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

• Chromosome Segregation
• Cytokinesis
• MitoticCellCycle
• Annotation Complete Checklist (in progress Val)
• AnnotationCompleteGenes

Useful Links

• Useful Links

Documentation (in progress)

• Curation Tool

• PomBase User Documentation Drafts

• General PomBase Curator Documentation
  • GO
    • GO ontology structure
    • GO Annotation guidelines (includes fission yeast specific guidelines, and pre- vs. post-composing GO terms)
  • Phenotype Annotation Guidelines
    • Pre- vs. post-composing phenotype terms with conditions
  • Gene Expression
  • Complementation (needs updating)
  • Modification
  • Annotating (sequence) features in Artemis (needs updating)
  • Protein feature annotation (needs updating-val)
  • Genetic and physical Interactions (needs updating-val)
  • Status and Species Distribution? (needs updating-val)
  • General Annotation Extension Guidelines
  • Describing Residues

• Data Handling and creation Protocols
  • External GO Data
  • EMBL resubmission
  • GO submission
  • PhenotypeMapping for PMID:23697806

• Ensembl browser track labelling
• HTP data file validation and upload instructions to send when we receive a form submission
• Files Used By EsyN

• 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

• GOslims For unknown project

• 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
  • RelationsAndTransitivity
  • multi_gene_phenotypes

• 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

• Student project ideas
  • Student Project?

• Outreach
  • Pombelist Notifications Pending or curation spotlight

Inventories

• Distant orthologs
• Ortholog Table Updates
• Pombe Gene Losses
• S.c. genes with no pombe orthologs
• Wild-type Pombe characteristics
• Example genes with various features

Reports

• Progress Reports

Deprecated pages

• Known Drug Targets
  • Creating a ProteinComplexInventory
• 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
• Physically Unmapped Genes and Proteins

• Chado
  • Storage of genotypes and phenotypes in Chado

The PomBase Team

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