Links to sites using the PO

Ontology Listing Services

Agroportal

Bioportal

EBI OLS

OBO Foundry

OntoFox- web-based Ontology tool that fetches ontology terms and axioms

OntoBee

A to F

Annotare- Array Express experiment submission tool

• Ref: Annotare—a tool for annotating high-throughput biomedical investigations and resulting data Bioinformatics, Volume 26, Issue 19, 1 October 2010, Pages 2470–2471

Arapheno - search by TO or EO, weird versions

BRENDA- mostly uses BTO, but old version of PO, TO and EO are on it

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AgBase- only has annotations to GO

ARTADE2DB- link not working?

Biolod.org example page: non-secretory trichome see also: plant structure - site and links not working?

Brassibase- No PO on their site

cosmoss- No PO on their site

Cyverse- mirror site of planteome, otherwise not sure how it is being used

G to L

Gramene Archive-

Gramene Biomart- can filter by PO and GO

Grape genome database

Query page CRIBI- Grape genes are annotated to PO terms

Live Plant Image Group- has links to browse PO, but not sure how it is used

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Gene Ontology- No PO or TO?

ISA Tools Software Suite

M to P

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: MAGIC: access portal to a cross-platform gene expression compendium for maize- Fu et al (2014), Bioinformatics. doi: 10.1093/bioinformatics/btt739

MaizeGDB- PO annotations are listed on Gene pages from Sekhon study:

Maize cell Genomics database- images tagged with PO ids

Manually Curated Database of Rice Proteins- tagged with TO terms

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

Metabolomics Standards Initiative- PO is recommended in MSI standards

Morphodb- Cool PO browser with links to annotated data from lettuce and sunflower, really old version of PO

Phenopsis - from INRA, information system dedicated to the model plant Arabidopsis thaliana; ontology terms are out of date on here, links go go to the EBI OLS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: PO terms

POEAS- Plant Ontology Enrichment Analysis Server, automated Plant Phenomic Analysis Using Plant Ontology

PRIDE- In query, there are a list of parameter types to choose from. If you pick PO, you get a list of terms.

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The Integrated Databases of Plant Omics Data- link not working

OntoBrowser- interactive ontology navigator and ontology-based image retrieval system. It makes use of an ontology to retrieve images. page not loading...

Plant Phenome- on Biolod, links not functional

Ontology page- link to ontology browser is not functional

Plantsystematics.org- ?? cant find any PO ref

R to Z

RARGEII- RIKEN Arabidopsis Genome Encyclopedia, Search mutant lines by phenotypes- use PO or PATO

Riken- link not working...

Solanaceae Genome network (SGN)- can browse/search by GO,PO, SO, PATO

SoyBase- AmiGO browser of Soy Ontology terms, not mapped to PO or TO

SuperFamily - need to address some issues here, not an "Arabidopsis Plant Ontology".

Traitnet- no ontology searches etc from their site...

Uniprot keywords- can search for GO terms, no use of PO ??

Virtual plant- browse the Plant Ontology to see Arabidopsis genes annotated to that term

TAIR - GO_and_PO_Annotations can be downloaded, browse by ontology terms

Others?

not actually using the PO but should be:

Bio-Array Resource for Plant Biology (BAR)

Crop Ontology

Genevestigator