Links to sites using the PO

From Plant Ontology Wiki
Jump to navigationJump to search
The printable version is no longer supported and may have rendering errors. Please update your browser bookmarks and please use the default browser print function instead.

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


_______________________________________________________________________

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

_____________________________________________________________________________________________________________

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

_________________________________________________________________________________________________________

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

________________________________________________________________________________________________

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