Links to sites using the PO

Ontology Listing Services

Agroportal

Bioportal

EBI OLS

OBO Foundry

A to G

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

Compositae Genomics Project: Morphdb

Grape genome database

Query page CRIBI- Grape genes are annotated to PO terms

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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

G to L

Gene Ontology- No PO or TO?

Gramene- http://archive.gramene.org/plant_ontology/

Gramene Biomart- can filter by PO and GO

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

ISA

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

M to P

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

• 'MAize Gene expressIon Compendium'. It is 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.
• plant ontology annotations

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

Maize cell Genomics database- JCVI

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

Manually Curated Database of Rice Proteins- tagged with TO terms

Metalife- ????

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

PO integration in MSI standards

NASC Ontology page- link to ontology browser is not functional

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

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

OntoBee

Plantsystematics.org- ?? cant find any PO ref

Phenopsis - information system dedicated to the model plant Arabidopsis thaliana; ontology terms are out of date on here, go to the EBI OLS,

POEAS - POEAS: 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.

The Integrated Databases of Plant Omics Data- link not working

Plant Phenome- on Biolod, links not functional

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