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Selecting a Compound

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

Selecting a Disease

Search Term

The caBIO Portlet Templated Search tool allows end users to

specify keyword queries or to

execute case-insensitive searches for genes that are associated with compounds. You may also 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. Not all brand names for pharmacological substances are included in the Cancer Gene Index.

Info
titleNote

Although the Cancer Gene Index refers to pharmacological substances as "compounds," caBIO and the NCI Thesaurus

refers to

use the

concept as

term "agents" for this concept.

"

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.

character, will match zero or more characters (for example, "etoposide*" or "*etoposide*"

). The "*" wild card characters will match zero or more characters after your search, and "?" replaces exactly one additional character

instead of "etoposide phosphate"). For example, a search for "etoposide" will return nearly 875 gene-

agent

compound pairs that are related to that exact term, whereas a search for "*etop*" returns

nearly

about 900 gene-

disease

compound pairs, where genes match terms that include "etopophos," "etoposide" and "etoposide phosphate."

warning

titleWarning

Not all brand names for pharmacological compounds are included in the Cancer Gene Index.

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 tool

compound 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.

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Info
titleNote

If you do not find an appropriate term, you may try inserting a single question mark after your search term (

e.g.

for example, "etopo?") to increase the number of retrieved terms.

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).

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A table of genes, your compound/agent concept search

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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, agent term, and a PubMed identifier

for will be returned or if

. Each row represents a single gene-compound association.

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

Tip
titleTip

If you have used your own search term,

try using of the

the Cancer Gene Index may use a different term for the same compound concept. Try using of the compound's generic name if you used the brand name, the "*"

or "?"
Note
titleRetrieved Gene-Agent Associations

If your search term matches more than one Cancer Gene Index compound/agent term, the same gene may be associated with one or more of the matched compound/agent terms.

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Validating Your Retrieved Results

A fully-featured search tool would allow you to limit your searches to results that have been validated

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.

character or a more general search term (for example, "*etopo*" instead of "etoposide-fluorouracil").

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Note
titleSaving Your Search Results

To save your search results, copy and paste them into a text editor or spreadsheet.


Validating Your Retrieved Gene-Agent Results

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 set

or 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

records

record.

To perform these checks, click on any gene-compound result row in order to view its Gene-Disease Association information. Gene-

Disease

Agent Assocation data

includes

include the Gene Term, Gene Symbol, Agent Term, Agent 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 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 (

3

1,

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" (

4

2, middle and right

green

blue boxes in middle panel). If you wish to exclude data from cell lines,

loom

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.

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Note
titleNote

If you accidentally navigate to somewhere else in

caBIO by clicking on the wrong link in the Object Viewer

the caBIO Object Browser 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 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

disease

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 disease

parent, sister, and child agent concept terms and perform a Templated

searches

search for each

parent or child

concept.

To view

disease

compound 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

etopo"), and click the Search button (3). If required, select your exact search term from the list to view the NCI Term page.

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Agent Search PageImage Added

You may view parent and child terms for any disease term by clicking on the Relationships tab (blue box). For example, "

ovarian serous adenocarcinoma

Epipodophyllotoxin Compound" has the children "

ovarian serous cystadenocarcinoma

2-Ethylhydrazide," "Etoposide Phosphate," "Etoposide," "GL331," "Podophyllin," and "

ovarian serous papillary adenocarcinoma

Teniposide" and the parent terms "

malignant ovarian serous tumor

Antineoplastic Plant Product ," "ovarian adenocarcinoma," and "

serous adenocarcinoma

Topoisomerase-II Inhibitor ." Alternatively, if you would like to view parent, sister, and child concepts and find where your term fits in the entire

disease column

agent hierarchy, click the red View in Hierarchy button (green box).

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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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Agent HierarchyImage Added