume annotation extensions usefully.  For example, an annotation to 'cytosol' part of 'postsynapse' will NOT be grouped under postsynapse by the vast majority of tools.  How can we fix this!?  Can we provide 'folded' temp terms for at least some AE relationships: @ a minimum, part_of + occurs_in.
** Demo of how this works in Jenkins inference pipeline (Heiko)
* Progress on documentation (10 min) - David OS/Rama

===Protein2GO===
* Protein2GO: 15 min - demo/new features + 5 min discussion (ECO codes) - Aleksandra Shypitsyna

===Traceability of annotations===
* When one annotation is derived from another (manually or logically) it would be useful to have an easy way to point back to the existing annotation (and not just a gene product). Tony Sawford

===MicroRNA guideline summary===
* Brief overview (15 min) - Rachael Huntley

===Reactome Annotations===
*Reactome Annotations: TAS or EXP? (Harold; Peter)
**Brought up in 2007 (http://gocwiki.geneontology.org/index.php/2007_GOC_Action_Items). Thought resolved here: http://gocwiki.geneontology.org/index.php/GO_18th_Consortium_Meeting_Action_Items (2009)

===Resolution on chromatin binding===
* chromatin binding vs localization to chromatin (15 min) - Ruth, Karen, others?

===Resolution on regulation of activity===

* Would you annotate a protein involved in localisation (or regulation of localisation) of X to ‘regulation of X activity’ ?