Annotation Conf. Call 2017-01-10

Bluejeans

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Agenda

Next Consortium Meeting

• June 1-3, 2017
• The regular meeting will be followed by two optional workshop days on LEGO and Reactome curation on June 4 and 5
• Pankaj Jaiswal has graciously offered to host the meeting at Oregon State University in Corvallis, Oregon
• He has set up a really nice meeting webpage at https://sites.google.com/view/goc2017
• Please register!

Review of Jenkins Pipeline

View GAF builds in Jenkins

• GAF checks
  • Annotation Rules and Error Files
    • Jenkins GAF checks with red status cannot be inspected
      • Jenkins builds that fail do not display the most recent errors file, so curators can't check what needs to be fixed
    • GOA annotation checks on GAFs are more stringent than Jenkins checks (should be same?)
      • Annotation QC checks employed by GOA and Jenkins should be in sync
    • Convert old annotation_qc.xml
      • Annotation rules on github
  • Inferred annotations (annotations created by logical inference)
    • Inter-ontology links
      • Source: GOC
      • PomBase inferred GAF missing annotations
      • Remove all single-step BP classes
  • Annotations inferred from annotation extensions (fold-based predictions)
    • Source: GOC-OWL
    • GOC-OWL inference pipeline concerns
      • Annotations are now being generated from 'folded' terms
      • Concerns about:
        • evidence code used
        • qualifiers
        • redundancy with existing manual annotations
        • misuse of AEs leading to erroneous assertions
      • Change assigned_by for GOC OWL inferences to be able to distinguish from F-P
  • Evidence Codes used for Inferred Annotations
    • GOC-OWL inference pipeline concerns
    • Add inter-ontology links to go-basic and stop materializing inferred annotations from inter-ontology links
    • Remove constraint on IEP only applying to BP

Working Groups

• At the November 2016 USC meeting, we agreed to establish working groups for several topics.
• If they haven't already, groups need to set up meeting schedule and agendas
  • Annotation Guidelines for High Throughput Experiments
    • Helen Attrill (FB)
    • Stacia Engel (SGD)
    • Pascale Gaudet (SIB)
    • Ruth Lovering (UCL)
    • Kimberly Van Auken (WB)
  • Working group to finalize transcription decision tree
    • Marcio Acencio (NTNU)
    • Karen Christie (MGI)
    • Rachael Huntely (UCL)
  • Working group to review use of ECO codes
    • David Hill (MGI)
    • Note also that there is an ECO workshop at this year's ISB meeting

LEGO Modeling Discussions

• We would like to reserve the second Tuesday annotation call of each month for discussion of LEGO modeling.
• The proposal is to have two presenters each month for an ~30 minute discussion of their model.
• The goal is to get more people comfortable with LEGO modeling and increase the number of processes represented by LEGO models in GO.
• Please sign-up for a time slot here: LEGO Discussion Rota
• We would like to do this on a volunteer basis, so please consider taking a turn.
• We all benefit from discussing modeling issues from across a broad spectrum of organisms, and there is likely commonality amongst the pathways and processes that we are trying to represent.

Minutes

On call: Alice, Chris, David H., David OS, George, Giulia, Harold, Helen, Jim, Karen, Kimberly, Li, Melanie, Midori, Moni, Pasclae, Penelope, Petra, Rachael, Ruth, Sabrina, Stan, Terry, Val

Regrets: Paola

QC Pipeline

• Two pipelines - Jenkins and Mike Cherry's checking scripts
• Focus of this call - Jenkins pipeline
  • GAF checks have been failing - red balls
    • Due to an upstream failure in ontology build, was not being caught, but affected GAF check pipeline
    • This was an edge case, but has now been addressed such that the inconsistency check will happen upstream of the GAF check
• Annotation rules
  • See github link
    • Rules include those from Mike's original checking script, tool-based rules (e.g., Protein2GO), Jenkins rules
    • Rules were in XML, and a web page documented each rule in a human-readable format
    • Replacing system with a markdown and yaml file
    • Still need a page for human readable review (script will pick up the content of the md file for display)
    • These files are to be used for software developers to implement
    • Working on universal implementation of all of these rules on top of the graphstore that Jim is implemeting
• Jenkins annotation inference pipelines
  • Inter-ontology links and annotation deepening
  • Evidence codes
    • First implementation used IC evidence code
    • But, now preserving original evidence code
    • However, these annotations may really be the result of a combinatorial evidence chain