Plant Ontology Wiki po-mw_wikidb http://wiki.plantontology.org/index.php/Main_Page MediaWiki 1.35.0 first-letter Media Special Talk User User talk Plant Ontology Wiki Plant Ontology Wiki talk File File talk MediaWiki MediaWiki talk Template Template talk Help Help talk Category Category talk In Discussion In Discussion talk 0 1 26256 26255 2016-10-12T20:45:38Z Cooperl 9 /* PO Releases and Database Updates */ 26256 wikitext text/x-wiki <big>'''Welcome to the Plant Ontology Wiki'''</big> == Plant Ontology Consortium Resources == * [http://www.plantontology.org Plant Ontology Home] * [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] == About the Plant Ontology project == * [[ PO_Project_Overview|Overview of the PO project ]] * [[ 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. == Other == [[Calendar]] (POC outreach schedule) == Wiki meta links == * [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:FAQ MediaWiki FAQ] * [http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list] 9gfxfr2izd2zt0c6ioqk6ln2b5ln98e