From Plant Ontology Wiki
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.
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
- Creative Commons License
- Plant Ontology Response to OBO Foundry Review
PO Releases and Database Updates
Visit the pages below for specific details on each release
Next Release: Release 21 Tentatively Scheduled for the Spring 2014
Latest Release #20: August 2013 Release_20
Release #19 January, 2013 Release_19
Release #18 July 2012 Release
Release #17 April 2012 Release Page
Release #16 October 2011 Release Page
Release #15 May 2011 Release Page
Release #14 Jan 2011 Release Page
Release #13 October 2010 Release Page
POC weekly meetings
POC workshops and other meetings
PRO-PO-GO_Meeting Buffalo, NY May 2013
NASC Nottingham Arabidopsis Stock Centre
* New *
- Potential new collaborators:
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)
- Link to the PO_DBXref.txt on the SVN of the dbxRefs currently in use. There is also a link to this from our "Documentation" page on te PO site.
- To submit files to the SVN- please see: Developers_SVN_Guide
PO Annotations page links to Category:Annotations
- Zea mays_Leaf_Dev_Li et al,_2010
Growth Stage Mappings
- 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.
- How to use the Github Issues 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
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.
- link to Dbxrefs file on SVN: dbxrefs
Note: As of Aug. 2015 the DbXref file is located in the Planteome GitHub Repository/common files
- 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.
- Xrefs to SourceForge trackers in the OBO file: There are two types of xrefs: prior to mid 2013, they were entered as: OBO_SF_PO:XXXXXXX (7 digit number). After the revision of the SourceForge tracker software in mid 2013, the new Xref format is: OBO_SF2_PO:xxx
- Helpful hint: to create a link in the tracker to another tracker, use: [plant-ontology-po-term-requests:#xxx]
Requesting new ontology terms, or changes to existing terms
Calendar (POC outreach schedule)