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titleDocumentation Table of Contents
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titleNeed Additional Help?

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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 Printing multiple pages.

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titleHaving Trouble Reading the Text?

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

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{scrollbar:icons=false} {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] {panel} {tip:title=Need Additional Help?}If you need additional support, please contact the [NCICB Support Group|http://ncicb.nci.nih.gov/support].{tip} {info:title=To 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 [WikiTrainFAQsTips:How do I print multiple pages?]. {info} {info:title=Having Trouble Reading the Text?}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:wikicontent:Exit Disclaimer to Include|name=ExitDisclaimer|nopanel=true}.{info} {column} {column} h1. Searching for Genes Associated with a Disease To use the [caBIO Home Page Freestyle Lexical Mine|http://cabioapi.nci.nih.gov/cabio43/Home.action] tool to find genes that are associated with a cancer-related disease, begin typing keywords into the search field. Because the tool suggests caBIO terms that match the characters you have entered, it is relatively easy to find a disease term that matches your desired disease concept. !DiseaseSearch.jpg|alt="Disease Search"! If you would like to search for any disease term that contains a string use the special character "\*." For example, "ovarian serous adenocarcinoma" would only return objects that have attributes containing this _exact_ disease term, but "\*ovarian\*" will retrieve objects with attributes containing any term with the string "ovarian." After entering a search term (1), click the Submit button (2) to retrieve results. Although you may limit your search by clicking on the {{more options ...}} link, this is not required (3). {tip:title=Tip}If you have cannot find an appropriate search term, click the {{Contact Us}} link for help.{tip} !DiseaseSearch2.jpg|alt="Disease Search 2"! h1.Search Results The caBIO Home Page Freestyle Lexical Mine will retrieve objects with attributes that match your search term. These objects are grouped by type, which are shown as tabs at the top of the results page. To view genes that are associated with your disease term of interest, click the Evidence tab at the top of the page (1). Each row in the Evidence results table is a truncated view of an {{Evidence}} object (that is, not all attributes and methods are shown on this page), where columns include: * the class and identifier ({{Class/Id}}), * evidence of the gene-disease association ({{Sentence}}), * whether the evidence was collected from experiments involving cell lines ([{{Cellline Status}}|Data, Metadata, and Annotations#Indicators]), * whether the evidence is negative that is, gene X is not associated with disease or compound Y; [{{Negation Status}}|Data, Metadata, and Annotations#Indicators]), * the PubMed identifier for the abstract from which the evidence was extracted ({{Pubmed Id}}), and * whether the status of the sentence ([{{Sentence Status}}|Data, Metadata, and Annotations#sentence status flags]). For additional information on the attributes of the {{Evidence}} type objects, refer to the section [Data, Metadata, and Annotations|https://wiki.nci.nih.gov/x/zC1yAQ]. !PortalFreestyleDiseaseResults_Evidence.jpg|alt="Portal Freestyle Disease Results"! h1. Finding the Gene Associated with the Evidence To discover which gene is associated with each piece of evidence, click on the {{Class/Id}} link for the desired object. This will open the full {{Evidence}} type object. Scroll over to the right, and click on {{getGeneFunctionAssociationCollection}} method link (1) to view the {{Gene Disease Association}} type object. This object has a role attribute that contains one or more [Role Codes|Data, Metadata, and Annotations#Role Codes] or [Role Details|Data, Metadata, and Annotations#Role Details] that describe the nature of the gene-disease relationship, as well as a notation that the Cancer Gene Index is the source of these data. {tip:title=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 to other data by [expert human curators|https://wiki.nci.nih.gov/x/DS9yAQ], select only {{Evidence}} objects where the {{Sentence Status}} is {{finished}} and the {{Negation Status}} is {{no}}.{tip} {info:title=Note}A single piece of evidence may have multiple Role Codes and Role Details describing the gene-disease association, and the evidence may also describe gene-compound associations. Thus, after clicking the {{getGeneFunctionAssociationCollection}} link, you may see multiple retrieved objects of type {{
Column

Searching for Genes Associated with a Disease

To use the caBIO Home Page Freestyle Lexical Mine tool to find genes that are associated with a cancer-related disease, begin typing keywords into the search field. Because the tool suggests caBIO terms that match the characters you have entered, it is relatively easy to find a disease term that matches your desired disease concept.

Disease SearchImage Added

If you would like to search for any disease term that contains a string use the special character "*." For example, "ovarian serous adenocarcinoma" would only return objects that have attributes containing this exact disease term, but "*ovarian*" will retrieve objects with attributes containing any term with the string "ovarian."

After entering a search term (1), click the Submit button (2) to retrieve results. Although you may limit your search by clicking on the more options ... link, this is not required (3).

Tip
titleTip

If you have cannot find an appropriate search term, click the Contact Us link for help.

Disease Search 2Image Added

Search Results

The caBIO Home Page Freestyle Lexical Mine will retrieve objects with attributes that match your search term. These objects are grouped by type, which are shown as tabs at the top of the results page. To view genes that are associated with your disease term of interest, click the Evidence tab at the top of the page (1).

Each row in the Evidence results table is a truncated view of an Evidence object (that is, not all attributes and methods are shown on this page), where columns include:

  • the class and identifier (Class/Id),
  • evidence of the gene-disease association (Sentence),
  • whether the evidence was collected from experiments involving cell lines ( Cellline Status ),
  • whether the evidence is negative that is, gene X is not associated with disease or compound Y; Negation Status ),
  • the PubMed identifier for the abstract from which the evidence was extracted (Pubmed Id), and
  • whether the status of the sentence ( Sentence Status ).

For additional information on the attributes of the Evidence type objects, refer to the section Data, Metadata, and Annotations.

Portal Freestyle Disease ResultsImage Added

Finding the Gene Associated with the Evidence

To discover which gene is associated with each piece of evidence, click on the Class/Id link for the desired object. This will open the full Evidence type object. Scroll over to the right, and click on getGeneFunctionAssociationCollection method link (1) to view the Gene Disease Association type object. This object has a role attribute that contains one or more Role Codes or Role Details that describe the nature of the gene-disease relationship, as well as a notation that the Cancer Gene Index is the source of these data.

Tip
titleTip

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 to other data by expert human curators, select only Evidence objects where the Sentence Status is finished and the Negation Status is no.

Info
titleNote

A single piece of evidence may have multiple Role Codes and Role Details describing the gene-disease association, and the evidence may also describe gene-compound associations. Thus, after clicking the getGeneFunctionAssociationCollection link, you may see multiple retrieved objects of type

gov.nih.nci.cabio.domain.GeneDiseaseAssociation

}}

and

even

multiple

object

retrieved

records

of

type

{{

gov.nih.nci.cabio.domain.GeneAgentAssociation

}}.{info} Click on the {{getGene}} link

.

Click on the getGene link (2)

to

access

the

related

{{

Gene

}}

object

(bottom

panel).

This

{{

Gene

}}

object

contains

the

full

name

and

HUGO

Gene

Symbol

in

the

{{

fullName

}}

and

{{

hugoSymbol

}}

columns

(3),

for

example,

for

the

gene

associated

with

the

disease

of

interest

and

a

specific

piece

of

evidence.

To

explore

additional

genes

associated

with

the

disease

term

of

interest,

navigate

back

to

the

evidence

page

and

repeat

this

process. !SimpleDiseaseDOV.jpg|alt="Simple Disease DOV"! {note:title=Be Careful}If you find yourself in a part of the object model that you do not understand or if you get confused, stop and navigate your web browser back to the search results page with the Evidence tab.{note} For your reference, the subset of caBIO classes that are related to the Cancer Gene Index are shown [here|https://wiki.nci.nih.gov/x/mTNyAQ]. The full model is available on the [caBIO gForge page|http://gforge.nci.nih.gov/frs/download.php/7830/caBIO_4.3.1.eap], but you must have the [Enterprise Architect|http://www.sparxsystems.com.au/] modeling tool to view this file. h1.Disease Ontologies As you become comfortable navigating the caBIO object model, you may wish to start using additional method links to discover the pathway/s in which a particular Cancer Gene Index gene is involved, clinical protocol information for a disease or compound, and other related data. It is also possible to view disease ontologies for a given gene-disease concept pair by navigating through the object model to records for objects in the class {{Disease Ontology}}, {{

process.

Simple Disease DOVImage Added

Note
titleBe Careful

If you find yourself in a part of the object model that you do not understand or if you get confused, stop and navigate your web browser back to the search results page with the Evidence tab.

For your reference, the subset of caBIO classes that are related to the Cancer Gene Index are shown. The full model is available on the NCI SVN, but you must have the Enterprise Architect

Multiexcerpt include
nopaneltrue
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modeling tool to view this file.

Disease Ontologies

As you become comfortable navigating the caBIO object model, you may wish to start using additional method links to discover the pathway/s in which a particular Cancer Gene Index gene is involved, clinical protocol information for a disease or compound, and other related data. It is also possible to view disease ontologies for a given gene-disease concept pair by navigating through the object model to records for objects in the class Disease Ontology, gov.nih.nci.cabio.domain.DiseaseOntology

}}

.

This

can

be

helpful

if

you

would

like

to

search

for

genes

that

are

associated

with

parent,

sister,

or

child

concepts

to

you

disease

search

term.

You

can

reach

these

records

from

either

the

Disease

Ontology

tab

of

the

main

search

result

page

or

by

clicking

through

the

model

starting

from

retrieved

{{

Evidence

}}

type

objects.

To

view

related

disease

concepts

from

the

Disease

Ontology

tab,

click

on

the

tab

and

select

the

any

hyperlink

in

the

{{

Class/Id

}}

column.

This

will

reveal

a

{{

Disease

Ontology

}}

type

object.

If

you

would

like

to

view

parent

or

child

disease

concepts

linked

with

an

evidence

object,

select

the

{{

getGeneFunctionAssociationCollection

}}

link

on

the

Evidence

object

page

(1)

and

then

click

the

{{

getDiseaseOntology

}}

link

in

the

{{

GeneDiseaseAssociation

}}

object

record

(2).

Once

you

have

pulled

up

a

{{

Disease

Ontology

}}

record,

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.

{note:title=Note}If the disease concept of interest has neither parent nor child concepts, you must search the [NCI Thesaurus|http://nciterms.nci.nih.gov/] using your disease term or EVS ID listed in the EVS ID column of the Disease Ontology object or use the [EVS API|https://wiki.nci.nih.gov/x/paSl].{note} h1. NCI Thesaurus Disease Ontologies To view disease ontologies in the NCI Thesaurus, 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 (2, "ovarian serous adenocarcinoma") or NCI Thesaurus concept code (for example, "C7550", and click the Search button (3). If required, select your exact search term from the list to view the NCI Term page {tip:title=Identifier Tip}The EVS Identifier for a term is also its NCI Thesaurus Concept Code.{tip} !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}

Note
titleNote

If the disease concept of interest has neither parent nor child concepts, you must search the NCI Thesaurus using your disease term or EVS ID listed in the EVS ID column of the Disease Ontology object or use the EVS API.

NCI Thesaurus Disease Ontologies

To view disease ontologies in the NCI Thesaurus, open a new browser tab or window and navigate to the NCI Thesaurus web page, enter in your disease term (2, "ovarian serous adenocarcinoma") or NCI Thesaurus concept code (for example, "C7550", and click the Search button (3). If required, select your exact search term from the list to view the NCI Term page

Tip
titleIdentifier Tip

The EVS Identifier for a term is also its NCI Thesaurus Concept Code.

NCIt 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" 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).

NCIt Disease Ontology SearchImage Added