h1. Search for Biological Entities Gene Query Overview
The [caBIO Home Page Search for Biological Entities|http://cabioapi.nci.nih.gov/cabio43/Home.action] is a flexible tool, and the workflow presented here is just one of the ways that it can be used. These steps illustrate how to query a specific type of Cancer Gene Index-associated object to identify those with attributes that are associated with your gene search term.
h1. 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|http://www.genenames.org] {multi-excerpt-include:wikicontent:Exit Disclaimer to Include|name=ExitDisclaimer|nopanel=true}. 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|http://nciterms.nci.nih.gov/] 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:title=Tip}You may use the question mark wild card character after your search term (for example, "top2?") when using {{Exact Match}} or {{Begins With}}.{tip}
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.
h1. 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 Gene/Disease tables.
{tip:title=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.{tip}
!PortalSEBGeneSearch.jpg|alt="Portal SEB GeneSearch!
The following subsections describe how to view associated [#disease terms] and [#compound terms]
{anchor:compound terms}
h2. Gene-Compound Association Results
In the Gene/Agent tables, columns include each object's identifier, the [Role Code and/or Role Detail|Data, Metadata, and Annotations#Role] 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}}.
!SBEGAresults.jpg|alt="SBEGA results"!
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|https://wiki.nci.nih.gov/x/DS9yAQ] section.
{tip:title=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, you should first view the {{Evidence}} objects (bottom panel) and scroll to the right to check that the [{{sentenceStatus}}|Data, Metadata, and Annotations#sentence status flags] is "finished" and [{{negationIndicator}}|Data, Metadata, and Annotations#Indicators] 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.
!PortalSEBGeneResults.jpg|"Porgal SEB GeneResults"!
{anchor:disease terms}
h2. Gene-Disease Association Results
Retrieved gene-disease results are listed as records in a single table, which includes each object's identifier, the [Role Code and/or Role Detail|Data, Metadata, and Annotations#Role] 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}}.
!SBEgdResults.jpg|alt="SBEgd Results"!
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).
{tip:title=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, you should first view the {{Evidence}} objects (bottom panel) and scroll to the right to check that the [{{sentenceStatus}}|Data, Metadata, and Annotations#sentence status flags] is "finished" and [{{negationIndicator}}|Data, Metadata, and Annotations#Indicators] 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). Black double lines indicated breaks in the view of an object in this figure. 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.
!TemplatedSearchGOV2.jpg|alt="Templated Search GOV2"!
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