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Ontology Database
Type ID or keyword to search    
select ontology (optional)   Gene (GO)  Plant structure (PO)  Growth stage (GRO)
Trait (TO)    Environment (EO) Taxonomy(GR_tax) 		[e.g. flower or TO:0000303]
 
grain_icon Find help on ontology Search  | Browse  | Query results  | Term details  | Associations  | Term to term relationships  | More information 

Ontology (Controlled Vocabulary) Help

Search:

You can search the ontology database by using either of the following queries:

You can limit your searches by checking any one or more of the ontology types (GO/PO/GRO/TO/EO/GR_tax) below the text search box

Remember that different ontologies are for different purposes and do not overlap with each other. For more information on each ontology type please visit the current ontologies section.

Query results:

The query results table will give you a list of terms that matched your search. This table includes. See an example search for culm  by selecting the ontology type "plant structure(PO)". In this example you will see that "culm" is a synonym of "stem".

Browse:

If you are not familiar with the ontology types, their usage, term names, and the  term_id or accessions, we recommend using the browse option available from the current ontologies section to find an appropriate term and the datasets associated with it. Or follow the tutorial. You will find associated with each term a number of objects as listed in the table below. To view all the associations please consult the association section of this help document.

Ontology Associated object types
Gene OntologyEnsembl rice genes (from rice genome assembly)
Proteins from SWISSPROT-TrEMBL
Plant Ontology
    Plant structure or anatomy (PO)
    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

Term details:

In this part of the ontology browser it displays details of one TO/PO/GRO/GO terms one at a time, along with additional information on term name, term ID, synonym, definition, comments, derivation, list of parent and children terms, followed by a section on associated object types (see following section).

In the "derivation" section the [i] or [p] or [d] symbols suggest how a given term is related to the term below (child)/above (parent) its position in the ontology tree. For more information, please see term to term relationships section.

When the associations are displayed next to a term, it means that a term name was used in descibing a given object (gene/protein/QTL/mapset) either directly or sometimes indirectly to one of its children term in the tree. All the associations from a detailed level term(s) (children) are accumulated by a parent term. Therefore as we move up towards the general terms, in the derived tree, the number of associations increase.


Associations:

In order to find the associations (genes / qtl / proteins / mapsets) to a term of your interest, please see the number next to your term (e.g.there are  #115 phenotype associations to the term stem (PO0009047). You can view the detail list of these associations by scrolling to the section of the page below the term details.

The association table displays total number of objects (QTL/phenotype gene/EnsEMBL gene/proteins) and associations with "term name". The number of associations could be more than the number of objects because of the greater number of evidences (citations) that were used in making the associations.

Click on any one of the appropriate hyperlinked text and that will take you to a page displaying a table with a list of objects types/associations you selected.

On the associations page the results table will provide information on following:
# All the information in the columns can be sorted as you prefer by clicking the column header/title.
# The association page displays 25 associations at a time.
# The associations can be downloaded as a zip file by clicking the "Download button" present at the top right corner of the association table.
Want to learn more about how each term is related to its parent and child(ren) terms, take a look athe the following section. You may also like to visit the online tutorial.

Term to term relationships:

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).


More information:

For more information on how to use ontologies and downloads please follow the following links.

Current Ontologies   | Documentation   | Evidence code   | FTP   | Ontology suggestion   | Associations   | Publications   | Tutorial   | FAQ