Searching for Diseases and Compounds Associated with a Gene

To use the caBIO Home Page Freestyle Lexical Mine tool to find diseases and pharmacological substances that are associated with a gene, begin typing the HUGO gene name

into the search field. Because the Freestyle Lexical Mine suggests caBIO terms that match the characters you have entered, it is relatively easy to find a gene term that matches your desired gene concept.

If you would like to search for any gene that contains a string use the special character "*." For example, "C4BPA" would only return objects with attributes that match this exact gene, but "C4BP*" will retrieve objects with attributes containing "C4BPA" and "C4BPB."

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 that match your gene search term. These objects are grouped by type, which are shown as tabs at the top of the results page. To view diseases and compounds that are associated with your gene search term, 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 the columns include:

• the class and identifier (Class/Id),
• evidence of the gene-disease or gene-compound 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 these attributes, refer to the section Data, Metadata, and Annotations.

Finding Diseases or Compounds Associated with the Evidence

To discover which disease and/or compound 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 and/or Gene Agent Association type objects. The GeneFunctionAssocation type object has a role attribute that contains Role Codes or Role Details that describe the nature of the gene-disease and gene-compound relationship, as well as a notation that the Cancer Gene Index is the source of these data.

The following subsections provide step-by-step guidance on how to find #disease terms or #compound terms.

Finding Disease Terms

To view associated disease terms that are linked to the Gene Disease Association type object, click on the getDiseaseOntology link (2) to access the related DiseaseOntology object (bottom panel). This DiseaseOntology object contains the disease name and EVS Identifier in the name and EVSid columns (3), for example, for the disease associated with the gene of interest and a specific piece of evidence.

To explore additional diseases associated with the gene 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 here.The full model is available on the caBIO gForge page, but you must have the Enterprise Architect

modeling tool to view this file.

Finding Compound Terms

Evidence may also be associated with compounds. To view associated compound terms that are linked to any Gene Agent Association type object, click on the getAgent link (2) to access the related Agent object (bottom panel). This object contains the compound name and EVS Identifier in the name and EVSid columns (3), for example, for the compound associated with the gene of interest and a specific piece of evidence.

To explore additional compounds associated with the gene 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 here. The full model is available on the caBIO gForge page, but you must have the Enterprise Architect

modeling tool to view this file.