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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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titleDocumentation Table of Contents
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{info} {column} {column} h1. Selecting a Gene Search Term The [caBIO Portlet Templated Search|http://cagrid-portal.nci.nih.gov/web/guest/community?p_p_id=cabioportlet_WAR_cabioportlets_INSTANCE_R7dp&p_p_lifecycle=1&p_p_state=normal&p_p_mode=view&p_p_col_id=column-1&p_p_col_count=1&_cabioportlet_WAR_cabioportlets_INSTANCE_R7dp__spage=%2Fportlet_action%2Fcabioportlet%2FdiseaseToGenesQuery&_cabioportlet_WAR_cabioportlets_INSTANCE_R7dp__sorig=%2Fportlet_action%2Fcabioportlet%2FdiseaseToGenesQuery%2Fresults] 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_ gene terms in the Cancer Gene Index. If you would like to search for a specific gene (for example, only for "BMP7"), you may use the gene's [HUGO gene symbol|http://www.genenames.org/]

Column

Selecting a Gene 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 gene terms in the Cancer Gene Index.

If you would like to search for a specific gene (for example, only for "BMP7"), you may use the gene's HUGO gene symbol

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.

If

you

would

like

to

search

for

diseases

and

compounds

that

are

associated

with

a

related

genes

(for

example,

"BMP2,"

"BMP3,"

"BMP5",

and

"BMP7"),

use

the

\

*

wild

card

character,

which

matches

zero

or

more

characters,

in

your

search

terms

(for

example,

"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."

h1.

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

(for

example,

"BMP7"

or

"BMP*"),

and

click

the

Search

button

(4).

{

Info
:
title
=
Note
}

Although

the

Cancer

Gene

Index

refers

to

pharmacological

substances

as

"compounds,"

caBIO

refers

to

the

concept

as

"agents."

{info} !PortletGeneSearch.jpg|alt="Portlet GeneSearch"! The {{Gene to

Portlet GeneSearchImage Added

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

single

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

any

Cancer

Gene

Index

gene

symbol

or

if

no

disease

or

compound

is

associated

with

your

gene

search

term.

{warning:title=

Warning
titleWarning!
}

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.{warning} !PortletGeneResult.jpg|alt="Portlet GeneResult"! {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 Results caBIO houses the 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. In order to select only your desired data, you must access to caBIO Object Graph Browser to manually check the negation status of and find other annotations for each retrieved record. h2. Validating Your Retrieved Compound Results To perform this validation, click on any gene-compound result row in order to view its Gene-Agent Association information. Gene-Agent Association data include the Gene Term, Gene Symbol, Agent Term, Agent Identifier, Sentence PubMed Identifier, Sentence Evidence, [Evidence Code|Data, Metadata, and Annotations#Evidence Codes], and [Role|Data, Metadata, and Annotations#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). !TemplatedSearchGGA2.jpg|alt="Templated Search GGA2"! This will open up a the Gene-Agent Association 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}}|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." If you want to see additional information about the agent, navigate back to the Gene-Agent Association in your browser and click on {{getAgent}} (3, blue box in top panel). This will open an {{Agent}} object, in which you may see the name and EVS Identifier for the associated compound (4, blue boxes in bottom panel). !TemplatedSearchGOV2.jpg|alt-"Templated Search GOV2"! {note:title=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!{note} 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. h2. Validating Your Retrieved Disease Results To validate gene-disease associations click on any row in the Gene-Disease Association results table. This will open the concept pair's Gene-Disease Association information. These 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|Data, Metadata, and Annotations#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). !TemplatedSearchGGA.jpg|alt="Templated Search GGA"! This will open up a the Gene-Disease Assocation object in a new window or tab in your web browser. Click on the {{getEvidenceCollection}} link (1, 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-disease association. Gene-disease pairs with true relationships were validated as being true associations by human curators have a [{{sentenceStatus}}|Data, Metadata, and Annotations#sentence status flags] set to "finished" and a [{{negationStatus}}|Data, Metadata, and Annotations#Indicators] set to "no" (2, green boxes in the middle panel). If you wish to exclude data from cell lines, for example, the [{{celllineStatus}}|Data, Metadata, and Annotations#Indicators] must be be "no." If you want to see some additional information about the disease, navigate back to the Gene-Disease Association object in your browser, and click on {{getDiseaseOntology}} (3, blue box in top panel). This will open a {{Disease Ontology}} record, in which you may see the name and EVS Identifier for the associated disease (4, blue boxes in bottom panel). !TemplatedSearchGOV.jpg|alt="Templated Search GOV"! {note:title=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!{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 in the results table. h1. New Gene to Disease/Agent Searches 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). !PortletGeneReset.jpg|alt="Portlet GeneReset"! {column} {section}

results.

Portlet GeneResultImage Added

Note
titleSaving Your Search Results

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

Validating Your Results

caBIO houses the 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. In order to select only your desired data, you must access to caBIO Object Graph Browser to manually check the negation status of and find other annotations for each retrieved record.

Validating Your Retrieved Compound Results

To perform this validation, click on any gene-compound result row in order to view its Gene-Agent Association information. Gene-Agent Association data include the Gene Term, Gene Symbol, Agent Term, Agent Identifier, 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 GGA2Image Added

This will open up a the Gene-Agent Association 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, for example, the celllineStatus must be be "no." If you want to see additional information about the agent, navigate back to the Gene-Agent Association in your browser and click on getAgent (3, blue box in top panel). This will open an Agent object, in which you may see the name and EVS Identifier for the associated compound (4, blue boxes in bottom panel).

Image Added

Note
titleNote

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 Disease Results

To validate gene-disease associations click on any row in the Gene-Disease Association results table. This will open the concept pair's Gene-Disease Association information. These 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 GGAImage Added

This will open up a the Gene-Disease Assocation object in a new window or tab in your web browser. Click on the getEvidenceCollection link (1, 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-disease association. Gene-disease pairs with true relationships were validated as being true associations by human curators have a sentenceStatus set to "finished" and a negationStatus set to "no" (2, green boxes in the middle panel). If you wish to exclude data from cell lines, for example, the celllineStatus must be be "no." If you want to see some additional information about the disease, navigate back to the Gene-Disease Association object in your browser, and click on getDiseaseOntology (3, blue box in top panel). This will open a Disease Ontology record, in which you may see the name and EVS Identifier for the associated disease (4, blue boxes in bottom panel).

Templated Search GOVImage Added

Note
titleNote

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-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 in the results table.

New Gene to Disease/Agent Searches

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).

Portlet GeneResetImage Added