Version 70 (modified by 6 years ago) (diff) | ,
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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
- http://geneontology.org/GO.downloads.files.shtml#ref
- 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
General Ontology Links
- Other trackers
- Subversion SVN tour and manual
- 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
- FYPO fypo-simple.obo, which is what Kim loads into Canto, or full FYPO
- 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)