An ontology is a standardized (controlled) glossary of keywords arranged in a structured order or a network based on biological concepts. Each vocabulary term has a fixed term identification and a definition. It allows the users to query the different databases or subsections of a database using the same keywords and query strings (provided those different databases have implemented the commonly adopted ontologies).

Yes. Please refer to the Ontology database Help documents, tutorial, and release notes (http://www.gramene.org/tutorials/ontologies.html)

Gramene uses the following types of controlled vocabularies (ontologies): Plant Ontology (TM) (http://www.gramene.org/plant_ontology/index.html#po) (PO) - Gramene is collaborating with The Plant Ontology Consortium (POC) ( www.plantontology.org to develop a controlled vocabulary for plant structure (anatomy) and growth stages. Cereal Plant structure (PO)(morphology, organs, tissue and cell types) - The controlled vocabulary of plant structures representing organs, tissue and cell types. Examples are stamen, gynoecium, petal, parenchyma, guard cell, etc Cereal Plant Growth stages (GRO)(plant growth and developmental stages) - The controlled vocabulary of growth and developmental stages in various cereal plants. Examples are germination, seedling, booting, flowering, etc. Available only for rice, maize, sorghum, wheat, wheat, oat and barley. Trait Ontology (TM) (http://www.gramene.org/plant_ontology/index.html#to) - Trait ontology is a controlled vocabulary to describe each trait as a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature individual. Examples are glutinous endosperm, disease resistance, plant height, photosensitivity, male sterility, etc. Gene Ontology (GO)- Copyright Gene Ontology Consortium. (http://www.gramene.org/plant_ontology/index.html#go) - Developed by the Gene Ontology Consortium (GOC) to help annotate information on gene products (not the genes) using the following three organizing principles: Molecular function - The tasks performed by individual gene products; example is Rubisco Biological process - Broad biological goals, such as photosynthesis or ripening, that are accomplished by ordered assemblies of molecular functions. Cellular component - Subcellular structures, locations, and macromolecular complexes; examples include chloroplast, telomere, vacuole, nucleus, etc. Environment Ontology (EO) - EO is a controlled vocabulary to describe different types of supplemental environments that have been reported in the experimental profiles of gene expression and phenotype (mutant and QTL) studies on cereal plants. Taxonomy Ontology (GR_tax) - GR_tax is a representation of the taxonomy tree in the ontology format. Each term in this ontology can represent subspecies, species, genus, order, class or any rank in the classification. Primarily derived from NCBI Taxonomy, the revisions were made as and when/where required in the rankings. The rank of genome types was added by this project. This taxonomy ontology focuses on the Poaceae (Gramineae) family of plant taxonomy only.

The Trait and Plant Ontologies (http://www.plantontology.org) are developed in house with the help from databases like MaizeGDB, GrainGenes and IRIS. If you are interested in their development we encourage you to contact us by sending an e-mail to Gramene at gramene@gramene.org. The Gene Ontologies are developed by the Gene Ontology Consortium (GOC) (http://www.geneontology.org) in which Gramene actively participates. You can contact the GOC by e-mail at go@geneontology.org.

Yes. You are encouraged to do so. Please use the Ontology submission form. (http://www.gramene.org/plant_ontology/submission). For help on the submission, please consult http://www.gramene.org/documentation/cvo_help.html.

You are encouraged to use the ontologies in the curation of your own datasets. For this you may use the download facility (text dump) available from Gramene (http://www.gramene.org/plant_ontology/index.html#ontology).

You can get the most up-to-date list of Gene Ontology associations to a protein or gene from the "Association" link on the Ontology Database's navigation bar. (http://www.gramene.org/plant_ontology/index.html#assoc)

The seven digit number next to the term such as GRO:0005297 (plant ontology term) / GO:0003674 (gene ontology term) / TO:0000387 (trait ontology term) is a unique identifier of a given ontology term.

This suggests the number of unique associations (protein/genes) to a given term. However, the associations are sometimes not direct, they are indirect associations accumulated from the various child terms (view an example of a term's derivation at http://www.gramene.org/db/ontology/search_term?id=TO:0000303).

These represent the relationship type of a given term to its parent term (view an example of a term's derivation. [i] stands for "INSTANCE OF / IS A / TYPE OF" and [p] stands for "PART OF". Example 1. Seed is an instance of whole plant: whole plant --[i] seed Example 2. Embryo is an instance of whole plant and is also part of seed: whole plant --[i] embryo ---[i] seed ----[p] embryo

This symbol suggests that this term has an extended tree that carries various children terms with PART OF and IS A relationships.

To download the data, you may use the download facility (text dump) available from Gramene. (http://www.gramene.org/plant_ontology/index.html#ontology)

#1 Go to 'Search" section of the navigation bar (next to the Gramene icon) on top left of the Gramene page and from the drop down select 'All-GrameneMart' #2 on the GrameneMart page that opens, select the data set 'Oryza sativa genes (TIGR3)' and click the button 'next'. [if you want the data set from a particular chromosome, select the chromosome before hitting the 'next' button]. # it will automatically select all the entries for loci/genes found in the rice genome assembly. (e.g. 58752 total entries). # then click the button 'next', which will take you to a features page # On the features page from the gene/gene attributes section select the 'TIGR Gene LOC ID" and make a second selection of the GO ID and Description from 'Gene/External References section'. # after this go to the bottom of this page and select your 'output format' and 'file compression' and click the button 'export' # e.g. if you have selected for output format 'text, tab separated' and file compression 'gzip', by clicking the 'export' it will prompt you the save or open as a normal function, where you would like to save your file. Since it is a compressed file you will be required to unzip it.

We do not have the actual trait ontology term for rheological traits from wheat because we have not added the QTLs associated with them in Gramene database. As soon as we have the QTLs available for these traits from GrainGenes we will incorporate the traits in Gramene. The following papers have reported such traits: http://grain.jouy.inra.fr/cgi-bin/graingenes/report.cgi?class=reference;id=174 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=15965651&dopt=Abstract. In the meantime if you simply need the trait ontology term for rheological trait and associated parameters such as dough extensibility and Rmax we can add them to the Trait Ontology. Please send us the appropriate definition of the terms and their assay method.

Yes. We provide the gene ontology associations to Uniprot proteins from Hordeum (various species). From the Gene Ontology listed on http://www.gramene.org/plant_ontology/index.html#ontology you will need to browse Molecular Function, Biological Process, Cellular Component. Click on "browse" and go to the protein section of the annotations to select the Hordeum species you are interested in. For example, under "Molecular Function" there are 989 protein annotations for Hordeum vulgare [Gramene release #24]. Click on that number and from the results page you can download the GO annotations by clicking the 'download' button located in the top-right of the results table. You can then use the downloaded files to map the GO terms to the probe sets from your species. However in order to do this a mapping to Uniprot database accessions is required for the other species.

All of the data available at Gramene is in the public domain, and thus is freely available. Gramene does not require nor administer license agreements. However, as indicated on the web-page at http://www.gramene.org/plant_ontology/ the different ontologies come from various sources, and these sources should be acknowledged. The Gene Ontology (GO) terms and definitions are from the Gene Ontology Consortium, and the Plant Ontology (PO) terms are from the Plant Ontology Consortium. The Trait Ontology (TO), Environment Ontology (EO) and Taxonomy Ontology (Gr_Tax) are from Gramene. PO now offers Plant Growth and Development stages terms, in addition to Plant Structure terms, and Gramene is now using the PO terms instead of the GRO terms, which are no longer used.