Table 1 Description of applied ontologies

Plant Ontology (PO) [27]

Plant anatomy and morphology and development stages

http://www.plantontology.org/

Gene Ontology (GO) [29]

Biological processes, cellular components and molecular functions

http://geneontology.org/

Chemical Entities of Biological Interest ontology (ChEBI) [43]

Molecular entities focused on ‘small’ chemical compounds.

http://www.ebi.ac.uk/chebi/

Phenotypic Qualities Ontology (PATO) [16,19]

Phenotypic qualities

http://obofoundry.org/wiki/index.php/PATO:Main_Page

Plant Experimental Conditions Ontology (EO)

Treatments, growing conditions, and/or study types

http://planteome.org/amigo/cgi-bin/crop_amigo/term_details?term=EO:0007359

NCBI taxonomy (NCBITAXON)

A curated classification and nomenclature for all of the organisms in the public sequence databases.

http://www.ncbi.nlm.nih.gov/taxonomy

Relation Ontology (RO) [41]

Core upper-level relations and biology-specific relations

https://code.google.com/p/obo-relations/