Gramene’s Ontologies Tutorial Gramene v. 26 Gramene’s Ontologies Tutorial This database is a collective resource of structured controlled vocabularies (Ontologies) for knowledge domains and their associations. Knowledge Domains: Plant Ontology (PO) Plant Structure (morphology, organs, tissue and cell types) and Development* Growth stages (plant growth and developmental stages) Trait Ontology (TO) Plant traits and phenotypes  Gene Ontology (GO)   Molecular function Biological process Cellular component Environment Ontology (EO) Gramene's taxonomy ontology (GR_tax) Associations: 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. 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 2/16/2019

Tutorial Tips Note! Although we continually work to make Gramene compatible with all browsers, there are problems with some browser versions. If you're having difficulty viewing Gramene, try using a different browser. Please report any problems with browsers through Gramene Feedback. Images shown may not be up to date, so results on your searches may be different, or the data may be displayed in a different order. 2/16/2019

Click here to open ontology search Gramene Home Page www.gramene.org Go to the Gramene Home page (http://www.gramene.org) Click the ‘Ontology’ link from the navigation bar menu on top of the page. Click here to open ontology search 2/16/2019

Module Home-Page layout Module home pages provide the following information: Searching/Browsing – links to different types of searches. Other Tools – if applicable, links to different tools used in this module. Help – links to help pages, tutorials, release notes, FAQ and other helpful documentation. Download – information on where to download the database. Feedback – How to contact Gramene Acknowledgements – Other programs that contribute to this data. Quicklinks and external links – when appropriate these links are provided. 2/16/2019

Ontology Home Page or Click here if you need more help on Ontology 2. Click to browse terms or to learn more about their use and key concepts. or 1. Type term name and click search. (option- to limit a search, click box of desired ontology type) On the Ontology database entry page, users have the (1) browse and (2) search options to begin using the database. 2/16/2019

Browsing the Ontology Database 3. Click on “BROWSE” to navigate through the desired ontology type. 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. 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 Ontology - Ensembl rice genes (from rice genome assembly), Proteins from SWISSPROT-TrEMBL Plant Ontology - Plant structure or anatomy (PO) - phenotype genes Cereal plant growth stages (GRO) - phenotype genes Trait Ontology - Phenotype genes, QTL Environment Ontology - Coming soon Gramene Taxonomy Ontology - Proteins from SWISSPROT-TrEMBL, QTL, Map sets 2/16/2019

Searching the Ontology Database Type your query e.g. Example is a search for function alpha-amylase 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) Click search icon 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". You can search the ontology database by using either of the following queries: Term name (e.g. stem length, alpha-amylase, Zea mays, etc.) Term_id or an accession (e.g. 303 or TO:0000303) Synonyms (e.g. culm length) Or any word that you think can fetch an appropriate query result (EXCEPT THE GENE NAMES AND SYMBOLS). 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. 2/16/2019

Gene Ontology (GO) search results Definition of the ontology term Exact ontology term 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 "plant structure(PO)". In this example you will see that "culm" is a synonym of "stem". Synonyms (if any) Ontology Accession for the ontology term. Select to view detailed information. (see next slide) 2/16/2019

Ontology Term Accession Detail Exact ontology term The lineage of alpha-amylase activity as a molecular function Links to source that originally developed this ontology. + Indicates expandable tree. Click on term to expand. Number of database objects associated in the database with this term. Definition of the term External references used for defining terms or making associations. 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. 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: 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 "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) Term-term relationship [i]: IS A (type of) – see help file for more information Click to expand. Click to get a complete list of associations with the given ontology term (see next slide.) 2/16/2019

Ontology Associations Click to view the term and its children (indirectly associated to parent term if any) for which the object type was annotated see previous slide) Method used to ascertain this association. Click on code for description. 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. Links to the original entry in Gramene database. Click for TIGR gene report in Gramene. (See Genomes Tutorial) 2/16/2019

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: 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. 2/16/2019

Other Options From Ontologies The lower half of the ontologies home page offers other helpful resources. Link to Evidence Code definitions. (see next slide) Click to submit your ontology suggestions Click to download ontologies Learn more about ontologies from these publications 2/16/2019

Evidence Codes This is a list of evidence codes used in curation at Gramene. These are the basis for ascertaining associations. 2/16/2019

FAQs Search FAQ Feedback: Submit a question to Gramene Click to expand or collapse a question or answer 2/16/2019

Help Use Help file for assistance on developing a search, understanding the results, or in understanding ontologies. 2/16/2019

Action Steps: Things you can do 1) Make Suggestions Send us your review of the terms, definitions and relationships to ensure accuracy. Suggest new terms, definitions, or improvements to current structures. If you find incorrect associations, let us know. 2) Use Ontologies Use current ontology terms in describing your data in publications and databases. 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. 2/16/2019

Email Gramene at gramene@gramene.org Contact Gramene Use the feedback button, located at the top of every page, to provide feedback or to ask questions about Gramene. or Email Gramene at gramene@gramene.org 2/16/2019