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
- 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
- Jenkins GAF checks with red status cannot be inspected
- Inferred annotations (annotations created by logical inference)
- Inter-ontology links
- 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
- Annotation Rules and Error Files
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
- Annotation Guidelines for High Throughput Experiments
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, Stacia, Stan, Terry, Val
Regrets: Paola
QC Pipelines
- 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
- GAF checks have been failing - red balls
- 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
- See github link
- Jenkins annotation inference pipelines
- Inter-ontology links and annotation deepening
- Evidence codes in general
- First implementation used IC evidence code
- But, now preserving original evidence code and using GOC as contributed by entry
- However, these annotations may really be the result of a combinatorial evidence chain
- Annotations from deepening
- Two main issues:
- When IC was used, primary GO ID was in the With/From but new annotation was from extension
- Also some relations, such as regulates_o_occurs_in, if not used correctly will result in incorrect annotations
- These annotations will need to be fixed to get the correct inferred annotation
- How many annotations have actually used this relation?
- Need examples of each of these relations in LEGO models - DOCUMENTATION
- Need distinction between has_regulation_target and the chained relations that also use regulates_o
- Protein2GO now has the options to use the chained relations, but there isn't sufficient documentation about how and when to use them!
- Annotations may be correct, but the inference is wrong
- See the MAPK example in the GOC-OWL inference github ticket
- ACTION ITEM: Look at annotations that use a regulation term and occurs_in in the AE to check on these annotations to make sure annotation deepening is correct
- ACTION ITEM: Make sure that annotation extensions in tools use the more human readable relation name
- Two main issues: