Sample Code Cookbook

This page lists use cases and provides examples of how these questions can be answered using NCBO software (web services and widgets), and includes links to code samples and documentation.

Use Cases

• I have a list of terms that were used to annotate a data set, how can I see if any of these terms exist in standard ontologies?
  • Use the Search Web service to search for your term in all ontologies in BioPortal. If you have a small list of terms, searching each term individually via the BioPortal Search UI may be sufficient. Otherwise, for a long list of terms, use the Search Web service directly.
    • Search Web service documentation: http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Search_services
    • Example code: https://bmir-gforge.stanford.edu/gf/project/client_examples/scmsvn/?action=browse&path=%2Ftrunk%2F

• I would like to find all terms mapped from my ontology to other ontologies in BioPortal
  • Use the Mapping web service to find terms in other BioPortal ontologies similar to terms in your ontology. These mappings include mapping generated manually (DbXrefs) and programatically (LOOM).
    • Mapping Web service documentation: http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Mapping_Service
    • Example code: https://bmir-gforge.stanford.edu/gf/project/client_examples/scmsvn/?action=browse&path=%2Ftrunk%2FPerl%2FExtractMappings%2F

• I am the curator for a database and need to triage papers to identify which papers from PubMed to curate to add new information to my database
  • Use the Annotator web service to identify ontology terms in textual data.
    • Annotator Web service documentation: http://www.bioontology.org/wiki/index.php/Annotator_Web_service
    • Example code:

• I have PubMed abstracts and want to link information in the abstracts to my database of interest.
  • Process the text with the Annotator web service. If your database of interest is included in the NCBO Resource Index you can search the database(s) for records that contain these terms. See http://www.bioontology.org/wiki/index.php/Resource_Index for more details on the Resource Index web service.

• I have a web form with fields I would like to users to fill-in with a specific set of terms from the Gene Ontology.
  • Generate this subset of terms and then load this ontology as a view of the Gene Ontology (http://bioportal.bioontology.org/ontologies/44532#views). Then choose the ontology-term autocomplete widget from the Widgets page (http://bioportal.bioontology.org/ontologies/44532#widgets) and select the "Get Code" button for Javascript that you can add to your web form.

• I would like to include the graph display of my ontology on my web site.
  • Choose the Visualization widget from the widgets page (e.g. http://bioportal.bioontology.org/ontologies/44532#widgets) for your ontology of interest and select the "Get Code" button to add the ontology graph to your web site.

• I would like to get all terms from an ontology and re-format the data to use in my own system.
  • Use the "Get all terms" web service (http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Get_all_terms_using_the_specific_ontology_version_id and http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Get_all_terms_using_the_virtual_ontology_id) to get a list of all of the terms and all details about each term, e.g. synonyms, definition, subclass, etc.