Links to sites using the PO

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Ontology Listing Services, etc

Agroportal

Bioportal

Crop Ontology- PO is listed along with the crop-specific onotlogies

EBI OLS

OBO Foundry

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

OntoBee- A linked data server designed for ontologies, the goal is to facilitate ontology data sharing, visualization, query, integration, and analysis.

ISA Tools Software Suite- Use of ontologies is recommended

Metabolomics Standards Initiative- PO is recommended in MSI standards

AgBioData Site- Consortium of agricultural biological databases and associated resources

A to F

Annotare- Array Express experiment submission tool- supports an ontology widget that is enabled with ontology look-up services of the NCBO Bioportal

Arapheno - search by TO or EO, weird versions

Brassica Information Portal - TO and PO terms can be used to search, have requested new terms (#391 and #392)

BRENDA- Enzyme Database, mostly uses BTO, but old version of PO, TO and EO are on their Ontology explorer


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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- Old ontology browsers, can browse PO, TO, PECO, and GO

Gramene Biomart- can filter by PO and GO

Grape genome database

Query page CRIBI- Grape genes are annotated to PO terms

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Gene Ontology- No PO or TO?

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

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

MaizeGDB Genes- 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- Data is tagged with PO, TO and PECO 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

The Compositae Genome Project (CGP)- Morphodb Cool PO browser with links to annotated data from lettuce and sunflower, really old version of PO

Oryzabase PO Version - Japanese version of old PO (plant structures only translated)

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

POEAS- Plant Ontology Enrichment Analysis Server, automated Plant Phenomic Analysis Using Plant Ontology terms based on genes from Arabidopsis thaliana


Plant-specimen-contextual-data-consensus

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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

NASC Ontology page- link to ontology browser is not functional

Oryzabase- no links to PO terms

Plantsystematics.org- ?? cant find any PO ref

PRIDE- PRoteomics IDEntifications (PRIDE) database, used to have a ontology query, but cannot find it now

R to Z

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

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

SuperFamily Phenotype Browser

  • Prefix changed to AP - 'Arabidopsis Plant ontology' with 2 subontologies (PAN for Plant ANatomical entity, PDE for Plant structure DEvelopment stage), "AP:0025099" used here is equivalent to "PO:0025099" in original ontology
  • need to address some issues here, not an "Arabidopsis Plant Ontology"

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

Wheat Data Interoperability Guidelines - Recommendations prepared by the Wheat Data Interoperability Working Group, of the Research Data Alliance

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

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

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

Others?

not actually using the PO but should be:

Bio-Array Resource for Plant Biology (BAR)

Genevestigator

Personal tools
IN DISCUSSION