View source for Links to sites using the PO

=Ontology Listing Services, etc= 
[http://agroportal.lirmm.fr/ Agroportal]

[http://bioportal.bioontology.org/ Bioportal]

[http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=PO EBI OLS] 

[http://www.obofoundry.org/ OBO Foundry]

[http://ontofox.hegroup.org/ OntoFox]- web-based Ontology tool that fetches ontology terms and axioms

[http://www.ontobee.org/ OntoBee]

[http://isatab.sourceforge.net/ ISA Tools Software Suite]- Use of ontologies is recommended

[http://www.metabolomics-msi.org/ Metabolomics Standards Initiative]- PO is recommended in MSI standards

=A to F=
[https://www.ebi.ac.uk/fg/annotare/ Annotare]- Array Express experiment submission tool

* Ref: [https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btq462 Annotare—a tool for annotating high-throughput biomedical investigations and resulting data] Bioinformatics, Volume 26, Issue 19, 1 October 2010, Pages 2470–2471

[https://arapheno.1001genomes.org/ontology/PTO/ Arapheno] - search by TO or EO, weird versions

[http://www.brenda-enzymes.info/ BRENDA]- mostly uses BTO, but old version of PO, TO and EO are on it

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[http://www.agbase.msstate.edu/ AgBase]- only has annotations to GO

[https://database.riken.jp/sw/ ARTADE2DB]- link not working?

[http://biolod.org/ Biolod.org] example page: [http://biolod.org/class/cria131u4510i/PO_0004510 non-secretory trichome]
see also: [http://biolod.org/database/ria131i/PO_class_structure_Plant_structure plant structure] - site and links not working?

[http://brassibase.cos.uni-heidelberg.de/ Brassibase]- No PO on their site

[http://www.cosmoss.org/ cosmoss]- No PO on their site

[http://www.cyverse.org/ Cyverse]- mirror site of planteome, otherwise not sure how it is being used

=G to L=

[http://archive.gramene.org/plant_ontology/ Gramene Archive]- Old ontology browsers

[http://ensembl.gramene.org/biomart/martview/a5af63c60de7ebc805c5f558d7459deb Gramene Biomart]- can filter by PO and GO

[http://genomes.cribi.unipd.it/grape/ Grape genome database] 

[http://genomes.cribi.unipd.it/cgi-bin/pqs2/query.pl?release=v1#Ontologies Query page CRIBI]- Grape genes are annotated to PO terms

[https://sites.google.com/site/liveplantimagegroup/home Live Plant Image Group]- has links to browse PO, but not sure how it is used

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[http://www.geneontology.org/ Gene Ontology]- No PO or TO?

=M to P=

[http://bioinformatics.intec.ugent.be/magic/ MAGIC]- 'MAize Gene expressIon Compendium'- a web-based interface for exploring and analyzing a comprehensive maize-specific cross-platform expression compendium. 
* This compendium was constructed by collecting, homogenizing and formally annotating publicly available microarrays from Gene Expression Omnibus (GEO), and ArrayExpress. Includes plant ontology annotations
* REF: [https://academic.oup.com/bioinformatics/article/30/9/1316/234066/MAGIC-access-portal-to-a-cross-platform-gene MAGIC: access portal to a cross-platform gene expression compendium for maize]-  Fu et al (2014), Bioinformatics. doi: 10.1093/bioinformatics/btt739

[http://maizegdb.org/gene_center/gene/GRMZM2G119578 MaizeGDB Genes]- PO annotations are listed on Gene pages from Sekhon study.

[http://maize.jcvi.org/cellgenomics/ecell.php?search=10 Maize cell Genomics database]- images tagged with PO ids 

[http://www.genomeindia.org/biocuration/ Manually Curated Database of Rice Proteins]- tagged with TO terms

[http://services.cbib.u-bordeaux2.fr/MERYB/vocabulary/ontology.php?section=2&sel=&expand=1&term_id=603&specie= Metabolomic Repository Bordeaux MeRy]- plant metabolomics platform allowing the storage and visualisation of Nuclear Magnetic Resonance (NMR) metabolic profiles from plants, but has old version of PO and EO

[http://compgenomics.ucdavis.edu/morphodb/analysis/viewOntology.php Morphodb]- Cool PO browser with links to annotated data from lettuce and sunflower, really old version of PO

[https://shigen.nig.ac.jp/rice/oryzabase/ Oryzabase]- 


[http://bioweb.supagro.inra.fr/phenopsis/ Phenopsis] - from INRA, information system dedicated to the model plant Arabidopsis thaliana; ontology terms are out of date on here, links go go to the EBI OLS
* see page: [http://bioweb.supagro.inra.fr/phenopsis/ConsulterOrgane.php PO terms]

[http://caps.ncbs.res.in/poeas/index.html POEAS]- Plant Ontology Enrichment Analysis Server, automated Plant Phenomic Analysis Using Plant Ontology terms based on genes from Arabidopsis thaliana

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[https://database.riken.jp/sw/en/Home/cria301u1i/ The Integrated Databases of Plant Omics Data]- link not working

[http://www.cs.utexas.edu/~miranker/studentWeb/OntobrowserHomePage.html OntoBrowser]- interactive ontology navigator and ontology-based image retrieval system. It makes use of an ontology to retrieve images. page not loading...

[http://biolod.org/database/ria224i/Plant_Phenome Plant Phenome]- on Biolod, links not functional

[http://arabidopsis.info/NASC Ontology page]- link to ontology browser is not functional

[http://www.plantsystematics.org Plantsystematics.org]- ?? cant find any PO ref

[https://www.ebi.ac.uk/pride/archive/ PRIDE]- PRoteomics IDEntifications (PRIDE) database, used to have a ontology query, but cannot find it now

=R to Z=

[http://rarge-v2.psc.riken.jp/ RARGEII]- RIKEN Arabidopsis Genome Encyclopedia, Search mutant lines by phenotypes- use PO or PATO

[http://semantic-json.org/sw/wiki/en/cria160s1ria160s5i/#applications Riken]- link not working...

[http://solgenomics.net/tools/onto/index.pl Solanaceae Genome network (SGN)]- can browse/search by GO,PO, SO, PATO

[https://soybase.org/ SoyBase]- AmiGO browser of Soy Ontology terms, not mapped to PO or TO

[http://supfam.cs.bris.ac.uk/SUPERFAMILY/cgi-bin/phenotype.cgi?search=AP%3A0025099 SuperFamily] - need to address some issues here, not an "Arabidopsis Plant Ontology".

[http://traitnet.ecoinformatics.org/ Traitnet]- no ontology searches etc from their site...

[http://www.uniprot.org/keywords/ Uniprot keywords]- can search for GO terms, no use of PO ??

[http://virtualplant.bio.nyu.edu/cgi-bin/vpweb/ Virtual plant]- browse the Plant Ontology to see Arabidopsis genes annotated to that term

[https://www.arabidopsis.org/ TAIR] - GO_and_PO_Annotations can be downloaded, browse by ontology terms

=Others?=
not actually using the PO but should be:

[http://bar.utoronto.ca/welcome.htm Bio-Array Resource for Plant Biology (BAR)] 

[http://www.cropontology.org/ Crop Ontology]	

[https://www.genevestigator.com/gv/plant.jsp Genevestigator]