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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]
{panel}
{tip:title=Need Additional Help?}If you need additional support, please contact [Application Support|mailto:ncicb@pop.nci.nih.gov].{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?].
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Section
Column
width30%
Panel
titlePage Contents
Table of Contents
maxLevel4
Panel
titleDocumentation Table of Contents
Tip
titleNeed Additional Help?

If you need additional support, please contact Application Support.

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?.

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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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.

{info} {column} {column} h1. Searching for Compounds Associated with a Compound 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 pharmacological substance, 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 compound search term that matches your desired compound concept. !AgentSearch.jpg! If you would like to search for any compound term that contains a string use the special character "\*." For example, "cisplatin" would only return objects that are associated with this _exact_ compound term, but "cisp\*" will retrieve objects that are associated with any term that contains the string "cisp." 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} !AgentSearch2.jpg! 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 compound term, 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 (i.e., not all attributes and methods are shown on this page), where the columns include: * the class and identifier ({{Class/Id}}), * evidence of the gene-compound association ({{Sentence}}), * whether the evidence was collected from experiments involving cell lines ([{{Cellline Status}}|Data, Metadata, and Annotations#Indicators]), * whether the evidence is negative (i.e., gene X is not associated with 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 these attributes of the {{Evidence}} type objects, refer to the section [Data, Metadata, and Annotations|https://wiki.nci.nih.gov/x/zC1yAQ]. {info:title=Note}Although the Cancer Gene Index refers to pharmacological substances as "compounds" or "drugs," caBIO and the NCI Thesaurus use the term "agent" for the same concept.{info} !PortalFreestyleAgentResults_Evidence.jpg! 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 Agent 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-compound/agent relationship, as well as a notation that the Cancer Gene Index is the source of these data. {warning:title=Warning}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, select only {{Evidence}} objects where the {{Sentence Status}} is {{finished}} and {{Negation Indicator}} is {{no}}.{warning} {info:title=Note}A single piece of evidence may have multiple Role Codes and Role Details describing the gene-compound association, and the evidence may also describe gene-disease associations. Thus, after clicking the {{getGeneFunctionAssociationCollection}} link, you may see multiple retrieved objects of type {{Gene Agent Association}}, {{

Column

Searching for Compounds Associated with a Compound

To use the caBIO Home Page Freestyle Lexical Mine tool to find genes that are associated with a pharmacological substance, 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 compound search term that matches your desired compound concept.

Image Added

If you would like to search for any compound term that contains a string use the special character "*." For example, "cisplatin" would only return objects that are associated with this exact compound term, but "cisp*" will retrieve objects that are associated with any term that contains the string "cisp."

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.

Image 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 compound term, 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 (i.e., not all attributes and methods are shown on this page), where the columns include:

  • the class and identifier (Class/Id),
  • evidence of the gene-compound association (Sentence),
  • whether the evidence was collected from experiments involving cell lines (Cellline Status),
  • whether the evidence is negative (i.e., gene X is not associated with 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 these attributes of the Evidence type objects, refer to the section Data, Metadata, and Annotations.

Info
titleNote

Although the Cancer Gene Index refers to pharmacological substances as "compounds" or "drugs," caBIO and the NCI Thesaurus use the term "agent" for the same concept.

Image 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 Agent 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-compound/agent relationship, as well as a notation that the Cancer Gene Index is the source of these data.

Warning
titleWarning

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, select only Evidence objects where the Sentence Status is finished and Negation Indicator is no.

Info
titleNote

A single piece of evidence may have multiple Role Codes and Role Details describing the gene-compound association, and the evidence may also describe gene-disease associations. Thus, after clicking the getGeneFunctionAssociationCollection link, you may see multiple retrieved objects of type Gene Agent Association, gov.nih.nci.cabio.domain.GeneAgentAssociation

}}

,

and

even

multiple

object

retrieved

records

of

type

{{

Gene

Disease

Association

}}

,

{{

gov.nih.nci.cabio.domain.GeneDiseaseAssociation

}}.{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

compound

of

interest

and

a

specific

piece

of

evidence.

!SimpleAgentDOV.jpg! To explore additional genes associated with the compound term, navigate back to the evidence page and repeat this process. {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 caBIO 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/]

Image Added

To explore additional genes associated with the compound term, navigate back to the evidence page and repeat this process.

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 here. The full caBIO model is available on the caBIO gForge page, but you must have the Enterprise Architect

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{multi-excerpt-include:wikicontent:Exit Disclaimer to Include|name=ExitDisclaimer|nopanel=true}

 modeling 
 
 tool 
 
 to 
 
 view 
 
 this 
 
 file.



h1.
Agent 
 
 Ontologies


If 
 
 you 
 
 would 
 
 like 
 
 to 
 
 search 
 
 for 
 
 genes 
 
 that 
 
 are 
 
 associated 
 
 with 
 
 parent, 
 
 sister, 
 
 or 
 
 child 
 
 concepts 
 
 to 
 
 your 
 
 compound/agent 
 
 search 
 
 term, 
 
 you 
 
 must 
 
 use 
 
 the 
 
 NCI 
 
 Thesaurus. 
 
 To 
 
 view 
 
 these 
 
 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 
 
 compound 
 
 term 
 
 (2, 
 
 "etoposide") 
 
 or 
 
 NCI 
 
 Thesaurus 
 
 concept 
 
 code 
 
 (e.g., 
 
 "C491"), 
 
 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}

!AgentSearchPage.jpg!

You may view parent and child terms for any compound term by clicking on the Relationships tab (blue box). For example, "etoposide" has the no child terms and the parent term "Epipodophyllotoxin Compound." Alternatively, if you would like to view parent, sister, and child concepts as well as where your term fits in the entire agent hierarchy, click the red View in Hierarchy button (green box). 

!AgentHierarchy.jpg!
{column}
{section}
Image Added
You may view parent and child terms for any compound term by clicking on the Relationships tab (blue box). For example, "etoposide" has the no child terms and the parent term "Epipodophyllotoxin Compound." Alternatively, if you would like to view parent, sister, and child concepts as well as where your term fits in the entire agent hierarchy, click the red View in Hierarchy button (green box). 
Image Added