IEDB Assay Types

The Experimental data present in the IEDB demonstrates antibody, T cell, or MHC recognition of an epitope. Thus, the assays can be grouped into the categories of T Cell Assays, B Cell Assays, and MHC Ligand Assays. These selections can be made on the Home Page or on the Results Page.  Additionally, one may further narrow search results to very specific experimental methods using the Assay Finder.

The Assay Finder is used to facilitate the selection of one or more assay types and presents the assay types of each category in a hierarchical tree format.  The Assay Finder for T Cell, B cell, and MHC Ligand assays can be found on the results page and also their respective Specialized Search pages.  The Assay Finder may be browsed by clicking open any node of the tree or may be searched by utilizing drop down menus to select from the types of assays present in the IEDB.  Browsing the tree allows users to select parent nodes of sets of similar assays. Searching by the drop down menus allows users to search by assay Name, Method, Measured response, or the Units of a quantitative value that was captured. As shown below, once a search has been performed, such as for "IFNg release", the Assay Finder returns those assays measuring that response. In this case, 8 records were returned. Icons present in the Search Results allow one to select any assay by clicking the "plus sign" or to view any assay in the context of the hierarchical tree by clicking on the "Highlight" icon. Users may also click on any node of the tree to select that node as a search criteria. Once all desired assay types have been selected, users must click "Apply" to add these search parameters to their larger query of the IEDB data. Clicking "Apply" will close the Assay Finder and return the user back to the larger search interface, consisting of many other fields and Finders.

Assay Definitions

Assays used by the IEDB are dependent upon The Ontology for Biomedical Investigations (OBI) http://obi-ontology.org/page/Main_Page.

This formal ontology is an integrated ontology for the description of biological and clinical investigations. As the IEDB encounters new assay types in the literature, they are added to OBI. To read assay definitions, synonyms, full term names, and see their relationships to other assay terms, use the OBI linkout in the Finder Results table.

By using OBI to describe experimental assays, the data of the IEDB becomes interoperable with other resources utilizing OBI, enabling sophisticated queries and enforcing logical reasoning. To read more about OBI, see this publication: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0154556