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{section}
{column:width=30%}
{panel:title=Page Contents}
{toc:maxLevel=4}
{panel}
{panel:title=Documentation Table of Contents}
* [Documentation Main Page|https://wiki.nci.nih.gov/x/hC5yAQ]
* [Creation of the Cancer Gene Index|https://wiki.nci.nih.gov/x/DS9yAQ]
* [Data, Metadata, and Annotations|https://wiki.nci.nih.gov/x/zC1yAQ]
* [Cancer Gene Index Gene-Disease and Gene-Compound XML Documents|https://wiki.nci.nih.gov/x/8i1yAQ]
* [caBIO APIs|https://wiki.nci.nih.gov/x/7zByAQ]
* [Cancer Gene Index Shared Parsed Data and Code|https://wiki.nci.nih.gov/x/hzJyAQ]
* [caBIO Portlet Templated Searches|https://wiki.nci.nih.gov/x/0C9yAQ]
* [caBIO Home Page|https://wiki.nci.nih.gov/x/TTByAQ]
* [caBIO iPhone Application|https://wiki.nci.nih.gov/x/VDFyAQ]
* [caBIO Portlet Simple Searches|https://wiki.nci.nih.gov/x/-TByAQ]
* [Glossary|https://wiki.nci.nih.gov/x/si9yAQ]
* [Credits and Resources|https://wiki.nci.nih.gov/x/yS9yAQ]
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{info} {column} {column} h1. Selecting a Disease Search Term The [caBIO Portlet Templated Search|http://cagrid-portal.nci.nih.gov/web/guest/community;jsessionid=E1218755391349E44FD04AD235F26193?p_p_id=cabioportlet_WAR_cabioportlets_INSTANCE_R7dp&p_p_lifecycle=0&p_p_state=normal&p_p_mode=view&p_p_col_id=column-1&p_p_col_count=1&_cabioportlet_WAR_cabioportlets_INSTANCE_R7dp_struts_action=%2Fcabioportlet%2Fview&tabs1=Templated%20Searches] tool allows end users to search

Column

Selecting a Disease Search Term

The caBIO Portlet Templated Search tool allows end users to search (case-insensitive)

for

genes

that

are

associated

with

a

disease

name

or

disease

keywords.

You

may

also

search

for

genes

that

match

a

specific

disease

concept

term

or

concept

code

from

the

NCI

Thesaurus.

These

keywords,

terms

or

codes

must

match

_

exact

_

disease

terms

in

the

Cancer

Gene

Index.

If

you

would

like

to

use

keywords

to

find

genes

that

are

associated

with

a

general

type

of

cancer

(that

is,

any

cancer

involving

the

ovaries

as

opposed

to

a

specific

disease

like

"ovarian

serous

adenocarcinoma"),

it

is

highly

recommended

that

you

use

the

"

\

*"

wild

card

character,

which

will

match

zero

or

more

characters,

in

your

search

terms

(for

example,

"ovarian

\

*"

or

"

\

*ovarian

\

*").

For

example,

a

search

for

"ovarian

cancer"

will

return

nearly

2,500

genes

that

are

related

to

the

_

exact

_

term

"ovarian

cancer,"

whereas

a

search

for

"

\

*ovarian

\

*"

returns

nearly

9,000

gene-disease

pairs,

where

genes

were

associated

in

the

literature

with

terms

that

include

"ovarian

adenocarcinoma,"

"ovarian

adenocarcinomas,"

"ovarian

borderline

tumor,"

"ovarian

brenner

tumor,"

"ovarian

cancer,"

etc.

If

you

would

like

to

search

for

a

specific

disease

(for

example,

only

for

"ovarian

papillary

serous

adenocarcinoma"),

you

can

try

an

_

ad

hoc

_

query.

These

search

terms

may

not

match

a

Cancer

Gene

Index

disease

term,

and

thus

it

is

recommended

that

you

first

query

the

NCI

Thesaurus

for

your

desired

term.

Navigate

to

the

[

NCI

Thesaurus

web

page

|http://nciterms.nci.nih.gov/]

and

select

the

Contains

radio

button

(1).

Enter

in

one

or

more

keywords

(2,

for

example

"malignant

ovarian"),

and

click

the

Search

button

(3).

A

list

of

all

NCI

Thesaurus

terms

that

contain

your

keyword/s

will

be

retrieved. !NCItSearchPage.jpg|alt="NCIt Search Page"! {tip:title=Note} If you do not find an appropriate term, try inserting a single question mark after your search term (for example, "malignant ovar?") to increase the number of retrieved terms.{tip} 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). 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. !NCItDiseaseResult.jpg|alt="NCIT Disease Result"! h1. Using Templated Search Tool to Retrieve Gene-Disease Concept Pairs 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 (for example, "\*ovarian\*" or "ovarian serous adenocarcinoma"), and click the Search button (4). !PortletDiseaseSearch.jpg|alt="Portlet Disease Search"! The {{Diseases to Genes query}} returns all of the genes that were associated in MEDLINE abstracts with your disease search term, and each result represents one piece of evidence of a gene-disease association. These results are presented in table consisting of three columns which include: HUGO Gene Symbol, NCI Thesaurus disease term, and a PubMed identifier. Each row represents a single gene-disease association. If no genes are associated with your disease term, you will receive a "No results found" message. If you have used your own search term, the Cancer Gene Index may use a different disease term for the same disease concept. Try using of the "\*" wild card character or a different search term (for example, "ovar\*" or "ovarian\*serous\*" instead of "ovarian serous adenoma"). !PortletDiseaseReset.jpg|alt="Portlet Disease Reset"! {note:title=Saving Your Search Results}To save your search results, copy and paste them into a text editor or spreadsheet.{note} h1. Validating Your Retrieved Gene-Disease 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|https://wiki.nci.nih.gov/x/DS9yAQ] or originated from cell lines or non-human organisms. Queries cannot be limited by these or other annotations (for example, [gene status flags|Data, Metadata, and Annotations#gene status flags], or curator [comments|Data, Metadata, and Annotations#comments]). Thus, you must access to caBIO Object Graph Browser to manually check the negation status of and find other annotations for each of retrieved record. To perform these checks, click on any gene-disease result row in order to view its Gene-Disease Association information. Gene-Disease Assocation data include the Gene Term, Gene Symbol, Disease Term, Disease Symbol, Sentence PubMed Identifier, Sentence Evidence, [Evidence Code|Data, Metadata, and Annotations#Evidence Codes], and [Role Code or Detail|Data, Metadata, and Annotations#Role] (1). Next, click on the {{Open this record in the caBIO Object Graph Browser}} at the bottom of the page (2). !TemplatedSearchGDA.jpg|alt="Templated Search GDA"! This will open up a the full Gene-Disease Assocation record in a new tab in your web browser. Click on the {{getEvidenceCollection}} link (3, green box) to open the associated Evidence record, which contains all of the annotations made by the curator for that particular piece of evidence of a gene-disease association. Gene-disease associations with validated relationships have a [{{sentenceStatus}}|Data, Metadata, and Annotations#sentence status flags] set to "finished" and a [{{negationStatus}}|Data, Metadata, and Annotations#Indicators] set to "no" (4, middle and right green boxes). If you wish to exclude data from cell lines, for example, the [{{celllineStatus}}|Data, Metadata, and Annotations#Indicators] must be be "no" (4, left green box). Additional information on these and other data in the Evidence record may be found in the [Data, Metadata, and Annotations|https://wiki.nci.nih.gov/x/zC1yAQ] section. !TemplatedSearchDOV.jpg|alt="Templated Search DOV"! {note:title=Note}If you accidentally navigate to somewhere else in caBIO Object Browser and are confused, stop and go back in your web browser!{note} Once you have finished reviewing the gene-disease 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-disease pairs. To search for genes associated with these additional disease concepts, return to your Templated Search results page and click the {{Disease to Genes}} link (1), click the Reset button (2) or manually delete your existing search, 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). !PortletDiseaseReset.jpg|alt="Portlet Disease Reset"! h1. Disease Ontologies Although 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 a new browser tab or window and navigate to the [NCI Thesaurus web page|http://nciterms.nci.nih.gov/], 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. !NCItSearchPage.jpg|alt+"NCIT Search 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). !NCItDiseaseOntologySearch.jpg|alt="NCIt Disease Ontology Search! {column} {section}

retrieved.

NCIt Search PageImage Added

Tip
titleNote

If you do not find an appropriate term, try inserting a single question mark after your search term (for example, "malignant ovar?") 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).

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.

NCIT Disease ResultImage Added

Using Templated Search Tool to Retrieve Gene-Disease Concept Pairs

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 (for example, "*ovarian*" or "ovarian serous adenocarcinoma"), and click the Search button (4).

Portlet Disease SearchImage Added

The Diseases to Genes query returns all of the genes that were associated in MEDLINE abstracts with your disease search term, and each result represents one piece of evidence of a gene-disease association. These results are presented in table consisting of three columns which include: HUGO Gene Symbol, NCI Thesaurus disease term, and a PubMed identifier. Each row represents a single gene-disease association.

If no genes are associated with your disease term, you will receive a "No results found" message. If you have used your own search term, the Cancer Gene Index may use a different disease term for the same disease concept. Try using of the "*" wild card character or a different search term (for example, "ovar*" or "ovarian*serous*" instead of "ovarian serous adenoma").

Portlet Disease ResetImage Added

Note
titleSaving Your Search Results

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

Validating Your Retrieved Gene-Disease 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 or originated from cell lines 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 negation status of and find other annotations for each of retrieved record.

To perform these checks, click on any gene-disease result row in order to view its Gene-Disease Association information. Gene-Disease Assocation data include the Gene Term, Gene Symbol, Disease Term, Disease Symbol, Sentence PubMed Identifier, Sentence Evidence, Evidence Code, and Role Code or Detail (1).

Next, click on the Open this record in the caBIO Object Graph Browser at the bottom of the page (2).

Templated Search GDAImage Added

This will open up a the full Gene-Disease Assocation record in a new tab in your web browser. Click on the getEvidenceCollection link (3, green box) to open the associated Evidence record, which contains all of the annotations made by the curator for that particular piece of evidence of a gene-disease association. Gene-disease associations with validated relationships 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, for example, the celllineStatus must be be "no" (4, left green box). Additional information on these and other data in the Evidence record may be found in the Data, Metadata, and Annotations section.

Templated Search DOVImage Added

Note
titleNote

If you accidentally navigate to somewhere else in caBIO Object Browser and are confused, stop and go back in your web browser!

Once you have finished reviewing the gene-disease 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-disease pairs.

To search for genes associated with these additional disease concepts, return to your Templated Search results page and click the Disease to Genes link (1), click the Reset button (2) or manually delete your existing search, 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).

Portlet Disease ResetImage Added

Disease Ontologies

Although 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 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.

Image 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" 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).

Image Added