Version 337 (modified by val_wood, 9 years ago) (diff)


PomBase Curator Meetings


Next Items, in rough order of priority

  • Abstracts (IN PROGRESS)
  • 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)
  • annotation intersects, rules update (Val IN PROGRESS)
    • Antonia will paste in her "protein glycosylation" so far
    • Val will make poster/slides/text
  • Documentation update (IN PROGRESS)
    • linking to specific curation tool documentation
    • documentation for gene pages, update
  • consider name for species distribution
  • Discuss and look over NOTs
    • eg fnx1
  • Chromosome notation
  • Discuss if ISS should be filtered ISS isn't in the list. We have IEA, IEP, NAS, RCA, TAS and IC.
  • 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?)
  • cell wall assembly and biogenesis

  • systematic IDs for transposons (make SF item)
  • 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.
  • Decreased transcr vs inviable.
  • 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'?)).
  • 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?)
  • Make a mapping of relations to display on pages
    • Draft now in Dropbox/pombase/PomBase_website/extension_relation_display_text.txt (2012-09-17)
  • Discussion about has_part and how it affects curation
    • 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 ...
  • 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
  • extension syntax e.g.

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

  • postponed Regulation rules (ongoing, will do when Val has done basic documentation/"rules")
  • Session approval (list of things to check), Val in progress
  • qualifier documentation for "controlled curations"
  • pombase budding yeast and human orthologs (postponed until new human orthologs appear in PomBase?), updating orthologs, and ortholog tables
  • disease ontology
  • Sort out definitions

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
  • Pre- vs post-composing terms
    • background (older comments):
      • We've decided to make some phenotype terms obsolete and use conditions to capture temperature, carbon source, nitrogen source, etc. Last call to review the affected terms -- are there any that we should keep after all?
        • normal growth at high temperature FYPO:0000674
        • viable at high temperature FYPO:0000282
        • sensitive to cold FYPO:0000080
        • sensitive to high osmolarity FYPO:0000081
        • sensitive to high temperature FYPO:0000082
        • slow growth at high temperature FYPO:0000247
        • normal cell growth on ammonia nitrogen source FYPO:0000242
        • normal cell growth on proline nitrogen source FYPO:0000243
        • slow cell growth on ammonia nitrogen source FYPO:0000249
        • slow cell growth on proline nitrogen source FYPO:0000250
        • slow cell growth on galactose carbon source FYPO:0000251
        • slow cell growth on glycerol/ethanol carbon source FYPO:0000442
        • increased cell growth rate on glucose carbon source FYPO:0000637
        • slow cell growth on glycerol carbon source FYPO:0000684
    • update 2012-03-09: I'm now thinking of keeping just heat sensitive (FYPO:82) and cold sensitive (FYPO:80) as a practical matter -- lots of community curators/users will search for them! The rest could probably still go, converted to parent + condition(s).
    • update 2012-06-12 (based on discussion in May): actually still thinking about this. It's a "when to pre- or post-compose terms" question, analogous to GO terms + extensions. Thoughts in progress noted here.

  • Curation tool related, progress towards launch
  • SF related
  • Making IC annotations (in Artemis)

Help/ Documentation plan

  • FAQ update
  • Ensembl Help update
  • Curation tool help update

Data types/ Data descriptions


  • Implications of sequence change for residues and alleles , checks curators need to take, also need to discuss this with Mark
  • Trancription overhaul ....documentation etc (terms for sequence specific transcription factors)
  • contributes_to qualifier


  • Are all things which can be migrated from the wiki to the curation tool?

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

HAve been liasing with Emily and . Emiliy's documentation on this should be available shortly, so we will revisit when this is available...

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
  • Matrix (interseciton of processes)
  • 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


  • Discuss GO "response to"
  • 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


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