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Using the caBIO Portlet Templated Search to Find Disease and Compounds Associated with a Gene
Selecting a Disease Search Term
The caBIO Portlet Templated Search tool allows end users to execute case-insensitive searches for the diseases and compounds that are associated with a gene concept. These search terms must match exact (case-insensitive) gene terms in the Cancer Gene Index.
If you would like to search for a specific gene (e.g., only for "BMP7"), you may use the gene's HUGO gene symbol.
If you would like to search for diseases and compounds that are associated with a related genes (e.g., "BMP2," "BMP3," "BMP5", and "BMP7"), use the * wild card character, which matches zero or more characters, in your search terms (e.g., "BMP*"). For example, a search for "bmp7" will return nearly 210 results that are related to that exact term, whereas a search for "bmp*" returns nearly 2,200 results, where genes match terms that include "BMP1," "BMP2," and "BMPR2."
Using Templated Search Tool to Retrieve Gene-Disease and Gene-Compound Concept Pairs
To search for Cancer Gene Index gene-disease and gene-compound data on the Templated Search page, click on the Cancer Gene Index Category node (1) and choose the Gene to Diseases/Agents query option (2). Manually delete the suggested search term "C4BPA" (3), enter your compound term or concept code into the text box (e.g., "BMP7" or "BMP*"), and click the Search button (4).
Note
Although the Cancer Gene Index refers to pharmacological substances as "compounds," caBIO refers to the concept as "agents."
The Gene to Diseases/Agents query returns Gene/Agent Association and Gene/Disease Association results in a tabular form. Each table consists of three columns which include: HUGO Gene Symbol, NCI Thesaurus disease or compound term, and a PubMed identifier. Each row represents a piece of evidence (i.e. a sentence extracted from MEDLINE abstracts) supporting the gene-disease or gene-compound association. You will will receive a "No results found" message if you have used a search term that does not match the Cancer Gene Index gene symbol or if no disease or compound are associated with your gene search term.
Warning
At this time, you cannot download your search results. Instead, you must copy them into a text editor or spreadsheet.
Note
Your first result page will likely contain a Gene/Agent Association and Gene/Disease Association table. This does not mean that all of the gene-compound associations are given on the first page. Instead you must continue to review subsequent results pages to find all gene-compound and gene-disease association results.
Validating Your Retrieved Gene-Disease 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 or gene-compound associations or as not originating 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 search result.
To perform this validation, click on any gene-disease or gene-compound result row in order to view its Gene-Disease Association or Gene-Agent 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). GAdditional 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-Agent 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-compound association. Gene-compound 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, look 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.
Note
If you accidentally navigate to somewhere else in caBIO by clicking on the wrong link in the Object Viewer and are confused, stop and go back!
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.
Validating Your Retrieved Gene-Compound/Agent Results
To validate gene-compound/agent associations click on any row in a Gene-Agent Association results table in order to view the concept pair's Gene-Agent Association information. These data include 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 metadata and data 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-Agent Assocation object in a new window or 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-compound association. Gene-compound 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, look 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.
Note
If you accidentally navigate to somewhere else in caBIO by clicking on the wrong link in the Object Viewer and are confused, go back!
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 diseases and compounds/agents associated with other genes, return to your Templated Search results page, if needed, and click the Gene to Diseases/Agents link (1), hit the Reset button (2), enter a new gene symbol (3), and click Search (4). If you would like to select a new query option, click Return to Templates (below 2 and 4).
