Ontologies

Links to the most up to date versions of ontology flat files are provided below. Definitions of the terms in all ontologies are contained in respective definition files. You may wish to download the flat files and view them by using a stand alone ontology browser DAG-EDIT

Current Ontologies
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(in OBO format)

Trait Ontology^TM (TO)

It 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.

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Ontology + Definitions

Gene Ontology^TM (GO)

Developed by the Gene Ontology Consortium to help annotate information on gene products (not the genes) using the following three organizing principles of molecular function, biological process and cellular component. Copyright © Gene Ontology Consortium.

All ontologies + Definitions

Molecular Function: The tasks performed by individual gene products; example is Rubisco

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Biological Process: Broad biological goals, such as photosynthesis or ripening, that are accomplished by ordered assemblies of molecular functions.

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Cellular Component: Subcellular structures, locations, and macromolecular complexes; examples include chloroplast, telomere, vacuole, nucleus, etc. .

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Plant Ontology^TM (PO)

Gramene is collaborating with The Plant Ontology Consortium (POC) to develop a controlled vocabulary for plant structure (anatomy) and growth stages.

Plant Structure (PO): The controlled vocabulary of plant structures representing organs, tissue and cell types. Examples are stamen, gynoecium, petal, parenchyma, guard cell, etc.

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Ontology + Definitions

Cereal Plant Growth Stages (GRO): 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.

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Ontology + Definitions

Environment Ontology (EO)

It represents 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.

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Ontology + Definitions

Taxonomy Ontology (GR_tax)

It 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.

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Ontology + Definitions

Gazetteer Ontology (GAZ)

GAZ is developed by a group of experts and researchers including those from Gramene database. GAZ represents a first step towards an open source gazetteer, constructed on ontological principles (controlled vocabulary), that describes places and place names and the relations between them. In Gramene databse we have used GAZ in the Diversity database to annotate the source site of germplasm colelction.

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Ontology + Definitions

Current Ontologies	Browse	Download (in OBO format)
Trait Ontology^TM (TO) It 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.	BROWSE	Ontology + Definitions

Gene Ontology^TM (GO) Developed by the Gene Ontology Consortium to help annotate information on gene products (not the genes) using the following three organizing principles of molecular function, biological process and cellular component. Copyright © Gene Ontology Consortium.		All ontologies + Definitions
Molecular Function: The tasks performed by individual gene products; example is Rubisco	BROWSE	-"-
Biological Process: Broad biological goals, such as photosynthesis or ripening, that are accomplished by ordered assemblies of molecular functions.	BROWSE	-"-
Cellular Component: Subcellular structures, locations, and macromolecular complexes; examples include chloroplast, telomere, vacuole, nucleus, etc. .	BROWSE	-"-

Plant Ontology^TM (PO) Gramene is collaborating with The Plant Ontology Consortium (POC) to develop a controlled vocabulary for plant structure (anatomy) and growth stages.
Plant Structure (PO): The controlled vocabulary of plant structures representing organs, tissue and cell types. Examples are stamen, gynoecium, petal, parenchyma, guard cell, etc.	BROWSE	Ontology + Definitions
Cereal Plant Growth Stages (GRO): 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.	BROWSE	Ontology + Definitions

Environment Ontology (EO) It represents 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.	BROWSE	Ontology + Definitions

Taxonomy Ontology (GR_tax) It 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.	BROWSE	Ontology + Definitions

Gazetteer Ontology (GAZ) GAZ is developed by a group of experts and researchers including those from Gramene database. GAZ represents a first step towards an open source gazetteer, constructed on ontological principles (controlled vocabulary), that describes places and place names and the relations between them. In Gramene databse we have used GAZ in the Diversity database to annotate the source site of germplasm colelction.	BROWSE	Ontology + Definitions

Last modified: Mon Apr 28 18:17:14 2008