Remember that different ontologies are for different purposes and do not overlap with each other.For more information on each ontology type for selection of terms please visit the Browsepage.
Browsing ontology requires an understanding the concept of a hierarchical tree. Each ontology begins with a root term which encompasses all the ontology's terms. Terms are related to each other and are described as parent terms and child terms. Clicking on a term in an ontology will expand it to display it's child terms. For more information on the types of parent-child relationships in ontologies, see the term to term relationships section.
Ontology | Associated object types |
Gene Ontology | Ensembl rice genes (from rice genome assembly) Proteins from SWISSPROT-TrEMBL |
Plant Ontology
Cereal plant growth stages (GRO) |
phenotype genes phenotype genes |
Trait Ontology | Phenotype genes QTL |
Environment Ontology | Coming soon |
Gramene Taxonomy Ontology |
Proteins from SWISSPROT-TrEMBL QTL Map sets |
Current Ontologies | Browse by a specific ontology, get a general introduction to the ontologies in Gramene, or download the ontologies and definitions. |
Tutorial | More in-depth than the help pages, use the tutorial for an example of using the database, see how it integrates other datasets, and get tips to increase your data search efficiency. |
FAQ | Frequently Asked Questions - see what questions users have asked, and get the developers answers. |
Release Notes | For more information about the most recent release. |
Evidence codes | Defines the evidence codes and explains how they are used for PO annotation of genes/gene products/phenotypes |
Download | |
Associations | See Acknowledgements |
Ontology suggestion | Suggest an ontology term. |
Every vocabulary term in the ontology has a parent and can have children of its own. As described below, these terms have a predefined set of relationship types among themselves. These relationship types are based on the biological concepts to depict the correct association to each other. Thus such an organization of vocabularies allow the users to navigate their searches using either a higher level/more generic concept. If desired they can also perform the queries using a finer level or much detailed set of terms. For example in the following image, a user can enter the search using the word "root" and can get a list of all the genes that are expresed in this plant part. However if one wishes to know what genes are expressed in "root cortex", there is an option to browse down the tree or search using the term name to find specifically all the genes that are expressed in "root cortex".
Please note that terms in the ontology may have more than one parent (e.g. trichoblast, has two parents, cell and root. Same as root hair).