Searching for Genes Associated with a Disease

To use the caBIO Home Page Freestyle Lexical Mine tool to find genes that are associated with a cancer-related disease, begin typing keywords into the search field. Because the tool suggests caBIO terms that match the characters you have entered, it is relatively easy to find a disease term that matches your desired disease concept.

If you would like to search for any disease term that contains a string use the special character "*." For example, "ovarian serous adenocarcinoma" would only return objects that have attributes containing this exact disease term, but "*ovarian*" will retrieve objects with attributes containing any term with the string "ovarian."

After entering a search term (1), click the Submit button (2) to retrieve results. Although you may limit your search by clicking on the more options ... link, this is not required (3).

Search Results

The caBIO Home Page Freestyle Lexical Mine will retrieve objects with attributes that match your search term. These objects are grouped by type, which are shown as tabs at the top of the results page. To view genes that are associated with your disease term of interest, click the Evidence tab at the top of the page (1).

Each row in the Evidence results table is a truncated view of an Evidence object (that is, not all attributes and methods are shown on this page), where columns include:

• the class and identifier (Class/Id),
• evidence of the gene-disease association (Sentence),
• whether the evidence was collected from experiments involving cell lines ( Cellline Status ),
• whether the evidence is negative that is, gene X is not associated with disease or compound Y; Negation Status ),
• the PubMed identifier for the abstract from which the evidence was extracted (Pubmed Id), and
• whether the status of the sentence ( Sentence Status ).

For additional information on the attributes of the Evidence type objects, refer to the section Data, Metadata, and Annotations.

Finding the Gene Associated with the Evidence

To discover which gene is associated with each piece of evidence, click on the Class/Id link for the desired object. This will open the full Evidence type object. Scroll over to the right, and click on getGeneFunctionAssociationCollection method link (1) to view the Gene Disease Association type object. This object has a role attribute that contains one or more Role Codes or Role Details that describe the nature of the gene-disease relationship, as well as a notation that the Cancer Gene Index is the source of these data.

Click on the getGene link (2) to access the related Gene object (bottom panel). This Gene object contains the full name and HUGO Gene Symbol in the fullName and hugoSymbol columns (3), for example, for the gene associated with the disease of interest and a specific piece of evidence.

To explore additional genes associated with the disease term of interest, navigate back to the evidence page and repeat this process.

For your reference, the subset of caBIO classes that are related to the Cancer Gene Index are shown. The full model is available on the NCI SVN, but you must have the Enterprise Architect modeling tool to view this file.

Disease Ontologies

As you become comfortable navigating the caBIO object model, you may wish to start using additional method links to discover the pathway/s in which a particular Cancer Gene Index gene is involved, clinical protocol information for a disease or compound, and other related data. It is also possible to view disease ontologies for a given gene-disease concept pair by navigating through the object model to records for objects in the class Disease Ontology, gov.nih.nci.cabio.domain.DiseaseOntology. This can be helpful if you would like to search for genes that are associated with parent, sister, or child concepts to you disease search term.

You can reach these records from either the Disease Ontology tab of the main search result page or by clicking through the model starting from retrieved Evidence type objects. To view related disease concepts from the Disease Ontology tab, click on the tab and select the any hyperlink in the Class/Id column. This will reveal a Disease Ontology type object. If you would like to view parent or child disease concepts linked with an evidence object, select the getGeneFunctionAssociationCollection link on the Evidence object page (1) and then click the getDiseaseOntology link in the GeneDiseaseAssociation object record (2). Once you have pulled up a Disease Ontology record, 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.

NCI Thesaurus Disease Ontologies

To view disease ontologies in the NCI Thesaurus, open a new browser tab or window and navigate to the NCI Thesaurus web page, enter in your disease term (2, "ovarian serous adenocarcinoma") or NCI Thesaurus concept code (for example, "C7550", and click the Search button (3). If required, select your exact search term from the list to view the NCI Term page

You may view parent and child terms for any disease term by clicking on the Relationships tab (blue box). For example, "ovarian serous adenocarcinoma" has the children "ovarian serous cystadenocarcinoma" and "ovarian serous papillary adenocarcinoma" and the parent terms "malignant ovarian serous tumor," "ovarian adenocarcinoma," and "serous adenocarcinoma." Alternatively, if you would like to view where your term fits in the entire disease hierarchy, click the red View in Hierarchy button (green box).