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<big>'''Welcome to the Plant Ontology Wiki'''</big>
 
<big>'''Welcome to the Plant Ontology Wiki'''</big>
 +
  
 
== Plant Ontology Consortium Resources ==  
 
== Plant Ontology Consortium Resources ==  
 
* [http://www.plantontology.org Plant Ontology Home]
 
* [http://www.plantontology.org Plant Ontology Home]
 
* [http://plantontology.org/amigo/go.cgi Search or browse the Plant Ontology]
 
* [http://plantontology.org/amigo/go.cgi Search or browse the Plant Ontology]
 +
* [http://plantontology.org/docs/release_notes/index.html Release notes] the most recent information on the database and website changes.
 
* [http://plantontology.org/download/download.html Downloads]
 
* [http://plantontology.org/download/download.html Downloads]
  
−
== About the project ==  
+
== About the Plant Ontology project ==  
−
* [http://plantontology.org/docs/otherdocs/poc_project.html Overview of the PO project]
+
* [[ PO_Project_Overview|Overview of the PO project ]]
−
* [http://plantontology.org/docs/otherdocs/charter.html Poc charter] Describes the Consortium's responsibilities and how can you participate in its activities.  
+
* [[ POC_Charter|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/
 +
 
 +
[[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 #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 ===
 +
[[POC_Meetings_Minutes|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]]
 +
 
 +
[[POC Technical Issues Page]]
 +
 
 +
==Affiliated Ontologies==
 +
[[Plant Disease Ontology]]
 +
 
 +
[[Plant Stress Ontology]]
 +
 
 +
[[Plant Trait Ontology]]
 +
 
 +
[[Plant Environment Ontology]]
 +
 
 +
[[Cell Ontology]]
 +
 
 +
[[Gene Ontology]]
 +
 
 +
[[GCP Crop Ontology]]
 +
 
 +
[[Ontology for Biomedical Investigations]]
 +
 
 +
[[Plant Phenotype Ontology]]
 +
 
 +
[http://code.google.com/p/popcomm-ontology/ Population and Community Ontology]
 +
 
 +
==POC Collaborators==
 +
[[ABRC]]
 +
 
 +
[[AgBase]]
 +
 
 +
[[Agron-Omics]]
 +
 
 +
[[Angiosperm Phylogeny Web Glossary]]
 +
 
 +
[[BAR]]
 +
 
 +
[[Cosmoss-_Physcomitrella]]
 +
 
 +
[[CRIBI- Grape Genomics]]
 +
 
 +
[[Flora of North America- FNA]]
 +
 
 +
[[Genome Database for Rosaceae]]
 +
 
 +
[[Gramene]]
 +
 
 +
[[Live Plant Image Group]]
 +
 
 +
[[MaizeGDB]]
 +
 
 +
[[MorphoBank]]
 +
 
 +
[[Minimal Anatomical Terminology]]
 +
 
 +
[[NASC]] Nottingham Arabidopsis Stock Centre
 +
 
 +
[[OBO Foundry]]
 +
 
 +
[[Oryzabase]]
 +
 
 +
[[Oak Ridge National Lab-ORNL]]
 +
 
 +
[[Phenoscape]]
 +
 
 +
[[PlantSystematics.org]]
 +
 
 +
[[PLEXdb]]
 +
 
 +
[http://solgenomics.net/tools/onto/index.pl Solanaceae Genome network (SGN) ]
 +
 
 +
[[SoyBase]]
 +
 
 +
[[SSWAP]]
 +
 
 +
[[TraitNet]]
 +
 
 +
[[Wood Anatomy]]
 +
 
 +
'''* New *'''
 +
 
 +
[[Wheat Gene Catalog]]
 +
 
 +
[[JSTOR Herbarium Annotations]]
 +
 
 +
- Potential new collaborators:
 +
 
 +
[[eMonocot]]
 +
 
 +
[[CoGe]]
 +
 
 +
[[Cycad Pages]]
 +
 
 +
[[Oregon Flora Project]]
 +
 
 +
[[MASISH- Maize Seed In Situ Hybridization database]]
 +
 
 +
[[International Society of Root Research]]
 +
 
 +
[[List of user group contacts]]
 +
 
 +
==[[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]
 +
 
 +
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.
 +
 
 +
===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.
 +
 
 +
* To submit files to the SVN- please see: [[Developers_SVN_Guide]]
 +
 
 +
===PO Annotations pages===
 +
* Links to [http://wiki.plantontology.org/index.php/Category:Annotations 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:
 +
* [[Oryza_sativa_LCM_Tang_et_al,_2010]]
 +
 
 +
==Growth Stage Mappings==
 +
 
 +
Link to [https://github.com/Planteome/plant-ontology/tree/master/mapping2po Mapping files on the Planteome GitHub]
 +
 
 +
*[[Arabidopsis-boyes-stages]]
 +
 
 +
== Outreach ==
 +
* [[POC_Outreach_Events|POC outreach activities and presentations]] by year
 +
* [[Plant Ontology Tutorials]]
 +
* [http://plantontology.org/docs/presentations/demo/poc-demo-1.html 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
 +
 
 +
*[[PO in the media]]
 +
 
 +
==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'''
 +
* [[Relations in the Plant Ontology]]
 +
* [http://code.google.com/p/obo-relations/ OBO relation ontology]
 +
* [http://wiki.geneontology.org/index.php/Reasoner_Overview Reasoner Overview]
 +
 
 +
===Principles, Rationales and Key Organizing Rules of the PO===
 +
''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.
 +
* [[Growth_Stages_Ontology_Principles|Growth Stages Ontology]] and [[Growth_Stages_Ontology_FAQ|frequently asked  questions]]
 +
* [[Developmental_Stages_Ontology_Principles|Developmental Stages Ontology]]
 +
 
 +
''' Formats of the Ontology Files'''
 +
* OBO format: The Plant Ontology follows the Gene Ontology's: [http://www.geneontology.org/GO.format.obo-1_2.shtml 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 [http://protege.stanford.edu Protege] software.
 +
 
 +
 
 +
''' Ontology accessions '''
 +
* [[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]'''''
 +
 
 +
* [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
 +
** 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.
  
−
== Plant Ontology Development Guidelines ==
+
== Other ==
−
* [http://plantontology.org/docs/otherdocs/ontology_doc.html Developers style guide] provides key concepts and stylistic aspects of PO.
+
[[Calendar]] (POC outreach schedule)
−
'''Principles, rationals and key organizing rules of the PO'''
 
−
** [http://plantontology.org/docs/otherdocs/principles_rationales.html Plant structure ontology] Rationale for high nodes in the ontology, examples and explanation of three "patterns" of the ontology structure.
 
−
** [http://plantontology.org/docs/growth/growth_stages.html Growth Stages Ontology]
 
−
** [http://plantontology.org/docs/development/developmental_stages.html Developmental Stages Ontology]
 
−
* [http://plantontology.org/docs/numbers/number.html Ontology Accessions] Guide to unique accessions/ids associated to each PO term.
 
−
* [http://plantontology.org/docs/dbxref/PO_DBXref.txt DBXrefs] Provides a list of the database cross reference abbreviations used in the ontology files and the database.
 
−
''' Flat file formats '''
 
−
* [http://www.geneontology.org/GO.format.obo-1_2.shtml Ontology file format]
 
−
* [http://plantontology.org/docs/otherdocs/assoc-file-format.html Annotation file formats] If your database/project would like to submit the annotations to the PO database, please consult the suggested file format.
 
  
 
== Wiki meta links ==
 
== Wiki meta links ==
 
* [http://meta.wikimedia.org/wiki/Help:Contents User's Guide]
 
* [http://meta.wikimedia.org/wiki/Help:Contents User's Guide]
 +
* [http://www.mediawiki.org/wiki/Help:Formatting Wiki syntax]
 
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
 
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
 
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
 
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
 
* [http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]
 
* [http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]

Latest revision as of 20:45, 12 October 2016

Welcome to the Plant Ontology Wiki


Plant Ontology Consortium Resources

About the Plant Ontology project

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/

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 #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 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

POC Technical Issues Page

Affiliated Ontologies

Plant Disease Ontology

Plant Stress Ontology

Plant Trait Ontology

Plant Environment Ontology

Cell Ontology

Gene Ontology

GCP Crop Ontology

Ontology for Biomedical Investigations

Plant Phenotype Ontology

Population and Community Ontology

POC Collaborators

ABRC

AgBase

Agron-Omics

Angiosperm Phylogeny Web Glossary

BAR

Cosmoss-_Physcomitrella

CRIBI- Grape Genomics

Flora of North America- FNA

Genome Database for Rosaceae

Gramene

Live Plant Image Group

MaizeGDB

MorphoBank

Minimal Anatomical Terminology

NASC Nottingham Arabidopsis Stock Centre

OBO Foundry

Oryzabase

Oak Ridge National Lab-ORNL

Phenoscape

PlantSystematics.org

PLEXdb

Solanaceae Genome network (SGN)

SoyBase

SSWAP

TraitNet

Wood Anatomy

* New *

Wheat Gene Catalog

JSTOR Herbarium Annotations

- Potential new collaborators:

eMonocot

CoGe

Cycad Pages

Oregon Flora Project

MASISH- Maize Seed In Situ Hybridization database

International Society of Root Research

List of user group contacts

Links to sites using the PO

Preparation of Ontology Annotation Files

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.

Demo of deldupe Rfunction1.png


Information about how to use column 16:

Other Helpful Info:

  • 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.

PO Annotations pages


In progress:

Growth Stage Mappings

Link to Mapping files on the Planteome GitHub

Outreach

Publications and Other Resources

  • Related Publications References and citations of interest on ontology, published by the PO consortium and collaborators.

If you are aware of a publication that is not on this list, please send us the citation and we will add it.

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.

Formats of the Ontology Files


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

Other

Calendar (POC outreach schedule)

Wiki meta links

Retrieved from "http://wiki.plantontology.org/index.php?title=Main_Page&oldid=26256"