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Overview
The caBIO Portal Search for Biological Entities is a flexible tool, and the worklow presented here is just one of the ways that it can be used. These steps illustrate how to query a specific type object to identify those with attributes that are associated with your gene search term. This tool may be useful if you want to view only specific types of objects related to Cancer Gene Index.
Identifying a Gene Search Term
In order to search for genes that are associated with a given disease, you must first have a HUGO gene symbol. Although it is much easier to use the HUGO gene symbol, you may also use the gene's NCI Thesaurus concept code. To find this code, navigate to the NCI Thesaurus web page and select the Contains radio button (1). Enter you gene symbol (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).
Tip
You may use the question mark wild card character after your search term (e.g., "bmp?") when using Exact Match or {{Begins With}.
Select the desired result from the list of retrieved thesaurus terms in order to view the term's concept page. You may use Thesaurus Code (1) with the Search for Biological Entities tool.
Using the Search for Biological Entities Tool
Compounds and diseases associated with a particular gene in the Cancer Gene Index data may be accessed by selecting the Gene class in the package gov.nih.nci.cabio.domain. The line breaks in the tree represent classes that have been removed for space. Enter the HUGO gene symbol in the symbol field or the NCI Thesaurus gene concept code in the id field, select gov.nih.nci.cabio.domain.GeneFunctionAssociation as the Search Object, and click Submit. Retrieved results are shown as records in Gene/Agent and/or Gene/Disease tables.
Tip
Although the Cancer Gene Index refers to pharmacological substances by the term "compound" or even "drug," caBIO and the NCI Thesaurus use the term "agent" for this concept.
Gene-Compound Association Results
In the Gene/Agent tables, columns include each object's identifier, the Role Code and/or Role Detail associated with the gene-compound or gene-disease concept pair, notation that the data derive from the Cancer Gene Index, and three method links - getGene, getEvidenceCollection, and getAgent. To view the 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). For additional information on these data and metadata, refer to the Data, Metadata, and Annotations section.
Search Tip
If you do not want to spend time navigating through the caBIO object model for candidate gene-compound associations that were found to be false positives, unclear, or redundant to other data, you should first view the Evidence objects (bottom panel) and scroll to the right to check that the sentenceStatus is "finished" and negationIndicator is no before clicking through to gene name information in the Gene object.tip
Click the getAgent method link to the name and EVS identifier of the associated compound term in the fullName and EVSid columns, respectively.
!SEBGENEGeneResults!
Gene-Disease Association Results
Retrieved gene-disease 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-disease concept pair, notation that the data derive from the Cancer Gene Index, and three method links - getGene, getEvidenceCollection, and getDiseaseOntology. To view the gene-disease 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).
Search Tip
If you do not want to spend time navigating through the caBIO object model for candidate gene-disease associations that were found to be false positives, unclear, or redundant to other data, you should first view the Evidence objects (bottom panel) and scroll to the right to check that the sentenceStatus is "finished" and negationIndicator is no before clicking through to gene name information in the DiseaseOntology object.tip
Click the getDiseaseOntology method link to the name and EVS identifier of the associated disease term in the fullName and EVSid columns, respectively. You may also view parent and child concepts for your disease of interest and explore gene-disease associations with those disease concepts, as well (2). You can find parent disease concepts by scrolling to the right and selecting the getParentDiseaseOntologyRelationshipCollection link; child disease concepts can be accessed by clicking on the getChildDiseaseOntologyRelationshipCollection link.
