If you would like to search for a specific compound (e.g.for example, only for "Etoposide Phosphate"), you may have trouble matching your ad hoc query term to a Cancer Gene Index compound term. In these instances, it is highly recommended that you search the NCI Thesaurus for the term that matches your desired term prior to querying the Templated Search toolcompound concept. Navigate to the NCI Thesaurus web page and select the "Contains" radio button (1). Enter in one or more keywords (2, e.g. for example "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 Contact Us link at the bottom of the web page for help (4).

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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) , or 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..

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Using Templated Search Tool to Retrieve Gene-Compound Concept Pairs

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

The Agent to Genes query returns all of the genes that were associated in MEDLINE abstracts with your compound search term. These results are presented in table consisting of three columns which include: HUGO gene symbol, NCI Thesaurus agent term, and a PubMed identifier. Each row represents a piece of evidence (i.e. a sentence extracted from MEDLINE abstracts) supporting the single gene-compound association.

If no genes are associated with your compound term, you will receive a "No results found" message.

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 compound term.

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Validating Your Retrieved Gene-Agent Results

A fully-featured search tool would allow you to limit your searches to results that have been validated caBIO houses all Cancer Gene Index gene-disease association annotations, including information on whether the association was found to be negative by the Cancer Gene Index project's human curators as being true gene-compound associations or that do not come or originated from cell lines . Currently, however, the Templated Search does not allow such limits to be setor non-human organisms. Queries cannot be limited by these or other annotations (for example, gene status flags, or curator comments). Thus, you must access to caBIO Object Graph Browser to manually check the validity of negation status of and find other annotations for each of the retrieved recordsrecord.

To perform these checks, click on any gene-compound result row in order to view its Gene-Disease Association information. Gene-Agent Assocation data includes include the Gene Term, Gene Symbol, Agent Term, Agent Symbol, Sentence PubMed Identifier, Sentence Evidence, Evidence Code, and 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).

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This will open up a the Gene-Agent Assocation object in a new window or tab in your web browser. Click on the getEvidenceCollection link (31, green blue box) to open the full Evidence record (middle panel), which contains all of the annotations made by the curator for that particular piece of evidence of a gene-compound association. Gene-compound associations with true relationships that were validated as being true associations by human curators have a sentenceStatus set to "finished" and a negationStatus set to "no" (42, middle and right green blue boxes in middle panel). If you wish to exclude data from cell lines, look for example, the celllineStatus to must be be "no" (4, left green box). ." Additional information on these items and other Evidence record data may be found in the Data, Metadata, and Annotations section.

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 Return to Results link in blue to continue evaluating retrieved gene-compound pairs in the results table.

To search for genes associated with these additional compound concepts, return to your Templated Search results page if needed and click . Click the Agent to Genes link (1), click hit the Reset button (2) or manually delete the search contents, 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).

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Agent Ontologies

Although the NCI Thesaurus contains information about compound agent ontologies, the caBIO Templated Search does not currently allow you to leverage implement this hierarchical compound information. In the future, this feature may be implemented in this tool, but for now, Thus, you must searching search the NCI Thesaurus for these ontological compound parent, sister, and child agent concept terms and perform a Templated search for each parent or child concept.

The Cancer Gene Index includes the NCI Thesaurus term "Pharmacologic Substance," its child concepts, and all of their NCI Thesaurus synonyms.