Difference between revisions of "Main Page"
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Visit the pages below for specific details on each release | Visit the pages below for specific details on each release | ||
| − | Next Release: | + | Next Release: After Jan 2016, the PO releases will be part of the Planteome Releases see: http://planteome.org/ |
| − | + | [[For Next Release:]] | |
| + | |||
| + | Past Releases: | ||
| + | |||
| + | Last PO Release October 2015 [[Release 21]] | ||
| + | |||
| + | Release #20: August 2013 [[Release_20]] | ||
Release #19 January, 2013 [[Release_19]] | Release #19 January, 2013 [[Release_19]] | ||
| Line 36: | Line 42: | ||
Release #13 [[October 2010 Release Page]] | Release #13 [[October 2010 Release Page]] | ||
| + | |||
| + | *''' Protocols page for Plant Ontology Releases: [[PO Release SOP Page]]''' | ||
== POC Meetings == | == POC Meetings == | ||
| Line 155: | Line 163: | ||
==[[Links to sites using the PO]]== | ==[[Links to sites using the PO]]== | ||
| − | == | + | == Preparation of Ontology 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 [http://www.geneontology.org/GO.format.gaf-2_0.shtml GO gaf 2.0 format] | * 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 [http://www.geneontology.org/GO.format.gaf-2_0.shtml GO gaf 2.0 format] | ||
| − | * | + | |
| + | Before submitting new association files please do the following checks: | ||
| + | |||
| + | * Remove any duplicated rows | ||
| + | |||
| + | * Remove rows where contents of column 1 through column 15 are identical to any other row. | ||
| + | |||
| + | * Remove rows containing identical information in all columns aside from column 11 (synonym), and the synonyms should be added to the identical row using a "pipe" | | ||
| + | |||
| + | eg: Autophagy|Isoamylase | ||
| + | |||
| + | * Rows containing information in column 16 should be kept | ||
| + | |||
| + | * Rows containing duplicate information in columns 1-15, but lacking information in column 16 should be removed. These rows cause duplicate information to be displayed in the browser. | ||
| + | |||
| + | * See the image below for an example of duplicate rows differing in only column 16, in this case, the highlighted row would be removed to avoid duplications in annotation. | ||
| + | |||
| + | [[File:Demo_of_deldupe_Rfunction1.png]] | ||
| + | |||
| + | |||
| + | ===Information about how to use column 16: === | ||
| + | * Please consult the guidelines for using the column 16 [[PO_Annotation_Extensions_(column_16)]] | ||
| + | |||
* See also [https://docs.google.com/spreadsheet/ccc?key=0AhrY0qRdO4budHRqaklJcmJxRjlaVnV6UGlyd0xWbHc&hl=en_US Google docs spread sheet] with specific suggestions of what terms and relations to put in column 16. | * See also [https://docs.google.com/spreadsheet/ccc?key=0AhrY0qRdO4budHRqaklJcmJxRjlaVnV6UGlyd0xWbHc&hl=en_US Google docs spread sheet] with specific suggestions of what terms and relations to put in column 16. | ||
| − | |||
| + | ===Other Helpful Info:=== | ||
| + | |||
| + | * Adding [["Associated to" links]] to GO (final table column in the association view) | ||
* Link to the [https://github.com/Planteome/common-files-for-ref-ontologies/blob/master/PO_DBXref.txt PO_DBXref.txt] on the GitHub of the dbxRefs currently in use. There is also a link to this from our "Documentation" page on the PO site. | * Link to the [https://github.com/Planteome/common-files-for-ref-ontologies/blob/master/PO_DBXref.txt PO_DBXref.txt] on the GitHub of the dbxRefs currently in use. There is also a link to this from our "Documentation" page on the PO site. | ||
| − | |||
* To submit files to the SVN- please see: [[Developers_SVN_Guide]] | * To submit files to the SVN- please see: [[Developers_SVN_Guide]] | ||
| − | + | ===PO Annotations pages=== | |
| − | PO Annotations | + | * Links to [http://wiki.plantontology.org/index.php/Category:Annotations Category:Annotations] |
* [[Arabidopsis_Schmid_2005]] | * [[Arabidopsis_Schmid_2005]] | ||
| + | * [[Plant_Pheontype_Pilot_Project_2015]] | ||
* [[Oryza_sativa_LCM_Aya_et_al,_2011]] | * [[Oryza_sativa_LCM_Aya_et_al,_2011]] | ||
* [[Oryza_sativa,_IMP,_Gramene_Genes]] | * [[Oryza_sativa,_IMP,_Gramene_Genes]] | ||
| Line 177: | Line 208: | ||
* [[Zea mays_Leaf_Dev_Li et al,_2010]] | * [[Zea mays_Leaf_Dev_Li et al,_2010]] | ||
* [[Zea_mays_IEP_Sekhon]] | * [[Zea_mays_IEP_Sekhon]] | ||
| + | *[[SoyBase_QTL]] | ||
| + | |||
In progress: | In progress: | ||
| Line 191: | Line 224: | ||
* [[Plant Ontology Tutorials]] | * [[Plant Ontology Tutorials]] | ||
* [http://plantontology.org/docs/presentations/demo/poc-demo-1.html Introduction to the project] (slide show) | * [http://plantontology.org/docs/presentations/demo/poc-demo-1.html Introduction to the project] (slide show) | ||
| − | * [[How to use the | + | * [[How to use the GitHub Issues]] to request new terms or changes to existing term. |
== Publications and Other Resources== | == Publications and Other Resources== | ||
| Line 217: | Line 250: | ||
===Principles, Rationales and Key Organizing Rules of the PO=== | ===Principles, Rationales and Key Organizing Rules of the PO=== | ||
| − | |||
''The first three pages listed below are not up to date.'' | ''The first three pages listed below are not up to date.'' | ||
* [[Plant_Structure_Principles_Rules|Plant Structure Ontology]] Rationale for high nodes in the ontology, examples and explanation of three "patterns" of the ontology structure. | * [[Plant_Structure_Principles_Rules|Plant Structure Ontology]] Rationale for high nodes in the ontology, examples and explanation of three "patterns" of the ontology structure. | ||
* [[Growth_Stages_Ontology_Principles|Growth Stages Ontology]] and [[Growth_Stages_Ontology_FAQ|frequently asked questions]] | * [[Growth_Stages_Ontology_Principles|Growth Stages Ontology]] and [[Growth_Stages_Ontology_FAQ|frequently asked questions]] | ||
* [[Developmental_Stages_Ontology_Principles|Developmental Stages Ontology]] | * [[Developmental_Stages_Ontology_Principles|Developmental Stages Ontology]] | ||
| − | |||
| − | |||
''' Formats of the Ontology Files''' | ''' Formats of the Ontology Files''' | ||
| Line 233: | Line 263: | ||
* [[Accession_IDS_Guide|Guide to unique accessions/ids associated to each PO term]] | * [[Accession_IDS_Guide|Guide to unique accessions/ids associated to each PO term]] | ||
| − | + | '''Creating Dbxrefs to outside Sources:''' | |
| − | ''' | ||
| − | |||
'''''Note: As of Aug. 2015 the DbXref file is located in the [https://github.com/Planteome/common-files-for-ref-ontologies Planteome GitHub Repository/common files]''''' | '''''Note: As of Aug. 2015 the DbXref file is located in the [https://github.com/Planteome/common-files-for-ref-ontologies Planteome GitHub Repository/common files]''''' | ||
| Line 241: | Line 269: | ||
* [https://github.com/Planteome/common-files-for-ref-ontologies/blob/master/PO_DBXref.txt Database cross reference file on GitHub- current] | * [https://github.com/Planteome/common-files-for-ref-ontologies/blob/master/PO_DBXref.txt Database cross reference file on GitHub- current] | ||
| − | + | ====Requesting new ontology terms, or changes to existing terms ==== | |
| − | * | + | * Link to [https://github.com/Planteome/plant-ontology/issues Plant Ontology GitHub Issues Tracker] |
| − | |||
* Xref to the GitHub trackers: PO_GIT:xyz | * Xref to the GitHub trackers: PO_GIT:xyz | ||
| − | |||
** Helpful hint: to create a link in the tracker to another tracker, use: '#xyz' | ** Helpful hint: to create a link in the tracker to another tracker, use: '#xyz' | ||
| + | * Xrefs to (now deprecated) 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 | ||
| + | |||
| + | |||
| + | ====PO-Refs==== | ||
| + | * 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. | |
| − | * | ||
== Other == | == Other == | ||
Latest revision as of 20:45, 12 October 2016
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
- 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: After Jan 2016, the PO releases will be part of the Planteome Releases see: http://planteome.org/
Past Releases:
Last PO Release October 2015 Release 21
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
- Protocols page for Plant Ontology Releases: PO Release SOP Page
POC Meetings
POC weekly meetings
Minutes of the Plant Ontology Consortium meetings
POC workshops and other meetings
PRO-PO-GO_Meeting Buffalo, NY May 2013
Plant_Ontology_and_Crop_Annotation_Workshop_OSU_2012
Wood_anatomy_ontology_meeting,_2012_at_NYBG,_agenda
POC Meeting at NYBG; Sept 10th-11th, 2011
POC Meeting and Workshop Nov 4th to 6th, 2010; NYBG, Bronx, NY
POC_Meeting and Workshop June 29th and 30th, 2010 Corvallis, OR
Affiliated Ontologies
Ontology for Biomedical Investigations
Population and Community Ontology
POC Collaborators
Angiosperm Phylogeny Web Glossary
Minimal Anatomical Terminology
NASC Nottingham Arabidopsis Stock Centre
Solanaceae Genome network (SGN)
* New *
- Potential new collaborators:
MASISH- Maize Seed In Situ Hybridization database
International Society of Root Research
Links to sites using the PO
Preparation of Ontology 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
Before submitting new association files please do the following checks:
- Remove any duplicated rows
- Remove rows where contents of column 1 through column 15 are identical to any other row.
- Remove rows containing identical information in all columns aside from column 11 (synonym), and the synonyms should be added to the identical row using a "pipe" |
eg: Autophagy|Isoamylase
- Rows containing information in column 16 should be kept
- Rows containing duplicate information in columns 1-15, but lacking information in column 16 should be removed. These rows cause duplicate information to be displayed in the browser.
- See the image below for an example of duplicate rows differing in only column 16, in this case, the highlighted row would be removed to avoid duplications in annotation.
Information about how to use column 16:
- Please consult the guidelines for using the column 16 PO_Annotation_Extensions_(column_16)
- See also Google docs spread sheet with specific suggestions of what terms and relations to put in column 16.
Other Helpful Info:
- Adding "Associated to" links to GO (final table column in the association view)
- Link to the PO_DBXref.txt on the GitHub of the dbxRefs currently in use. There is also a link to this from our "Documentation" page on the PO site.
- To submit files to the SVN- please see: Developers_SVN_Guide
PO Annotations pages
- Links to Category:Annotations
- Arabidopsis_Schmid_2005
- Plant_Pheontype_Pilot_Project_2015
- Oryza_sativa_LCM_Aya_et_al,_2011
- Oryza_sativa,_IMP,_Gramene_Genes
- Vitis_vinifera;_grape
- Zea mays_Leaf_Dev_Li et al,_2010
- Zea_mays_IEP_Sekhon
- SoyBase_QTL
In progress:
Growth Stage Mappings
Link to Mapping files on the Planteome GitHub
Outreach
- POC outreach activities and presentations by year
- Plant Ontology Tutorials
- Introduction to the project (slide show)
- 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
- PO Developers Guide
- To submit files to the SVN- please see: Developers_SVN_Guide
- To submit files to the GitHub repository- please see: Developers_GitHub_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
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.
Ontology accessions
Creating Dbxrefs to outside Sources:
Note: As of Aug. 2015 the DbXref file is located in the Planteome GitHub Repository/common files
Requesting new ontology terms, or changes to existing terms
- Xref to the GitHub trackers: PO_GIT:xyz
- Helpful hint: to create a link in the tracker to another tracker, use: '#xyz'
- Xrefs to (now deprecated) 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
PO-Refs
- 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.
Other
Calendar (POC outreach schedule)
