Using the caBIO Portlet Templated Search to Find Genes Associated with a Disease

Selecting a Disease Search Term

The caBIO Portlet Templated Search tool allows end users to specify keyword queries or to search for genes that match a specific disease concept term or concept code from the NCI Thesaurus. These keywords, terms or codes must match exact disease terms in the Cancer Gene Index.

If you would like to use keywords to find genes that are associated with a general type of cancer, such as any cancer involving the ovaries, as opposed to a specific disease ("ovarian serous adenocarcinoma"), it is highly recommended that you use the * or even ? wild card characters in your search terms (e.g., "ovarian*" or "*ovarian*serous*"). The "*" wild card characters will match zero or more characters after your search, and "?" replaces exactly one additional character. For example, a search for "ovarian cancer" will return nearly 2,500 genes that are related to the term "ovarian cancer," whereas a search for "ovarian*" returns nearly 7,000 gene-disease pairs, where genes match terms that include "ovarian adenocarcinoma," "ovarian adenocarcinomas," "ovarian borderline tumor," "ovarian brenner tumor," "ovarian cancer," etc.

If you would like to search for a specific disease (e.g., only for "ovarian papillary serous adenocarcinoma"), it is highly recommended that you search the NCI Thesaurus for your desired term prior to querying the Templated Search tool. Navigate to the NCI Thesaurus web page and select the Contains radio button (1). Enter in one or more keywords (2, e.g. "malignant ovarian"), and click the Search button (3). A list of all NCI Thesaurus terms that contain your keyword/s will be retrieved.

If after trying these tips and using various keywords you still cannot find the term for which you were looking, click on the Contact Us link at the bottom of the web page for help (4).

Once you find your desired NCI Thesaurus term in the list of retrieved results, click on its name in order to navigate to its concept page. For searching caBIO, you may use the NCI Thesaurus Preferred Name (1), the NCI Thesaurus Code (2), or even one of the term's synonyms and abbreviations. The Preferred Name and NCI Thesaurus code are present both at the top of the concept page and within the Terms and Properties section of the web page.

Using Templated Search Tool to Retrieve Gene-Disease Concept Pairs

To search for Cancer Gene Index gene-disease data on the Templated Search page, click on the Cancer Gene Index Category node (1) and choose the Disease to Genes query option (2). Manually delete the suggested search term "fibroadenoma" (3), enter your disease term or concept code into the text box (e.g., "ovarian*" or "ovarian serous adenocarcinoma"), and click the Search button (4).

A table of genes, your disease concept search term, and a PubMed identifier for will be returned or if no genes are associated with your disease term (e.g., "ovarian serous adenocarcinoma"), you will receive a "No results found" message. If you have used your own search term, try using of the "*" or "?" wild card characters. If you have used the NCI Thesaurus to find a specific term or code and there is no typographical error in your query, the Cancer Gene Index does not contain genes associated with that disease term.

Validating Your Retrieved Results

A fully-featured search tool would allow you to limit your searches to results that have been validated by the Cancer Gene Index project's human curators as being true gene-disease associations or that do not come from cell lines. Currently, however, the Templated Search does not allow such limits to be set. Thus, you must access to caBIO Object Graph Browser to manually check the validity of each of the retrieved records.

To perform these checks, click on any gene-disease result row in order to view its Gene-Disease Association information. Gene-Disease Assocation data includes the Gene Term, Gene Symbol, Disease Term, Disease Symbol, Sentence PubMed Identifier, Sentence Evidence, Data, Metadata, and Annotations#Evidence Code, and Data, Metadata, and Annotations#Role Code or Detail (1). Additional information on these items may be found in the Data, Metadata, and Annotations section.

Next, click on the Open this record in the caBIO Object Graph Browser at the bottom of the page (2).

This will open up a the Gene-Disease Assocation object in a new tab in your web browser. Click on the getEvidenceCollection link (3, green box) to open the full Evidence record, which contains all of the annotations made by the curator for that particular piece of evidence of a gene-disease association. Gene-disease associations with true relationships were validated as being true associations by human curators have a sentenceStatus set to "finished" and a negationStatus set to "no" (4, middle and right green boxes). If you wish to exclude data from cell lines, loom for the celllineStatus to be "no" (4, left green box). Additional information on these items may be found in the Data, Metadata, and Annotations section.

Once you have finished reviewing the gene-disease association in the caBIO Object Graph Browser, return to the caBIO Portlet web browser tab or window, and click the Return to Results link in blue to continue evaluating retrieved gene-disease pairs.

To search for genes associated with these additional disease concepts, return to your Templated Search results page and click the Disease to Genes link (1), click the Reset button (2), enter additional search terms or concept codes (3), and click Search (4). If you would like to select a new query option, click Return to Templates (below 2 and 4).

Disease Ontologies

Cancers are complicated diseases, as is the nomenclature. The NCI Thesaurus contains information about disease ontologies, but the caBIO Templated Search does not currently allow you to leverage this hierarchical disease information. In the future, this feature may be implemented in the Templated Search tool, but for now, you may find the names and NCI Thesaurus Codes for the parent or child concepts of your disease search term by searching the NCI Thesaurus.

To view disease ontologies, open a new browser tab or window and navigate to the NCI Thesaurus web page, enter in your disease term or NCI Thesaurus concept code (2, "ovarian serous adenocarcinoma"), 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).

Instead, try searching for a more general disease term in the NCI Thesaurus. To find this, open a new browser tab or window and navigate to the NCI Thesaurus web page, enter in your disease term or NCI Thesaurus concept code (2, "ovarian serous adenocarcinoma"), and click the Search button (3). If required, select your exact search term from the list to view the NCI Term page. You may use the parent and child disease concepts listed the Relationships tab (3) for your Templated Search or you may find all related disease term in the Thesaurus disease hierarchy by clicking the red View in Hierarchy button (4).

NCI THESAURUS RELATIONSHIPS AND HIERARCHY