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If after trying these tips and using various keywords you still cannot find the term for which you were looking, click on the Figure 3.1.!!!!!! 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. Figure 3.2!!!!! Using Templated Search Toolto Retrieve Gene-Disease Concept Pairs
Templated Search tool to find genes associated with a disease | Templated Search tool to find genes associated with a disease | 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.for example, "*ovarian*" or "ovarian serous adenocarcinoma"), and click the Search button (4).*Figure 3.3. !!!!!!! The If 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. Note |
If you have used your own search term, the Cancer Gene Index may use a different disease term ,for the same gene may be associated with one or more of the matched disease terms. These genes appear multiple times in your retrieved results.If you have used your own search term, try disease concept. Try using of the "*" wild card character with more general terms. 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 exact disease term. 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 or a different search term (for example, "ovar*" or "ovarian*serous*" instead of "ovarian serous adenoma").
Validating Your Retrieved Gene-Disease ResultscaBIO houses all Cancer Gene Index gene-disease association annotations, including information on whether the association was found to be negative 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 or originated from cell lines , but currently 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 negation status of and find other annotations for each of these retrieved recordsrecord. To perform these checks, first click on any gene-disease result row in order to view its Gene-Disease Association information. Gene-Disease Assocation data includes include the Gene Term, Gene Symbol, Disease Term, Disease Symbol, Sentence PubMed Identifier, Sentence Evidence, Data, Metadata, and Annotations#Evidence Evidence Code, and Data, Metadata, and Annotations#Role Role Code or Detail (1). Additional information on these items may be found in the Data, Metadata, and Annotations section. Next, click on the NEW FIGURE HERE!!!! This will open up a the full Gene-Disease Assocation object record in a new tab in your web browser. Click on the
Once you have finished reviewing the gene-disease association in the caBIO Object Graph Browser, return to the caBIO Portlet tab in your web browser tab or window, and click the Cancers are complicated diseases, as is the nomenclature. For example, "ovarian serous adenocarcinoma" is closely related to, but distinct from, "ovarian serous cystadenocarcinoma," "ovarian serous papillary adenocarcinoma," and "malignant ovarian serous tumor." If you utilize the Templated Search tool to query for "ovarian serous adenocarcinoma" you will only uncover genes related to this exact term. Unfortunately, you cannot yet use this tool to simultaneously retrieve records for closely related disease terms and instead must repeat the To search for genes associated with these additional disease concepts, return to your Templated Search results page and click the Disease OntologiesAlthough the NCI Thesaurus contains information about disease ontologies, the caBIO Templated Search does not implement this hierarchical disease information. Thus, you must search the NCI Thesaurus for these parent, sister, and child disease concept terms and perform a Templated searches for each concept. To view disease ontologies, open 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. 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 disease ontologies parent and child terms for any disease term by clicking on the Relationships tab (3) and reviewing the parent and child concepts, or you may see 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 by clicking , click the red View in Hierarchy button (4). NCIt SEARCH FIGURE OVARIAN ADENOCARCINOMA HERE!!! To search for genes associated with these additional disease concepts, return to your Templated Search results page and click the green box). Figure 3.4. Resetting the Cancer Gene Index Disease to Genes caBIO Templated Search. |