Version 403 (modified by val_wood, 9 years ago) (diff)


PomBase Curator Meetings


Next Items, in rough order of priority

Monday 22 April

  • follow up from below: Antonia will paste in her "protein glycosylation" so far (DONE)
  • check that the qualative/quantitve expression stuff is all documented and working OK (need list of allowed qualifiers etc) (DONE OR IN PROGRESS)
  • Call with Kim to chat about Curation tool :
    • request to curate a paper e-mail, revisions (IN PROGRESS WE 3 VW,MH,AL, will do thorough testing once next batch of changes are made to test)
  • PomBase? User Documentation Drafts (see wiki, mainly done, we should check these through for details (i.e where TMHMMs from) and move onto jira for mark to link to page sections, and announce) (IN PROGRESS, MODT POMBASE USER DOCUMENTATION IS IN PLACE, NEED TO LINK FROM SPECIFIC PAGE SECTIONS TO HELP, and ANNOUNCE)
  • make some FYPO terms unavaiable for direct annotation. There are lots of terms where it should be possible to make a more specific phenotype annotation (i.e swollen, elongated, multinucleate, aseptate etc), where it is possible that we did not know this when we made the original annotation. We should slowly look through these and move down. An example but not a great one: we should make the curation tool force people to annotate more specifically for these. For example they should never be able to annotate to a term which does not specify vegetative/ vs G0/ meiotic etc.... (DISCUSSED, AS WE NOTICE TERMS WE CAN ADD THIS SUBSET, AND "DO NOT ANNOTATE" COMMENT. ASKED KIM TO ADD A WARNING TO LOGS)

  • "response to" phenotype only?
    • Antonia: when to use cellular response to terms (I know they should not be used for expression data and not to use 'toxin' or 'drug'. But what if there is a sensitivity/growth assay? they are sort of informative are they not - I just want a reminder).
    • It seems odd that sty1 will only be annotated to "response to oxidative stress" via 'regulation....'

its almost as if we need a term "signalling in response to oxidative stress"


  • Group call

General issues:

  • ISB/ GO meeting (GMOD (canto/ chado), curation rules (function prediction people)
  • nextPomBase build

Individual Updates & Priorities

  • Val priorities: cell cycle report and related annotation updates, import of deletion project morphology phenotypes (~5000 annotations), curation session approval, curation, off work 2 weeks, tidy wiki, curation tool video (Val will look at S/ware and or contact Gulietta), more consistency rules, community curation launch preparation

  • Midori (FYPO, queries for Val, now in progress)
  • Antonia (RT, more curation)
  • Kim (Community curation release items )
    • V 35 build, is ready for curators for checking
  • MArk (version 34 tickets, will check open RT tickets)
    • V34 will be hopefully be live for 29th
    • Sam's data, seems to be some discreapancy in the amount of data but should be between 2-4 annotatiosn per gene?
  • If time go through curation tracker, and see what con be done quickly

Tuesday 23rd April

A.M 11.00 Group call

General Val ISB/ GO meeting (GMOD (canto/ chado), curation rules (function prediction people) curation session approval, curation, off work 2 weeks, tidy wiki), curation tool video

  • nextPomBase build

Individual Updates & Priorities

  • Val (cell cycle report & annotation updates, import of morphology phenotypes, consistency rules)
  • Midori (FYPO)
  • Antonia (RT)
  • Kim ( Community curation release)
  • MArk (version 34 tickets)

Monday 6 May

Go ahead or cancel?

Tue 22 May

Go ahead or cancel?

Next plan dates, no room booked

  • Galaxy demo, pombe specific example (would the bent cells work?)


  • keep a look out for these: look for others in response waiting file I changed the evidence for the IGI annotations to ISO because it wasn't really shown in this paper that it is involved in those processes, it only rescued a growth defect in cerevisiae ortholog mutant
  • check all community curation flags set on approved papers

For any papers you have sent out, can you check that the "community curatable" flag is set in the triag (also that they have triage status "curatable", some appear to have had the papers added, but the status wasn't set (probably because it was added directly rather than by the automated paper load).

  • Val: I might have put some things through to abnormal chromosome/chromatin organization that should probably be morphology...could you have a look out for them?

(we should do queries on this for V 34 and V35 to check)

  • localization dependency


  • Use of inhibited by...used for "biological inhibition" (i.e regulation) and exogenous inhibition...discuss?
  • discuss what should be the default text for searching terms etc (see e-mail with subject "default text")
  • How to alert users to scope of terms with 'during vegetative growth' in synonyms and xps, but not the term names? Could rename all, or add to defs, or add comments. (IN PROGRESS)
    • i) Midori will add "vegetative growth to definitions"
    • ii) We will ask Kim if it is possible to have a "group" to use a different synonym_type_def and if we did this would it be possible to display this term name as a default for these terms in the curation tool
    • iii) if not we will add to term names (will be a bit clunky on gene pages)
    (example processes localisation to centromere/ spindle pole body duplication)
  • GO regulation of process discuss, make guidelines
    • Signal transduction upstream of transcription (adenylate cyclase, git pathway)
    • regulation of transcription regulating process (gene specific transcription)
      • Martins paper PMID:19101542
      • Charlies gits
        • consider git1 barrier septum assembly annotation
    • Protein modification and regulation
      • see email exchange with David/SGD
      • curs/97535c919f7436fe (Winston lab paper)
    • relationship of chromatin silencing to transcription, see mcl1 (upstream effect?)
  • Discussion about has_part and how it affects curation
    • see e.g. in e-mail folder NTR: srebp catabolism
    • e.g wnt signalling has_part MAP kinase
    • e.g. primer synthesis
    • you can't infer annotations in either direction over a has_part relation, but if you want to see the "whole" for a gene that's annotated to the "part", that's ok ...
  • extension syntax e.g.

annotation_extension=requires_modification(MOD:00046),​ residue=S462​ or annotation_extension=requires_modification(MOD:00046,​ residue=S462​)

Phenotype ontology (Midori 2012-02-29)

  • Annotations: how to represent when alleles of interest are studied with another (non-null) allele of the same gene present
    • email sent 2012-06-27
    • example: mcm2 alleles in PMID:9383050
      • several different mcm2-x alleles assayed on plasmids, with mcm2+, mcm2delta, or mcm2 allele cdc19-P1 on chromosome

Data types/ Data descriptions

Specific Curation issues, biology

  • Trancription overhaul ....documentation etc (terms for sequence specific transcription factors)
  • cell wall assembly and biogenesis

  • where does conjugation begin, (is signalling from pheromone part of conjugation, or regulation of conjugation? Juan says regulation)


  • Are all things which can be migrated from the wiki to the curation tool?
  • controlled curation, still need to cover genome org/pathway/protein sequence feature/warning
  • Discuss annotation consistency between complexes and process (should we suggest complex/process links?)

Future tasks to discuss with Mark

  • User configuration of gene pages (discuss in detail in future)
    • Ability to collapse/open sections by default
    • Ability to configure order of sections on gene pages
    • Some sections may become so long that we need to rethink how redundant data is presented (Antonia's examples)
  • Discuss column 17 display (this might result in a new jira item)
  • Where did the annotation_extension data preview go (It was nearly right....)

Future Meeting Discussion Items, please move forward if more urgent

Low Priority

Quality Control and consistency checks

  • Compare to existing curation
  • Compare to orthologs
  • look at domain data
  • other complex subunits
  • MAking annotation inferences using existing annotations
    • carbohydrate metabolism and cell surface -> extracellular polysaccharide metabolic process???
    • transcription related (appropriate TF and DNA binding terms)
    • vesicel mediated transport / intracellualr protein transport
    • telomeric DNA binding -> telomeric region
    • GTPase -> GTP binding


  • More on Pfam, false negatives, clans
  • localization dependencies
  • Gene naming and GNC
  • Broader annotation consistency checks, Matrix project, GO slim term comparison
  • taxon restrictions
  • improving annotation for uncharacterised genes
  • updating products
  • Regulation
    • Direct vs indirect
    • e.g autophagy example
    • regulation of cell cycle and signal transduction
    • start and end of a process
  • Function/process links
  • Updating EMBL
  • Download data formats (gff etc)
  • editing sequence in Artemis
  • systematic reduction of the orphan set


  • pombe budding yeast and human orthologs (POSTPONED until new human orthologs appear in PomBase?), updating orthologs, and ortholog tables
  • qualifier documentation for "controlled curations"
  • sort out the reference pombe strain h90. Currently the taxon ID is used (briefly discussed - keep as is or change ref strain to h90 (and if so make a 'pretend sequence'?)).
  • Annotating sequence features
    • promoter features, ID? and syntax
    • we need a way to physically annotate the processed and unprocessed peptides and attach SO terms directly to them (we could do this now using misc_feature and a SO term, and we couldn't use them as objects to annotate to directly in Artemis/Chado?)
  • Implications of sequence changes for residues and alleles , checks curators need to take, also need to discuss this with Mark
  • Annotating tRNA's: what did we decide about this? (can't add genes to tool, what ontology to use..). SO says that they can give us SOM terms.
  • Regulation rules (ongoing, will do when Val has done basic documentation/"rules") (POSTPONED)
  • Making IC annotations (in Artemis) (I don't know if there is still anything to discuss about this?)
  • Session approval (list of things to check), seems to be working OK, but we could do with a list of basic checks
  • systematic IDs for transposons (make SF item) ...postponed until needed
  • Dealing with diploids
    • how to specify a diploid genotype, and capture the info in curation tool
    • what to do when haploid spore phenotype depends on genotype of the parent diploid

POSTPONED, no changes required at present, qualifier is not used much

  • postponed dephosphorylation etc (see Chado load error logs)
  • postponed GO through enrichment and slimming and update FAQ
  • postponed until Kim gets further, low priority revisit complementation
  • Discuss if ISS should be filtered ISS isn't in the list. We have IEA, IEP, NAS, RCA, TAS and IC. POSTPONED< Still thinking about this
  • disease ontology (Postponed until we have disease ontology IDs)
  • consider name for species distribution (pending inspiration)
  • Discuss and look over NOTs (postponed)