Main Page
Welcome to the Plant Ontology Wiki
Plant Ontology Consortium Resources
- Plant Ontology Home
- Search or browse the Plant Ontology
- Release notes the most recent information on the database and website changes.
- Downloads
About the Plant Ontology project
- Overview of the PO project
- POC charter Describes the Consortium's responsibilities and how can you participate in its activities.
- Citing POC How to cite POC in your article
- File:PO brochure final (LC 7-21-11).pdf
PO Releases and Database Updates
Visit the pages below for specific details on each release
Next Scheduled Release:
Tentatively scheduled for: Early November Release_19
POC Meetings
POC weekly meetings
Minutes of the Plant Ontology Consortium meetings
POC workshops and other meetings
POC_Meeting and Workshop June 29th and 30th, 2010 Corvallis, OR
POC Meeting and Workshop Nov 4th to 6th, 2010; NYBG, Bronx, NY
POC Meeting at NYBG; Sept 10th-11th, 2011
Wood_anatomy_ontology_meeting,_2012_at_NYBG,_agenda
Plant_Ontology_and_Crop_Annotation_Workshop_OSU_2012
POC Collaborators and Affiliated Ontologies
Angiosperm Phylogeny Web Glossary
Minimal Anatomical Terminology
NASC Nottingham Arabidopsis Stock Centre
Ontology for Biomedical Investigations
Population and Community Ontology
Solanaceae Genome network (SGN)
* New *
Potential new collaborators:
MASISH- Maize Seed In Situ Hybridization database
International Society of Root Research
Ontology Annotations
PO Annotations page links to Category:Annotations
Outreach
- POC outreach activities and presentations by year
- Plant Ontology Tutorials
- Introduction to the project (slide show)
- How to use the SourceForge tracker to request new terms or changes to existing term.
Publications and Other Resources
- Related Publications References and citations of interest on ontology, published by the PO consortium and collaborators.
- Plant Ontology Citations Publications from outside the consortium that discuss the PO or use it in their analyses.
If you are aware of a publication that is not on this list, please send us the citation and we will add it.
- Ontology Resources Links to other projects working on ontologies
Plant Ontology Development Guidelines
Developers style guide
Descriptions of relations in the PO
Principles, Rationales and Key Organizing Rules of the PO
The first three pages listed below are not up to date.
- Plant Structure Ontology Rationale for high nodes in the ontology, examples and explanation of three "patterns" of the ontology structure.
- Growth Stages Ontology and frequently asked questions
- Developmental Stages Ontology
- Protocols page for Plant Ontology Releases: PO Release SOP Page
Ontology accessions
DBXrefs
- link to Dbxrefs file on SVN: dbxrefs
- Database cross reference file on the SVN- current
- Custom references maintained by PO, for items without a standard url abbreviation, can be viewed at PO references
- the Plant Ontology curators page provides a list of ontology curators and editors, with their affiliations.
Formats of the Ontology Files
- OBO format: The Plant Ontology follows the Gene Ontology's: OBO Flat File Format Specification, version 1.2
- OWL Format: The Plant Ontology is also available in Web Ontology Language (OWL) as rdf/xhml, which can be viewed and editing using Protege software.
Preparation and Display of Annotation Files
- If your database/project would like to submit annotations to the PO database, please consult the suggested file format: Annotation Association File Format and the GO gaf 2.0 format
- For more information about how to use column 16: PO_Annotation_Extensions_(column_16)#Specific_suggestions_for_column_16
- See also Google docs spread sheet with specific suggestions of what terms and relations to put in column 16.
- Adding "Associated to" links to GO (final table column in the association view)
Requesting new ontology terms, or changes to existing terms
- Link to Source Forge tracker
- Wiki page with instructions on How to use the Source Forge tracker.
Other
Calendar (POC outreach schedule)
