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

Canto Test Tool

• Test tool, Canto front page : ​http://curation.pombase.org/test/docs/canto_front
  • this page exists so we can look at the changes to the Canto home page before release
• Test Tool, front page: ​http://curation.pombase.org/test/

Chado

• ​All Chado views and reports
• ​annotation extensions
• ​cvs
• ​All controlled vocabularies in Chado
• ​Sequence feature types and counts loaded into Chado
• ​Chado dumps and warnings

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 (a.k.a. dbxrefs) ​plain text or ​pretty web formatting
    • Reference collection ​plain text or ​pretty web formatting

• Taxon constraints
  • taxon "triggers" obo file ​GO web link to file or see revision history at ​GO CVSweb (links to current and past versions of the files)
  • PomBase annotation report ​GO web link or ​CVSweb link

• Annotation extension relations listed under "ontologies" below
• ​GO SourceForge trackers
  • ​Ontology term requests
  • ​Annotation issues

General Ontology Links

• Other trackers
  • ​Sequence Ontology
  • ​PATO
  • ​Evidence code ontology (ECO)
  • ​PRO

• 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 ​fypo-simple.obo, which is what Kim loads into Canto, or ​full FYPO
    • to see relations used in the ontology, look at the "Typedef" stanzas at the bottom of the ​FYPO editing file
  • PECO (phenotype conditions) ​https://sourceforge.net/p/pombase/code/HEAD/tree/phenotype_ontology/peco.obo
  • GO ​GO basic (used for Chado load) or ​complete core GO
  • SO ​https://sourceforge.net/p/song/svn/HEAD/tree/trunk/so-xp.obo
  • PATO ​http://purl.obolibrary.org/obo/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
    • Current release: ​https://code.google.com/p/evidenceontology/source/browse/trunk/eco.obo
    • Editors' version (pre-release): ​https://code.google.com/p/evidenceontology/source/browse/trunk/eco-edit.obo
  • RO ​http://purl.obolibrary.org/obo/ro.obo
  • GO annotation extension relations
    • GO relations file (includes extension relations and others): ​http://purl.obolibrary.org/obo/go/extensions/gorel.obo
    • QuickGO graphical view: ​http://www.ebi.ac.uk/QuickGO/AnnotationExtensionRelations.html

• Other
  • PRO home page ​http://pir.georgetown.edu/pro/

Website links

• How to report when scary error messages appear on PomBase web pages: ​Jira PB-1394 (last comment)