Overview

The caBIO Portal Search for Biological Entities tool is useful for querying a specific type object to identify those with attributes that are associated with your gene , disease, or 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

Gene Search Term

In order to search for genes that are associated with a given disease, you must first have either an NCI Thesaurus term or EVS Identifier/NCI Thesaurus Identifier for the disease or compound of interest. To find both of these valuesa 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. If you have never used the NCI Thesaurus before, and select the Contains radio button so that the search will return any terms that contain your keywords (1). Enter you keyword/s 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).

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 (21) with the Search for Biological Entities tool.

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If you would like to uncover disease ontologies and also query the Biological Entities functionality for parent and child concepts, 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 you may view where the term fits in the terminology hierarchy by clicking View in Hierarchy (green box).

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Using the Search for Biological Entities

Tool

Compounds and diseases To search for genes that are associated with a particular disease, in the Domain Packages tree (1) expand the gene in the Cancer Gene Index data may be accessed by selecting the Gene class in the package gov.nih.nci.cabio.domain package tree node (2) and select DiseaseOntology class (3). In the gov.nih.nci.cabio.domain.DiseaseOntology search form, provide the disease term NCI Thesaurus concept code in the EVSid field (4a) or the disease NCI Thesaurus term name in the name field (4b). Select the {{. 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.GeneDiseaseAssociation from GeneFunctionAssociation as the Search Object drop-down list (5), and click the Submit button (6).

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Retrieved results are listed shown as records in Gene/Agent and/or Gene/Disease tables.

Gene-Compound Association Results

In the Gene/Agent tables, columns include a single table (top panel), which includes 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 getDiseaseOntology getAgent. 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). 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).

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 (Figure 5.9, 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.

!SEBGENEAgentResults!

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).

Warning! If you do not want to spend time navigating through the caBIO object model for candidate gene-disease and gene-compound associations that were found to be false positives, unclear, or redundant to other data, you should first view the Evidence objects (Figure 5.9, bottom panel) and scroll to the right to check that the Sentence Status sentenceStatus is "finished" and negationIndicator is [[no}} before clicking through to gene name information in the Gene DiseaseOntology object.tip

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Click the getDiseaseOntology method link in any retrieved result should you wish to 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.

Warning! caBIO may not always contain the most up-to-date disease ontology data from the NCI Thesaurus. If the disease concept of interest has neither parent nor child concepts, search the NCI Thesaurus using your disease term or EVS ID listed in the Disease Ontology object, if you have not done so already.

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