Welcome to the PomBase Wiki

This wiki accompanies ​PomBase, a comprehensive resource for researchers working the fission yeast Schizosaccharomyces pombe. PomBase combines structural and functional annotation, literature curation and access to large-scale data sets. Enjoy!

Meetings

• PomBase Planning Meetings - Agendas and Minutes
• PomBase Curator Meeting - Agendas and Action Items
• PomBase group call- Minutes/Actions

Annotation priorities

• Annotation Priorities
• Annotation Complete Checklist (in progress Val)

Useful Links

• Useful Links
• List of Pombase components and links to their repositories?

Documentation (in progress)

• Curation Tool

• PomBase User Documentation Drafts

• General PomBase Curator Documentation
  • Curation Guidelines?
    • GO Annotation guidelines (includes fission yeast specific guidelines, and pre- vs. post-composing GO terms)
    • Pre- vs. post-composing phenotype terms with conditions
    • ​Annotation Extensions, Ontologies used so far and examples (merge this into Annotation extension documentation)
    • Gene Expression
    • Complementation
    • Modification
    • Annotating (sequence) features in Artemis
    • Protein feature annotation
    • Genetic and physical Interactions
    • Status and Species Distribution?

• Data Handling and creation Protocols
  • External GO Data
  • EMBL resubmission
  • GO submission
  • PhenotypeMapping for PMID:23697806
  • Creating a ProteinComplexInventory
  • Ensembl browser track labelling

• Nomenclature
  • Gene Nomenclature, will eventually move under "About" on pombase.org
  • Gene Product Nomenclature
  • Naming antisense transcripts

• Documentation for in-house ontologies
  • Fission Yeast Phenotype Ontology

Work in progress

• Curation Tool
  • Curation tool Features (completed in progress and pending)
  • GO terms we may not require in the curation tool (too specific)
  • Annotation Extensions proposal
  • Multi-gene phenotypes

• PomBase Website
  • Canned queries for PomBase query tool
  • BioGRID bait/hit notation mapping
  • PomBase release testing

• Curation
  • Extension ID types

• Curation Consistency and QC
  • Matrix Project
  • Database Sanity Checks (syntax)
  • Database Sanity Checks (biology)
    • Possible rules for phenotypes
  • List of approximate results for a set of test queries

• Thoughts on regulation
  • Regulation

• File formats
  • Phenotype Import Export draft format

• Curation

• Phenotypes to map to unstressed

• Sequence analysis
  • Pfam submissions in progress

• Outreach
  • Pombelist Notifications Pending or curation spotlight
• Chado
  • Storage of genotypes and phenotypes in Chado

=*​Complete list of controlled vocabularies in Chado

Inventories

• Known Drug Targets
• Physically Unmapped Genes and Proteins
• Distant orthologs
• Ortholog Table Updates
• Pombe Gene Losses

• S.c. genes with no pombe orthologs
• Wild-type Pombe characteristics
• Example genes with various features

Projects

• Community Curation Initiative?

Reports

• Progress Reports

Mailing Lists

• ​pombelist - the fission yeast community mailing list (Mailman info page)
• ​SourceForge mailing lists - topics parallel trackers

Trackers

• ​SourceForge trackers
  • ​Curation tool
• ​Jira tracker for Ensembl
• ​Community helpdesk tracker

Deprecated pages

• Curator Training Papers
• PomBase Technical Meeting - Agendas and Action Items
• Questions to bring up at in-house meeting page was empty so moved here...
• PRO IDs for modified forms of S. pombe proteins - wasn't kept up to date; see Dropbox/pombase/ontologies/PR/pombe_mini_PR.obo instead
• Protein Feature Documentation - content now in pombase.org documentation
• Reference Genomes Information and Progress
• Lucene search issues (none pending)
• Qualifiers Used (will be mostly deprecated)
• Curation tool brainstorming page
• describing residues modified or mutated (Artemis)
• Papers with no PMID
• Papers costing ¬£¬£ to access
• Complementation Annotations to transfer
• Qualifiers used

The PomBase Team

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For a complete list of local wiki pages, see TitleIndex.