https://wiki.geneontology.org/api.php?action=feedcontributions&user=Suzi&feedformat=atomGO Wiki - User contributions [en]2024-03-29T01:19:14ZUser contributionsMediaWiki 1.40.0https://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2018-12-18&diff=72463Annotation Conf. Call 2018-12-182018-12-18T16:10:01Z<p>Suzi: </p>
<hr />
<div>= Meeting URL =<br />
*https://stanford.zoom.us/j/976175422<br />
<br />
== GO Conference Calls ==<br />
*Tuesdays at 8am PDT<br />
**1st Tuesday: Alliance Biological Function<br />
**2nd Tuesday: GO Consortium<br />
**3rd Tuesday: GO-CAM Working Group<br />
**4th Tuesday: GO-CAM Working Group<br />
**5th Tuesday: Alliance Biological Function<br />
*One Zoom URL for all - https://stanford.zoom.us/j/976175422<br />
<br />
= Agenda = <br />
<br />
== Progress Reports ==<br />
*Thank you to everyone who submitted or worked on a progress report.<br />
*Any questions or outstanding issues?<br />
<br />
== Annotation Review Stats ==<br />
*We will discuss the overall progress on annotation review for 2018.<br />
*[https://docs.google.com/spreadsheets/d/1P2C_PMJtgBNiIxBeDMPvmf992f3sL7ZCw8Z-l0ZAVmk/edit#gid=0 Annotation Review Summary]<br />
<br />
== HTP Publication ==<br />
*Congratulations and thanks to Helen and the HTP working group on the acceptance (with minor revisions) of the Database manuscript on annotating GO from HTP experiments.<br />
<br />
== Ontology Editor's Geneva Meeting ==<br />
*The ontology editor's met in Geneva last week to discuss plans to align reactions amongst GO - Rhea - Reactome.<br />
*The plan is that, going forward, Rhea reactions will be the authoritative source for GO catalytic activity terms.<br />
*We also reviewed and discussed conversion of Reactome pathways to GO-CAM models (Ben Good's work).<br />
**Proposal for new RO relations to describe participants in reactions and metabolic processes.<br />
***This proposal will address the incorrect inferences that are currently generated from GO-CAM due to insufficient equivalence axioms in the ontology.<br />
**Touched on representation of protein complexes in GO-CAM.<br />
**Working on a report of genes annotated to a process and regulation of that process (broadly speaking) for future curation review.<br />
<br />
== Pipeline - PAINT annotations ==<br />
*Retrieving PAINT annotations for MODs<br />
*PAINT annotations that have gone through QA/QC pipeline can be retrieved from MOD-specific production annotation files on snapshot or current<br />
<br />
== Annotation Guidelines ==<br />
*We would like to discuss new guidelines written for annotating from mutant phenotypes:<br />
**[http://wiki.geneontology.org/index.php/Annotation#Annotating_from_phenotypes Annotating from phenotypes]<br />
<br />
== 2019 ==<br />
*Next consortium-wide call: Tuesday, January 8th, 2019<br />
<br />
= Minutes =<br />
*On call: Chris G., Chris, M., Suzi L., David, Giulia, Kevin, Kimberly, Laurent-Philippe, Li, Michele, Midori, Pascale, Patrick, Paul T., Sabrina, Seth, Shur-Jen, Stan, Tanya <br />
<br />
<br />
[[Category:Annotation Working Group]]</div>Suzihttps://wiki.geneontology.org/index.php?title=Other_Organisms_and_Viruses_(2005-2013)&diff=72231Other Organisms and Viruses (2005-2013)2018-11-26T23:41:23Z<p>Suzi: /* Terms and structure */</p>
<hr />
<div>=Multi-Organism Process=<br />
<br />
Multi-organism process and its children were created in Jan 2005 in collaboration with the Plant-Associated Microbe GO interest group (PAMGO) to describe interactions that occur between organisms of different species, and to subsume the existing terms that described interactions between organisms, e.g. pathogenesis and host-pathogen interaction. These terms were felt to be too 'host-centric', due to their reference to the disease process and their non-systematic placement in the ontologies. Further terms were added after the November 2005 content meeting to flesh out the node further.<br />
<br />
Complementary terms exist for annotating cellular locations such as host cell nucleus; see the cellular component guidelines for more details. The GO annotation conventions have a guide to annotating with these terms and how to represent the other organism in the interaction.<br />
<br />
=Terms and structure=<br />
<br />
Multi-organism processes are categorized according to the nature of the interaction (behavioral or physiological), and by whether they are inter- or intra-species. Interspecies interactions of an intimate or co-dependent nature fall under the term symbiosis, encompassing mutualism through parasitism, which covers all types of symbiosis between species, including mutualism (where the association is advantageous to one, or usually both, organisms) and parasitism (where the association is advantageous to one organism but detrimental to the other). All new terms that describe interactions between organisms should be placed in the interaction between organisms node under the appropriate parent(s).<br />
<br />
The node is structured broadly like this (not all terms shown):<br />
<br />
multi-organism process<br />
[i] interspecies interaction between organisms<br />
---[i] symbiosis, encompassing mutualism through parasitism<br />
[i] intraspecies interaction between organisms<br />
<br />
Symbiotic relationships may be between two organisms of similar sizes or of differing sizes, and most of the processes under symbiosis, encompassing mutualism through parasitism have child terms to specify the sizes of the organisms involved. These terms use the nomenclature host for the larger organism and symbiont for the smaller organism. For interactions where there is no clear host or symbiont, the wording other organism is used, and terms are appended with during symbiotic interaction to make it clear that they represent processes occurring during symbiosis.<br />
<br />
symbiosis, encompassing mutualism through parasitism<br />
[i] acquisition of nutrients from other organism during symbiotic interaction<br />
---[i] acquisition of nutrients from host<br />
---[i] acquisition of nutrients from symbiont<br />
[i] interaction with host<br />
---[i] acquisition of nutrients from host<br />
[i] interaction with symbiont<br />
---[i] acquisition of nutrients from symbiont<br />
<br />
Some processes may occur as part of symbiosis or outside it; the structure to represent such a process is illustrated below. Note that terms representing non-symbiotic interactions between organisms should use the wording another organism to refer to the second organism.<br />
<br />
interaction between organisms<br />
[i] physiological interaction between organisms<br />
---[i] killing of cells of another organism<br />
------[i] killing of cells of other organism during symbiotic interaction<br />
---------[i] killing of host cells<br />
---------[i] killing of symbiont cells<br />
[i] interspecies interaction between organisms<br />
---[i] symbiosis, encompassing mutualism through parasitism<br />
------[i] killing of cells of other organism during symbiotic interaction<br />
---------[i] killing of host cells<br />
---------[i] killing of symbiont cells<br />
<br />
==More reading material==<br />
[https://docs.google.com/document/d/196nLKiQ2Go4toilCq226w7u0p52odvCkq-bU5qgtzu0/edit?usp=sharing host_symbiont_annotation doc from Chris]<br />
<br />
=Standard Definitions=<br />
<br />
*'''[process involving] other organism during symbiotic interaction''': [definition of process], where the two organisms are in a symbiotic relationship. <br />
<br />
*'''[process involving] host''': [definition of process]. The host is defined as the larger of the organisms involved in a symbiotic interaction. <br />
<br />
*'''[process involving] symbiont''': [definition of process]. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction. <br />
<br />
Taking the process acquisition of nutrients as an example, the terms and definitions would be as follows:<br />
<br />
*'''acquisition of nutrients from other organism during symbiotic interaction''': The production of structures and/or molecules in an organism that are required for the acquisition and/or utilization of nutrients obtained from a second organism, where the two organisms are in a symbiotic relationship. <br />
*'''acquisition of nutrients from host''': The production of structures and/or molecules in an organism that are required for the acquisition and/or utilization of nutrients obtained from its host. The host is defined as the larger of the organisms involved in a symbiotic interaction. <br />
*'''acquisition of nutrients from symbiont''': The production of structures and/or molecules in an organism that are required for the acquisition and/or utilization of nutrients obtained from its symbiont. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction. <br />
<br />
=Hosts, Symbionts and Viruses=<br />
<br />
The cellular component ontology provides terms to complement those in the biological process ontology representing multi-organism processes. There are two main locations for these terms: the first set, for the representation of the larger organism in the interaction, can be found under host in extraorganismal space; the second set are to capture virus components, and are under the term virion.<br />
<br />
cellular_component<br />
[i] extracellular region<br />
---[p] extracellular region part<br />
------[i] extraorganismal space<br />
---------[i] host<br />
...<br />
[i] virion<br />
<br />
Viruses should be annotated like any other organism involved in a multi-organism process, using cellular component terms such as host cell cytoplasm or host cell nucleus. Locations in the virus itself are found under the term virion.<br />
<br />
<br />
<br />
The GO annotation conventions have a guide to annotating with these terms and how to represent the other organism in the interaction. '''DOES THAT STILL EXIST ?'''<br />
<br />
==2013 Virus cross-products==<br />
* [[Virus_call_2013-11-27]]<br />
** Jane, Becky, Chris, David OS <br />
** better way to represent viral modulation of cell activity<br />
** terms that reference a specific host protein, where the virus modulates one or more functions of that protein<br />
** Processes where the differentia is that it involves a virus<br />
<br />
==2009-2012 Virus work==<br />
Jane Lomax, Rebecca Foulger, Brenley McIntosh - July 2012<br />
Michelle Gwinn Giglio, Candace Collmer, Ariane Toussaint, Alexander Diehl, Fiona McCarthy, Marcus Chibucos<br />
<br />
* '''Summary''': [[Virus_terms_(Completed_2012)]]<br />
* [[Virus_ontology_devt_July_2012]]<br />
* [[Spanins_and_Holins]] 14 August 2012 <br />
* [[Brenley's_Suggested_Terms]] 16 August 2012<br />
<br />
==Phage calls 2012==<br />
* [[Phage_jamboree-_I_July_31st_2012]]<br />
* [[Phage_jamboree-_II_August_2nd_2012]]<br />
* [[Phage_call_August_9th_2012]]<br />
* [[Phage_call_August_21st-23rd_2012]]<br />
* [[Phage_call_August_30th_2012]]<br />
* [[Phage_call_September_6th_2012]]<br />
<br />
<br />
==Virus discussions 2009==<br />
* Michelle, Candace, Marcus, Fiona, Jane, Alex, Ariane, Brenley, Fiona <br />
* [[First_email_for_virus-term_overhaul,_march_09]]<br />
** The terms themselves are a real jumble with no overall structure, and the annotations we have a mainly to a small number of these terms (e.g. GO:0019059 : initiation of viral infection, GO:0019047 : provirus integration, GO:0019061 : uncoating of virus)<br />
* [[Viral_term_WebEx_meeting_june_3_2009]]<br />
** lysis/lysogeny split<br />
** discussion of top-level term names and whether 'viral reproduction encompassed all viral processes. Perhaps use 'viral-host interaction' instead?<br />
** discussion of the annotation of 'abnormal' processes<br />
** necessity to have a specific 'viral' term - for example 'viral transcription' (or not)<br />
* [[Viral term WebEx meeting august 21 2009]]<br />
** Creating separate viral v/s host terms.<br />
** Reproduction v/s growth v/s development<br />
** Symbiont granularity (unicellular vs multicellular)<br />
* [[Candace's_email_21_July_2009]]<br />
** GO:0009626 : plant-type hypersensitive response<br />
** GO:0034053 : modulation by symbiont of host defense-related programmed cell death<br />
<br />
<br />
----<br />
[[Category:GO Editors]][[Category:Ontology]] [[Category:Viruses]]<br />
[[Notes_on_specific_terms |Back to: Notes on specific terms]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2018_Montreal_GOC_Meeting_Logistics&diff=700172018 Montreal GOC Meeting Logistics2018-07-04T21:07:43Z<p>Suzi: /* Attendees */</p>
<hr />
<div><br />
=Start and end of meeting=<br />
To be announced <br />
<br />
=Registration fee=<br />
To be announced <br />
<br />
=Meeting site=<br />
'''Université du Québec à Montreal (UQAM), Pavillon Président-Kennedy'''<br />
* 201 Avenue du Président-Kennedy, Montréal, QC H2X 3Y7<br />
* Location: https://goo.gl/V1ZrsJ<br />
<br />
=Call-in information=<br />
To be announced<br />
<br />
=Travel=<br />
<br />
<br />
<br />
=Accommodations=<br />
<br />
Two options: Delta Hotel and Hotel Zero1<br />
<br />
==1) Delta Hotel Montreal==<br />
* https://www.marriott.com/hotels/travel/yuldb-delta-hotels-montreal/<br />
* '''Address:''' 475 President-Kennedy Avenue, Montreal, QC H3A 1J7<br />
* '''Directions to meeting venue:''' https://goo.gl/ha8fay<br />
* '''Phone:''' 1 (514) 286-1986<br />
* '''Reservation:''' Call Marriott Reservations at 1 (844) 860-3753<br />
** Book under: UQAM GO Meeting 2018<br />
** All reservations must be guaranteed with a major credit card.<br />
* '''Rate available until Tuesday, September 18, 2018'''. <br />
* '''Cancellation policy''': Individual reservations may be cancelled up until 48 hours local time prior to arrival with no penalty. Cancellations received after this time will be subject to one night’s room & tax, applied to the credit card used to guarantee the reservation.<br />
* '''Rates for October 16th-19th'''<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Room Type <br />
! Daily rate (excl tax)<br />
! Daily rate (incl tax; estimate)<br />
|-<br />
| Single/Double<br />
| CAN $188<br />
| CAN $222<br />
|-<br />
| Triple<br />
| CAN $208 <br />
| CAN $246<br />
|-<br />
| Quad<br />
| CAN $228<br />
| CAN $270<br />
|-<br />
|}<br />
<br />
<br />
'''Rate includes: '''<br />
* Free WiFi in room (+ wires) and WiFi in all public areas<br />
* Breakfast not included<br />
* Gym<br />
* Parking available: On-site parking: CAN $ 26.50 daily; Valet parking: CAN $32 daily<br />
<br />
==2) Hotel Zero1 Montreal== <br />
* http://www.zero1-mtl.com/en/default.html<br />
* '''Address:''' 1 RenéLévesque Est Montréal QC H2X 3Z5<br />
* '''Directions to meeting venue:''' https://goo.gl/1BkxYh<br />
* '''Phone:''' 1 (514) 871-9696 / 1 (855) 301-0001<br />
* '''Reservation:''' Call the hotel at 1 (514) 871-9696 / 1 (855) 301-0001<br />
** Book under: GO meeting at UQAM<br />
** All reservations must be guaranteed with a major credit card.<br />
* '''Rate available until August 15th, 2018'''. <br />
* '''Cancellation policy''': Inform the hotel in writing 48 hours prior to arrival date. If no notice is received, a penalty of one night (including all taxes) will be charged on the credit card on file (no show). <br />
* Upon arrival of the participant at the hotel, a deposit corresponding to the total accommodation fees (including taxes) + a security deposit will be due. <br />
* '''Rates for October 16th-19th'''<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Room Type <br />
! Daily rate (excl tax)<br />
! Daily rate (incl tax; estimate)<br />
|-<br />
| "Pop room" - 1 queen bed <br />
| CAN $169<br />
| CAN $200<br />
|-<br />
|}<br />
<br />
'''Rate includes: '''<br />
* Free WiFi in room and all public areas<br />
* Free local calls<br />
* Shower only<br />
* Gym (seems small)<br />
* American buffet breakfast included at the Z Tapas Lounge<br />
* Valet service available for CAN $28.00/day + applicable taxes.<br />
<br />
=Food=<br />
* World-famous Montreal bagels: http://www.stviateurbagel.com/ and https://fairmountbagel.com/ (both open 24 hours, in case you need a 3 am warm snack)<br />
<br />
=Bicycling and walking / running=<br />
* The venue is less than 1 km away from Par Mont Royal, great for walking and running (and biking is you like small hills): https://goo.gl/v5fyYq<br />
* Bike rental places: https://www.yelp.ca/search?cflt=bikerentals&find_loc=Montreal%2C+QC<br />
* If you have an afternoon, rent a bike or roller blades in the Old port and bike the Canal Lachine<br />
<br />
=To do and see=<br />
* Quartier des spectacles (the venue is right in that neighborhood): https://www.quartierdesspectacles.com/en/<br />
* Rue Saint-Denis: http://www.ruesaintdenis.ca/en/<br />
* Boulevard Saint-Laurent ("La Main"): http://boulevardsaintlaurent.com/en/<br />
* Mile End neighborhood (a couple of km North/East of the venue; very trendy right now): https://localfoodtours.com/montreal/10-things-to-do-in-the-mile-end-montreal/<br />
* Old port: http://www.oldportofmontreal.com/<br />
* Old Montreal: https://www.mtl.org/en/explore/neighbourhoods/old-montreal<br />
<br />
=Attendees=<br />
Please add your name to the table if you intend to attend the meeting, and the dinner, so we can get a headcount estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name <br />
! Organization <br />
! Attend the GOC dinner (Thursday 18th)? <br />
! Food restrictions<br />
|-<br />
| Pascale Gaudet<br />
| SIB/GO Central<br />
| Yes<br />
| <br />
|-<br />
| Val Wood<br />
| PomBase<br />
| Yes<br />
| <br />
|-<br />
| Suzanna Lewis<br />
| BBOP/LBNL<br />
| Yes<br />
| <br />
|-<br />
|}<br />
<br />
=Remote attendees=<br />
If you plan to attend remotely, please sign up here and indicate the sessions you are likely to attend:<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name <br />
! Organization <br />
|-<br />
|}<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2018_NYU_GOC_Meeting_Agenda&diff=687402018 NYU GOC Meeting Agenda2018-05-06T22:19:11Z<p>Suzi: /* Live version now here */</p>
<hr />
<div>= DO NOT EDIT=<br />
==<em>[https://docs.google.com/document/d/1Px8AgghIABKaGP174Av2XYXQ8NfUrkMRT1yJ8kwCgx4/edit?usp=sharing Live version now here in Google Drive]</em>==<br />
<br />
= Suggestions for topics=<br />
<br />
== Intro/Overview ==<br />
Paul T<br />
* Mention Alliance <br />
* Beginning new fiscal year<br />
<br />
== Infrastructure Projects ==<br />
<br />
* Release pipeline/new release cycle [https://github.com/orgs/geneontology/projects/11] (Seth, Eric)<br />
** Documentation https://github.com/geneontology/go-site/issues/555<br />
** UPDATE: Injection of PAINT annotations at GO Central (Huaiyu)<br />
** Discussion: Injection of GPADs derived from production GO-CAMs (Chris)<br />
** Automated QC (Eric, Kimberly)<br />
* public API (Nathan, Deepak)<br />
** Example of use: Ribbon (Nathan)<br />
* Interaction with data commons (Paul/Chris)<br />
* Enrichment analysis in the cloud (Paul/Chris)<br />
<br />
== GO-CAM and Noctua Project == <br />
<br />
* Noctua status reports<br />
** 1.0 Release [https://github.com/orgs/geneontology/projects/6] Seth, Chris<br />
** Tour of the Noctua Form: Tremayne, Paul<br />
** Importing Reactome into Noctua: Ben, David<br />
** Seeding models from GAFs: Dustin, Eric<br />
** Roll-out plan: Kimberly<br />
* Community usage of GO-CAMs<br />
** GO-CAM landing page [https://github.com/geneontology/go-site/issues/558] (Laurent-Phillippe)<br />
** Export to other formats and import into other databases (Laurent-Phillippe)<br />
** Loading GO-CAM annotations into MODS- The MGI Experience (David H)<br />
<br />
== Noctua Form hands-on session ==<br />
(Paul's suggestion) - 1.5h <br />
All curators should come with a paper or pathway that they would like to curate.<br />
Suggestion: curate signaling pathways?<br />
<br />
== Documentation and Outreach ==<br />
<br />
* Presentation of update website/Report on Documentation jamboree<br />
** New HTP annotations guidelines<br />
* Outreach plans (Suzi A)<br />
** SOPs for groups that want to submit annotations to the GOC<br />
* Licensing and community annotation (Seth?) <br / > With the possibility of a wider pool of annotation ingest, we should consider a copyright re-assignment policy to the GOC, getting pass-through agreements from re-used upstream resources (the http://reusabledata.org evaluation of Reactome, while possibly out of date, can be illustrative in the context of bulk model import), as well as the legal nature of the GOC.<br />
* Seth has included some copyright re-assignment text to the Noctua sign-up, especially as we are starting to take non-GOC annotations and users.<br />
* Slims maintenance update - Pascale /Chris<br />
<br />
<br />
<br />
== Projects ==<br />
<br />
=== Signaling Workshop Project ===<br />
Paul/Pascale: Can we give an overview/lessons learned summary ? General principles: <br />
* start and end of pathways<br />
* underannotation<br />
* overannotation<br />
* what does it mean to be part of a pathway/upstream/etc<br />
<br />
* Canonical Wnt Signaling (Kimberly VA and Helen) (https://github.com/geneontology/go-annotation/issues/1595)<br />
** Report on Ontology Changes<br />
** Report on Annotation Review<br />
*** Reviews Completed<br />
*** Reviews Outstanding<br />
*** New Annotation Practice Guidelines<br />
<br />
* MAPK Cascade (DavidH and SabrinaT) (https://github.com/geneontology/go-annotation/issues/1592)<br />
** Report on ontology changes<br />
** Report on Annotation Review<br />
*** Reviews Completed<br />
*** Reviews Outstanding<br />
*** New Annotation Practice Guidelines<br />
<br />
* GPCR signaling (Pascale or Petra)(https://github.com/geneontology/go-annotation/issues/1591)<br />
** Report on ontology changes<br />
** Report on Annotation Review<br />
*** Reviews Completed<br />
*** Reviews Outstanding<br />
*** New Annotation Practice Guidelines<br />
<br />
* JAK/STAT cascade (Ruth Lovering) (https://github.com/geneontology/go-annotation/issues/1628)<br />
** Report on ontology changes<br />
** Report on Annotation Review<br />
*** Reviews Completed<br />
*** Reviews Outstanding<br />
*** New Annotation Practice Guidelines<br />
<br />
===Tickets to discuss===<br />
* GP annotations to terms that refer to 'drugs' (DavidH)<br />
** https://github.com/geneontology/go-ontology/issues/15379<br />
<br />
=== Protein Complex working group report ===<br />
<br />
* Various tickets about complexes<br />
** https://github.com/geneontology/go-ontology/issues/15211<br />
** https://github.com/geneontology/go-ontology/issues/11094<br />
** https://github.com/geneontology/go-ontology/issues/11382<br />
** https://github.com/geneontology/go-ontology/issues/14375<br />
<br />
<br />
===Update MF refactor=== <br />
Pascale<br />
<br />
===Update: Tx refactor===<br />
Pascale<br />
<br />
== PAINT update == <br />
Huaiyu ~30-45 minutes<br />
<br />
== GP2Term Relations ==<br />
GitHub Project: [https://github.com/orgs/geneontology/projects/13] (Suzi L, Kimberly)<br />
** See [[:Category:Gene_Product_to_Term_Relations]]<br />
** UPDATE: GP2Term Relations coming from Noctua (Chris)<br />
** UPDATE/discussion: Enabling usage by users and bioinformaticians (Deepak, Laurent-Phillippe)<br />
** UPDATE: Display in AmiGO (Suzi L, Seth)<br />
<br />
== Quality Control Projects == <br />
<br />
* Report: QC group: annotation review stats<br />
* Cancer signaling pathways review (note: I also have this under GP2Term relations below; Chris)<br />
** Case study: [http://xena.ucsc.edu/ Xena] and cancer signaling project, [http://xenademo.berkeleybop.io/xena/ demo] (Suzi L)<br />
<br />
===Ideas for QC approaches===<br />
*Estimating literature coverage in curation*<br />
**(Requested by SAB and all the time)<br />
***Get stats for <br />
**** # genes with some annotation (IBA | EXP - separately - exclude HTP and probably ‘protein binding') <br />
**** # annotations per gene -> group by: >100 annotations, 50-100 annotations, 10-50 annotations, <10 annotations<br />
**** # papers per gene -> group by: >100 papers, 50-100 papers, 10-50 papers, <10 papers<br />
<br />
== External Projects==<br />
* Impact of GO qualifiers on Alliance gene descriptions (Mary D)<br />
<br />
=Sunday PM=<br />
==Breakout sessions ==<br />
===Alignment of Rhea, Reactome, IntAct and GO===<br />
Alan B, Peter D, Sandra/Birgit, Jim, Ben?<br />
With their recommendations for moving forward. GH ticket is here [https://github.com/geneontology/go-ontology/issues/14984] <br />
<br />
<br />
===QA and metrics===<br />
Suzi, Val, Kimberly, Pascale, Eric .. ?<br />
<br />
=Will we be talking about those??=<br />
== Future New Projects ==<br />
<br />
==Evolutionary taxon relations== <br />
(Paul, Chris)<br />
<br />
==Tickets==<br />
* Redundant annotations: <BR><br />
** https://github.com/geneontology/go-annotation/issues/1879<br />
<br />
* Main GAF file: providing a high confidence GAF file<br />
** https://github.com/geneontology/go-ontology/issues/15498<br />
<br />
* GOC-OWL inference pipeline concerns <br />
**https://github.com/geneontology/go-annotation/issues/1487<br />
<br />
==Other potential topics==<br />
* Documentation of rules: Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928<br />
* 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<br />
<br />
== Suggestions for topics Fall 2018==<br />
*'Response to' workshop (similar to the signaling WS)<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2018_NYU_GOC_Meeting_Agenda&diff=687392018 NYU GOC Meeting Agenda2018-05-06T22:18:35Z<p>Suzi: </p>
<hr />
<div>= DO NOT EDIT=<br />
==<em>[https://docs.google.com/document/d/1Px8AgghIABKaGP174Av2XYXQ8NfUrkMRT1yJ8kwCgx4/edit?usp=sharing Live version now here]</em>==<br />
= Suggestions for topics=<br />
<br />
== Intro/Overview ==<br />
Paul T<br />
* Mention Alliance <br />
* Beginning new fiscal year<br />
<br />
== Infrastructure Projects ==<br />
<br />
* Release pipeline/new release cycle [https://github.com/orgs/geneontology/projects/11] (Seth, Eric)<br />
** Documentation https://github.com/geneontology/go-site/issues/555<br />
** UPDATE: Injection of PAINT annotations at GO Central (Huaiyu)<br />
** Discussion: Injection of GPADs derived from production GO-CAMs (Chris)<br />
** Automated QC (Eric, Kimberly)<br />
* public API (Nathan, Deepak)<br />
** Example of use: Ribbon (Nathan)<br />
* Interaction with data commons (Paul/Chris)<br />
* Enrichment analysis in the cloud (Paul/Chris)<br />
<br />
== GO-CAM and Noctua Project == <br />
<br />
* Noctua status reports<br />
** 1.0 Release [https://github.com/orgs/geneontology/projects/6] Seth, Chris<br />
** Tour of the Noctua Form: Tremayne, Paul<br />
** Importing Reactome into Noctua: Ben, David<br />
** Seeding models from GAFs: Dustin, Eric<br />
** Roll-out plan: Kimberly<br />
* Community usage of GO-CAMs<br />
** GO-CAM landing page [https://github.com/geneontology/go-site/issues/558] (Laurent-Phillippe)<br />
** Export to other formats and import into other databases (Laurent-Phillippe)<br />
** Loading GO-CAM annotations into MODS- The MGI Experience (David H)<br />
<br />
== Noctua Form hands-on session ==<br />
(Paul's suggestion) - 1.5h <br />
All curators should come with a paper or pathway that they would like to curate.<br />
Suggestion: curate signaling pathways?<br />
<br />
== Documentation and Outreach ==<br />
<br />
* Presentation of update website/Report on Documentation jamboree<br />
** New HTP annotations guidelines<br />
* Outreach plans (Suzi A)<br />
** SOPs for groups that want to submit annotations to the GOC<br />
* Licensing and community annotation (Seth?) <br / > With the possibility of a wider pool of annotation ingest, we should consider a copyright re-assignment policy to the GOC, getting pass-through agreements from re-used upstream resources (the http://reusabledata.org evaluation of Reactome, while possibly out of date, can be illustrative in the context of bulk model import), as well as the legal nature of the GOC.<br />
* Seth has included some copyright re-assignment text to the Noctua sign-up, especially as we are starting to take non-GOC annotations and users.<br />
* Slims maintenance update - Pascale /Chris<br />
<br />
<br />
<br />
== Projects ==<br />
<br />
=== Signaling Workshop Project ===<br />
Paul/Pascale: Can we give an overview/lessons learned summary ? General principles: <br />
* start and end of pathways<br />
* underannotation<br />
* overannotation<br />
* what does it mean to be part of a pathway/upstream/etc<br />
<br />
* Canonical Wnt Signaling (Kimberly VA and Helen) (https://github.com/geneontology/go-annotation/issues/1595)<br />
** Report on Ontology Changes<br />
** Report on Annotation Review<br />
*** Reviews Completed<br />
*** Reviews Outstanding<br />
*** New Annotation Practice Guidelines<br />
<br />
* MAPK Cascade (DavidH and SabrinaT) (https://github.com/geneontology/go-annotation/issues/1592)<br />
** Report on ontology changes<br />
** Report on Annotation Review<br />
*** Reviews Completed<br />
*** Reviews Outstanding<br />
*** New Annotation Practice Guidelines<br />
<br />
* GPCR signaling (Pascale or Petra)(https://github.com/geneontology/go-annotation/issues/1591)<br />
** Report on ontology changes<br />
** Report on Annotation Review<br />
*** Reviews Completed<br />
*** Reviews Outstanding<br />
*** New Annotation Practice Guidelines<br />
<br />
* JAK/STAT cascade (Ruth Lovering) (https://github.com/geneontology/go-annotation/issues/1628)<br />
** Report on ontology changes<br />
** Report on Annotation Review<br />
*** Reviews Completed<br />
*** Reviews Outstanding<br />
*** New Annotation Practice Guidelines<br />
<br />
===Tickets to discuss===<br />
* GP annotations to terms that refer to 'drugs' (DavidH)<br />
** https://github.com/geneontology/go-ontology/issues/15379<br />
<br />
=== Protein Complex working group report ===<br />
<br />
* Various tickets about complexes<br />
** https://github.com/geneontology/go-ontology/issues/15211<br />
** https://github.com/geneontology/go-ontology/issues/11094<br />
** https://github.com/geneontology/go-ontology/issues/11382<br />
** https://github.com/geneontology/go-ontology/issues/14375<br />
<br />
<br />
===Update MF refactor=== <br />
Pascale<br />
<br />
===Update: Tx refactor===<br />
Pascale<br />
<br />
== PAINT update == <br />
Huaiyu ~30-45 minutes<br />
<br />
== GP2Term Relations ==<br />
GitHub Project: [https://github.com/orgs/geneontology/projects/13] (Suzi L, Kimberly)<br />
** See [[:Category:Gene_Product_to_Term_Relations]]<br />
** UPDATE: GP2Term Relations coming from Noctua (Chris)<br />
** UPDATE/discussion: Enabling usage by users and bioinformaticians (Deepak, Laurent-Phillippe)<br />
** UPDATE: Display in AmiGO (Suzi L, Seth)<br />
<br />
== Quality Control Projects == <br />
<br />
* Report: QC group: annotation review stats<br />
* Cancer signaling pathways review (note: I also have this under GP2Term relations below; Chris)<br />
** Case study: [http://xena.ucsc.edu/ Xena] and cancer signaling project, [http://xenademo.berkeleybop.io/xena/ demo] (Suzi L)<br />
<br />
===Ideas for QC approaches===<br />
*Estimating literature coverage in curation*<br />
**(Requested by SAB and all the time)<br />
***Get stats for <br />
**** # genes with some annotation (IBA | EXP - separately - exclude HTP and probably ‘protein binding') <br />
**** # annotations per gene -> group by: >100 annotations, 50-100 annotations, 10-50 annotations, <10 annotations<br />
**** # papers per gene -> group by: >100 papers, 50-100 papers, 10-50 papers, <10 papers<br />
<br />
== External Projects==<br />
* Impact of GO qualifiers on Alliance gene descriptions (Mary D)<br />
<br />
=Sunday PM=<br />
==Breakout sessions ==<br />
===Alignment of Rhea, Reactome, IntAct and GO===<br />
Alan B, Peter D, Sandra/Birgit, Jim, Ben?<br />
With their recommendations for moving forward. GH ticket is here [https://github.com/geneontology/go-ontology/issues/14984] <br />
<br />
<br />
===QA and metrics===<br />
Suzi, Val, Kimberly, Pascale, Eric .. ?<br />
<br />
=Will we be talking about those??=<br />
== Future New Projects ==<br />
<br />
==Evolutionary taxon relations== <br />
(Paul, Chris)<br />
<br />
==Tickets==<br />
* Redundant annotations: <BR><br />
** https://github.com/geneontology/go-annotation/issues/1879<br />
<br />
* Main GAF file: providing a high confidence GAF file<br />
** https://github.com/geneontology/go-ontology/issues/15498<br />
<br />
* GOC-OWL inference pipeline concerns <br />
**https://github.com/geneontology/go-annotation/issues/1487<br />
<br />
==Other potential topics==<br />
* Documentation of rules: Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928<br />
* 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<br />
<br />
== Suggestions for topics Fall 2018==<br />
*'Response to' workshop (similar to the signaling WS)<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2018_NYU_GOC_Meeting_Agenda&diff=687382018 NYU GOC Meeting Agenda2018-05-06T22:17:48Z<p>Suzi: </p>
<hr />
<div>= DO NOT EDIT=<br />
<em>[https://docs.google.com/document/d/1Px8AgghIABKaGP174Av2XYXQ8NfUrkMRT1yJ8kwCgx4/edit?usp=sharing Live version now here]</em><br />
= Suggestions for topics=<br />
<br />
== Intro/Overview ==<br />
Paul T<br />
* Mention Alliance <br />
* Beginning new fiscal year<br />
<br />
== Infrastructure Projects ==<br />
<br />
* Release pipeline/new release cycle [https://github.com/orgs/geneontology/projects/11] (Seth, Eric)<br />
** Documentation https://github.com/geneontology/go-site/issues/555<br />
** UPDATE: Injection of PAINT annotations at GO Central (Huaiyu)<br />
** Discussion: Injection of GPADs derived from production GO-CAMs (Chris)<br />
** Automated QC (Eric, Kimberly)<br />
* public API (Nathan, Deepak)<br />
** Example of use: Ribbon (Nathan)<br />
* Interaction with data commons (Paul/Chris)<br />
* Enrichment analysis in the cloud (Paul/Chris)<br />
<br />
== GO-CAM and Noctua Project == <br />
<br />
* Noctua status reports<br />
** 1.0 Release [https://github.com/orgs/geneontology/projects/6] Seth, Chris<br />
** Tour of the Noctua Form: Tremayne, Paul<br />
** Importing Reactome into Noctua: Ben, David<br />
** Seeding models from GAFs: Dustin, Eric<br />
** Roll-out plan: Kimberly<br />
* Community usage of GO-CAMs<br />
** GO-CAM landing page [https://github.com/geneontology/go-site/issues/558] (Laurent-Phillippe)<br />
** Export to other formats and import into other databases (Laurent-Phillippe)<br />
** Loading GO-CAM annotations into MODS- The MGI Experience (David H)<br />
<br />
== Noctua Form hands-on session ==<br />
(Paul's suggestion) - 1.5h <br />
All curators should come with a paper or pathway that they would like to curate.<br />
Suggestion: curate signaling pathways?<br />
<br />
== Documentation and Outreach ==<br />
<br />
* Presentation of update website/Report on Documentation jamboree<br />
** New HTP annotations guidelines<br />
* Outreach plans (Suzi A)<br />
** SOPs for groups that want to submit annotations to the GOC<br />
* Licensing and community annotation (Seth?) <br / > With the possibility of a wider pool of annotation ingest, we should consider a copyright re-assignment policy to the GOC, getting pass-through agreements from re-used upstream resources (the http://reusabledata.org evaluation of Reactome, while possibly out of date, can be illustrative in the context of bulk model import), as well as the legal nature of the GOC.<br />
* Seth has included some copyright re-assignment text to the Noctua sign-up, especially as we are starting to take non-GOC annotations and users.<br />
* Slims maintenance update - Pascale /Chris<br />
<br />
<br />
<br />
== Projects ==<br />
<br />
=== Signaling Workshop Project ===<br />
Paul/Pascale: Can we give an overview/lessons learned summary ? General principles: <br />
* start and end of pathways<br />
* underannotation<br />
* overannotation<br />
* what does it mean to be part of a pathway/upstream/etc<br />
<br />
* Canonical Wnt Signaling (Kimberly VA and Helen) (https://github.com/geneontology/go-annotation/issues/1595)<br />
** Report on Ontology Changes<br />
** Report on Annotation Review<br />
*** Reviews Completed<br />
*** Reviews Outstanding<br />
*** New Annotation Practice Guidelines<br />
<br />
* MAPK Cascade (DavidH and SabrinaT) (https://github.com/geneontology/go-annotation/issues/1592)<br />
** Report on ontology changes<br />
** Report on Annotation Review<br />
*** Reviews Completed<br />
*** Reviews Outstanding<br />
*** New Annotation Practice Guidelines<br />
<br />
* GPCR signaling (Pascale or Petra)(https://github.com/geneontology/go-annotation/issues/1591)<br />
** Report on ontology changes<br />
** Report on Annotation Review<br />
*** Reviews Completed<br />
*** Reviews Outstanding<br />
*** New Annotation Practice Guidelines<br />
<br />
* JAK/STAT cascade (Ruth Lovering) (https://github.com/geneontology/go-annotation/issues/1628)<br />
** Report on ontology changes<br />
** Report on Annotation Review<br />
*** Reviews Completed<br />
*** Reviews Outstanding<br />
*** New Annotation Practice Guidelines<br />
<br />
===Tickets to discuss===<br />
* GP annotations to terms that refer to 'drugs' (DavidH)<br />
** https://github.com/geneontology/go-ontology/issues/15379<br />
<br />
=== Protein Complex working group report ===<br />
<br />
* Various tickets about complexes<br />
** https://github.com/geneontology/go-ontology/issues/15211<br />
** https://github.com/geneontology/go-ontology/issues/11094<br />
** https://github.com/geneontology/go-ontology/issues/11382<br />
** https://github.com/geneontology/go-ontology/issues/14375<br />
<br />
<br />
===Update MF refactor=== <br />
Pascale<br />
<br />
===Update: Tx refactor===<br />
Pascale<br />
<br />
== PAINT update == <br />
Huaiyu ~30-45 minutes<br />
<br />
== GP2Term Relations ==<br />
GitHub Project: [https://github.com/orgs/geneontology/projects/13] (Suzi L, Kimberly)<br />
** See [[:Category:Gene_Product_to_Term_Relations]]<br />
** UPDATE: GP2Term Relations coming from Noctua (Chris)<br />
** UPDATE/discussion: Enabling usage by users and bioinformaticians (Deepak, Laurent-Phillippe)<br />
** UPDATE: Display in AmiGO (Suzi L, Seth)<br />
<br />
== Quality Control Projects == <br />
<br />
* Report: QC group: annotation review stats<br />
* Cancer signaling pathways review (note: I also have this under GP2Term relations below; Chris)<br />
** Case study: [http://xena.ucsc.edu/ Xena] and cancer signaling project, [http://xenademo.berkeleybop.io/xena/ demo] (Suzi L)<br />
<br />
===Ideas for QC approaches===<br />
*Estimating literature coverage in curation*<br />
**(Requested by SAB and all the time)<br />
***Get stats for <br />
**** # genes with some annotation (IBA | EXP - separately - exclude HTP and probably ‘protein binding') <br />
**** # annotations per gene -> group by: >100 annotations, 50-100 annotations, 10-50 annotations, <10 annotations<br />
**** # papers per gene -> group by: >100 papers, 50-100 papers, 10-50 papers, <10 papers<br />
<br />
== External Projects==<br />
* Impact of GO qualifiers on Alliance gene descriptions (Mary D)<br />
<br />
=Sunday PM=<br />
==Breakout sessions ==<br />
===Alignment of Rhea, Reactome, IntAct and GO===<br />
Alan B, Peter D, Sandra/Birgit, Jim, Ben?<br />
With their recommendations for moving forward. GH ticket is here [https://github.com/geneontology/go-ontology/issues/14984] <br />
<br />
<br />
===QA and metrics===<br />
Suzi, Val, Kimberly, Pascale, Eric .. ?<br />
<br />
=Will we be talking about those??=<br />
== Future New Projects ==<br />
<br />
==Evolutionary taxon relations== <br />
(Paul, Chris)<br />
<br />
==Tickets==<br />
* Redundant annotations: <BR><br />
** https://github.com/geneontology/go-annotation/issues/1879<br />
<br />
* Main GAF file: providing a high confidence GAF file<br />
** https://github.com/geneontology/go-ontology/issues/15498<br />
<br />
* GOC-OWL inference pipeline concerns <br />
**https://github.com/geneontology/go-annotation/issues/1487<br />
<br />
==Other potential topics==<br />
* Documentation of rules: Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928<br />
* 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<br />
<br />
== Suggestions for topics Fall 2018==<br />
*'Response to' workshop (similar to the signaling WS)<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2018_NYU_GOC_Meeting_Agenda&diff=687252018 NYU GOC Meeting Agenda2018-05-02T20:46:14Z<p>Suzi: /* Quality Control Projects */</p>
<hr />
<div><br />
= Suggestions for topics=<br />
<br />
== Intro/Overview ==<br />
Paul T<br />
* Mention Alliance <br />
* Beginning new fiscal year<br />
<br />
== Infrastructure Projects ==<br />
<br />
* Release pipeline/new release cycle [https://github.com/orgs/geneontology/projects/11] (Seth, Eric)<br />
** Documentation https://github.com/geneontology/go-site/issues/555<br />
** UPDATE: Injection of PAINT annotations at GO Central (Huaiyu)<br />
** Discussion: Injection of GPADs derived from production GO-CAMs (Chris)<br />
** Automated QC (Eric, Kimberly)<br />
* public API (Nathan, Deepak)<br />
** Example of use: Ribbon (Nathan)<br />
* Interaction with data commons (Paul/Chris)<br />
* Enrichment analysis in the cloud (Paul/Chris)<br />
<br />
== GO-CAM and Noctua Project == <br />
<br />
* Noctua status reports<br />
** 1.0 Release [https://github.com/orgs/geneontology/projects/6] Seth, Chris<br />
** Tour of the Noctua Form: Tremayne, Paul<br />
** Importing Reactome into Noctua: Ben, David<br />
** Seeding models from GAFs: Dustin, Eric<br />
** Roll-out plan: Kimberley<br />
* Community usage of GO-CAMs<br />
** GO-CAM landing page [https://github.com/geneontology/go-site/issues/558] (Laurent-Phillippe)<br />
** Export to other formats and import into other databases (Laurent-Phillippe)<br />
** Loading GO-CAM annotations into MODS- The MGI Experience (David H)<br />
<br />
== Noctua Form hands-on session ==<br />
(Paul's suggestion) - 1.5h <br />
All curators should come with a paper or pathway that they would like to curate.<br />
Suggestion: curate signaling pathways?<br />
<br />
== Documentation and Outreach ==<br />
<br />
* Presentation of update website/Report on Documentation jamboree<br />
* Outreach plans (Suzi A)<br />
** SOPs for groups that want to submit annotations to the GOC<br />
* Licensing and community annotation (Seth?) <br / > With the possibility of a wider pool of annotation ingest, we should consider a copyright re-assignment policy to the GOC, getting pass-through agreements from re-used upstream resources (the http://reusabledata.org evaluation of Reactome, while possibly out of date, can be illustrative in the context of bulk model import), as well as the legal nature of the GOC.<br />
<br />
== Projects ==<br />
<br />
=== Signaling Workshop Project ===<br />
Paul/Pascale: Can we give an overview/lessons learned summary ? General principles: <br />
* start and end of pathways<br />
* underannotation<br />
* overannotation<br />
* what does it mean to be part of a pathway/upstream/etc<br />
<br />
* Canonical Wnt Signaling (Kimberly VA and Helen) (https://github.com/geneontology/go-annotation/issues/1595)<br />
** Report on Ontology Changes<br />
** Report on Annotation Review<br />
*** Reviews Completed<br />
*** Reviews Outstanding<br />
*** New Annotation Practice Guidelines<br />
<br />
* MAPK Cascade (DavidH and SabrinaT) (https://github.com/geneontology/go-annotation/issues/1592)<br />
** Report on ontology changes<br />
** Report on Annotation Review<br />
*** Reviews Completed<br />
*** Reviews Outstanding<br />
*** New Annotation Practice Guidelines<br />
<br />
* GPCR signaling (Pascale or Petra)(https://github.com/geneontology/go-annotation/issues/1591)<br />
** Report on ontology changes<br />
** Report on Annotation Review<br />
*** Reviews Completed<br />
*** Reviews Outstanding<br />
*** New Annotation Practice Guidelines<br />
<br />
* JAK/STAT cascade (Ruth Lovering) (https://github.com/geneontology/go-annotation/issues/1628)<br />
** Report on ontology changes<br />
** Report on Annotation Review<br />
*** Reviews Completed<br />
*** Reviews Outstanding<br />
*** New Annotation Practice Guidelines<br />
<br />
=== Other projects ===<br />
<br />
* HTP annotations : present annotation guidelines<br />
* Complex working group report<br />
** Various tickets about complexes<br />
*** https://github.com/geneontology/go-ontology/issues/15211<br />
*** https://github.com/geneontology/go-ontology/issues/11094<br />
*** https://github.com/geneontology/go-ontology/issues/11382<br />
*** https://github.com/geneontology/go-ontology/issues/14375<br />
* Update MF refactor (Pascale)<br />
* Update: Tx refactor (Pascale)<br />
<br />
== PAINT update == <br />
Huaiyu ~30-45 minutes<br />
<br />
== GP2Term Relations ==<br />
GitHub Project: [https://github.com/orgs/geneontology/projects/13] (Suzi L, Kimberly)<br />
** See [[:Category:Gene_Product_to_Term_Relations]]<br />
** UPDATE: GP2Term Relations coming from Noctua (Chris)<br />
** UPDATE/discussion: Enabling usage by users and bioinformaticians (Deepak, Laurent-Phillippe)<br />
** UPDATE: Display in AmiGO (Suzi L, Seth)<br />
<br />
== Quality Control Projects == <br />
<br />
* Report: QC group: annotation review stats<br />
* Cancer signaling pathways review (note: I also have this under GP2Term relations below; Chris)<br />
** Case study: [http://xena.ucsc.edu/ Xena] and cancer signaling project, [http://xenademo.berkeleybop.io/xena/ demo] (Suzi L)<br />
<br />
===Ideas for QC approaches===<br />
*Estimating literature coverage in curation*<br />
**(Requested by SAB and all the time)<br />
***Get stats for <br />
**** # genes with some annotation (IBA | EXP - separately - exclude HTP and probably ‘protein binding') <br />
**** # annotations per gene -> group by: >100 annotations, 50-100 annotations, 10-50 annotations, <10 annotations<br />
**** # papers per gene -> group by: >100 papers, 50-100 papers, 10-50 papers, <10 papers<br />
<br />
== External Projects==<br />
* Impact of GO qualifiers on Alliance gene descriptions (Mary D)<br />
<br />
<br />
==Breakout sessions==<br />
===Alignment of Rhea, Reactome, IntAct and GO===<br />
<br />
With their recommendations for moving forward. GH ticket is here [https://github.com/geneontology/go-ontology/issues/14984] (Jim, Ben?)<br />
<br />
<br />
===QA and metrics===<br />
<br />
=Will we be talking about those??=<br />
== Future New Projects ==<br />
<br />
==Evolutionary taxon relations== <br />
(Paul, Chris)<br />
<br />
==Tickets==<br />
* GP annotations to terms that refer to 'drugs'<br />
** https://github.com/geneontology/go-ontology/issues/15379<br />
<br />
* Redundant annotations: <BR><br />
** https://github.com/geneontology/go-annotation/issues/1879<br />
<br />
* Main GAF file: providing a high confidence GAF file<br />
** https://github.com/geneontology/go-ontology/issues/15498<br />
<br />
* GOC-OWL inference pipeline concerns <br />
**https://github.com/geneontology/go-annotation/issues/1487<br />
<br />
==Other potential topics==<br />
* Documentation of rules: Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928<br />
* 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<br />
<br />
== Suggestions for topics Fall 2018==<br />
*'Response to' workshop (similar to the signaling WS)<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2018_NYU_GOC_Meeting_Agenda&diff=687242018 NYU GOC Meeting Agenda2018-05-02T20:43:51Z<p>Suzi: /* Quality Control Projects */</p>
<hr />
<div><br />
= Suggestions for topics=<br />
<br />
== Intro/Overview ==<br />
Paul T<br />
* Mention Alliance <br />
* Beginning new fiscal year<br />
<br />
== Infrastructure Projects ==<br />
<br />
* Release pipeline/new release cycle [https://github.com/orgs/geneontology/projects/11] (Seth, Eric)<br />
** Documentation https://github.com/geneontology/go-site/issues/555<br />
** UPDATE: Injection of PAINT annotations at GO Central (Huaiyu)<br />
** Discussion: Injection of GPADs derived from production GO-CAMs (Chris)<br />
** Automated QC (Eric, Kimberly)<br />
* public API (Nathan, Deepak)<br />
** Example of use: Ribbon (Nathan)<br />
* Interaction with data commons (Paul/Chris)<br />
* Enrichment analysis in the cloud (Paul/Chris)<br />
<br />
== GO-CAM and Noctua Project == <br />
<br />
* Noctua status reports<br />
** 1.0 Release [https://github.com/orgs/geneontology/projects/6] Seth, Chris<br />
** Tour of the Noctua Form: Tremayne, Paul<br />
** Importing Reactome into Noctua: Ben, David<br />
** Seeding models from GAFs: Dustin, Eric<br />
** Roll-out plan: Kimberley<br />
* Community usage of GO-CAMs<br />
** GO-CAM landing page [https://github.com/geneontology/go-site/issues/558] (Laurent-Phillippe)<br />
** Export to other formats and import into other databases (Laurent-Phillippe)<br />
** Loading GO-CAM annotations into MODS- The MGI Experience (David H)<br />
<br />
== Noctua Form hands-on session ==<br />
(Paul's suggestion) - 1.5h <br />
All curators should come with a paper or pathway that they would like to curate.<br />
Suggestion: curate signaling pathways?<br />
<br />
== Documentation and Outreach ==<br />
<br />
* Presentation of update website/Report on Documentation jamboree<br />
* Outreach plans (Suzi A)<br />
** SOPs for groups that want to submit annotations to the GOC<br />
* Licensing and community annotation (Seth?) <br / > With the possibility of a wider pool of annotation ingest, we should consider a copyright re-assignment policy to the GOC, getting pass-through agreements from re-used upstream resources (the http://reusabledata.org evaluation of Reactome, while possibly out of date, can be illustrative in the context of bulk model import), as well as the legal nature of the GOC.<br />
<br />
== Projects ==<br />
<br />
=== Signaling Workshop Project ===<br />
Paul/Pascale: Can we give an overview/lessons learned summary ? General principles: <br />
* start and end of pathways<br />
* underannotation<br />
* overannotation<br />
* what does it mean to be part of a pathway/upstream/etc<br />
<br />
* Canonical Wnt Signaling (Kimberly VA and Helen) (https://github.com/geneontology/go-annotation/issues/1595)<br />
** Report on Ontology Changes<br />
** Report on Annotation Review<br />
*** Reviews Completed<br />
*** Reviews Outstanding<br />
*** New Annotation Practice Guidelines<br />
<br />
* MAPK Cascade (DavidH and SabrinaT) (https://github.com/geneontology/go-annotation/issues/1592)<br />
** Report on ontology changes<br />
** Report on Annotation Review<br />
*** Reviews Completed<br />
*** Reviews Outstanding<br />
*** New Annotation Practice Guidelines<br />
<br />
* GPCR signaling (Pascale or Petra)(https://github.com/geneontology/go-annotation/issues/1591)<br />
** Report on ontology changes<br />
** Report on Annotation Review<br />
*** Reviews Completed<br />
*** Reviews Outstanding<br />
*** New Annotation Practice Guidelines<br />
<br />
* JAK/STAT cascade (Ruth Lovering) (https://github.com/geneontology/go-annotation/issues/1628)<br />
** Report on ontology changes<br />
** Report on Annotation Review<br />
*** Reviews Completed<br />
*** Reviews Outstanding<br />
*** New Annotation Practice Guidelines<br />
<br />
=== Other projects ===<br />
<br />
* HTP annotations : present annotation guidelines<br />
* Complex working group report<br />
** Various tickets about complexes<br />
*** https://github.com/geneontology/go-ontology/issues/15211<br />
*** https://github.com/geneontology/go-ontology/issues/11094<br />
*** https://github.com/geneontology/go-ontology/issues/11382<br />
*** https://github.com/geneontology/go-ontology/issues/14375<br />
* Update MF refactor (Pascale)<br />
* Update: Tx refactor (Pascale)<br />
<br />
== PAINT update == <br />
Huaiyu ~30-45 minutes<br />
<br />
== GP2Term Relations ==<br />
GitHub Project: [https://github.com/orgs/geneontology/projects/13] (Suzi L, Kimberly)<br />
** See [[:Category:Gene_Product_to_Term_Relations]]<br />
** UPDATE: GP2Term Relations coming from Noctua (Chris)<br />
** UPDATE/discussion: Enabling usage by users and bioinformaticians (Deepak, Laurent-Phillippe)<br />
** UPDATE: Display in AmiGO (Suzi L, Seth)<br />
<br />
== Quality Control Projects == <br />
<br />
* Report: QC group: annotation review stats<br />
* Cancer signaling pathways review (note: I also have this under GP2Term relations below; Chris)<br />
** Case study: [http://xena.ucsc.edu/ Xena] and cancer signaling project (Suzi L)<br />
<br />
===Ideas for QC approaches===<br />
*Estimating literature coverage in curation*<br />
**(Requested by SAB and all the time)<br />
***Get stats for <br />
**** # genes with some annotation (IBA | EXP - separately - exclude HTP and probably ‘protein binding') <br />
**** # annotations per gene -> group by: >100 annotations, 50-100 annotations, 10-50 annotations, <10 annotations<br />
**** # papers per gene -> group by: >100 papers, 50-100 papers, 10-50 papers, <10 papers<br />
<br />
== External Projects==<br />
* Impact of GO qualifiers on Alliance gene descriptions (Mary D)<br />
<br />
<br />
==Breakout sessions==<br />
===Alignment of Rhea, Reactome, IntAct and GO===<br />
<br />
With their recommendations for moving forward. GH ticket is here [https://github.com/geneontology/go-ontology/issues/14984] (Jim, Ben?)<br />
<br />
<br />
===QA and metrics===<br />
<br />
=Will we be talking about those??=<br />
== Future New Projects ==<br />
<br />
==Evolutionary taxon relations== <br />
(Paul, Chris)<br />
<br />
==Tickets==<br />
* GP annotations to terms that refer to 'drugs'<br />
** https://github.com/geneontology/go-ontology/issues/15379<br />
<br />
* Redundant annotations: <BR><br />
** https://github.com/geneontology/go-annotation/issues/1879<br />
<br />
* Main GAF file: providing a high confidence GAF file<br />
** https://github.com/geneontology/go-ontology/issues/15498<br />
<br />
* GOC-OWL inference pipeline concerns <br />
**https://github.com/geneontology/go-annotation/issues/1487<br />
<br />
==Other potential topics==<br />
* Documentation of rules: Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928<br />
* 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<br />
<br />
== Suggestions for topics Fall 2018==<br />
*'Response to' workshop (similar to the signaling WS)<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2018_NYU_SAB_Meeting_Agenda&diff=682772018 NYU SAB Meeting Agenda2018-03-26T19:57:17Z<p>Suzi: /* Important points from the 2015 SAB report */</p>
<hr />
<div>[[Category: GO Consortium Meetings]]<br />
<br />
==date: May 15, 2018 ==<br />
<br />
=TO DO=<br />
* Go over last SAB report, make sure we've addressed everything <br />
<br />
<br />
* What materials do we need to prepare in advance ? <br />
** Update on priorities/progress<br />
** Metrics of our accomplishments <br />
<br />
* Are there any specific questions we have for the SAB?<br />
<br />
<br />
=What we'd like to show=<br />
* Noctua 1.0: demo, show groups using it<br />
<br />
=Important points from the 2015 SAB report=<br />
* Organization of the GOC<br />
** Goals<br />
** GOC projects and resources<br />
** QA group<br />
* Tools: <br />
** PAINT<br />
*** update functionality, pipeline<br />
*** show impact using one of Suzi's TCGA cancer pathways<br />
** Noctua<br />
*** Ask David H to report MGI's experience with Noctua<br />
** Capella: paper viewer tool<br />
* Broader community initiatives <br />
** Developer community: R packages for GO (technical outreach)<br />
** Draft some best practices for the developer community (See also paper - reproduciblity with GO PMID:29572502)<br />
** Best practices document for using GO, including GO enrichment (Paul)<br />
** Suggestion to have a “Certified GO tool developer” program with badges (not implement but what do people think ? can we also do that for curators? <br />
** Can GO partner with other enrichment tools beyond panther? <br />
** Make GO data available via web services to help people keep their data up to date (ongoing)<br />
** What is the future of https://github.com/cmungall/term-enrichment-protocol for standardizing among various enrichment tools? (not updated since 2014) <br />
** Create an index of external tools that have been evaluated by key standard metrics and this could translate into a gold star rating system on the GO website -> '''No resources to do that'''<br />
<br />
* Provide geneontology.org progress/usage metrics, particularly usage of enrichment analysis and compare to DAVID stats - see 2017 progress report for ideas<br />
** GO should provide more information about literature coverage in curation, so that users are better-informed about potential gaps and progress in annotation.<br />
* Outreach group<br />
<br />
=Questions we'd like to ask=<br />
* Should we push out GO-CAMs into pathway databases like pathwaycommons, ndex, ...?<br />
* Are there other communities that the SAB recommends/suggests we connect with ?</div>Suzihttps://wiki.geneontology.org/index.php?title=2018_NYU_GOC_Meeting_Agenda&diff=678282018 NYU GOC Meeting Agenda2018-03-07T16:33:50Z<p>Suzi: </p>
<hr />
<div><br />
== Suggestions for topics==<br />
* Presentation of update website/Report on Documentation jamboree<br />
* Report on ontology development group (see https://github.com/geneontology/go-ontology/milestone/5)<br />
** action item review<br />
* Report: Annotation group (https://github.com/geneontology/go-annotation/milestone/2)<br />
** Status Signaling workshop tasks<br />
* Report: QC group: annotation review stats <br />
** Cancer signaling pathways review<br />
* HTP annotations : present annotation guidelines<br />
* Complex working group report <br />
<br />
<br />
* Report from ontology group on alignment of Rhea, Reactome, IntAct and GO with their recommendations for moving forward. GH ticket is here [https://github.com/geneontology/go-ontology/issues/14984]<br />
<br />
<br />
* Noctua status report (announce 1.0 release). Complete roll-out plan for introducing other GOC members to its use<br />
<br />
<br />
== Suggestions for topics Fall 2018==<br />
*'Response to' workshop (similar to the signaling WS)<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2018_NYU_GOC_Meeting_Agenda&diff=678272018 NYU GOC Meeting Agenda2018-03-07T16:32:39Z<p>Suzi: </p>
<hr />
<div><br />
== Suggestions for topics==<br />
* Presentation of update website/Report on Documentation jamboree<br />
* Report on ontology development group (see https://github.com/geneontology/go-ontology/milestone/5)<br />
** action item review<br />
* Report: Annotation group<br />
** Status Signaling workshop tasks<br />
* Report: QC group: annotation review stats <br />
** Cancer signaling pathways review<br />
* HTP annotations : present annotation guidelines<br />
* Complex working group report <br />
<br />
<br />
* Report from ontology group on alignment of Rhea, Reactome, IntAct and GO with their recommendations for moving forward. GH ticket is here [https://github.com/geneontology/go-ontology/issues/14984]<br />
<br />
<br />
* Noctua status report (announce 1.0 release). Complete roll-out plan for introducing other GOC members to its use<br />
<br />
<br />
== Suggestions for topics Fall 2018==<br />
*'Response to' workshop (similar to the signaling WS)<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2018_NYU_GOC_Meeting_Agenda&diff=678262018 NYU GOC Meeting Agenda2018-03-07T16:29:00Z<p>Suzi: </p>
<hr />
<div><br />
== Suggestions for topics==<br />
* Presentation of update website/Report on Documentation jamboree<br />
* Report on ontology development group <br />
* Report: Annotation group<br />
** Status Signaling workshop tasks<br />
* Report: QC group: annotation review stats <br />
** Cancer signaling pathways review<br />
* HTP annotations : present annotation guidelines<br />
* Complex working group report <br />
<br />
<br />
* Report from ontology group on alignment of Rhea, Reactome, IntAct and GO with their recommendations for moving forward. GH ticket is here [https://github.com/geneontology/go-ontology/issues/14984]<br />
<br />
<br />
* Noctua status report (announce 1.0 release). Complete roll-out plan for introducing other GOC members to its use<br />
<br />
<br />
== Suggestions for topics Fall 2018==<br />
*'Response to' workshop (similar to the signaling WS)<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2018_NYU_GOC_Meeting_Agenda&diff=678212018 NYU GOC Meeting Agenda2018-03-07T16:17:22Z<p>Suzi: </p>
<hr />
<div><br />
== Suggestions for topics==<br />
* Presentation of update website/Report on Documentation jamboree<br />
* Report on ontology development group <br />
* Report: Annotation group<br />
** Status Signaling workshop tasks<br />
* Report: QC group: annotation review stats <br />
** Cancer signaling pathways review<br />
* HTP annotations : present annotation guidelines<br />
<br />
<br />
* Report from ontology group on alignment of Rhea, Reactome, IntAct and GO with their recommendations for moving forward. GH ticket is here [https://github.com/geneontology/go-ontology/issues/14984]<br />
<br />
<br />
* Noctua status report (announce 1.0 release). Complete roll-out plan for introducing other GOC members to its use<br />
<br />
<br />
== Suggestions for topics Fall 2018==<br />
*'Response to' workshop (similar to the signaling WS)<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2018_NYU_GOC_Meeting_Agenda&diff=678202018 NYU GOC Meeting Agenda2018-03-07T16:15:50Z<p>Suzi: </p>
<hr />
<div><br />
== Suggestions for topics==<br />
* Presentation of update website/Report on Documentation jamboree<br />
* Report on ontology development group <br />
* Report: Annotation group<br />
** Status Signaling workshop tasks<br />
* Report: QC group: annotation review stats <br />
** Cancer signaling pathways review<br />
* HTP annotations : present annotation guidelines<br />
<br />
<br />
* Report from ontology group on alignment of Rhea, Reactome, IntAct and GO with their recommendations for moving forward. GH ticket is here [https://github.com/geneontology/go-ontology/issues/14984]<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Suggestions for topics Fall 2018==<br />
*'Response to' workshop (similar to the signaling WS)<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2018_NYU_GOC_Meeting_Agenda&diff=678192018 NYU GOC Meeting Agenda2018-03-07T16:15:02Z<p>Suzi: </p>
<hr />
<div><br />
== Suggestions for topics==<br />
* Presentation of update website/Report on Documentation jamboree<br />
* Report on ontology development group <br />
* Report: Annotation group<br />
** Status Signaling workshop tasks<br />
* Report: QC group: annotation review stats <br />
* HTP annotations : present annotation guidelines<br />
<br />
<br />
* Report from ontology group on alignment of Rhea, Reactome, IntAct and GO with their recommendations for moving forward. GH ticket is here [https://github.com/geneontology/go-ontology/issues/14984]<br />
<br />
<br />
<br />
<br />
<br />
<br />
== Suggestions for topics Fall 2018==<br />
*'Response to' workshop (similar to the signaling WS)<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2018_NYU_GOC_Meeting_Logistics&diff=675322018 NYU GOC Meeting Logistics2018-02-16T02:30:20Z<p>Suzi: /* Attendees */</p>
<hr />
<div>More details will be available in the next few weeks. Meanwhile, here is some information to help you make travel arrangements. The meeting will start first thing on Saturday May 12 (so plan to arrive on Friday) and will end on Monday May 14 early enough in the afternoon to allow people to get to the airport for overnight flights to Europe.<br><br>See you in May!<br />
<br />
==Registration fee==<br />
Amount and payment details to be determined, but we hope to keep the amount low and find a convenient way to pay.<br />
<br />
==Meeting site==<br />
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; the meeting room is immediately on your left at street level.<br />
<br />
=Travel=<br />
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.<br />
==[https://www.jfkairport.com/#/ Kennedy Airport] details==<br />
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.<br />
==[https://www.newarkairport.com/#/ Newark Airport] details==<br />
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.)<br />
<br />
==[http://laguardiaairport.com/ LaGuardia Airport] details==<br />
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.<br />
<br />
==By train==<br />
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).<br />
<br />
==By car==<br />
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.<br />
<br />
=Accommodations=<br />
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 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.<br />
<br />
=Attendees=<br />
Please add your name to the table if you intend to attend the meeting, and the dinner (Sunday), so we can get a headcount estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Attend the GOC meeting?<br />
! Attend the GOC dinner?<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|-<br />
| Suzanna Lewis<br />
| GO@LBNL<br />
| Yes<br />
| Yes<br />
|-<br />
| David Hill<br />
| MGI/GOC<br />
| Yes<br />
| No<br />
|-<br />
|Judy Blake<br />
| MGI/GOC<br />
| Yes<br />
| Yes<br />
|-<br />
|Pascale Gaudet<br />
| SIB/GOC<br />
| Yes<br />
| Yes<br />
|-<br />
|Seth Carbon<br />
| LBL<br />
| Yes<br />
| Yes<br />
|-<br />
|Stacia Engel<br />
| SGD Stanford<br />
| Yes<br />
| Yes<br />
|-<br />
|Mike Cherry<br />
| SGD Stanford<br />
| Yes<br />
| Yes<br />
|-<br />
|}<br />
<br />
If you plan to attend remotely, please sign up here and indicate the sessions you are likely to attend:<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Saturday AM<br />
! Saturday PM<br />
! Sunday AM<br />
! Sunday PM<br />
! Monday AM<br />
|-<br />
| Joe Placeholder<br />
| none<br />
| yes<br />
| no<br />
| no<br />
| no<br />
| yes<br />
|-<br />
|}<br />
<br />
AM sessions will start at approximately 9 AM EDT / 2 PM BST / 6 AM PDT; PM sessions will start at approximately 2 PM EDT / 7 PM BST / 11 AM PDT.<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=Consortium_Meetings_and_Workshops&diff=65417Consortium Meetings and Workshops2017-10-05T16:33:45Z<p>Suzi: </p>
<hr />
<div>=GOC Meetings=<br />
==2018==<br />
*Next GOC meeting to be held May 12-14 at NYU, more details coming soon<br />
*"20th" anniversary meeting to be held in Montreal some time in the fall<br />
<br />
==2017==<br />
<br />
* GOC Meeting, Cambridge, UK, October 2-4, 2017<br />
** [[2017 Cambridge GOC Meeting Logistics]]<br />
** [[2017 Cambridge GOC Meeting Agenda]]<br />
** [[2017 Cambridge GOC Signalling Workshop]]<br />
* GOC GO Editors Workshop II, Berkeley, Aug 15-17<br />
**[[2017 Berkeley GO Editors Workshop II]]<br />
* GOC Meeting, Corvallis, Oregon, June 1-3 (plus workshops June 4-5), 2017<br />
** Logistics: https://sites.google.com/view/goc2017<br />
** [[2017 Corvallis GOC Meeting Agenda]]<br />
* GOC Protege Training Meeting Feb. 22, 23, and 24<br />
**[[Protege-OWL_Berkeley_Training_Logistics]]<br />
**Agenda: https://github.com/geneontology/protege-tutorial<br />
**Example tickets<br />
*** Adding a term: https://github.com/geneontology/go-ontology/issues/12996<br />
*** Obsoleting terms: https://github.com/geneontology/go-ontology/issues/12923<br />
*** Adding a term to a slim: https://github.com/geneontology/go-ontology/issues/13031<br />
*** Adding a taxon restriction:<br />
*** Merging terms https://github.com/geneontology/go-ontology/issues/12782<br />
<br />
==2016==<br />
* GOC Meeting, Los Angeles, November 4-6, 2016<br />
** [[2016 Los Angeles GOC Meeting Logistics]] <br />
** [[2016 Los Angeles GOC Meeting Agenda]]<br />
* Hinxton LEGO/Noctua Training, Hinxton, August 31 - September 02, 2016<br />
** [[2016 Hinxton LEGO/Noctua Training Logistics]] <br />
** [[2016 Hinxton LEGO/Noctua Training Agenda]]<br />
* GOC Meeting, Geneva, Switzerland, April 15-16, 2016<br />
** [[2016 Geneva GOC Meeting Logistics]] <br />
** [[2016 Geneva GOC Meeting Agenda]]<br />
<br />
==2015==<br />
* LEGO Jamboree, Geneva, Switzerland, December 8-10, 2015<br />
** [[2015 LEGO Jamboree Logistics]]<br />
* GOC Meeting, Washington, DC, August 30 - September 2, 2015<br />
** [[2015 Washington DC GOC Meeting Logistics]] <br />
** [[2015 Washington DC GOC Meeting Agenda]]<br />
** [[2015 Washington DC GOC Meeting Minutes]] <br />
** [[2015 Washington DC GOC Symposium Agenda]] <br />
** [[2015 Washington DC GOC Scientific Advisory Board Meeting Agenda]]<br />
* GOC All Hands Teleconference, April 1, 2015 <br />
** [[April 2015 GOC Teleconference Agenda and Logistics]]<br />
** [[April 2015 GOC Teleconference Minutes]]<br />
<br />
==2014==<br />
* GOC Meeting, Barcelona, October 13-15, 2014<br />
** [[2014 Barcelona Meeting Logistics]]<br />
** [[2014_Barcelona GOC Meeting_Agenda]]<br />
** [https://docs.google.com/document/d/1NonH97s8xEpDdx6DfonKPKI_RdHbbG-yft85UZtUmF0/edit#heading=h.2hxg96gzn5xe 2014 Barcelona Meeting Minutes]<br />
* PAINT Jamboree, Stanford CA, July 28-31, 2014<br />
** [[PAINT 2014 Summer Jamboree Kickoff Meeting Logistics]]<br />
* GOC Meeting, College Station, TX, March 16-17, 2014<br />
** [[2014 College Station Logistics]] <br />
** [[2014 College Station GOC Meeting Agenda]]<br />
<br />
==2013==<br />
* GOC Meeting, Bar Harbor, Maine, October (3), 4-6, 2013<br />
** [[2013 Bar Harbor Logistics]] <br />
** [[2013 Bar Harbor GOC Meeting Agenda]] <br />
** [[2013 GO Challenge]]<br />
* GOC Meeting, Cambridge, UK, April 11 - 13, 2013<br />
** [[2013 Cambridge Logistics]]<br />
** [[2013 Cambridge GOC Meeting Agenda]]<br />
** [[2013 Cambridge GOC Scientific Advisory Board Meeting Agenda]]<br />
* [http://www.ebi.ac.uk/biocuration2013/ BioCurator]<br />
<br />
==2012==<br />
*PAINT Training meeting, Stanford, Dec 10-13 2012<br />
** [[2012 PAINT workshop Logistics]] | [[2012 PAINT]] <br />
* GOC Meeting, Caltech, Pasadena, October 7 - 9, 2012<br />
** [[2012 Caltech GOC Meeting Logistics]] - [http://wiki.geneontology.org/index.php/2012_GOC_Meeting_Caltech 2012 Caltech GOC Meeting Agenda]<br />
* CAT Meeting, Caltech<br />
** [http://wiki.geneontology.org/index.php/Common_Annotation_Framework_Specification#Working_Meeting.2C_Caltech.2C_June_4th-8th.2C_2012 CAT meeting]<br />
* GOC Annotation Meeting, Stanford University, 26-28th February 2012<br />
** [[2012 Stanford Annotation Meeting Logistics]] - [http://wiki.geneontology.org/index.php/2012_Annotation_Meeting_Stanford 2012 Annotation Meeting Agenda]<br />
* [[Hinxton OBO-Edit/Protege 4 workshop Jan 2012 | Protege/OWL workshop]], Hinxton, UK, 30-31st Jan 2012<br />
<br />
==2011==<br />
* GOC meeting, University College London, 7-9th November 2011<br />
** [[2011 UCL Meeting Logistics]] - [[2011 UCL Meeting Agenda]]<br />
<br />
* GOC meeting, University of Southern California, 19-21st May 2011<br />
** [[2011 USC Meeting Logistics]] - [[2011 USC Meeting Agenda]] - [[2011 USC Meeting Action Items]] - [[File:minutes_LA2011.pdf]] Photo<br />
<br />
* UCL GO [http://www.ucl.ac.uk/cardiovasculargeneontology/Outreach/Annotation_Workshops Annotation workshop] London, 6-7th April 2011<br />
<br />
==2010==<br />
* The Jackson Laboratory, Bar Harbor, Maine, GOC Sept 7-9, 2010<br />
** [[2010 Bar Harbor Minutes]]<br />
<br />
* GO annotation camp, Centre Médical Universitaire (CMU) Geneva, Switzerland, June 16-18 2010<br />
** [[2010 GO camp Meeting Logistics]] - [[2010_GO_camp_Meeting_Agenda]]<br />
** [http://wiki.geneontology.org/index.php/Talk:2010_GO_camp_Meeting_Agenda GO camp Meeting Minutes]<br />
* Leland Stanford Jr. University, Stanford, California, GOC March 30-31 & SAB April 1, 2010<br />
** [[2010 Stanford Meeting Minutes]]<br />
<br />
==2009==<br />
* [[Cambridge GO Consortium Meeting | Cambridge Combined GO Consortium and SAB Meeting]] Jesus College, Cambridge, UK, September 23-25, 2009 -- [[2009 Cambridge Meeting Logistics]] <br />
** [[GOC Meeting Minutes September 2009|GOC Meeting Minutes September 2009]]<br />
<br />
<br />
* [[Oregon GO Consortium Meeting]] Eugene, Oregon, March 30, 31, 2009 -- '''[[2009_Oregon_Meeting_Logistics|2009 Oregon Meeting Logistics]]'''<br />
* [[Oregon Reference Genomes Meeting]] Eugene, Oregon, April 1, 2009 -- '''[[2009_Oregon_Meeting_Logistics|2009 Oregon Meeting Logistics]]'''<br />
<br />
==2008==<br />
* [[20th GO Consortium Meeting]] Montreal, October 21-22, 2008 -- '''[[October 2008 Meeting Logistics]]'''<br />
** [[20th_GO_Consortium_Meeting_Minutes | 20th GO Consortium Meeting minutes]]<br />
* [[Oct 2008 SAB Meeting]] Montreal, October 23, 2008 -- '''[[October 2008 Meeting Logistics]]'''<br />
<br />
<br />
* [[SLC GO Reference Genome Project Meeting]], April 20-21, 2008 Univ. of Utah, Salt Lake City, Utah<br />
** [[Reference Genome Meeting Minutes April 2008|Reference Genome Meeting Minutes April 2008]]<br />
** [[April 2008 Meeting logistics summary]]<br />
* [[GO Field Trip]], Afternoon of April 21, 2008: Antelope Island<br />
** [[wildlife and birds seen]] - List of Birds and Mammals<br />
* [[SLC GO Consortium Meeting]], April 22-23, 2008 Univ of Utah, Salt Lake City, Utah Photo:[[http://www.geneontology.org/photo_GO_SaltLakeCity.shtml]]<br />
** [[SLC GO Consortium Meeting Minutes April 2008|SLC GO Consortium Meeting Meeting Minutes April 2008]]<br />
** [[April 2008 Meeting logistics summary]]<br />
* Please [[http://gocwiki.geneontology.org/index.php/Register#Registration_for_April_2008_GO_Meetings_at_University_of_Utah.2C_SLC Register]] for one or both meetings.<br />
<br />
==2007==<br />
*[[GO Reference Genome Meeting]], Sept 26-27th, 2007 Princeton, New Jersey<br />
** [[Reference Genome minutes|Reference Genome minutes]]<br />
** [[September 2007 Meeting logistics summary]]<br />
*[[GO 3rd Advisors Meeting]], September 25th, 2007 Princeton, New Jersey<br />
** [[SAB minutes|Minutes from SAB]]<br />
** [[September 2007 Meeting logistics summary]]<br />
* [[GO 18th Consortium Meeting]], September 23-24th, 2007 Princeton, New Jersey. Photo:[[http://www.geneontology.org/images/photo_GOC_20070923.jpg]]<br />
** [[GO 18th Consortium Meeting Minutes Day 1|Draft Minutes Day 1]]<br />
** [[GO 18th Consortium Meeting Minutes Day 2|Draft Minutes Day 2]]<br />
** [[GO 18th Consortium Meeting Action Items ]]<br />
** [[Outstanding Action Items from 17th GOC Meeting, Cambridge UK]]<br />
** [[September 2007 Meeting logistics summary]]<br />
*[[GO Consortium Meeting 2007]], January 7-10th, 2007 Cambridge UK Photo:[[http://www.geneontology.org/photo_GO_JesusCollege.shtml]], Minutes:[[http://www.geneontology.org/meeting/minutes/20070108_Cambridge.doc]]<br />
*[[GO Advisors Meeting]], September 7th, 2006 Seattle Washington<br />
*Third Annotation Camp, July 10-14th, 2006 Stanford University. Photo:[[http://www.geneontology.org/photo_GO_Annotation_Camp_20060714.shtml]], Minutes:[[http://www.geneontology.org/meeting/minutes/20060710_GOannotCamp_Stanford.pdf]]<br />
----<br />
<br />
==Progress Reports for GOC Meetings==<br />
#Meeting Progress Reports 2011<br />
## [[Meeting_Progress_Reports_November_2011]]<br />
## [[Meeting_Progress_Reports_May_2011]]<br />
#Meeting Progress Reports 2010<br />
## [[Meeting_Progress_Reports_September_2010]]<br />
## [[Meeting_Progress_Reports_March_2010]]<br />
#Meeting Progress Reports 2009<br />
##[[Meeting_Progress_Reports_September_2009]]<br />
##[[Meeting_Progress_Reports_March_2009]]<br />
##[[Meeting_Progress_Reports_September_2009]]<br />
#Meeting Progress Reports 2008<br />
##[[Meeting_Progress_Report_April_2008]]<br />
##[[Meeting Progress Reports October 2008]]<br />
#[[Converting .doc or .docx to Wiki]]<br />
<br />
==Progress Report Templates==<br />
# [[MOD template]] (wiki)<br />
# [[Ontology Development template]]<br />
# [[Outreach and Advocacy report template]]<br />
# [[SO progress report template]]<br />
<br />
==Publications, tutorials, talks, posters==<br />
# [[Publications, tutorials, talks, posters]]<br />
<br />
<br />
[[Category:Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Agenda&diff=653972017 Cambridge GOC Meeting Agenda2017-10-03T10:16:26Z<p>Suzi: /* WHY creating slims - Intro to slim philosophy */</p>
<hr />
<div>GOC Meeting, Cambridge , October 2-4, 2017<br />
<br />
=To all speakers=<br />
Please add your slides to the google drive:<br />
https://drive.google.com/drive/folders/0B7bEr6HANSlGSHY3c2JqNEs2ZUk<br />
=Minutes=<br />
https://docs.google.com/document/d/1Y9_Mvqes3op36TPHgfaS7K5FHnGZLgUApghIFYyUKR8/edit#heading=h.638rbn3dlj1z<br />
=Monday 2nd October 9:00 a.m.=<br />
==Welcome, overview, vision, introductions==<br />
GO PIs<br />
==GO handbook presentation==<br />
===The Gene Ontology and the meaning of biological function (Paul T)===<br />
<br />
<br />
===Translating research data into Gene Ontology annotations (Pascale)=== <br />
(includes a discussion of the issue: background knowledge & protein domains<br />
https://github.com/geneontology/go-annotation/issues/1621)<br />
<br />
===Gene Ontology - annotation extensions (Ruth)===<br />
<br />
=Coffee break 10:30=<br />
<br />
==Ontology Issues and Updates==<br />
===Update on MF refactoring (Pascale and Paul T)===<br />
<br />
===Qualifiers/Relation issues (Kimberly and Chris)===<br />
<br />
====Refresher on Qualifiers/Relations (Chris)====<br />
<br />
https://docs.google.com/presentation/d/1aSr1kguPM9im_SHWGVVDe-7T0PNyvJUnXhMZk54on6Y/edit?usp=sharing<br />
<br />
====Biological Process Relations: Use of Qualifiers in Legacy Annotations====<br />
Proposal: We will apply the general qualifier to all legacy annotations. Each group can provide more specific qualifiers if they have a mechanism to distinguish. <br />
====Regulates relations (Kimberly)====<br />
Adding new qualifiers for the relation between a gene/gene product and a GO term. <br />
*Corvallis discussion:* What should the default relation be? How will we handle regulation? Use a relation, involved in regulation of, or use the precomposed regulation term?<br />
Ruth: There are now 3 ways to say the same thing: - involved_in_regulation_of X - involved_in X regulation - involved_in BP regulates(X)<br />
For annotation purposes and for our users we want one.<br />
DOS: Good point. These are semantically identical, but I agree we need to find a way to only have one: by convention for classic GO annotation and by filtering the output of inference for noctua output. Proposal: If a named regulation class exists: involved_in X regulation ...if not: involved_in {some BP} regulates(X) NOTE: If there was an annotation in Noctua such as ‘regulation of’ ‘very specific term’ and there was no term as ‘regulation of very specific term’ the GOC pipeline would create the annotation to the parent term: ‘regulation of less specific term’. Q: Is this implemented ?<br />
<br />
=Lunch 12:30=<br />
<br />
===Molecular Function Relations===<br />
====Multiple qualifiers for an annotation (Huaiyu)====<br />
<br />
===Cellular Component Relations===<br />
<br />
====CC component annotation guidelines (Kimberly)====<br />
*CC component annotation: what does it mean ? Kimberly to do 1 proposal (out of 3 alternatives)<br />
1. where the protein is active 2. two different meanings: enables or the right RO (part:of, ie just found there) 3. part_of (low information value!)<br />
<br />
*colocalizes with<br />
<br />
==Annotation guidelines and issues (part one)==<br />
===Signaling (Kimberly and David)===<br />
*Report from signaling workshop: David /Kimberly<br />
*Signaling: First attempt at Annotation consistency 2.0 - Kimberly to report on the approach and the outcome.<br />
Discussion points: Limited participation (self-selected to participate). One recommendation may be to ask all active curators to participate, even at some low level https://github.com/orgs/geneontology/projects/<br />
<br />
==Ontology WG update: David==<br />
<br />
=Coffee break 15:30=<br />
===Overview of GO annotations/Noctua (Kimberly & Chris)===<br />
====Getting Noctua ready for production (Kimberly & Seth)====<br />
*Kimberly & Seth Blocking issues list:<br />
** <strike>When importing an annotation from AmiGO using a companion / buddy, source providedBy should be retained <br /> https://github.com/geneontology/noctua/issues/459 </strike><br />
** GAF exports<br />
*** providedBy should be used in GPAD export <br /> https://github.com/geneontology/noctua/issues/502<br />
*** ...<br />
*Action Item Corvallis 2017/06:<br />
**Provide ways for users to recover and digest GO-CAM units (Gene Ontology-based Causal Activity Model). Ideas include rule-based generations of text statements from model, cytoscape view of network described, etc.<br /><small>I believe that this is a more exploratory and open project. We now offer an RDF enpoint, in addition to the APIs we already have, as well as the proposed feeding from AmiGO. If this is still open in the future, it may be very good Hackathon material. Needs more discussion.</small><br />
**ECO codes available for use in Noctua should show how they map up to a classic GO code, and there should be an alert for curators when they are using a code that does NOT map up to a classic code <br /><small>There is no ticket for such functionality. This would likely have to be written into Minerva or as a pre/post check on (some) server.</small><br />
**PRO IDs for use in Noctua <br />https://github.com/geneontology/noctua/issues/429 <br />https://github.com/geneontology/noctua/issues/122<br />
**Fix GPAD export from Noctua <br />https://github.com/geneontology/noctua/issues/418<br />
**Add a SPARTA workbench <br />https://github.com/geneontology/noctua/issues/465<br />
**Working group discussion of evidence on complex Noctua models (Kimberly?)<br />
<br />
====Noctua table view demo (Chris)====<br />
<br />
==Project updates ==<br />
====Report on transcription work/Noctua templates: Astrid GREEKC consortium====<br />
====Report of Reactome-GO connection: David H/Peter D====<br />
<br />
<br />
=Evening: Poster session 17:00=<br />
<br />
=Tuesday 3rd October 9:00 a.m.=<br />
<br />
==Project updates - continued ==<br />
====AGR - report to GOC: PIs====<br />
====SynGO meeting report: Paul T====<br />
<br />
===Documentation and GitHub overview (Kimberly/Seth/David/Pascale)===<br />
Kimberly Action Items Corvallis 2017/06<br />
*Continue with the consolidation of all documentation for ontology editing, and remove all old documents.<br />
*Review annotation documentation and add to github and readthedocs.<br />
*Make sure to mark obsolete pages/doc as such and add a link to the new relevant doc<br />
*Solicit annotation documentation from participating groups for consolidation.<br />
*Make sure to mark docs with ‘Date last reviewed’ so it’s easy for users to know when the documentation was last touched.<br />
*Pascale: additional information associated with GO terms, see GitHub ticket?<br />
*Add and follow action items at https://github.com/orgs/geneontology/projects/3<br />
<br />
<br />
'''How GO now uses GitHub for project management and guidelines for contributors'''<br />
*Where is information relevant to everyone's need<br />
*Groups (Groups.yaml)<br />
*Members<br />
*Etc<br />
<br />
<br />
==Annotation guidelines and issues (part two)==<br />
<br />
===Centralization of InterPro2GO annotations (Paul T)===<br />
Proposal (follow-up from Geneva 2016): <br />
*GO database pulls directly from InterPro2GO for UniProt Reference Proteomes<br />
*MOD identifier is used as primary gene identifier<br />
*Annotations are given "contributed by" InterPro<br />
*MODs pull from GO database, no need to maintain separate InterPro pipelines<br />
<br />
===HTP guidelines (Helen)===<br />
Helen - 15 minutes Report on progress from HTP working group<br />
https://docs.google.com/presentation/d/1oLkKWRSNQ-wWB_CCDxcb3a84hXsfkjl4Jp-kAEkhQUQ/edit#slide=id.g26c97bd257_1_57<br />
*Draft Guidelines https://docs.google.com/document/d/1ScIeclAzUXMe-tU6n0lVfsSwMHpOeNb7uK8On9-iKXc/edit?usp=sharing%7CHTP<br />
<br />
*Provision of new evidence code<br />
*Implementation & adding to guidelines<br />
<br />
==Transcription annotations decision tree==<br />
Ruth Action Items Corvallis 2017/06<br />
*David OS to create transcription regulator activity (proposed by Paul T)<br />
*Proposed changes to decision tree in Corvallis:<br />
**Simplified from previous version. Essentially a choice between ‘regulating transcription by RNA polymerase II’ or ‘regulating gene expression’<br />
**Annotation 5 = contributes_to sequence-specific DNA binding<br />
David: when people do enrichment, they don’t drop contributes_to (ie., pay attention to qualifiers), so all those proteins will come down as ‘DNA binding’ Action item: replace ‘annotation 5’ with ISS annotation (if DNA binding domain) or contributes to annotation 5 with ISS annotation if no DNA binding domain and domains to suggest coactivator<br />
*<br />
**Annotation 3 = nuclear chromatin<br />
Not everyone comfortable with this (ex., Stacia, David) Shouldn’t it be ‘colocalizes_with’? It was previously agreed that the definition for nuclear chromatin: The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus. Source:PMID:20404130 was to be applied. The proteins here include all associated proteins, not limited to just histones. With this statement the TFs are then contributing to chromatin, rather than binding to chromatin or colocalizing with it.<br />
*<br />
**Decision tree to be put up on GOC website.<br />
**Should annotation 4 exist? (Ruth)<br />
<br />
==PAINT update (Huaiyu)==<br />
Huaiyu Action Items Corvallis 2017/06:<br />
*Encourage discussion between PAINT curators and other annotators about terms not used for propagation<br />
*Report how many annotations per species are used for annotation propagation; could even supply this number for propagation specifically to human genes<br />
*Ruth and Huaiyu (others?) will discuss making use of groups that have already annotated specific gene lists to annotate the corresponding PAINT families.<br />
*Smooth out the challenge mechanism to make it easier to do make and resolve<br />
the challenges, identify terms that may be problematic and would benefit from consistency exercises and discussion.<br />
*Get a list of families where terms have not been propagated (?) - Please check this one for clarity.<br />
(added to github project board) Develop mechanism to trigger review of annotated PAINT families.<br />
<br />
<br />
<br />
==Community Support==<br />
===Citing GO (Paul T)===<br />
*Web page<br />
*Tool providers: Action Item Corvallis 2017/06: someone to represent GOC and contact GO tool providers to display version information and state this information needs to be included in any subsequent publication. Plus list the GOC paper to reference, as well as the tool provider reference. See: https://github.com/geneontology/go-site/issues/359 and https://github.com/geneontology/go-site/issues/360<br />
<br />
===Enrichment (Paul T & Suzi)===<br />
*Web page <br />
*Paul Pavlidis…<br />
*Data Commons work<br />
<br />
===GO_Slims (Val, Suzi, Mary)===<br />
====WHY creating slims - Intro to slim philosophy====<br />
* Suzi: For genome overviews, for profiling an individual gene, for particular taxa, for a particular area of biology. Criteria for evaluating a slim<br />
* Val: Slimming tips [https://docs.google.com/presentation/d/1oXzxaJpkm46irdMA0fbKohUgcx5Qm2xkbraZ83ttPXw/edit?usp=sharing_eil&ts=59cd0de3 Slimming tips]<br />
Includes Slim uses, Creating a biologically useful slim (complete coverage by aspect, biologically useful terms i.e sufficient granularity, avoiding single step process terms (i.e functions), different slims for different purposes) (Val: 20 mins)<br />
<br />
====Use and maintenance of slims (Mary)====<br />
Mary: algorithm - 15 minutes<br />
<br />
====HOW to make slims (Chris)====<br />
Yaml format for creating slims/types of slims/target organisms<br />
<br />
* https://github.com/geneontology/go-ontology/issues/12780<br />
* https://github.com/geneontology/go-ontology/issues/14028<br />
* https://github.com/geneontology/go-ontology/issues/12554<br />
<br />
====GO presentation of slims====<br />
Suzi: GO ribbon<br />
Group discussion: how should we present slims in GO: Multiple or one ?<br />
How many slims will be available? How will we represent multiple slims? <br />
(Pascale asks: what are our resources for this? what is the priority? which slims is GO responsible for?)<br />
<br />
=Wednesday 4th October 9:00 a.m.=<br />
==Ongoing work==<br />
===AmiGO (Follow up with Seth)===<br />
*In general, while several of the AmiGO issues are high-priority, there has been limited bandwidth to tackle them in the context of continuing work on Noctua and the replacement pipeline. Several fixes are queued up and will be available before the upcoming SAB meeting.<br />
**In response to: in base_statistics, plotly graph for "Experimental annotation publications by assigner" is confusing https://github.com/geneontology/amigo/issues/429<br />
**From Pascale's question: My understanding is that there are essentially no resources for AmiGO right now so any AmiGO issue is low priority. Is this correct?<br />
<br />
===The Fate of Simple Processes===<br />
*analysis of gene products annotated to phosphorylation but not annotated to a kinase MF term. What did these annotations actually mean? Curators would need to review. Timeline? Deadline? Working group? One possibility would be to use part_of/involved_in relation to phosphorylation for genes also annotated to kinase MF, and causally_upstream_of_or_within for others until curators can re-evaluate.<br />
*Other considerations:<br />
**Helen: are there many the single-step processes?<br />
**Paul: user-oriented approach - is it a useful grouping for our users?<br />
**Ruth: we need to think about the meaning beyond just “phosphorylation”<br />
**Ruth: what are the consequences of removing “phosphorylation” and what happens to all its children?<br />
**Pascale Q: providing that we remove the processes, would it affect the term enrichment analysis?<br />
<br />
===BP refactoring===<br />
*Defining “Cellular Process” and “Multi-Organism Process” terms<br />
*Action item: the comments/examples/notes should be captured, working group to discuss this.<br />
<br />
===Proteoforms===<br />
Establish a working group for when and how to use proteoforms in annotation. (Kimberly with Harold and Li)<br />
===Usability issues===<br />
*What do users want?<br />
**truth (summary/story/model)?<br />
**fishing expeditions?<br />
**api access?<br />
** appropriate licensing<br />
*Who are our users?<br />
**geneticists?<br />
**clinicians?<br />
**computational biologists?<br />
***aggregators<br />
*Use cases: https://github.com/geneontology/go-ontology/issues/13606<br />
*Perhaps discussion of examples of how the GOC members are engaging with the community and how we can do better in the future (suggested by Helen).<br />
* Val: What happened to the user survey? PomBase collected 70 responses from our users but I never heard a summary of the findings at a subsequent meeting. Could somebody give an overview of the results?<br />
<br />
==Addition items - If time allows==<br />
Chris: Where should documentation on term usage go in the ontology? We'd like to create a new type of annotation in Protégé, but the details of the implementation need to be worked out. <br />
<br />
<br />
==Viral processes update (Pascale)==<br />
Action Items Corvallis 2017/06 Check whether the incorporated changes could affect the host proteins. Document the use cases. '''Nothing to report - depends on where documentation will be hosted'''<br />
<br />
==Action Item Review==<br />
<br />
=Wednesday noon-ish Fin=<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Agenda&diff=653962017 Cambridge GOC Meeting Agenda2017-10-03T10:15:44Z<p>Suzi: /* WHY creating slims - Intro to slim philosophy */</p>
<hr />
<div>GOC Meeting, Cambridge , October 2-4, 2017<br />
<br />
=To all speakers=<br />
Please add your slides to the google drive:<br />
https://drive.google.com/drive/folders/0B7bEr6HANSlGSHY3c2JqNEs2ZUk<br />
=Minutes=<br />
https://docs.google.com/document/d/1Y9_Mvqes3op36TPHgfaS7K5FHnGZLgUApghIFYyUKR8/edit#heading=h.638rbn3dlj1z<br />
=Monday 2nd October 9:00 a.m.=<br />
==Welcome, overview, vision, introductions==<br />
GO PIs<br />
==GO handbook presentation==<br />
===The Gene Ontology and the meaning of biological function (Paul T)===<br />
<br />
<br />
===Translating research data into Gene Ontology annotations (Pascale)=== <br />
(includes a discussion of the issue: background knowledge & protein domains<br />
https://github.com/geneontology/go-annotation/issues/1621)<br />
<br />
===Gene Ontology - annotation extensions (Ruth)===<br />
<br />
=Coffee break 10:30=<br />
<br />
==Ontology Issues and Updates==<br />
===Update on MF refactoring (Pascale and Paul T)===<br />
<br />
===Qualifiers/Relation issues (Kimberly and Chris)===<br />
<br />
====Refresher on Qualifiers/Relations (Chris)====<br />
<br />
https://docs.google.com/presentation/d/1aSr1kguPM9im_SHWGVVDe-7T0PNyvJUnXhMZk54on6Y/edit?usp=sharing<br />
<br />
====Biological Process Relations: Use of Qualifiers in Legacy Annotations====<br />
Proposal: We will apply the general qualifier to all legacy annotations. Each group can provide more specific qualifiers if they have a mechanism to distinguish. <br />
====Regulates relations (Kimberly)====<br />
Adding new qualifiers for the relation between a gene/gene product and a GO term. <br />
*Corvallis discussion:* What should the default relation be? How will we handle regulation? Use a relation, involved in regulation of, or use the precomposed regulation term?<br />
Ruth: There are now 3 ways to say the same thing: - involved_in_regulation_of X - involved_in X regulation - involved_in BP regulates(X)<br />
For annotation purposes and for our users we want one.<br />
DOS: Good point. These are semantically identical, but I agree we need to find a way to only have one: by convention for classic GO annotation and by filtering the output of inference for noctua output. Proposal: If a named regulation class exists: involved_in X regulation ...if not: involved_in {some BP} regulates(X) NOTE: If there was an annotation in Noctua such as ‘regulation of’ ‘very specific term’ and there was no term as ‘regulation of very specific term’ the GOC pipeline would create the annotation to the parent term: ‘regulation of less specific term’. Q: Is this implemented ?<br />
<br />
=Lunch 12:30=<br />
<br />
===Molecular Function Relations===<br />
====Multiple qualifiers for an annotation (Huaiyu)====<br />
<br />
===Cellular Component Relations===<br />
<br />
====CC component annotation guidelines (Kimberly)====<br />
*CC component annotation: what does it mean ? Kimberly to do 1 proposal (out of 3 alternatives)<br />
1. where the protein is active 2. two different meanings: enables or the right RO (part:of, ie just found there) 3. part_of (low information value!)<br />
<br />
*colocalizes with<br />
<br />
==Annotation guidelines and issues (part one)==<br />
===Signaling (Kimberly and David)===<br />
*Report from signaling workshop: David /Kimberly<br />
*Signaling: First attempt at Annotation consistency 2.0 - Kimberly to report on the approach and the outcome.<br />
Discussion points: Limited participation (self-selected to participate). One recommendation may be to ask all active curators to participate, even at some low level https://github.com/orgs/geneontology/projects/<br />
<br />
==Ontology WG update: David==<br />
<br />
=Coffee break 15:30=<br />
===Overview of GO annotations/Noctua (Kimberly & Chris)===<br />
====Getting Noctua ready for production (Kimberly & Seth)====<br />
*Kimberly & Seth Blocking issues list:<br />
** <strike>When importing an annotation from AmiGO using a companion / buddy, source providedBy should be retained <br /> https://github.com/geneontology/noctua/issues/459 </strike><br />
** GAF exports<br />
*** providedBy should be used in GPAD export <br /> https://github.com/geneontology/noctua/issues/502<br />
*** ...<br />
*Action Item Corvallis 2017/06:<br />
**Provide ways for users to recover and digest GO-CAM units (Gene Ontology-based Causal Activity Model). Ideas include rule-based generations of text statements from model, cytoscape view of network described, etc.<br /><small>I believe that this is a more exploratory and open project. We now offer an RDF enpoint, in addition to the APIs we already have, as well as the proposed feeding from AmiGO. If this is still open in the future, it may be very good Hackathon material. Needs more discussion.</small><br />
**ECO codes available for use in Noctua should show how they map up to a classic GO code, and there should be an alert for curators when they are using a code that does NOT map up to a classic code <br /><small>There is no ticket for such functionality. This would likely have to be written into Minerva or as a pre/post check on (some) server.</small><br />
**PRO IDs for use in Noctua <br />https://github.com/geneontology/noctua/issues/429 <br />https://github.com/geneontology/noctua/issues/122<br />
**Fix GPAD export from Noctua <br />https://github.com/geneontology/noctua/issues/418<br />
**Add a SPARTA workbench <br />https://github.com/geneontology/noctua/issues/465<br />
**Working group discussion of evidence on complex Noctua models (Kimberly?)<br />
<br />
====Noctua table view demo (Chris)====<br />
<br />
==Project updates ==<br />
====Report on transcription work/Noctua templates: Astrid GREEKC consortium====<br />
====Report of Reactome-GO connection: David H/Peter D====<br />
<br />
<br />
=Evening: Poster session 17:00=<br />
<br />
=Tuesday 3rd October 9:00 a.m.=<br />
<br />
==Project updates - continued ==<br />
====AGR - report to GOC: PIs====<br />
====SynGO meeting report: Paul T====<br />
<br />
===Documentation and GitHub overview (Kimberly/Seth/David/Pascale)===<br />
Kimberly Action Items Corvallis 2017/06<br />
*Continue with the consolidation of all documentation for ontology editing, and remove all old documents.<br />
*Review annotation documentation and add to github and readthedocs.<br />
*Make sure to mark obsolete pages/doc as such and add a link to the new relevant doc<br />
*Solicit annotation documentation from participating groups for consolidation.<br />
*Make sure to mark docs with ‘Date last reviewed’ so it’s easy for users to know when the documentation was last touched.<br />
*Pascale: additional information associated with GO terms, see GitHub ticket?<br />
*Add and follow action items at https://github.com/orgs/geneontology/projects/3<br />
<br />
<br />
'''How GO now uses GitHub for project management and guidelines for contributors'''<br />
*Where is information relevant to everyone's need<br />
*Groups (Groups.yaml)<br />
*Members<br />
*Etc<br />
<br />
<br />
==Annotation guidelines and issues (part two)==<br />
<br />
===Centralization of InterPro2GO annotations (Paul T)===<br />
Proposal (follow-up from Geneva 2016): <br />
*GO database pulls directly from InterPro2GO for UniProt Reference Proteomes<br />
*MOD identifier is used as primary gene identifier<br />
*Annotations are given "contributed by" InterPro<br />
*MODs pull from GO database, no need to maintain separate InterPro pipelines<br />
<br />
===HTP guidelines (Helen)===<br />
Helen - 15 minutes Report on progress from HTP working group<br />
https://docs.google.com/presentation/d/1oLkKWRSNQ-wWB_CCDxcb3a84hXsfkjl4Jp-kAEkhQUQ/edit#slide=id.g26c97bd257_1_57<br />
*Draft Guidelines https://docs.google.com/document/d/1ScIeclAzUXMe-tU6n0lVfsSwMHpOeNb7uK8On9-iKXc/edit?usp=sharing%7CHTP<br />
<br />
*Provision of new evidence code<br />
*Implementation & adding to guidelines<br />
<br />
==Transcription annotations decision tree==<br />
Ruth Action Items Corvallis 2017/06<br />
*David OS to create transcription regulator activity (proposed by Paul T)<br />
*Proposed changes to decision tree in Corvallis:<br />
**Simplified from previous version. Essentially a choice between ‘regulating transcription by RNA polymerase II’ or ‘regulating gene expression’<br />
**Annotation 5 = contributes_to sequence-specific DNA binding<br />
David: when people do enrichment, they don’t drop contributes_to (ie., pay attention to qualifiers), so all those proteins will come down as ‘DNA binding’ Action item: replace ‘annotation 5’ with ISS annotation (if DNA binding domain) or contributes to annotation 5 with ISS annotation if no DNA binding domain and domains to suggest coactivator<br />
*<br />
**Annotation 3 = nuclear chromatin<br />
Not everyone comfortable with this (ex., Stacia, David) Shouldn’t it be ‘colocalizes_with’? It was previously agreed that the definition for nuclear chromatin: The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus. Source:PMID:20404130 was to be applied. The proteins here include all associated proteins, not limited to just histones. With this statement the TFs are then contributing to chromatin, rather than binding to chromatin or colocalizing with it.<br />
*<br />
**Decision tree to be put up on GOC website.<br />
**Should annotation 4 exist? (Ruth)<br />
<br />
==PAINT update (Huaiyu)==<br />
Huaiyu Action Items Corvallis 2017/06:<br />
*Encourage discussion between PAINT curators and other annotators about terms not used for propagation<br />
*Report how many annotations per species are used for annotation propagation; could even supply this number for propagation specifically to human genes<br />
*Ruth and Huaiyu (others?) will discuss making use of groups that have already annotated specific gene lists to annotate the corresponding PAINT families.<br />
*Smooth out the challenge mechanism to make it easier to do make and resolve<br />
the challenges, identify terms that may be problematic and would benefit from consistency exercises and discussion.<br />
*Get a list of families where terms have not been propagated (?) - Please check this one for clarity.<br />
(added to github project board) Develop mechanism to trigger review of annotated PAINT families.<br />
<br />
<br />
<br />
==Community Support==<br />
===Citing GO (Paul T)===<br />
*Web page<br />
*Tool providers: Action Item Corvallis 2017/06: someone to represent GOC and contact GO tool providers to display version information and state this information needs to be included in any subsequent publication. Plus list the GOC paper to reference, as well as the tool provider reference. See: https://github.com/geneontology/go-site/issues/359 and https://github.com/geneontology/go-site/issues/360<br />
<br />
===Enrichment (Paul T & Suzi)===<br />
*Web page <br />
*Paul Pavlidis…<br />
*Data Commons work<br />
<br />
===GO_Slims (Val, Suzi, Mary)===<br />
====WHY creating slims - Intro to slim philosophy====<br />
* Suzi: For genome overviews, for profiling an individual gene, for particular taxa, for a particular area of biology<br />
* Val: Slimming tips [https://docs.google.com/presentation/d/1oXzxaJpkm46irdMA0fbKohUgcx5Qm2xkbraZ83ttPXw/edit?usp=sharing_eil&ts=59cd0de3 Slimming tips]<br />
Includes Slim uses, Creating a biologically useful slim (complete coverage by aspect, biologically useful terms i.e sufficient granularity, avoiding single step process terms (i.e functions), different slims for different purposes) (Val: 20 mins)<br />
<br />
====Use and maintenance of slims (Mary)====<br />
Mary: algorithm - 15 minutes<br />
<br />
====HOW to make slims (Chris)====<br />
Yaml format for creating slims/types of slims/target organisms<br />
<br />
* https://github.com/geneontology/go-ontology/issues/12780<br />
* https://github.com/geneontology/go-ontology/issues/14028<br />
* https://github.com/geneontology/go-ontology/issues/12554<br />
<br />
====GO presentation of slims====<br />
Suzi: GO ribbon<br />
Group discussion: how should we present slims in GO: Multiple or one ?<br />
How many slims will be available? How will we represent multiple slims? <br />
(Pascale asks: what are our resources for this? what is the priority? which slims is GO responsible for?)<br />
<br />
=Wednesday 4th October 9:00 a.m.=<br />
==Ongoing work==<br />
===AmiGO (Follow up with Seth)===<br />
*In general, while several of the AmiGO issues are high-priority, there has been limited bandwidth to tackle them in the context of continuing work on Noctua and the replacement pipeline. Several fixes are queued up and will be available before the upcoming SAB meeting.<br />
**In response to: in base_statistics, plotly graph for "Experimental annotation publications by assigner" is confusing https://github.com/geneontology/amigo/issues/429<br />
**From Pascale's question: My understanding is that there are essentially no resources for AmiGO right now so any AmiGO issue is low priority. Is this correct?<br />
<br />
===The Fate of Simple Processes===<br />
*analysis of gene products annotated to phosphorylation but not annotated to a kinase MF term. What did these annotations actually mean? Curators would need to review. Timeline? Deadline? Working group? One possibility would be to use part_of/involved_in relation to phosphorylation for genes also annotated to kinase MF, and causally_upstream_of_or_within for others until curators can re-evaluate.<br />
*Other considerations:<br />
**Helen: are there many the single-step processes?<br />
**Paul: user-oriented approach - is it a useful grouping for our users?<br />
**Ruth: we need to think about the meaning beyond just “phosphorylation”<br />
**Ruth: what are the consequences of removing “phosphorylation” and what happens to all its children?<br />
**Pascale Q: providing that we remove the processes, would it affect the term enrichment analysis?<br />
<br />
===BP refactoring===<br />
*Defining “Cellular Process” and “Multi-Organism Process” terms<br />
*Action item: the comments/examples/notes should be captured, working group to discuss this.<br />
<br />
===Proteoforms===<br />
Establish a working group for when and how to use proteoforms in annotation. (Kimberly with Harold and Li)<br />
===Usability issues===<br />
*What do users want?<br />
**truth (summary/story/model)?<br />
**fishing expeditions?<br />
**api access?<br />
** appropriate licensing<br />
*Who are our users?<br />
**geneticists?<br />
**clinicians?<br />
**computational biologists?<br />
***aggregators<br />
*Use cases: https://github.com/geneontology/go-ontology/issues/13606<br />
*Perhaps discussion of examples of how the GOC members are engaging with the community and how we can do better in the future (suggested by Helen).<br />
* Val: What happened to the user survey? PomBase collected 70 responses from our users but I never heard a summary of the findings at a subsequent meeting. Could somebody give an overview of the results?<br />
<br />
==Addition items - If time allows==<br />
Chris: Where should documentation on term usage go in the ontology? We'd like to create a new type of annotation in Protégé, but the details of the implementation need to be worked out. <br />
<br />
<br />
==Viral processes update (Pascale)==<br />
Action Items Corvallis 2017/06 Check whether the incorporated changes could affect the host proteins. Document the use cases. '''Nothing to report - depends on where documentation will be hosted'''<br />
<br />
==Action Item Review==<br />
<br />
=Wednesday noon-ish Fin=<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Agenda&diff=653952017 Cambridge GOC Meeting Agenda2017-10-03T10:14:50Z<p>Suzi: /* GO_Slims */</p>
<hr />
<div>GOC Meeting, Cambridge , October 2-4, 2017<br />
<br />
=To all speakers=<br />
Please add your slides to the google drive:<br />
https://drive.google.com/drive/folders/0B7bEr6HANSlGSHY3c2JqNEs2ZUk<br />
=Minutes=<br />
https://docs.google.com/document/d/1Y9_Mvqes3op36TPHgfaS7K5FHnGZLgUApghIFYyUKR8/edit#heading=h.638rbn3dlj1z<br />
=Monday 2nd October 9:00 a.m.=<br />
==Welcome, overview, vision, introductions==<br />
GO PIs<br />
==GO handbook presentation==<br />
===The Gene Ontology and the meaning of biological function (Paul T)===<br />
<br />
<br />
===Translating research data into Gene Ontology annotations (Pascale)=== <br />
(includes a discussion of the issue: background knowledge & protein domains<br />
https://github.com/geneontology/go-annotation/issues/1621)<br />
<br />
===Gene Ontology - annotation extensions (Ruth)===<br />
<br />
=Coffee break 10:30=<br />
<br />
==Ontology Issues and Updates==<br />
===Update on MF refactoring (Pascale and Paul T)===<br />
<br />
===Qualifiers/Relation issues (Kimberly and Chris)===<br />
<br />
====Refresher on Qualifiers/Relations (Chris)====<br />
<br />
https://docs.google.com/presentation/d/1aSr1kguPM9im_SHWGVVDe-7T0PNyvJUnXhMZk54on6Y/edit?usp=sharing<br />
<br />
====Biological Process Relations: Use of Qualifiers in Legacy Annotations====<br />
Proposal: We will apply the general qualifier to all legacy annotations. Each group can provide more specific qualifiers if they have a mechanism to distinguish. <br />
====Regulates relations (Kimberly)====<br />
Adding new qualifiers for the relation between a gene/gene product and a GO term. <br />
*Corvallis discussion:* What should the default relation be? How will we handle regulation? Use a relation, involved in regulation of, or use the precomposed regulation term?<br />
Ruth: There are now 3 ways to say the same thing: - involved_in_regulation_of X - involved_in X regulation - involved_in BP regulates(X)<br />
For annotation purposes and for our users we want one.<br />
DOS: Good point. These are semantically identical, but I agree we need to find a way to only have one: by convention for classic GO annotation and by filtering the output of inference for noctua output. Proposal: If a named regulation class exists: involved_in X regulation ...if not: involved_in {some BP} regulates(X) NOTE: If there was an annotation in Noctua such as ‘regulation of’ ‘very specific term’ and there was no term as ‘regulation of very specific term’ the GOC pipeline would create the annotation to the parent term: ‘regulation of less specific term’. Q: Is this implemented ?<br />
<br />
=Lunch 12:30=<br />
<br />
===Molecular Function Relations===<br />
====Multiple qualifiers for an annotation (Huaiyu)====<br />
<br />
===Cellular Component Relations===<br />
<br />
====CC component annotation guidelines (Kimberly)====<br />
*CC component annotation: what does it mean ? Kimberly to do 1 proposal (out of 3 alternatives)<br />
1. where the protein is active 2. two different meanings: enables or the right RO (part:of, ie just found there) 3. part_of (low information value!)<br />
<br />
*colocalizes with<br />
<br />
==Annotation guidelines and issues (part one)==<br />
===Signaling (Kimberly and David)===<br />
*Report from signaling workshop: David /Kimberly<br />
*Signaling: First attempt at Annotation consistency 2.0 - Kimberly to report on the approach and the outcome.<br />
Discussion points: Limited participation (self-selected to participate). One recommendation may be to ask all active curators to participate, even at some low level https://github.com/orgs/geneontology/projects/<br />
<br />
==Ontology WG update: David==<br />
<br />
=Coffee break 15:30=<br />
===Overview of GO annotations/Noctua (Kimberly & Chris)===<br />
====Getting Noctua ready for production (Kimberly & Seth)====<br />
*Kimberly & Seth Blocking issues list:<br />
** <strike>When importing an annotation from AmiGO using a companion / buddy, source providedBy should be retained <br /> https://github.com/geneontology/noctua/issues/459 </strike><br />
** GAF exports<br />
*** providedBy should be used in GPAD export <br /> https://github.com/geneontology/noctua/issues/502<br />
*** ...<br />
*Action Item Corvallis 2017/06:<br />
**Provide ways for users to recover and digest GO-CAM units (Gene Ontology-based Causal Activity Model). Ideas include rule-based generations of text statements from model, cytoscape view of network described, etc.<br /><small>I believe that this is a more exploratory and open project. We now offer an RDF enpoint, in addition to the APIs we already have, as well as the proposed feeding from AmiGO. If this is still open in the future, it may be very good Hackathon material. Needs more discussion.</small><br />
**ECO codes available for use in Noctua should show how they map up to a classic GO code, and there should be an alert for curators when they are using a code that does NOT map up to a classic code <br /><small>There is no ticket for such functionality. This would likely have to be written into Minerva or as a pre/post check on (some) server.</small><br />
**PRO IDs for use in Noctua <br />https://github.com/geneontology/noctua/issues/429 <br />https://github.com/geneontology/noctua/issues/122<br />
**Fix GPAD export from Noctua <br />https://github.com/geneontology/noctua/issues/418<br />
**Add a SPARTA workbench <br />https://github.com/geneontology/noctua/issues/465<br />
**Working group discussion of evidence on complex Noctua models (Kimberly?)<br />
<br />
====Noctua table view demo (Chris)====<br />
<br />
==Project updates ==<br />
====Report on transcription work/Noctua templates: Astrid GREEKC consortium====<br />
====Report of Reactome-GO connection: David H/Peter D====<br />
<br />
<br />
=Evening: Poster session 17:00=<br />
<br />
=Tuesday 3rd October 9:00 a.m.=<br />
<br />
==Project updates - continued ==<br />
====AGR - report to GOC: PIs====<br />
====SynGO meeting report: Paul T====<br />
<br />
===Documentation and GitHub overview (Kimberly/Seth/David/Pascale)===<br />
Kimberly Action Items Corvallis 2017/06<br />
*Continue with the consolidation of all documentation for ontology editing, and remove all old documents.<br />
*Review annotation documentation and add to github and readthedocs.<br />
*Make sure to mark obsolete pages/doc as such and add a link to the new relevant doc<br />
*Solicit annotation documentation from participating groups for consolidation.<br />
*Make sure to mark docs with ‘Date last reviewed’ so it’s easy for users to know when the documentation was last touched.<br />
*Pascale: additional information associated with GO terms, see GitHub ticket?<br />
*Add and follow action items at https://github.com/orgs/geneontology/projects/3<br />
<br />
<br />
'''How GO now uses GitHub for project management and guidelines for contributors'''<br />
*Where is information relevant to everyone's need<br />
*Groups (Groups.yaml)<br />
*Members<br />
*Etc<br />
<br />
<br />
==Annotation guidelines and issues (part two)==<br />
<br />
===Centralization of InterPro2GO annotations (Paul T)===<br />
Proposal (follow-up from Geneva 2016): <br />
*GO database pulls directly from InterPro2GO for UniProt Reference Proteomes<br />
*MOD identifier is used as primary gene identifier<br />
*Annotations are given "contributed by" InterPro<br />
*MODs pull from GO database, no need to maintain separate InterPro pipelines<br />
<br />
===HTP guidelines (Helen)===<br />
Helen - 15 minutes Report on progress from HTP working group<br />
https://docs.google.com/presentation/d/1oLkKWRSNQ-wWB_CCDxcb3a84hXsfkjl4Jp-kAEkhQUQ/edit#slide=id.g26c97bd257_1_57<br />
*Draft Guidelines https://docs.google.com/document/d/1ScIeclAzUXMe-tU6n0lVfsSwMHpOeNb7uK8On9-iKXc/edit?usp=sharing%7CHTP<br />
<br />
*Provision of new evidence code<br />
*Implementation & adding to guidelines<br />
<br />
==Transcription annotations decision tree==<br />
Ruth Action Items Corvallis 2017/06<br />
*David OS to create transcription regulator activity (proposed by Paul T)<br />
*Proposed changes to decision tree in Corvallis:<br />
**Simplified from previous version. Essentially a choice between ‘regulating transcription by RNA polymerase II’ or ‘regulating gene expression’<br />
**Annotation 5 = contributes_to sequence-specific DNA binding<br />
David: when people do enrichment, they don’t drop contributes_to (ie., pay attention to qualifiers), so all those proteins will come down as ‘DNA binding’ Action item: replace ‘annotation 5’ with ISS annotation (if DNA binding domain) or contributes to annotation 5 with ISS annotation if no DNA binding domain and domains to suggest coactivator<br />
*<br />
**Annotation 3 = nuclear chromatin<br />
Not everyone comfortable with this (ex., Stacia, David) Shouldn’t it be ‘colocalizes_with’? It was previously agreed that the definition for nuclear chromatin: The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus. Source:PMID:20404130 was to be applied. The proteins here include all associated proteins, not limited to just histones. With this statement the TFs are then contributing to chromatin, rather than binding to chromatin or colocalizing with it.<br />
*<br />
**Decision tree to be put up on GOC website.<br />
**Should annotation 4 exist? (Ruth)<br />
<br />
==PAINT update (Huaiyu)==<br />
Huaiyu Action Items Corvallis 2017/06:<br />
*Encourage discussion between PAINT curators and other annotators about terms not used for propagation<br />
*Report how many annotations per species are used for annotation propagation; could even supply this number for propagation specifically to human genes<br />
*Ruth and Huaiyu (others?) will discuss making use of groups that have already annotated specific gene lists to annotate the corresponding PAINT families.<br />
*Smooth out the challenge mechanism to make it easier to do make and resolve<br />
the challenges, identify terms that may be problematic and would benefit from consistency exercises and discussion.<br />
*Get a list of families where terms have not been propagated (?) - Please check this one for clarity.<br />
(added to github project board) Develop mechanism to trigger review of annotated PAINT families.<br />
<br />
<br />
<br />
==Community Support==<br />
===Citing GO (Paul T)===<br />
*Web page<br />
*Tool providers: Action Item Corvallis 2017/06: someone to represent GOC and contact GO tool providers to display version information and state this information needs to be included in any subsequent publication. Plus list the GOC paper to reference, as well as the tool provider reference. See: https://github.com/geneontology/go-site/issues/359 and https://github.com/geneontology/go-site/issues/360<br />
<br />
===Enrichment (Paul T & Suzi)===<br />
*Web page <br />
*Paul Pavlidis…<br />
*Data Commons work<br />
<br />
===GO_Slims (Val, Suzi, Mary)===<br />
====WHY creating slims - Intro to slim philosophy====<br />
* Suzi: For overviews, for particular taxa, for a particular area of biology<br />
* Val: Slimming tips [https://docs.google.com/presentation/d/1oXzxaJpkm46irdMA0fbKohUgcx5Qm2xkbraZ83ttPXw/edit?usp=sharing_eil&ts=59cd0de3 Slimming tips]<br />
Includes Slim uses, Creating a biologically useful slim (complete coverage by aspect, biologically useful terms i.e sufficient granularity, avoiding single step process terms (i.e functions), different slims for different purposes) (Val: 20 mins)<br />
<br />
====Use and maintenance of slims (Mary)====<br />
Mary: algorithm - 15 minutes<br />
<br />
====HOW to make slims (Chris)====<br />
Yaml format for creating slims/types of slims/target organisms<br />
<br />
* https://github.com/geneontology/go-ontology/issues/12780<br />
* https://github.com/geneontology/go-ontology/issues/14028<br />
* https://github.com/geneontology/go-ontology/issues/12554<br />
<br />
====GO presentation of slims====<br />
Suzi: GO ribbon<br />
Group discussion: how should we present slims in GO: Multiple or one ?<br />
How many slims will be available? How will we represent multiple slims? <br />
(Pascale asks: what are our resources for this? what is the priority? which slims is GO responsible for?)<br />
<br />
=Wednesday 4th October 9:00 a.m.=<br />
==Ongoing work==<br />
===AmiGO (Follow up with Seth)===<br />
*In general, while several of the AmiGO issues are high-priority, there has been limited bandwidth to tackle them in the context of continuing work on Noctua and the replacement pipeline. Several fixes are queued up and will be available before the upcoming SAB meeting.<br />
**In response to: in base_statistics, plotly graph for "Experimental annotation publications by assigner" is confusing https://github.com/geneontology/amigo/issues/429<br />
**From Pascale's question: My understanding is that there are essentially no resources for AmiGO right now so any AmiGO issue is low priority. Is this correct?<br />
<br />
===The Fate of Simple Processes===<br />
*analysis of gene products annotated to phosphorylation but not annotated to a kinase MF term. What did these annotations actually mean? Curators would need to review. Timeline? Deadline? Working group? One possibility would be to use part_of/involved_in relation to phosphorylation for genes also annotated to kinase MF, and causally_upstream_of_or_within for others until curators can re-evaluate.<br />
*Other considerations:<br />
**Helen: are there many the single-step processes?<br />
**Paul: user-oriented approach - is it a useful grouping for our users?<br />
**Ruth: we need to think about the meaning beyond just “phosphorylation”<br />
**Ruth: what are the consequences of removing “phosphorylation” and what happens to all its children?<br />
**Pascale Q: providing that we remove the processes, would it affect the term enrichment analysis?<br />
<br />
===BP refactoring===<br />
*Defining “Cellular Process” and “Multi-Organism Process” terms<br />
*Action item: the comments/examples/notes should be captured, working group to discuss this.<br />
<br />
===Proteoforms===<br />
Establish a working group for when and how to use proteoforms in annotation. (Kimberly with Harold and Li)<br />
===Usability issues===<br />
*What do users want?<br />
**truth (summary/story/model)?<br />
**fishing expeditions?<br />
**api access?<br />
** appropriate licensing<br />
*Who are our users?<br />
**geneticists?<br />
**clinicians?<br />
**computational biologists?<br />
***aggregators<br />
*Use cases: https://github.com/geneontology/go-ontology/issues/13606<br />
*Perhaps discussion of examples of how the GOC members are engaging with the community and how we can do better in the future (suggested by Helen).<br />
* Val: What happened to the user survey? PomBase collected 70 responses from our users but I never heard a summary of the findings at a subsequent meeting. Could somebody give an overview of the results?<br />
<br />
==Addition items - If time allows==<br />
Chris: Where should documentation on term usage go in the ontology? We'd like to create a new type of annotation in Protégé, but the details of the implementation need to be worked out. <br />
<br />
<br />
==Viral processes update (Pascale)==<br />
Action Items Corvallis 2017/06 Check whether the incorporated changes could affect the host proteins. Document the use cases. '''Nothing to report - depends on where documentation will be hosted'''<br />
<br />
==Action Item Review==<br />
<br />
=Wednesday noon-ish Fin=<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Agenda&diff=653942017 Cambridge GOC Meeting Agenda2017-10-03T10:10:42Z<p>Suzi: /* GO_Slims */</p>
<hr />
<div>GOC Meeting, Cambridge , October 2-4, 2017<br />
<br />
=To all speakers=<br />
Please add your slides to the google drive:<br />
https://drive.google.com/drive/folders/0B7bEr6HANSlGSHY3c2JqNEs2ZUk<br />
=Minutes=<br />
https://docs.google.com/document/d/1Y9_Mvqes3op36TPHgfaS7K5FHnGZLgUApghIFYyUKR8/edit#heading=h.638rbn3dlj1z<br />
=Monday 2nd October 9:00 a.m.=<br />
==Welcome, overview, vision, introductions==<br />
GO PIs<br />
==GO handbook presentation==<br />
===The Gene Ontology and the meaning of biological function (Paul T)===<br />
<br />
<br />
===Translating research data into Gene Ontology annotations (Pascale)=== <br />
(includes a discussion of the issue: background knowledge & protein domains<br />
https://github.com/geneontology/go-annotation/issues/1621)<br />
<br />
===Gene Ontology - annotation extensions (Ruth)===<br />
<br />
=Coffee break 10:30=<br />
<br />
==Ontology Issues and Updates==<br />
===Update on MF refactoring (Pascale and Paul T)===<br />
<br />
===Qualifiers/Relation issues (Kimberly and Chris)===<br />
<br />
====Refresher on Qualifiers/Relations (Chris)====<br />
<br />
https://docs.google.com/presentation/d/1aSr1kguPM9im_SHWGVVDe-7T0PNyvJUnXhMZk54on6Y/edit?usp=sharing<br />
<br />
====Biological Process Relations: Use of Qualifiers in Legacy Annotations====<br />
Proposal: We will apply the general qualifier to all legacy annotations. Each group can provide more specific qualifiers if they have a mechanism to distinguish. <br />
====Regulates relations (Kimberly)====<br />
Adding new qualifiers for the relation between a gene/gene product and a GO term. <br />
*Corvallis discussion:* What should the default relation be? How will we handle regulation? Use a relation, involved in regulation of, or use the precomposed regulation term?<br />
Ruth: There are now 3 ways to say the same thing: - involved_in_regulation_of X - involved_in X regulation - involved_in BP regulates(X)<br />
For annotation purposes and for our users we want one.<br />
DOS: Good point. These are semantically identical, but I agree we need to find a way to only have one: by convention for classic GO annotation and by filtering the output of inference for noctua output. Proposal: If a named regulation class exists: involved_in X regulation ...if not: involved_in {some BP} regulates(X) NOTE: If there was an annotation in Noctua such as ‘regulation of’ ‘very specific term’ and there was no term as ‘regulation of very specific term’ the GOC pipeline would create the annotation to the parent term: ‘regulation of less specific term’. Q: Is this implemented ?<br />
<br />
=Lunch 12:30=<br />
<br />
===Molecular Function Relations===<br />
====Multiple qualifiers for an annotation (Huaiyu)====<br />
<br />
===Cellular Component Relations===<br />
<br />
====CC component annotation guidelines (Kimberly)====<br />
*CC component annotation: what does it mean ? Kimberly to do 1 proposal (out of 3 alternatives)<br />
1. where the protein is active 2. two different meanings: enables or the right RO (part:of, ie just found there) 3. part_of (low information value!)<br />
<br />
*colocalizes with<br />
<br />
==Annotation guidelines and issues (part one)==<br />
===Signaling (Kimberly and David)===<br />
*Report from signaling workshop: David /Kimberly<br />
*Signaling: First attempt at Annotation consistency 2.0 - Kimberly to report on the approach and the outcome.<br />
Discussion points: Limited participation (self-selected to participate). One recommendation may be to ask all active curators to participate, even at some low level https://github.com/orgs/geneontology/projects/<br />
<br />
==Ontology WG update: David==<br />
<br />
=Coffee break 15:30=<br />
===Overview of GO annotations/Noctua (Kimberly & Chris)===<br />
====Getting Noctua ready for production (Kimberly & Seth)====<br />
*Kimberly & Seth Blocking issues list:<br />
** <strike>When importing an annotation from AmiGO using a companion / buddy, source providedBy should be retained <br /> https://github.com/geneontology/noctua/issues/459 </strike><br />
** GAF exports<br />
*** providedBy should be used in GPAD export <br /> https://github.com/geneontology/noctua/issues/502<br />
*** ...<br />
*Action Item Corvallis 2017/06:<br />
**Provide ways for users to recover and digest GO-CAM units (Gene Ontology-based Causal Activity Model). Ideas include rule-based generations of text statements from model, cytoscape view of network described, etc.<br /><small>I believe that this is a more exploratory and open project. We now offer an RDF enpoint, in addition to the APIs we already have, as well as the proposed feeding from AmiGO. If this is still open in the future, it may be very good Hackathon material. Needs more discussion.</small><br />
**ECO codes available for use in Noctua should show how they map up to a classic GO code, and there should be an alert for curators when they are using a code that does NOT map up to a classic code <br /><small>There is no ticket for such functionality. This would likely have to be written into Minerva or as a pre/post check on (some) server.</small><br />
**PRO IDs for use in Noctua <br />https://github.com/geneontology/noctua/issues/429 <br />https://github.com/geneontology/noctua/issues/122<br />
**Fix GPAD export from Noctua <br />https://github.com/geneontology/noctua/issues/418<br />
**Add a SPARTA workbench <br />https://github.com/geneontology/noctua/issues/465<br />
**Working group discussion of evidence on complex Noctua models (Kimberly?)<br />
<br />
====Noctua table view demo (Chris)====<br />
<br />
==Project updates ==<br />
====Report on transcription work/Noctua templates: Astrid GREEKC consortium====<br />
====Report of Reactome-GO connection: David H/Peter D====<br />
<br />
<br />
=Evening: Poster session 17:00=<br />
<br />
=Tuesday 3rd October 9:00 a.m.=<br />
<br />
==Project updates - continued ==<br />
====AGR - report to GOC: PIs====<br />
====SynGO meeting report: Paul T====<br />
<br />
===Documentation and GitHub overview (Kimberly/Seth/David/Pascale)===<br />
Kimberly Action Items Corvallis 2017/06<br />
*Continue with the consolidation of all documentation for ontology editing, and remove all old documents.<br />
*Review annotation documentation and add to github and readthedocs.<br />
*Make sure to mark obsolete pages/doc as such and add a link to the new relevant doc<br />
*Solicit annotation documentation from participating groups for consolidation.<br />
*Make sure to mark docs with ‘Date last reviewed’ so it’s easy for users to know when the documentation was last touched.<br />
*Pascale: additional information associated with GO terms, see GitHub ticket?<br />
*Add and follow action items at https://github.com/orgs/geneontology/projects/3<br />
<br />
<br />
'''How GO now uses GitHub for project management and guidelines for contributors'''<br />
*Where is information relevant to everyone's need<br />
*Groups (Groups.yaml)<br />
*Members<br />
*Etc<br />
<br />
<br />
==Annotation guidelines and issues (part two)==<br />
<br />
===Centralization of InterPro2GO annotations (Paul T)===<br />
Proposal (follow-up from Geneva 2016): <br />
*GO database pulls directly from InterPro2GO for UniProt Reference Proteomes<br />
*MOD identifier is used as primary gene identifier<br />
*Annotations are given "contributed by" InterPro<br />
*MODs pull from GO database, no need to maintain separate InterPro pipelines<br />
<br />
===HTP guidelines (Helen)===<br />
Helen - 15 minutes Report on progress from HTP working group<br />
https://docs.google.com/presentation/d/1oLkKWRSNQ-wWB_CCDxcb3a84hXsfkjl4Jp-kAEkhQUQ/edit#slide=id.g26c97bd257_1_57<br />
*Draft Guidelines https://docs.google.com/document/d/1ScIeclAzUXMe-tU6n0lVfsSwMHpOeNb7uK8On9-iKXc/edit?usp=sharing%7CHTP<br />
<br />
*Provision of new evidence code<br />
*Implementation & adding to guidelines<br />
<br />
==Transcription annotations decision tree==<br />
Ruth Action Items Corvallis 2017/06<br />
*David OS to create transcription regulator activity (proposed by Paul T)<br />
*Proposed changes to decision tree in Corvallis:<br />
**Simplified from previous version. Essentially a choice between ‘regulating transcription by RNA polymerase II’ or ‘regulating gene expression’<br />
**Annotation 5 = contributes_to sequence-specific DNA binding<br />
David: when people do enrichment, they don’t drop contributes_to (ie., pay attention to qualifiers), so all those proteins will come down as ‘DNA binding’ Action item: replace ‘annotation 5’ with ISS annotation (if DNA binding domain) or contributes to annotation 5 with ISS annotation if no DNA binding domain and domains to suggest coactivator<br />
*<br />
**Annotation 3 = nuclear chromatin<br />
Not everyone comfortable with this (ex., Stacia, David) Shouldn’t it be ‘colocalizes_with’? It was previously agreed that the definition for nuclear chromatin: The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus. Source:PMID:20404130 was to be applied. The proteins here include all associated proteins, not limited to just histones. With this statement the TFs are then contributing to chromatin, rather than binding to chromatin or colocalizing with it.<br />
*<br />
**Decision tree to be put up on GOC website.<br />
**Should annotation 4 exist? (Ruth)<br />
<br />
==PAINT update (Huaiyu)==<br />
Huaiyu Action Items Corvallis 2017/06:<br />
*Encourage discussion between PAINT curators and other annotators about terms not used for propagation<br />
*Report how many annotations per species are used for annotation propagation; could even supply this number for propagation specifically to human genes<br />
*Ruth and Huaiyu (others?) will discuss making use of groups that have already annotated specific gene lists to annotate the corresponding PAINT families.<br />
*Smooth out the challenge mechanism to make it easier to do make and resolve<br />
the challenges, identify terms that may be problematic and would benefit from consistency exercises and discussion.<br />
*Get a list of families where terms have not been propagated (?) - Please check this one for clarity.<br />
(added to github project board) Develop mechanism to trigger review of annotated PAINT families.<br />
<br />
<br />
<br />
==Community Support==<br />
===Citing GO (Paul T)===<br />
*Web page<br />
*Tool providers: Action Item Corvallis 2017/06: someone to represent GOC and contact GO tool providers to display version information and state this information needs to be included in any subsequent publication. Plus list the GOC paper to reference, as well as the tool provider reference. See: https://github.com/geneontology/go-site/issues/359 and https://github.com/geneontology/go-site/issues/360<br />
<br />
===Enrichment (Paul T & Suzi)===<br />
*Web page <br />
*Paul Pavlidis…<br />
*Data Commons work<br />
<br />
===GO_Slims===<br />
====WHY creating slims - Intro to slim philosophy (Val, Suzi, Mary)====<br />
* Val: Slimming tips [https://docs.google.com/presentation/d/1oXzxaJpkm46irdMA0fbKohUgcx5Qm2xkbraZ83ttPXw/edit?usp=sharing_eil&ts=59cd0de3 Slimming tips]<br />
Includes Slim uses, Creating a biologically useful slim (complete coverage by aspect, biologically useful terms i.e sufficient granularity, avoiding single step process terms (i.e functions), different slims for different purposes) (Val: 20 mins)<br />
* Suzi: For overviews, for particular taxa, for a particular area of biology<br />
<br />
====HOW to make slims (Chris)====<br />
Yaml format for creating slims/types of slims/target organisms<br />
<br />
* https://github.com/geneontology/go-ontology/issues/12780<br />
* https://github.com/geneontology/go-ontology/issues/14028<br />
* https://github.com/geneontology/go-ontology/issues/12554<br />
<br />
====Use and maintenance of slims (Mary and Suzi)====<br />
Mary: algorithm - 15 minutes<br />
<br />
====GO presentation of slims====<br />
Suzi: GO ribbon<br />
Group discussion: how should we present slims in GO: Multiple or one ?<br />
How many slims will be available? How will we represent multiple slims? <br />
(Pascale asks: what are our resources for this? what is the priority? which slims is GO responsible for?)<br />
<br />
=Wednesday 4th October 9:00 a.m.=<br />
==Ongoing work==<br />
===AmiGO (Follow up with Seth)===<br />
*In general, while several of the AmiGO issues are high-priority, there has been limited bandwidth to tackle them in the context of continuing work on Noctua and the replacement pipeline. Several fixes are queued up and will be available before the upcoming SAB meeting.<br />
**In response to: in base_statistics, plotly graph for "Experimental annotation publications by assigner" is confusing https://github.com/geneontology/amigo/issues/429<br />
**From Pascale's question: My understanding is that there are essentially no resources for AmiGO right now so any AmiGO issue is low priority. Is this correct?<br />
<br />
===The Fate of Simple Processes===<br />
*analysis of gene products annotated to phosphorylation but not annotated to a kinase MF term. What did these annotations actually mean? Curators would need to review. Timeline? Deadline? Working group? One possibility would be to use part_of/involved_in relation to phosphorylation for genes also annotated to kinase MF, and causally_upstream_of_or_within for others until curators can re-evaluate.<br />
*Other considerations:<br />
**Helen: are there many the single-step processes?<br />
**Paul: user-oriented approach - is it a useful grouping for our users?<br />
**Ruth: we need to think about the meaning beyond just “phosphorylation”<br />
**Ruth: what are the consequences of removing “phosphorylation” and what happens to all its children?<br />
**Pascale Q: providing that we remove the processes, would it affect the term enrichment analysis?<br />
<br />
===BP refactoring===<br />
*Defining “Cellular Process” and “Multi-Organism Process” terms<br />
*Action item: the comments/examples/notes should be captured, working group to discuss this.<br />
<br />
===Proteoforms===<br />
Establish a working group for when and how to use proteoforms in annotation. (Kimberly with Harold and Li)<br />
===Usability issues===<br />
*What do users want?<br />
**truth (summary/story/model)?<br />
**fishing expeditions?<br />
**api access?<br />
** appropriate licensing<br />
*Who are our users?<br />
**geneticists?<br />
**clinicians?<br />
**computational biologists?<br />
***aggregators<br />
*Use cases: https://github.com/geneontology/go-ontology/issues/13606<br />
*Perhaps discussion of examples of how the GOC members are engaging with the community and how we can do better in the future (suggested by Helen).<br />
* Val: What happened to the user survey? PomBase collected 70 responses from our users but I never heard a summary of the findings at a subsequent meeting. Could somebody give an overview of the results?<br />
<br />
==Addition items - If time allows==<br />
Chris: Where should documentation on term usage go in the ontology? We'd like to create a new type of annotation in Protégé, but the details of the implementation need to be worked out. <br />
<br />
<br />
==Viral processes update (Pascale)==<br />
Action Items Corvallis 2017/06 Check whether the incorporated changes could affect the host proteins. Document the use cases. '''Nothing to report - depends on where documentation will be hosted'''<br />
<br />
==Action Item Review==<br />
<br />
=Wednesday noon-ish Fin=<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Agenda&diff=653042017 Cambridge GOC Meeting Agenda2017-09-27T00:34:09Z<p>Suzi: /* Wednesday 4th October */</p>
<hr />
<div>GOC Meeting, Cambridge , October 2-4, 2017<br />
<br />
=Monday 2nd October=<br />
==Welcome, overview, vision, introductions==<br />
GO PIs<br />
==GO handbook presentation==<br />
*The Gene Ontology and the meaning of biological function (Paul T)<br />
*Translating research data into Gene Ontology annotations (Pascale)<br />
*Gene Ontology - annotation extensions (Ruth)<br />
*GO as a biological systems model (Suzi, or Paul T if Suzi is late)<br />
Pascale will move slides to Google drive<br />
==Ontology Issues and Updates==<br />
===Update on MF refactoring (Pascale or Paul T)===<br />
====GitHub tutorial (Seth & Pascale)====<br />
How GO now uses GitHub for project management and guidelines for contributors<br />
*Where is information relevant to everyone's need<br />
*Groups (Groups.yaml)<br />
*Members<br />
*Etc<br />
<br />
===Qualifiers/Relation issues (Kimberly and Chris)===<br />
====Qualifiers/Relations in GPAD (Kimberly and Chris)====<br />
====Contributes_to guidelines====<br />
++ colocalizes with<br />
====Multiple qualifiers for an annotation (Huaiyu)====<br />
====Use of Qualifiers in Legacy Annotations====<br />
Pascale Proposal: We will apply the general qualifier to all legacy annotations. Each group can provide more specific qualifiers if they have a mechanism to distinguish. Action Items Corvallis 2017/06<br />
*Working group to decide what relations should be available in Protein2GO or other tools for manual annotations. Also decide when there are different ways of expressing the same thing, what way we will choose. What should the default gene/gene product relation be for legacy annotations?<br />
*Chris to work on reports that may help curators make decisions about what annotations can get more expressive qualifiers.<br />
<br />
====Regulates relations====<br />
Adding new qualifiers for the relation between a gene/gene product and a GO term What should the default relation be? How will we handle regulation? Use a relation, involved in regulation of, or use the precomposed regulation term?<br />
Ruth: There are now 3 ways to say the same thing: - involved_in_regulation_of X - involved_in X regulation - involved_in BP regulates(X)<br />
For annotation purposes and for our users we want one.<br />
DOS: Good point. These are semantically identical, but I agree we need to find a way to only have one: by convention for classic GO annotation and by filtering the output of inference for noctua output. Proposal: If a named regulation class exists: involved_in X regulation ...if not: involved_in {some BP} regulates(X) NOTE: If there was an annotation in Noctua such as ‘regulation of’ ‘very specific term’ and there was no term as ‘regulation of very specific term’ the GOC pipeline would create the annotation to the parent term: ‘regulation of less specific term’. Q: Is this implemented ?<br />
==Annotation guidelines and issues (part one)==<br />
===Signaling (Kimberly and David)===<br />
*Report from signaling workshop: David /Kimberly<br />
*Signaling: First attempt at Annotation consistency 2.0 - Kimberly to report on the approach and the outcome.<br />
Discussion points: Limited participation (self-selected to participate). One recommendation may be to ask all active curators to participate, even at some low level https://github.com/orgs/geneontology/projects/<br />
<br />
===Overview of GO annotations/Noctua (Kimberly & Chris)===<br />
====Getting Noctua ready for production====<br />
*Kimberly & Seth Blocking issues list: TO BE COMPLETED<br />
*Action Item Corvallis 2017/06:<br />
**Provide ways for users to recover and digest GO-CAM units (Gene Ontology-based Causal Activity Model). Ideas include rule-based generations of text statements from model, cytoscape view of network described, etc.<br />
**ECO codes available for use in Noctua should show how they map up to a classic GO code, and there should be an alert for curators when they are using a code that does NOT map up to a classic code<br />
**PRO IDs for use in Noctua<br />
**Fix GPAD export from Noctua https://github.com/geneontology/noctua/issues/418<br />
**Add a SPARTA workbench https://github.com/geneontology/noctua/issues/465<br />
**Working group discussion of evidence on complex Noctua models (Kimberly?)<br />
<br />
====Noctua table view demo (Chris)====<br />
<br />
==Project updates==<br />
*AGR - report to GOC: PIs<br />
*SynGO meeting report: Paul T<br />
*Report of Reactome-GO connection: David H/Peter D<br />
*Report on transcription work/Noctua templates: Astrid GREEKC consortium=<br />
=Evening: Poster session=<br />
<br />
=Tuesday 3rd October=<br />
==Annotation guidelines and issues (part two)==<br />
===CC component annotation guidelines (Kimberly)===<br />
CC component annotation: what does it mean ? Kimberly to do 1 proposal (out of 3 alternatives)<br />
1. where the protein is active 2. two different meanings: enables or the right RO (part:of, ie just found there) 3. part_of (low information value!)<br />
===Author intent & protein domains===<br />
Pascale /Ruth; IDA v IC v New evidence code https://github.com/geneontology/go-annotation/issues/1621 30 minutes discussion about issues; hopefully action items can come out of the discussion<br />
===Centralization of InterPro2GO annotations===<br />
Proposal (follow-up from Geneva 2016): (Paul T)<br />
*GO database pulls directly from InterPro2GO for UniProt Reference Proteomes<br />
*MOD identifier is used as primary gene identifier<br />
*Annotations are given "contributed by" InterPro<br />
*MODs pull from GO database, no need to maintain separate InterPro pipelines<br />
<br />
===HTP guidelines===<br />
Helen - 15 minutes Report on progress from HTP working group<br />
*Draft Guidelines https://docs.google.com/document/d/1ScIeclAzUXMe-tU6n0lVfsSwMHpOeNb7uK8On9-iKXc/edit?usp=sharing%7CHTP<br />
<br />
*Provision of new evidence code<br />
*Implementation & developing guidelines<br />
<br />
===Transcription annotations decision tree===<br />
Ruth Action Items Corvallis 2017/06<br />
*David OS to create transcription regulator activity (proposed by Paul T)<br />
*Proposed changes to decision tree in Corvallis:<br />
**Simplified from previous version. Essentially a choice between ‘regulating transcription by RNA polymerase II’ or ‘regulating gene expression’<br />
**Annotation 5 = contributes_to sequence-specific DNA binding<br />
David: when people do enrichment, they don’t drop contributes_to (ie., pay attention to qualifiers), so all those proteins will come down as ‘DNA binding’ Action item: replace ‘annotation 5’ with ISS annotation (if DNA binding domain) or contributes to annotation 5 with ISS annotation if no DNA binding domain and domains to suggest coactivator<br />
*<br />
**Annotation 3 = nuclear chromatin<br />
Not everyone comfortable with this (ex., Stacia, David) Shouldn’t it be ‘colocalizes_with’? It was previously agreed that the definition for nuclear chromatin: The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus. Source:PMID:20404130 was to be applied. The proteins here include all associated proteins, not limited to just histones. With this statement the TFs are then contributing to chromatin, rather than binding to chromatin or colocalizing with it.<br />
*<br />
**Decision tree to be put up on GOC website.<br />
**Should annotation 4 exist? (Ruth)<br />
<br />
===Annotation Documentation===<br />
Kimberly Action Items Corvallis 2017/06<br />
*Continue with the consolidation of all documentation for ontology editing, and remove all old documents.<br />
*Review annotation documentation and add to github and readthedocs.<br />
*Make sure to mark obsolete pages/doc as such and add a link to the new relevant doc<br />
*Solicit annotation documentation from participating groups for consolidation.<br />
*Make sure to mark docs with ‘Date last reviewed’ so it’s easy for users to know when the documentation was last touched.<br />
*Pascale: additional information associated with GO terms, see GitHub ticket?<br />
*Add and follow action items at https://github.com/orgs/geneontology/projects/3<br />
<br />
===Annotation quality control===<br />
====PAINT update (Huaiyu)====<br />
Huaiyu Action Items Corvallis 2017/06:<br />
*Encourage discussion between PAINT curators and other annotators about terms not used for propagation<br />
*Report how many annotations per species are used for annotation propagation; could even supply this number for propagation specifically to human genes<br />
*Ruth and Huaiyu (others?) will discuss making use of groups that have already annotated specific gene lists to annotate the corresponding PAINT families.<br />
*Smooth out the challenge mechanism to make it easier to do make and resolve<br />
the challenges, identify terms that may be problematic and would benefit from consistency exercises and discussion.<br />
*Get a list of families where terms have not been propagated (?) - Please check this one for clarity.<br />
(added to github project board) Develop mechanism to trigger review of annotated PAINT families.<br />
<br />
===Viral processes update (Pascale)===<br />
Action Items Corvallis 2017/06 Check whether the incorporated changes could affect the host proteins. Document the use cases.<br />
==Community Support==<br />
===Citing GO (Paul T)===<br />
*Web page<br />
*Tool providers: Action Item Corvallis 2017/06: someone to represent GOC and contact GO tool providers to display version information and state this information needs to be included in any subsequent publication. Plus list the GOC paper to reference, as well as the tool provider reference. See: https://github.com/geneontology/go-site/issues/359 and https://github.com/geneontology/go-site/issues/360<br />
===Enrichment (Paul T & Suzi)===<br />
*Web page <br />
*Paul Pavlidis…<br />
*Data Commons work<br />
<br />
===GO_Slims===<br />
====Philosophy (Val, Suzi)====<br />
Creating a biologically useful slim (complete coverage by aspect, biologically useful terms i.e sufficient granularity, avoiding single step process terms (i.e functions), different slims for different purposes: Judy, Mary D (+ Suzi, Val, etc). For overviews, for particular taxa, for a particular area of biology<br />
Specifications for slims from user's perspective (Val: 30 minutes)<br />
====HOW TO MAKE SLIMS (Chris)====<br />
Yaml format for creating slims/types of slims/target organisms<br />
====Use and maintenance of slims (Mary and Suzi)====<br />
Mary: algorithm - 15 minutes<br />
Suzi: GO ribbon<br />
<br />
=Wednesday 4th October=<br />
==Ongoing work==<br />
===AmiGO (Follow up with Seth)===<br />
*In general, while several of the AmiGO issues are high-priority, there has been limited bandwidth to tackle them in the context of continuing work on Noctua and the replacement pipeline. Several fixes are queued up and will be available before the upcoming SAB meeting.<br />
**In response to: in base_statistics, plotly graph for "Experimental annotation publications by assigner" is confusing https://github.com/geneontology/amigo/issues/429<br />
**From Pascale's question: My understanding is that there are essentially no resources for AmiGO right now so any AmiGO issue is low priority. Is this correct?<br />
<br />
===The Fate of Simple Processes===<br />
*analysis of gene products annotated to phosphorylation but not annotated to a kinase MF term. What did these annotations actually mean? Curators would need to review. Timeline? Deadline? Working group? One possibility would be to use part_of/involved_in relation to phosphorylation for genes also annotated to kinase MF, and causally_upstream_of_or_within for others until curators can re-evaluate.<br />
*Other considerations:<br />
**Helen: are there many the single-step processes?<br />
**Paul: user-oriented approach - is it a useful grouping for our users?<br />
**Ruth: we need to think about the meaning beyond just “phosphorylation”<br />
**Ruth: what are the consequences of removing “phosphorylation” and what happens to all its children?<br />
**Pascale Q: providing that we remove the processes, would it affect the term enrichment analysis?<br />
<br />
===BP refactoring===<br />
*Defining “Cellular Process” and “Multi-Organism Process” terms<br />
*Action item: the comments/examples/notes should be captured, working group to discuss this.<br />
<br />
===Proteoforms===<br />
Establish a working group for when and how to use proteoforms in annotation. (Kimberly with Harold and Li)<br />
===Usability issues===<br />
*What do users want?<br />
**truth (summary/story/model)?<br />
**fishing expeditions?<br />
**api access?<br />
*Who are our users?<br />
**geneticists?<br />
**clinicians?<br />
**computational biologists?<br />
*Use cases: https://github.com/geneontology/go-ontology/issues/13606<br />
*Perhaps discussion of examples of how the GOC members are engaging with the community and how we can do better in the future (suggested by Helen).<br />
==Action Item Review==<br />
<br />
=Wednesday noon-ish Fin=<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Agenda&diff=653032017 Cambridge GOC Meeting Agenda2017-09-27T00:33:09Z<p>Suzi: </p>
<hr />
<div>GOC Meeting, Cambridge , October 2-4, 2017<br />
<br />
=Monday 2nd October=<br />
==Welcome, overview, vision, introductions==<br />
GO PIs<br />
==GO handbook presentation==<br />
*The Gene Ontology and the meaning of biological function (Paul T)<br />
*Translating research data into Gene Ontology annotations (Pascale)<br />
*Gene Ontology - annotation extensions (Ruth)<br />
*GO as a biological systems model (Suzi, or Paul T if Suzi is late)<br />
Pascale will move slides to Google drive<br />
==Ontology Issues and Updates==<br />
===Update on MF refactoring (Pascale or Paul T)===<br />
====GitHub tutorial (Seth & Pascale)====<br />
How GO now uses GitHub for project management and guidelines for contributors<br />
*Where is information relevant to everyone's need<br />
*Groups (Groups.yaml)<br />
*Members<br />
*Etc<br />
<br />
===Qualifiers/Relation issues (Kimberly and Chris)===<br />
====Qualifiers/Relations in GPAD (Kimberly and Chris)====<br />
====Contributes_to guidelines====<br />
++ colocalizes with<br />
====Multiple qualifiers for an annotation (Huaiyu)====<br />
====Use of Qualifiers in Legacy Annotations====<br />
Pascale Proposal: We will apply the general qualifier to all legacy annotations. Each group can provide more specific qualifiers if they have a mechanism to distinguish. Action Items Corvallis 2017/06<br />
*Working group to decide what relations should be available in Protein2GO or other tools for manual annotations. Also decide when there are different ways of expressing the same thing, what way we will choose. What should the default gene/gene product relation be for legacy annotations?<br />
*Chris to work on reports that may help curators make decisions about what annotations can get more expressive qualifiers.<br />
<br />
====Regulates relations====<br />
Adding new qualifiers for the relation between a gene/gene product and a GO term What should the default relation be? How will we handle regulation? Use a relation, involved in regulation of, or use the precomposed regulation term?<br />
Ruth: There are now 3 ways to say the same thing: - involved_in_regulation_of X - involved_in X regulation - involved_in BP regulates(X)<br />
For annotation purposes and for our users we want one.<br />
DOS: Good point. These are semantically identical, but I agree we need to find a way to only have one: by convention for classic GO annotation and by filtering the output of inference for noctua output. Proposal: If a named regulation class exists: involved_in X regulation ...if not: involved_in {some BP} regulates(X) NOTE: If there was an annotation in Noctua such as ‘regulation of’ ‘very specific term’ and there was no term as ‘regulation of very specific term’ the GOC pipeline would create the annotation to the parent term: ‘regulation of less specific term’. Q: Is this implemented ?<br />
==Annotation guidelines and issues (part one)==<br />
===Signaling (Kimberly and David)===<br />
*Report from signaling workshop: David /Kimberly<br />
*Signaling: First attempt at Annotation consistency 2.0 - Kimberly to report on the approach and the outcome.<br />
Discussion points: Limited participation (self-selected to participate). One recommendation may be to ask all active curators to participate, even at some low level https://github.com/orgs/geneontology/projects/<br />
<br />
===Overview of GO annotations/Noctua (Kimberly & Chris)===<br />
====Getting Noctua ready for production====<br />
*Kimberly & Seth Blocking issues list: TO BE COMPLETED<br />
*Action Item Corvallis 2017/06:<br />
**Provide ways for users to recover and digest GO-CAM units (Gene Ontology-based Causal Activity Model). Ideas include rule-based generations of text statements from model, cytoscape view of network described, etc.<br />
**ECO codes available for use in Noctua should show how they map up to a classic GO code, and there should be an alert for curators when they are using a code that does NOT map up to a classic code<br />
**PRO IDs for use in Noctua<br />
**Fix GPAD export from Noctua https://github.com/geneontology/noctua/issues/418<br />
**Add a SPARTA workbench https://github.com/geneontology/noctua/issues/465<br />
**Working group discussion of evidence on complex Noctua models (Kimberly?)<br />
<br />
====Noctua table view demo (Chris)====<br />
<br />
==Project updates==<br />
*AGR - report to GOC: PIs<br />
*SynGO meeting report: Paul T<br />
*Report of Reactome-GO connection: David H/Peter D<br />
*Report on transcription work/Noctua templates: Astrid GREEKC consortium=<br />
=Evening: Poster session=<br />
<br />
=Tuesday 3rd October=<br />
==Annotation guidelines and issues (part two)==<br />
===CC component annotation guidelines (Kimberly)===<br />
CC component annotation: what does it mean ? Kimberly to do 1 proposal (out of 3 alternatives)<br />
1. where the protein is active 2. two different meanings: enables or the right RO (part:of, ie just found there) 3. part_of (low information value!)<br />
===Author intent & protein domains===<br />
Pascale /Ruth; IDA v IC v New evidence code https://github.com/geneontology/go-annotation/issues/1621 30 minutes discussion about issues; hopefully action items can come out of the discussion<br />
===Centralization of InterPro2GO annotations===<br />
Proposal (follow-up from Geneva 2016): (Paul T)<br />
*GO database pulls directly from InterPro2GO for UniProt Reference Proteomes<br />
*MOD identifier is used as primary gene identifier<br />
*Annotations are given "contributed by" InterPro<br />
*MODs pull from GO database, no need to maintain separate InterPro pipelines<br />
<br />
===HTP guidelines===<br />
Helen - 15 minutes Report on progress from HTP working group<br />
*Draft Guidelines https://docs.google.com/document/d/1ScIeclAzUXMe-tU6n0lVfsSwMHpOeNb7uK8On9-iKXc/edit?usp=sharing%7CHTP<br />
<br />
*Provision of new evidence code<br />
*Implementation & developing guidelines<br />
<br />
===Transcription annotations decision tree===<br />
Ruth Action Items Corvallis 2017/06<br />
*David OS to create transcription regulator activity (proposed by Paul T)<br />
*Proposed changes to decision tree in Corvallis:<br />
**Simplified from previous version. Essentially a choice between ‘regulating transcription by RNA polymerase II’ or ‘regulating gene expression’<br />
**Annotation 5 = contributes_to sequence-specific DNA binding<br />
David: when people do enrichment, they don’t drop contributes_to (ie., pay attention to qualifiers), so all those proteins will come down as ‘DNA binding’ Action item: replace ‘annotation 5’ with ISS annotation (if DNA binding domain) or contributes to annotation 5 with ISS annotation if no DNA binding domain and domains to suggest coactivator<br />
*<br />
**Annotation 3 = nuclear chromatin<br />
Not everyone comfortable with this (ex., Stacia, David) Shouldn’t it be ‘colocalizes_with’? It was previously agreed that the definition for nuclear chromatin: The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus. Source:PMID:20404130 was to be applied. The proteins here include all associated proteins, not limited to just histones. With this statement the TFs are then contributing to chromatin, rather than binding to chromatin or colocalizing with it.<br />
*<br />
**Decision tree to be put up on GOC website.<br />
**Should annotation 4 exist? (Ruth)<br />
<br />
===Annotation Documentation===<br />
Kimberly Action Items Corvallis 2017/06<br />
*Continue with the consolidation of all documentation for ontology editing, and remove all old documents.<br />
*Review annotation documentation and add to github and readthedocs.<br />
*Make sure to mark obsolete pages/doc as such and add a link to the new relevant doc<br />
*Solicit annotation documentation from participating groups for consolidation.<br />
*Make sure to mark docs with ‘Date last reviewed’ so it’s easy for users to know when the documentation was last touched.<br />
*Pascale: additional information associated with GO terms, see GitHub ticket?<br />
*Add and follow action items at https://github.com/orgs/geneontology/projects/3<br />
<br />
===Annotation quality control===<br />
====PAINT update (Huaiyu)====<br />
Huaiyu Action Items Corvallis 2017/06:<br />
*Encourage discussion between PAINT curators and other annotators about terms not used for propagation<br />
*Report how many annotations per species are used for annotation propagation; could even supply this number for propagation specifically to human genes<br />
*Ruth and Huaiyu (others?) will discuss making use of groups that have already annotated specific gene lists to annotate the corresponding PAINT families.<br />
*Smooth out the challenge mechanism to make it easier to do make and resolve<br />
the challenges, identify terms that may be problematic and would benefit from consistency exercises and discussion.<br />
*Get a list of families where terms have not been propagated (?) - Please check this one for clarity.<br />
(added to github project board) Develop mechanism to trigger review of annotated PAINT families.<br />
<br />
===Viral processes update (Pascale)===<br />
Action Items Corvallis 2017/06 Check whether the incorporated changes could affect the host proteins. Document the use cases.<br />
==Community Support==<br />
===Citing GO (Paul T)===<br />
*Web page<br />
*Tool providers: Action Item Corvallis 2017/06: someone to represent GOC and contact GO tool providers to display version information and state this information needs to be included in any subsequent publication. Plus list the GOC paper to reference, as well as the tool provider reference. See: https://github.com/geneontology/go-site/issues/359 and https://github.com/geneontology/go-site/issues/360<br />
===Enrichment (Paul T & Suzi)===<br />
*Web page <br />
*Paul Pavlidis…<br />
*Data Commons work<br />
<br />
===GO_Slims===<br />
====Philosophy (Val, Suzi)====<br />
Creating a biologically useful slim (complete coverage by aspect, biologically useful terms i.e sufficient granularity, avoiding single step process terms (i.e functions), different slims for different purposes: Judy, Mary D (+ Suzi, Val, etc). For overviews, for particular taxa, for a particular area of biology<br />
Specifications for slims from user's perspective (Val: 30 minutes)<br />
====HOW TO MAKE SLIMS (Chris)====<br />
Yaml format for creating slims/types of slims/target organisms<br />
====Use and maintenance of slims (Mary and Suzi)====<br />
Mary: algorithm - 15 minutes<br />
Suzi: GO ribbon<br />
<br />
=Wednesday 4th October=<br />
==Ongoing work==<br />
===AmiGO (Follow up with Seth)===<br />
*In general, while several of the AmiGO issues are high-priority, there has been limited bandwidth to tackle them in the context of continuing work on Noctua and the replacement pipeline. Several fixes are queued up and will be available before the upcoming SAB meeting.<br />
**In response to: in base_statistics, plotly graph for "Experimental annotation publications by assigner" is confusing https://github.com/geneontology/amigo/issues/429<br />
**From Pascale's question: My understanding is that there are essentially no resources for AmiGO right now so any AmiGO issue is low priority. Is this correct?<br />
<br />
===The Fate of Simple Processes===<br />
*analysis of gene products annotated to phosphorylation but not annotated to a kinase MF term. What did these annotations actually mean? Curators would need to review. Timeline? Deadline? Working group? One possibility would be to use part_of/involved_in relation to phosphorylation for genes also annotated to kinase MF, and causally_upstream_of_or_within for others until curators can re-evaluate.<br />
*Other considerations:<br />
**Helen: are there many the single-step processes?<br />
**Paul: user-oriented approach - is it a useful grouping for our users?<br />
**Ruth: we need to think about the meaning beyond just “phosphorylation”<br />
**Ruth: what are the consequences of removing “phosphorylation” and what happens to all its children?<br />
**Pascale Q: providing that we remove the processes, would it affect the term enrichment analysis?<br />
<br />
===BP refactoring===<br />
*Defining “Cellular Process” and “Multi-Organism Process” terms<br />
*Action item: the comments/examples/notes should be captured, working group to discuss this.<br />
<br />
===Proteoforms===<br />
Establish a working group for when and how to use proteoforms in annotation. (Kimberly with Harold and Li)<br />
===Usability issues===<br />
*What do users want?<br />
**truth (summary/story/model)?<br />
**fishing expeditions?<br />
**api access?<br />
*Who are our users?<br />
**geneticists?<br />
**clinicians?<br />
**computational biologists?<br />
*Use cases: https://github.com/geneontology/go-ontology/issues/13606<br />
*Perhaps discussion of examples of how the GOC members are engaging with the community and how we can do better in the future (suggested by Helen).<br />
<br />
=Wednesday noon-ish Fin=<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Agenda&diff=653022017 Cambridge GOC Meeting Agenda2017-09-27T00:30:18Z<p>Suzi: /* Usability issues */</p>
<hr />
<div>GOC Meeting, Cambridge , October 2-4, 2017<br />
<br />
=Monday 2nd October=<br />
==Welcome, overview, vision, introductions==<br />
GO PIs<br />
==GO handbook presentation==<br />
*The Gene Ontology and the meaning of biological function (Paul T)<br />
*Translating research data into Gene Ontology annotations (Pascale)<br />
*Gene Ontology - annotation extensions (Ruth)<br />
*GO as a biological systems model (Suzi, or Paul T if Suzi is late)<br />
Pascale will move slides to Google drive<br />
==Ontology Issues and Updates==<br />
===Update on MF refactoring (Pascale or Paul T)===<br />
====GitHub tutorial (Seth & Pascale)====<br />
How GO now uses GitHub for project management and guidelines for contributors<br />
*Where is information relevant to everyone's need<br />
*Groups (Groups.yaml)<br />
*Members<br />
*Etc<br />
<br />
===Qualifiers/Relation issues (Kimberly and Chris)===<br />
====Qualifiers/Relations in GPAD (Kimberly and Chris)====<br />
====Contributes_to guidelines====<br />
++ colocalizes with<br />
====Multiple qualifiers for an annotation (Huaiyu)====<br />
====Use of Qualifiers in Legacy Annotations====<br />
Pascale Proposal: We will apply the general qualifier to all legacy annotations. Each group can provide more specific qualifiers if they have a mechanism to distinguish. Action Items Corvallis 2017/06<br />
*Working group to decide what relations should be available in Protein2GO or other tools for manual annotations. Also decide when there are different ways of expressing the same thing, what way we will choose. What should the default gene/gene product relation be for legacy annotations?<br />
*Chris to work on reports that may help curators make decisions about what annotations can get more expressive qualifiers.<br />
<br />
====Regulates relations====<br />
Adding new qualifiers for the relation between a gene/gene product and a GO term What should the default relation be? How will we handle regulation? Use a relation, involved in regulation of, or use the precomposed regulation term?<br />
Ruth: There are now 3 ways to say the same thing: - involved_in_regulation_of X - involved_in X regulation - involved_in BP regulates(X)<br />
For annotation purposes and for our users we want one.<br />
DOS: Good point. These are semantically identical, but I agree we need to find a way to only have one: by convention for classic GO annotation and by filtering the output of inference for noctua output. Proposal: If a named regulation class exists: involved_in X regulation ...if not: involved_in {some BP} regulates(X) NOTE: If there was an annotation in Noctua such as ‘regulation of’ ‘very specific term’ and there was no term as ‘regulation of very specific term’ the GOC pipeline would create the annotation to the parent term: ‘regulation of less specific term’. Q: Is this implemented ?<br />
==Project updates==<br />
*AGR - report to GOC: PIs<br />
*SynGO meeting report: Paul T<br />
*Report of Reactome-GO connection: David H/Peter D<br />
*Report on transcription work/Noctua templates: Astrid GREEKC consortium=<br />
=Evening: Poster session=<br />
<br />
=Tuesday 3rd October=<br />
==Annotation guidelines and issues (part one)==<br />
===Signaling (Kimberly and David)===<br />
*Report from signaling workshop: David /Kimberly<br />
*Signaling: First attempt at Annotation consistency 2.0 - Kimberly to report on the approach and the outcome.<br />
Discussion points: Limited participation (self-selected to participate). One recommendation may be to ask all active curators to participate, even at some low level https://github.com/orgs/geneontology/projects/<br />
<br />
===Overview of GO annotations/Noctua (Kimberly & Chris)===<br />
====Getting Noctua ready for production====<br />
*Kimberly & Seth Blocking issues list: TO BE COMPLETED<br />
*Action Item Corvallis 2017/06:<br />
**Provide ways for users to recover and digest GO-CAM units (Gene Ontology-based Causal Activity Model). Ideas include rule-based generations of text statements from model, cytoscape view of network described, etc.<br />
**ECO codes available for use in Noctua should show how they map up to a classic GO code, and there should be an alert for curators when they are using a code that does NOT map up to a classic code<br />
**PRO IDs for use in Noctua<br />
**Fix GPAD export from Noctua https://github.com/geneontology/noctua/issues/418<br />
**Add a SPARTA workbench https://github.com/geneontology/noctua/issues/465<br />
**Working group discussion of evidence on complex Noctua models (Kimberly?)<br />
<br />
====Noctua table view demo (Chris)====<br />
<br />
===CC component annotation guidelines (Kimberly)===<br />
CC component annotation: what does it mean ? Kimberly to do 1 proposal (out of 3 alternatives)<br />
1. where the protein is active 2. two different meanings: enables or the right RO (part:of, ie just found there) 3. part_of (low information value!)<br />
===Author intent & protein domains===<br />
Pascale /Ruth; IDA v IC v New evidence code https://github.com/geneontology/go-annotation/issues/1621 30 minutes discussion about issues; hopefully action items can come out of the discussion<br />
===Centralization of InterPro2GO annotations===<br />
Proposal (follow-up from Geneva 2016): (Paul T)<br />
*GO database pulls directly from InterPro2GO for UniProt Reference Proteomes<br />
*MOD identifier is used as primary gene identifier<br />
*Annotations are given "contributed by" InterPro<br />
*MODs pull from GO database, no need to maintain separate InterPro pipelines<br />
<br />
==Annotation guidelines and issues (part two)==<br />
===HTP guidelines===<br />
Helen - 15 minutes Report on progress from HTP working group<br />
*Draft Guidelines https://docs.google.com/document/d/1ScIeclAzUXMe-tU6n0lVfsSwMHpOeNb7uK8On9-iKXc/edit?usp=sharing%7CHTP<br />
<br />
*Provision of new evidence code<br />
*Implementation & developing guidelines<br />
<br />
===Transcription annotations decision tree===<br />
Ruth Action Items Corvallis 2017/06<br />
*David OS to create transcription regulator activity (proposed by Paul T)<br />
*Proposed changes to decision tree in Corvallis:<br />
**Simplified from previous version. Essentially a choice between ‘regulating transcription by RNA polymerase II’ or ‘regulating gene expression’<br />
**Annotation 5 = contributes_to sequence-specific DNA binding<br />
David: when people do enrichment, they don’t drop contributes_to (ie., pay attention to qualifiers), so all those proteins will come down as ‘DNA binding’ Action item: replace ‘annotation 5’ with ISS annotation (if DNA binding domain) or contributes to annotation 5 with ISS annotation if no DNA binding domain and domains to suggest coactivator<br />
*<br />
**Annotation 3 = nuclear chromatin<br />
Not everyone comfortable with this (ex., Stacia, David) Shouldn’t it be ‘colocalizes_with’? It was previously agreed that the definition for nuclear chromatin: The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus. Source:PMID:20404130 was to be applied. The proteins here include all associated proteins, not limited to just histones. With this statement the TFs are then contributing to chromatin, rather than binding to chromatin or colocalizing with it.<br />
*<br />
**Decision tree to be put up on GOC website.<br />
**Should annotation 4 exist? (Ruth)<br />
<br />
===Annotation Documentation===<br />
Kimberly Action Items Corvallis 2017/06<br />
*Continue with the consolidation of all documentation for ontology editing, and remove all old documents.<br />
*Review annotation documentation and add to github and readthedocs.<br />
*Make sure to mark obsolete pages/doc as such and add a link to the new relevant doc<br />
*Solicit annotation documentation from participating groups for consolidation.<br />
*Make sure to mark docs with ‘Date last reviewed’ so it’s easy for users to know when the documentation was last touched.<br />
*Pascale: additional information associated with GO terms, see GitHub ticket?<br />
*Add and follow action items at https://github.com/orgs/geneontology/projects/3<br />
<br />
===Annotation quality control===<br />
====PAINT update (Huaiyu)====<br />
Huaiyu Action Items Corvallis 2017/06:<br />
*Encourage discussion between PAINT curators and other annotators about terms not used for propagation<br />
*Report how many annotations per species are used for annotation propagation; could even supply this number for propagation specifically to human genes<br />
*Ruth and Huaiyu (others?) will discuss making use of groups that have already annotated specific gene lists to annotate the corresponding PAINT families.<br />
*Smooth out the challenge mechanism to make it easier to do make and resolve<br />
the challenges, identify terms that may be problematic and would benefit from consistency exercises and discussion.<br />
*Get a list of families where terms have not been propagated (?) - Please check this one for clarity.<br />
(added to github project board) Develop mechanism to trigger review of annotated PAINT families.<br />
<br />
===Viral processes update (Pascale)===<br />
Action Items Corvallis 2017/06 Check whether the incorporated changes could affect the host proteins. Document the use cases.<br />
==Community Support==<br />
===Citing GO (Paul T)===<br />
*Web page<br />
*Tool providers: Action Item Corvallis 2017/06: someone to represent GOC and contact GO tool providers to display version information and state this information needs to be included in any subsequent publication. Plus list the GOC paper to reference, as well as the tool provider reference. See: https://github.com/geneontology/go-site/issues/359 and https://github.com/geneontology/go-site/issues/360<br />
===Enrichment (Paul T & Suzi)===<br />
*Web page <br />
*Paul Pavlidis…<br />
*Data Commons work<br />
<br />
===GO_Slims===<br />
====Philosophy (Val, Suzi)====<br />
Creating a biologically useful slim (complete coverage by aspect, biologically useful terms i.e sufficient granularity, avoiding single step process terms (i.e functions), different slims for different purposes: Judy, Mary D (+ Suzi, Val, etc). For overviews, for particular taxa, for a particular area of biology<br />
Specifications for slims from user's perspective (Val: 30 minutes)<br />
====HOW TO MAKE SLIMS (Chris)====<br />
Yaml format for creating slims/types of slims/target organisms<br />
====Use and maintenance of slims (Mary and Suzi)====<br />
Mary: algorithm - 15 minutes<br />
Suzi: GO ribbon<br />
<br />
=Wednesday 4th October=<br />
==Ongoing work==<br />
===AmiGO (Follow up with Seth)===<br />
*In general, while several of the AmiGO issues are high-priority, there has been limited bandwidth to tackle them in the context of continuing work on Noctua and the replacement pipeline. Several fixes are queued up and will be available before the upcoming SAB meeting.<br />
**In response to: in base_statistics, plotly graph for "Experimental annotation publications by assigner" is confusing https://github.com/geneontology/amigo/issues/429<br />
**From Pascale's question: My understanding is that there are essentially no resources for AmiGO right now so any AmiGO issue is low priority. Is this correct?<br />
<br />
===The Fate of Simple Processes===<br />
*analysis of gene products annotated to phosphorylation but not annotated to a kinase MF term. What did these annotations actually mean? Curators would need to review. Timeline? Deadline? Working group? One possibility would be to use part_of/involved_in relation to phosphorylation for genes also annotated to kinase MF, and causally_upstream_of_or_within for others until curators can re-evaluate.<br />
*Other considerations:<br />
**Helen: are there many the single-step processes?<br />
**Paul: user-oriented approach - is it a useful grouping for our users?<br />
**Ruth: we need to think about the meaning beyond just “phosphorylation”<br />
**Ruth: what are the consequences of removing “phosphorylation” and what happens to all its children?<br />
**Pascale Q: providing that we remove the processes, would it affect the term enrichment analysis?<br />
<br />
===BP refactoring===<br />
*Defining “Cellular Process” and “Multi-Organism Process” terms<br />
*Action item: the comments/examples/notes should be captured, working group to discuss this.<br />
<br />
===Proteoforms===<br />
Establish a working group for when and how to use proteoforms in annotation. (Kimberly with Harold and Li)<br />
===Usability issues===<br />
*What do users want?<br />
**truth (summary/story/model)?<br />
**fishing expeditions?<br />
**api access?<br />
*Who are our users?<br />
**geneticists?<br />
**clinicians?<br />
**computational biologists?<br />
*Use cases: https://github.com/geneontology/go-ontology/issues/13606<br />
*Perhaps discussion of examples of how the GOC members are engaging with the community and how we can do better in the future (suggested by Helen).<br />
<br />
=Wednesday noon-ish Fin=<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Agenda&diff=653012017 Cambridge GOC Meeting Agenda2017-09-27T00:29:31Z<p>Suzi: /* BP refactoring */</p>
<hr />
<div>GOC Meeting, Cambridge , October 2-4, 2017<br />
<br />
=Monday 2nd October=<br />
==Welcome, overview, vision, introductions==<br />
GO PIs<br />
==GO handbook presentation==<br />
*The Gene Ontology and the meaning of biological function (Paul T)<br />
*Translating research data into Gene Ontology annotations (Pascale)<br />
*Gene Ontology - annotation extensions (Ruth)<br />
*GO as a biological systems model (Suzi, or Paul T if Suzi is late)<br />
Pascale will move slides to Google drive<br />
==Ontology Issues and Updates==<br />
===Update on MF refactoring (Pascale or Paul T)===<br />
====GitHub tutorial (Seth & Pascale)====<br />
How GO now uses GitHub for project management and guidelines for contributors<br />
*Where is information relevant to everyone's need<br />
*Groups (Groups.yaml)<br />
*Members<br />
*Etc<br />
<br />
===Qualifiers/Relation issues (Kimberly and Chris)===<br />
====Qualifiers/Relations in GPAD (Kimberly and Chris)====<br />
====Contributes_to guidelines====<br />
++ colocalizes with<br />
====Multiple qualifiers for an annotation (Huaiyu)====<br />
====Use of Qualifiers in Legacy Annotations====<br />
Pascale Proposal: We will apply the general qualifier to all legacy annotations. Each group can provide more specific qualifiers if they have a mechanism to distinguish. Action Items Corvallis 2017/06<br />
*Working group to decide what relations should be available in Protein2GO or other tools for manual annotations. Also decide when there are different ways of expressing the same thing, what way we will choose. What should the default gene/gene product relation be for legacy annotations?<br />
*Chris to work on reports that may help curators make decisions about what annotations can get more expressive qualifiers.<br />
<br />
====Regulates relations====<br />
Adding new qualifiers for the relation between a gene/gene product and a GO term What should the default relation be? How will we handle regulation? Use a relation, involved in regulation of, or use the precomposed regulation term?<br />
Ruth: There are now 3 ways to say the same thing: - involved_in_regulation_of X - involved_in X regulation - involved_in BP regulates(X)<br />
For annotation purposes and for our users we want one.<br />
DOS: Good point. These are semantically identical, but I agree we need to find a way to only have one: by convention for classic GO annotation and by filtering the output of inference for noctua output. Proposal: If a named regulation class exists: involved_in X regulation ...if not: involved_in {some BP} regulates(X) NOTE: If there was an annotation in Noctua such as ‘regulation of’ ‘very specific term’ and there was no term as ‘regulation of very specific term’ the GOC pipeline would create the annotation to the parent term: ‘regulation of less specific term’. Q: Is this implemented ?<br />
==Project updates==<br />
*AGR - report to GOC: PIs<br />
*SynGO meeting report: Paul T<br />
*Report of Reactome-GO connection: David H/Peter D<br />
*Report on transcription work/Noctua templates: Astrid GREEKC consortium=<br />
=Evening: Poster session=<br />
<br />
=Tuesday 3rd October=<br />
==Annotation guidelines and issues (part one)==<br />
===Signaling (Kimberly and David)===<br />
*Report from signaling workshop: David /Kimberly<br />
*Signaling: First attempt at Annotation consistency 2.0 - Kimberly to report on the approach and the outcome.<br />
Discussion points: Limited participation (self-selected to participate). One recommendation may be to ask all active curators to participate, even at some low level https://github.com/orgs/geneontology/projects/<br />
<br />
===Overview of GO annotations/Noctua (Kimberly & Chris)===<br />
====Getting Noctua ready for production====<br />
*Kimberly & Seth Blocking issues list: TO BE COMPLETED<br />
*Action Item Corvallis 2017/06:<br />
**Provide ways for users to recover and digest GO-CAM units (Gene Ontology-based Causal Activity Model). Ideas include rule-based generations of text statements from model, cytoscape view of network described, etc.<br />
**ECO codes available for use in Noctua should show how they map up to a classic GO code, and there should be an alert for curators when they are using a code that does NOT map up to a classic code<br />
**PRO IDs for use in Noctua<br />
**Fix GPAD export from Noctua https://github.com/geneontology/noctua/issues/418<br />
**Add a SPARTA workbench https://github.com/geneontology/noctua/issues/465<br />
**Working group discussion of evidence on complex Noctua models (Kimberly?)<br />
<br />
====Noctua table view demo (Chris)====<br />
<br />
===CC component annotation guidelines (Kimberly)===<br />
CC component annotation: what does it mean ? Kimberly to do 1 proposal (out of 3 alternatives)<br />
1. where the protein is active 2. two different meanings: enables or the right RO (part:of, ie just found there) 3. part_of (low information value!)<br />
===Author intent & protein domains===<br />
Pascale /Ruth; IDA v IC v New evidence code https://github.com/geneontology/go-annotation/issues/1621 30 minutes discussion about issues; hopefully action items can come out of the discussion<br />
===Centralization of InterPro2GO annotations===<br />
Proposal (follow-up from Geneva 2016): (Paul T)<br />
*GO database pulls directly from InterPro2GO for UniProt Reference Proteomes<br />
*MOD identifier is used as primary gene identifier<br />
*Annotations are given "contributed by" InterPro<br />
*MODs pull from GO database, no need to maintain separate InterPro pipelines<br />
<br />
==Annotation guidelines and issues (part two)==<br />
===HTP guidelines===<br />
Helen - 15 minutes Report on progress from HTP working group<br />
*Draft Guidelines https://docs.google.com/document/d/1ScIeclAzUXMe-tU6n0lVfsSwMHpOeNb7uK8On9-iKXc/edit?usp=sharing%7CHTP<br />
<br />
*Provision of new evidence code<br />
*Implementation & developing guidelines<br />
<br />
===Transcription annotations decision tree===<br />
Ruth Action Items Corvallis 2017/06<br />
*David OS to create transcription regulator activity (proposed by Paul T)<br />
*Proposed changes to decision tree in Corvallis:<br />
**Simplified from previous version. Essentially a choice between ‘regulating transcription by RNA polymerase II’ or ‘regulating gene expression’<br />
**Annotation 5 = contributes_to sequence-specific DNA binding<br />
David: when people do enrichment, they don’t drop contributes_to (ie., pay attention to qualifiers), so all those proteins will come down as ‘DNA binding’ Action item: replace ‘annotation 5’ with ISS annotation (if DNA binding domain) or contributes to annotation 5 with ISS annotation if no DNA binding domain and domains to suggest coactivator<br />
*<br />
**Annotation 3 = nuclear chromatin<br />
Not everyone comfortable with this (ex., Stacia, David) Shouldn’t it be ‘colocalizes_with’? It was previously agreed that the definition for nuclear chromatin: The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus. Source:PMID:20404130 was to be applied. The proteins here include all associated proteins, not limited to just histones. With this statement the TFs are then contributing to chromatin, rather than binding to chromatin or colocalizing with it.<br />
*<br />
**Decision tree to be put up on GOC website.<br />
**Should annotation 4 exist? (Ruth)<br />
<br />
===Annotation Documentation===<br />
Kimberly Action Items Corvallis 2017/06<br />
*Continue with the consolidation of all documentation for ontology editing, and remove all old documents.<br />
*Review annotation documentation and add to github and readthedocs.<br />
*Make sure to mark obsolete pages/doc as such and add a link to the new relevant doc<br />
*Solicit annotation documentation from participating groups for consolidation.<br />
*Make sure to mark docs with ‘Date last reviewed’ so it’s easy for users to know when the documentation was last touched.<br />
*Pascale: additional information associated with GO terms, see GitHub ticket?<br />
*Add and follow action items at https://github.com/orgs/geneontology/projects/3<br />
<br />
===Annotation quality control===<br />
====PAINT update (Huaiyu)====<br />
Huaiyu Action Items Corvallis 2017/06:<br />
*Encourage discussion between PAINT curators and other annotators about terms not used for propagation<br />
*Report how many annotations per species are used for annotation propagation; could even supply this number for propagation specifically to human genes<br />
*Ruth and Huaiyu (others?) will discuss making use of groups that have already annotated specific gene lists to annotate the corresponding PAINT families.<br />
*Smooth out the challenge mechanism to make it easier to do make and resolve<br />
the challenges, identify terms that may be problematic and would benefit from consistency exercises and discussion.<br />
*Get a list of families where terms have not been propagated (?) - Please check this one for clarity.<br />
(added to github project board) Develop mechanism to trigger review of annotated PAINT families.<br />
<br />
===Viral processes update (Pascale)===<br />
Action Items Corvallis 2017/06 Check whether the incorporated changes could affect the host proteins. Document the use cases.<br />
==Community Support==<br />
===Citing GO (Paul T)===<br />
*Web page<br />
*Tool providers: Action Item Corvallis 2017/06: someone to represent GOC and contact GO tool providers to display version information and state this information needs to be included in any subsequent publication. Plus list the GOC paper to reference, as well as the tool provider reference. See: https://github.com/geneontology/go-site/issues/359 and https://github.com/geneontology/go-site/issues/360<br />
===Enrichment (Paul T & Suzi)===<br />
*Web page <br />
*Paul Pavlidis…<br />
*Data Commons work<br />
<br />
===GO_Slims===<br />
====Philosophy (Val, Suzi)====<br />
Creating a biologically useful slim (complete coverage by aspect, biologically useful terms i.e sufficient granularity, avoiding single step process terms (i.e functions), different slims for different purposes: Judy, Mary D (+ Suzi, Val, etc). For overviews, for particular taxa, for a particular area of biology<br />
Specifications for slims from user's perspective (Val: 30 minutes)<br />
====HOW TO MAKE SLIMS (Chris)====<br />
Yaml format for creating slims/types of slims/target organisms<br />
====Use and maintenance of slims (Mary and Suzi)====<br />
Mary: algorithm - 15 minutes<br />
Suzi: GO ribbon<br />
<br />
=Wednesday 4th October=<br />
==Ongoing work==<br />
===AmiGO (Follow up with Seth)===<br />
*In general, while several of the AmiGO issues are high-priority, there has been limited bandwidth to tackle them in the context of continuing work on Noctua and the replacement pipeline. Several fixes are queued up and will be available before the upcoming SAB meeting.<br />
**In response to: in base_statistics, plotly graph for "Experimental annotation publications by assigner" is confusing https://github.com/geneontology/amigo/issues/429<br />
**From Pascale's question: My understanding is that there are essentially no resources for AmiGO right now so any AmiGO issue is low priority. Is this correct?<br />
<br />
===The Fate of Simple Processes===<br />
*analysis of gene products annotated to phosphorylation but not annotated to a kinase MF term. What did these annotations actually mean? Curators would need to review. Timeline? Deadline? Working group? One possibility would be to use part_of/involved_in relation to phosphorylation for genes also annotated to kinase MF, and causally_upstream_of_or_within for others until curators can re-evaluate.<br />
*Other considerations:<br />
**Helen: are there many the single-step processes?<br />
**Paul: user-oriented approach - is it a useful grouping for our users?<br />
**Ruth: we need to think about the meaning beyond just “phosphorylation”<br />
**Ruth: what are the consequences of removing “phosphorylation” and what happens to all its children?<br />
**Pascale Q: providing that we remove the processes, would it affect the term enrichment analysis?<br />
<br />
===BP refactoring===<br />
*Defining “Cellular Process” and “Multi-Organism Process” terms<br />
*Action item: the comments/examples/notes should be captured, working group to discuss this.<br />
<br />
===Proteoforms===<br />
Establish a working group for when and how to use proteoforms in annotation. (Kimberly with Harold and Li)<br />
===Usability issues===<br />
What do users want?<br />
truth (summary/story/model)?<br />
fishing expeditions?<br />
api access?<br />
Who are our users?<br />
geneticists?<br />
clinicians?<br />
computational biologists?<br />
Use cases: https://github.com/geneontology/go-ontology/issues/13606<br />
Perhaps discussion of examples of how the GOC members are engaging with the community and how we can do better in the future (suggested by Helen).<br />
=Wednesday noon-ish Fin=<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Agenda&diff=653002017 Cambridge GOC Meeting Agenda2017-09-27T00:29:20Z<p>Suzi: /* The Fate of Simple Processes */</p>
<hr />
<div>GOC Meeting, Cambridge , October 2-4, 2017<br />
<br />
=Monday 2nd October=<br />
==Welcome, overview, vision, introductions==<br />
GO PIs<br />
==GO handbook presentation==<br />
*The Gene Ontology and the meaning of biological function (Paul T)<br />
*Translating research data into Gene Ontology annotations (Pascale)<br />
*Gene Ontology - annotation extensions (Ruth)<br />
*GO as a biological systems model (Suzi, or Paul T if Suzi is late)<br />
Pascale will move slides to Google drive<br />
==Ontology Issues and Updates==<br />
===Update on MF refactoring (Pascale or Paul T)===<br />
====GitHub tutorial (Seth & Pascale)====<br />
How GO now uses GitHub for project management and guidelines for contributors<br />
*Where is information relevant to everyone's need<br />
*Groups (Groups.yaml)<br />
*Members<br />
*Etc<br />
<br />
===Qualifiers/Relation issues (Kimberly and Chris)===<br />
====Qualifiers/Relations in GPAD (Kimberly and Chris)====<br />
====Contributes_to guidelines====<br />
++ colocalizes with<br />
====Multiple qualifiers for an annotation (Huaiyu)====<br />
====Use of Qualifiers in Legacy Annotations====<br />
Pascale Proposal: We will apply the general qualifier to all legacy annotations. Each group can provide more specific qualifiers if they have a mechanism to distinguish. Action Items Corvallis 2017/06<br />
*Working group to decide what relations should be available in Protein2GO or other tools for manual annotations. Also decide when there are different ways of expressing the same thing, what way we will choose. What should the default gene/gene product relation be for legacy annotations?<br />
*Chris to work on reports that may help curators make decisions about what annotations can get more expressive qualifiers.<br />
<br />
====Regulates relations====<br />
Adding new qualifiers for the relation between a gene/gene product and a GO term What should the default relation be? How will we handle regulation? Use a relation, involved in regulation of, or use the precomposed regulation term?<br />
Ruth: There are now 3 ways to say the same thing: - involved_in_regulation_of X - involved_in X regulation - involved_in BP regulates(X)<br />
For annotation purposes and for our users we want one.<br />
DOS: Good point. These are semantically identical, but I agree we need to find a way to only have one: by convention for classic GO annotation and by filtering the output of inference for noctua output. Proposal: If a named regulation class exists: involved_in X regulation ...if not: involved_in {some BP} regulates(X) NOTE: If there was an annotation in Noctua such as ‘regulation of’ ‘very specific term’ and there was no term as ‘regulation of very specific term’ the GOC pipeline would create the annotation to the parent term: ‘regulation of less specific term’. Q: Is this implemented ?<br />
==Project updates==<br />
*AGR - report to GOC: PIs<br />
*SynGO meeting report: Paul T<br />
*Report of Reactome-GO connection: David H/Peter D<br />
*Report on transcription work/Noctua templates: Astrid GREEKC consortium=<br />
=Evening: Poster session=<br />
<br />
=Tuesday 3rd October=<br />
==Annotation guidelines and issues (part one)==<br />
===Signaling (Kimberly and David)===<br />
*Report from signaling workshop: David /Kimberly<br />
*Signaling: First attempt at Annotation consistency 2.0 - Kimberly to report on the approach and the outcome.<br />
Discussion points: Limited participation (self-selected to participate). One recommendation may be to ask all active curators to participate, even at some low level https://github.com/orgs/geneontology/projects/<br />
<br />
===Overview of GO annotations/Noctua (Kimberly & Chris)===<br />
====Getting Noctua ready for production====<br />
*Kimberly & Seth Blocking issues list: TO BE COMPLETED<br />
*Action Item Corvallis 2017/06:<br />
**Provide ways for users to recover and digest GO-CAM units (Gene Ontology-based Causal Activity Model). Ideas include rule-based generations of text statements from model, cytoscape view of network described, etc.<br />
**ECO codes available for use in Noctua should show how they map up to a classic GO code, and there should be an alert for curators when they are using a code that does NOT map up to a classic code<br />
**PRO IDs for use in Noctua<br />
**Fix GPAD export from Noctua https://github.com/geneontology/noctua/issues/418<br />
**Add a SPARTA workbench https://github.com/geneontology/noctua/issues/465<br />
**Working group discussion of evidence on complex Noctua models (Kimberly?)<br />
<br />
====Noctua table view demo (Chris)====<br />
<br />
===CC component annotation guidelines (Kimberly)===<br />
CC component annotation: what does it mean ? Kimberly to do 1 proposal (out of 3 alternatives)<br />
1. where the protein is active 2. two different meanings: enables or the right RO (part:of, ie just found there) 3. part_of (low information value!)<br />
===Author intent & protein domains===<br />
Pascale /Ruth; IDA v IC v New evidence code https://github.com/geneontology/go-annotation/issues/1621 30 minutes discussion about issues; hopefully action items can come out of the discussion<br />
===Centralization of InterPro2GO annotations===<br />
Proposal (follow-up from Geneva 2016): (Paul T)<br />
*GO database pulls directly from InterPro2GO for UniProt Reference Proteomes<br />
*MOD identifier is used as primary gene identifier<br />
*Annotations are given "contributed by" InterPro<br />
*MODs pull from GO database, no need to maintain separate InterPro pipelines<br />
<br />
==Annotation guidelines and issues (part two)==<br />
===HTP guidelines===<br />
Helen - 15 minutes Report on progress from HTP working group<br />
*Draft Guidelines https://docs.google.com/document/d/1ScIeclAzUXMe-tU6n0lVfsSwMHpOeNb7uK8On9-iKXc/edit?usp=sharing%7CHTP<br />
<br />
*Provision of new evidence code<br />
*Implementation & developing guidelines<br />
<br />
===Transcription annotations decision tree===<br />
Ruth Action Items Corvallis 2017/06<br />
*David OS to create transcription regulator activity (proposed by Paul T)<br />
*Proposed changes to decision tree in Corvallis:<br />
**Simplified from previous version. Essentially a choice between ‘regulating transcription by RNA polymerase II’ or ‘regulating gene expression’<br />
**Annotation 5 = contributes_to sequence-specific DNA binding<br />
David: when people do enrichment, they don’t drop contributes_to (ie., pay attention to qualifiers), so all those proteins will come down as ‘DNA binding’ Action item: replace ‘annotation 5’ with ISS annotation (if DNA binding domain) or contributes to annotation 5 with ISS annotation if no DNA binding domain and domains to suggest coactivator<br />
*<br />
**Annotation 3 = nuclear chromatin<br />
Not everyone comfortable with this (ex., Stacia, David) Shouldn’t it be ‘colocalizes_with’? It was previously agreed that the definition for nuclear chromatin: The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus. Source:PMID:20404130 was to be applied. The proteins here include all associated proteins, not limited to just histones. With this statement the TFs are then contributing to chromatin, rather than binding to chromatin or colocalizing with it.<br />
*<br />
**Decision tree to be put up on GOC website.<br />
**Should annotation 4 exist? (Ruth)<br />
<br />
===Annotation Documentation===<br />
Kimberly Action Items Corvallis 2017/06<br />
*Continue with the consolidation of all documentation for ontology editing, and remove all old documents.<br />
*Review annotation documentation and add to github and readthedocs.<br />
*Make sure to mark obsolete pages/doc as such and add a link to the new relevant doc<br />
*Solicit annotation documentation from participating groups for consolidation.<br />
*Make sure to mark docs with ‘Date last reviewed’ so it’s easy for users to know when the documentation was last touched.<br />
*Pascale: additional information associated with GO terms, see GitHub ticket?<br />
*Add and follow action items at https://github.com/orgs/geneontology/projects/3<br />
<br />
===Annotation quality control===<br />
====PAINT update (Huaiyu)====<br />
Huaiyu Action Items Corvallis 2017/06:<br />
*Encourage discussion between PAINT curators and other annotators about terms not used for propagation<br />
*Report how many annotations per species are used for annotation propagation; could even supply this number for propagation specifically to human genes<br />
*Ruth and Huaiyu (others?) will discuss making use of groups that have already annotated specific gene lists to annotate the corresponding PAINT families.<br />
*Smooth out the challenge mechanism to make it easier to do make and resolve<br />
the challenges, identify terms that may be problematic and would benefit from consistency exercises and discussion.<br />
*Get a list of families where terms have not been propagated (?) - Please check this one for clarity.<br />
(added to github project board) Develop mechanism to trigger review of annotated PAINT families.<br />
<br />
===Viral processes update (Pascale)===<br />
Action Items Corvallis 2017/06 Check whether the incorporated changes could affect the host proteins. Document the use cases.<br />
==Community Support==<br />
===Citing GO (Paul T)===<br />
*Web page<br />
*Tool providers: Action Item Corvallis 2017/06: someone to represent GOC and contact GO tool providers to display version information and state this information needs to be included in any subsequent publication. Plus list the GOC paper to reference, as well as the tool provider reference. See: https://github.com/geneontology/go-site/issues/359 and https://github.com/geneontology/go-site/issues/360<br />
===Enrichment (Paul T & Suzi)===<br />
*Web page <br />
*Paul Pavlidis…<br />
*Data Commons work<br />
<br />
===GO_Slims===<br />
====Philosophy (Val, Suzi)====<br />
Creating a biologically useful slim (complete coverage by aspect, biologically useful terms i.e sufficient granularity, avoiding single step process terms (i.e functions), different slims for different purposes: Judy, Mary D (+ Suzi, Val, etc). For overviews, for particular taxa, for a particular area of biology<br />
Specifications for slims from user's perspective (Val: 30 minutes)<br />
====HOW TO MAKE SLIMS (Chris)====<br />
Yaml format for creating slims/types of slims/target organisms<br />
====Use and maintenance of slims (Mary and Suzi)====<br />
Mary: algorithm - 15 minutes<br />
Suzi: GO ribbon<br />
<br />
=Wednesday 4th October=<br />
==Ongoing work==<br />
===AmiGO (Follow up with Seth)===<br />
*In general, while several of the AmiGO issues are high-priority, there has been limited bandwidth to tackle them in the context of continuing work on Noctua and the replacement pipeline. Several fixes are queued up and will be available before the upcoming SAB meeting.<br />
**In response to: in base_statistics, plotly graph for "Experimental annotation publications by assigner" is confusing https://github.com/geneontology/amigo/issues/429<br />
**From Pascale's question: My understanding is that there are essentially no resources for AmiGO right now so any AmiGO issue is low priority. Is this correct?<br />
<br />
===The Fate of Simple Processes===<br />
*analysis of gene products annotated to phosphorylation but not annotated to a kinase MF term. What did these annotations actually mean? Curators would need to review. Timeline? Deadline? Working group? One possibility would be to use part_of/involved_in relation to phosphorylation for genes also annotated to kinase MF, and causally_upstream_of_or_within for others until curators can re-evaluate.<br />
*Other considerations:<br />
**Helen: are there many the single-step processes?<br />
**Paul: user-oriented approach - is it a useful grouping for our users?<br />
**Ruth: we need to think about the meaning beyond just “phosphorylation”<br />
**Ruth: what are the consequences of removing “phosphorylation” and what happens to all its children?<br />
**Pascale Q: providing that we remove the processes, would it affect the term enrichment analysis?<br />
<br />
===BP refactoring===<br />
Defining “Cellular Process” and “Multi-Organism Process” terms<br />
Action item: the comments/examples/notes should be captured, working group to discuss this.<br />
===Proteoforms===<br />
Establish a working group for when and how to use proteoforms in annotation. (Kimberly with Harold and Li)<br />
===Usability issues===<br />
What do users want?<br />
truth (summary/story/model)?<br />
fishing expeditions?<br />
api access?<br />
Who are our users?<br />
geneticists?<br />
clinicians?<br />
computational biologists?<br />
Use cases: https://github.com/geneontology/go-ontology/issues/13606<br />
Perhaps discussion of examples of how the GOC members are engaging with the community and how we can do better in the future (suggested by Helen).<br />
=Wednesday noon-ish Fin=<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Agenda&diff=652992017 Cambridge GOC Meeting Agenda2017-09-27T00:28:57Z<p>Suzi: /* AmiGO (Follow up with Seth) */</p>
<hr />
<div>GOC Meeting, Cambridge , October 2-4, 2017<br />
<br />
=Monday 2nd October=<br />
==Welcome, overview, vision, introductions==<br />
GO PIs<br />
==GO handbook presentation==<br />
*The Gene Ontology and the meaning of biological function (Paul T)<br />
*Translating research data into Gene Ontology annotations (Pascale)<br />
*Gene Ontology - annotation extensions (Ruth)<br />
*GO as a biological systems model (Suzi, or Paul T if Suzi is late)<br />
Pascale will move slides to Google drive<br />
==Ontology Issues and Updates==<br />
===Update on MF refactoring (Pascale or Paul T)===<br />
====GitHub tutorial (Seth & Pascale)====<br />
How GO now uses GitHub for project management and guidelines for contributors<br />
*Where is information relevant to everyone's need<br />
*Groups (Groups.yaml)<br />
*Members<br />
*Etc<br />
<br />
===Qualifiers/Relation issues (Kimberly and Chris)===<br />
====Qualifiers/Relations in GPAD (Kimberly and Chris)====<br />
====Contributes_to guidelines====<br />
++ colocalizes with<br />
====Multiple qualifiers for an annotation (Huaiyu)====<br />
====Use of Qualifiers in Legacy Annotations====<br />
Pascale Proposal: We will apply the general qualifier to all legacy annotations. Each group can provide more specific qualifiers if they have a mechanism to distinguish. Action Items Corvallis 2017/06<br />
*Working group to decide what relations should be available in Protein2GO or other tools for manual annotations. Also decide when there are different ways of expressing the same thing, what way we will choose. What should the default gene/gene product relation be for legacy annotations?<br />
*Chris to work on reports that may help curators make decisions about what annotations can get more expressive qualifiers.<br />
<br />
====Regulates relations====<br />
Adding new qualifiers for the relation between a gene/gene product and a GO term What should the default relation be? How will we handle regulation? Use a relation, involved in regulation of, or use the precomposed regulation term?<br />
Ruth: There are now 3 ways to say the same thing: - involved_in_regulation_of X - involved_in X regulation - involved_in BP regulates(X)<br />
For annotation purposes and for our users we want one.<br />
DOS: Good point. These are semantically identical, but I agree we need to find a way to only have one: by convention for classic GO annotation and by filtering the output of inference for noctua output. Proposal: If a named regulation class exists: involved_in X regulation ...if not: involved_in {some BP} regulates(X) NOTE: If there was an annotation in Noctua such as ‘regulation of’ ‘very specific term’ and there was no term as ‘regulation of very specific term’ the GOC pipeline would create the annotation to the parent term: ‘regulation of less specific term’. Q: Is this implemented ?<br />
==Project updates==<br />
*AGR - report to GOC: PIs<br />
*SynGO meeting report: Paul T<br />
*Report of Reactome-GO connection: David H/Peter D<br />
*Report on transcription work/Noctua templates: Astrid GREEKC consortium=<br />
=Evening: Poster session=<br />
<br />
=Tuesday 3rd October=<br />
==Annotation guidelines and issues (part one)==<br />
===Signaling (Kimberly and David)===<br />
*Report from signaling workshop: David /Kimberly<br />
*Signaling: First attempt at Annotation consistency 2.0 - Kimberly to report on the approach and the outcome.<br />
Discussion points: Limited participation (self-selected to participate). One recommendation may be to ask all active curators to participate, even at some low level https://github.com/orgs/geneontology/projects/<br />
<br />
===Overview of GO annotations/Noctua (Kimberly & Chris)===<br />
====Getting Noctua ready for production====<br />
*Kimberly & Seth Blocking issues list: TO BE COMPLETED<br />
*Action Item Corvallis 2017/06:<br />
**Provide ways for users to recover and digest GO-CAM units (Gene Ontology-based Causal Activity Model). Ideas include rule-based generations of text statements from model, cytoscape view of network described, etc.<br />
**ECO codes available for use in Noctua should show how they map up to a classic GO code, and there should be an alert for curators when they are using a code that does NOT map up to a classic code<br />
**PRO IDs for use in Noctua<br />
**Fix GPAD export from Noctua https://github.com/geneontology/noctua/issues/418<br />
**Add a SPARTA workbench https://github.com/geneontology/noctua/issues/465<br />
**Working group discussion of evidence on complex Noctua models (Kimberly?)<br />
<br />
====Noctua table view demo (Chris)====<br />
<br />
===CC component annotation guidelines (Kimberly)===<br />
CC component annotation: what does it mean ? Kimberly to do 1 proposal (out of 3 alternatives)<br />
1. where the protein is active 2. two different meanings: enables or the right RO (part:of, ie just found there) 3. part_of (low information value!)<br />
===Author intent & protein domains===<br />
Pascale /Ruth; IDA v IC v New evidence code https://github.com/geneontology/go-annotation/issues/1621 30 minutes discussion about issues; hopefully action items can come out of the discussion<br />
===Centralization of InterPro2GO annotations===<br />
Proposal (follow-up from Geneva 2016): (Paul T)<br />
*GO database pulls directly from InterPro2GO for UniProt Reference Proteomes<br />
*MOD identifier is used as primary gene identifier<br />
*Annotations are given "contributed by" InterPro<br />
*MODs pull from GO database, no need to maintain separate InterPro pipelines<br />
<br />
==Annotation guidelines and issues (part two)==<br />
===HTP guidelines===<br />
Helen - 15 minutes Report on progress from HTP working group<br />
*Draft Guidelines https://docs.google.com/document/d/1ScIeclAzUXMe-tU6n0lVfsSwMHpOeNb7uK8On9-iKXc/edit?usp=sharing%7CHTP<br />
<br />
*Provision of new evidence code<br />
*Implementation & developing guidelines<br />
<br />
===Transcription annotations decision tree===<br />
Ruth Action Items Corvallis 2017/06<br />
*David OS to create transcription regulator activity (proposed by Paul T)<br />
*Proposed changes to decision tree in Corvallis:<br />
**Simplified from previous version. Essentially a choice between ‘regulating transcription by RNA polymerase II’ or ‘regulating gene expression’<br />
**Annotation 5 = contributes_to sequence-specific DNA binding<br />
David: when people do enrichment, they don’t drop contributes_to (ie., pay attention to qualifiers), so all those proteins will come down as ‘DNA binding’ Action item: replace ‘annotation 5’ with ISS annotation (if DNA binding domain) or contributes to annotation 5 with ISS annotation if no DNA binding domain and domains to suggest coactivator<br />
*<br />
**Annotation 3 = nuclear chromatin<br />
Not everyone comfortable with this (ex., Stacia, David) Shouldn’t it be ‘colocalizes_with’? It was previously agreed that the definition for nuclear chromatin: The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus. Source:PMID:20404130 was to be applied. The proteins here include all associated proteins, not limited to just histones. With this statement the TFs are then contributing to chromatin, rather than binding to chromatin or colocalizing with it.<br />
*<br />
**Decision tree to be put up on GOC website.<br />
**Should annotation 4 exist? (Ruth)<br />
<br />
===Annotation Documentation===<br />
Kimberly Action Items Corvallis 2017/06<br />
*Continue with the consolidation of all documentation for ontology editing, and remove all old documents.<br />
*Review annotation documentation and add to github and readthedocs.<br />
*Make sure to mark obsolete pages/doc as such and add a link to the new relevant doc<br />
*Solicit annotation documentation from participating groups for consolidation.<br />
*Make sure to mark docs with ‘Date last reviewed’ so it’s easy for users to know when the documentation was last touched.<br />
*Pascale: additional information associated with GO terms, see GitHub ticket?<br />
*Add and follow action items at https://github.com/orgs/geneontology/projects/3<br />
<br />
===Annotation quality control===<br />
====PAINT update (Huaiyu)====<br />
Huaiyu Action Items Corvallis 2017/06:<br />
*Encourage discussion between PAINT curators and other annotators about terms not used for propagation<br />
*Report how many annotations per species are used for annotation propagation; could even supply this number for propagation specifically to human genes<br />
*Ruth and Huaiyu (others?) will discuss making use of groups that have already annotated specific gene lists to annotate the corresponding PAINT families.<br />
*Smooth out the challenge mechanism to make it easier to do make and resolve<br />
the challenges, identify terms that may be problematic and would benefit from consistency exercises and discussion.<br />
*Get a list of families where terms have not been propagated (?) - Please check this one for clarity.<br />
(added to github project board) Develop mechanism to trigger review of annotated PAINT families.<br />
<br />
===Viral processes update (Pascale)===<br />
Action Items Corvallis 2017/06 Check whether the incorporated changes could affect the host proteins. Document the use cases.<br />
==Community Support==<br />
===Citing GO (Paul T)===<br />
*Web page<br />
*Tool providers: Action Item Corvallis 2017/06: someone to represent GOC and contact GO tool providers to display version information and state this information needs to be included in any subsequent publication. Plus list the GOC paper to reference, as well as the tool provider reference. See: https://github.com/geneontology/go-site/issues/359 and https://github.com/geneontology/go-site/issues/360<br />
===Enrichment (Paul T & Suzi)===<br />
*Web page <br />
*Paul Pavlidis…<br />
*Data Commons work<br />
<br />
===GO_Slims===<br />
====Philosophy (Val, Suzi)====<br />
Creating a biologically useful slim (complete coverage by aspect, biologically useful terms i.e sufficient granularity, avoiding single step process terms (i.e functions), different slims for different purposes: Judy, Mary D (+ Suzi, Val, etc). For overviews, for particular taxa, for a particular area of biology<br />
Specifications for slims from user's perspective (Val: 30 minutes)<br />
====HOW TO MAKE SLIMS (Chris)====<br />
Yaml format for creating slims/types of slims/target organisms<br />
====Use and maintenance of slims (Mary and Suzi)====<br />
Mary: algorithm - 15 minutes<br />
Suzi: GO ribbon<br />
<br />
=Wednesday 4th October=<br />
==Ongoing work==<br />
===AmiGO (Follow up with Seth)===<br />
*In general, while several of the AmiGO issues are high-priority, there has been limited bandwidth to tackle them in the context of continuing work on Noctua and the replacement pipeline. Several fixes are queued up and will be available before the upcoming SAB meeting.<br />
**In response to: in base_statistics, plotly graph for "Experimental annotation publications by assigner" is confusing https://github.com/geneontology/amigo/issues/429<br />
**From Pascale's question: My understanding is that there are essentially no resources for AmiGO right now so any AmiGO issue is low priority. Is this correct?<br />
<br />
===The Fate of Simple Processes===<br />
analysis of gene products annotated to phosphorylation but not annotated to a kinase MF term. What did these annotations actually mean? Curators would need to review. Timeline? Deadline? Working group? One possibility would be to use part_of/involved_in relation to phosphorylation for genes also annotated to kinase MF, and causally_upstream_of_or_within for others until curators can re-evaluate.<br />
Other considerations:<br />
Helen: are there many the single-step processes?<br />
Paul: user-oriented approach - is it a useful grouping for our users?<br />
Ruth: we need to think about the meaning beyond just “phosphorylation”<br />
Ruth: what are the consequences of removing “phosphorylation” and what happens to all its children?<br />
Pascale Q: providing that we remove the processes, would it affect the term enrichment analysis?<br />
===BP refactoring===<br />
Defining “Cellular Process” and “Multi-Organism Process” terms<br />
Action item: the comments/examples/notes should be captured, working group to discuss this.<br />
===Proteoforms===<br />
Establish a working group for when and how to use proteoforms in annotation. (Kimberly with Harold and Li)<br />
===Usability issues===<br />
What do users want?<br />
truth (summary/story/model)?<br />
fishing expeditions?<br />
api access?<br />
Who are our users?<br />
geneticists?<br />
clinicians?<br />
computational biologists?<br />
Use cases: https://github.com/geneontology/go-ontology/issues/13606<br />
Perhaps discussion of examples of how the GOC members are engaging with the community and how we can do better in the future (suggested by Helen).<br />
=Wednesday noon-ish Fin=<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Agenda&diff=652982017 Cambridge GOC Meeting Agenda2017-09-27T00:28:03Z<p>Suzi: /* PAINT update (Huaiyu) */</p>
<hr />
<div>GOC Meeting, Cambridge , October 2-4, 2017<br />
<br />
=Monday 2nd October=<br />
==Welcome, overview, vision, introductions==<br />
GO PIs<br />
==GO handbook presentation==<br />
*The Gene Ontology and the meaning of biological function (Paul T)<br />
*Translating research data into Gene Ontology annotations (Pascale)<br />
*Gene Ontology - annotation extensions (Ruth)<br />
*GO as a biological systems model (Suzi, or Paul T if Suzi is late)<br />
Pascale will move slides to Google drive<br />
==Ontology Issues and Updates==<br />
===Update on MF refactoring (Pascale or Paul T)===<br />
====GitHub tutorial (Seth & Pascale)====<br />
How GO now uses GitHub for project management and guidelines for contributors<br />
*Where is information relevant to everyone's need<br />
*Groups (Groups.yaml)<br />
*Members<br />
*Etc<br />
<br />
===Qualifiers/Relation issues (Kimberly and Chris)===<br />
====Qualifiers/Relations in GPAD (Kimberly and Chris)====<br />
====Contributes_to guidelines====<br />
++ colocalizes with<br />
====Multiple qualifiers for an annotation (Huaiyu)====<br />
====Use of Qualifiers in Legacy Annotations====<br />
Pascale Proposal: We will apply the general qualifier to all legacy annotations. Each group can provide more specific qualifiers if they have a mechanism to distinguish. Action Items Corvallis 2017/06<br />
*Working group to decide what relations should be available in Protein2GO or other tools for manual annotations. Also decide when there are different ways of expressing the same thing, what way we will choose. What should the default gene/gene product relation be for legacy annotations?<br />
*Chris to work on reports that may help curators make decisions about what annotations can get more expressive qualifiers.<br />
<br />
====Regulates relations====<br />
Adding new qualifiers for the relation between a gene/gene product and a GO term What should the default relation be? How will we handle regulation? Use a relation, involved in regulation of, or use the precomposed regulation term?<br />
Ruth: There are now 3 ways to say the same thing: - involved_in_regulation_of X - involved_in X regulation - involved_in BP regulates(X)<br />
For annotation purposes and for our users we want one.<br />
DOS: Good point. These are semantically identical, but I agree we need to find a way to only have one: by convention for classic GO annotation and by filtering the output of inference for noctua output. Proposal: If a named regulation class exists: involved_in X regulation ...if not: involved_in {some BP} regulates(X) NOTE: If there was an annotation in Noctua such as ‘regulation of’ ‘very specific term’ and there was no term as ‘regulation of very specific term’ the GOC pipeline would create the annotation to the parent term: ‘regulation of less specific term’. Q: Is this implemented ?<br />
==Project updates==<br />
*AGR - report to GOC: PIs<br />
*SynGO meeting report: Paul T<br />
*Report of Reactome-GO connection: David H/Peter D<br />
*Report on transcription work/Noctua templates: Astrid GREEKC consortium=<br />
=Evening: Poster session=<br />
<br />
=Tuesday 3rd October=<br />
==Annotation guidelines and issues (part one)==<br />
===Signaling (Kimberly and David)===<br />
*Report from signaling workshop: David /Kimberly<br />
*Signaling: First attempt at Annotation consistency 2.0 - Kimberly to report on the approach and the outcome.<br />
Discussion points: Limited participation (self-selected to participate). One recommendation may be to ask all active curators to participate, even at some low level https://github.com/orgs/geneontology/projects/<br />
<br />
===Overview of GO annotations/Noctua (Kimberly & Chris)===<br />
====Getting Noctua ready for production====<br />
*Kimberly & Seth Blocking issues list: TO BE COMPLETED<br />
*Action Item Corvallis 2017/06:<br />
**Provide ways for users to recover and digest GO-CAM units (Gene Ontology-based Causal Activity Model). Ideas include rule-based generations of text statements from model, cytoscape view of network described, etc.<br />
**ECO codes available for use in Noctua should show how they map up to a classic GO code, and there should be an alert for curators when they are using a code that does NOT map up to a classic code<br />
**PRO IDs for use in Noctua<br />
**Fix GPAD export from Noctua https://github.com/geneontology/noctua/issues/418<br />
**Add a SPARTA workbench https://github.com/geneontology/noctua/issues/465<br />
**Working group discussion of evidence on complex Noctua models (Kimberly?)<br />
<br />
====Noctua table view demo (Chris)====<br />
<br />
===CC component annotation guidelines (Kimberly)===<br />
CC component annotation: what does it mean ? Kimberly to do 1 proposal (out of 3 alternatives)<br />
1. where the protein is active 2. two different meanings: enables or the right RO (part:of, ie just found there) 3. part_of (low information value!)<br />
===Author intent & protein domains===<br />
Pascale /Ruth; IDA v IC v New evidence code https://github.com/geneontology/go-annotation/issues/1621 30 minutes discussion about issues; hopefully action items can come out of the discussion<br />
===Centralization of InterPro2GO annotations===<br />
Proposal (follow-up from Geneva 2016): (Paul T)<br />
*GO database pulls directly from InterPro2GO for UniProt Reference Proteomes<br />
*MOD identifier is used as primary gene identifier<br />
*Annotations are given "contributed by" InterPro<br />
*MODs pull from GO database, no need to maintain separate InterPro pipelines<br />
<br />
==Annotation guidelines and issues (part two)==<br />
===HTP guidelines===<br />
Helen - 15 minutes Report on progress from HTP working group<br />
*Draft Guidelines https://docs.google.com/document/d/1ScIeclAzUXMe-tU6n0lVfsSwMHpOeNb7uK8On9-iKXc/edit?usp=sharing%7CHTP<br />
<br />
*Provision of new evidence code<br />
*Implementation & developing guidelines<br />
<br />
===Transcription annotations decision tree===<br />
Ruth Action Items Corvallis 2017/06<br />
*David OS to create transcription regulator activity (proposed by Paul T)<br />
*Proposed changes to decision tree in Corvallis:<br />
**Simplified from previous version. Essentially a choice between ‘regulating transcription by RNA polymerase II’ or ‘regulating gene expression’<br />
**Annotation 5 = contributes_to sequence-specific DNA binding<br />
David: when people do enrichment, they don’t drop contributes_to (ie., pay attention to qualifiers), so all those proteins will come down as ‘DNA binding’ Action item: replace ‘annotation 5’ with ISS annotation (if DNA binding domain) or contributes to annotation 5 with ISS annotation if no DNA binding domain and domains to suggest coactivator<br />
*<br />
**Annotation 3 = nuclear chromatin<br />
Not everyone comfortable with this (ex., Stacia, David) Shouldn’t it be ‘colocalizes_with’? It was previously agreed that the definition for nuclear chromatin: The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus. Source:PMID:20404130 was to be applied. The proteins here include all associated proteins, not limited to just histones. With this statement the TFs are then contributing to chromatin, rather than binding to chromatin or colocalizing with it.<br />
*<br />
**Decision tree to be put up on GOC website.<br />
**Should annotation 4 exist? (Ruth)<br />
<br />
===Annotation Documentation===<br />
Kimberly Action Items Corvallis 2017/06<br />
*Continue with the consolidation of all documentation for ontology editing, and remove all old documents.<br />
*Review annotation documentation and add to github and readthedocs.<br />
*Make sure to mark obsolete pages/doc as such and add a link to the new relevant doc<br />
*Solicit annotation documentation from participating groups for consolidation.<br />
*Make sure to mark docs with ‘Date last reviewed’ so it’s easy for users to know when the documentation was last touched.<br />
*Pascale: additional information associated with GO terms, see GitHub ticket?<br />
*Add and follow action items at https://github.com/orgs/geneontology/projects/3<br />
<br />
===Annotation quality control===<br />
====PAINT update (Huaiyu)====<br />
Huaiyu Action Items Corvallis 2017/06:<br />
*Encourage discussion between PAINT curators and other annotators about terms not used for propagation<br />
*Report how many annotations per species are used for annotation propagation; could even supply this number for propagation specifically to human genes<br />
*Ruth and Huaiyu (others?) will discuss making use of groups that have already annotated specific gene lists to annotate the corresponding PAINT families.<br />
*Smooth out the challenge mechanism to make it easier to do make and resolve<br />
the challenges, identify terms that may be problematic and would benefit from consistency exercises and discussion.<br />
*Get a list of families where terms have not been propagated (?) - Please check this one for clarity.<br />
(added to github project board) Develop mechanism to trigger review of annotated PAINT families.<br />
<br />
===Viral processes update (Pascale)===<br />
Action Items Corvallis 2017/06 Check whether the incorporated changes could affect the host proteins. Document the use cases.<br />
==Community Support==<br />
===Citing GO (Paul T)===<br />
*Web page<br />
*Tool providers: Action Item Corvallis 2017/06: someone to represent GOC and contact GO tool providers to display version information and state this information needs to be included in any subsequent publication. Plus list the GOC paper to reference, as well as the tool provider reference. See: https://github.com/geneontology/go-site/issues/359 and https://github.com/geneontology/go-site/issues/360<br />
===Enrichment (Paul T & Suzi)===<br />
*Web page <br />
*Paul Pavlidis…<br />
*Data Commons work<br />
<br />
===GO_Slims===<br />
====Philosophy (Val, Suzi)====<br />
Creating a biologically useful slim (complete coverage by aspect, biologically useful terms i.e sufficient granularity, avoiding single step process terms (i.e functions), different slims for different purposes: Judy, Mary D (+ Suzi, Val, etc). For overviews, for particular taxa, for a particular area of biology<br />
Specifications for slims from user's perspective (Val: 30 minutes)<br />
====HOW TO MAKE SLIMS (Chris)====<br />
Yaml format for creating slims/types of slims/target organisms<br />
====Use and maintenance of slims (Mary and Suzi)====<br />
Mary: algorithm - 15 minutes<br />
Suzi: GO ribbon<br />
<br />
=Wednesday 4th October=<br />
==Ongoing work==<br />
===AmiGO (Follow up with Seth)===<br />
In general, while several of the AmiGO issues are high-priority, there has been limited bandwidth to tackle them in the context of continuing work on Noctua and the replacement pipeline. Several fixes are queued up and will be available before the upcoming SAB meeting.<br />
In response to: in base_statistics, plotly graph for "Experimental annotation publications by assigner" is confusing https://github.com/geneontology/amigo/issues/429<br />
From Pascale's question: My understanding is that there are essentially no resources for AmiGO right now so any AmiGO issue is low priority. Is this correct?<br />
===The Fate of Simple Processes===<br />
analysis of gene products annotated to phosphorylation but not annotated to a kinase MF term. What did these annotations actually mean? Curators would need to review. Timeline? Deadline? Working group? One possibility would be to use part_of/involved_in relation to phosphorylation for genes also annotated to kinase MF, and causally_upstream_of_or_within for others until curators can re-evaluate.<br />
Other considerations:<br />
Helen: are there many the single-step processes?<br />
Paul: user-oriented approach - is it a useful grouping for our users?<br />
Ruth: we need to think about the meaning beyond just “phosphorylation”<br />
Ruth: what are the consequences of removing “phosphorylation” and what happens to all its children?<br />
Pascale Q: providing that we remove the processes, would it affect the term enrichment analysis?<br />
===BP refactoring===<br />
Defining “Cellular Process” and “Multi-Organism Process” terms<br />
Action item: the comments/examples/notes should be captured, working group to discuss this.<br />
===Proteoforms===<br />
Establish a working group for when and how to use proteoforms in annotation. (Kimberly with Harold and Li)<br />
===Usability issues===<br />
What do users want?<br />
truth (summary/story/model)?<br />
fishing expeditions?<br />
api access?<br />
Who are our users?<br />
geneticists?<br />
clinicians?<br />
computational biologists?<br />
Use cases: https://github.com/geneontology/go-ontology/issues/13606<br />
Perhaps discussion of examples of how the GOC members are engaging with the community and how we can do better in the future (suggested by Helen).<br />
=Wednesday noon-ish Fin=<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Agenda&diff=652972017 Cambridge GOC Meeting Agenda2017-09-27T00:27:39Z<p>Suzi: /* Annotation Documentation */</p>
<hr />
<div>GOC Meeting, Cambridge , October 2-4, 2017<br />
<br />
=Monday 2nd October=<br />
==Welcome, overview, vision, introductions==<br />
GO PIs<br />
==GO handbook presentation==<br />
*The Gene Ontology and the meaning of biological function (Paul T)<br />
*Translating research data into Gene Ontology annotations (Pascale)<br />
*Gene Ontology - annotation extensions (Ruth)<br />
*GO as a biological systems model (Suzi, or Paul T if Suzi is late)<br />
Pascale will move slides to Google drive<br />
==Ontology Issues and Updates==<br />
===Update on MF refactoring (Pascale or Paul T)===<br />
====GitHub tutorial (Seth & Pascale)====<br />
How GO now uses GitHub for project management and guidelines for contributors<br />
*Where is information relevant to everyone's need<br />
*Groups (Groups.yaml)<br />
*Members<br />
*Etc<br />
<br />
===Qualifiers/Relation issues (Kimberly and Chris)===<br />
====Qualifiers/Relations in GPAD (Kimberly and Chris)====<br />
====Contributes_to guidelines====<br />
++ colocalizes with<br />
====Multiple qualifiers for an annotation (Huaiyu)====<br />
====Use of Qualifiers in Legacy Annotations====<br />
Pascale Proposal: We will apply the general qualifier to all legacy annotations. Each group can provide more specific qualifiers if they have a mechanism to distinguish. Action Items Corvallis 2017/06<br />
*Working group to decide what relations should be available in Protein2GO or other tools for manual annotations. Also decide when there are different ways of expressing the same thing, what way we will choose. What should the default gene/gene product relation be for legacy annotations?<br />
*Chris to work on reports that may help curators make decisions about what annotations can get more expressive qualifiers.<br />
<br />
====Regulates relations====<br />
Adding new qualifiers for the relation between a gene/gene product and a GO term What should the default relation be? How will we handle regulation? Use a relation, involved in regulation of, or use the precomposed regulation term?<br />
Ruth: There are now 3 ways to say the same thing: - involved_in_regulation_of X - involved_in X regulation - involved_in BP regulates(X)<br />
For annotation purposes and for our users we want one.<br />
DOS: Good point. These are semantically identical, but I agree we need to find a way to only have one: by convention for classic GO annotation and by filtering the output of inference for noctua output. Proposal: If a named regulation class exists: involved_in X regulation ...if not: involved_in {some BP} regulates(X) NOTE: If there was an annotation in Noctua such as ‘regulation of’ ‘very specific term’ and there was no term as ‘regulation of very specific term’ the GOC pipeline would create the annotation to the parent term: ‘regulation of less specific term’. Q: Is this implemented ?<br />
==Project updates==<br />
*AGR - report to GOC: PIs<br />
*SynGO meeting report: Paul T<br />
*Report of Reactome-GO connection: David H/Peter D<br />
*Report on transcription work/Noctua templates: Astrid GREEKC consortium=<br />
=Evening: Poster session=<br />
<br />
=Tuesday 3rd October=<br />
==Annotation guidelines and issues (part one)==<br />
===Signaling (Kimberly and David)===<br />
*Report from signaling workshop: David /Kimberly<br />
*Signaling: First attempt at Annotation consistency 2.0 - Kimberly to report on the approach and the outcome.<br />
Discussion points: Limited participation (self-selected to participate). One recommendation may be to ask all active curators to participate, even at some low level https://github.com/orgs/geneontology/projects/<br />
<br />
===Overview of GO annotations/Noctua (Kimberly & Chris)===<br />
====Getting Noctua ready for production====<br />
*Kimberly & Seth Blocking issues list: TO BE COMPLETED<br />
*Action Item Corvallis 2017/06:<br />
**Provide ways for users to recover and digest GO-CAM units (Gene Ontology-based Causal Activity Model). Ideas include rule-based generations of text statements from model, cytoscape view of network described, etc.<br />
**ECO codes available for use in Noctua should show how they map up to a classic GO code, and there should be an alert for curators when they are using a code that does NOT map up to a classic code<br />
**PRO IDs for use in Noctua<br />
**Fix GPAD export from Noctua https://github.com/geneontology/noctua/issues/418<br />
**Add a SPARTA workbench https://github.com/geneontology/noctua/issues/465<br />
**Working group discussion of evidence on complex Noctua models (Kimberly?)<br />
<br />
====Noctua table view demo (Chris)====<br />
<br />
===CC component annotation guidelines (Kimberly)===<br />
CC component annotation: what does it mean ? Kimberly to do 1 proposal (out of 3 alternatives)<br />
1. where the protein is active 2. two different meanings: enables or the right RO (part:of, ie just found there) 3. part_of (low information value!)<br />
===Author intent & protein domains===<br />
Pascale /Ruth; IDA v IC v New evidence code https://github.com/geneontology/go-annotation/issues/1621 30 minutes discussion about issues; hopefully action items can come out of the discussion<br />
===Centralization of InterPro2GO annotations===<br />
Proposal (follow-up from Geneva 2016): (Paul T)<br />
*GO database pulls directly from InterPro2GO for UniProt Reference Proteomes<br />
*MOD identifier is used as primary gene identifier<br />
*Annotations are given "contributed by" InterPro<br />
*MODs pull from GO database, no need to maintain separate InterPro pipelines<br />
<br />
==Annotation guidelines and issues (part two)==<br />
===HTP guidelines===<br />
Helen - 15 minutes Report on progress from HTP working group<br />
*Draft Guidelines https://docs.google.com/document/d/1ScIeclAzUXMe-tU6n0lVfsSwMHpOeNb7uK8On9-iKXc/edit?usp=sharing%7CHTP<br />
<br />
*Provision of new evidence code<br />
*Implementation & developing guidelines<br />
<br />
===Transcription annotations decision tree===<br />
Ruth Action Items Corvallis 2017/06<br />
*David OS to create transcription regulator activity (proposed by Paul T)<br />
*Proposed changes to decision tree in Corvallis:<br />
**Simplified from previous version. Essentially a choice between ‘regulating transcription by RNA polymerase II’ or ‘regulating gene expression’<br />
**Annotation 5 = contributes_to sequence-specific DNA binding<br />
David: when people do enrichment, they don’t drop contributes_to (ie., pay attention to qualifiers), so all those proteins will come down as ‘DNA binding’ Action item: replace ‘annotation 5’ with ISS annotation (if DNA binding domain) or contributes to annotation 5 with ISS annotation if no DNA binding domain and domains to suggest coactivator<br />
*<br />
**Annotation 3 = nuclear chromatin<br />
Not everyone comfortable with this (ex., Stacia, David) Shouldn’t it be ‘colocalizes_with’? It was previously agreed that the definition for nuclear chromatin: The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus. Source:PMID:20404130 was to be applied. The proteins here include all associated proteins, not limited to just histones. With this statement the TFs are then contributing to chromatin, rather than binding to chromatin or colocalizing with it.<br />
*<br />
**Decision tree to be put up on GOC website.<br />
**Should annotation 4 exist? (Ruth)<br />
<br />
===Annotation Documentation===<br />
Kimberly Action Items Corvallis 2017/06<br />
*Continue with the consolidation of all documentation for ontology editing, and remove all old documents.<br />
*Review annotation documentation and add to github and readthedocs.<br />
*Make sure to mark obsolete pages/doc as such and add a link to the new relevant doc<br />
*Solicit annotation documentation from participating groups for consolidation.<br />
*Make sure to mark docs with ‘Date last reviewed’ so it’s easy for users to know when the documentation was last touched.<br />
*Pascale: additional information associated with GO terms, see GitHub ticket?<br />
*Add and follow action items at https://github.com/orgs/geneontology/projects/3<br />
<br />
===Annotation quality control===<br />
====PAINT update (Huaiyu)====<br />
Huaiyu Action Items Corvallis 2017/06:<br />
Encourage discussion between PAINT curators and other annotators about terms not used for propagation<br />
Report how many annotations per species are used for annotation propagation; could even supply this number for propagation specifically to human genes<br />
Ruth and Huaiyu (others?) will discuss making use of groups that have already annotated specific gene lists to annotate the corresponding PAINT families.<br />
Smooth out the challenge mechanism to make it easier to do make and resolve<br />
the challenges, identify terms that may be problematic and would benefit from consistency exercises and discussion.<br />
Get a list of families where terms have not been propagated (?) - Please check this one for clarity.<br />
(added to github project board) Develop mechanism to trigger review of annotated PAINT families.<br />
===Viral processes update (Pascale)===<br />
Action Items Corvallis 2017/06 Check whether the incorporated changes could affect the host proteins. Document the use cases.<br />
==Community Support==<br />
===Citing GO (Paul T)===<br />
*Web page<br />
*Tool providers: Action Item Corvallis 2017/06: someone to represent GOC and contact GO tool providers to display version information and state this information needs to be included in any subsequent publication. Plus list the GOC paper to reference, as well as the tool provider reference. See: https://github.com/geneontology/go-site/issues/359 and https://github.com/geneontology/go-site/issues/360<br />
===Enrichment (Paul T & Suzi)===<br />
*Web page <br />
*Paul Pavlidis…<br />
*Data Commons work<br />
<br />
===GO_Slims===<br />
====Philosophy (Val, Suzi)====<br />
Creating a biologically useful slim (complete coverage by aspect, biologically useful terms i.e sufficient granularity, avoiding single step process terms (i.e functions), different slims for different purposes: Judy, Mary D (+ Suzi, Val, etc). For overviews, for particular taxa, for a particular area of biology<br />
Specifications for slims from user's perspective (Val: 30 minutes)<br />
====HOW TO MAKE SLIMS (Chris)====<br />
Yaml format for creating slims/types of slims/target organisms<br />
====Use and maintenance of slims (Mary and Suzi)====<br />
Mary: algorithm - 15 minutes<br />
Suzi: GO ribbon<br />
<br />
=Wednesday 4th October=<br />
==Ongoing work==<br />
===AmiGO (Follow up with Seth)===<br />
In general, while several of the AmiGO issues are high-priority, there has been limited bandwidth to tackle them in the context of continuing work on Noctua and the replacement pipeline. Several fixes are queued up and will be available before the upcoming SAB meeting.<br />
In response to: in base_statistics, plotly graph for "Experimental annotation publications by assigner" is confusing https://github.com/geneontology/amigo/issues/429<br />
From Pascale's question: My understanding is that there are essentially no resources for AmiGO right now so any AmiGO issue is low priority. Is this correct?<br />
===The Fate of Simple Processes===<br />
analysis of gene products annotated to phosphorylation but not annotated to a kinase MF term. What did these annotations actually mean? Curators would need to review. Timeline? Deadline? Working group? One possibility would be to use part_of/involved_in relation to phosphorylation for genes also annotated to kinase MF, and causally_upstream_of_or_within for others until curators can re-evaluate.<br />
Other considerations:<br />
Helen: are there many the single-step processes?<br />
Paul: user-oriented approach - is it a useful grouping for our users?<br />
Ruth: we need to think about the meaning beyond just “phosphorylation”<br />
Ruth: what are the consequences of removing “phosphorylation” and what happens to all its children?<br />
Pascale Q: providing that we remove the processes, would it affect the term enrichment analysis?<br />
===BP refactoring===<br />
Defining “Cellular Process” and “Multi-Organism Process” terms<br />
Action item: the comments/examples/notes should be captured, working group to discuss this.<br />
===Proteoforms===<br />
Establish a working group for when and how to use proteoforms in annotation. (Kimberly with Harold and Li)<br />
===Usability issues===<br />
What do users want?<br />
truth (summary/story/model)?<br />
fishing expeditions?<br />
api access?<br />
Who are our users?<br />
geneticists?<br />
clinicians?<br />
computational biologists?<br />
Use cases: https://github.com/geneontology/go-ontology/issues/13606<br />
Perhaps discussion of examples of how the GOC members are engaging with the community and how we can do better in the future (suggested by Helen).<br />
=Wednesday noon-ish Fin=<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Agenda&diff=652962017 Cambridge GOC Meeting Agenda2017-09-27T00:26:56Z<p>Suzi: /* Transcription annotations decision tree */</p>
<hr />
<div>GOC Meeting, Cambridge , October 2-4, 2017<br />
<br />
=Monday 2nd October=<br />
==Welcome, overview, vision, introductions==<br />
GO PIs<br />
==GO handbook presentation==<br />
*The Gene Ontology and the meaning of biological function (Paul T)<br />
*Translating research data into Gene Ontology annotations (Pascale)<br />
*Gene Ontology - annotation extensions (Ruth)<br />
*GO as a biological systems model (Suzi, or Paul T if Suzi is late)<br />
Pascale will move slides to Google drive<br />
==Ontology Issues and Updates==<br />
===Update on MF refactoring (Pascale or Paul T)===<br />
====GitHub tutorial (Seth & Pascale)====<br />
How GO now uses GitHub for project management and guidelines for contributors<br />
*Where is information relevant to everyone's need<br />
*Groups (Groups.yaml)<br />
*Members<br />
*Etc<br />
<br />
===Qualifiers/Relation issues (Kimberly and Chris)===<br />
====Qualifiers/Relations in GPAD (Kimberly and Chris)====<br />
====Contributes_to guidelines====<br />
++ colocalizes with<br />
====Multiple qualifiers for an annotation (Huaiyu)====<br />
====Use of Qualifiers in Legacy Annotations====<br />
Pascale Proposal: We will apply the general qualifier to all legacy annotations. Each group can provide more specific qualifiers if they have a mechanism to distinguish. Action Items Corvallis 2017/06<br />
*Working group to decide what relations should be available in Protein2GO or other tools for manual annotations. Also decide when there are different ways of expressing the same thing, what way we will choose. What should the default gene/gene product relation be for legacy annotations?<br />
*Chris to work on reports that may help curators make decisions about what annotations can get more expressive qualifiers.<br />
<br />
====Regulates relations====<br />
Adding new qualifiers for the relation between a gene/gene product and a GO term What should the default relation be? How will we handle regulation? Use a relation, involved in regulation of, or use the precomposed regulation term?<br />
Ruth: There are now 3 ways to say the same thing: - involved_in_regulation_of X - involved_in X regulation - involved_in BP regulates(X)<br />
For annotation purposes and for our users we want one.<br />
DOS: Good point. These are semantically identical, but I agree we need to find a way to only have one: by convention for classic GO annotation and by filtering the output of inference for noctua output. Proposal: If a named regulation class exists: involved_in X regulation ...if not: involved_in {some BP} regulates(X) NOTE: If there was an annotation in Noctua such as ‘regulation of’ ‘very specific term’ and there was no term as ‘regulation of very specific term’ the GOC pipeline would create the annotation to the parent term: ‘regulation of less specific term’. Q: Is this implemented ?<br />
==Project updates==<br />
*AGR - report to GOC: PIs<br />
*SynGO meeting report: Paul T<br />
*Report of Reactome-GO connection: David H/Peter D<br />
*Report on transcription work/Noctua templates: Astrid GREEKC consortium=<br />
=Evening: Poster session=<br />
<br />
=Tuesday 3rd October=<br />
==Annotation guidelines and issues (part one)==<br />
===Signaling (Kimberly and David)===<br />
*Report from signaling workshop: David /Kimberly<br />
*Signaling: First attempt at Annotation consistency 2.0 - Kimberly to report on the approach and the outcome.<br />
Discussion points: Limited participation (self-selected to participate). One recommendation may be to ask all active curators to participate, even at some low level https://github.com/orgs/geneontology/projects/<br />
<br />
===Overview of GO annotations/Noctua (Kimberly & Chris)===<br />
====Getting Noctua ready for production====<br />
*Kimberly & Seth Blocking issues list: TO BE COMPLETED<br />
*Action Item Corvallis 2017/06:<br />
**Provide ways for users to recover and digest GO-CAM units (Gene Ontology-based Causal Activity Model). Ideas include rule-based generations of text statements from model, cytoscape view of network described, etc.<br />
**ECO codes available for use in Noctua should show how they map up to a classic GO code, and there should be an alert for curators when they are using a code that does NOT map up to a classic code<br />
**PRO IDs for use in Noctua<br />
**Fix GPAD export from Noctua https://github.com/geneontology/noctua/issues/418<br />
**Add a SPARTA workbench https://github.com/geneontology/noctua/issues/465<br />
**Working group discussion of evidence on complex Noctua models (Kimberly?)<br />
<br />
====Noctua table view demo (Chris)====<br />
<br />
===CC component annotation guidelines (Kimberly)===<br />
CC component annotation: what does it mean ? Kimberly to do 1 proposal (out of 3 alternatives)<br />
1. where the protein is active 2. two different meanings: enables or the right RO (part:of, ie just found there) 3. part_of (low information value!)<br />
===Author intent & protein domains===<br />
Pascale /Ruth; IDA v IC v New evidence code https://github.com/geneontology/go-annotation/issues/1621 30 minutes discussion about issues; hopefully action items can come out of the discussion<br />
===Centralization of InterPro2GO annotations===<br />
Proposal (follow-up from Geneva 2016): (Paul T)<br />
*GO database pulls directly from InterPro2GO for UniProt Reference Proteomes<br />
*MOD identifier is used as primary gene identifier<br />
*Annotations are given "contributed by" InterPro<br />
*MODs pull from GO database, no need to maintain separate InterPro pipelines<br />
<br />
==Annotation guidelines and issues (part two)==<br />
===HTP guidelines===<br />
Helen - 15 minutes Report on progress from HTP working group<br />
*Draft Guidelines https://docs.google.com/document/d/1ScIeclAzUXMe-tU6n0lVfsSwMHpOeNb7uK8On9-iKXc/edit?usp=sharing%7CHTP<br />
<br />
*Provision of new evidence code<br />
*Implementation & developing guidelines<br />
<br />
===Transcription annotations decision tree===<br />
Ruth Action Items Corvallis 2017/06<br />
*David OS to create transcription regulator activity (proposed by Paul T)<br />
*Proposed changes to decision tree in Corvallis:<br />
**Simplified from previous version. Essentially a choice between ‘regulating transcription by RNA polymerase II’ or ‘regulating gene expression’<br />
**Annotation 5 = contributes_to sequence-specific DNA binding<br />
David: when people do enrichment, they don’t drop contributes_to (ie., pay attention to qualifiers), so all those proteins will come down as ‘DNA binding’ Action item: replace ‘annotation 5’ with ISS annotation (if DNA binding domain) or contributes to annotation 5 with ISS annotation if no DNA binding domain and domains to suggest coactivator<br />
*<br />
**Annotation 3 = nuclear chromatin<br />
Not everyone comfortable with this (ex., Stacia, David) Shouldn’t it be ‘colocalizes_with’? It was previously agreed that the definition for nuclear chromatin: The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus. Source:PMID:20404130 was to be applied. The proteins here include all associated proteins, not limited to just histones. With this statement the TFs are then contributing to chromatin, rather than binding to chromatin or colocalizing with it.<br />
*<br />
**Decision tree to be put up on GOC website.<br />
**Should annotation 4 exist? (Ruth)<br />
<br />
===Annotation Documentation===<br />
Kimberly Action Items Corvallis 2017/06<br />
Continue with the consolidation of all documentation for ontology editing, and remove all old documents.<br />
Review annotation documentation and add to github and readthedocs.<br />
Make sure to mark obsolete pages/doc as such and add a link to the new relevant doc<br />
Solicit annotation documentation from participating groups for consolidation.<br />
Make sure to mark docs with ‘Date last reviewed’ so it’s easy for users to know when the documentation was last touched.<br />
Pascale: additional information associated with GO terms, see GitHub ticket?<br />
Add and follow action items at https://github.com/orgs/geneontology/projects/3<br />
===Annotation quality control===<br />
====PAINT update (Huaiyu)====<br />
Huaiyu Action Items Corvallis 2017/06:<br />
Encourage discussion between PAINT curators and other annotators about terms not used for propagation<br />
Report how many annotations per species are used for annotation propagation; could even supply this number for propagation specifically to human genes<br />
Ruth and Huaiyu (others?) will discuss making use of groups that have already annotated specific gene lists to annotate the corresponding PAINT families.<br />
Smooth out the challenge mechanism to make it easier to do make and resolve<br />
the challenges, identify terms that may be problematic and would benefit from consistency exercises and discussion.<br />
Get a list of families where terms have not been propagated (?) - Please check this one for clarity.<br />
(added to github project board) Develop mechanism to trigger review of annotated PAINT families.<br />
===Viral processes update (Pascale)===<br />
Action Items Corvallis 2017/06 Check whether the incorporated changes could affect the host proteins. Document the use cases.<br />
==Community Support==<br />
===Citing GO (Paul T)===<br />
*Web page<br />
*Tool providers: Action Item Corvallis 2017/06: someone to represent GOC and contact GO tool providers to display version information and state this information needs to be included in any subsequent publication. Plus list the GOC paper to reference, as well as the tool provider reference. See: https://github.com/geneontology/go-site/issues/359 and https://github.com/geneontology/go-site/issues/360<br />
===Enrichment (Paul T & Suzi)===<br />
*Web page <br />
*Paul Pavlidis…<br />
*Data Commons work<br />
<br />
===GO_Slims===<br />
====Philosophy (Val, Suzi)====<br />
Creating a biologically useful slim (complete coverage by aspect, biologically useful terms i.e sufficient granularity, avoiding single step process terms (i.e functions), different slims for different purposes: Judy, Mary D (+ Suzi, Val, etc). For overviews, for particular taxa, for a particular area of biology<br />
Specifications for slims from user's perspective (Val: 30 minutes)<br />
====HOW TO MAKE SLIMS (Chris)====<br />
Yaml format for creating slims/types of slims/target organisms<br />
====Use and maintenance of slims (Mary and Suzi)====<br />
Mary: algorithm - 15 minutes<br />
Suzi: GO ribbon<br />
<br />
=Wednesday 4th October=<br />
==Ongoing work==<br />
===AmiGO (Follow up with Seth)===<br />
In general, while several of the AmiGO issues are high-priority, there has been limited bandwidth to tackle them in the context of continuing work on Noctua and the replacement pipeline. Several fixes are queued up and will be available before the upcoming SAB meeting.<br />
In response to: in base_statistics, plotly graph for "Experimental annotation publications by assigner" is confusing https://github.com/geneontology/amigo/issues/429<br />
From Pascale's question: My understanding is that there are essentially no resources for AmiGO right now so any AmiGO issue is low priority. Is this correct?<br />
===The Fate of Simple Processes===<br />
analysis of gene products annotated to phosphorylation but not annotated to a kinase MF term. What did these annotations actually mean? Curators would need to review. Timeline? Deadline? Working group? One possibility would be to use part_of/involved_in relation to phosphorylation for genes also annotated to kinase MF, and causally_upstream_of_or_within for others until curators can re-evaluate.<br />
Other considerations:<br />
Helen: are there many the single-step processes?<br />
Paul: user-oriented approach - is it a useful grouping for our users?<br />
Ruth: we need to think about the meaning beyond just “phosphorylation”<br />
Ruth: what are the consequences of removing “phosphorylation” and what happens to all its children?<br />
Pascale Q: providing that we remove the processes, would it affect the term enrichment analysis?<br />
===BP refactoring===<br />
Defining “Cellular Process” and “Multi-Organism Process” terms<br />
Action item: the comments/examples/notes should be captured, working group to discuss this.<br />
===Proteoforms===<br />
Establish a working group for when and how to use proteoforms in annotation. (Kimberly with Harold and Li)<br />
===Usability issues===<br />
What do users want?<br />
truth (summary/story/model)?<br />
fishing expeditions?<br />
api access?<br />
Who are our users?<br />
geneticists?<br />
clinicians?<br />
computational biologists?<br />
Use cases: https://github.com/geneontology/go-ontology/issues/13606<br />
Perhaps discussion of examples of how the GOC members are engaging with the community and how we can do better in the future (suggested by Helen).<br />
=Wednesday noon-ish Fin=<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Agenda&diff=652952017 Cambridge GOC Meeting Agenda2017-09-27T00:26:07Z<p>Suzi: /* Transcription annotations decision tree */</p>
<hr />
<div>GOC Meeting, Cambridge , October 2-4, 2017<br />
<br />
=Monday 2nd October=<br />
==Welcome, overview, vision, introductions==<br />
GO PIs<br />
==GO handbook presentation==<br />
*The Gene Ontology and the meaning of biological function (Paul T)<br />
*Translating research data into Gene Ontology annotations (Pascale)<br />
*Gene Ontology - annotation extensions (Ruth)<br />
*GO as a biological systems model (Suzi, or Paul T if Suzi is late)<br />
Pascale will move slides to Google drive<br />
==Ontology Issues and Updates==<br />
===Update on MF refactoring (Pascale or Paul T)===<br />
====GitHub tutorial (Seth & Pascale)====<br />
How GO now uses GitHub for project management and guidelines for contributors<br />
*Where is information relevant to everyone's need<br />
*Groups (Groups.yaml)<br />
*Members<br />
*Etc<br />
<br />
===Qualifiers/Relation issues (Kimberly and Chris)===<br />
====Qualifiers/Relations in GPAD (Kimberly and Chris)====<br />
====Contributes_to guidelines====<br />
++ colocalizes with<br />
====Multiple qualifiers for an annotation (Huaiyu)====<br />
====Use of Qualifiers in Legacy Annotations====<br />
Pascale Proposal: We will apply the general qualifier to all legacy annotations. Each group can provide more specific qualifiers if they have a mechanism to distinguish. Action Items Corvallis 2017/06<br />
*Working group to decide what relations should be available in Protein2GO or other tools for manual annotations. Also decide when there are different ways of expressing the same thing, what way we will choose. What should the default gene/gene product relation be for legacy annotations?<br />
*Chris to work on reports that may help curators make decisions about what annotations can get more expressive qualifiers.<br />
<br />
====Regulates relations====<br />
Adding new qualifiers for the relation between a gene/gene product and a GO term What should the default relation be? How will we handle regulation? Use a relation, involved in regulation of, or use the precomposed regulation term?<br />
Ruth: There are now 3 ways to say the same thing: - involved_in_regulation_of X - involved_in X regulation - involved_in BP regulates(X)<br />
For annotation purposes and for our users we want one.<br />
DOS: Good point. These are semantically identical, but I agree we need to find a way to only have one: by convention for classic GO annotation and by filtering the output of inference for noctua output. Proposal: If a named regulation class exists: involved_in X regulation ...if not: involved_in {some BP} regulates(X) NOTE: If there was an annotation in Noctua such as ‘regulation of’ ‘very specific term’ and there was no term as ‘regulation of very specific term’ the GOC pipeline would create the annotation to the parent term: ‘regulation of less specific term’. Q: Is this implemented ?<br />
==Project updates==<br />
*AGR - report to GOC: PIs<br />
*SynGO meeting report: Paul T<br />
*Report of Reactome-GO connection: David H/Peter D<br />
*Report on transcription work/Noctua templates: Astrid GREEKC consortium=<br />
=Evening: Poster session=<br />
<br />
=Tuesday 3rd October=<br />
==Annotation guidelines and issues (part one)==<br />
===Signaling (Kimberly and David)===<br />
*Report from signaling workshop: David /Kimberly<br />
*Signaling: First attempt at Annotation consistency 2.0 - Kimberly to report on the approach and the outcome.<br />
Discussion points: Limited participation (self-selected to participate). One recommendation may be to ask all active curators to participate, even at some low level https://github.com/orgs/geneontology/projects/<br />
<br />
===Overview of GO annotations/Noctua (Kimberly & Chris)===<br />
====Getting Noctua ready for production====<br />
*Kimberly & Seth Blocking issues list: TO BE COMPLETED<br />
*Action Item Corvallis 2017/06:<br />
**Provide ways for users to recover and digest GO-CAM units (Gene Ontology-based Causal Activity Model). Ideas include rule-based generations of text statements from model, cytoscape view of network described, etc.<br />
**ECO codes available for use in Noctua should show how they map up to a classic GO code, and there should be an alert for curators when they are using a code that does NOT map up to a classic code<br />
**PRO IDs for use in Noctua<br />
**Fix GPAD export from Noctua https://github.com/geneontology/noctua/issues/418<br />
**Add a SPARTA workbench https://github.com/geneontology/noctua/issues/465<br />
**Working group discussion of evidence on complex Noctua models (Kimberly?)<br />
<br />
====Noctua table view demo (Chris)====<br />
<br />
===CC component annotation guidelines (Kimberly)===<br />
CC component annotation: what does it mean ? Kimberly to do 1 proposal (out of 3 alternatives)<br />
1. where the protein is active 2. two different meanings: enables or the right RO (part:of, ie just found there) 3. part_of (low information value!)<br />
===Author intent & protein domains===<br />
Pascale /Ruth; IDA v IC v New evidence code https://github.com/geneontology/go-annotation/issues/1621 30 minutes discussion about issues; hopefully action items can come out of the discussion<br />
===Centralization of InterPro2GO annotations===<br />
Proposal (follow-up from Geneva 2016): (Paul T)<br />
*GO database pulls directly from InterPro2GO for UniProt Reference Proteomes<br />
*MOD identifier is used as primary gene identifier<br />
*Annotations are given "contributed by" InterPro<br />
*MODs pull from GO database, no need to maintain separate InterPro pipelines<br />
<br />
==Annotation guidelines and issues (part two)==<br />
===HTP guidelines===<br />
Helen - 15 minutes Report on progress from HTP working group<br />
*Draft Guidelines https://docs.google.com/document/d/1ScIeclAzUXMe-tU6n0lVfsSwMHpOeNb7uK8On9-iKXc/edit?usp=sharing%7CHTP<br />
<br />
*Provision of new evidence code<br />
*Implementation & developing guidelines<br />
<br />
===Transcription annotations decision tree===<br />
Ruth Action Items Corvallis 2017/06<br />
*David OS to create transcription regulator activity (proposed by Paul T)<br />
*Proposed changes to decision tree in Corvallis:<br />
**Simplified from previous version. Essentially a choice between ‘regulating transcription by RNA polymerase II’ or ‘regulating gene expression’<br />
**Annotation 5 = contributes_to sequence-specific DNA binding<br />
David: when people do enrichment, they don’t drop contributes_to (ie., pay attention to qualifiers), so all those proteins will come down as ‘DNA binding’ Action item: replace ‘annotation 5’ with ISS annotation (if DNA binding domain) or contributes to annotation 5 with ISS annotation if no DNA binding domain and domains to suggest coactivator<br />
**Annotation 3 = nuclear chromatin<br />
Not everyone comfortable with this (ex., Stacia, David) Shouldn’t it be ‘colocalizes_with’? It was previously agreed that the definition for nuclear chromatin: The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus. Source:PMID:20404130 was to be applied. The proteins here include all associated proteins, not limited to just histones. With this statement the TFs are then contributing to chromatin, rather than binding to chromatin or colocalizing with it.<br />
Decision tree to be put up on GOC website.<br />
Should annotation 4 exist? (Ruth)<br />
<br />
===Annotation Documentation===<br />
Kimberly Action Items Corvallis 2017/06<br />
Continue with the consolidation of all documentation for ontology editing, and remove all old documents.<br />
Review annotation documentation and add to github and readthedocs.<br />
Make sure to mark obsolete pages/doc as such and add a link to the new relevant doc<br />
Solicit annotation documentation from participating groups for consolidation.<br />
Make sure to mark docs with ‘Date last reviewed’ so it’s easy for users to know when the documentation was last touched.<br />
Pascale: additional information associated with GO terms, see GitHub ticket?<br />
Add and follow action items at https://github.com/orgs/geneontology/projects/3<br />
===Annotation quality control===<br />
====PAINT update (Huaiyu)====<br />
Huaiyu Action Items Corvallis 2017/06:<br />
Encourage discussion between PAINT curators and other annotators about terms not used for propagation<br />
Report how many annotations per species are used for annotation propagation; could even supply this number for propagation specifically to human genes<br />
Ruth and Huaiyu (others?) will discuss making use of groups that have already annotated specific gene lists to annotate the corresponding PAINT families.<br />
Smooth out the challenge mechanism to make it easier to do make and resolve<br />
the challenges, identify terms that may be problematic and would benefit from consistency exercises and discussion.<br />
Get a list of families where terms have not been propagated (?) - Please check this one for clarity.<br />
(added to github project board) Develop mechanism to trigger review of annotated PAINT families.<br />
===Viral processes update (Pascale)===<br />
Action Items Corvallis 2017/06 Check whether the incorporated changes could affect the host proteins. Document the use cases.<br />
==Community Support==<br />
===Citing GO (Paul T)===<br />
*Web page<br />
*Tool providers: Action Item Corvallis 2017/06: someone to represent GOC and contact GO tool providers to display version information and state this information needs to be included in any subsequent publication. Plus list the GOC paper to reference, as well as the tool provider reference. See: https://github.com/geneontology/go-site/issues/359 and https://github.com/geneontology/go-site/issues/360<br />
===Enrichment (Paul T & Suzi)===<br />
*Web page <br />
*Paul Pavlidis…<br />
*Data Commons work<br />
<br />
===GO_Slims===<br />
====Philosophy (Val, Suzi)====<br />
Creating a biologically useful slim (complete coverage by aspect, biologically useful terms i.e sufficient granularity, avoiding single step process terms (i.e functions), different slims for different purposes: Judy, Mary D (+ Suzi, Val, etc). For overviews, for particular taxa, for a particular area of biology<br />
Specifications for slims from user's perspective (Val: 30 minutes)<br />
====HOW TO MAKE SLIMS (Chris)====<br />
Yaml format for creating slims/types of slims/target organisms<br />
====Use and maintenance of slims (Mary and Suzi)====<br />
Mary: algorithm - 15 minutes<br />
Suzi: GO ribbon<br />
<br />
=Wednesday 4th October=<br />
==Ongoing work==<br />
===AmiGO (Follow up with Seth)===<br />
In general, while several of the AmiGO issues are high-priority, there has been limited bandwidth to tackle them in the context of continuing work on Noctua and the replacement pipeline. Several fixes are queued up and will be available before the upcoming SAB meeting.<br />
In response to: in base_statistics, plotly graph for "Experimental annotation publications by assigner" is confusing https://github.com/geneontology/amigo/issues/429<br />
From Pascale's question: My understanding is that there are essentially no resources for AmiGO right now so any AmiGO issue is low priority. Is this correct?<br />
===The Fate of Simple Processes===<br />
analysis of gene products annotated to phosphorylation but not annotated to a kinase MF term. What did these annotations actually mean? Curators would need to review. Timeline? Deadline? Working group? One possibility would be to use part_of/involved_in relation to phosphorylation for genes also annotated to kinase MF, and causally_upstream_of_or_within for others until curators can re-evaluate.<br />
Other considerations:<br />
Helen: are there many the single-step processes?<br />
Paul: user-oriented approach - is it a useful grouping for our users?<br />
Ruth: we need to think about the meaning beyond just “phosphorylation”<br />
Ruth: what are the consequences of removing “phosphorylation” and what happens to all its children?<br />
Pascale Q: providing that we remove the processes, would it affect the term enrichment analysis?<br />
===BP refactoring===<br />
Defining “Cellular Process” and “Multi-Organism Process” terms<br />
Action item: the comments/examples/notes should be captured, working group to discuss this.<br />
===Proteoforms===<br />
Establish a working group for when and how to use proteoforms in annotation. (Kimberly with Harold and Li)<br />
===Usability issues===<br />
What do users want?<br />
truth (summary/story/model)?<br />
fishing expeditions?<br />
api access?<br />
Who are our users?<br />
geneticists?<br />
clinicians?<br />
computational biologists?<br />
Use cases: https://github.com/geneontology/go-ontology/issues/13606<br />
Perhaps discussion of examples of how the GOC members are engaging with the community and how we can do better in the future (suggested by Helen).<br />
=Wednesday noon-ish Fin=<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Agenda&diff=652942017 Cambridge GOC Meeting Agenda2017-09-27T00:24:58Z<p>Suzi: /* HTP guidelines */</p>
<hr />
<div>GOC Meeting, Cambridge , October 2-4, 2017<br />
<br />
=Monday 2nd October=<br />
==Welcome, overview, vision, introductions==<br />
GO PIs<br />
==GO handbook presentation==<br />
*The Gene Ontology and the meaning of biological function (Paul T)<br />
*Translating research data into Gene Ontology annotations (Pascale)<br />
*Gene Ontology - annotation extensions (Ruth)<br />
*GO as a biological systems model (Suzi, or Paul T if Suzi is late)<br />
Pascale will move slides to Google drive<br />
==Ontology Issues and Updates==<br />
===Update on MF refactoring (Pascale or Paul T)===<br />
====GitHub tutorial (Seth & Pascale)====<br />
How GO now uses GitHub for project management and guidelines for contributors<br />
*Where is information relevant to everyone's need<br />
*Groups (Groups.yaml)<br />
*Members<br />
*Etc<br />
<br />
===Qualifiers/Relation issues (Kimberly and Chris)===<br />
====Qualifiers/Relations in GPAD (Kimberly and Chris)====<br />
====Contributes_to guidelines====<br />
++ colocalizes with<br />
====Multiple qualifiers for an annotation (Huaiyu)====<br />
====Use of Qualifiers in Legacy Annotations====<br />
Pascale Proposal: We will apply the general qualifier to all legacy annotations. Each group can provide more specific qualifiers if they have a mechanism to distinguish. Action Items Corvallis 2017/06<br />
*Working group to decide what relations should be available in Protein2GO or other tools for manual annotations. Also decide when there are different ways of expressing the same thing, what way we will choose. What should the default gene/gene product relation be for legacy annotations?<br />
*Chris to work on reports that may help curators make decisions about what annotations can get more expressive qualifiers.<br />
<br />
====Regulates relations====<br />
Adding new qualifiers for the relation between a gene/gene product and a GO term What should the default relation be? How will we handle regulation? Use a relation, involved in regulation of, or use the precomposed regulation term?<br />
Ruth: There are now 3 ways to say the same thing: - involved_in_regulation_of X - involved_in X regulation - involved_in BP regulates(X)<br />
For annotation purposes and for our users we want one.<br />
DOS: Good point. These are semantically identical, but I agree we need to find a way to only have one: by convention for classic GO annotation and by filtering the output of inference for noctua output. Proposal: If a named regulation class exists: involved_in X regulation ...if not: involved_in {some BP} regulates(X) NOTE: If there was an annotation in Noctua such as ‘regulation of’ ‘very specific term’ and there was no term as ‘regulation of very specific term’ the GOC pipeline would create the annotation to the parent term: ‘regulation of less specific term’. Q: Is this implemented ?<br />
==Project updates==<br />
*AGR - report to GOC: PIs<br />
*SynGO meeting report: Paul T<br />
*Report of Reactome-GO connection: David H/Peter D<br />
*Report on transcription work/Noctua templates: Astrid GREEKC consortium=<br />
=Evening: Poster session=<br />
<br />
=Tuesday 3rd October=<br />
==Annotation guidelines and issues (part one)==<br />
===Signaling (Kimberly and David)===<br />
*Report from signaling workshop: David /Kimberly<br />
*Signaling: First attempt at Annotation consistency 2.0 - Kimberly to report on the approach and the outcome.<br />
Discussion points: Limited participation (self-selected to participate). One recommendation may be to ask all active curators to participate, even at some low level https://github.com/orgs/geneontology/projects/<br />
<br />
===Overview of GO annotations/Noctua (Kimberly & Chris)===<br />
====Getting Noctua ready for production====<br />
*Kimberly & Seth Blocking issues list: TO BE COMPLETED<br />
*Action Item Corvallis 2017/06:<br />
**Provide ways for users to recover and digest GO-CAM units (Gene Ontology-based Causal Activity Model). Ideas include rule-based generations of text statements from model, cytoscape view of network described, etc.<br />
**ECO codes available for use in Noctua should show how they map up to a classic GO code, and there should be an alert for curators when they are using a code that does NOT map up to a classic code<br />
**PRO IDs for use in Noctua<br />
**Fix GPAD export from Noctua https://github.com/geneontology/noctua/issues/418<br />
**Add a SPARTA workbench https://github.com/geneontology/noctua/issues/465<br />
**Working group discussion of evidence on complex Noctua models (Kimberly?)<br />
<br />
====Noctua table view demo (Chris)====<br />
<br />
===CC component annotation guidelines (Kimberly)===<br />
CC component annotation: what does it mean ? Kimberly to do 1 proposal (out of 3 alternatives)<br />
1. where the protein is active 2. two different meanings: enables or the right RO (part:of, ie just found there) 3. part_of (low information value!)<br />
===Author intent & protein domains===<br />
Pascale /Ruth; IDA v IC v New evidence code https://github.com/geneontology/go-annotation/issues/1621 30 minutes discussion about issues; hopefully action items can come out of the discussion<br />
===Centralization of InterPro2GO annotations===<br />
Proposal (follow-up from Geneva 2016): (Paul T)<br />
*GO database pulls directly from InterPro2GO for UniProt Reference Proteomes<br />
*MOD identifier is used as primary gene identifier<br />
*Annotations are given "contributed by" InterPro<br />
*MODs pull from GO database, no need to maintain separate InterPro pipelines<br />
<br />
==Annotation guidelines and issues (part two)==<br />
===HTP guidelines===<br />
Helen - 15 minutes Report on progress from HTP working group<br />
*Draft Guidelines https://docs.google.com/document/d/1ScIeclAzUXMe-tU6n0lVfsSwMHpOeNb7uK8On9-iKXc/edit?usp=sharing%7CHTP<br />
<br />
*Provision of new evidence code<br />
*Implementation & developing guidelines<br />
<br />
===Transcription annotations decision tree===<br />
Ruth Action Items Corvallis 2017/06<br />
David OS to create transcription regulator activity (proposed by Paul T)<br />
Proposed changes to decision tree in Corvallis:<br />
Simplified from previous version. Essentially a choice between ‘regulating transcription by RNA polymerase II’ or ‘regulating gene expression’<br />
Annotation 5 = contributes_to sequence-specific DNA binding<br />
David: when people do enrichment, they don’t drop contributes_to (ie., pay attention to qualifiers), so all those proteins will come down as ‘DNA binding’ Action item: replace ‘annotation 5’ with ISS annotation (if DNA binding domain) or contributes to annotation 5 with ISS annotation if no DNA binding domain and domains to suggest coactivator<br />
Annotation 3 = nuclear chromatin<br />
Not everyone comfortable with this (ex., Stacia, David) Shouldn’t it be ‘colocalizes_with’? It was previously agreed that the definition for nuclear chromatin: The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus. Source:PMID:20404130 was to be applied. The proteins here include all associated proteins, not limited to just histones. With this statement the TFs are then contributing to chromatin, rather than binding to chromatin or colocalizing with it.<br />
Decision tree to be put up on GOC website.<br />
Should annotation 4 exist? (Ruth)<br />
<br />
===Annotation Documentation===<br />
Kimberly Action Items Corvallis 2017/06<br />
Continue with the consolidation of all documentation for ontology editing, and remove all old documents.<br />
Review annotation documentation and add to github and readthedocs.<br />
Make sure to mark obsolete pages/doc as such and add a link to the new relevant doc<br />
Solicit annotation documentation from participating groups for consolidation.<br />
Make sure to mark docs with ‘Date last reviewed’ so it’s easy for users to know when the documentation was last touched.<br />
Pascale: additional information associated with GO terms, see GitHub ticket?<br />
Add and follow action items at https://github.com/orgs/geneontology/projects/3<br />
===Annotation quality control===<br />
====PAINT update (Huaiyu)====<br />
Huaiyu Action Items Corvallis 2017/06:<br />
Encourage discussion between PAINT curators and other annotators about terms not used for propagation<br />
Report how many annotations per species are used for annotation propagation; could even supply this number for propagation specifically to human genes<br />
Ruth and Huaiyu (others?) will discuss making use of groups that have already annotated specific gene lists to annotate the corresponding PAINT families.<br />
Smooth out the challenge mechanism to make it easier to do make and resolve<br />
the challenges, identify terms that may be problematic and would benefit from consistency exercises and discussion.<br />
Get a list of families where terms have not been propagated (?) - Please check this one for clarity.<br />
(added to github project board) Develop mechanism to trigger review of annotated PAINT families.<br />
===Viral processes update (Pascale)===<br />
Action Items Corvallis 2017/06 Check whether the incorporated changes could affect the host proteins. Document the use cases.<br />
==Community Support==<br />
===Citing GO (Paul T)===<br />
*Web page<br />
*Tool providers: Action Item Corvallis 2017/06: someone to represent GOC and contact GO tool providers to display version information and state this information needs to be included in any subsequent publication. Plus list the GOC paper to reference, as well as the tool provider reference. See: https://github.com/geneontology/go-site/issues/359 and https://github.com/geneontology/go-site/issues/360<br />
===Enrichment (Paul T & Suzi)===<br />
*Web page <br />
*Paul Pavlidis…<br />
*Data Commons work<br />
<br />
===GO_Slims===<br />
====Philosophy (Val, Suzi)====<br />
Creating a biologically useful slim (complete coverage by aspect, biologically useful terms i.e sufficient granularity, avoiding single step process terms (i.e functions), different slims for different purposes: Judy, Mary D (+ Suzi, Val, etc). For overviews, for particular taxa, for a particular area of biology<br />
Specifications for slims from user's perspective (Val: 30 minutes)<br />
====HOW TO MAKE SLIMS (Chris)====<br />
Yaml format for creating slims/types of slims/target organisms<br />
====Use and maintenance of slims (Mary and Suzi)====<br />
Mary: algorithm - 15 minutes<br />
Suzi: GO ribbon<br />
<br />
=Wednesday 4th October=<br />
==Ongoing work==<br />
===AmiGO (Follow up with Seth)===<br />
In general, while several of the AmiGO issues are high-priority, there has been limited bandwidth to tackle them in the context of continuing work on Noctua and the replacement pipeline. Several fixes are queued up and will be available before the upcoming SAB meeting.<br />
In response to: in base_statistics, plotly graph for "Experimental annotation publications by assigner" is confusing https://github.com/geneontology/amigo/issues/429<br />
From Pascale's question: My understanding is that there are essentially no resources for AmiGO right now so any AmiGO issue is low priority. Is this correct?<br />
===The Fate of Simple Processes===<br />
analysis of gene products annotated to phosphorylation but not annotated to a kinase MF term. What did these annotations actually mean? Curators would need to review. Timeline? Deadline? Working group? One possibility would be to use part_of/involved_in relation to phosphorylation for genes also annotated to kinase MF, and causally_upstream_of_or_within for others until curators can re-evaluate.<br />
Other considerations:<br />
Helen: are there many the single-step processes?<br />
Paul: user-oriented approach - is it a useful grouping for our users?<br />
Ruth: we need to think about the meaning beyond just “phosphorylation”<br />
Ruth: what are the consequences of removing “phosphorylation” and what happens to all its children?<br />
Pascale Q: providing that we remove the processes, would it affect the term enrichment analysis?<br />
===BP refactoring===<br />
Defining “Cellular Process” and “Multi-Organism Process” terms<br />
Action item: the comments/examples/notes should be captured, working group to discuss this.<br />
===Proteoforms===<br />
Establish a working group for when and how to use proteoforms in annotation. (Kimberly with Harold and Li)<br />
===Usability issues===<br />
What do users want?<br />
truth (summary/story/model)?<br />
fishing expeditions?<br />
api access?<br />
Who are our users?<br />
geneticists?<br />
clinicians?<br />
computational biologists?<br />
Use cases: https://github.com/geneontology/go-ontology/issues/13606<br />
Perhaps discussion of examples of how the GOC members are engaging with the community and how we can do better in the future (suggested by Helen).<br />
=Wednesday noon-ish Fin=<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Agenda&diff=652932017 Cambridge GOC Meeting Agenda2017-09-27T00:23:30Z<p>Suzi: /* Noctua table view demo */</p>
<hr />
<div>GOC Meeting, Cambridge , October 2-4, 2017<br />
<br />
=Monday 2nd October=<br />
==Welcome, overview, vision, introductions==<br />
GO PIs<br />
==GO handbook presentation==<br />
*The Gene Ontology and the meaning of biological function (Paul T)<br />
*Translating research data into Gene Ontology annotations (Pascale)<br />
*Gene Ontology - annotation extensions (Ruth)<br />
*GO as a biological systems model (Suzi, or Paul T if Suzi is late)<br />
Pascale will move slides to Google drive<br />
==Ontology Issues and Updates==<br />
===Update on MF refactoring (Pascale or Paul T)===<br />
====GitHub tutorial (Seth & Pascale)====<br />
How GO now uses GitHub for project management and guidelines for contributors<br />
*Where is information relevant to everyone's need<br />
*Groups (Groups.yaml)<br />
*Members<br />
*Etc<br />
<br />
===Qualifiers/Relation issues (Kimberly and Chris)===<br />
====Qualifiers/Relations in GPAD (Kimberly and Chris)====<br />
====Contributes_to guidelines====<br />
++ colocalizes with<br />
====Multiple qualifiers for an annotation (Huaiyu)====<br />
====Use of Qualifiers in Legacy Annotations====<br />
Pascale Proposal: We will apply the general qualifier to all legacy annotations. Each group can provide more specific qualifiers if they have a mechanism to distinguish. Action Items Corvallis 2017/06<br />
*Working group to decide what relations should be available in Protein2GO or other tools for manual annotations. Also decide when there are different ways of expressing the same thing, what way we will choose. What should the default gene/gene product relation be for legacy annotations?<br />
*Chris to work on reports that may help curators make decisions about what annotations can get more expressive qualifiers.<br />
<br />
====Regulates relations====<br />
Adding new qualifiers for the relation between a gene/gene product and a GO term What should the default relation be? How will we handle regulation? Use a relation, involved in regulation of, or use the precomposed regulation term?<br />
Ruth: There are now 3 ways to say the same thing: - involved_in_regulation_of X - involved_in X regulation - involved_in BP regulates(X)<br />
For annotation purposes and for our users we want one.<br />
DOS: Good point. These are semantically identical, but I agree we need to find a way to only have one: by convention for classic GO annotation and by filtering the output of inference for noctua output. Proposal: If a named regulation class exists: involved_in X regulation ...if not: involved_in {some BP} regulates(X) NOTE: If there was an annotation in Noctua such as ‘regulation of’ ‘very specific term’ and there was no term as ‘regulation of very specific term’ the GOC pipeline would create the annotation to the parent term: ‘regulation of less specific term’. Q: Is this implemented ?<br />
==Project updates==<br />
*AGR - report to GOC: PIs<br />
*SynGO meeting report: Paul T<br />
*Report of Reactome-GO connection: David H/Peter D<br />
*Report on transcription work/Noctua templates: Astrid GREEKC consortium=<br />
=Evening: Poster session=<br />
<br />
=Tuesday 3rd October=<br />
==Annotation guidelines and issues (part one)==<br />
===Signaling (Kimberly and David)===<br />
*Report from signaling workshop: David /Kimberly<br />
*Signaling: First attempt at Annotation consistency 2.0 - Kimberly to report on the approach and the outcome.<br />
Discussion points: Limited participation (self-selected to participate). One recommendation may be to ask all active curators to participate, even at some low level https://github.com/orgs/geneontology/projects/<br />
<br />
===Overview of GO annotations/Noctua (Kimberly & Chris)===<br />
====Getting Noctua ready for production====<br />
*Kimberly & Seth Blocking issues list: TO BE COMPLETED<br />
*Action Item Corvallis 2017/06:<br />
**Provide ways for users to recover and digest GO-CAM units (Gene Ontology-based Causal Activity Model). Ideas include rule-based generations of text statements from model, cytoscape view of network described, etc.<br />
**ECO codes available for use in Noctua should show how they map up to a classic GO code, and there should be an alert for curators when they are using a code that does NOT map up to a classic code<br />
**PRO IDs for use in Noctua<br />
**Fix GPAD export from Noctua https://github.com/geneontology/noctua/issues/418<br />
**Add a SPARTA workbench https://github.com/geneontology/noctua/issues/465<br />
**Working group discussion of evidence on complex Noctua models (Kimberly?)<br />
<br />
====Noctua table view demo (Chris)====<br />
<br />
===CC component annotation guidelines (Kimberly)===<br />
CC component annotation: what does it mean ? Kimberly to do 1 proposal (out of 3 alternatives)<br />
1. where the protein is active 2. two different meanings: enables or the right RO (part:of, ie just found there) 3. part_of (low information value!)<br />
===Author intent & protein domains===<br />
Pascale /Ruth; IDA v IC v New evidence code https://github.com/geneontology/go-annotation/issues/1621 30 minutes discussion about issues; hopefully action items can come out of the discussion<br />
===Centralization of InterPro2GO annotations===<br />
Proposal (follow-up from Geneva 2016): (Paul T)<br />
*GO database pulls directly from InterPro2GO for UniProt Reference Proteomes<br />
*MOD identifier is used as primary gene identifier<br />
*Annotations are given "contributed by" InterPro<br />
*MODs pull from GO database, no need to maintain separate InterPro pipelines<br />
<br />
==Annotation guidelines and issues (part two)==<br />
===HTP guidelines===<br />
Helen - 15 minutes Report on progress from HTP working group<br />
Draft Guidelines Guidelines draft<br />
Action Items Corvallis 2017<br />
Provision of new evidence code<br />
Implementation & developing guidelines<br />
===Transcription annotations decision tree===<br />
Ruth Action Items Corvallis 2017/06<br />
David OS to create transcription regulator activity (proposed by Paul T)<br />
Proposed changes to decision tree in Corvallis:<br />
Simplified from previous version. Essentially a choice between ‘regulating transcription by RNA polymerase II’ or ‘regulating gene expression’<br />
Annotation 5 = contributes_to sequence-specific DNA binding<br />
David: when people do enrichment, they don’t drop contributes_to (ie., pay attention to qualifiers), so all those proteins will come down as ‘DNA binding’ Action item: replace ‘annotation 5’ with ISS annotation (if DNA binding domain) or contributes to annotation 5 with ISS annotation if no DNA binding domain and domains to suggest coactivator<br />
Annotation 3 = nuclear chromatin<br />
Not everyone comfortable with this (ex., Stacia, David) Shouldn’t it be ‘colocalizes_with’? It was previously agreed that the definition for nuclear chromatin: The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus. Source:PMID:20404130 was to be applied. The proteins here include all associated proteins, not limited to just histones. With this statement the TFs are then contributing to chromatin, rather than binding to chromatin or colocalizing with it.<br />
Decision tree to be put up on GOC website.<br />
Should annotation 4 exist? (Ruth)<br />
<br />
===Annotation Documentation===<br />
Kimberly Action Items Corvallis 2017/06<br />
Continue with the consolidation of all documentation for ontology editing, and remove all old documents.<br />
Review annotation documentation and add to github and readthedocs.<br />
Make sure to mark obsolete pages/doc as such and add a link to the new relevant doc<br />
Solicit annotation documentation from participating groups for consolidation.<br />
Make sure to mark docs with ‘Date last reviewed’ so it’s easy for users to know when the documentation was last touched.<br />
Pascale: additional information associated with GO terms, see GitHub ticket?<br />
Add and follow action items at https://github.com/orgs/geneontology/projects/3<br />
===Annotation quality control===<br />
====PAINT update (Huaiyu)====<br />
Huaiyu Action Items Corvallis 2017/06:<br />
Encourage discussion between PAINT curators and other annotators about terms not used for propagation<br />
Report how many annotations per species are used for annotation propagation; could even supply this number for propagation specifically to human genes<br />
Ruth and Huaiyu (others?) will discuss making use of groups that have already annotated specific gene lists to annotate the corresponding PAINT families.<br />
Smooth out the challenge mechanism to make it easier to do make and resolve<br />
the challenges, identify terms that may be problematic and would benefit from consistency exercises and discussion.<br />
Get a list of families where terms have not been propagated (?) - Please check this one for clarity.<br />
(added to github project board) Develop mechanism to trigger review of annotated PAINT families.<br />
===Viral processes update (Pascale)===<br />
Action Items Corvallis 2017/06 Check whether the incorporated changes could affect the host proteins. Document the use cases.<br />
==Community Support==<br />
===Citing GO (Paul T)===<br />
*Web page<br />
*Tool providers: Action Item Corvallis 2017/06: someone to represent GOC and contact GO tool providers to display version information and state this information needs to be included in any subsequent publication. Plus list the GOC paper to reference, as well as the tool provider reference. See: https://github.com/geneontology/go-site/issues/359 and https://github.com/geneontology/go-site/issues/360<br />
===Enrichment (Paul T & Suzi)===<br />
*Web page <br />
*Paul Pavlidis…<br />
*Data Commons work<br />
<br />
===GO_Slims===<br />
====Philosophy (Val, Suzi)====<br />
Creating a biologically useful slim (complete coverage by aspect, biologically useful terms i.e sufficient granularity, avoiding single step process terms (i.e functions), different slims for different purposes: Judy, Mary D (+ Suzi, Val, etc). For overviews, for particular taxa, for a particular area of biology<br />
Specifications for slims from user's perspective (Val: 30 minutes)<br />
====HOW TO MAKE SLIMS (Chris)====<br />
Yaml format for creating slims/types of slims/target organisms<br />
====Use and maintenance of slims (Mary and Suzi)====<br />
Mary: algorithm - 15 minutes<br />
Suzi: GO ribbon<br />
<br />
=Wednesday 4th October=<br />
==Ongoing work==<br />
===AmiGO (Follow up with Seth)===<br />
In general, while several of the AmiGO issues are high-priority, there has been limited bandwidth to tackle them in the context of continuing work on Noctua and the replacement pipeline. Several fixes are queued up and will be available before the upcoming SAB meeting.<br />
In response to: in base_statistics, plotly graph for "Experimental annotation publications by assigner" is confusing https://github.com/geneontology/amigo/issues/429<br />
From Pascale's question: My understanding is that there are essentially no resources for AmiGO right now so any AmiGO issue is low priority. Is this correct?<br />
===The Fate of Simple Processes===<br />
analysis of gene products annotated to phosphorylation but not annotated to a kinase MF term. What did these annotations actually mean? Curators would need to review. Timeline? Deadline? Working group? One possibility would be to use part_of/involved_in relation to phosphorylation for genes also annotated to kinase MF, and causally_upstream_of_or_within for others until curators can re-evaluate.<br />
Other considerations:<br />
Helen: are there many the single-step processes?<br />
Paul: user-oriented approach - is it a useful grouping for our users?<br />
Ruth: we need to think about the meaning beyond just “phosphorylation”<br />
Ruth: what are the consequences of removing “phosphorylation” and what happens to all its children?<br />
Pascale Q: providing that we remove the processes, would it affect the term enrichment analysis?<br />
===BP refactoring===<br />
Defining “Cellular Process” and “Multi-Organism Process” terms<br />
Action item: the comments/examples/notes should be captured, working group to discuss this.<br />
===Proteoforms===<br />
Establish a working group for when and how to use proteoforms in annotation. (Kimberly with Harold and Li)<br />
===Usability issues===<br />
What do users want?<br />
truth (summary/story/model)?<br />
fishing expeditions?<br />
api access?<br />
Who are our users?<br />
geneticists?<br />
clinicians?<br />
computational biologists?<br />
Use cases: https://github.com/geneontology/go-ontology/issues/13606<br />
Perhaps discussion of examples of how the GOC members are engaging with the community and how we can do better in the future (suggested by Helen).<br />
=Wednesday noon-ish Fin=<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Agenda&diff=652922017 Cambridge GOC Meeting Agenda2017-09-27T00:22:45Z<p>Suzi: /* Centralization of InterPro2GO annotations */</p>
<hr />
<div>GOC Meeting, Cambridge , October 2-4, 2017<br />
<br />
=Monday 2nd October=<br />
==Welcome, overview, vision, introductions==<br />
GO PIs<br />
==GO handbook presentation==<br />
*The Gene Ontology and the meaning of biological function (Paul T)<br />
*Translating research data into Gene Ontology annotations (Pascale)<br />
*Gene Ontology - annotation extensions (Ruth)<br />
*GO as a biological systems model (Suzi, or Paul T if Suzi is late)<br />
Pascale will move slides to Google drive<br />
==Ontology Issues and Updates==<br />
===Update on MF refactoring (Pascale or Paul T)===<br />
====GitHub tutorial (Seth & Pascale)====<br />
How GO now uses GitHub for project management and guidelines for contributors<br />
*Where is information relevant to everyone's need<br />
*Groups (Groups.yaml)<br />
*Members<br />
*Etc<br />
<br />
===Qualifiers/Relation issues (Kimberly and Chris)===<br />
====Qualifiers/Relations in GPAD (Kimberly and Chris)====<br />
====Contributes_to guidelines====<br />
++ colocalizes with<br />
====Multiple qualifiers for an annotation (Huaiyu)====<br />
====Use of Qualifiers in Legacy Annotations====<br />
Pascale Proposal: We will apply the general qualifier to all legacy annotations. Each group can provide more specific qualifiers if they have a mechanism to distinguish. Action Items Corvallis 2017/06<br />
*Working group to decide what relations should be available in Protein2GO or other tools for manual annotations. Also decide when there are different ways of expressing the same thing, what way we will choose. What should the default gene/gene product relation be for legacy annotations?<br />
*Chris to work on reports that may help curators make decisions about what annotations can get more expressive qualifiers.<br />
<br />
====Regulates relations====<br />
Adding new qualifiers for the relation between a gene/gene product and a GO term What should the default relation be? How will we handle regulation? Use a relation, involved in regulation of, or use the precomposed regulation term?<br />
Ruth: There are now 3 ways to say the same thing: - involved_in_regulation_of X - involved_in X regulation - involved_in BP regulates(X)<br />
For annotation purposes and for our users we want one.<br />
DOS: Good point. These are semantically identical, but I agree we need to find a way to only have one: by convention for classic GO annotation and by filtering the output of inference for noctua output. Proposal: If a named regulation class exists: involved_in X regulation ...if not: involved_in {some BP} regulates(X) NOTE: If there was an annotation in Noctua such as ‘regulation of’ ‘very specific term’ and there was no term as ‘regulation of very specific term’ the GOC pipeline would create the annotation to the parent term: ‘regulation of less specific term’. Q: Is this implemented ?<br />
==Project updates==<br />
*AGR - report to GOC: PIs<br />
*SynGO meeting report: Paul T<br />
*Report of Reactome-GO connection: David H/Peter D<br />
*Report on transcription work/Noctua templates: Astrid GREEKC consortium=<br />
=Evening: Poster session=<br />
<br />
=Tuesday 3rd October=<br />
==Annotation guidelines and issues (part one)==<br />
===Signaling (Kimberly and David)===<br />
*Report from signaling workshop: David /Kimberly<br />
*Signaling: First attempt at Annotation consistency 2.0 - Kimberly to report on the approach and the outcome.<br />
Discussion points: Limited participation (self-selected to participate). One recommendation may be to ask all active curators to participate, even at some low level https://github.com/orgs/geneontology/projects/<br />
<br />
===Overview of GO annotations/Noctua (Kimberly & Chris)===<br />
====Getting Noctua ready for production====<br />
*Kimberly & Seth Blocking issues list: TO BE COMPLETED<br />
*Action Item Corvallis 2017/06:<br />
**Provide ways for users to recover and digest GO-CAM units (Gene Ontology-based Causal Activity Model). Ideas include rule-based generations of text statements from model, cytoscape view of network described, etc.<br />
**ECO codes available for use in Noctua should show how they map up to a classic GO code, and there should be an alert for curators when they are using a code that does NOT map up to a classic code<br />
**PRO IDs for use in Noctua<br />
**Fix GPAD export from Noctua https://github.com/geneontology/noctua/issues/418<br />
**Add a SPARTA workbench https://github.com/geneontology/noctua/issues/465<br />
**Working group discussion of evidence on complex Noctua models (Kimberly?)<br />
<br />
====Noctua table view demo====<br />
===CC component annotation guidelines (Kimberly)===<br />
CC component annotation: what does it mean ? Kimberly to do 1 proposal (out of 3 alternatives)<br />
1. where the protein is active 2. two different meanings: enables or the right RO (part:of, ie just found there) 3. part_of (low information value!)<br />
===Author intent & protein domains===<br />
Pascale /Ruth; IDA v IC v New evidence code https://github.com/geneontology/go-annotation/issues/1621 30 minutes discussion about issues; hopefully action items can come out of the discussion<br />
===Centralization of InterPro2GO annotations===<br />
Proposal (follow-up from Geneva 2016): (Paul T)<br />
*GO database pulls directly from InterPro2GO for UniProt Reference Proteomes<br />
*MOD identifier is used as primary gene identifier<br />
*Annotations are given "contributed by" InterPro<br />
*MODs pull from GO database, no need to maintain separate InterPro pipelines<br />
<br />
==Annotation guidelines and issues (part two)==<br />
===HTP guidelines===<br />
Helen - 15 minutes Report on progress from HTP working group<br />
Draft Guidelines Guidelines draft<br />
Action Items Corvallis 2017<br />
Provision of new evidence code<br />
Implementation & developing guidelines<br />
===Transcription annotations decision tree===<br />
Ruth Action Items Corvallis 2017/06<br />
David OS to create transcription regulator activity (proposed by Paul T)<br />
Proposed changes to decision tree in Corvallis:<br />
Simplified from previous version. Essentially a choice between ‘regulating transcription by RNA polymerase II’ or ‘regulating gene expression’<br />
Annotation 5 = contributes_to sequence-specific DNA binding<br />
David: when people do enrichment, they don’t drop contributes_to (ie., pay attention to qualifiers), so all those proteins will come down as ‘DNA binding’ Action item: replace ‘annotation 5’ with ISS annotation (if DNA binding domain) or contributes to annotation 5 with ISS annotation if no DNA binding domain and domains to suggest coactivator<br />
Annotation 3 = nuclear chromatin<br />
Not everyone comfortable with this (ex., Stacia, David) Shouldn’t it be ‘colocalizes_with’? It was previously agreed that the definition for nuclear chromatin: The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus. Source:PMID:20404130 was to be applied. The proteins here include all associated proteins, not limited to just histones. With this statement the TFs are then contributing to chromatin, rather than binding to chromatin or colocalizing with it.<br />
Decision tree to be put up on GOC website.<br />
Should annotation 4 exist? (Ruth)<br />
<br />
===Annotation Documentation===<br />
Kimberly Action Items Corvallis 2017/06<br />
Continue with the consolidation of all documentation for ontology editing, and remove all old documents.<br />
Review annotation documentation and add to github and readthedocs.<br />
Make sure to mark obsolete pages/doc as such and add a link to the new relevant doc<br />
Solicit annotation documentation from participating groups for consolidation.<br />
Make sure to mark docs with ‘Date last reviewed’ so it’s easy for users to know when the documentation was last touched.<br />
Pascale: additional information associated with GO terms, see GitHub ticket?<br />
Add and follow action items at https://github.com/orgs/geneontology/projects/3<br />
===Annotation quality control===<br />
====PAINT update (Huaiyu)====<br />
Huaiyu Action Items Corvallis 2017/06:<br />
Encourage discussion between PAINT curators and other annotators about terms not used for propagation<br />
Report how many annotations per species are used for annotation propagation; could even supply this number for propagation specifically to human genes<br />
Ruth and Huaiyu (others?) will discuss making use of groups that have already annotated specific gene lists to annotate the corresponding PAINT families.<br />
Smooth out the challenge mechanism to make it easier to do make and resolve<br />
the challenges, identify terms that may be problematic and would benefit from consistency exercises and discussion.<br />
Get a list of families where terms have not been propagated (?) - Please check this one for clarity.<br />
(added to github project board) Develop mechanism to trigger review of annotated PAINT families.<br />
===Viral processes update (Pascale)===<br />
Action Items Corvallis 2017/06 Check whether the incorporated changes could affect the host proteins. Document the use cases.<br />
==Community Support==<br />
===Citing GO (Paul T)===<br />
*Web page<br />
*Tool providers: Action Item Corvallis 2017/06: someone to represent GOC and contact GO tool providers to display version information and state this information needs to be included in any subsequent publication. Plus list the GOC paper to reference, as well as the tool provider reference. See: https://github.com/geneontology/go-site/issues/359 and https://github.com/geneontology/go-site/issues/360<br />
===Enrichment (Paul T & Suzi)===<br />
*Web page <br />
*Paul Pavlidis…<br />
*Data Commons work<br />
<br />
===GO_Slims===<br />
====Philosophy (Val, Suzi)====<br />
Creating a biologically useful slim (complete coverage by aspect, biologically useful terms i.e sufficient granularity, avoiding single step process terms (i.e functions), different slims for different purposes: Judy, Mary D (+ Suzi, Val, etc). For overviews, for particular taxa, for a particular area of biology<br />
Specifications for slims from user's perspective (Val: 30 minutes)<br />
====HOW TO MAKE SLIMS (Chris)====<br />
Yaml format for creating slims/types of slims/target organisms<br />
====Use and maintenance of slims (Mary and Suzi)====<br />
Mary: algorithm - 15 minutes<br />
Suzi: GO ribbon<br />
<br />
=Wednesday 4th October=<br />
==Ongoing work==<br />
===AmiGO (Follow up with Seth)===<br />
In general, while several of the AmiGO issues are high-priority, there has been limited bandwidth to tackle them in the context of continuing work on Noctua and the replacement pipeline. Several fixes are queued up and will be available before the upcoming SAB meeting.<br />
In response to: in base_statistics, plotly graph for "Experimental annotation publications by assigner" is confusing https://github.com/geneontology/amigo/issues/429<br />
From Pascale's question: My understanding is that there are essentially no resources for AmiGO right now so any AmiGO issue is low priority. Is this correct?<br />
===The Fate of Simple Processes===<br />
analysis of gene products annotated to phosphorylation but not annotated to a kinase MF term. What did these annotations actually mean? Curators would need to review. Timeline? Deadline? Working group? One possibility would be to use part_of/involved_in relation to phosphorylation for genes also annotated to kinase MF, and causally_upstream_of_or_within for others until curators can re-evaluate.<br />
Other considerations:<br />
Helen: are there many the single-step processes?<br />
Paul: user-oriented approach - is it a useful grouping for our users?<br />
Ruth: we need to think about the meaning beyond just “phosphorylation”<br />
Ruth: what are the consequences of removing “phosphorylation” and what happens to all its children?<br />
Pascale Q: providing that we remove the processes, would it affect the term enrichment analysis?<br />
===BP refactoring===<br />
Defining “Cellular Process” and “Multi-Organism Process” terms<br />
Action item: the comments/examples/notes should be captured, working group to discuss this.<br />
===Proteoforms===<br />
Establish a working group for when and how to use proteoforms in annotation. (Kimberly with Harold and Li)<br />
===Usability issues===<br />
What do users want?<br />
truth (summary/story/model)?<br />
fishing expeditions?<br />
api access?<br />
Who are our users?<br />
geneticists?<br />
clinicians?<br />
computational biologists?<br />
Use cases: https://github.com/geneontology/go-ontology/issues/13606<br />
Perhaps discussion of examples of how the GOC members are engaging with the community and how we can do better in the future (suggested by Helen).<br />
=Wednesday noon-ish Fin=<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Agenda&diff=652912017 Cambridge GOC Meeting Agenda2017-09-27T00:22:30Z<p>Suzi: /* Centralization of InterPro2GO annotations */</p>
<hr />
<div>GOC Meeting, Cambridge , October 2-4, 2017<br />
<br />
=Monday 2nd October=<br />
==Welcome, overview, vision, introductions==<br />
GO PIs<br />
==GO handbook presentation==<br />
*The Gene Ontology and the meaning of biological function (Paul T)<br />
*Translating research data into Gene Ontology annotations (Pascale)<br />
*Gene Ontology - annotation extensions (Ruth)<br />
*GO as a biological systems model (Suzi, or Paul T if Suzi is late)<br />
Pascale will move slides to Google drive<br />
==Ontology Issues and Updates==<br />
===Update on MF refactoring (Pascale or Paul T)===<br />
====GitHub tutorial (Seth & Pascale)====<br />
How GO now uses GitHub for project management and guidelines for contributors<br />
*Where is information relevant to everyone's need<br />
*Groups (Groups.yaml)<br />
*Members<br />
*Etc<br />
<br />
===Qualifiers/Relation issues (Kimberly and Chris)===<br />
====Qualifiers/Relations in GPAD (Kimberly and Chris)====<br />
====Contributes_to guidelines====<br />
++ colocalizes with<br />
====Multiple qualifiers for an annotation (Huaiyu)====<br />
====Use of Qualifiers in Legacy Annotations====<br />
Pascale Proposal: We will apply the general qualifier to all legacy annotations. Each group can provide more specific qualifiers if they have a mechanism to distinguish. Action Items Corvallis 2017/06<br />
*Working group to decide what relations should be available in Protein2GO or other tools for manual annotations. Also decide when there are different ways of expressing the same thing, what way we will choose. What should the default gene/gene product relation be for legacy annotations?<br />
*Chris to work on reports that may help curators make decisions about what annotations can get more expressive qualifiers.<br />
<br />
====Regulates relations====<br />
Adding new qualifiers for the relation between a gene/gene product and a GO term What should the default relation be? How will we handle regulation? Use a relation, involved in regulation of, or use the precomposed regulation term?<br />
Ruth: There are now 3 ways to say the same thing: - involved_in_regulation_of X - involved_in X regulation - involved_in BP regulates(X)<br />
For annotation purposes and for our users we want one.<br />
DOS: Good point. These are semantically identical, but I agree we need to find a way to only have one: by convention for classic GO annotation and by filtering the output of inference for noctua output. Proposal: If a named regulation class exists: involved_in X regulation ...if not: involved_in {some BP} regulates(X) NOTE: If there was an annotation in Noctua such as ‘regulation of’ ‘very specific term’ and there was no term as ‘regulation of very specific term’ the GOC pipeline would create the annotation to the parent term: ‘regulation of less specific term’. Q: Is this implemented ?<br />
==Project updates==<br />
*AGR - report to GOC: PIs<br />
*SynGO meeting report: Paul T<br />
*Report of Reactome-GO connection: David H/Peter D<br />
*Report on transcription work/Noctua templates: Astrid GREEKC consortium=<br />
=Evening: Poster session=<br />
<br />
=Tuesday 3rd October=<br />
==Annotation guidelines and issues (part one)==<br />
===Signaling (Kimberly and David)===<br />
*Report from signaling workshop: David /Kimberly<br />
*Signaling: First attempt at Annotation consistency 2.0 - Kimberly to report on the approach and the outcome.<br />
Discussion points: Limited participation (self-selected to participate). One recommendation may be to ask all active curators to participate, even at some low level https://github.com/orgs/geneontology/projects/<br />
<br />
===Overview of GO annotations/Noctua (Kimberly & Chris)===<br />
====Getting Noctua ready for production====<br />
*Kimberly & Seth Blocking issues list: TO BE COMPLETED<br />
*Action Item Corvallis 2017/06:<br />
**Provide ways for users to recover and digest GO-CAM units (Gene Ontology-based Causal Activity Model). Ideas include rule-based generations of text statements from model, cytoscape view of network described, etc.<br />
**ECO codes available for use in Noctua should show how they map up to a classic GO code, and there should be an alert for curators when they are using a code that does NOT map up to a classic code<br />
**PRO IDs for use in Noctua<br />
**Fix GPAD export from Noctua https://github.com/geneontology/noctua/issues/418<br />
**Add a SPARTA workbench https://github.com/geneontology/noctua/issues/465<br />
**Working group discussion of evidence on complex Noctua models (Kimberly?)<br />
<br />
====Noctua table view demo====<br />
===CC component annotation guidelines (Kimberly)===<br />
CC component annotation: what does it mean ? Kimberly to do 1 proposal (out of 3 alternatives)<br />
1. where the protein is active 2. two different meanings: enables or the right RO (part:of, ie just found there) 3. part_of (low information value!)<br />
===Author intent & protein domains===<br />
Pascale /Ruth; IDA v IC v New evidence code https://github.com/geneontology/go-annotation/issues/1621 30 minutes discussion about issues; hopefully action items can come out of the discussion<br />
===Centralization of InterPro2GO annotations===<br />
Proposal (follow-up from Geneva 2016): (Paul T)<br />
**GO database pulls directly from InterPro2GO for UniProt Reference Proteomes<br />
**MOD identifier is used as primary gene identifier<br />
**Annotations are given "contributed by" InterPro<br />
**MODs pull from GO database, no need to maintain separate InterPro pipelines<br />
<br />
==Annotation guidelines and issues (part two)==<br />
===HTP guidelines===<br />
Helen - 15 minutes Report on progress from HTP working group<br />
Draft Guidelines Guidelines draft<br />
Action Items Corvallis 2017<br />
Provision of new evidence code<br />
Implementation & developing guidelines<br />
===Transcription annotations decision tree===<br />
Ruth Action Items Corvallis 2017/06<br />
David OS to create transcription regulator activity (proposed by Paul T)<br />
Proposed changes to decision tree in Corvallis:<br />
Simplified from previous version. Essentially a choice between ‘regulating transcription by RNA polymerase II’ or ‘regulating gene expression’<br />
Annotation 5 = contributes_to sequence-specific DNA binding<br />
David: when people do enrichment, they don’t drop contributes_to (ie., pay attention to qualifiers), so all those proteins will come down as ‘DNA binding’ Action item: replace ‘annotation 5’ with ISS annotation (if DNA binding domain) or contributes to annotation 5 with ISS annotation if no DNA binding domain and domains to suggest coactivator<br />
Annotation 3 = nuclear chromatin<br />
Not everyone comfortable with this (ex., Stacia, David) Shouldn’t it be ‘colocalizes_with’? It was previously agreed that the definition for nuclear chromatin: The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus. Source:PMID:20404130 was to be applied. The proteins here include all associated proteins, not limited to just histones. With this statement the TFs are then contributing to chromatin, rather than binding to chromatin or colocalizing with it.<br />
Decision tree to be put up on GOC website.<br />
Should annotation 4 exist? (Ruth)<br />
<br />
===Annotation Documentation===<br />
Kimberly Action Items Corvallis 2017/06<br />
Continue with the consolidation of all documentation for ontology editing, and remove all old documents.<br />
Review annotation documentation and add to github and readthedocs.<br />
Make sure to mark obsolete pages/doc as such and add a link to the new relevant doc<br />
Solicit annotation documentation from participating groups for consolidation.<br />
Make sure to mark docs with ‘Date last reviewed’ so it’s easy for users to know when the documentation was last touched.<br />
Pascale: additional information associated with GO terms, see GitHub ticket?<br />
Add and follow action items at https://github.com/orgs/geneontology/projects/3<br />
===Annotation quality control===<br />
====PAINT update (Huaiyu)====<br />
Huaiyu Action Items Corvallis 2017/06:<br />
Encourage discussion between PAINT curators and other annotators about terms not used for propagation<br />
Report how many annotations per species are used for annotation propagation; could even supply this number for propagation specifically to human genes<br />
Ruth and Huaiyu (others?) will discuss making use of groups that have already annotated specific gene lists to annotate the corresponding PAINT families.<br />
Smooth out the challenge mechanism to make it easier to do make and resolve<br />
the challenges, identify terms that may be problematic and would benefit from consistency exercises and discussion.<br />
Get a list of families where terms have not been propagated (?) - Please check this one for clarity.<br />
(added to github project board) Develop mechanism to trigger review of annotated PAINT families.<br />
===Viral processes update (Pascale)===<br />
Action Items Corvallis 2017/06 Check whether the incorporated changes could affect the host proteins. Document the use cases.<br />
==Community Support==<br />
===Citing GO (Paul T)===<br />
*Web page<br />
*Tool providers: Action Item Corvallis 2017/06: someone to represent GOC and contact GO tool providers to display version information and state this information needs to be included in any subsequent publication. Plus list the GOC paper to reference, as well as the tool provider reference. See: https://github.com/geneontology/go-site/issues/359 and https://github.com/geneontology/go-site/issues/360<br />
===Enrichment (Paul T & Suzi)===<br />
*Web page <br />
*Paul Pavlidis…<br />
*Data Commons work<br />
<br />
===GO_Slims===<br />
====Philosophy (Val, Suzi)====<br />
Creating a biologically useful slim (complete coverage by aspect, biologically useful terms i.e sufficient granularity, avoiding single step process terms (i.e functions), different slims for different purposes: Judy, Mary D (+ Suzi, Val, etc). For overviews, for particular taxa, for a particular area of biology<br />
Specifications for slims from user's perspective (Val: 30 minutes)<br />
====HOW TO MAKE SLIMS (Chris)====<br />
Yaml format for creating slims/types of slims/target organisms<br />
====Use and maintenance of slims (Mary and Suzi)====<br />
Mary: algorithm - 15 minutes<br />
Suzi: GO ribbon<br />
<br />
=Wednesday 4th October=<br />
==Ongoing work==<br />
===AmiGO (Follow up with Seth)===<br />
In general, while several of the AmiGO issues are high-priority, there has been limited bandwidth to tackle them in the context of continuing work on Noctua and the replacement pipeline. Several fixes are queued up and will be available before the upcoming SAB meeting.<br />
In response to: in base_statistics, plotly graph for "Experimental annotation publications by assigner" is confusing https://github.com/geneontology/amigo/issues/429<br />
From Pascale's question: My understanding is that there are essentially no resources for AmiGO right now so any AmiGO issue is low priority. Is this correct?<br />
===The Fate of Simple Processes===<br />
analysis of gene products annotated to phosphorylation but not annotated to a kinase MF term. What did these annotations actually mean? Curators would need to review. Timeline? Deadline? Working group? One possibility would be to use part_of/involved_in relation to phosphorylation for genes also annotated to kinase MF, and causally_upstream_of_or_within for others until curators can re-evaluate.<br />
Other considerations:<br />
Helen: are there many the single-step processes?<br />
Paul: user-oriented approach - is it a useful grouping for our users?<br />
Ruth: we need to think about the meaning beyond just “phosphorylation”<br />
Ruth: what are the consequences of removing “phosphorylation” and what happens to all its children?<br />
Pascale Q: providing that we remove the processes, would it affect the term enrichment analysis?<br />
===BP refactoring===<br />
Defining “Cellular Process” and “Multi-Organism Process” terms<br />
Action item: the comments/examples/notes should be captured, working group to discuss this.<br />
===Proteoforms===<br />
Establish a working group for when and how to use proteoforms in annotation. (Kimberly with Harold and Li)<br />
===Usability issues===<br />
What do users want?<br />
truth (summary/story/model)?<br />
fishing expeditions?<br />
api access?<br />
Who are our users?<br />
geneticists?<br />
clinicians?<br />
computational biologists?<br />
Use cases: https://github.com/geneontology/go-ontology/issues/13606<br />
Perhaps discussion of examples of how the GOC members are engaging with the community and how we can do better in the future (suggested by Helen).<br />
=Wednesday noon-ish Fin=<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Agenda&diff=652902017 Cambridge GOC Meeting Agenda2017-09-27T00:22:11Z<p>Suzi: /* Centralization of InterPro2GO annotations */</p>
<hr />
<div>GOC Meeting, Cambridge , October 2-4, 2017<br />
<br />
=Monday 2nd October=<br />
==Welcome, overview, vision, introductions==<br />
GO PIs<br />
==GO handbook presentation==<br />
*The Gene Ontology and the meaning of biological function (Paul T)<br />
*Translating research data into Gene Ontology annotations (Pascale)<br />
*Gene Ontology - annotation extensions (Ruth)<br />
*GO as a biological systems model (Suzi, or Paul T if Suzi is late)<br />
Pascale will move slides to Google drive<br />
==Ontology Issues and Updates==<br />
===Update on MF refactoring (Pascale or Paul T)===<br />
====GitHub tutorial (Seth & Pascale)====<br />
How GO now uses GitHub for project management and guidelines for contributors<br />
*Where is information relevant to everyone's need<br />
*Groups (Groups.yaml)<br />
*Members<br />
*Etc<br />
<br />
===Qualifiers/Relation issues (Kimberly and Chris)===<br />
====Qualifiers/Relations in GPAD (Kimberly and Chris)====<br />
====Contributes_to guidelines====<br />
++ colocalizes with<br />
====Multiple qualifiers for an annotation (Huaiyu)====<br />
====Use of Qualifiers in Legacy Annotations====<br />
Pascale Proposal: We will apply the general qualifier to all legacy annotations. Each group can provide more specific qualifiers if they have a mechanism to distinguish. Action Items Corvallis 2017/06<br />
*Working group to decide what relations should be available in Protein2GO or other tools for manual annotations. Also decide when there are different ways of expressing the same thing, what way we will choose. What should the default gene/gene product relation be for legacy annotations?<br />
*Chris to work on reports that may help curators make decisions about what annotations can get more expressive qualifiers.<br />
<br />
====Regulates relations====<br />
Adding new qualifiers for the relation between a gene/gene product and a GO term What should the default relation be? How will we handle regulation? Use a relation, involved in regulation of, or use the precomposed regulation term?<br />
Ruth: There are now 3 ways to say the same thing: - involved_in_regulation_of X - involved_in X regulation - involved_in BP regulates(X)<br />
For annotation purposes and for our users we want one.<br />
DOS: Good point. These are semantically identical, but I agree we need to find a way to only have one: by convention for classic GO annotation and by filtering the output of inference for noctua output. Proposal: If a named regulation class exists: involved_in X regulation ...if not: involved_in {some BP} regulates(X) NOTE: If there was an annotation in Noctua such as ‘regulation of’ ‘very specific term’ and there was no term as ‘regulation of very specific term’ the GOC pipeline would create the annotation to the parent term: ‘regulation of less specific term’. Q: Is this implemented ?<br />
==Project updates==<br />
*AGR - report to GOC: PIs<br />
*SynGO meeting report: Paul T<br />
*Report of Reactome-GO connection: David H/Peter D<br />
*Report on transcription work/Noctua templates: Astrid GREEKC consortium=<br />
=Evening: Poster session=<br />
<br />
=Tuesday 3rd October=<br />
==Annotation guidelines and issues (part one)==<br />
===Signaling (Kimberly and David)===<br />
*Report from signaling workshop: David /Kimberly<br />
*Signaling: First attempt at Annotation consistency 2.0 - Kimberly to report on the approach and the outcome.<br />
Discussion points: Limited participation (self-selected to participate). One recommendation may be to ask all active curators to participate, even at some low level https://github.com/orgs/geneontology/projects/<br />
<br />
===Overview of GO annotations/Noctua (Kimberly & Chris)===<br />
====Getting Noctua ready for production====<br />
*Kimberly & Seth Blocking issues list: TO BE COMPLETED<br />
*Action Item Corvallis 2017/06:<br />
**Provide ways for users to recover and digest GO-CAM units (Gene Ontology-based Causal Activity Model). Ideas include rule-based generations of text statements from model, cytoscape view of network described, etc.<br />
**ECO codes available for use in Noctua should show how they map up to a classic GO code, and there should be an alert for curators when they are using a code that does NOT map up to a classic code<br />
**PRO IDs for use in Noctua<br />
**Fix GPAD export from Noctua https://github.com/geneontology/noctua/issues/418<br />
**Add a SPARTA workbench https://github.com/geneontology/noctua/issues/465<br />
**Working group discussion of evidence on complex Noctua models (Kimberly?)<br />
<br />
====Noctua table view demo====<br />
===CC component annotation guidelines (Kimberly)===<br />
CC component annotation: what does it mean ? Kimberly to do 1 proposal (out of 3 alternatives)<br />
1. where the protein is active 2. two different meanings: enables or the right RO (part:of, ie just found there) 3. part_of (low information value!)<br />
===Author intent & protein domains===<br />
Pascale /Ruth; IDA v IC v New evidence code https://github.com/geneontology/go-annotation/issues/1621 30 minutes discussion about issues; hopefully action items can come out of the discussion<br />
===Centralization of InterPro2GO annotations===<br />
*Proposal (follow-up from Geneva 2016): (Paul T)<br />
**GO database pulls directly from InterPro2GO for UniProt Reference Proteomes<br />
**MOD identifier is used as primary gene identifier<br />
**Annotations are given "contributed by" InterPro<br />
**MODs pull from GO database, no need to maintain separate InterPro pipelines<br />
<br />
==Annotation guidelines and issues (part two)==<br />
===HTP guidelines===<br />
Helen - 15 minutes Report on progress from HTP working group<br />
Draft Guidelines Guidelines draft<br />
Action Items Corvallis 2017<br />
Provision of new evidence code<br />
Implementation & developing guidelines<br />
===Transcription annotations decision tree===<br />
Ruth Action Items Corvallis 2017/06<br />
David OS to create transcription regulator activity (proposed by Paul T)<br />
Proposed changes to decision tree in Corvallis:<br />
Simplified from previous version. Essentially a choice between ‘regulating transcription by RNA polymerase II’ or ‘regulating gene expression’<br />
Annotation 5 = contributes_to sequence-specific DNA binding<br />
David: when people do enrichment, they don’t drop contributes_to (ie., pay attention to qualifiers), so all those proteins will come down as ‘DNA binding’ Action item: replace ‘annotation 5’ with ISS annotation (if DNA binding domain) or contributes to annotation 5 with ISS annotation if no DNA binding domain and domains to suggest coactivator<br />
Annotation 3 = nuclear chromatin<br />
Not everyone comfortable with this (ex., Stacia, David) Shouldn’t it be ‘colocalizes_with’? It was previously agreed that the definition for nuclear chromatin: The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus. Source:PMID:20404130 was to be applied. The proteins here include all associated proteins, not limited to just histones. With this statement the TFs are then contributing to chromatin, rather than binding to chromatin or colocalizing with it.<br />
Decision tree to be put up on GOC website.<br />
Should annotation 4 exist? (Ruth)<br />
<br />
===Annotation Documentation===<br />
Kimberly Action Items Corvallis 2017/06<br />
Continue with the consolidation of all documentation for ontology editing, and remove all old documents.<br />
Review annotation documentation and add to github and readthedocs.<br />
Make sure to mark obsolete pages/doc as such and add a link to the new relevant doc<br />
Solicit annotation documentation from participating groups for consolidation.<br />
Make sure to mark docs with ‘Date last reviewed’ so it’s easy for users to know when the documentation was last touched.<br />
Pascale: additional information associated with GO terms, see GitHub ticket?<br />
Add and follow action items at https://github.com/orgs/geneontology/projects/3<br />
===Annotation quality control===<br />
====PAINT update (Huaiyu)====<br />
Huaiyu Action Items Corvallis 2017/06:<br />
Encourage discussion between PAINT curators and other annotators about terms not used for propagation<br />
Report how many annotations per species are used for annotation propagation; could even supply this number for propagation specifically to human genes<br />
Ruth and Huaiyu (others?) will discuss making use of groups that have already annotated specific gene lists to annotate the corresponding PAINT families.<br />
Smooth out the challenge mechanism to make it easier to do make and resolve<br />
the challenges, identify terms that may be problematic and would benefit from consistency exercises and discussion.<br />
Get a list of families where terms have not been propagated (?) - Please check this one for clarity.<br />
(added to github project board) Develop mechanism to trigger review of annotated PAINT families.<br />
===Viral processes update (Pascale)===<br />
Action Items Corvallis 2017/06 Check whether the incorporated changes could affect the host proteins. Document the use cases.<br />
==Community Support==<br />
===Citing GO (Paul T)===<br />
*Web page<br />
*Tool providers: Action Item Corvallis 2017/06: someone to represent GOC and contact GO tool providers to display version information and state this information needs to be included in any subsequent publication. Plus list the GOC paper to reference, as well as the tool provider reference. See: https://github.com/geneontology/go-site/issues/359 and https://github.com/geneontology/go-site/issues/360<br />
===Enrichment (Paul T & Suzi)===<br />
*Web page <br />
*Paul Pavlidis…<br />
*Data Commons work<br />
<br />
===GO_Slims===<br />
====Philosophy (Val, Suzi)====<br />
Creating a biologically useful slim (complete coverage by aspect, biologically useful terms i.e sufficient granularity, avoiding single step process terms (i.e functions), different slims for different purposes: Judy, Mary D (+ Suzi, Val, etc). For overviews, for particular taxa, for a particular area of biology<br />
Specifications for slims from user's perspective (Val: 30 minutes)<br />
====HOW TO MAKE SLIMS (Chris)====<br />
Yaml format for creating slims/types of slims/target organisms<br />
====Use and maintenance of slims (Mary and Suzi)====<br />
Mary: algorithm - 15 minutes<br />
Suzi: GO ribbon<br />
<br />
=Wednesday 4th October=<br />
==Ongoing work==<br />
===AmiGO (Follow up with Seth)===<br />
In general, while several of the AmiGO issues are high-priority, there has been limited bandwidth to tackle them in the context of continuing work on Noctua and the replacement pipeline. Several fixes are queued up and will be available before the upcoming SAB meeting.<br />
In response to: in base_statistics, plotly graph for "Experimental annotation publications by assigner" is confusing https://github.com/geneontology/amigo/issues/429<br />
From Pascale's question: My understanding is that there are essentially no resources for AmiGO right now so any AmiGO issue is low priority. Is this correct?<br />
===The Fate of Simple Processes===<br />
analysis of gene products annotated to phosphorylation but not annotated to a kinase MF term. What did these annotations actually mean? Curators would need to review. Timeline? Deadline? Working group? One possibility would be to use part_of/involved_in relation to phosphorylation for genes also annotated to kinase MF, and causally_upstream_of_or_within for others until curators can re-evaluate.<br />
Other considerations:<br />
Helen: are there many the single-step processes?<br />
Paul: user-oriented approach - is it a useful grouping for our users?<br />
Ruth: we need to think about the meaning beyond just “phosphorylation”<br />
Ruth: what are the consequences of removing “phosphorylation” and what happens to all its children?<br />
Pascale Q: providing that we remove the processes, would it affect the term enrichment analysis?<br />
===BP refactoring===<br />
Defining “Cellular Process” and “Multi-Organism Process” terms<br />
Action item: the comments/examples/notes should be captured, working group to discuss this.<br />
===Proteoforms===<br />
Establish a working group for when and how to use proteoforms in annotation. (Kimberly with Harold and Li)<br />
===Usability issues===<br />
What do users want?<br />
truth (summary/story/model)?<br />
fishing expeditions?<br />
api access?<br />
Who are our users?<br />
geneticists?<br />
clinicians?<br />
computational biologists?<br />
Use cases: https://github.com/geneontology/go-ontology/issues/13606<br />
Perhaps discussion of examples of how the GOC members are engaging with the community and how we can do better in the future (suggested by Helen).<br />
=Wednesday noon-ish Fin=<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Agenda&diff=652892017 Cambridge GOC Meeting Agenda2017-09-27T00:21:11Z<p>Suzi: /* Getting Noctua ready for production */</p>
<hr />
<div>GOC Meeting, Cambridge , October 2-4, 2017<br />
<br />
=Monday 2nd October=<br />
==Welcome, overview, vision, introductions==<br />
GO PIs<br />
==GO handbook presentation==<br />
*The Gene Ontology and the meaning of biological function (Paul T)<br />
*Translating research data into Gene Ontology annotations (Pascale)<br />
*Gene Ontology - annotation extensions (Ruth)<br />
*GO as a biological systems model (Suzi, or Paul T if Suzi is late)<br />
Pascale will move slides to Google drive<br />
==Ontology Issues and Updates==<br />
===Update on MF refactoring (Pascale or Paul T)===<br />
====GitHub tutorial (Seth & Pascale)====<br />
How GO now uses GitHub for project management and guidelines for contributors<br />
*Where is information relevant to everyone's need<br />
*Groups (Groups.yaml)<br />
*Members<br />
*Etc<br />
<br />
===Qualifiers/Relation issues (Kimberly and Chris)===<br />
====Qualifiers/Relations in GPAD (Kimberly and Chris)====<br />
====Contributes_to guidelines====<br />
++ colocalizes with<br />
====Multiple qualifiers for an annotation (Huaiyu)====<br />
====Use of Qualifiers in Legacy Annotations====<br />
Pascale Proposal: We will apply the general qualifier to all legacy annotations. Each group can provide more specific qualifiers if they have a mechanism to distinguish. Action Items Corvallis 2017/06<br />
*Working group to decide what relations should be available in Protein2GO or other tools for manual annotations. Also decide when there are different ways of expressing the same thing, what way we will choose. What should the default gene/gene product relation be for legacy annotations?<br />
*Chris to work on reports that may help curators make decisions about what annotations can get more expressive qualifiers.<br />
<br />
====Regulates relations====<br />
Adding new qualifiers for the relation between a gene/gene product and a GO term What should the default relation be? How will we handle regulation? Use a relation, involved in regulation of, or use the precomposed regulation term?<br />
Ruth: There are now 3 ways to say the same thing: - involved_in_regulation_of X - involved_in X regulation - involved_in BP regulates(X)<br />
For annotation purposes and for our users we want one.<br />
DOS: Good point. These are semantically identical, but I agree we need to find a way to only have one: by convention for classic GO annotation and by filtering the output of inference for noctua output. Proposal: If a named regulation class exists: involved_in X regulation ...if not: involved_in {some BP} regulates(X) NOTE: If there was an annotation in Noctua such as ‘regulation of’ ‘very specific term’ and there was no term as ‘regulation of very specific term’ the GOC pipeline would create the annotation to the parent term: ‘regulation of less specific term’. Q: Is this implemented ?<br />
==Project updates==<br />
*AGR - report to GOC: PIs<br />
*SynGO meeting report: Paul T<br />
*Report of Reactome-GO connection: David H/Peter D<br />
*Report on transcription work/Noctua templates: Astrid GREEKC consortium=<br />
=Evening: Poster session=<br />
<br />
=Tuesday 3rd October=<br />
==Annotation guidelines and issues (part one)==<br />
===Signaling (Kimberly and David)===<br />
*Report from signaling workshop: David /Kimberly<br />
*Signaling: First attempt at Annotation consistency 2.0 - Kimberly to report on the approach and the outcome.<br />
Discussion points: Limited participation (self-selected to participate). One recommendation may be to ask all active curators to participate, even at some low level https://github.com/orgs/geneontology/projects/<br />
<br />
===Overview of GO annotations/Noctua (Kimberly & Chris)===<br />
====Getting Noctua ready for production====<br />
*Kimberly & Seth Blocking issues list: TO BE COMPLETED<br />
*Action Item Corvallis 2017/06:<br />
**Provide ways for users to recover and digest GO-CAM units (Gene Ontology-based Causal Activity Model). Ideas include rule-based generations of text statements from model, cytoscape view of network described, etc.<br />
**ECO codes available for use in Noctua should show how they map up to a classic GO code, and there should be an alert for curators when they are using a code that does NOT map up to a classic code<br />
**PRO IDs for use in Noctua<br />
**Fix GPAD export from Noctua https://github.com/geneontology/noctua/issues/418<br />
**Add a SPARTA workbench https://github.com/geneontology/noctua/issues/465<br />
**Working group discussion of evidence on complex Noctua models (Kimberly?)<br />
<br />
====Noctua table view demo====<br />
===CC component annotation guidelines (Kimberly)===<br />
CC component annotation: what does it mean ? Kimberly to do 1 proposal (out of 3 alternatives)<br />
1. where the protein is active 2. two different meanings: enables or the right RO (part:of, ie just found there) 3. part_of (low information value!)<br />
===Author intent & protein domains===<br />
Pascale /Ruth; IDA v IC v New evidence code https://github.com/geneontology/go-annotation/issues/1621 30 minutes discussion about issues; hopefully action items can come out of the discussion<br />
===Centralization of InterPro2GO annotations===<br />
Proposal (follow-up from Geneva 2016): (Paul T)<br />
GO database pulls directly from InterPro2GO for UniProt Reference Proteomes<br />
MOD identifier is used as primary gene identifier<br />
Annotations are given "contributed by" InterPro<br />
MODs pull from GO database, no need to maintain separate InterPro pipelines<br />
==Annotation guidelines and issues (part two)==<br />
===HTP guidelines===<br />
Helen - 15 minutes Report on progress from HTP working group<br />
Draft Guidelines Guidelines draft<br />
Action Items Corvallis 2017<br />
Provision of new evidence code<br />
Implementation & developing guidelines<br />
===Transcription annotations decision tree===<br />
Ruth Action Items Corvallis 2017/06<br />
David OS to create transcription regulator activity (proposed by Paul T)<br />
Proposed changes to decision tree in Corvallis:<br />
Simplified from previous version. Essentially a choice between ‘regulating transcription by RNA polymerase II’ or ‘regulating gene expression’<br />
Annotation 5 = contributes_to sequence-specific DNA binding<br />
David: when people do enrichment, they don’t drop contributes_to (ie., pay attention to qualifiers), so all those proteins will come down as ‘DNA binding’ Action item: replace ‘annotation 5’ with ISS annotation (if DNA binding domain) or contributes to annotation 5 with ISS annotation if no DNA binding domain and domains to suggest coactivator<br />
Annotation 3 = nuclear chromatin<br />
Not everyone comfortable with this (ex., Stacia, David) Shouldn’t it be ‘colocalizes_with’? It was previously agreed that the definition for nuclear chromatin: The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus. Source:PMID:20404130 was to be applied. The proteins here include all associated proteins, not limited to just histones. With this statement the TFs are then contributing to chromatin, rather than binding to chromatin or colocalizing with it.<br />
Decision tree to be put up on GOC website.<br />
Should annotation 4 exist? (Ruth)<br />
<br />
===Annotation Documentation===<br />
Kimberly Action Items Corvallis 2017/06<br />
Continue with the consolidation of all documentation for ontology editing, and remove all old documents.<br />
Review annotation documentation and add to github and readthedocs.<br />
Make sure to mark obsolete pages/doc as such and add a link to the new relevant doc<br />
Solicit annotation documentation from participating groups for consolidation.<br />
Make sure to mark docs with ‘Date last reviewed’ so it’s easy for users to know when the documentation was last touched.<br />
Pascale: additional information associated with GO terms, see GitHub ticket?<br />
Add and follow action items at https://github.com/orgs/geneontology/projects/3<br />
===Annotation quality control===<br />
====PAINT update (Huaiyu)====<br />
Huaiyu Action Items Corvallis 2017/06:<br />
Encourage discussion between PAINT curators and other annotators about terms not used for propagation<br />
Report how many annotations per species are used for annotation propagation; could even supply this number for propagation specifically to human genes<br />
Ruth and Huaiyu (others?) will discuss making use of groups that have already annotated specific gene lists to annotate the corresponding PAINT families.<br />
Smooth out the challenge mechanism to make it easier to do make and resolve<br />
the challenges, identify terms that may be problematic and would benefit from consistency exercises and discussion.<br />
Get a list of families where terms have not been propagated (?) - Please check this one for clarity.<br />
(added to github project board) Develop mechanism to trigger review of annotated PAINT families.<br />
===Viral processes update (Pascale)===<br />
Action Items Corvallis 2017/06 Check whether the incorporated changes could affect the host proteins. Document the use cases.<br />
==Community Support==<br />
===Citing GO (Paul T)===<br />
*Web page<br />
*Tool providers: Action Item Corvallis 2017/06: someone to represent GOC and contact GO tool providers to display version information and state this information needs to be included in any subsequent publication. Plus list the GOC paper to reference, as well as the tool provider reference. See: https://github.com/geneontology/go-site/issues/359 and https://github.com/geneontology/go-site/issues/360<br />
===Enrichment (Paul T & Suzi)===<br />
*Web page <br />
*Paul Pavlidis…<br />
*Data Commons work<br />
<br />
===GO_Slims===<br />
====Philosophy (Val, Suzi)====<br />
Creating a biologically useful slim (complete coverage by aspect, biologically useful terms i.e sufficient granularity, avoiding single step process terms (i.e functions), different slims for different purposes: Judy, Mary D (+ Suzi, Val, etc). For overviews, for particular taxa, for a particular area of biology<br />
Specifications for slims from user's perspective (Val: 30 minutes)<br />
====HOW TO MAKE SLIMS (Chris)====<br />
Yaml format for creating slims/types of slims/target organisms<br />
====Use and maintenance of slims (Mary and Suzi)====<br />
Mary: algorithm - 15 minutes<br />
Suzi: GO ribbon<br />
<br />
=Wednesday 4th October=<br />
==Ongoing work==<br />
===AmiGO (Follow up with Seth)===<br />
In general, while several of the AmiGO issues are high-priority, there has been limited bandwidth to tackle them in the context of continuing work on Noctua and the replacement pipeline. Several fixes are queued up and will be available before the upcoming SAB meeting.<br />
In response to: in base_statistics, plotly graph for "Experimental annotation publications by assigner" is confusing https://github.com/geneontology/amigo/issues/429<br />
From Pascale's question: My understanding is that there are essentially no resources for AmiGO right now so any AmiGO issue is low priority. Is this correct?<br />
===The Fate of Simple Processes===<br />
analysis of gene products annotated to phosphorylation but not annotated to a kinase MF term. What did these annotations actually mean? Curators would need to review. Timeline? Deadline? Working group? One possibility would be to use part_of/involved_in relation to phosphorylation for genes also annotated to kinase MF, and causally_upstream_of_or_within for others until curators can re-evaluate.<br />
Other considerations:<br />
Helen: are there many the single-step processes?<br />
Paul: user-oriented approach - is it a useful grouping for our users?<br />
Ruth: we need to think about the meaning beyond just “phosphorylation”<br />
Ruth: what are the consequences of removing “phosphorylation” and what happens to all its children?<br />
Pascale Q: providing that we remove the processes, would it affect the term enrichment analysis?<br />
===BP refactoring===<br />
Defining “Cellular Process” and “Multi-Organism Process” terms<br />
Action item: the comments/examples/notes should be captured, working group to discuss this.<br />
===Proteoforms===<br />
Establish a working group for when and how to use proteoforms in annotation. (Kimberly with Harold and Li)<br />
===Usability issues===<br />
What do users want?<br />
truth (summary/story/model)?<br />
fishing expeditions?<br />
api access?<br />
Who are our users?<br />
geneticists?<br />
clinicians?<br />
computational biologists?<br />
Use cases: https://github.com/geneontology/go-ontology/issues/13606<br />
Perhaps discussion of examples of how the GOC members are engaging with the community and how we can do better in the future (suggested by Helen).<br />
=Wednesday noon-ish Fin=<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Agenda&diff=652882017 Cambridge GOC Meeting Agenda2017-09-27T00:20:49Z<p>Suzi: /* Getting Noctua ready for production */</p>
<hr />
<div>GOC Meeting, Cambridge , October 2-4, 2017<br />
<br />
=Monday 2nd October=<br />
==Welcome, overview, vision, introductions==<br />
GO PIs<br />
==GO handbook presentation==<br />
*The Gene Ontology and the meaning of biological function (Paul T)<br />
*Translating research data into Gene Ontology annotations (Pascale)<br />
*Gene Ontology - annotation extensions (Ruth)<br />
*GO as a biological systems model (Suzi, or Paul T if Suzi is late)<br />
Pascale will move slides to Google drive<br />
==Ontology Issues and Updates==<br />
===Update on MF refactoring (Pascale or Paul T)===<br />
====GitHub tutorial (Seth & Pascale)====<br />
How GO now uses GitHub for project management and guidelines for contributors<br />
*Where is information relevant to everyone's need<br />
*Groups (Groups.yaml)<br />
*Members<br />
*Etc<br />
<br />
===Qualifiers/Relation issues (Kimberly and Chris)===<br />
====Qualifiers/Relations in GPAD (Kimberly and Chris)====<br />
====Contributes_to guidelines====<br />
++ colocalizes with<br />
====Multiple qualifiers for an annotation (Huaiyu)====<br />
====Use of Qualifiers in Legacy Annotations====<br />
Pascale Proposal: We will apply the general qualifier to all legacy annotations. Each group can provide more specific qualifiers if they have a mechanism to distinguish. Action Items Corvallis 2017/06<br />
*Working group to decide what relations should be available in Protein2GO or other tools for manual annotations. Also decide when there are different ways of expressing the same thing, what way we will choose. What should the default gene/gene product relation be for legacy annotations?<br />
*Chris to work on reports that may help curators make decisions about what annotations can get more expressive qualifiers.<br />
<br />
====Regulates relations====<br />
Adding new qualifiers for the relation between a gene/gene product and a GO term What should the default relation be? How will we handle regulation? Use a relation, involved in regulation of, or use the precomposed regulation term?<br />
Ruth: There are now 3 ways to say the same thing: - involved_in_regulation_of X - involved_in X regulation - involved_in BP regulates(X)<br />
For annotation purposes and for our users we want one.<br />
DOS: Good point. These are semantically identical, but I agree we need to find a way to only have one: by convention for classic GO annotation and by filtering the output of inference for noctua output. Proposal: If a named regulation class exists: involved_in X regulation ...if not: involved_in {some BP} regulates(X) NOTE: If there was an annotation in Noctua such as ‘regulation of’ ‘very specific term’ and there was no term as ‘regulation of very specific term’ the GOC pipeline would create the annotation to the parent term: ‘regulation of less specific term’. Q: Is this implemented ?<br />
==Project updates==<br />
*AGR - report to GOC: PIs<br />
*SynGO meeting report: Paul T<br />
*Report of Reactome-GO connection: David H/Peter D<br />
*Report on transcription work/Noctua templates: Astrid GREEKC consortium=<br />
=Evening: Poster session=<br />
<br />
=Tuesday 3rd October=<br />
==Annotation guidelines and issues (part one)==<br />
===Signaling (Kimberly and David)===<br />
*Report from signaling workshop: David /Kimberly<br />
*Signaling: First attempt at Annotation consistency 2.0 - Kimberly to report on the approach and the outcome.<br />
Discussion points: Limited participation (self-selected to participate). One recommendation may be to ask all active curators to participate, even at some low level https://github.com/orgs/geneontology/projects/<br />
<br />
===Overview of GO annotations/Noctua (Kimberly & Chris)===<br />
====Getting Noctua ready for production====<br />
*Kimberly & Seth Blocking issues list: TO BE COMPLETED<br />
*Action Item Corvallis 2017/06:<br />
**Provide ways for users to recover and digest GO-CAM units (Gene Ontology-based Causal Activity Model). Ideas include rule-based generations of text statements from model, cytoscape view of network described, etc.<br />
**ECO codes available for use in Noctua should show how they map up to a classic GO code, and there should be an alert for curators when they are using a code that does NOT map up to a classic code<br />
**PRO IDs for use in Noctua<br />
**Fix GPAD export from Noctua https://github.com/geneontology/noctua/issues/418<br />
**Add a SPARTA workbench https://github.com/geneontology/noctua/issues/465<br />
**Action Item Corvallis 2017/06: Working group discussion of evidence on complex Noctua models (Kimberly?)<br />
<br />
====Noctua table view demo====<br />
===CC component annotation guidelines (Kimberly)===<br />
CC component annotation: what does it mean ? Kimberly to do 1 proposal (out of 3 alternatives)<br />
1. where the protein is active 2. two different meanings: enables or the right RO (part:of, ie just found there) 3. part_of (low information value!)<br />
===Author intent & protein domains===<br />
Pascale /Ruth; IDA v IC v New evidence code https://github.com/geneontology/go-annotation/issues/1621 30 minutes discussion about issues; hopefully action items can come out of the discussion<br />
===Centralization of InterPro2GO annotations===<br />
Proposal (follow-up from Geneva 2016): (Paul T)<br />
GO database pulls directly from InterPro2GO for UniProt Reference Proteomes<br />
MOD identifier is used as primary gene identifier<br />
Annotations are given "contributed by" InterPro<br />
MODs pull from GO database, no need to maintain separate InterPro pipelines<br />
==Annotation guidelines and issues (part two)==<br />
===HTP guidelines===<br />
Helen - 15 minutes Report on progress from HTP working group<br />
Draft Guidelines Guidelines draft<br />
Action Items Corvallis 2017<br />
Provision of new evidence code<br />
Implementation & developing guidelines<br />
===Transcription annotations decision tree===<br />
Ruth Action Items Corvallis 2017/06<br />
David OS to create transcription regulator activity (proposed by Paul T)<br />
Proposed changes to decision tree in Corvallis:<br />
Simplified from previous version. Essentially a choice between ‘regulating transcription by RNA polymerase II’ or ‘regulating gene expression’<br />
Annotation 5 = contributes_to sequence-specific DNA binding<br />
David: when people do enrichment, they don’t drop contributes_to (ie., pay attention to qualifiers), so all those proteins will come down as ‘DNA binding’ Action item: replace ‘annotation 5’ with ISS annotation (if DNA binding domain) or contributes to annotation 5 with ISS annotation if no DNA binding domain and domains to suggest coactivator<br />
Annotation 3 = nuclear chromatin<br />
Not everyone comfortable with this (ex., Stacia, David) Shouldn’t it be ‘colocalizes_with’? It was previously agreed that the definition for nuclear chromatin: The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus. Source:PMID:20404130 was to be applied. The proteins here include all associated proteins, not limited to just histones. With this statement the TFs are then contributing to chromatin, rather than binding to chromatin or colocalizing with it.<br />
Decision tree to be put up on GOC website.<br />
Should annotation 4 exist? (Ruth)<br />
<br />
===Annotation Documentation===<br />
Kimberly Action Items Corvallis 2017/06<br />
Continue with the consolidation of all documentation for ontology editing, and remove all old documents.<br />
Review annotation documentation and add to github and readthedocs.<br />
Make sure to mark obsolete pages/doc as such and add a link to the new relevant doc<br />
Solicit annotation documentation from participating groups for consolidation.<br />
Make sure to mark docs with ‘Date last reviewed’ so it’s easy for users to know when the documentation was last touched.<br />
Pascale: additional information associated with GO terms, see GitHub ticket?<br />
Add and follow action items at https://github.com/orgs/geneontology/projects/3<br />
===Annotation quality control===<br />
====PAINT update (Huaiyu)====<br />
Huaiyu Action Items Corvallis 2017/06:<br />
Encourage discussion between PAINT curators and other annotators about terms not used for propagation<br />
Report how many annotations per species are used for annotation propagation; could even supply this number for propagation specifically to human genes<br />
Ruth and Huaiyu (others?) will discuss making use of groups that have already annotated specific gene lists to annotate the corresponding PAINT families.<br />
Smooth out the challenge mechanism to make it easier to do make and resolve<br />
the challenges, identify terms that may be problematic and would benefit from consistency exercises and discussion.<br />
Get a list of families where terms have not been propagated (?) - Please check this one for clarity.<br />
(added to github project board) Develop mechanism to trigger review of annotated PAINT families.<br />
===Viral processes update (Pascale)===<br />
Action Items Corvallis 2017/06 Check whether the incorporated changes could affect the host proteins. Document the use cases.<br />
==Community Support==<br />
===Citing GO (Paul T)===<br />
*Web page<br />
*Tool providers: Action Item Corvallis 2017/06: someone to represent GOC and contact GO tool providers to display version information and state this information needs to be included in any subsequent publication. Plus list the GOC paper to reference, as well as the tool provider reference. See: https://github.com/geneontology/go-site/issues/359 and https://github.com/geneontology/go-site/issues/360<br />
===Enrichment (Paul T & Suzi)===<br />
*Web page <br />
*Paul Pavlidis…<br />
*Data Commons work<br />
<br />
===GO_Slims===<br />
====Philosophy (Val, Suzi)====<br />
Creating a biologically useful slim (complete coverage by aspect, biologically useful terms i.e sufficient granularity, avoiding single step process terms (i.e functions), different slims for different purposes: Judy, Mary D (+ Suzi, Val, etc). For overviews, for particular taxa, for a particular area of biology<br />
Specifications for slims from user's perspective (Val: 30 minutes)<br />
====HOW TO MAKE SLIMS (Chris)====<br />
Yaml format for creating slims/types of slims/target organisms<br />
====Use and maintenance of slims (Mary and Suzi)====<br />
Mary: algorithm - 15 minutes<br />
Suzi: GO ribbon<br />
<br />
=Wednesday 4th October=<br />
==Ongoing work==<br />
===AmiGO (Follow up with Seth)===<br />
In general, while several of the AmiGO issues are high-priority, there has been limited bandwidth to tackle them in the context of continuing work on Noctua and the replacement pipeline. Several fixes are queued up and will be available before the upcoming SAB meeting.<br />
In response to: in base_statistics, plotly graph for "Experimental annotation publications by assigner" is confusing https://github.com/geneontology/amigo/issues/429<br />
From Pascale's question: My understanding is that there are essentially no resources for AmiGO right now so any AmiGO issue is low priority. Is this correct?<br />
===The Fate of Simple Processes===<br />
analysis of gene products annotated to phosphorylation but not annotated to a kinase MF term. What did these annotations actually mean? Curators would need to review. Timeline? Deadline? Working group? One possibility would be to use part_of/involved_in relation to phosphorylation for genes also annotated to kinase MF, and causally_upstream_of_or_within for others until curators can re-evaluate.<br />
Other considerations:<br />
Helen: are there many the single-step processes?<br />
Paul: user-oriented approach - is it a useful grouping for our users?<br />
Ruth: we need to think about the meaning beyond just “phosphorylation”<br />
Ruth: what are the consequences of removing “phosphorylation” and what happens to all its children?<br />
Pascale Q: providing that we remove the processes, would it affect the term enrichment analysis?<br />
===BP refactoring===<br />
Defining “Cellular Process” and “Multi-Organism Process” terms<br />
Action item: the comments/examples/notes should be captured, working group to discuss this.<br />
===Proteoforms===<br />
Establish a working group for when and how to use proteoforms in annotation. (Kimberly with Harold and Li)<br />
===Usability issues===<br />
What do users want?<br />
truth (summary/story/model)?<br />
fishing expeditions?<br />
api access?<br />
Who are our users?<br />
geneticists?<br />
clinicians?<br />
computational biologists?<br />
Use cases: https://github.com/geneontology/go-ontology/issues/13606<br />
Perhaps discussion of examples of how the GOC members are engaging with the community and how we can do better in the future (suggested by Helen).<br />
=Wednesday noon-ish Fin=<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Agenda&diff=652872017 Cambridge GOC Meeting Agenda2017-09-27T00:19:24Z<p>Suzi: /* Signaling (Kimberly and David) */</p>
<hr />
<div>GOC Meeting, Cambridge , October 2-4, 2017<br />
<br />
=Monday 2nd October=<br />
==Welcome, overview, vision, introductions==<br />
GO PIs<br />
==GO handbook presentation==<br />
*The Gene Ontology and the meaning of biological function (Paul T)<br />
*Translating research data into Gene Ontology annotations (Pascale)<br />
*Gene Ontology - annotation extensions (Ruth)<br />
*GO as a biological systems model (Suzi, or Paul T if Suzi is late)<br />
Pascale will move slides to Google drive<br />
==Ontology Issues and Updates==<br />
===Update on MF refactoring (Pascale or Paul T)===<br />
====GitHub tutorial (Seth & Pascale)====<br />
How GO now uses GitHub for project management and guidelines for contributors<br />
*Where is information relevant to everyone's need<br />
*Groups (Groups.yaml)<br />
*Members<br />
*Etc<br />
<br />
===Qualifiers/Relation issues (Kimberly and Chris)===<br />
====Qualifiers/Relations in GPAD (Kimberly and Chris)====<br />
====Contributes_to guidelines====<br />
++ colocalizes with<br />
====Multiple qualifiers for an annotation (Huaiyu)====<br />
====Use of Qualifiers in Legacy Annotations====<br />
Pascale Proposal: We will apply the general qualifier to all legacy annotations. Each group can provide more specific qualifiers if they have a mechanism to distinguish. Action Items Corvallis 2017/06<br />
*Working group to decide what relations should be available in Protein2GO or other tools for manual annotations. Also decide when there are different ways of expressing the same thing, what way we will choose. What should the default gene/gene product relation be for legacy annotations?<br />
*Chris to work on reports that may help curators make decisions about what annotations can get more expressive qualifiers.<br />
<br />
====Regulates relations====<br />
Adding new qualifiers for the relation between a gene/gene product and a GO term What should the default relation be? How will we handle regulation? Use a relation, involved in regulation of, or use the precomposed regulation term?<br />
Ruth: There are now 3 ways to say the same thing: - involved_in_regulation_of X - involved_in X regulation - involved_in BP regulates(X)<br />
For annotation purposes and for our users we want one.<br />
DOS: Good point. These are semantically identical, but I agree we need to find a way to only have one: by convention for classic GO annotation and by filtering the output of inference for noctua output. Proposal: If a named regulation class exists: involved_in X regulation ...if not: involved_in {some BP} regulates(X) NOTE: If there was an annotation in Noctua such as ‘regulation of’ ‘very specific term’ and there was no term as ‘regulation of very specific term’ the GOC pipeline would create the annotation to the parent term: ‘regulation of less specific term’. Q: Is this implemented ?<br />
==Project updates==<br />
*AGR - report to GOC: PIs<br />
*SynGO meeting report: Paul T<br />
*Report of Reactome-GO connection: David H/Peter D<br />
*Report on transcription work/Noctua templates: Astrid GREEKC consortium=<br />
=Evening: Poster session=<br />
<br />
=Tuesday 3rd October=<br />
==Annotation guidelines and issues (part one)==<br />
===Signaling (Kimberly and David)===<br />
*Report from signaling workshop: David /Kimberly<br />
*Signaling: First attempt at Annotation consistency 2.0 - Kimberly to report on the approach and the outcome.<br />
Discussion points: Limited participation (self-selected to participate). One recommendation may be to ask all active curators to participate, even at some low level https://github.com/orgs/geneontology/projects/<br />
<br />
===Overview of GO annotations/Noctua (Kimberly & Chris)===<br />
====Getting Noctua ready for production====<br />
Kimberly & Seth Blocking issues list: TO BE COMPLETED<br />
Action Item Corvallis 2017/06:<br />
Provide ways for users to recover and digest GO-CAM units (Gene Ontology-based Causal Activity Model). Ideas include rule-based generations of text statements from model, cytoscape view of network described, etc.<br />
ECO codes available for use in Noctua should show how they map up to a classic GO code, and there should be an alert for curators when they are using a code that does NOT map up to a classic code<br />
PRO IDs for use in Noctua<br />
Fix GPAD export from Noctua https://github.com/geneontology/noctua/issues/418<br />
Add a SPARTA workbench https://github.com/geneontology/noctua/issues/465<br />
Action Item Corvallis 2017/06:<br />
Working group discussion of evidence on complex Noctua models (Kimberly?)<br />
====Noctua table view demo====<br />
===CC component annotation guidelines (Kimberly)===<br />
CC component annotation: what does it mean ? Kimberly to do 1 proposal (out of 3 alternatives)<br />
1. where the protein is active 2. two different meanings: enables or the right RO (part:of, ie just found there) 3. part_of (low information value!)<br />
===Author intent & protein domains===<br />
Pascale /Ruth; IDA v IC v New evidence code https://github.com/geneontology/go-annotation/issues/1621 30 minutes discussion about issues; hopefully action items can come out of the discussion<br />
===Centralization of InterPro2GO annotations===<br />
Proposal (follow-up from Geneva 2016): (Paul T)<br />
GO database pulls directly from InterPro2GO for UniProt Reference Proteomes<br />
MOD identifier is used as primary gene identifier<br />
Annotations are given "contributed by" InterPro<br />
MODs pull from GO database, no need to maintain separate InterPro pipelines<br />
==Annotation guidelines and issues (part two)==<br />
===HTP guidelines===<br />
Helen - 15 minutes Report on progress from HTP working group<br />
Draft Guidelines Guidelines draft<br />
Action Items Corvallis 2017<br />
Provision of new evidence code<br />
Implementation & developing guidelines<br />
===Transcription annotations decision tree===<br />
Ruth Action Items Corvallis 2017/06<br />
David OS to create transcription regulator activity (proposed by Paul T)<br />
Proposed changes to decision tree in Corvallis:<br />
Simplified from previous version. Essentially a choice between ‘regulating transcription by RNA polymerase II’ or ‘regulating gene expression’<br />
Annotation 5 = contributes_to sequence-specific DNA binding<br />
David: when people do enrichment, they don’t drop contributes_to (ie., pay attention to qualifiers), so all those proteins will come down as ‘DNA binding’ Action item: replace ‘annotation 5’ with ISS annotation (if DNA binding domain) or contributes to annotation 5 with ISS annotation if no DNA binding domain and domains to suggest coactivator<br />
Annotation 3 = nuclear chromatin<br />
Not everyone comfortable with this (ex., Stacia, David) Shouldn’t it be ‘colocalizes_with’? It was previously agreed that the definition for nuclear chromatin: The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus. Source:PMID:20404130 was to be applied. The proteins here include all associated proteins, not limited to just histones. With this statement the TFs are then contributing to chromatin, rather than binding to chromatin or colocalizing with it.<br />
Decision tree to be put up on GOC website.<br />
Should annotation 4 exist? (Ruth)<br />
<br />
===Annotation Documentation===<br />
Kimberly Action Items Corvallis 2017/06<br />
Continue with the consolidation of all documentation for ontology editing, and remove all old documents.<br />
Review annotation documentation and add to github and readthedocs.<br />
Make sure to mark obsolete pages/doc as such and add a link to the new relevant doc<br />
Solicit annotation documentation from participating groups for consolidation.<br />
Make sure to mark docs with ‘Date last reviewed’ so it’s easy for users to know when the documentation was last touched.<br />
Pascale: additional information associated with GO terms, see GitHub ticket?<br />
Add and follow action items at https://github.com/orgs/geneontology/projects/3<br />
===Annotation quality control===<br />
====PAINT update (Huaiyu)====<br />
Huaiyu Action Items Corvallis 2017/06:<br />
Encourage discussion between PAINT curators and other annotators about terms not used for propagation<br />
Report how many annotations per species are used for annotation propagation; could even supply this number for propagation specifically to human genes<br />
Ruth and Huaiyu (others?) will discuss making use of groups that have already annotated specific gene lists to annotate the corresponding PAINT families.<br />
Smooth out the challenge mechanism to make it easier to do make and resolve<br />
the challenges, identify terms that may be problematic and would benefit from consistency exercises and discussion.<br />
Get a list of families where terms have not been propagated (?) - Please check this one for clarity.<br />
(added to github project board) Develop mechanism to trigger review of annotated PAINT families.<br />
===Viral processes update (Pascale)===<br />
Action Items Corvallis 2017/06 Check whether the incorporated changes could affect the host proteins. Document the use cases.<br />
==Community Support==<br />
===Citing GO (Paul T)===<br />
*Web page<br />
*Tool providers: Action Item Corvallis 2017/06: someone to represent GOC and contact GO tool providers to display version information and state this information needs to be included in any subsequent publication. Plus list the GOC paper to reference, as well as the tool provider reference. See: https://github.com/geneontology/go-site/issues/359 and https://github.com/geneontology/go-site/issues/360<br />
===Enrichment (Paul T & Suzi)===<br />
*Web page <br />
*Paul Pavlidis…<br />
*Data Commons work<br />
<br />
===GO_Slims===<br />
====Philosophy (Val, Suzi)====<br />
Creating a biologically useful slim (complete coverage by aspect, biologically useful terms i.e sufficient granularity, avoiding single step process terms (i.e functions), different slims for different purposes: Judy, Mary D (+ Suzi, Val, etc). For overviews, for particular taxa, for a particular area of biology<br />
Specifications for slims from user's perspective (Val: 30 minutes)<br />
====HOW TO MAKE SLIMS (Chris)====<br />
Yaml format for creating slims/types of slims/target organisms<br />
====Use and maintenance of slims (Mary and Suzi)====<br />
Mary: algorithm - 15 minutes<br />
Suzi: GO ribbon<br />
<br />
=Wednesday 4th October=<br />
==Ongoing work==<br />
===AmiGO (Follow up with Seth)===<br />
In general, while several of the AmiGO issues are high-priority, there has been limited bandwidth to tackle them in the context of continuing work on Noctua and the replacement pipeline. Several fixes are queued up and will be available before the upcoming SAB meeting.<br />
In response to: in base_statistics, plotly graph for "Experimental annotation publications by assigner" is confusing https://github.com/geneontology/amigo/issues/429<br />
From Pascale's question: My understanding is that there are essentially no resources for AmiGO right now so any AmiGO issue is low priority. Is this correct?<br />
===The Fate of Simple Processes===<br />
analysis of gene products annotated to phosphorylation but not annotated to a kinase MF term. What did these annotations actually mean? Curators would need to review. Timeline? Deadline? Working group? One possibility would be to use part_of/involved_in relation to phosphorylation for genes also annotated to kinase MF, and causally_upstream_of_or_within for others until curators can re-evaluate.<br />
Other considerations:<br />
Helen: are there many the single-step processes?<br />
Paul: user-oriented approach - is it a useful grouping for our users?<br />
Ruth: we need to think about the meaning beyond just “phosphorylation”<br />
Ruth: what are the consequences of removing “phosphorylation” and what happens to all its children?<br />
Pascale Q: providing that we remove the processes, would it affect the term enrichment analysis?<br />
===BP refactoring===<br />
Defining “Cellular Process” and “Multi-Organism Process” terms<br />
Action item: the comments/examples/notes should be captured, working group to discuss this.<br />
===Proteoforms===<br />
Establish a working group for when and how to use proteoforms in annotation. (Kimberly with Harold and Li)<br />
===Usability issues===<br />
What do users want?<br />
truth (summary/story/model)?<br />
fishing expeditions?<br />
api access?<br />
Who are our users?<br />
geneticists?<br />
clinicians?<br />
computational biologists?<br />
Use cases: https://github.com/geneontology/go-ontology/issues/13606<br />
Perhaps discussion of examples of how the GOC members are engaging with the community and how we can do better in the future (suggested by Helen).<br />
=Wednesday noon-ish Fin=<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Agenda&diff=652862017 Cambridge GOC Meeting Agenda2017-09-27T00:18:24Z<p>Suzi: /* Use of Qualifiers in Legacy Annotations */</p>
<hr />
<div>GOC Meeting, Cambridge , October 2-4, 2017<br />
<br />
=Monday 2nd October=<br />
==Welcome, overview, vision, introductions==<br />
GO PIs<br />
==GO handbook presentation==<br />
*The Gene Ontology and the meaning of biological function (Paul T)<br />
*Translating research data into Gene Ontology annotations (Pascale)<br />
*Gene Ontology - annotation extensions (Ruth)<br />
*GO as a biological systems model (Suzi, or Paul T if Suzi is late)<br />
Pascale will move slides to Google drive<br />
==Ontology Issues and Updates==<br />
===Update on MF refactoring (Pascale or Paul T)===<br />
====GitHub tutorial (Seth & Pascale)====<br />
How GO now uses GitHub for project management and guidelines for contributors<br />
*Where is information relevant to everyone's need<br />
*Groups (Groups.yaml)<br />
*Members<br />
*Etc<br />
<br />
===Qualifiers/Relation issues (Kimberly and Chris)===<br />
====Qualifiers/Relations in GPAD (Kimberly and Chris)====<br />
====Contributes_to guidelines====<br />
++ colocalizes with<br />
====Multiple qualifiers for an annotation (Huaiyu)====<br />
====Use of Qualifiers in Legacy Annotations====<br />
Pascale Proposal: We will apply the general qualifier to all legacy annotations. Each group can provide more specific qualifiers if they have a mechanism to distinguish. Action Items Corvallis 2017/06<br />
*Working group to decide what relations should be available in Protein2GO or other tools for manual annotations. Also decide when there are different ways of expressing the same thing, what way we will choose. What should the default gene/gene product relation be for legacy annotations?<br />
*Chris to work on reports that may help curators make decisions about what annotations can get more expressive qualifiers.<br />
<br />
====Regulates relations====<br />
Adding new qualifiers for the relation between a gene/gene product and a GO term What should the default relation be? How will we handle regulation? Use a relation, involved in regulation of, or use the precomposed regulation term?<br />
Ruth: There are now 3 ways to say the same thing: - involved_in_regulation_of X - involved_in X regulation - involved_in BP regulates(X)<br />
For annotation purposes and for our users we want one.<br />
DOS: Good point. These are semantically identical, but I agree we need to find a way to only have one: by convention for classic GO annotation and by filtering the output of inference for noctua output. Proposal: If a named regulation class exists: involved_in X regulation ...if not: involved_in {some BP} regulates(X) NOTE: If there was an annotation in Noctua such as ‘regulation of’ ‘very specific term’ and there was no term as ‘regulation of very specific term’ the GOC pipeline would create the annotation to the parent term: ‘regulation of less specific term’. Q: Is this implemented ?<br />
==Project updates==<br />
*AGR - report to GOC: PIs<br />
*SynGO meeting report: Paul T<br />
*Report of Reactome-GO connection: David H/Peter D<br />
*Report on transcription work/Noctua templates: Astrid GREEKC consortium=<br />
=Evening: Poster session=<br />
<br />
=Tuesday 3rd October=<br />
==Annotation guidelines and issues (part one)==<br />
===Signaling (Kimberly and David)===<br />
Report from signaling workshop: David /Kimberly<br />
Signaling: First attempt at Annotation consistency 2.0 - Kimberly to report on the approach and the outcome.<br />
Discussion points: Limited participation (self-selected to participate). One recommendation may be to ask all active curators to participate, even at some low level https://github.com/orgs/geneontology/projects/<br />
===Overview of GO annotations/Noctua (Kimberly & Chris)===<br />
====Getting Noctua ready for production====<br />
Kimberly & Seth Blocking issues list: TO BE COMPLETED<br />
Action Item Corvallis 2017/06:<br />
Provide ways for users to recover and digest GO-CAM units (Gene Ontology-based Causal Activity Model). Ideas include rule-based generations of text statements from model, cytoscape view of network described, etc.<br />
ECO codes available for use in Noctua should show how they map up to a classic GO code, and there should be an alert for curators when they are using a code that does NOT map up to a classic code<br />
PRO IDs for use in Noctua<br />
Fix GPAD export from Noctua https://github.com/geneontology/noctua/issues/418<br />
Add a SPARTA workbench https://github.com/geneontology/noctua/issues/465<br />
Action Item Corvallis 2017/06:<br />
Working group discussion of evidence on complex Noctua models (Kimberly?)<br />
====Noctua table view demo====<br />
===CC component annotation guidelines (Kimberly)===<br />
CC component annotation: what does it mean ? Kimberly to do 1 proposal (out of 3 alternatives)<br />
1. where the protein is active 2. two different meanings: enables or the right RO (part:of, ie just found there) 3. part_of (low information value!)<br />
===Author intent & protein domains===<br />
Pascale /Ruth; IDA v IC v New evidence code https://github.com/geneontology/go-annotation/issues/1621 30 minutes discussion about issues; hopefully action items can come out of the discussion<br />
===Centralization of InterPro2GO annotations===<br />
Proposal (follow-up from Geneva 2016): (Paul T)<br />
GO database pulls directly from InterPro2GO for UniProt Reference Proteomes<br />
MOD identifier is used as primary gene identifier<br />
Annotations are given "contributed by" InterPro<br />
MODs pull from GO database, no need to maintain separate InterPro pipelines<br />
==Annotation guidelines and issues (part two)==<br />
===HTP guidelines===<br />
Helen - 15 minutes Report on progress from HTP working group<br />
Draft Guidelines Guidelines draft<br />
Action Items Corvallis 2017<br />
Provision of new evidence code<br />
Implementation & developing guidelines<br />
===Transcription annotations decision tree===<br />
Ruth Action Items Corvallis 2017/06<br />
David OS to create transcription regulator activity (proposed by Paul T)<br />
Proposed changes to decision tree in Corvallis:<br />
Simplified from previous version. Essentially a choice between ‘regulating transcription by RNA polymerase II’ or ‘regulating gene expression’<br />
Annotation 5 = contributes_to sequence-specific DNA binding<br />
David: when people do enrichment, they don’t drop contributes_to (ie., pay attention to qualifiers), so all those proteins will come down as ‘DNA binding’ Action item: replace ‘annotation 5’ with ISS annotation (if DNA binding domain) or contributes to annotation 5 with ISS annotation if no DNA binding domain and domains to suggest coactivator<br />
Annotation 3 = nuclear chromatin<br />
Not everyone comfortable with this (ex., Stacia, David) Shouldn’t it be ‘colocalizes_with’? It was previously agreed that the definition for nuclear chromatin: The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus. Source:PMID:20404130 was to be applied. The proteins here include all associated proteins, not limited to just histones. With this statement the TFs are then contributing to chromatin, rather than binding to chromatin or colocalizing with it.<br />
Decision tree to be put up on GOC website.<br />
Should annotation 4 exist? (Ruth)<br />
<br />
===Annotation Documentation===<br />
Kimberly Action Items Corvallis 2017/06<br />
Continue with the consolidation of all documentation for ontology editing, and remove all old documents.<br />
Review annotation documentation and add to github and readthedocs.<br />
Make sure to mark obsolete pages/doc as such and add a link to the new relevant doc<br />
Solicit annotation documentation from participating groups for consolidation.<br />
Make sure to mark docs with ‘Date last reviewed’ so it’s easy for users to know when the documentation was last touched.<br />
Pascale: additional information associated with GO terms, see GitHub ticket?<br />
Add and follow action items at https://github.com/orgs/geneontology/projects/3<br />
===Annotation quality control===<br />
====PAINT update (Huaiyu)====<br />
Huaiyu Action Items Corvallis 2017/06:<br />
Encourage discussion between PAINT curators and other annotators about terms not used for propagation<br />
Report how many annotations per species are used for annotation propagation; could even supply this number for propagation specifically to human genes<br />
Ruth and Huaiyu (others?) will discuss making use of groups that have already annotated specific gene lists to annotate the corresponding PAINT families.<br />
Smooth out the challenge mechanism to make it easier to do make and resolve<br />
the challenges, identify terms that may be problematic and would benefit from consistency exercises and discussion.<br />
Get a list of families where terms have not been propagated (?) - Please check this one for clarity.<br />
(added to github project board) Develop mechanism to trigger review of annotated PAINT families.<br />
===Viral processes update (Pascale)===<br />
Action Items Corvallis 2017/06 Check whether the incorporated changes could affect the host proteins. Document the use cases.<br />
==Community Support==<br />
===Citing GO (Paul T)===<br />
*Web page<br />
*Tool providers: Action Item Corvallis 2017/06: someone to represent GOC and contact GO tool providers to display version information and state this information needs to be included in any subsequent publication. Plus list the GOC paper to reference, as well as the tool provider reference. See: https://github.com/geneontology/go-site/issues/359 and https://github.com/geneontology/go-site/issues/360<br />
===Enrichment (Paul T & Suzi)===<br />
*Web page <br />
*Paul Pavlidis…<br />
*Data Commons work<br />
<br />
===GO_Slims===<br />
====Philosophy (Val, Suzi)====<br />
Creating a biologically useful slim (complete coverage by aspect, biologically useful terms i.e sufficient granularity, avoiding single step process terms (i.e functions), different slims for different purposes: Judy, Mary D (+ Suzi, Val, etc). For overviews, for particular taxa, for a particular area of biology<br />
Specifications for slims from user's perspective (Val: 30 minutes)<br />
====HOW TO MAKE SLIMS (Chris)====<br />
Yaml format for creating slims/types of slims/target organisms<br />
====Use and maintenance of slims (Mary and Suzi)====<br />
Mary: algorithm - 15 minutes<br />
Suzi: GO ribbon<br />
<br />
=Wednesday 4th October=<br />
==Ongoing work==<br />
===AmiGO (Follow up with Seth)===<br />
In general, while several of the AmiGO issues are high-priority, there has been limited bandwidth to tackle them in the context of continuing work on Noctua and the replacement pipeline. Several fixes are queued up and will be available before the upcoming SAB meeting.<br />
In response to: in base_statistics, plotly graph for "Experimental annotation publications by assigner" is confusing https://github.com/geneontology/amigo/issues/429<br />
From Pascale's question: My understanding is that there are essentially no resources for AmiGO right now so any AmiGO issue is low priority. Is this correct?<br />
===The Fate of Simple Processes===<br />
analysis of gene products annotated to phosphorylation but not annotated to a kinase MF term. What did these annotations actually mean? Curators would need to review. Timeline? Deadline? Working group? One possibility would be to use part_of/involved_in relation to phosphorylation for genes also annotated to kinase MF, and causally_upstream_of_or_within for others until curators can re-evaluate.<br />
Other considerations:<br />
Helen: are there many the single-step processes?<br />
Paul: user-oriented approach - is it a useful grouping for our users?<br />
Ruth: we need to think about the meaning beyond just “phosphorylation”<br />
Ruth: what are the consequences of removing “phosphorylation” and what happens to all its children?<br />
Pascale Q: providing that we remove the processes, would it affect the term enrichment analysis?<br />
===BP refactoring===<br />
Defining “Cellular Process” and “Multi-Organism Process” terms<br />
Action item: the comments/examples/notes should be captured, working group to discuss this.<br />
===Proteoforms===<br />
Establish a working group for when and how to use proteoforms in annotation. (Kimberly with Harold and Li)<br />
===Usability issues===<br />
What do users want?<br />
truth (summary/story/model)?<br />
fishing expeditions?<br />
api access?<br />
Who are our users?<br />
geneticists?<br />
clinicians?<br />
computational biologists?<br />
Use cases: https://github.com/geneontology/go-ontology/issues/13606<br />
Perhaps discussion of examples of how the GOC members are engaging with the community and how we can do better in the future (suggested by Helen).<br />
=Wednesday noon-ish Fin=<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Agenda&diff=652852017 Cambridge GOC Meeting Agenda2017-09-27T00:17:29Z<p>Suzi: /* Project updates */</p>
<hr />
<div>GOC Meeting, Cambridge , October 2-4, 2017<br />
<br />
=Monday 2nd October=<br />
==Welcome, overview, vision, introductions==<br />
GO PIs<br />
==GO handbook presentation==<br />
*The Gene Ontology and the meaning of biological function (Paul T)<br />
*Translating research data into Gene Ontology annotations (Pascale)<br />
*Gene Ontology - annotation extensions (Ruth)<br />
*GO as a biological systems model (Suzi, or Paul T if Suzi is late)<br />
Pascale will move slides to Google drive<br />
==Ontology Issues and Updates==<br />
===Update on MF refactoring (Pascale or Paul T)===<br />
====GitHub tutorial (Seth & Pascale)====<br />
How GO now uses GitHub for project management and guidelines for contributors<br />
*Where is information relevant to everyone's need<br />
*Groups (Groups.yaml)<br />
*Members<br />
*Etc<br />
<br />
===Qualifiers/Relation issues (Kimberly and Chris)===<br />
====Qualifiers/Relations in GPAD (Kimberly and Chris)====<br />
====Contributes_to guidelines====<br />
++ colocalizes with<br />
====Multiple qualifiers for an annotation (Huaiyu)====<br />
====Use of Qualifiers in Legacy Annotations====<br />
Pascale Proposal: We will apply the general qualifier to all legacy annotations. Each group can provide more specific qualifiers if they have a mechanism to distinguish. Action Items Corvallis 2017/06<br />
Working group to decide what relations should be available in Protein2GO or other tools for manual annotations. Also decide when there are different ways of expressing the same thing, what way we will choose. What should the default gene/gene product relation be for legacy annotations?<br />
Chris to work on reports that may help curators make decisions about what annotations can get more expressive qualifiers.<br />
====Regulates relations====<br />
Adding new qualifiers for the relation between a gene/gene product and a GO term What should the default relation be? How will we handle regulation? Use a relation, involved in regulation of, or use the precomposed regulation term?<br />
Ruth: There are now 3 ways to say the same thing: - involved_in_regulation_of X - involved_in X regulation - involved_in BP regulates(X)<br />
For annotation purposes and for our users we want one.<br />
DOS: Good point. These are semantically identical, but I agree we need to find a way to only have one: by convention for classic GO annotation and by filtering the output of inference for noctua output. Proposal: If a named regulation class exists: involved_in X regulation ...if not: involved_in {some BP} regulates(X) NOTE: If there was an annotation in Noctua such as ‘regulation of’ ‘very specific term’ and there was no term as ‘regulation of very specific term’ the GOC pipeline would create the annotation to the parent term: ‘regulation of less specific term’. Q: Is this implemented ?<br />
==Project updates==<br />
*AGR - report to GOC: PIs<br />
*SynGO meeting report: Paul T<br />
*Report of Reactome-GO connection: David H/Peter D<br />
*Report on transcription work/Noctua templates: Astrid GREEKC consortium=<br />
=Evening: Poster session=<br />
<br />
=Tuesday 3rd October=<br />
==Annotation guidelines and issues (part one)==<br />
===Signaling (Kimberly and David)===<br />
Report from signaling workshop: David /Kimberly<br />
Signaling: First attempt at Annotation consistency 2.0 - Kimberly to report on the approach and the outcome.<br />
Discussion points: Limited participation (self-selected to participate). One recommendation may be to ask all active curators to participate, even at some low level https://github.com/orgs/geneontology/projects/<br />
===Overview of GO annotations/Noctua (Kimberly & Chris)===<br />
====Getting Noctua ready for production====<br />
Kimberly & Seth Blocking issues list: TO BE COMPLETED<br />
Action Item Corvallis 2017/06:<br />
Provide ways for users to recover and digest GO-CAM units (Gene Ontology-based Causal Activity Model). Ideas include rule-based generations of text statements from model, cytoscape view of network described, etc.<br />
ECO codes available for use in Noctua should show how they map up to a classic GO code, and there should be an alert for curators when they are using a code that does NOT map up to a classic code<br />
PRO IDs for use in Noctua<br />
Fix GPAD export from Noctua https://github.com/geneontology/noctua/issues/418<br />
Add a SPARTA workbench https://github.com/geneontology/noctua/issues/465<br />
Action Item Corvallis 2017/06:<br />
Working group discussion of evidence on complex Noctua models (Kimberly?)<br />
====Noctua table view demo====<br />
===CC component annotation guidelines (Kimberly)===<br />
CC component annotation: what does it mean ? Kimberly to do 1 proposal (out of 3 alternatives)<br />
1. where the protein is active 2. two different meanings: enables or the right RO (part:of, ie just found there) 3. part_of (low information value!)<br />
===Author intent & protein domains===<br />
Pascale /Ruth; IDA v IC v New evidence code https://github.com/geneontology/go-annotation/issues/1621 30 minutes discussion about issues; hopefully action items can come out of the discussion<br />
===Centralization of InterPro2GO annotations===<br />
Proposal (follow-up from Geneva 2016): (Paul T)<br />
GO database pulls directly from InterPro2GO for UniProt Reference Proteomes<br />
MOD identifier is used as primary gene identifier<br />
Annotations are given "contributed by" InterPro<br />
MODs pull from GO database, no need to maintain separate InterPro pipelines<br />
==Annotation guidelines and issues (part two)==<br />
===HTP guidelines===<br />
Helen - 15 minutes Report on progress from HTP working group<br />
Draft Guidelines Guidelines draft<br />
Action Items Corvallis 2017<br />
Provision of new evidence code<br />
Implementation & developing guidelines<br />
===Transcription annotations decision tree===<br />
Ruth Action Items Corvallis 2017/06<br />
David OS to create transcription regulator activity (proposed by Paul T)<br />
Proposed changes to decision tree in Corvallis:<br />
Simplified from previous version. Essentially a choice between ‘regulating transcription by RNA polymerase II’ or ‘regulating gene expression’<br />
Annotation 5 = contributes_to sequence-specific DNA binding<br />
David: when people do enrichment, they don’t drop contributes_to (ie., pay attention to qualifiers), so all those proteins will come down as ‘DNA binding’ Action item: replace ‘annotation 5’ with ISS annotation (if DNA binding domain) or contributes to annotation 5 with ISS annotation if no DNA binding domain and domains to suggest coactivator<br />
Annotation 3 = nuclear chromatin<br />
Not everyone comfortable with this (ex., Stacia, David) Shouldn’t it be ‘colocalizes_with’? It was previously agreed that the definition for nuclear chromatin: The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus. Source:PMID:20404130 was to be applied. The proteins here include all associated proteins, not limited to just histones. With this statement the TFs are then contributing to chromatin, rather than binding to chromatin or colocalizing with it.<br />
Decision tree to be put up on GOC website.<br />
Should annotation 4 exist? (Ruth)<br />
<br />
===Annotation Documentation===<br />
Kimberly Action Items Corvallis 2017/06<br />
Continue with the consolidation of all documentation for ontology editing, and remove all old documents.<br />
Review annotation documentation and add to github and readthedocs.<br />
Make sure to mark obsolete pages/doc as such and add a link to the new relevant doc<br />
Solicit annotation documentation from participating groups for consolidation.<br />
Make sure to mark docs with ‘Date last reviewed’ so it’s easy for users to know when the documentation was last touched.<br />
Pascale: additional information associated with GO terms, see GitHub ticket?<br />
Add and follow action items at https://github.com/orgs/geneontology/projects/3<br />
===Annotation quality control===<br />
====PAINT update (Huaiyu)====<br />
Huaiyu Action Items Corvallis 2017/06:<br />
Encourage discussion between PAINT curators and other annotators about terms not used for propagation<br />
Report how many annotations per species are used for annotation propagation; could even supply this number for propagation specifically to human genes<br />
Ruth and Huaiyu (others?) will discuss making use of groups that have already annotated specific gene lists to annotate the corresponding PAINT families.<br />
Smooth out the challenge mechanism to make it easier to do make and resolve<br />
the challenges, identify terms that may be problematic and would benefit from consistency exercises and discussion.<br />
Get a list of families where terms have not been propagated (?) - Please check this one for clarity.<br />
(added to github project board) Develop mechanism to trigger review of annotated PAINT families.<br />
===Viral processes update (Pascale)===<br />
Action Items Corvallis 2017/06 Check whether the incorporated changes could affect the host proteins. Document the use cases.<br />
==Community Support==<br />
===Citing GO (Paul T)===<br />
*Web page<br />
*Tool providers: Action Item Corvallis 2017/06: someone to represent GOC and contact GO tool providers to display version information and state this information needs to be included in any subsequent publication. Plus list the GOC paper to reference, as well as the tool provider reference. See: https://github.com/geneontology/go-site/issues/359 and https://github.com/geneontology/go-site/issues/360<br />
===Enrichment (Paul T & Suzi)===<br />
*Web page <br />
*Paul Pavlidis…<br />
*Data Commons work<br />
<br />
===GO_Slims===<br />
====Philosophy (Val, Suzi)====<br />
Creating a biologically useful slim (complete coverage by aspect, biologically useful terms i.e sufficient granularity, avoiding single step process terms (i.e functions), different slims for different purposes: Judy, Mary D (+ Suzi, Val, etc). For overviews, for particular taxa, for a particular area of biology<br />
Specifications for slims from user's perspective (Val: 30 minutes)<br />
====HOW TO MAKE SLIMS (Chris)====<br />
Yaml format for creating slims/types of slims/target organisms<br />
====Use and maintenance of slims (Mary and Suzi)====<br />
Mary: algorithm - 15 minutes<br />
Suzi: GO ribbon<br />
<br />
=Wednesday 4th October=<br />
==Ongoing work==<br />
===AmiGO (Follow up with Seth)===<br />
In general, while several of the AmiGO issues are high-priority, there has been limited bandwidth to tackle them in the context of continuing work on Noctua and the replacement pipeline. Several fixes are queued up and will be available before the upcoming SAB meeting.<br />
In response to: in base_statistics, plotly graph for "Experimental annotation publications by assigner" is confusing https://github.com/geneontology/amigo/issues/429<br />
From Pascale's question: My understanding is that there are essentially no resources for AmiGO right now so any AmiGO issue is low priority. Is this correct?<br />
===The Fate of Simple Processes===<br />
analysis of gene products annotated to phosphorylation but not annotated to a kinase MF term. What did these annotations actually mean? Curators would need to review. Timeline? Deadline? Working group? One possibility would be to use part_of/involved_in relation to phosphorylation for genes also annotated to kinase MF, and causally_upstream_of_or_within for others until curators can re-evaluate.<br />
Other considerations:<br />
Helen: are there many the single-step processes?<br />
Paul: user-oriented approach - is it a useful grouping for our users?<br />
Ruth: we need to think about the meaning beyond just “phosphorylation”<br />
Ruth: what are the consequences of removing “phosphorylation” and what happens to all its children?<br />
Pascale Q: providing that we remove the processes, would it affect the term enrichment analysis?<br />
===BP refactoring===<br />
Defining “Cellular Process” and “Multi-Organism Process” terms<br />
Action item: the comments/examples/notes should be captured, working group to discuss this.<br />
===Proteoforms===<br />
Establish a working group for when and how to use proteoforms in annotation. (Kimberly with Harold and Li)<br />
===Usability issues===<br />
What do users want?<br />
truth (summary/story/model)?<br />
fishing expeditions?<br />
api access?<br />
Who are our users?<br />
geneticists?<br />
clinicians?<br />
computational biologists?<br />
Use cases: https://github.com/geneontology/go-ontology/issues/13606<br />
Perhaps discussion of examples of how the GOC members are engaging with the community and how we can do better in the future (suggested by Helen).<br />
=Wednesday noon-ish Fin=<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Agenda&diff=652842017 Cambridge GOC Meeting Agenda2017-09-27T00:16:28Z<p>Suzi: </p>
<hr />
<div>GOC Meeting, Cambridge , October 2-4, 2017<br />
<br />
=Monday 2nd October=<br />
==Welcome, overview, vision, introductions==<br />
GO PIs<br />
==GO handbook presentation==<br />
*The Gene Ontology and the meaning of biological function (Paul T)<br />
*Translating research data into Gene Ontology annotations (Pascale)<br />
*Gene Ontology - annotation extensions (Ruth)<br />
*GO as a biological systems model (Suzi, or Paul T if Suzi is late)<br />
Pascale will move slides to Google drive<br />
==Ontology Issues and Updates==<br />
===Update on MF refactoring (Pascale or Paul T)===<br />
====GitHub tutorial (Seth & Pascale)====<br />
How GO now uses GitHub for project management and guidelines for contributors<br />
*Where is information relevant to everyone's need<br />
*Groups (Groups.yaml)<br />
*Members<br />
*Etc<br />
<br />
===Qualifiers/Relation issues (Kimberly and Chris)===<br />
====Qualifiers/Relations in GPAD (Kimberly and Chris)====<br />
====Contributes_to guidelines====<br />
++ colocalizes with<br />
====Multiple qualifiers for an annotation (Huaiyu)====<br />
====Use of Qualifiers in Legacy Annotations====<br />
Pascale Proposal: We will apply the general qualifier to all legacy annotations. Each group can provide more specific qualifiers if they have a mechanism to distinguish. Action Items Corvallis 2017/06<br />
Working group to decide what relations should be available in Protein2GO or other tools for manual annotations. Also decide when there are different ways of expressing the same thing, what way we will choose. What should the default gene/gene product relation be for legacy annotations?<br />
Chris to work on reports that may help curators make decisions about what annotations can get more expressive qualifiers.<br />
====Regulates relations====<br />
Adding new qualifiers for the relation between a gene/gene product and a GO term What should the default relation be? How will we handle regulation? Use a relation, involved in regulation of, or use the precomposed regulation term?<br />
Ruth: There are now 3 ways to say the same thing: - involved_in_regulation_of X - involved_in X regulation - involved_in BP regulates(X)<br />
For annotation purposes and for our users we want one.<br />
DOS: Good point. These are semantically identical, but I agree we need to find a way to only have one: by convention for classic GO annotation and by filtering the output of inference for noctua output. Proposal: If a named regulation class exists: involved_in X regulation ...if not: involved_in {some BP} regulates(X) NOTE: If there was an annotation in Noctua such as ‘regulation of’ ‘very specific term’ and there was no term as ‘regulation of very specific term’ the GOC pipeline would create the annotation to the parent term: ‘regulation of less specific term’. Q: Is this implemented ?<br />
==Project updates==<br />
*AGR - report to GOC: PIs<br />
*SynGO meeting report: Paul T<br />
*Report of Reactome-GO connection: David H/Peter D<br />
*Report on transcription work/Noctua templates: Astrid GREEKC consortium=<br />
Evening: Poster session<br />
=Tuesday 3rd October=<br />
==Annotation guidelines and issues (part one)==<br />
===Signaling (Kimberly and David)===<br />
Report from signaling workshop: David /Kimberly<br />
Signaling: First attempt at Annotation consistency 2.0 - Kimberly to report on the approach and the outcome.<br />
Discussion points: Limited participation (self-selected to participate). One recommendation may be to ask all active curators to participate, even at some low level https://github.com/orgs/geneontology/projects/<br />
===Overview of GO annotations/Noctua (Kimberly & Chris)===<br />
====Getting Noctua ready for production====<br />
Kimberly & Seth Blocking issues list: TO BE COMPLETED<br />
Action Item Corvallis 2017/06:<br />
Provide ways for users to recover and digest GO-CAM units (Gene Ontology-based Causal Activity Model). Ideas include rule-based generations of text statements from model, cytoscape view of network described, etc.<br />
ECO codes available for use in Noctua should show how they map up to a classic GO code, and there should be an alert for curators when they are using a code that does NOT map up to a classic code<br />
PRO IDs for use in Noctua<br />
Fix GPAD export from Noctua https://github.com/geneontology/noctua/issues/418<br />
Add a SPARTA workbench https://github.com/geneontology/noctua/issues/465<br />
Action Item Corvallis 2017/06:<br />
Working group discussion of evidence on complex Noctua models (Kimberly?)<br />
====Noctua table view demo====<br />
===CC component annotation guidelines (Kimberly)===<br />
CC component annotation: what does it mean ? Kimberly to do 1 proposal (out of 3 alternatives)<br />
1. where the protein is active 2. two different meanings: enables or the right RO (part:of, ie just found there) 3. part_of (low information value!)<br />
===Author intent & protein domains===<br />
Pascale /Ruth; IDA v IC v New evidence code https://github.com/geneontology/go-annotation/issues/1621 30 minutes discussion about issues; hopefully action items can come out of the discussion<br />
===Centralization of InterPro2GO annotations===<br />
Proposal (follow-up from Geneva 2016): (Paul T)<br />
GO database pulls directly from InterPro2GO for UniProt Reference Proteomes<br />
MOD identifier is used as primary gene identifier<br />
Annotations are given "contributed by" InterPro<br />
MODs pull from GO database, no need to maintain separate InterPro pipelines<br />
==Annotation guidelines and issues (part two)==<br />
===HTP guidelines===<br />
Helen - 15 minutes Report on progress from HTP working group<br />
Draft Guidelines Guidelines draft<br />
Action Items Corvallis 2017<br />
Provision of new evidence code<br />
Implementation & developing guidelines<br />
===Transcription annotations decision tree===<br />
Ruth Action Items Corvallis 2017/06<br />
David OS to create transcription regulator activity (proposed by Paul T)<br />
Proposed changes to decision tree in Corvallis:<br />
Simplified from previous version. Essentially a choice between ‘regulating transcription by RNA polymerase II’ or ‘regulating gene expression’<br />
Annotation 5 = contributes_to sequence-specific DNA binding<br />
David: when people do enrichment, they don’t drop contributes_to (ie., pay attention to qualifiers), so all those proteins will come down as ‘DNA binding’ Action item: replace ‘annotation 5’ with ISS annotation (if DNA binding domain) or contributes to annotation 5 with ISS annotation if no DNA binding domain and domains to suggest coactivator<br />
Annotation 3 = nuclear chromatin<br />
Not everyone comfortable with this (ex., Stacia, David) Shouldn’t it be ‘colocalizes_with’? It was previously agreed that the definition for nuclear chromatin: The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus. Source:PMID:20404130 was to be applied. The proteins here include all associated proteins, not limited to just histones. With this statement the TFs are then contributing to chromatin, rather than binding to chromatin or colocalizing with it.<br />
Decision tree to be put up on GOC website.<br />
Should annotation 4 exist? (Ruth)<br />
<br />
===Annotation Documentation===<br />
Kimberly Action Items Corvallis 2017/06<br />
Continue with the consolidation of all documentation for ontology editing, and remove all old documents.<br />
Review annotation documentation and add to github and readthedocs.<br />
Make sure to mark obsolete pages/doc as such and add a link to the new relevant doc<br />
Solicit annotation documentation from participating groups for consolidation.<br />
Make sure to mark docs with ‘Date last reviewed’ so it’s easy for users to know when the documentation was last touched.<br />
Pascale: additional information associated with GO terms, see GitHub ticket?<br />
Add and follow action items at https://github.com/orgs/geneontology/projects/3<br />
===Annotation quality control===<br />
====PAINT update (Huaiyu)====<br />
Huaiyu Action Items Corvallis 2017/06:<br />
Encourage discussion between PAINT curators and other annotators about terms not used for propagation<br />
Report how many annotations per species are used for annotation propagation; could even supply this number for propagation specifically to human genes<br />
Ruth and Huaiyu (others?) will discuss making use of groups that have already annotated specific gene lists to annotate the corresponding PAINT families.<br />
Smooth out the challenge mechanism to make it easier to do make and resolve<br />
the challenges, identify terms that may be problematic and would benefit from consistency exercises and discussion.<br />
Get a list of families where terms have not been propagated (?) - Please check this one for clarity.<br />
(added to github project board) Develop mechanism to trigger review of annotated PAINT families.<br />
===Viral processes update (Pascale)===<br />
Action Items Corvallis 2017/06 Check whether the incorporated changes could affect the host proteins. Document the use cases.<br />
==Community Support==<br />
===Citing GO (Paul T)===<br />
*Web page<br />
*Tool providers: Action Item Corvallis 2017/06: someone to represent GOC and contact GO tool providers to display version information and state this information needs to be included in any subsequent publication. Plus list the GOC paper to reference, as well as the tool provider reference. See: https://github.com/geneontology/go-site/issues/359 and https://github.com/geneontology/go-site/issues/360<br />
===Enrichment (Paul T & Suzi)===<br />
*Web page <br />
*Paul Pavlidis…<br />
*Data Commons work<br />
<br />
===GO_Slims===<br />
====Philosophy (Val, Suzi)====<br />
Creating a biologically useful slim (complete coverage by aspect, biologically useful terms i.e sufficient granularity, avoiding single step process terms (i.e functions), different slims for different purposes: Judy, Mary D (+ Suzi, Val, etc). For overviews, for particular taxa, for a particular area of biology<br />
Specifications for slims from user's perspective (Val: 30 minutes)<br />
====HOW TO MAKE SLIMS (Chris)====<br />
Yaml format for creating slims/types of slims/target organisms<br />
====Use and maintenance of slims (Mary and Suzi)====<br />
Mary: algorithm - 15 minutes<br />
Suzi: GO ribbon<br />
<br />
=Wednesday 4th October=<br />
==Ongoing work==<br />
===AmiGO (Follow up with Seth)===<br />
In general, while several of the AmiGO issues are high-priority, there has been limited bandwidth to tackle them in the context of continuing work on Noctua and the replacement pipeline. Several fixes are queued up and will be available before the upcoming SAB meeting.<br />
In response to: in base_statistics, plotly graph for "Experimental annotation publications by assigner" is confusing https://github.com/geneontology/amigo/issues/429<br />
From Pascale's question: My understanding is that there are essentially no resources for AmiGO right now so any AmiGO issue is low priority. Is this correct?<br />
===The Fate of Simple Processes===<br />
analysis of gene products annotated to phosphorylation but not annotated to a kinase MF term. What did these annotations actually mean? Curators would need to review. Timeline? Deadline? Working group? One possibility would be to use part_of/involved_in relation to phosphorylation for genes also annotated to kinase MF, and causally_upstream_of_or_within for others until curators can re-evaluate.<br />
Other considerations:<br />
Helen: are there many the single-step processes?<br />
Paul: user-oriented approach - is it a useful grouping for our users?<br />
Ruth: we need to think about the meaning beyond just “phosphorylation”<br />
Ruth: what are the consequences of removing “phosphorylation” and what happens to all its children?<br />
Pascale Q: providing that we remove the processes, would it affect the term enrichment analysis?<br />
===BP refactoring===<br />
Defining “Cellular Process” and “Multi-Organism Process” terms<br />
Action item: the comments/examples/notes should be captured, working group to discuss this.<br />
===Proteoforms===<br />
Establish a working group for when and how to use proteoforms in annotation. (Kimberly with Harold and Li)<br />
===Usability issues===<br />
What do users want?<br />
truth (summary/story/model)?<br />
fishing expeditions?<br />
api access?<br />
Who are our users?<br />
geneticists?<br />
clinicians?<br />
computational biologists?<br />
Use cases: https://github.com/geneontology/go-ontology/issues/13606<br />
Perhaps discussion of examples of how the GOC members are engaging with the community and how we can do better in the future (suggested by Helen).<br />
=Wednesday noon-ish Fin=<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2017_Berkeley_GO_Editors_Workshop_II&diff=647442017 Berkeley GO Editors Workshop II2017-08-08T21:50:16Z<p>Suzi: </p>
<hr />
<div>= Party! (or at least dinner together) =<br />
*Where: [https://goo.gl/maps/UsbWRZLMFMy 2 Biehs Court, Oakland, CA 94618]<br />
*When: Wednesday, August 16 (whenever the meeting closes down and you get over there)<br />
*Ideas for what you'd like to eat? And drink?<br />
<br />
= Agenda (Draft) =<br />
<br />
== Topics ==<br />
<br />
=== Fundamentals ===<br />
* Understanding OWL reasoning. A practical sessions with problem solving exercises, covering:<br />
* Equivalent Class, SubClass; Relations: Characteristics, hierarchy, chains, domain and range; GCIs; advanced querying; explanations.<br />
* Understanding the current GO relation set. (A practical session with problem solving exercises + aim to develop better doc)<br />
* The art of designing robust equivalence axioms & design patterns ( editors would like more guidelines on how to construct these.)<br />
<br />
=== Infrastructure ===<br />
* Design pattern infrastructure<br />
* Pipelines and how they run, both imports and file output. Starting jobs with ROBOT.<br />
* Build failures<br />
* Document the various fail messages and how to correct the issues.<br />
* Ontology work for GO-CAM<br />
** QC-checking property chains and relations that will be used for GPAD generation<br />
** Removing the part_of o regulates chains--- Do we want to instantiate all of the current inferences before removal?<br />
<br />
=== Content ===<br />
* Problematic GitHub tickets/mini Projects<br />
** Pascale: #13731 <br />
* Review the accumulated use cases for GO from ontology ticket #13606. Discuss how we can continue to best meet the needs of our various communities.<br />
<br />
= Logistics =<br />
<br />
== Accommodations ==<br />
<br />
* http://www.fourpointssanfranciscobaybridge.com/<br />
<br />
Getting there:<br />
<br />
* [https://www.google.com/maps/dir/Four+Points+by+Sheraton+San+Francisco+Bay+Bridge,+Powell+Street,+Emeryville,+CA/MacArthur+BART+Station,+40th+Street,+Oakland,+CA/@37.8346259,-122.2866117,15z/am=t/data=!3m1!5s0x80857e0870dbdd83:0x571df460c4d9d3cb!4m14!4m13!1m5!1m1!1s0x80857e44a03ff3e3:0xc502416c1c31eb3a!2m2!1d-122.2939195!2d37.8381923!1m5!1m1!1s0x80857de2a98ae50d:0xc5fce433b2157d9f!2m2!1d-122.267047!2d37.8290643!3e3 shuttle from MacArthur BART]<br />
<br />
Taxis also available from either MacArthur or Ashby<br />
<br />
== Meeting Location ==<br />
<br />
[http://biosciopsatberkeley.lbl.gov/location/aquatic-park-office/ Berkeley Lab, Aquatic Park Offices]<br />
<br />
Lawrence Berkeley National Laboratory (LBNL), Aquatic Park office of Biosciences Operations at Berkeley<br />
Physical address: 717 Potter Street, Berkeley, CA 94710<br />
<br />
Meeting room: room 181<br />
<br />
=== Travel between hotel and meeting ===<br />
<br />
* [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]<br />
* [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 ]<br />
* Taxi/Lyft/Uber<br />
<br />
Aim to be at the lab for 9am<br />
<br />
== Participants ==<br />
<br />
{| {{Prettytable}}<br />
|-<br />
! Name<br />
! Organization<br />
! Comments<br />
|-<br />
| David Hill<br />
| Jackson Laboratory<br />
| <br />
|<br />
|-<br />
|Harold Drabkin<br />
| Jackson Laboratory<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| Caltech<br />
| Arriving SFO Monday, 8/14, 5:03PM<br />
|-<br />
| Pascale Gaudet<br />
| SIB Swiss Institute of Bioinformatics<br />
| <br />
|-<br />
| David Osumi-Sutherland<br />
| EBI<br />
| <br />
|-<br />
| Karen Christie<br />
| Jackson Laboratory<br />
| <br />
|-<br />
| Tanya Berardini<br />
| TAIR/Phoenix<br />
| <br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
|<br />
|-<br />
|}<br />
<br />
LBL:<br />
<br />
* Chris Mungall<br />
* Eric Douglass<br />
* Monica Munoz-Torres<br />
* Seth Carbon<br />
<br />
[[Category:Meetings]]<br />
[[Category:Protege]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Signalling_Workshop&diff=642382017 Cambridge GOC Signalling Workshop2017-07-05T18:08:46Z<p>Suzi: /* Attendees */</p>
<hr />
<div>==Planned Schedule== <br />
<br />
* '''Sunday October 1st''': <br />
:* Meeting will run from 9am to 5:00pm.<br />
<br />
==Agenda==<br />
<br />
[[Signalling Workshop Agenda ]]<br />
<br />
==Minutes and useful links==<br />
<br />
[https://docs.google.com/document/d/1wCzCkPL9ft20ZP5XnTn8IQAcxoFEduaBmzVWKN0hbU0/edit?usp=sharing google minutes] Signaling workshop hopefully this link will enable everyone to edit the doc<br />
<br />
[http://wiki.geneontology.org/index.php/Annotation_Conf._Call_2017-06-27 27June17 annotation call minutes]<br />
<br />
[http://www.geneontology.org/page/go-annotation-conventions#ligand annotation conventions ligand]<br />
<br />
[http://wiki.geneontology.org/index.php/Signaling Ontology signaling project started 2009]<br />
<br />
==Items agreed==<br />
Hopefully no further discussion required:<br />
# All signaling ontology terms should have a defined start and end - work on the ontology is required<br />
# GO-CAM models will be created to present clear views of what is part of a pathway, what regulates the pathway, and what is causally upstream of the pathway<br />
# The Cambridge meeting will focus on a selection of specific pathways<br />
# Annotation conference calls will spend some time (approx 20 min each call) looking at these<br />
<br />
==Pre-meeting github tickets==<br />
<br />
[https://github.com/geneontology/go-annotation/projects/4 signaling project at GitHub]<br />
<br />
==Attendees==<br />
Please add your name to the table and indicate if you intend to participate in the pre-meeting discussions<br />
<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Participate in pre-meeting discussions<br />
! Request funding for Saturday night hotel accommodation near meeting<br />
! Interested in attending Sunday 1st October<br />
<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
| Yes<br />
|-<br />
| Suzanna Lewis<br />
| BBOP (LBNL)<br />
| Yes<br />
| Maybe?<br />
| Yes<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
| Yes<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
| Yes<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Rachael Huntley<br />
| UCL<br />
| Yes<br />
| No<br />
| Yes<br />
|-<br />
| Sandra Orchard<br />
| EBI-IntAct<br />
| <br />
| No<br />
| Yes<br />
|-<br />
| David Hill<br />
| GOC/Jackson Laboratory<br />
| Yes<br />
| <br />
| Yes<br />
|-<br />
| Judy Blake<br />
| GOC/MGI (Jackson)<br />
| <br />
| <br />
| Yes<br />
|-<br />
| Stacia Engel<br />
| SGD<br />
| <br />
| <br />
| Yes<br />
|-<br />
| Kimberly Van Auken<br />
| Wormbase<br />
| Yes<br />
| <br />
| Yes<br />
|-<br />
| Sabrina Toro<br />
| Zfin<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Doug Howe<br />
| Zfin<br />
| <br />
| <br />
| Maybe<br />
|-<br />
| Pascale Gaudet<br />
| GOC/nextprot<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Tanya Berardini/TAIR rep<br />
| TAIR<br />
| Yes<br />
| Maybe<br />
| Yes but may not make it<br />
|-<br />
| Chris Mungall<br />
| LBNL<br />
| To the extent I can<br />
| Yes<br />
| Yes<br />
|}<br />
<br />
<br />
<br />
[[Category: GO Consortium Meetings]] <br />
[[Category: Working Groups]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Signalling_Workshop&diff=642372017 Cambridge GOC Signalling Workshop2017-07-05T18:06:12Z<p>Suzi: /* Attendees */</p>
<hr />
<div>==Planned Schedule== <br />
<br />
* '''Sunday October 1st''': <br />
:* Meeting will run from 9am to 5:00pm.<br />
<br />
==Agenda==<br />
<br />
[[Signalling Workshop Agenda ]]<br />
<br />
==Minutes and useful links==<br />
<br />
[https://docs.google.com/document/d/1wCzCkPL9ft20ZP5XnTn8IQAcxoFEduaBmzVWKN0hbU0/edit?usp=sharing google minutes] Signaling workshop hopefully this link will enable everyone to edit the doc<br />
<br />
[http://wiki.geneontology.org/index.php/Annotation_Conf._Call_2017-06-27 27June17 annotation call minutes]<br />
<br />
[http://www.geneontology.org/page/go-annotation-conventions#ligand annotation conventions ligand]<br />
<br />
[http://wiki.geneontology.org/index.php/Signaling Ontology signaling project started 2009]<br />
<br />
==Items agreed==<br />
Hopefully no further discussion required:<br />
# All signaling ontology terms should have a defined start and end - work on the ontology is required<br />
# GO-CAM models will be created to present clear views of what is part of a pathway, what regulates the pathway, and what is causally upstream of the pathway<br />
# The Cambridge meeting will focus on a selection of specific pathways<br />
# Annotation conference calls will spend some time (approx 20 min each call) looking at these<br />
<br />
==Pre-meeting github tickets==<br />
<br />
[https://github.com/geneontology/go-annotation/projects/4 signaling project at GitHub]<br />
<br />
==Attendees==<br />
Please add your name to the table and indicate if you intend to participate in the pre-meeting discussions<br />
<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Participate in pre-meeting discussions<br />
! Request funding for Saturday night hotel accommodation near meeting<br />
! Interested in attending Sunday 1st October<br />
<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
| Yes<br />
|-<br />
| Suzanna Lewis<br />
| BBOP (LBNL)<br />
| Yes<br />
| No<br />
| Yes<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
| Yes<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
| Yes<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Rachael Huntley<br />
| UCL<br />
| Yes<br />
| No<br />
| Yes<br />
|-<br />
| Sandra Orchard<br />
| EBI-IntAct<br />
| <br />
| No<br />
| Yes<br />
|-<br />
| David Hill<br />
| GOC/Jackson Laboratory<br />
| Yes<br />
| <br />
| Yes<br />
|-<br />
| Judy Blake<br />
| GOC/MGI (Jackson)<br />
| <br />
| <br />
| Yes<br />
|-<br />
| Stacia Engel<br />
| SGD<br />
| <br />
| <br />
| Yes<br />
|-<br />
| Kimberly Van Auken<br />
| Wormbase<br />
| Yes<br />
| <br />
| Yes<br />
|-<br />
| Sabrina Toro<br />
| Zfin<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Doug Howe<br />
| Zfin<br />
| <br />
| <br />
| Maybe<br />
|-<br />
| Pascale Gaudet<br />
| GOC/nextprot<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Tanya Berardini/TAIR rep<br />
| TAIR<br />
| Yes<br />
| Maybe<br />
| Yes but may not make it<br />
|-<br />
| Chris Mungall<br />
| LBNL<br />
| To the extent I can<br />
| Yes<br />
| Yes<br />
|}<br />
<br />
<br />
<br />
[[Category: GO Consortium Meetings]] <br />
[[Category: Working Groups]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Logistics&diff=640262017 Cambridge GOC Meeting Logistics2017-06-02T18:44:29Z<p>Suzi: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Cambridge , October 2-4, 2017=<br />
<br />
* Location: <br />
** [http://www.unicen.cam.ac.uk/ Cambridge University Centre]<br />
<br />
<br />
==Registration==<br />
* Please register at: <br />
<br />
==Consortium dinner ==<br />
<br />
To be added<br />
<br />
==Planned Schedule== <br />
<br />
* '''Monday October 2nd''': <br />
:* Meeting will run from 9am to 5pm. <br />
<br />
*'''Tuesday October 3rd''': <br />
:* Meeting will run from 9am to 5pm.<br />
<br />
*'''Wednesday October 4th''': <br />
:* Meeting will run from 9am to 1pm.<br />
:* Optional break out groups may follow.<br />
<br />
==Meeting Venue and Directions==<br />
* Address Granta Place, Mill Lane, Cambridge, CB2 1RU<br />
** [https://map.cam.ac.uk/University+Centre#52.201128,0.116362,18 Map]<br />
<br />
===Arriving===<br />
* International Flights and travel to Cambridge (to be added)<br />
<br />
===Meeting Dinner===<br />
* Dinner will be on Monday or Tuesday evening<br />
<br />
==Attendees==<br />
Please add your name to the table if you intend to attend the meeting, the dinner, so we can get a headcount estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! Are you planning to attend the GOC dinner<br />
<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|-<br />
| Midori Harris<br />
| PomBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|-<br />
| Paola Roncaglia<br />
| EMBL-EBI<br />
| Yes<br />
| Yes<br />
|-<br />
| Petra Fey<br />
| dictyBase<br />
| Yes<br />
| Yes<br />
|-<br />
| Suzanna Lewis<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|-<br />
| Chris Mungall<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|-<br />
| Seth Carbon<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|-<br />
| Moni Munoz-Torres<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Yes<br />
| Yes<br />
|-<br />
| Rachael Huntley<br />
| UCL<br />
| Yes<br />
| Yes<br />
|-<br />
| Nancy Campbell<br />
| UCL<br />
| Yes<br />
| Yes<br />
|-<br />
| Barbara Kramarz<br />
| UCL<br />
| Yes<br />
| Yes<br />
|-<br />
| Sandra Orchard<br />
| EBI-IntAct<br />
| Yes<br />
| Yes<br />
|-<br />
| Birgit Meldal<br />
| EBI-IntAct<br />
| Yes<br />
| Yes<br />
|-<br />
| David Hill<br />
| GOC/Jackson Laboratory<br />
| Yes<br />
| Yes<br />
|-<br />
| Judy Blake<br />
| GOC/MGI (Jackson)<br />
| Yes<br />
| Yes<br />
|}<br />
<br />
NOT attending:<br />
<br />
Peter D'Eustachio<br />
<br />
==Accommodations==<br />
<br />
<br />
== Local activities ==<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2017_Corvallis_GOC_Meeting_Agenda&diff=639772017 Corvallis GOC Meeting Agenda2017-05-29T23:06:04Z<p>Suzi: /* Noctua and SIGNOR2 (Chris & Paul T) */</p>
<hr />
<div>=Thursday June 1=<br />
==8-9am Breakfast and setup==<br />
==Welcome, schedule and logistics==<br />
*Remote attendees call in via Bluejeans: https://bluejeans.com/993661940<br />
*Introductions<br />
==Overview of Objectives for Upcoming Year==<br />
*Aim1: Provide a comprehensive model of biological knowledge focused on human biology<br />
**Ontology<br />
***MF refactoring completed<br />
***BP refactoring underway, including annotation qualifiers<br />
**Annotation<br />
***N# of pathways annotated according to prioritized list (Paul S to provide)<br />
***Complete the incorporation of new annotation groups/sources: SynGO, SIGNOR<br />
*Aim 2: Provide the “hub” for a broad community of scientists to extend and modify the GO<br />
**Pipeline transition completed (**almost** -- chris)<br />
**Noctua rolled out to all GO curation groups<br />
***Evidence issues resolved in Noctua<br />
**Documentation for ontology request guidelines completed<br />
*Aim 3: Apply biological knowledge obtained in model organisms to human biology<br />
**PAINT annotations going directly into GO database (not via MODs)<br />
**PAINT annotation completed for all families with experimental annotations<br />
**Established alert system for ongoing review of annotated families<br />
*Aim 4: Maintain the integrity and quality of new and existing annotations<br />
**Ongoing annotation consistency exercises (conference calls and github) will now include a write-up (or blog) as case studies to be published on the web site.<br />
**An automated rule-based annotation QA system will be put into place that will be refined/extended based on input from the consistency exercises and PAINT curators<br />
**Establishment of an agreed upon policy for when annotations will be removed (and put this policy into action)<br />
*Am 5: Enable the scientific community to make full use of the GO data resources<br />
**Fixed existing problems with enrichment analysis<br />
**Website?<br />
**Outreach?<br />
<br />
==Infrastructure (Aim 2—Provide a “hub”)==<br />
===Pipeline Migration (Seth & Chris 20 mins) (Goal 2.a)===<br />
===New APIs (Seth & Chris 10 mins)===<br />
===TermGenie replacement* (Dan 20 mins)===<br />
*https://github.com/geneontology/go-ontology/issues/13472<br />
<br />
==12-1pm Lunch==<br />
===Graph Store update (Eric 10 mins)===<br />
===Licensing and GO (Seth 20 mins)===<br />
*Where we currently stand with licensing and possible issues<br />
*What others do with our data<br />
===GO and Related Projects===<br />
*Planteome (Chris, Seth, and Pankaj): How GO and Planteome contribute to one another<br />
*SIGNOR (Chris and Paul T) and SynGO (Ruth?) annotation incorporation (Goal 1.b.ii)<br />
**https://github.com/geneontology/noctua/issues/413<br />
**https://github.com/geneontology/noctua/issues/418<br />
*AGR<br />
**Parts of GO infrastructure being re-used by AGR (Chris)<br />
***db-xrefs.yaml<br />
**Data Formats (Chris)<br />
***BGI and GPI<br />
***Gene association JSON<br />
**Ribbon demo (Suzi)<br />
*Other Projects<br />
**BioCaddie and db-xrefs.yaml (Chris)<br />
**Monarch (Chris)<br />
**Panther?<br />
==3-3:30pm snacks==<br />
===Identifiers (Chris)===<br />
*Replacing double MGI (Chris)<br />
**https://github.com/geneontology/go-site/issues/346<br />
**https://github.com/geneontology/go-site/pull/338 (AGR)<br />
==Ontology (Aim 1—a comprehensive model of biological knowledge)==<br />
===Update on Ontology Editing: David + Chris 20min===<br />
*Design Pattern Updates: David OS + Chris 20 mins<br />
*Ontology Documentation: Moni 10 mins (Goal 2.c)<br />
*Curator notes and propagation<br />
**https://github.com/geneontology/go-ontology/issues/13384<br />
*Proposal: text mining github tickets for ontology terms (Chris, Kimberley)<br />
===MF refactoring (Paul, DavidOS 30 mins) (Goal 1.a.i)===<br />
*Issues: https://github.com/geneontology/molecular_function_refactoring/issues<br />
*Emphasis on practical implications for LEGO curation (templates).<br />
===ECO===<br />
*Mapping to classic GO evidence codes. The official mapping of IMP to ECO is insufficiently broad. Should cover non-genetic perturbations (e.g. pharmacological).<br />
**https://github.com/evidenceontology/evidenceontology/issues/117<br />
*There are lots of things under the ECO code that maps to IDA that are perturbations, not assays e.g.<br />
**https://github.com/evidenceontology/evidenceontology/issues/123#issuecomment-281041854<br />
<br />
===Noctua and SIGNOR2 (Chris & Paul T)===<br />
*https://github.com/geneontology/noctua/issues/413<br />
*Additional document - https://docs.google.com/document/d/1QpfUY_LgeIryMj6EEAE05FXLE_894GalkerBU8dMuVU/edit#<br />
<br />
===Straw man BP refactor Chris (Goal 1.a.ii)===<br />
<br />
==6:00pm onwards mixer==<br />
<br />
=Friday June 2=<br />
==8-9am Breakfast==<br />
==Ontology continued…==<br />
===The fate of simple processes===<br />
*What do we consider a single-step process and what is their future?<br />
**GH ticket about single step processes https://github.com/geneontology/go-ontology/issues/12859<br />
**Is this a single step process? https://github.com/geneontology/go-ontology/issues/13012<br />
*The distinction between cellular processes and processes, do we need it?<br />
**GH ticket about cellular processes: https://github.com/geneontology/go-ontology/issues/12849<br />
<br />
==Annotation (Aims 1, 3, & 4—integrity and quality)==<br />
===Noctua Update (Seth & Chris 10 mins)===<br />
===Noctua rollout to curation groups (Goal 2.b)===<br />
*Current plan:<br />
**SGD (June, July)<br />
**WormBase (August, September)<br />
**Swiss-Prot (October)<br />
**Others? Issues?<br />
===GAFs and GPADs from Noctua models (David and Seth, 30 mins)===<br />
* Where do we stand?<br />
**https://github.com/geneontology/noctua/issues/418<br />
**Challenges with complex models (evidence) (Goal 2.b.i)<br />
**All of PRO IDS should be available in Noctua (ids for human, pombe, etc); can these be loaded from PRO directly (PRO to supply a GPI file).<br />
**GP-CC Should we allow direct GO part_of CC assertion (rather than via GO <-- enabled_by MF occurs_in --> CC). This is more accurate in some cases e.g. for membrane components.<br />
===Use of Qualifiers in Legacy Annotations (needs to come before pipeline??)===<br />
*RO subset for use with GAF/GPAD in qualifier column (Chris/Kimberly/DavidOS)<br />
*New qualifiers for biological processes<br />
*Incorporate expanded list of GP-GO term relations into annotation tools and files<br />
*Regulation and causality<br />
<br />
==12-1pm Lunch==<br />
<br />
===Focused Pathway annotation (Goal 1.b.i)===<br />
===Contacts for Curation Groups (Pascale & David)===<br />
Some annotation groups are now gone (no longer annotating), therefore, can't dispute annotations and have no mechanism to update or change them, if needed. We need to have a mechanism for tracking the status better github go-annotation tracker for annotation disputes can we have some GOC superuser status in Protein2GO that allows GO curators to update annotations Some groups like JCVI, PAMGO no longer annotate - can GOC take control of these experimental annotations?<br />
===PAINT update (Chris, Karen, Suzi, Pascale and Huaiyu)===<br />
*Analysis of the PAINT annotations (Karen and Huaiyu).<br />
*Plan for production services/pipeline for PAINT annotations (Chris)<br />
*Reverse flow (Goal 3.a)<br />
*Completion of all families with exp. evidence (Goal 3.b)<br />
*Initial implementation of alert system: what are the requirements? (Goal 3.c)<br />
===Annotation QC issues===<br />
====Consistency exercises (written case studies - Goal 4.a)====<br />
<br />
====GO Rules System (Eric) (Goal 4.b)====<br />
<br />
====QA from PAINT - automated rule-based annotation QA (Pascale) (Goal 4.b)====<br />
<br />
====How do annotation groups handle obsoleting/deprecating GO annotations? (led by someone from SGD or Val?) (Goal 4.c)====<br />
<br />
====Consistent use of the type field in GAFs and GPAD (Chris)====<br />
*E.g. https://github.com/geneontology/go-annotation/issues/1554<br />
<br />
==3:30pm Networking and Recreational outing==<br />
<br />
==6:00pm — Dinner==<br />
<br />
==Saturday June 3==<br />
==8-9am Breakfast==<br />
==Annotation continued…==<br />
===Annotation QC issues continued…===<br />
====HTP papers (Helen, Pascale & Sylvain)====<br />
*See notes /list of papers:<br />
<br />
====Transcription-Factor decision tree (Ruth - 20 mins)====<br />
*https://github.com/geneontology/go-annotation/issues/1463<br />
<br />
====Modified protein binding (Pascale & Sylvain)====<br />
*https://github.com/geneontology/go-ontology/issues/12787<br />
===Annotation of Viral Processes===<br />
*13214<br />
*Taxon restriction?<br />
*Annotation of host proteins involved in, or co-opted for, viral reproduction<br />
*Transcription, translation of viral genome<br />
*DOS proposal for multi-organism annotation (reviving old proposal) - poss allowing non-canonical function to be separable<br />
<br />
==12-1pm Lunch==<br />
==Community relations (Aim 5—enabling the community)==<br />
===Enrichment Analysis (Val & Seth) (Goal 5.a)===<br />
*by default have the enrichment tool run directly on the GO annotation dataset<br />
*by default enable loading a background<br />
*currently missing a substantial number of annotations (e.g. fission yeast)<br />
*Via ontobio python library (Chris)<br />
**Example jupyter notebook: https://github.com/biolink/ontobio/blob/master/notebooks/Phenotype_Enrichment.ipynb<br />
===Website? (Goal 5.b)===<br />
===Outreach? (Goal 5.c)===<br />
<br />
==3-5:30-pm Networking and Recreation==<br />
<br />
==5:30pm POSTERS and mixer==<br />
<br />
= Attendees =<br />
<br />
Please add your name to the table if you intend to attend the meeting, the dinner, the Noctua workshop, and the Reactome workshop so we can get a headcount estimate. Thank you!<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! Are you planning to attend the GOC dinner<br />
! Are you bringing a poster? how many?<br />
! Are you planning to attend the Noctua workshop the day after the meeting, Sunday, June 4th?<br />
! Are you planning to attend the Reactome workshop on Monday, June 5th?<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase<br />
| Y<br />
| Y<br />
|<br />
| N<br />
| N<br />
|-<br />
| Helen Attrill<br />
| FlyBase<br />
| Y<br />
| Y<br />
|<br />
| N<br />
| N<br />
|-<br />
| Judy Blake<br />
| MGI<br />
| Y<br />
| Y<br />
| Y-1<br />
| N<br />
| N<br />
|-<br />
| Seth Carbon<br />
| Berkeley/LBL<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Mike Cherry<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Laurel Cooper<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Stacia Engel<br />
| SGD<br />
| Y<br />
| N<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Priyanka Garg<br />
| <br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Parul Gupta<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Tom Hayman<br />
| RGD<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Emily Heald<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| David Hill<br />
| MGI<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Doug Howe<br />
| ZFIN<br />
| Y<br />
| maybe<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Ceri Van Slyke<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Sridhar Ramachandran<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| David Fashena<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Leyla Ruzica<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Pankaj Jaiswal<br />
| Reactome/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Stan Laulederkind<br />
| RGD<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Suzi Lewis<br />
| Berkeley/LBL<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Y<br />
| Y<br />
| Y-3<br />
| Y<br />
| Y<br />
|-<br />
| Austin Meier<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Moni Munoz-Torres<br />
| Berkeley/LBL<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| N<br />
|-<br />
| Sushma Naithani<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Darren Natale<br />
| PRO<br />
| Y<br />
| <br />
|<br />
| N<br />
| N<br />
|-<br />
| Sabrina Toro<br />
| Zfin<br />
| Y<br />
| maybe<br />
| N<br />
| Y<br />
| Y<br />
|-<br />
| Kimberly Van Auken<br />
| WB<br />
| Y<br />
| Y<br />
| Y (1)<br />
| Y<br />
| Y<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Peter D'Eustachio<br />
| Reactome<br />
| Y<br />
| Y<br />
| N?<br />
| Y<br />
| Y<br />
|-<br />
| Maria Martin<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| N<br />
| N<br />
|-<br />
| Tony Sawford<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Alice Shypitsyna<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| Y<br />
| ?<br />
|-<br />
| George Georghiou<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| Y<br />
| Y<br />
|-<br />
| Pascale Gaudet<br />
| GOC/SIB Swiss Institute of Bioinformtaics<br />
| Y<br />
| Y<br />
| ?<br />
| Y<br />
| Y<br />
|-<br />
|-<br />
| David OS<br />
| EBI<br />
| Y<br />
| Y<br />
| N<br />
| AM<br />
| N<br />
|-<br />
| Malcolm Fisher<br />
| Xenbase<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| Y<br />
|-<br />
|}<br />
<br />
*NOT ATTENDING:<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2017_Corvallis_GOC_Meeting_Agenda&diff=639762017 Corvallis GOC Meeting Agenda2017-05-29T23:05:08Z<p>Suzi: /* ECO */</p>
<hr />
<div>=Thursday June 1=<br />
==8-9am Breakfast and setup==<br />
==Welcome, schedule and logistics==<br />
*Remote attendees call in via Bluejeans: https://bluejeans.com/993661940<br />
*Introductions<br />
==Overview of Objectives for Upcoming Year==<br />
*Aim1: Provide a comprehensive model of biological knowledge focused on human biology<br />
**Ontology<br />
***MF refactoring completed<br />
***BP refactoring underway, including annotation qualifiers<br />
**Annotation<br />
***N# of pathways annotated according to prioritized list (Paul S to provide)<br />
***Complete the incorporation of new annotation groups/sources: SynGO, SIGNOR<br />
*Aim 2: Provide the “hub” for a broad community of scientists to extend and modify the GO<br />
**Pipeline transition completed (**almost** -- chris)<br />
**Noctua rolled out to all GO curation groups<br />
***Evidence issues resolved in Noctua<br />
**Documentation for ontology request guidelines completed<br />
*Aim 3: Apply biological knowledge obtained in model organisms to human biology<br />
**PAINT annotations going directly into GO database (not via MODs)<br />
**PAINT annotation completed for all families with experimental annotations<br />
**Established alert system for ongoing review of annotated families<br />
*Aim 4: Maintain the integrity and quality of new and existing annotations<br />
**Ongoing annotation consistency exercises (conference calls and github) will now include a write-up (or blog) as case studies to be published on the web site.<br />
**An automated rule-based annotation QA system will be put into place that will be refined/extended based on input from the consistency exercises and PAINT curators<br />
**Establishment of an agreed upon policy for when annotations will be removed (and put this policy into action)<br />
*Am 5: Enable the scientific community to make full use of the GO data resources<br />
**Fixed existing problems with enrichment analysis<br />
**Website?<br />
**Outreach?<br />
<br />
==Infrastructure (Aim 2—Provide a “hub”)==<br />
===Pipeline Migration (Seth & Chris 20 mins) (Goal 2.a)===<br />
===New APIs (Seth & Chris 10 mins)===<br />
===TermGenie replacement* (Dan 20 mins)===<br />
*https://github.com/geneontology/go-ontology/issues/13472<br />
<br />
==12-1pm Lunch==<br />
===Graph Store update (Eric 10 mins)===<br />
===Licensing and GO (Seth 20 mins)===<br />
*Where we currently stand with licensing and possible issues<br />
*What others do with our data<br />
===GO and Related Projects===<br />
*Planteome (Chris, Seth, and Pankaj): How GO and Planteome contribute to one another<br />
*SIGNOR (Chris and Paul T) and SynGO (Ruth?) annotation incorporation (Goal 1.b.ii)<br />
**https://github.com/geneontology/noctua/issues/413<br />
**https://github.com/geneontology/noctua/issues/418<br />
*AGR<br />
**Parts of GO infrastructure being re-used by AGR (Chris)<br />
***db-xrefs.yaml<br />
**Data Formats (Chris)<br />
***BGI and GPI<br />
***Gene association JSON<br />
**Ribbon demo (Suzi)<br />
*Other Projects<br />
**BioCaddie and db-xrefs.yaml (Chris)<br />
**Monarch (Chris)<br />
**Panther?<br />
==3-3:30pm snacks==<br />
===Identifiers (Chris)===<br />
*Replacing double MGI (Chris)<br />
**https://github.com/geneontology/go-site/issues/346<br />
**https://github.com/geneontology/go-site/pull/338 (AGR)<br />
==Ontology (Aim 1—a comprehensive model of biological knowledge)==<br />
===Update on Ontology Editing: David + Chris 20min===<br />
*Design Pattern Updates: David OS + Chris 20 mins<br />
*Ontology Documentation: Moni 10 mins (Goal 2.c)<br />
*Curator notes and propagation<br />
**https://github.com/geneontology/go-ontology/issues/13384<br />
*Proposal: text mining github tickets for ontology terms (Chris, Kimberley)<br />
===MF refactoring (Paul, DavidOS 30 mins) (Goal 1.a.i)===<br />
*Issues: https://github.com/geneontology/molecular_function_refactoring/issues<br />
*Emphasis on practical implications for LEGO curation (templates).<br />
===ECO===<br />
*Mapping to classic GO evidence codes. The official mapping of IMP to ECO is insufficiently broad. Should cover non-genetic perturbations (e.g. pharmacological).<br />
**https://github.com/evidenceontology/evidenceontology/issues/117<br />
*There are lots of things under the ECO code that maps to IDA that are perturbations, not assays e.g.<br />
**https://github.com/evidenceontology/evidenceontology/issues/123#issuecomment-281041854<br />
<br />
===Noctua and SIGNOR2 (Chris & Paul T)===<br />
*https://github.com/geneontology/noctua/issues/413<br />
**Additional document - https://docs.google.com/document/d/1QpfUY_LgeIryMj6EEAE05FXLE_894GalkerBU8dMuVU/edit#<br />
===Straw man BP refactor Chris (Goal 1.a.ii)===<br />
<br />
==6:00pm onwards mixer==<br />
<br />
=Friday June 2=<br />
==8-9am Breakfast==<br />
==Ontology continued…==<br />
===The fate of simple processes===<br />
*What do we consider a single-step process and what is their future?<br />
**GH ticket about single step processes https://github.com/geneontology/go-ontology/issues/12859<br />
**Is this a single step process? https://github.com/geneontology/go-ontology/issues/13012<br />
*The distinction between cellular processes and processes, do we need it?<br />
**GH ticket about cellular processes: https://github.com/geneontology/go-ontology/issues/12849<br />
<br />
==Annotation (Aims 1, 3, & 4—integrity and quality)==<br />
===Noctua Update (Seth & Chris 10 mins)===<br />
===Noctua rollout to curation groups (Goal 2.b)===<br />
*Current plan:<br />
**SGD (June, July)<br />
**WormBase (August, September)<br />
**Swiss-Prot (October)<br />
**Others? Issues?<br />
===GAFs and GPADs from Noctua models (David and Seth, 30 mins)===<br />
* Where do we stand?<br />
**https://github.com/geneontology/noctua/issues/418<br />
**Challenges with complex models (evidence) (Goal 2.b.i)<br />
**All of PRO IDS should be available in Noctua (ids for human, pombe, etc); can these be loaded from PRO directly (PRO to supply a GPI file).<br />
**GP-CC Should we allow direct GO part_of CC assertion (rather than via GO <-- enabled_by MF occurs_in --> CC). This is more accurate in some cases e.g. for membrane components.<br />
===Use of Qualifiers in Legacy Annotations (needs to come before pipeline??)===<br />
*RO subset for use with GAF/GPAD in qualifier column (Chris/Kimberly/DavidOS)<br />
*New qualifiers for biological processes<br />
*Incorporate expanded list of GP-GO term relations into annotation tools and files<br />
*Regulation and causality<br />
<br />
==12-1pm Lunch==<br />
<br />
===Focused Pathway annotation (Goal 1.b.i)===<br />
===Contacts for Curation Groups (Pascale & David)===<br />
Some annotation groups are now gone (no longer annotating), therefore, can't dispute annotations and have no mechanism to update or change them, if needed. We need to have a mechanism for tracking the status better github go-annotation tracker for annotation disputes can we have some GOC superuser status in Protein2GO that allows GO curators to update annotations Some groups like JCVI, PAMGO no longer annotate - can GOC take control of these experimental annotations?<br />
===PAINT update (Chris, Karen, Suzi, Pascale and Huaiyu)===<br />
*Analysis of the PAINT annotations (Karen and Huaiyu).<br />
*Plan for production services/pipeline for PAINT annotations (Chris)<br />
*Reverse flow (Goal 3.a)<br />
*Completion of all families with exp. evidence (Goal 3.b)<br />
*Initial implementation of alert system: what are the requirements? (Goal 3.c)<br />
===Annotation QC issues===<br />
====Consistency exercises (written case studies - Goal 4.a)====<br />
<br />
====GO Rules System (Eric) (Goal 4.b)====<br />
<br />
====QA from PAINT - automated rule-based annotation QA (Pascale) (Goal 4.b)====<br />
<br />
====How do annotation groups handle obsoleting/deprecating GO annotations? (led by someone from SGD or Val?) (Goal 4.c)====<br />
<br />
====Consistent use of the type field in GAFs and GPAD (Chris)====<br />
*E.g. https://github.com/geneontology/go-annotation/issues/1554<br />
<br />
==3:30pm Networking and Recreational outing==<br />
<br />
==6:00pm — Dinner==<br />
<br />
==Saturday June 3==<br />
==8-9am Breakfast==<br />
==Annotation continued…==<br />
===Annotation QC issues continued…===<br />
====HTP papers (Helen, Pascale & Sylvain)====<br />
*See notes /list of papers:<br />
<br />
====Transcription-Factor decision tree (Ruth - 20 mins)====<br />
*https://github.com/geneontology/go-annotation/issues/1463<br />
<br />
====Modified protein binding (Pascale & Sylvain)====<br />
*https://github.com/geneontology/go-ontology/issues/12787<br />
===Annotation of Viral Processes===<br />
*13214<br />
*Taxon restriction?<br />
*Annotation of host proteins involved in, or co-opted for, viral reproduction<br />
*Transcription, translation of viral genome<br />
*DOS proposal for multi-organism annotation (reviving old proposal) - poss allowing non-canonical function to be separable<br />
<br />
==12-1pm Lunch==<br />
==Community relations (Aim 5—enabling the community)==<br />
===Enrichment Analysis (Val & Seth) (Goal 5.a)===<br />
*by default have the enrichment tool run directly on the GO annotation dataset<br />
*by default enable loading a background<br />
*currently missing a substantial number of annotations (e.g. fission yeast)<br />
*Via ontobio python library (Chris)<br />
**Example jupyter notebook: https://github.com/biolink/ontobio/blob/master/notebooks/Phenotype_Enrichment.ipynb<br />
===Website? (Goal 5.b)===<br />
===Outreach? (Goal 5.c)===<br />
<br />
==3-5:30-pm Networking and Recreation==<br />
<br />
==5:30pm POSTERS and mixer==<br />
<br />
= Attendees =<br />
<br />
Please add your name to the table if you intend to attend the meeting, the dinner, the Noctua workshop, and the Reactome workshop so we can get a headcount estimate. Thank you!<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! Are you planning to attend the GOC dinner<br />
! Are you bringing a poster? how many?<br />
! Are you planning to attend the Noctua workshop the day after the meeting, Sunday, June 4th?<br />
! Are you planning to attend the Reactome workshop on Monday, June 5th?<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase<br />
| Y<br />
| Y<br />
|<br />
| N<br />
| N<br />
|-<br />
| Helen Attrill<br />
| FlyBase<br />
| Y<br />
| Y<br />
|<br />
| N<br />
| N<br />
|-<br />
| Judy Blake<br />
| MGI<br />
| Y<br />
| Y<br />
| Y-1<br />
| N<br />
| N<br />
|-<br />
| Seth Carbon<br />
| Berkeley/LBL<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Mike Cherry<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Laurel Cooper<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Stacia Engel<br />
| SGD<br />
| Y<br />
| N<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Priyanka Garg<br />
| <br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Parul Gupta<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Tom Hayman<br />
| RGD<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Emily Heald<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| David Hill<br />
| MGI<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Doug Howe<br />
| ZFIN<br />
| Y<br />
| maybe<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Ceri Van Slyke<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Sridhar Ramachandran<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| David Fashena<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Leyla Ruzica<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Pankaj Jaiswal<br />
| Reactome/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Stan Laulederkind<br />
| RGD<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Suzi Lewis<br />
| Berkeley/LBL<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Y<br />
| Y<br />
| Y-3<br />
| Y<br />
| Y<br />
|-<br />
| Austin Meier<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Moni Munoz-Torres<br />
| Berkeley/LBL<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| N<br />
|-<br />
| Sushma Naithani<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Darren Natale<br />
| PRO<br />
| Y<br />
| <br />
|<br />
| N<br />
| N<br />
|-<br />
| Sabrina Toro<br />
| Zfin<br />
| Y<br />
| maybe<br />
| N<br />
| Y<br />
| Y<br />
|-<br />
| Kimberly Van Auken<br />
| WB<br />
| Y<br />
| Y<br />
| Y (1)<br />
| Y<br />
| Y<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Peter D'Eustachio<br />
| Reactome<br />
| Y<br />
| Y<br />
| N?<br />
| Y<br />
| Y<br />
|-<br />
| Maria Martin<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| N<br />
| N<br />
|-<br />
| Tony Sawford<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Alice Shypitsyna<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| Y<br />
| ?<br />
|-<br />
| George Georghiou<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| Y<br />
| Y<br />
|-<br />
| Pascale Gaudet<br />
| GOC/SIB Swiss Institute of Bioinformtaics<br />
| Y<br />
| Y<br />
| ?<br />
| Y<br />
| Y<br />
|-<br />
|-<br />
| David OS<br />
| EBI<br />
| Y<br />
| Y<br />
| N<br />
| AM<br />
| N<br />
|-<br />
| Malcolm Fisher<br />
| Xenbase<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| Y<br />
|-<br />
|}<br />
<br />
*NOT ATTENDING:<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2017_Corvallis_GOC_Meeting_Agenda&diff=639752017 Corvallis GOC Meeting Agenda2017-05-29T23:04:45Z<p>Suzi: /* ECO */</p>
<hr />
<div>=Thursday June 1=<br />
==8-9am Breakfast and setup==<br />
==Welcome, schedule and logistics==<br />
*Remote attendees call in via Bluejeans: https://bluejeans.com/993661940<br />
*Introductions<br />
==Overview of Objectives for Upcoming Year==<br />
*Aim1: Provide a comprehensive model of biological knowledge focused on human biology<br />
**Ontology<br />
***MF refactoring completed<br />
***BP refactoring underway, including annotation qualifiers<br />
**Annotation<br />
***N# of pathways annotated according to prioritized list (Paul S to provide)<br />
***Complete the incorporation of new annotation groups/sources: SynGO, SIGNOR<br />
*Aim 2: Provide the “hub” for a broad community of scientists to extend and modify the GO<br />
**Pipeline transition completed (**almost** -- chris)<br />
**Noctua rolled out to all GO curation groups<br />
***Evidence issues resolved in Noctua<br />
**Documentation for ontology request guidelines completed<br />
*Aim 3: Apply biological knowledge obtained in model organisms to human biology<br />
**PAINT annotations going directly into GO database (not via MODs)<br />
**PAINT annotation completed for all families with experimental annotations<br />
**Established alert system for ongoing review of annotated families<br />
*Aim 4: Maintain the integrity and quality of new and existing annotations<br />
**Ongoing annotation consistency exercises (conference calls and github) will now include a write-up (or blog) as case studies to be published on the web site.<br />
**An automated rule-based annotation QA system will be put into place that will be refined/extended based on input from the consistency exercises and PAINT curators<br />
**Establishment of an agreed upon policy for when annotations will be removed (and put this policy into action)<br />
*Am 5: Enable the scientific community to make full use of the GO data resources<br />
**Fixed existing problems with enrichment analysis<br />
**Website?<br />
**Outreach?<br />
<br />
==Infrastructure (Aim 2—Provide a “hub”)==<br />
===Pipeline Migration (Seth & Chris 20 mins) (Goal 2.a)===<br />
===New APIs (Seth & Chris 10 mins)===<br />
===TermGenie replacement* (Dan 20 mins)===<br />
*https://github.com/geneontology/go-ontology/issues/13472<br />
<br />
==12-1pm Lunch==<br />
===Graph Store update (Eric 10 mins)===<br />
===Licensing and GO (Seth 20 mins)===<br />
*Where we currently stand with licensing and possible issues<br />
*What others do with our data<br />
===GO and Related Projects===<br />
*Planteome (Chris, Seth, and Pankaj): How GO and Planteome contribute to one another<br />
*SIGNOR (Chris and Paul T) and SynGO (Ruth?) annotation incorporation (Goal 1.b.ii)<br />
**https://github.com/geneontology/noctua/issues/413<br />
**https://github.com/geneontology/noctua/issues/418<br />
*AGR<br />
**Parts of GO infrastructure being re-used by AGR (Chris)<br />
***db-xrefs.yaml<br />
**Data Formats (Chris)<br />
***BGI and GPI<br />
***Gene association JSON<br />
**Ribbon demo (Suzi)<br />
*Other Projects<br />
**BioCaddie and db-xrefs.yaml (Chris)<br />
**Monarch (Chris)<br />
**Panther?<br />
==3-3:30pm snacks==<br />
===Identifiers (Chris)===<br />
*Replacing double MGI (Chris)<br />
**https://github.com/geneontology/go-site/issues/346<br />
**https://github.com/geneontology/go-site/pull/338 (AGR)<br />
==Ontology (Aim 1—a comprehensive model of biological knowledge)==<br />
===Update on Ontology Editing: David + Chris 20min===<br />
*Design Pattern Updates: David OS + Chris 20 mins<br />
*Ontology Documentation: Moni 10 mins (Goal 2.c)<br />
*Curator notes and propagation<br />
**https://github.com/geneontology/go-ontology/issues/13384<br />
*Proposal: text mining github tickets for ontology terms (Chris, Kimberley)<br />
===MF refactoring (Paul, DavidOS 30 mins) (Goal 1.a.i)===<br />
*Issues: https://github.com/geneontology/molecular_function_refactoring/issues<br />
*Emphasis on practical implications for LEGO curation (templates).<br />
===ECO===<br />
*Mapping to classic GO evidence codes. The official mapping of IMP to ECO is insufficiently broad. Should cover non-genetic perturbations (e.g. pharmacological).<br />
**https://github.com/evidenceontology/evidenceontology/issues/117<br />
*There are lots of things under the ECO code that maps to IDA that are perturbations, not assays e.g. **https://github.com/evidenceontology/evidenceontology/issues/123#issuecomment-281041854<br />
<br />
===Noctua and SIGNOR2 (Chris & Paul T)===<br />
*https://github.com/geneontology/noctua/issues/413<br />
**Additional document - https://docs.google.com/document/d/1QpfUY_LgeIryMj6EEAE05FXLE_894GalkerBU8dMuVU/edit#<br />
===Straw man BP refactor Chris (Goal 1.a.ii)===<br />
<br />
==6:00pm onwards mixer==<br />
<br />
=Friday June 2=<br />
==8-9am Breakfast==<br />
==Ontology continued…==<br />
===The fate of simple processes===<br />
*What do we consider a single-step process and what is their future?<br />
**GH ticket about single step processes https://github.com/geneontology/go-ontology/issues/12859<br />
**Is this a single step process? https://github.com/geneontology/go-ontology/issues/13012<br />
*The distinction between cellular processes and processes, do we need it?<br />
**GH ticket about cellular processes: https://github.com/geneontology/go-ontology/issues/12849<br />
<br />
==Annotation (Aims 1, 3, & 4—integrity and quality)==<br />
===Noctua Update (Seth & Chris 10 mins)===<br />
===Noctua rollout to curation groups (Goal 2.b)===<br />
*Current plan:<br />
**SGD (June, July)<br />
**WormBase (August, September)<br />
**Swiss-Prot (October)<br />
**Others? Issues?<br />
===GAFs and GPADs from Noctua models (David and Seth, 30 mins)===<br />
* Where do we stand?<br />
**https://github.com/geneontology/noctua/issues/418<br />
**Challenges with complex models (evidence) (Goal 2.b.i)<br />
**All of PRO IDS should be available in Noctua (ids for human, pombe, etc); can these be loaded from PRO directly (PRO to supply a GPI file).<br />
**GP-CC Should we allow direct GO part_of CC assertion (rather than via GO <-- enabled_by MF occurs_in --> CC). This is more accurate in some cases e.g. for membrane components.<br />
===Use of Qualifiers in Legacy Annotations (needs to come before pipeline??)===<br />
*RO subset for use with GAF/GPAD in qualifier column (Chris/Kimberly/DavidOS)<br />
*New qualifiers for biological processes<br />
*Incorporate expanded list of GP-GO term relations into annotation tools and files<br />
*Regulation and causality<br />
<br />
==12-1pm Lunch==<br />
<br />
===Focused Pathway annotation (Goal 1.b.i)===<br />
===Contacts for Curation Groups (Pascale & David)===<br />
Some annotation groups are now gone (no longer annotating), therefore, can't dispute annotations and have no mechanism to update or change them, if needed. We need to have a mechanism for tracking the status better github go-annotation tracker for annotation disputes can we have some GOC superuser status in Protein2GO that allows GO curators to update annotations Some groups like JCVI, PAMGO no longer annotate - can GOC take control of these experimental annotations?<br />
===PAINT update (Chris, Karen, Suzi, Pascale and Huaiyu)===<br />
*Analysis of the PAINT annotations (Karen and Huaiyu).<br />
*Plan for production services/pipeline for PAINT annotations (Chris)<br />
*Reverse flow (Goal 3.a)<br />
*Completion of all families with exp. evidence (Goal 3.b)<br />
*Initial implementation of alert system: what are the requirements? (Goal 3.c)<br />
===Annotation QC issues===<br />
====Consistency exercises (written case studies - Goal 4.a)====<br />
<br />
====GO Rules System (Eric) (Goal 4.b)====<br />
<br />
====QA from PAINT - automated rule-based annotation QA (Pascale) (Goal 4.b)====<br />
<br />
====How do annotation groups handle obsoleting/deprecating GO annotations? (led by someone from SGD or Val?) (Goal 4.c)====<br />
<br />
====Consistent use of the type field in GAFs and GPAD (Chris)====<br />
*E.g. https://github.com/geneontology/go-annotation/issues/1554<br />
<br />
==3:30pm Networking and Recreational outing==<br />
<br />
==6:00pm — Dinner==<br />
<br />
==Saturday June 3==<br />
==8-9am Breakfast==<br />
==Annotation continued…==<br />
===Annotation QC issues continued…===<br />
====HTP papers (Helen, Pascale & Sylvain)====<br />
*See notes /list of papers:<br />
<br />
====Transcription-Factor decision tree (Ruth - 20 mins)====<br />
*https://github.com/geneontology/go-annotation/issues/1463<br />
<br />
====Modified protein binding (Pascale & Sylvain)====<br />
*https://github.com/geneontology/go-ontology/issues/12787<br />
===Annotation of Viral Processes===<br />
*13214<br />
*Taxon restriction?<br />
*Annotation of host proteins involved in, or co-opted for, viral reproduction<br />
*Transcription, translation of viral genome<br />
*DOS proposal for multi-organism annotation (reviving old proposal) - poss allowing non-canonical function to be separable<br />
<br />
==12-1pm Lunch==<br />
==Community relations (Aim 5—enabling the community)==<br />
===Enrichment Analysis (Val & Seth) (Goal 5.a)===<br />
*by default have the enrichment tool run directly on the GO annotation dataset<br />
*by default enable loading a background<br />
*currently missing a substantial number of annotations (e.g. fission yeast)<br />
*Via ontobio python library (Chris)<br />
**Example jupyter notebook: https://github.com/biolink/ontobio/blob/master/notebooks/Phenotype_Enrichment.ipynb<br />
===Website? (Goal 5.b)===<br />
===Outreach? (Goal 5.c)===<br />
<br />
==3-5:30-pm Networking and Recreation==<br />
<br />
==5:30pm POSTERS and mixer==<br />
<br />
= Attendees =<br />
<br />
Please add your name to the table if you intend to attend the meeting, the dinner, the Noctua workshop, and the Reactome workshop so we can get a headcount estimate. Thank you!<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! Are you planning to attend the GOC dinner<br />
! Are you bringing a poster? how many?<br />
! Are you planning to attend the Noctua workshop the day after the meeting, Sunday, June 4th?<br />
! Are you planning to attend the Reactome workshop on Monday, June 5th?<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase<br />
| Y<br />
| Y<br />
|<br />
| N<br />
| N<br />
|-<br />
| Helen Attrill<br />
| FlyBase<br />
| Y<br />
| Y<br />
|<br />
| N<br />
| N<br />
|-<br />
| Judy Blake<br />
| MGI<br />
| Y<br />
| Y<br />
| Y-1<br />
| N<br />
| N<br />
|-<br />
| Seth Carbon<br />
| Berkeley/LBL<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Mike Cherry<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Laurel Cooper<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Stacia Engel<br />
| SGD<br />
| Y<br />
| N<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Priyanka Garg<br />
| <br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Parul Gupta<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Tom Hayman<br />
| RGD<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Emily Heald<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| David Hill<br />
| MGI<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Doug Howe<br />
| ZFIN<br />
| Y<br />
| maybe<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Ceri Van Slyke<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Sridhar Ramachandran<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| David Fashena<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Leyla Ruzica<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Pankaj Jaiswal<br />
| Reactome/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Stan Laulederkind<br />
| RGD<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Suzi Lewis<br />
| Berkeley/LBL<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Y<br />
| Y<br />
| Y-3<br />
| Y<br />
| Y<br />
|-<br />
| Austin Meier<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Moni Munoz-Torres<br />
| Berkeley/LBL<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| N<br />
|-<br />
| Sushma Naithani<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Darren Natale<br />
| PRO<br />
| Y<br />
| <br />
|<br />
| N<br />
| N<br />
|-<br />
| Sabrina Toro<br />
| Zfin<br />
| Y<br />
| maybe<br />
| N<br />
| Y<br />
| Y<br />
|-<br />
| Kimberly Van Auken<br />
| WB<br />
| Y<br />
| Y<br />
| Y (1)<br />
| Y<br />
| Y<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Peter D'Eustachio<br />
| Reactome<br />
| Y<br />
| Y<br />
| N?<br />
| Y<br />
| Y<br />
|-<br />
| Maria Martin<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| N<br />
| N<br />
|-<br />
| Tony Sawford<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Alice Shypitsyna<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| Y<br />
| ?<br />
|-<br />
| George Georghiou<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| Y<br />
| Y<br />
|-<br />
| Pascale Gaudet<br />
| GOC/SIB Swiss Institute of Bioinformtaics<br />
| Y<br />
| Y<br />
| ?<br />
| Y<br />
| Y<br />
|-<br />
|-<br />
| David OS<br />
| EBI<br />
| Y<br />
| Y<br />
| N<br />
| AM<br />
| N<br />
|-<br />
| Malcolm Fisher<br />
| Xenbase<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| Y<br />
|-<br />
|}<br />
<br />
*NOT ATTENDING:<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzihttps://wiki.geneontology.org/index.php?title=2017_Corvallis_GOC_Meeting_Agenda&diff=639742017 Corvallis GOC Meeting Agenda2017-05-29T23:04:19Z<p>Suzi: /* Ontology (Aim 1—a comprehensive model of biological knowledge) */</p>
<hr />
<div>=Thursday June 1=<br />
==8-9am Breakfast and setup==<br />
==Welcome, schedule and logistics==<br />
*Remote attendees call in via Bluejeans: https://bluejeans.com/993661940<br />
*Introductions<br />
==Overview of Objectives for Upcoming Year==<br />
*Aim1: Provide a comprehensive model of biological knowledge focused on human biology<br />
**Ontology<br />
***MF refactoring completed<br />
***BP refactoring underway, including annotation qualifiers<br />
**Annotation<br />
***N# of pathways annotated according to prioritized list (Paul S to provide)<br />
***Complete the incorporation of new annotation groups/sources: SynGO, SIGNOR<br />
*Aim 2: Provide the “hub” for a broad community of scientists to extend and modify the GO<br />
**Pipeline transition completed (**almost** -- chris)<br />
**Noctua rolled out to all GO curation groups<br />
***Evidence issues resolved in Noctua<br />
**Documentation for ontology request guidelines completed<br />
*Aim 3: Apply biological knowledge obtained in model organisms to human biology<br />
**PAINT annotations going directly into GO database (not via MODs)<br />
**PAINT annotation completed for all families with experimental annotations<br />
**Established alert system for ongoing review of annotated families<br />
*Aim 4: Maintain the integrity and quality of new and existing annotations<br />
**Ongoing annotation consistency exercises (conference calls and github) will now include a write-up (or blog) as case studies to be published on the web site.<br />
**An automated rule-based annotation QA system will be put into place that will be refined/extended based on input from the consistency exercises and PAINT curators<br />
**Establishment of an agreed upon policy for when annotations will be removed (and put this policy into action)<br />
*Am 5: Enable the scientific community to make full use of the GO data resources<br />
**Fixed existing problems with enrichment analysis<br />
**Website?<br />
**Outreach?<br />
<br />
==Infrastructure (Aim 2—Provide a “hub”)==<br />
===Pipeline Migration (Seth & Chris 20 mins) (Goal 2.a)===<br />
===New APIs (Seth & Chris 10 mins)===<br />
===TermGenie replacement* (Dan 20 mins)===<br />
*https://github.com/geneontology/go-ontology/issues/13472<br />
<br />
==12-1pm Lunch==<br />
===Graph Store update (Eric 10 mins)===<br />
===Licensing and GO (Seth 20 mins)===<br />
*Where we currently stand with licensing and possible issues<br />
*What others do with our data<br />
===GO and Related Projects===<br />
*Planteome (Chris, Seth, and Pankaj): How GO and Planteome contribute to one another<br />
*SIGNOR (Chris and Paul T) and SynGO (Ruth?) annotation incorporation (Goal 1.b.ii)<br />
**https://github.com/geneontology/noctua/issues/413<br />
**https://github.com/geneontology/noctua/issues/418<br />
*AGR<br />
**Parts of GO infrastructure being re-used by AGR (Chris)<br />
***db-xrefs.yaml<br />
**Data Formats (Chris)<br />
***BGI and GPI<br />
***Gene association JSON<br />
**Ribbon demo (Suzi)<br />
*Other Projects<br />
**BioCaddie and db-xrefs.yaml (Chris)<br />
**Monarch (Chris)<br />
**Panther?<br />
==3-3:30pm snacks==<br />
===Identifiers (Chris)===<br />
*Replacing double MGI (Chris)<br />
**https://github.com/geneontology/go-site/issues/346<br />
**https://github.com/geneontology/go-site/pull/338 (AGR)<br />
==Ontology (Aim 1—a comprehensive model of biological knowledge)==<br />
===Update on Ontology Editing: David + Chris 20min===<br />
*Design Pattern Updates: David OS + Chris 20 mins<br />
*Ontology Documentation: Moni 10 mins (Goal 2.c)<br />
*Curator notes and propagation<br />
**https://github.com/geneontology/go-ontology/issues/13384<br />
*Proposal: text mining github tickets for ontology terms (Chris, Kimberley)<br />
===MF refactoring (Paul, DavidOS 30 mins) (Goal 1.a.i)===<br />
*Issues: https://github.com/geneontology/molecular_function_refactoring/issues<br />
*Emphasis on practical implications for LEGO curation (templates).<br />
===ECO===<br />
*Mapping to classic GO evidence codes. The official mapping of IMP to ECO is insufficiently broad. Should cover non-genetic perturbations (e.g. pharmacological).<br />
**https://github.com/evidenceontology/evidenceontology/issues/117<br />
*There are lots of things under the ECO code that maps to IDA that are perturbations, not assays e.g.: **https://github.com/evidenceontology/evidenceontology/issues/123#issuecomment-281041854<br />
===Noctua and SIGNOR2 (Chris & Paul T)===<br />
*https://github.com/geneontology/noctua/issues/413<br />
**Additional document - https://docs.google.com/document/d/1QpfUY_LgeIryMj6EEAE05FXLE_894GalkerBU8dMuVU/edit#<br />
===Straw man BP refactor Chris (Goal 1.a.ii)===<br />
<br />
==6:00pm onwards mixer==<br />
<br />
=Friday June 2=<br />
==8-9am Breakfast==<br />
==Ontology continued…==<br />
===The fate of simple processes===<br />
*What do we consider a single-step process and what is their future?<br />
**GH ticket about single step processes https://github.com/geneontology/go-ontology/issues/12859<br />
**Is this a single step process? https://github.com/geneontology/go-ontology/issues/13012<br />
*The distinction between cellular processes and processes, do we need it?<br />
**GH ticket about cellular processes: https://github.com/geneontology/go-ontology/issues/12849<br />
<br />
==Annotation (Aims 1, 3, & 4—integrity and quality)==<br />
===Noctua Update (Seth & Chris 10 mins)===<br />
===Noctua rollout to curation groups (Goal 2.b)===<br />
*Current plan:<br />
**SGD (June, July)<br />
**WormBase (August, September)<br />
**Swiss-Prot (October)<br />
**Others? Issues?<br />
===GAFs and GPADs from Noctua models (David and Seth, 30 mins)===<br />
* Where do we stand?<br />
**https://github.com/geneontology/noctua/issues/418<br />
**Challenges with complex models (evidence) (Goal 2.b.i)<br />
**All of PRO IDS should be available in Noctua (ids for human, pombe, etc); can these be loaded from PRO directly (PRO to supply a GPI file).<br />
**GP-CC Should we allow direct GO part_of CC assertion (rather than via GO <-- enabled_by MF occurs_in --> CC). This is more accurate in some cases e.g. for membrane components.<br />
===Use of Qualifiers in Legacy Annotations (needs to come before pipeline??)===<br />
*RO subset for use with GAF/GPAD in qualifier column (Chris/Kimberly/DavidOS)<br />
*New qualifiers for biological processes<br />
*Incorporate expanded list of GP-GO term relations into annotation tools and files<br />
*Regulation and causality<br />
<br />
==12-1pm Lunch==<br />
<br />
===Focused Pathway annotation (Goal 1.b.i)===<br />
===Contacts for Curation Groups (Pascale & David)===<br />
Some annotation groups are now gone (no longer annotating), therefore, can't dispute annotations and have no mechanism to update or change them, if needed. We need to have a mechanism for tracking the status better github go-annotation tracker for annotation disputes can we have some GOC superuser status in Protein2GO that allows GO curators to update annotations Some groups like JCVI, PAMGO no longer annotate - can GOC take control of these experimental annotations?<br />
===PAINT update (Chris, Karen, Suzi, Pascale and Huaiyu)===<br />
*Analysis of the PAINT annotations (Karen and Huaiyu).<br />
*Plan for production services/pipeline for PAINT annotations (Chris)<br />
*Reverse flow (Goal 3.a)<br />
*Completion of all families with exp. evidence (Goal 3.b)<br />
*Initial implementation of alert system: what are the requirements? (Goal 3.c)<br />
===Annotation QC issues===<br />
====Consistency exercises (written case studies - Goal 4.a)====<br />
<br />
====GO Rules System (Eric) (Goal 4.b)====<br />
<br />
====QA from PAINT - automated rule-based annotation QA (Pascale) (Goal 4.b)====<br />
<br />
====How do annotation groups handle obsoleting/deprecating GO annotations? (led by someone from SGD or Val?) (Goal 4.c)====<br />
<br />
====Consistent use of the type field in GAFs and GPAD (Chris)====<br />
*E.g. https://github.com/geneontology/go-annotation/issues/1554<br />
<br />
==3:30pm Networking and Recreational outing==<br />
<br />
==6:00pm — Dinner==<br />
<br />
==Saturday June 3==<br />
==8-9am Breakfast==<br />
==Annotation continued…==<br />
===Annotation QC issues continued…===<br />
====HTP papers (Helen, Pascale & Sylvain)====<br />
*See notes /list of papers:<br />
<br />
====Transcription-Factor decision tree (Ruth - 20 mins)====<br />
*https://github.com/geneontology/go-annotation/issues/1463<br />
<br />
====Modified protein binding (Pascale & Sylvain)====<br />
*https://github.com/geneontology/go-ontology/issues/12787<br />
===Annotation of Viral Processes===<br />
*13214<br />
*Taxon restriction?<br />
*Annotation of host proteins involved in, or co-opted for, viral reproduction<br />
*Transcription, translation of viral genome<br />
*DOS proposal for multi-organism annotation (reviving old proposal) - poss allowing non-canonical function to be separable<br />
<br />
==12-1pm Lunch==<br />
==Community relations (Aim 5—enabling the community)==<br />
===Enrichment Analysis (Val & Seth) (Goal 5.a)===<br />
*by default have the enrichment tool run directly on the GO annotation dataset<br />
*by default enable loading a background<br />
*currently missing a substantial number of annotations (e.g. fission yeast)<br />
*Via ontobio python library (Chris)<br />
**Example jupyter notebook: https://github.com/biolink/ontobio/blob/master/notebooks/Phenotype_Enrichment.ipynb<br />
===Website? (Goal 5.b)===<br />
===Outreach? (Goal 5.c)===<br />
<br />
==3-5:30-pm Networking and Recreation==<br />
<br />
==5:30pm POSTERS and mixer==<br />
<br />
= Attendees =<br />
<br />
Please add your name to the table if you intend to attend the meeting, the dinner, the Noctua workshop, and the Reactome workshop so we can get a headcount estimate. Thank you!<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! Are you planning to attend the GOC dinner<br />
! Are you bringing a poster? how many?<br />
! Are you planning to attend the Noctua workshop the day after the meeting, Sunday, June 4th?<br />
! Are you planning to attend the Reactome workshop on Monday, June 5th?<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase<br />
| Y<br />
| Y<br />
|<br />
| N<br />
| N<br />
|-<br />
| Helen Attrill<br />
| FlyBase<br />
| Y<br />
| Y<br />
|<br />
| N<br />
| N<br />
|-<br />
| Judy Blake<br />
| MGI<br />
| Y<br />
| Y<br />
| Y-1<br />
| N<br />
| N<br />
|-<br />
| Seth Carbon<br />
| Berkeley/LBL<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Mike Cherry<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Laurel Cooper<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Stacia Engel<br />
| SGD<br />
| Y<br />
| N<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Priyanka Garg<br />
| <br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Parul Gupta<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Tom Hayman<br />
| RGD<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Emily Heald<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| David Hill<br />
| MGI<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Doug Howe<br />
| ZFIN<br />
| Y<br />
| maybe<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Ceri Van Slyke<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Sridhar Ramachandran<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| David Fashena<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Leyla Ruzica<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Pankaj Jaiswal<br />
| Reactome/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Stan Laulederkind<br />
| RGD<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Suzi Lewis<br />
| Berkeley/LBL<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Y<br />
| Y<br />
| Y-3<br />
| Y<br />
| Y<br />
|-<br />
| Austin Meier<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Moni Munoz-Torres<br />
| Berkeley/LBL<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| N<br />
|-<br />
| Sushma Naithani<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Darren Natale<br />
| PRO<br />
| Y<br />
| <br />
|<br />
| N<br />
| N<br />
|-<br />
| Sabrina Toro<br />
| Zfin<br />
| Y<br />
| maybe<br />
| N<br />
| Y<br />
| Y<br />
|-<br />
| Kimberly Van Auken<br />
| WB<br />
| Y<br />
| Y<br />
| Y (1)<br />
| Y<br />
| Y<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Peter D'Eustachio<br />
| Reactome<br />
| Y<br />
| Y<br />
| N?<br />
| Y<br />
| Y<br />
|-<br />
| Maria Martin<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| N<br />
| N<br />
|-<br />
| Tony Sawford<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Alice Shypitsyna<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| Y<br />
| ?<br />
|-<br />
| George Georghiou<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| Y<br />
| Y<br />
|-<br />
| Pascale Gaudet<br />
| GOC/SIB Swiss Institute of Bioinformtaics<br />
| Y<br />
| Y<br />
| ?<br />
| Y<br />
| Y<br />
|-<br />
|-<br />
| David OS<br />
| EBI<br />
| Y<br />
| Y<br />
| N<br />
| AM<br />
| N<br />
|-<br />
| Malcolm Fisher<br />
| Xenbase<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| Y<br />
|-<br />
|}<br />
<br />
*NOT ATTENDING:<br />
<br />
[[Category: GO Consortium Meetings]]</div>Suzi