Useful Links for PomBase Curators

a collection of links to useful sites, files, and other resources that we haven't fit in to any other wiki pages

Curation tool

• Curation tool (production) ​http://curation.pombase.org/pombe
• GO test version(uses UniProt accession ​http://oliver0.sysbiol.cam.ac.uk/uniprot/
• Curation tool PomBase? Test version ​http://curation.pombase.org/test
• Test session without genes ​http://curation.pombase.org/t
• Test session with genes ​http://curation.pombase.org/t/2

Chado

• All Chado views and reports ​internal ​external
• All controlled vocabularies in Chado ​internal or ​external
• Sequence feature types and counts loaded into Chado ​internal or ​external

GO related

• GO 'reference and evidence codes' section of Downloads page - notably, has links to the dbxref abbreviation collection
  • ​http://geneontology.org/GO.downloads.files.shtml#ref
    • Abbreviations ​plain text or ​pretty web formatting
    • Reference collection ​plain text or ​pretty web formatting

• ​GO SourceForge trackers
  • ​Ontology term requests
  • ​Annotation issues
  • ​Evidence code ontology (ECO) requests
  • ​DB xrefs

• ​TermGenie

General Ontology Links

• Other trackers
  • ​Sequence Ontology
  • ​PATO

• Subversion SVN tour and manual
  • ​http://svnbook.red-bean.com/en/1.6/svn.tour.cycle.html
  • ​http://svnbook.red-bean.com/en/1.6/index.html

• Ontologies
  • FYPO ​http://pombase.svn.sourceforge.net/viewvc/pombase/phenotype_ontology/fypo_edit.obo
  • GO ​http://geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo
  • SO ​http://song.cvs.sourceforge.net/*checkout*/song/ontology/so-xp.obo
  • PATO ​http://pato.googlecode.com/svn/trunk/quality.obo
  • CL ​http://purl.obolibrary.org/obo/cl.obo
  • PRO ​ftp://ftp.pir.georgetown.edu/databases/ontology/pro_obo/pro.obo
  • PSI-MOD ​http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/mod/data/PSI-MOD.obo
  • ECO NEW: ​http://code.google.com/p/evidenceontology/issues/list OLD: ​http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/evidence_code.obo
  • RO ​http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo
  • GO annotation extension relations ​http://www.geneontology.org/scratch

/xps/go_annotation_extension_relations.obo

• GO annotation extension view ​http://www.ebi.ac.uk/QuickGO/AnnotationExtensionRelations.html