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Using the caBIO Portlet Templated Search to Find Genes Associated with a CompoundSelecting a Disease Search TermThe caBIO Portlet Templated Search tool allows end users to specify keyword queries or to search for genes that match a specific compound concept term or concept code from the NCI Thesaurus. These keywords, terms or codes must match exact (case-insensitive) compound terms in the Cancer Gene Index.
If you would like to use keywords to find genes that are associated with a compound, either alone or in combination with another substance (e.g., as any substance containing "etoposide"), as opposed to a specific compound ("Etoposide Phosphate"), it is highly recommended that you use the * or even ? wild card characters in your search terms (e.g., "etoposide*" or "*etoposide*"). The "*" wild card characters will match zero or more characters after your search, and "?" replaces exactly one additional character. For example, a search for "etoposide" will return nearly 875 gene-agent pairs that are related to that exact term, whereas a search for "*etop*" returns nearly 900 gene-disease pairs, where genes match terms that include "etopophos," "etoposide" and "etoposide phosphate."
If you would like to search for a specific compound (e.g., only for "Etoposide Phosphate"), 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. "etoposide"), 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 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-Compound Concept PairsTo search for Cancer Gene Index gene-compound data on the Templated Search page, click on the A table of genes, your compound/agent concept search term, and a PubMed identifier for will be returned or if no genes are associated with your compound term, 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. If the tool still does not retrieve any results, no genes were found to be associated with your compound term.
Validating Your Retrieved ResultsA 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-compound 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-compound result row in order to view its Gene-Disease Association information. Gene-Disease Assocation data includes the Gene Term, Gene Symbol, Agent Term, Agent 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 This will open up a the Gene-Agent Assocation object in a new tab in your web browser. Click on the
Once you have finished reviewing the gene-compound association in the caBIO Object Graph Browser, return to the caBIO Portlet web browser tab or window, and click the To search for genes associated with these additional compound concepts, return to your Templated Search results page if needed and click the Agent OntologiesAlthough the NCI Thesaurus contains information about compound ontologies, the caBIO Templated Search does not currently allow you to leverage this hierarchical disease information. In the future, this feature may be implemented in this tool, but for now, you must searching the NCI Thesaurus for these ontological disease terms and perform a Templated searches for each parent or child concept. To view disease ontologies, open a new browser tab or window and navigate to the NCI Thesaurus web page, enter in your compound 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). ADD NOTE HERE AND GD - YOU CAN USE CABIO TO DO THIS< BUT IT IS MORE COMPLICATED THAN WE WILL GO INTO HERE. |
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