Annotation Conf. Call 2017-04-11

Bluejeans URL

https://bluejeans.com/993661940

Agenda

• Meeting agenda on geneontology/go-annotation

GOC Meeting, Corvallis, Oregon, June 1-3 (plus workshops June 4-5), 2017

• Logistics: https://sites.google.com/view/goc2017
• 2017 Corvallis GOC Meeting Agenda
  • Please check the table at the bottom of the Agenda page and add your name, if not already there. Also please double-check the information associated with your entry.

Jenkins Pipeline

• Redundant annotations coming from Function-Process inter-ontology links

PAINT Annotation Queries/Disputes Now in Github

• Tracking PAINT-related annotation queries/disputes in github
• Example

Ontology Terms that Refer to Specific Gene Products

• Ticket on geneontology/go-ontology
• Proposal is to remove ontology terms that refer to specific gene products

Proposed new Biological Process Annotation Qualifiers

• Use of Regulation Terms
• Gene products annotated to regulation term but no MF annotation
• Gene products annotated to both a process and regulation of that process

Working Groups

HTP Experiments

• Held first call on 2017-03-21
  • Agenda/Minutes
  • Google spreadsheet documenting HTP experiments

Transcription Decision Tree

• Reminder to review latest version linked from github ticket

Minutes

• On call: Alice, Chris, Emily, George, Guilia, Helen, Judy, Midori, Moni, Pascale, Petra, Rachael, Shur-Jen, Stan, Tanya, Terry, Suzi

Call Agendas on Github

• Will post meeting agenda on github so we can coordinate tickets with actionable items from calls/meetings

GOC Meeting - Corvallis, Oregon, June

• Register on Pankaj's Google site
• Also, please add your name to the table at the bottom of the agenda wiki page
• Agenda is currently a bit free-form, please add your items and the PIs will review and structure
• Next ontology editors call, editors will discuss what to present in Oregon

Redundant F-P Links

• AI: Create a new ticket, since the existing one has veered in several directions and is a bit confusing
• F-P links were always intended to just create annotations, using the same evidence code, for terms linked via the ontology
  • Some groups could not handle the inter-ontology links, so the annotations were generated
• Some duplicates do get generated
  • MGI removes exact duplicates
• PomBase noticed that less specific terms were being generated
• Should this be corrected in the code that generates the F-P propagated term?
  • Suzi - yes
• Some groups do make redundant annotations, even if to a less granular term
• Multiple annotations can indicate confidence in a given area of the ontology
• Redundancy should not affect enrichment analysis
• AI: Need to have better documentation about what will be generated by the inference pipelines
• Also note we still have the related issue of getting different annotations between Jenkins run remotely vs locally

PAINT Annotation Disputes Tracked Centrally in Github

• Previously, these issues where tracked in SourceForge
• Please create tickets on github geneontology/go-annotation
• Does this create extra work for Protein2GO users?
• Goal is trying to create a centralized place where PAINT GO annotations queries/disputes can be tracked
• Annotation queries can come from within GO or outside (e.g. users)