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Section
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titlePage Contents
Table of Contents
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titleDocumentation Table of Contents
Tip
titleNeed Additional Help?

If you need additional support, please contact the NCICB Support Group.

Info
titleTo Print the Guide

We recommend you print one wiki page of the guide at a time. To do this, click the printer icon at the top right of the page; then from the browser File menu, choose Print. Printing multiple pages at one time is more complex. For instructions, refer to How do I print multiple pages?.

Resizing

the

text

for

any

web

page

is

easy.

For

information

on

how

to

do

this

in

your

web

browser,

refer

to

this

[

W3C

tutorial|http://www.w3.org/WAI/changedesign] {multi-excerpt-include:

tutorial

Info
titleHaving Trouble Reading the Text?
Wiki Markup
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wikicontent:Exit

Disclaimer

to

Include

|name=ExitDisclaimer|nopanel=true}

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.

h1.

Search

for

Biological

Entities

Gene

Query

Overview

The

[

caBIO

Home

Page

Search

for

Biological

Entities

|http://cabioapi.nci.nih.gov/cabio43/Home.action]

is

a

flexible

tool,

and

the

workflow

presented

here

is

just

one

of

the

ways

that

it

can

be

used.

These

steps

illustrate

how

to

query

a

specific

type

of

Cancer

Gene

Index-associated

object

to

identify

those

with

attributes

that

are

associated

with

your

gene

search

term.

h1. Identifying a Gene Search Term In order to search for genes that are associated with a given disease, you must first have a [HUGO gene symbol|http://www.genenames.org] {multi-excerpt-include:wikicontent:Exit Disclaimer to Include|name=ExitDisclaimer|nopanel=true}. Although it is much easier to use the HUGO gene symbol, you may also use the gene's NCI Thesaurus concept code. To find this code, navigate to the [NCI Thesaurus web page|http://nciterms.nci.nih.gov/] and select the {{Contains}} radio button (1). Enter you gene symbol (2) and click the Search button (3). If you cannot find the term for which you were looking, click on the Contact Us link at the bottom of the web page (4). {tip:title=Tip}You may use the question mark wild card character after your search term (for example, "top2?") when using {{Exact Match}} or {{Begins With}}.{tip} Select the desired result from the list of retrieved thesaurus terms in order to view the term's concept page. You may use Thesaurus Code (1) with the Search for Biological Entities tool. h1. Using the Search for Biological Entities Tool Compounds and diseases associated with a particular gene in the Cancer Gene Index data may be accessed by selecting the {{Gene}} class in the package {{

Identifying a Gene Search Term

In order to search for genes that are associated with a given disease, you must first have a HUGO gene symbol

Column
Wiki Markup
Multiexcerpt include
wikicontent:Exit Disclaimer to Include
wikicontent:Exit Disclaimer to Include
nopaneltrue
MultiExcerptNameExitDisclaimer
PageWithExcerptwikicontent:Exit Disclaimer to Include
. Although it is much easier to use the HUGO gene symbol, you may also use the gene's NCI Thesaurus concept code. To find this code, navigate to the NCI Thesaurus web page and select the Contains radio button (1). Enter you gene symbol (2) and click the Search button (3). If you cannot find the term for which you were looking, click on the Contact Us link at the bottom of the web page (4).

Tip
titleTip

You may use the question mark wild card character after your search term (for example, "top2?") when using Exact Match or Begins With.

Select the desired result from the list of retrieved thesaurus terms in order to view the term's concept page. You may use Thesaurus Code (1) with the Search for Biological Entities tool.

Using the Search for Biological Entities Tool

Compounds and diseases associated with a particular gene in the Cancer Gene Index data may be accessed by selecting the Gene class in the package gov.nih.nci.cabio.domain

}}

.

The

line

breaks

in

the

tree

represent

classes

that

have

been

removed

for

space.

Enter

the

HUGO

gene

symbol

in

the

{{

symbol

}}

field

or

the

NCI

Thesaurus

gene

concept

code

in

the

{{

id

}}

field,

select

{{

gov.nih.nci.cabio.domain.GeneFunctionAssociation

}}

as

the

Search

Object,

and

click

Submit.

Retrieved

results

are

shown

as

records

in

Gene/Agent

and

Gene/Disease

tables.

Tip
titleTip

Although the Cancer Gene Index refers to pharmacological substances by the term "compound" or even

{tip:title=Tip}Although the Cancer Gene Index refers to pharmacological substances by the term "compound" or even

"drug,"

caBIO

and

the

NCI

Thesaurus

use

the

term

"agent"

for

this

concept.{tip} !PortalSEBGeneSearch.jpg|alt="Portal SEB GeneSearch! The following subsections describe how to view associated [#disease terms] and [#compound terms] {anchor:compound terms} h2. Gene-Compound Association Results In the Gene/Agent tables, columns include each object's identifier, the [Role Code and/or Role Detail|Data, Metadata, and Annotations#Role] associated with the gene-compound concept pair, notation that the data derive from the Cancer Gene Index, and three method links - {{getGene}}, {{getEvidenceCollection}}, and {{getAgent}}. !SBEGAresults.jpg|alt="SBEGA results"! To view the sentence and annotation information, select the {{getEvidenceCollection}} method (green box in top panel) to call up the associated {{Evidence}} type object (green box in middle panel). For additional information on these data and metadata, refer to the [Data, Metadata, and Annotations|https://wiki.nci.nih.gov/x/DS9yAQ] section. {tip:title=Search Tip}If you do not want to spend time navigating through the caBIO object model for candidate gene-compound associations that were found to be false positives, you should first view the {{Evidence}} objects (bottom panel) and scroll to the right to check that the [{{sentenceStatus}}|Data, Metadata, and Annotations#sentence status flags] is "finished" and [{{negationIndicator}}|Data, Metadata, and Annotations#Indicators] is {{no}} before clicking through to gene name information in the {{Gene}} object.{tip} Click the {{getAgent}} method link to the name and EVS identifier of the associated compound term in the {{fullName}} and {{EVSid}} columns, respectively. !PortalSEBGeneResults.jpg|"Porgal SEB GeneResults"! {anchor:disease terms} h2. Gene-Disease Association Results Retrieved gene-disease results are listed as records in a single table, which includes each object's identifier, the [Role Code and/or Role Detail|Data, Metadata, and Annotations#Role] associated with the gene-disease concept pair, notation that the data derive from the Cancer Gene Index, and three method links - {{getGene}}, {{getEvidenceCollection}}, and {{getDiseaseOntology}}. !SBEgdResults.jpg|alt="SBEgd Results"! To view the gene-disease sentence and annotation information, select the {{getEvidenceCollection}} method (green box in top panel) to call up the associated {{Evidence}} type object (green box in middle panel). {tip:title=Search Tip}If you do not want to spend time navigating through the caBIO object model for candidate gene-disease associations that were found to be false positives, you should first view the {{Evidence}} objects (bottom panel) and scroll to the right to check that the [{{sentenceStatus}}|Data, Metadata, and Annotations#sentence status flags] is "finished" and [{{negationIndicator}}|Data, Metadata, and Annotations#Indicators] is {{no}} before clicking through to gene name information in the {{DiseaseOntology}} object.{tip} Click the {{getDiseaseOntology}} method link to the name and EVS identifier of the associated disease term in the {{fullName}} and {{EVSid}} columns, respectively. You may also view parent and child concepts for your disease of interest and explore gene-disease associations with those disease concepts, as well (2). Black double lines indicated breaks in the view of an object in this figure. You can find parent disease concepts by scrolling to the right and selecting the {{getParentDiseaseOntologyRelationshipCollection}} link; child disease concepts can be accessed by clicking on the {{getChildDiseaseOntologyRelationshipCollection}} link. !TemplatedSearchGOV2.jpg|alt="Templated Search GOV2"!

concept.

Image Added

The following subsections describe how to view associated #disease terms and #compound terms

Anchor
compound terms
compound terms

Gene-Compound Association Results

In the Gene/Agent tables, columns include each object's identifier, the Role Code and/or Role Detail associated with the gene-compound concept pair, notation that the data derive from the Cancer Gene Index, and three method links - getGene, getEvidenceCollection, and getAgent.

SBEGA resultsImage Added

To view the sentence and annotation information, select the getEvidenceCollection method (green box in top panel) to call up the associated Evidence type object (green box in middle panel). For additional information on these data and metadata, refer to the Data, Metadata, and Annotations section.

Tip
titleSearch Tip

If you do not want to spend time navigating through the caBIO object model for candidate gene-compound associations that were found to be false positives, you should first view the Evidence objects (bottom panel) and scroll to the right to check that the sentenceStatus is "finished" and negationIndicator is no before clicking through to gene name information in the Gene object.

Click the getAgent method link to the name and EVS identifier of the associated compound term in the fullName and EVSid columns, respectively.

Image Added

Anchor
disease terms
disease terms

Gene-Disease Association Results

Retrieved gene-disease results are listed as records in a single table, which includes each object's identifier, the Role Code and/or Role Detail associated with the gene-disease concept pair, notation that the data derive from the Cancer Gene Index, and three method links - getGene, getEvidenceCollection, and getDiseaseOntology.

SBEgd ResultsImage Added

To view the gene-disease sentence and annotation information, select the getEvidenceCollection method (green box in top panel) to call up the associated Evidence type object (green box in middle panel).

Tip
titleSearch Tip

If you do not want to spend time navigating through the caBIO object model for candidate gene-disease associations that were found to be false positives, you should first view the Evidence objects (bottom panel) and scroll to the right to check that the sentenceStatus is "finished" and negationIndicator is no before clicking through to gene name information in the DiseaseOntology object.

Click the getDiseaseOntology method link to the name and EVS identifier of the associated disease term in the fullName and EVSid columns, respectively. You may also view parent and child concepts for your disease of interest and explore gene-disease associations with those disease concepts, as well (2). Black double lines indicated breaks in the view of an object in this figure. You can find parent disease concepts by scrolling to the right and selecting the getParentDiseaseOntologyRelationshipCollection link; child disease concepts can be accessed by clicking on the getChildDiseaseOntologyRelationshipCollection link.

Templated Search GOV2Image Added