Go to the Gramene Home page (http://www.gramene.org) Click the ‘Ontology’ link from the navigation bar menu on top of the page.
On the Ontology database entry page, users have the (1) browse and (2) search options to begin using the database.
To learn more about the different ontologies, go to the ‘Current Ontologies” section from the top of the page or simply scroll down after you open the ontology entry page. Follow the ‘Browse’ link to start navigating the ontology of choice.
An example using Gene Ontology (GO) to search for ‘alpha-amylase’. The search function can be used in a similar way to find plant structure, growth stages, environment, taxonomy and trait ontology terms. The query results table will give you a list of terms that matched your search. This table includes. Term accession: A stable ontology term id Aspect: suggesting a given term belongs to which type of ontology Term name: Name of the ontology term, by which it is called. Synonym: alternate names or aliases. Definition: A standardized definition of the term. See an example search for culm by selecting the ontology type &quot;plant structure(PO)&quot;. In this example you will see that &quot;culm&quot; is a synonym of &quot;stem&quot;.
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 &quot;derivation&quot; 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. 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 &quot;term name&quot;. 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: Term name Object type e.g. QTL/phenotype gene/EnsEMBL gene/proteins Object accession id. (Links to the respective gene/protein/QTL/Map set for detail information) Object symbol: a gene/protein symbol/a rice gene's locus id from the genome/QTL trait symbol/Mapset short name Object name: gene/protein/QTL tait/mapset full name/ Object synonyms: any aliases or QTL published symbol Object species: species with which the objects like QTL/phenotype gene/EnsEMBL gene/proteins is associated with Evidence: Any one or more of the experimental/evidence codes that determined the association of the object to the 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 &quot;root&quot; 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 &quot;root cortex&quot;, 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 &quot;root cortex&quot;. 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)
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 &quot;Download button&quot; present at the top right corner of the association table.
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.
Ontologies gramene tutorial
<ul><li>This database is a collective resource of structured controlled vocabularies (Ontologies) for knowledge domains and their associations. </li></ul><ul><li>Knowledge Domains: </li></ul><ul><ul><li>Plant Ontology ( PO ) </li></ul></ul><ul><ul><ul><li>Plant Structure (morphology, organs, tissue and cell types)* </li></ul></ul></ul><ul><ul><ul><li>Growth stages (plant growth and developmental stages) </li></ul></ul></ul><ul><ul><li>Trait Ontology ( TO ) </li></ul></ul><ul><ul><ul><li>Plant traits and phenotypes </li></ul></ul></ul><ul><ul><li>Gene Ontology ( GO ) </li></ul></ul><ul><ul><ul><li>Molecular function </li></ul></ul></ul><ul><ul><ul><li>Biological process </li></ul></ul></ul><ul><ul><ul><li>Cellular component </li></ul></ul></ul><ul><ul><li>Environment Ontology ( EO ) </li></ul></ul><ul><ul><li>Gramene's taxonomy ontology ( GR_tax ) </li></ul></ul><ul><li>Associations: </li></ul><ul><ul><li>Use this database to quickly find Ensembl rice genes (from TIGR’s rice genome assembly), proteins from SWISSPROT-TrEMBL representing Poaceae (grass) family, rice genes, QTL and map sets. </li></ul></ul>Gramene’s Ontologies Tutorial Note: 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 at Gramene Gramene v.20
Tutorial Help <ul><li>The hand icon indicates a link that allows you to go to the same page in your web browser. </li></ul>If you are viewing this tutorial with Adobe Acrobat Reader, click the "bookmarks" on the left hand side of the Reader for easier navigation. Action Options are noted in this type of font. Notes or comments use this style font.
Ontologies Map Ontologies Search Ontology Accession Aspect (Ontology) Synonyms Definition OntologyTerm Aspect Definition External References Derivation Annotations Ontology Term Name Object Object Accession Object Symbol Object Name Object Synonym Object Species Evidence Literature DB Genomes DB Maps DB Proteins DB Genes DB QTL DB Marker DB
Gramene Home Page Click here to open ontology search
Ontology Home Page Click here if you need more help on Ontology Click on the links of the ontologies to learn more about their use and key concepts. 2. Type term name and click search. ( option- to limit a search, click box of desired ontology type) 1. Click on “Current Ontologies” to browse terms or
Browsing the Ontology Database 3. Click on “BROWSE” to navigate through the desired ontology type.
Searching the Ontology Database Select “Gene Ontology” to search the GO database (or select one or more others appropriate to your term.) (Molecular Function is part of Gene Ontology) Type your query e.g. Example is a search for function alpha-amylase Click search
Gene Ontology (GO) search results Ontology Accession for the ontology term. Select to view detailed information. Exact ontology term Synonym s (if any) Definition of the ontology term
Ontology Term Accession Detail The lineage of alpha-amylase activity as a molecular function Term-term relationship [i]: IS A (type of) Number of database objects associated in the database with this term. Exact ontology term Definition of the term Click on link to get a complete list of set of genes/proteins/QTL/maps etc. that may be associated with the given ontology term ( see next slide for oryza sativa example.) Links to source that originally developed this ontology . External references used for defining or associated to synonyms Expandable tree. Click on term to expand.
Ontology Associations Links to the original entry in Gramene database. Click for TIGR gene report in Gramene. The term and its children (indirectly associated to parent term if any) for which the object type was annotated Click to download a zip file with tab delimited list of associations Method used to ascertain this association. Click on code for description. Clicking on the active column headers will sort by that column
Searching other ontologies Previous slides presented the gene ontology (GO) example. The same procedure must be followed if you would like to search other ontologies. The following table suggests the type of objects that are associated with different types of ontologies:
Other Options From Ontologyies Click to submit your ontology suggestions Learn more about Gramene ontologies Click to access download instructions Learn more about ontologies from these publications Click to learn about evidence used to make associations of ontology terms with different data types Click to download the associations Click to browse the frequently asked questions or access tutorial or help files.
Action Steps: Things you can do <ul><li>1) Make Suggestions </li></ul><ul><li>Send us your review of the terms, definitions and relationships to ensure accuracy. </li></ul><ul><li>Suggest new terms, definitions, or improvements to current structures. </li></ul><ul><li>If you find incorrect associations, let us know. </li></ul><ul><li>2) Use Ontologies </li></ul><ul><li>Use current ontology terms in describing your data in publications and databases. </li></ul><ul><li>If your project on cereal plants (especially rice [Oryza]) is generating data sets that may require these kinds of annotations and associations, we will be happy to help guide you through the annotation process and in setting up an Ontology database. </li></ul>
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