= Welcome to the !PomBase Wiki =

This wiki accompanies [http://www.pombase.org/ 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! [[BR]]

== Meetings ==

 
== Annotation priorities ==
 * [wiki:ChromosomeSegregation Chromosome Segregation] 
 * [wiki:Cytokinesis Cytokinesis] 
 * [wiki:MitoticCellCycle MitoticCellCycle] 
 * [wiki:AnnotationCompleteChecklist Annotation Complete Checklist]  (in progress Val)
 * [wiki:AnnotationCompleteGenes  AnnotationCompleteGenes]

== Work in progress ==

 * Curation
  * [wiki:RelationsAndTransitivity]
 
  * [wiki:annotationSanityChecks Database Sanity Checks (biology)]
   * [wiki:PhenotypeTests Possible rules for phenotypes ]
 
 * Thoughts on regulation
  * [wiki:RegulationPrinciplesIssuesQuestions Regulation]

== Inventories ==

 * [wiki:OrthologInventories Distant orthologs]
 * [wiki:OrthologTableUpdates Ortholog Table Updates]
 * [wiki:PombeGeneLosses Pombe Gene Losses]
 * [wiki:WildTypePhenotype Wild-type Pombe characteristics]



== Deprecated pages ==
 * [wiki:ProgressReports Progress Reports]
 * [wiki:ExampleGenes Example genes with various features]
  * [wiki:TermsSpecificity GO terms we may not require in the curation tool] (too specific)
 * [wiki:PhenotypesToMapToUnstressed Phenotypes to map to unstressed]
 * [wiki:BioGridBaitHitNotationMapping BioGRID bait/hit notation mapping]
 * [wiki:UsefulLinks Useful Links] 
 * [wiki:PhenotypeImportExportFormats Phenotype Import Export draft format]
 * !PomBase User Documentation Drafts
 * General !PomBase Curator Documentation
 * GO 
 *  [wiki:GOOntologyStructure GO ontology structure]
 * [wiki:GOAnnotationGuidelines GO Annotation guidelines] (includes fission yeast specific guidelines, and pre- vs. post-composing GO terms)
 * [wiki:PhenotypeAnnotationGuidelines Phenotype Annotation Guidelines]
 * [wiki:PrePostComposePhenotype Pre- vs. post-composing phenotype terms with conditions]
 * [wiki:CapturingGeneExpression Gene Expression]
 * [wiki:Complementation Complementation]  (needs updating)

 * [wiki:AnnotatingInArtemis Annotating (sequence) features in Artemis]  (needs updating)
 * [wiki:ProteinFeatureAnnotation Protein feature annotation]  (needs updating-val)
 * [wiki:GeneticAndPhysical Genetic and physical Interactions]  (needs updating-val)
 * [wiki:StatusAndSpeciesDistribution Status and Species Distribution]  (needs updating-val)
 * [wiki:GeneralAnnotationExtensionGuidelines  General Annotation Extension Guidelines]
 * [wiki:DescribingResidues Describing Residues]
   

 * Data Handling  and creation Protocols
  * [wiki:ExternalGOData External GO Data]
  * EMBL resubmission
  * GO submission
  * [wiki:HTPDataInstructions HTP data file validation and upload instructions] to send when we receive a form submission


 * Nomenclature
  * [wiki:Nomenclature Gene Nomenclature, will eventually move under "About" on pombase.org]
  * [wiki:GeneProductNaming Gene Product Nomenclature]
  * [wiki:AntisenseNaming Naming antisense transcripts]
 * [wiki:CurationToolFeatures Curation tool Features (completed in progress and pending)]
 * [wiki:FissionYeastPhenotypeOntology Fission Yeast Phenotype Ontology]
 * [wiki:PhenotypeMapping] for PMID:23697806
 * [wiki:OrthologInventoriesNoPom S.c. genes with no pombe orthologs]
 * [wiki:DrugTargets Known Drug Targets]
 * Creating a ProteinComplexInventory
 * [wiki:CuratorTrainingPapers Curator Training Papers]
 * [wiki:TechnicalMeeting PomBase Technical Meeting - Agendas and Action Items]
 * [wiki:InhouseMeetingQuestions Questions to bring up at in-house meeting] page was empty so moved here...
 * [wiki:PombeProIDs 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
 * [wiki:ProteinFeatureDocumentation Protein Feature Documentation] - content now in pombase.org documentation
 * [wiki:Reference_Genomes Reference Genomes Information and Progress]
 * [wiki:Lucene_issues Lucene search issues (none pending)]
 * [wiki:QualifiersUsed Qualifiers Used] (will be mostly deprecated)
 * [wiki:CurationToolBrainstorming Curation tool brainstorming page]
 * [wiki:DescribingResidues describing residues modified or mutated] (Artemis)
 * [wiki:PapersWithNoID Papers with no PMID] 
 * [wiki:PayToView Papers costing ££ to access] 
 * [wiki:ComplementationAnnotations Complementation Annotations to transfer]
 *  [wiki:QualifiersUsed Qualifiers used] 
 * [wiki:PhysicallyUnmappedGenesProteins Physically Unmapped Genes and Proteins]
 * [wiki:CurationToolMultiGenePhenotypes Multi-gene phenotypes in Canto]
 * [wiki:DocumentationForCurationTool Curation Tool]
 * [wiki:GOslims GOslims For unknown project]
 * [wiki:Modification Modification] 
  * [wiki:TrackRelabelling Ensembl browser track labelling]
 * [wiki:PlanningMeetings PomBase Planning Meetings - Agendas and Minutes]
 * [wiki:CuratorMeeting PomBase Curator Meeting - Agendas and Action Items]
 * [wiki:WeeklyGroupCall PomBase group call- Minutes/Actions]
* Chado
 * [wiki:ChadoGenotypesPhenotypes Storage of genotypes and phenotypes in Chado]
 * [wiki:PomBaseReleaseTesting PomBase release testing]
 * [wiki:IncludingAnnotationExtensions Annotation Extensions proposal]
 * [wiki:ExtensionIDTypes Extension ID types]
 * [wiki:CannedQueries Canned queries for  PomBase query tool] 
  * [wiki:DatabaseSanityChecks Database Sanity Checks (syntax)]

* Curation Consistency and QC
  * [wiki:MatrixProject Matrix Project]
  * [wiki:EsyNFiles Files Used By EsyN]

''The !PomBase Team''

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