standards > terminology artifact > DOI:10.25504/FAIRsharing.3ngg40

ready Plant Ontology

Abbreviation: PO

General Information
The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. The PO is under active development to expand to encompass terms and annotations from all plants.

This record replaces or incorporates the following deprecated resources:


Countries that developed this resource United States

Created in 2002

Taxonomic range

How to cite this record PO; Plant Ontology; DOI:; Last edited: Aug. 12, 2019, 4:16 p.m.; Last accessed: Oct 19 2019 8:58 p.m.

This record is maintained by cooperl  ORCID

Record updated: July 1, 2019, 7:55 p.m. by The FAIRsharing Team.

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Finding our way through phenotypes

Deans AR,Lewis SE,Huala E,Anzaldo SS,Ashburner M,Balhoff JP,Blackburn DC,Blake JA,Burleigh JG,Chanet B,Cooper LD,Courtot M,Csosz S,Cui H,Dahdul W,Das S,Dececchi TA,Dettai A,Diogo R,Druzinsky RE,Dumontier M,Franz NM,Friedrich F,Gkoutos GV,Haendel M,Harmon LJ,Hayamizu TF,He Y,Hines HM,Ibrahim N,Jackson LM,Jaiswal P,James-Zorn C,Kohler S,Lecointre G,Lapp H,Lawrence CJ,Le Novere N,Lundberg JG,Macklin J,Mast AR,Midford PE,Miko I,Mungall CJ,Oellrich A,Osumi-Sutherland D,Parkinson H,Ramirez MJ,Richter S,Robinson PN,Ruttenberg A,Schulz KS,Segerdell E,Seltmann KC,Sharkey MJ,Smith AD,Smith B,Specht CD,Squires RB,Thacker RW,Thessen A,Fernandez-Triana J,Vihinen M,Vize PD,Vogt L,Wall CE,Walls RL,Westerfeld M,Wharton RA,Wirkner CS,Woolley JB,Yoder MJ,Zorn AM,Mabee P
PLoS Biol 2015

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The plant ontology as a tool for comparative plant anatomy and genomic analyses.

Cooper L,Walls RL,Elser J,Gandolfo MA,Stevenson DW,Smith B,Preece J,Athreya B,Mungall CJ,Rensing S,Hiss M,Lang D,Reski R,Berardini TZ,Li D,Huala E,Schaeffer M,Menda N,Arnaud E,Shrestha R,Yamazaki Y,Jaiswal P
Plant Cell Physiol 2012

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The Plant Ontology: A Tool for Plant Genomics.

Cooper L,Jaiswal P
Methods Mol Biol 2015

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The plant ontology as a tool for comparative plant anatomy and genomic analyses.

Cooper L,Walls RL,Elser J,Gandolfo MA,Stevenson DW,Smith B,Preece J,Athreya B,Mungall CJ,Rensing S,Hiss M,Lang D,Reski R,Berardini TZ,Li D,Huala E,Schaeffer M,Menda N,Arnaud E,Shrestha R,Yamazaki Y,Jaiswal P
Plant Cell Physiol 2012

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Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages.

Jaiswal P,Avraham S,Ilic K,Kellogg EA,McCouch S,Pujar A,Reiser L,Rhee SY,Sachs MM,Schaeffer M,Stein L,Stevens P,Vincent L,Ware D,Zapata F
Comp Funct Genomics 2008

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The Plant Ontology Consortium and plant ontologies.

Comp Funct Genomics 2008

View Paper (PubMed) View Publication

The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations.

Avraham S,Tung CW,Ilic K,Jaiswal P,Kellogg EA,McCouch S,Pujar A,Reiser L,Rhee SY,Sachs MM,Schaeffer M,Stein L,Stevens P,Vincent L,Zapata F,Ware D
Nucleic Acids Res 2008

View Paper (PubMed) View Publication

PO Ontology Display

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Disclaimer: This widget assumes the availability of the ontology resources in the NCBO BioPortal.

View in OBO Foundry.

Implementing Databases (17)
MetaCrop 2.0
The MetaCrop resource contains information on the major metabolic pathways mainly in crops of agricultural and economic importance. The database includes manually curated information on reactions and the kinetic data associated with these reactions. Ontology terms are used and publication identification available to ease mining the data.

The Arabidopsis Information Resource
The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana.

Golm Metabolome Database
The Golm Metabolome Database (GMD) provides gas chromatography (GC) mass spectrometry (MS) reference spectra, reference metabolite profiles and tools for one of the most widespread routine technologies applied to the large scale screening and discovery of novel metabolic biomarkers.

Nottingham Arabidopsis Stock Centre Seeds Database
The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community.

Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants
Gramene's purpose is to provide added value to plant genomics data sets available within the public sector, which will facilitate researchers' ability to understand the plant genomes and take advantage of genomic sequence known in one species for identifying and understanding corresponding genes, pathways and phenotypes in other plant species.

Maize Genetics and Genomics Database
MaizeGDB is the maize research community's central repository for genetics and genomics information.

The Oryzabase is a comprehensive rice science database established in 2000 by rice researcher's committee in Japan. The Oryzabase consists of five parts, (1) genetic resource stock information, (2) gene dictionary, (3) chromosome maps, (4) mutant images, and (5) fundamental knowledge of rice science.

Genome Database for Rosaceae
The Genome Database for Rosaceae (GDR) is a curated and integrated web-based relational database providing centralized access to Rosaceae genomics and genetics data and analysis tools to facilitate cross-species utilization of data.

Manually Curated Database of Rice Proteins
‘Manually Curated Database of Rice Proteins’ (MCDRP) is a unique manually curated database based on published experimental data. Currently, the database has data for over 1800 rice proteins curated from > 4000 different experiments of over 400 research articles. Since every aspect of the experiment such as gene name, plant type, tissue and developmental stage has been digitized, experimental data can be rapidly accessed and integrated.

Genetic and Genomic Information System
GnpIS is a multispecies integrative information system dedicated to plant and fungi pests. It bridges genetic and genomic data, allowing researchers access to both genetic information (e.g. genetic maps, quantitative trait loci, association genetics, markers, polymorphisms, germplasms, phenotypes and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest. GnpIS is used by both large international projects and plant science departments at the French National Institute for Agricultural Research. It is regularly improved and released several times per year. GnpIS is accessible through a web portal and allows to browse different types of data either independently through dedicated interfaces or simultaneously using a quick search ('google like search') or advanced search (Biomart, Galaxy, Intermine) tools.

A resource providing data on bioentities and their associated ontology terms for Plant Biology. The database provides access to ontology-based annotations of genes, phenotypes and germplasms from about 90 plant species. A number of internal and external ontologies are used to annotate the biological data available from this resource.

Large-scale genomic data for the peanut have only become available in the last few years, with the advent of low-cost sequencing technologies. To make the data accessible to researchers and to integrate across diverse types of data, the International Peanut Genomics Consortium funded the development of PeanutBase. This database provides access to genetic maps and markers, locations of quantitative trait loci (QTLs), genome sequences, gene locations and sequences, gene families and correspondences with genes in other species, and descriptions of traits and growth characteristics. It also provides tools for exploration and analysis, including sequence of genomic and genic sequences, and keyword searches of genes, gene families, and QTL studies. These resources should facilitate breeding advancements in peanut, helping improve crop productivity and there are a variety of resources for peanut research around the web, ranging from tools for basic plant biology to information for growers and various sectors of the peanut industry to resources for plant breeders.

OBO Foundry
The Open Biological and Biomedical Ontology (OBO) Foundry is a collective of ontology developers that are committed to collaboration and adherence to shared principles. The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate. To achieve this, OBO Foundry participants voluntarily adhere to and contribute to the development of an evolving set of principles including open use, collaborative development, non-overlapping and strictly-scoped content, and common syntax and relations, based on ontology models that work well, such as the Gene Ontology (GO). The OBO Foundry is overseen by an Operations Committee with Editorial, Technical and Outreach working groups.

Brassica Information Portal
The Brassica Information Portal is a web repository for population and trait scoring information related to the Brassica breeding community. It provides information about quantitative trait loci and links curated Brassica phenotype experimental data with genotype information stored in external data sources. Advanced data submission capabilities and APIs enable users to store and publish their own study results in BIP. The repository can be easily browsed thanks to a set of user-friendly query interfaces.

BarleyBase is a public data resource of Affymetrix GeneChip data for plants.

Metabolomic Repository Bordeaux
MeRy-B is a plant metabolomics platform allowing the storage and visualisation of Nuclear Magnetic Resonance (NMR) metabolic profiles from plants.

DES-TOMATO is a topic-specific literature exploration system developed to allow the exploration of information related to tomato. The information provided in DES-TOMATO is obtained through the text-mining of available scientific literature, namely full-length articles in PubMed Central and titles and abstracts in PubMed.

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Grant Number(s)

  • 0822201 (National Science Foundation (NSF), USA)