Overview

The caBIO Portal Search for Biological Entities tool is useful for querying a specific type of object to identify those with attributes that are associated with your compound search term. This tool may is be useful if you want to view only specific types of objects related to Cancer Gene Index.

Identifying a Disease Search Term

In order to search for genes that are associated with a given compound, you must first have either an NCI Thesaurus term or EVS Identifier/NCI Thesaurus Identifier concept code for the compound of interest. To find both of these values, navigate to the NCI Thesaurus web page. If you have never used the NCI Thesaurus before, select the Select the Contains radio button so that the search will return any terms that contain your keywords (1). Enter you your keyword/s (2), and click the Search button (3). If you cannot find the term for which you were looking, click on the Contact Us link at the bottom of the web page (4).

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Select the desired result from the list of retrieved thesaurus terms in order to view the term's concept page. You may use either the Preferred Term (1) or the Thesaurus Code (2) with the Search for Biological Entities tool.

If you would like to uncover compound ontologies and also in order to query the Search Biological Entities functionality for parent and child concepts as well, you may find the names and NCI Thesaurus Codes for the immediate parent or child concepts by clicking on the Relationships tab (blue box) or . Alternatively, you may view where the term fits in the terminology hierarchy parent, sister, and child concepts by clicking View in Hierarchy (green box).

Using the Search for Biological Entities tool

To search for genes that are associated with a particular compound, in the Domain Packages tree (1) expand the gov.nih.nci.cabio.domain package tree node (2) and select Agent class (3). In the gov.nih.nci.cabio.domain.Agent search form, provide the compound term NCI Thesaurus concept code in the EVSid field (4a) or the disease NCI Thesaurus term name in the name field (4b). Select the {{gov.nih.nci.cabio.domain.GeneAgentAssociation from the Search Object drop-down list (5), and click the Submit button (6).

Retrieved results are listed as records in a single table (top panel), which includes each object's identifier, the Role Code and/or Role Detail associated with the gene-compound concept pair, notation that the data derive from the Cancer Gene Index, and three method links - getGene, getEvidenceCollection, and getAgent. To view the gene-disease compound sentence and annotation information, select the getEvidenceCollection method (green box in top panel) to call up the associated Evidence type object (green box in middle panel). Click on the getGene method link of any record (blue box in top panel) to access the related Gene object, which contains the full name and HUGO Gene Symbol in the fullName and hugoSymbol columns for the gene associated with the evidence and disease of interest (blue box in middle panel).Warning!

Click on the getGene method link of any record (blue box in top panel) to access the related Gene object, which contains the full name and HUGO Gene Symbol in the fullName and hugoSymbol columns for the gene associated with the evidence (blue box in middle panel).