To Print the Guide
We recommend you print one wiki page of the guide at a time. To do this, click the printer icon at the top right of the page; then from the browser File menu, choose Print. Printing multiple pages at one time is more complex. For instructions, refer to How do I print multiple pages?.
Searching for Diseases and Compounds Associated with a Gene
To use the caBIO Portal Freestyle Lexical Mine tool to find diseases and pharmacological substances that are associated with a gene, all you have to do is 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 (set of alphanumeric characters) use the special character "*" which will retrieve results will have zero or more characters in place of the asterisk. 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).
Tip
If you have cannot find an appropriate search term, click the Contact Us link for help.
Search Results
The caBIO Portal 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 (i.e., not all attributes and methods are shown on this page), whereas the columns show the attributes associated with the Evidence type: class and identifier (Class/Id), the evidence of the gene-disease association (Sentence), whether the evidence was collected from experiments involving cell lines (Cellline Status), whether the evidence is negative (i.e., 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 data, 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 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 and gene-compound relationship, as well as a notation that the Cancer Gene Index is the source of these data. For additional information on the meanings of the Role Codes and Details, refer to the section Data, Metadata, and Annotations.
Warning
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, select only Evidence objects where the Sentence Status is finished and the Negation Status is no.
Note
A single piece of evidence may have multiple Role Codes and Role Details describing the gene-disease or gene-compound association.
Finding Disease Terms
To view associated disease terms, 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.
Tip
The EVS Identifier is identical to the NCI Concept Code.
To explore additional diseases associated with the gene term of interest, navigate back to the evidence page and repeat this process.
Finding Compound Terms
Evidence may also be associated with compounds. To view associated compound terms, click on the getAgent link (2) to access the related Agent object (bottom panel). This Agent 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.
Be Careful
If you find yourself in a part of the object model that you do not understand or if you get confused, stop and navigate your web browser back to the search results page with the Evidence tab. For your reference, the subset of caBIO classes that are related to the Cancer Gene Index are shown in the figure below.
The full model is available on the caBIO gForge page, but you must have the Enterprise Architect modeling tool to view this file.
