Version 30 (modified by val_wood, 9 years ago) (diff)


Meetings held

6 Sept. 2011

  • Annotation extensions (with Chris, Emily, Jane; morning)
    • relations
      • direct and indirect regulation - has_regulation_target, plus child term(s) to be added (see what Chris has put in file)
      • when to use has_substrate - with MF catalytic activity terms
      • upstream & downstream
      • negating annotation extensions
  • Gene expression controlled curation
    • current capture of expression (some needs to migrate to annotation_extension)
    • how should we do this in future?
  • Phenotype modelling (with Kim & Mark; afternoon)
  • WT phenotypes

3/4 October 2011

  • As part of planning meeting Midori went through phenotype model for Chad (link to planning meeting minutes)
  • As follow on from phenotype modelling we drew up a draft workflow for capturing data in the curation tool (We will all work through this when curating phenotypes)
  • Midori went over basics of using subversion, esp. resolving conflicts
  • Bio-Curator meeting abstracts (Nov 30). hopefully Antonia can attend
  • General curation work

17/18 October 2011

  • Antonia's list

  • Regulation
    • Direct vs indirect
    • regulation of cell cycle and signal transduction
    • start and end of a process

3/4 November 2011

  • Identified and co-curated papers for undergraduate workshop

14 November 2011

  • round robin, next 2 weeks priorities etc

  • GO meeting debrief
  • Had a discussion about annotation extension When to pre-compose in ontology (during etc)
  • Also discussed phenotype curation, probably only need condition extension initially
  • Discussed how location required for process is equivalent to process dependent on localization to componet
  • need to migrate all required_for attached to components to process terms and move all dependent on to children
  • PomBase? release pending, discussion about a few thing required for release, and revised release date to 28th

15 November 2011

2 December 2011

  • round robin, next 2 weeks priorities etc
  • Midori OBO-Edit basics
    • loading viewing browsing searching etc (need to be able to view relations ontology)
  • Posters for biocuration

23-27 January 2012


  • RT versus jira (For a while we will probably stick with RT)
    • RT is now be configured so we see all responses.
    • Val demo how to configure dash to show all open/ closed items / assign itmes DONE
    • Val will encourage people to submit to helpdesk, or will summarize and post queries later
    • Note make sure any feedback received is appended to closed items as comments.
  • Proposed system:
    • Antonia monitors the helpdesk
    • Antonia decides if she can't answer the query who would be able to best answer (probably me at first for most legacy or data related questions, and Mark for inclusion of HTP datasets, Midori for PomBase website queries (including queries which will raise new jira tracker issues or feature requests), Antonia for requests to curate papers), but we can always reassign if they go to the wrong person...)
    • Once a query is answered Antonia will draft an FAQ item (if relevant) from the response, and send to Midori for editing and including in the PomBase FAQ
    • Hopefully after a year or so we will have answered most of the common queries and so increasing Antonia can increasingly point users directly to the FAQ.

Curation Tool

  • Getting feedback from authors on completed papers Val will write an email to send out with curation sessions We should keep a file of people who have been sent completed sessions as the next paper they should curate themselves

To discuss with Kim

  • Next things for Kim to work on (rough order) Curation tool

  • need to thrash out allele descriptions
  • Val needs to check that the proposal to change the tool fits with the phenotype format/model
  • 4. Annotation extensions
    • I.e which extensions need to be available for i) each ontology ii) each term
    • ii) annotation transfer of extensions and qualifier
  • 5. New datatypes, expression (dependent on outcome of discussion below), complementation (probably we will split out complementation as a curation type in the tool), protein sequence features (subset of SO)
    • GO through high priority SF items (1 & 2 above)

  • New features
    • See SF tracker


All items from discussion with mark added to relelvant jira tracker Other Action items

  • Download file options (val to document)
  • replacing current ftp site and download files (val to document) DONE

  • How to capture dephosphorylated/dephosphorylation DONE
  • pombelist FAQ proposal (putting pombelist "experimental" items into Susan F's FAQ)

6-7 February 2012

  • went through Antonia extensions (kim generated file with links to sessions)

Antonia will revise existing extensions to fit parser

  • extensions on phenotypes generally

Discussed that it is good practice to add targets to both phenotypes and GO terms, and that more generally extensions will be required for phenotypes, initially these wll need to be done by curators.

  • later we will be able to make links between phenotypes and GO terms
  • relations used in extensions will be reported by Kim during loading and the we can refine
  • Val went through some localization examples , e.g PMID:20298435
    • should the localization only be direct transport, anchoring, chaperoning? what about complex assembly, or part of a complex
    • decided localizations should be captured with GO if they were clearly "localisation" (i.e A- required for B). If possibly "complex dependent" i.e A required for B AND B required for A, should be phenotype only)

  • Using OBO-Edit, part 2: editing & saving
    • make a "condition" ontology

5-6 March 2012

Phenotype ontology

  • Should we keep some, all, or none of the "abnormal protein localization" terms? If some, which? Also see SF 3485679 (Midori 2012-02-29)
    • Decision as of 2012-03-05: keep all (unless a specific reason to obsolete a term crops up), because we'll need 'delayed' and therefore also a generic abnormal-process parent; pepper ontology with comments galore to explain which terms to use when.
    • Midori to try to sort out ontology structure with advice from George & Chris. It'll all work out somehow ...
  • Different terms if the mutated protein is mislocalized, or a target of the mutated protein is mislocalized? (Antonia 2012-03-01)
    • Decision as of 2012-03-05: use the same phenotype ontology term, and use an extension to identify which protein is mislocalized (always include an extension, to show that we know which protein was assayed).
  • Also, what extensions to use?
  • Discussed order of sections on Gene Summary pages/ NOT annotation submitted jira items
  • went through possible slides for Antonia's Biocurator presentation
  • Chased up follow up for user testing
  • went through protocol for assigning products (precedence now on wiki)

27th March 2012

  • Antonia's talk preparation
  • User testing discussion

17th April 2012

  • Skype with Kim to go through allele phenotype workflow

01 May 2012

EBI user testing, an planning meeting

14th May 2012

  • Go through new BioGRID documentation for genetic interactions, related to our items below.
    • capturing or inferring recessivity/dominence (and capturing heterozygosity or homozygosity in a diploid)
    • Will discuss when we have real life examples

  • Which relationship to use to represent target for normal protein localization..... (Midori suggested "assayed using" ...I'm happy to start with that...DONE,

23rd July 2012

  • Phenotype assumptions: do we want some 'default' conditions that are true for most experiments, unless otherwise stated? See for instance the terms decreased aerobic cell growth on glucose carbon source / slow cell growth / etc

DONE (in part) Decided to make some assumptions for "standard" conditions, and request terms for non standard conditions (if standard condition terms are requested, they can be added as synonymns and liberally commented)

  • Decide workflow for annotation transfer for phenotypes in the curation tool


  • workflow for curation tool, lab/person


  • Discussion about annotation specificity
    • curators collect examples of where they wondered whether they were going "too specific"
    • Curators to co-curate Espenshade papers to get a feel what degree of specificity we want to capture

DONE made some progress with this, basically in some cases for "response to" we will use extensions AND concurrent annotations so we don't have explosions of some conserved areas of the ontology which are likely to be otherwise conserved (especially when the same pathway can be triggered in response to various insults or depletions)

Also looked at a specific paper and decided that some compound terms were required to capture annotation specificity, AND there were a couple of possible issues with this existing part of the ontology (around SRBP signalling)

21st August 2012

  • Discussed with Mark:
  • Big item: display of annotation extensions (GO, FYPO), 'with' column (GO), alleles (FYPO), etc.
  • Other items:
    • set up regular meetings - one day of every other curator meeting, i.e. once every 4 weeks
    • gene page aesthetics (
    • improving notification about updates to "module", "biomarts", etc.
    • note for later meeting: collapsing display for annotations with lots of extensions

17th September 2012

5/6 th November 2012

  • N-matrix
  • skype with Kim, discussed multi gene phenotype worksflow in curation tool (see slides in dropbox)

7th Jan

  • Discussed how simple and site-wide PomBase? search should behave (midori will put on Jira tracker)
  • Discuss ad/disad of abolished enzyme activity as post composed...new_relation(GO:xxxxx) Discussed, and no time saving.
  • Gene expression data: we have a (sort of) temp solution for few compounds many genes. But no solution for 1000s of compounds + 1 gene. What to do with these? Eg. PMID:22840777 We discussed this and decided that what Antonia did here was adequate