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Gramene Ontology (Controlled Vocabulary) Database Help Document

Ontology search/browse options:

A. Quick Search

1. From the Ontologies home page, enter a keyword into the "Quick Search" Box. Keywords may include: Term name (e.g. days to heading, defense response, Zea mays); Term_id or an accession (e.g. 303 or TO:0000303); Synonyms (e.g. culm length or panicle); Or any word that you think can fetch an appropriate query result (EXCEPT THE GENE NAMES AND SYMBOLS).The default search uses wildcards, so a search for "flower" will include "flowering" and "smallflower".
2. Optionally limited your search by one or more ontologies by checking the desired ontology types (GO/PO/GRO/TO/EO/GR_tax) below the text search box.
3. To turn off the wildcard feature, check the "Exact Match" option.
4. Obsolete terms will not be returned by default. If you wish to include obsolete terms in your search, check the "Include Obsolete Terms" option.
5. Click on the search icon.

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 current ontologies section.

B. Browse Ontologies

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 discover an appropriate term and the datasets associated with it. Other guidance is offered in the tutorial.

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.

1. Click on the "Browse" link to the right of the ontology of interest.
2. The resulting page will be layed out in the manner of "Ontology Search Results", in the next Help Section. Go to the "Derivation" section to browse through the ontology's related terms.
3. Drill down through the ontology to locate terms of interest. But, keeping in mind that a term may have multiple parent terms, it may be desirable to move in both directions through the ontology. Each term will display a number after it, which reflects the number of associations in the Gramene database to that term. To understand associations, please consult the association section of this help document.

Ontology Search Results:

The query results table will give you a list of terms that matched your search. Select the term accession of the term of interest. In this part of the ontology browser it displays details of one TO/PO/GRO/GO term at a time, along with additional information on term name. Ontology Detail includes:
• Term name: Name of the ontology term, by which it is called.
• Term accession: A stable ontology term id
• Aspect: suggesting a given term belongs to which type of ontology
• Synonyms: alternate names or aliases.
• Definition: A standardized definition of the term.
• Source Ontology Database
• Derivation - This number in parentheses after a term refers to the number of associations a term has in the database. Click on child or parent terms to navigate the ontology. 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.
• Database Cross-References
• Parents: The parent term(s) of the term of interest.
• Children: The child term(s) of the term of interest. Learn more about how each term is related to its parent and child(ren) terms, please see term to term relationships section. You may also visit the online tutorial.
• Associations: In the Associations section, the number in parenthesis tells you how many associations there are in Gramene to your ontology term. Expand the section by clicking on "Associations". Associated "object types" (QTL/phenotype, gene/EnsEMBL, gene/protein, map set) will be identified, with objects grouped by species. "Object types" will vary for each ontology, as shown here:

  Ontology	Associated object types
  Gene Ontology	Ensembl 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

  • 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 term's child terms are accumulated by it (the parent term.) Therefore as we move up towards the general terms, in the derived tree, the number of associations increase.
  • The number of associations is identified for each species of each "object type". 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 associated species for an object and that will take you to a page displaying a table with a list of associations for the object type you selected with information on the following:
    
    • Term name - Ontology term
    • Object type e.g. QTL/phenotype gene/EnsEMBL gene/proteins
      
    • Object accession id - accession ID of the associated object in it's respective module (gene/protein/QTL/Map.) Follow these hyperlinks to view the object detail in that other module.
    • Object symbol: Object's symbol as defined in that particular module
    • Object name: Object's name as defined in the particular module
    • Object synonyms: any aliases for that object in the literature
    • Object species: species with which the object is associated
    • Evidence: Any one or more of the experimental/evidence codes that was used to determine the association of the object to the ontology term.
      
  • 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.

Other Resources

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.

Feedback

• Participate - Any suggestions for the addition, replacement or modification of the controlled vocabulary can be made via web based ontology submission.
• If you find any inconsistencies or mistakes, or have questions, please communicate them to us by clicking on the "feedback" link at the top of the Gramene pages or by going to the following URL: /db/feedback/send_feedback?refer_from=/rice_mutant/index.html Your suggestions and feedback are highly appreciated by the Gramene staff.

Term to term relationships:

*Note - Images may not be current with the database, but the concept is the same.

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".

Is a (instance of, type of): [i]

Used to describe the relationship between a child term that represents a specific type of a more general parent term.
For example in the following image: a guard cell is a type of cell; a root hair is a cell.


Part of: [p]

Used to indicate the relationship between a child term that is a part of the parent term.
For example in the following image: the root cortex is a part of root.


Develops from: [d] (used only in plant structure ontology)

Used to describe the relationship between a child term that develops from its parent term.
For example in the following image: the root hair develops from trichoblast.



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).

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