# Presentation: 524779

## caCORE TrainingEnterprise Vocabulary Services (EVS) Overview

- Course Number:		1030
- Target Audience: 		caDSR Users and Metadata Consumers

## Session Details:Training Objectives

**Upon successful completion of this session, you should be able to:**
- Explain the importance of standard vocabularies
- Describe the EVS initiative, components, and functionality
- Distinguish between the NCI Thesaurus and the NCI Metathesaurus to choose the best tool for the task at hand
- Access, browse, search the NCI Thesaurus and NCI Metathesaurus
- Evaluate search results to identify the best match
- Use EVS as a resource in choosing Common Data Elements (CDEs) and permissible values

## Session Details:Lesson Plan

**Lesson 1: Introduction to Enterprise Vocabulary Services (EVS)**
**Lesson 2: The NCI Thesaurus**
**Lesson 3: The NCI Metathesaurus**
**Lesson 4: EVS in Practice**

## Lesson 1: Introduction to Enterprise Vocabulary Services (EVS)

**In this lesson, you will learn how to:**
- Explain the importance of standard vocabularies
- Describe the EVS initiative
- Identify EVS components and functionality

**Notes:**
The first lesson covers the background and purpose of EVS and its components

## Introduction:Importance of Shared Meaning

**Why Are We Here?**
- Training: Why do we need this training?
- Location: Why am I in this particular room (virtual or physical)?
- Philosophical: Why do we exist?
**Asking the same question does not matter if each person interprets it differently**
**Shared meaning**** ****is important!**
- Asker
- Data Collector
- Responder
- Developer
- Researcher

**Notes:**
>Questions can be interpreted in a number of ways. If I ask the question ‘why are we here’, some of you might think:
Why do I need this training?
Why am I in this particular location?
Why do I exist?
Asking the same question is irrelevant if each person interprets it differently.
-shared meaning is important, especially since various users of data (those who ask for or collect versus providers or developers) have different perspectives.

The people who ask for/collect data rarely interact w/ developers/researchers, so there needs to be a different means for clarification.

## Introduction:Context Is Important

**Alcohol - rubbing vs. drinking**
**Colon - punctuation vs. organ**
**Mole - animal  vs. blemish vs. unit of measure vs. spy**
**Mouse - animal vs. computer navigation /data entry device **
**Probe – examination vs. investigation vs. instrument**

**Notes:**
>Context important in conveying meaning...These words all have very different meaning depending on words around it;  they are semantically ambiguous.
Alcohol....etc.

Point:  concepts can mean many different things in different contexts
It is important to consider context when comparing terms and choosing the right concept for your domain. 

## Introduction:Why Is a Standard Vocabulary Necessary?

**Facilitate translational research**
- Accelerate information sharing
- Accelerate discovery
**Facilitate the integration of diverse data systems throughout the cancer research community**
- Ensure validity of cross study data comparison and analysis
- Improve evaluation efficiency, safety, and efficacy
**Improve links between healthcare delivery system and clinical research trials**
- Increase accuracy and speed of data collection
- Increase patient safety
- Decrease approval time for safe and effective treatments

**Notes:**
>NCI’s goal is to prevent suffering and death from cancer by 2015.   A standard vocabulary is the vehicle for meeting these goals.
It can facilitate translational research which can in turn, speed info sharing and discovery
-SV can help in integrating diverse data systems across the cancer research community in order to ensure that data comparison and analysis is valid across studies, and to improve the efficiency, safety, and efficacy of evaluations
-And finally, it improves how healthcare delivery and clinical trials systems communicate, which will increase accuracy & speed of data collection and patient safety, and will decrease time it takes for treatments to be approved

## Introduction:Background/History on the EVS Project

**Established in 1999 by the NCI Director**
**Goal: Address NCI’s needs for controlled vocabulary and semantics**
**Active Collaborations:**
- Federal Agencies including National Institutes of Health (NIH), Food and Drug Administration (FDA), Department for Veterans Affairs (VA), and Centers for Disease Control (CDC)
- Standards Organizations such as Health Level Seven (HL7) and  Clinical Data Interchange Standards Consortium (CDISC)
- Cancer Centers
- Cancer Cooperative Groups
- Other Research Groups such as Microarray Gene Expression Data (MGED) Society

**Notes:**
The EVS project was Established in 1999 by the NCI Director
With the goal of addressing the NCI’s needs for a controlled vocabulary and semantics
Many people have been instrumental in progressing this project......Active Collaborations:
Federal Agencies including National Institutes of Health (NIH), Food and Drug Administration (FDA), Department for Veterans Affairs (VA), and Centers for Disease Control (CDC)
Standards Organizations such as Health Level Seven (HL7) and  Clinical Data Interchange Standards Consortium (CDISC)
Cancer Centers
Cancer Cooperative Groups
Other Research Groups such as Microarray Gene Expression Data (MGED) Society

## Introduction:Major Components of EVS

**NCI Thesaurus****	**
- Designed for application development: database coding, searching, and data mining
- NCI reference terminology (public domain, open source)
- 54,000 concepts covering agents, anatomy, biological processes, diseases, genes, gene products, and techniques/equipment
**NCI Metathesaurus**
- Designed for term mapping and document indexing across vocabularies
- Online dictionary and thesaurus
- Adaptation of National Library of Medicine’s Unified Medical Language System (UMLS) Metathesaurus
- 975,000+ concepts; 2,500,000 terms and phrases

**Notes:**
2 main components. Thes and meta.NCI Thesaurus  - Designed for application development, specifically to assist with database coding, searching, and data mining  -Is the NCI reference terminology (publicly accessible).  Over 54,000 biomedical concepts in more than 20 categories including agents, anatomy, gene, gene product.Meta - comprehensive biomedical terminology db.   Designed for term mapping and document indexing across vocabularies.  It is an online dictionary and thesaurus that has been adapted from the NLM UMLS – (covers Medicine, Nursing, Clinical Disciplines, and Biological Science).  Has over 975,000 concepts; 2 1⁄2 million terms and phrases---  I’d like to make distinction...   NCI Thesaurus is where look for immutable/absolute terms or concepts. Gives one definition, is more specific Whereas Meta like dictionary: find multiple, similar definitions that have slight differences in wording and emphasis.
Thes - Based on Description Logic meaning it expresses knowledge of concepts and concept hierarchies and you can see how Term/concept fits in a tree in terms of more general to more specific terms
Meta – uses Lexical Matching: in other words, it identifies concepts with similar word or word bases)
Open source = open content license.  Hierarchies – basis for semantic web languages

## Introduction:Concept Details...

**Name**
**Code (Concept Unique Identifier; CUI) **
- NCI Thesaurus code
- NCI Metathesaurus Concept Unique Identifier (NCI_META_CUI)
- UMLS concept code
**Properties**
- Definition(s)
- Synonym(s)
- Preferred name: the term NCI recommends for use in written and oral communication
- Links to use or related information in other external resources such as UMLS

**Notes:**
>Each concept in EVS has a name, code, and properties 
 the 2 unique identifiers are name and code 
 You want to use Code if you intend to use a concept in an external environment such as a database
Concepts have more than one code in most cases:
Example, NCI Thesaurus Code
NCI Metathesaurus Concept Unique Identifier (NCI_META_CUI),
And (UMLS) concept code.

Properties represent facts about the concept. 
Include # things; def, syn, preferred name (which is the term that NCI recommends for oral and written communication)
Info such as links to resources outside EVS, such as UMLS 

## Introduction:Concept Details

**Roles**
- Relationships with other concepts
- Taxonomy / Hierarchy
- Superconcepts / More General Concepts / Parents
- Subconcepts / More Specific Concepts / Children
- May be especially helpful in searching for and working with Common Data Elements (CDEs) in the Cancer Data Standards Repository (caDSR)

**Notes:**
>Roles are used to indicate relationships that exist between concepts in the Thesaurus.  The relationships are classified into hierarchies, 
Superconcepts:  are more general concepts, or Parents
Subconcepts are more specific concepts, or children
Ex., parent - Cancer, children – Prostate cancer, 
Roles may be especially helpful in searching for and working with CDEs in the caDSR, especially when browsing the tree stru

Relationships involve heritance/associations don’t

## Introduction:Keeping EVS Up to Date 

**Users**
- Content Drivers
**Subject Matter Experts**
- Terminology Modelers (PhDs, MDs, DPharms)
- Software Developers
- Operations and Maintenance
**Outside Reviewers**
- Via contract: e.g., College of American Pathology
- Via formal collaboration:  FDA, VA, CDC, caBIG Cancer Centers
- Via formal collaboration:  Standards Groups, Federal Agencies, Professional Societies, Universities

**Notes:**
>EVS is maintained by 3 groups of people
Users drive the content. 
Subject Matter Experts model, develop, and test the content. Include Terminology Modelers, Software Developers, involved in Operations and Maintenance
Outside reviewers critique, authorize, and give credibility to the content. Include people that are involved contractually, eg.,College of American Pathology 
Formally: FDA, CDC, caBIG Cancer Centers
Informally: 
Standards Groups  Health Level Seven (HL7), CDISC, Extended Metadata Registry (XMDR), IEEE Bioinformatics Standards Committee
Federal Agencies DoD, NASA, National Library of Medicine (NLM), Armed Forces Institute of Pathology
Professional Societies: Microarray Gene Expression Data Society (MGED), World Wide Web Consortium (W3C)
Universities: Harvard (Chembank Small Molecules Bioactives Database)
Minimum of 24 hr turn around time for suggestion of new term/definition.  Depends on content and the shape of the content.

## Introduction:How Can EVS Help You?

**Check and compare dictionary definitions**
**Find synonyms**
**Determine relationships to other concepts/terms**
**Identify and evaluate potential options when curating new Metadata or adding terms to permissible value lists **
**Provide links to related research publications**

## Introduction:Lesson 1 Review

**Now that you have successfully completed this lesson, you should be able to:**
- Explain the importance of standard vocabularies.
- Describe the EVS initiative.
- Identify EVS components and functionality.
**Any Questions?**

**Notes:**
1-to facilitate translational research, integrate diverse data systems, improve link b/t healthcare and clinical research
2-address NCI's needs for controlled vocabulary via software tools –NCI t and Meta- which access databases of terms
3-thes (1 specific definition, expressed in hierarchy, for use in db coding searching and mining) and meta (multiple, similar defs for use in indexing across vocabs)

## Lesson 2: The NCI Thesaurus

**In this lesson, you will learn how to:**
- Access the NCI Thesaurus.
- Browse the NCI Thesaurus.
- Use the NCI Thesaurus to search for terms.
- Evaluate search results to identify the best match.

## NCI Thesaurus:Accessing the NCI Thesaurus

**Ways to Access the NCI Thesaurus**
- _[http://](http://nciterms.nci.nih.gov/)__[nciterms.nci.nih.gov](http://nciterms.nci.nih.gov/)_** **
- Through CDE Browser
- Through CDE Curation Tool
- Through APIs
**Acceptable Browsers**
- Microsoft Internet Explorer 6 +
- Netscape 7 +
- Firefox 1 +
**JavaScript and Session Cookies**
- Must be enabled for search functions
- Automatically deleted when you exit
**Stylesheets**
- Must be enabled for correct display

**Notes:**
>publicly accessible: no account or password required.  

If questions or need help w/ any of this, you can call NCICB Application Support for assistance....next slide
...

To Adjust Browser security settings.
Microsoft Internet Explorer 6+ (Tools -> Internet Options -> Security -> Custom Level -> Adjust individual settings or Reset custom settings to Medium) 

Stylesheets – to enable, uncheck Tools/Options/Accessibility/disable stylesheets
API- application program interface, a set of routines, protocols that ,programmers use to build software

## NCI Thesaurus:NCICB Application Support

**Live Support: Monday – Friday 8 am – 8 pm Eastern Time**
- Telephone support is available Monday to Friday, 8 am – 8 pm Eastern Time, excluding government holidays.
- You may leave a message, send an email or submit a support request via the Web at any time.
- Specify the browser and tool (Thesaurus or Metathesaurus) you were using, the terminology you were viewing, and the error message you received.
**Email: ncicb@pop.nci.nih.gov**
**Phone: 301-451-4384**
**Toll-free: 888-478-4423**
**Web: **_[http://](http://ncicb.nci.nih.gov/NCICB/support)__[ncicb.nci.nih.gov](http://ncicb.nci.nih.gov/NCICB/support)__[/NCICB/support](http://ncicb.nci.nih.gov/NCICB/support)_** **

**Notes:**
Please specify browser and tool using, what terminology viewing, error msg

## NCI Thesaurus:NCI Terminology Browser

**NCI Thesaurus:****NCI Terminology Browser**

**http://nciterms.nci.nih.gov**

## NCI Thesaurus:Sources of Help

**NCI Thesaurus:****Sources of Help**

**View the NCI Browser Terminology Guide.**

**Check Known Issues if**
**you encounter problems.**

**Contact NCICB Application Support.**

**Notes:**
If having issues, 1st place look is Known Issues.  Help will launch the Browser Terminology Guide.
Contact us, Application Support.

## NCI Thesaurus:Select a Terminology

**Terminology Names**

**Date and/or Version**

**Terminology Descriptions**

**NCI Thesaurus:****Select a Terminology**

**Notes:**
Term browser welcomes you
NCI Thesaurus – is product of EVS and default, but can choose other Terminologies:
GO Ontology – Gene Ontology Consortium (updated Jan 2007)
SNOMED  - NOT FREE.  Only parts of SNOMED are in the NCIt. No definitions, but the terms sit in a tree and you figure out the definition of the term from the location in the tree.
MGED Ontology – Microarray Gene Expression Data Society
MedDRA – Snomed and Meddra for NCI use only
Pre-NCI Thesaurus (Reviewer Use Only):  Snapshot of the Thes vocabulary before release. This is Draft new content that has NOT been thru QC. 
Choose the terminology and Press Connect

## NCI Thesaurus:Connecting to the NCI Thesaurus

**Notes:**
White space – connection information

Sometimes gives you warning – cookies disabled. To fix:
Tools/Internet Options/Privacy/Advanced/Override and enable session cookies.
Then logout and re-Connect.

## NCI Thesaurus:Basic Navigation

**NCI Thesaurus:****Basic Navigation**

**Quick**
**Links**

**HELP: View NCI Terminology Browser Guide.**
**RESULTS: View Search results.**
**CUSTOMIZE: Customize your search.**
**ABOUT: View NCI Terminology Browser version.**
**BROWSE HIERARCHY: NCI Taxonomy Viewer**
**LOGOUT: Return to main screen to choose a different terminology.**

**Quick**
**Search**

**Concepts **
**Visited**

**Terminology **

**Advanced Search**

**Notes:**
>Horizontal links:
Read Slide (Help, Results, ...)
Click Browse hierarchy to start Taxonomy Viewer –Browse opens separate window of an expandable, hierarchical view of vocab chose. 

## NCI Thesaurus:Browsing: The NCI Taxonomy Viewer 

**Notes:**
Taxonomy view basically shows the concept neighborhood of the 20 parent concepts under which everything in NCIthes is organized.  
Clicking +/- (click next to gene product) will expand the tree so can see Parent/children (super/subconcept) relationship.
The term will appear in blue for easy identification
Once see leaf concepts or a dot, reached concept w/ no children.
So Messenger RNA is child/subconcept of Gene Product
See red.  Click messenger RNA details, minimize viewer, scroll down, see super/parent is gene product

## NCI Thesaurus:Advanced Search

**Limit results by Roles**

**Limit results by Properties**

**Limit results by Associations**

**Notes:**
Before more into details, ways to search. We saw search via browser, now quick and advanced
Show advanced search
Max is 25 but can change.
Can limit by:
-Association.
-Relationship to other concepts will limit results by Roles.
-Info about this concept will limit result by property (if asked: definition = *disease*)
Note: Advanced search defaults to an exact match. It does not automatically append a wildcard to the end of what you type.
Like the quick search does...

## NCI Thesaurus:Quick Search

**Type term or synonym**
- Quick Search defaults to checking preferred names and synonyms
**Use an asterisk ( * ) as the wildcard**
- You can put the asterisk before, in the middle, or at the end
- Quick Search automatically adds an asterisk at the end
**Set the maximum number of results you would like to see**
- Set at 10 – 250 results.
- Quick Search defaults to 25 results.
- Results are returned in order received rather than in order of best match
- The search engine will warn you if the number of hits exceeds the Max Results you have specified

**Notes:**
Change Max to 100
Search Chronic   Enter 
Slow - Can use asterisk as wildcard before, middle, or end (automatically adds at end so add or no).   Point out Concepts Visited. Quick Links. 
Results are returned in order received rather than in order of best match. (97)
Can use both red icons to evaluate your search results
Clicking on the (hover) Concept Neighborhood icon (don’t click) takes you to the term location in the Taxonomy Viewer so  that you can view parent  and child concepts 

Does anyone notice funny about first result?  It doesn’t have ‘chronic’ 
– Click Details.   Reason is because by default, the Quick Search searches the preferred name or synonym field. Scroll down and highlight ‘Chronic’ in Synonym.
Can change in Customize. Show both checked (very top and very bottom).  Remove Synonym.
 Must click ‘Save’ - Only saves for this session. 
Go   (84)
(default for other terminologies is to search ‘Concept name’)

## NCI Thesaurus:Customized Quick Search

**NCI Thesaurus:****Customized Quick Search**

**Include name and/or code**
**identifiers in your search**

**Search for a string in properties – matches words in any order**

**Specify exact match (no wildcard at end)**

**Select multiple Roles, Associations, & Properties to include in your search**

**Notes:**
Let’s go back to Customize
If click exact Match, Save, Name or code, Roles, Association, Properties.
Search Chronic, enter.  Have 1. 
Click details

Let’s go through some details....

Word Match works together with the concept properties list. When click and save Word Match, it disables everything except properties (don’t check).   Basically, it lets you search for a string in properties and matches words in any order.

## NCI Thesaurus:Search Results

**NCI Thesaurus:****Search Results**

**Clicking on the Concept **
**Neighborhood icon takes **
**you to the term location in**
**the Taxonomy Viewer so **
**that you can view parent **
**and child concepts **

**Clicking on the Concept Details icon**
**will display the concept’s identifiers,**
**roles, properties, parents, and children**

## NCI Thesaurus:Concept Details

**NCI Thesaurus:****Concept Details**

**Identifiers:**
**Name, Code**

**History: creation, **
**major changes, etc.**

**Properties**

**Graph: **
**diagram **
**of roles**

**NCI_META_CUI**
**(link to the NCI **
**Metathesaurus)**

**Notes:**
At top, can Bookmark this page to easily return 
(click) Printable Page, ->clearly organized view for printing
			contains universal Resource Identifier (URI) -for developers to point to the NCI DTS from within their ontology)
(click) History of concept: dates of all significant editing actions performed on concept (creation, modify, retire)
(click) Graph is diagram of roles/relationships among concepts. 2, select. This display can help you visualize the semantic relationships among the concepts in the vocabulary.  (So disease mod is superconcept)

So disease modifier is superconcept, as click, expands view

## NCI Thesaurus:Evaluating Your Search Result

**Concept Details**
- Identifiers
- Name, Code
- Information about This Concept (Properties)
- Definition, Synonyms, Preferred Name, Semantic Type, Links to External Resources
- Associations
- Relationships to Other Concepts (Roles)
- Superconcepts (Parents)
- Subconcepts (Children)
**Concept Neighborhood**
- Classification of the concept

**Notes:**
Concept Details
Identifiers – Name & Code (code something like C----)
Information about This Concept – lists properties like Definition, Synonyms, Preferred Name etc. 
Notice UML CUI – links to Meta (notice how different. Click)
Any Super or Subconcepts (parents & children)

Any Questions w/ detail view?

## NCI Thesaurus:Common Pitfalls to Avoid...

**Common Pitfall: **
**I am having trouble getting the search features to work. **
**Tips and Techniques:**
**Are you using a compatible browser?**
- Microsoft Internet Explorer 6 +
- Netscape Navigator 7 +
- Firefox 1 +
**Have you enabled JavaScript and cookies?**
- The Search function requires that JavaScript and session cookies be enabled. You can enable these by adjusting your browser’s security settings.

**Notes:**

You’re having trouble getting the search features to work.  Could be a simple thing – browser (see slide). Enabled Javascript and cookies?

But Lets say you’ve entered the exact term in the Quick Search box but aren’t seeing the term you want – Anyone? 
-Check your max results settings. The search engine returns the 1st things if finds, not necessarily the best hits.
-Maybe the term is in the synonym
Check customized settings e.g., ‘exact match’ box

## NCI Thesaurus:Common Pitfalls to Avoid...

**Common Pitfall:**
**I have entered the exact term in the Quick Search box but I am not getting the correct result. **
**Tips and Techniques:**
**Are you receiving the warning that hits exceed Max Results?**
- Check your Max Results setting. The search engine returns the first hits it finds, not necessarily the best hits.
**Have you tried customizing your search?**
- Click on Customize and choose “Exact match” to prevent the system from adding a wildcard at the end.
**Did you receive a synonym for the term your were searching?**
- Review results returned to check your data for synonyms for the term you were searching.

## NCI Thesaurus:Common Pitfalls to Avoid

**Common Pitfall: **
**I have entered the code in the Quick Search box but I am not getting the correct result. **
**Tips and Techniques:**
**Have you customized your search?**
- Quick Search defaults to searching the preferred names and synonyms.
- Clicking on the Customize option will allow you to search by code.
**Are you using the CUI?**
- The code you are using should start with a ‘C’.
- Make sure you are searching with the NCI Thesaurus Concept Code and not a caDSR Public ID or some other database code.

**Notes:**
Let’s say you entered the code in the Quick Search box but aren’t getting the correct result. 
Have to use Customize option to search by code
Make sure you are searching with the NCI Thesaurus Concept Code and not a 
caDSR Public ID or some other database code 

## NCI Thesaurus:Lesson 2 Review

**Now that you have successfully completed this lesson, you should be able to:**
- Access the NCI Thesaurus.
- Browse the NCI Thesaurus.
- Use the NCI Thesaurus to search for terms.
- Evaluate search results to identify the best match.
**Any Questions?**

## Lesson 3: The NCI Metathesaurus

**In this lesson, you will learn how to:**
- Access the NCI Metathesaurus.
- Browse the NCI Metathesaurus.
- Use the NCI Metathesaurus to search for terms.
- Evaluate search results to identify the best match.

## NCI Metathesaurus:Accessing the NCI Metathesaurus

**Ways to Access the NCI Metathesaurus**
- _[http://](http://ncimeta.nci.nih.gov/)__[ncimeta.nci.nih.gov](http://ncimeta.nci.nih.gov/)_** **
- Through the CDE Browser
- Through the CDE Curation Tool
- Through APIs
**Acceptable Browsers**
- Microsoft Internet Explorer 5+
- Netscape 6.2+
- Firefox 1+
**Recommendations**
- Set resolution to 1024 x 768 or higher for best display.
- Mac users may encounter issues. Click on “About” for more details.

**Notes:**
Do same w/ metathesaurus
Access through CDE Browser, Curation tool, APIs, and through Thesaurus too
Browsers.....similar as those for thesaurus (a little lower)
Let’s Login to meta.  Click EVS Home, link to Meta 

## NCI Metathesaurus:Connecting to the NCI Metathesaurus

**NCI Metathesaurus:****Connecting to the NCI Metathesaurus**

- _[http://](http://ncimeta.nci.nih.gov/)__[ncimeta.nci.nih.gov](http://ncimeta.nci.nih.gov/)_

**Notes:**
Here we can search the public version of NCI Metathesaurus.

Mentioned that Meta is based on NLM's UMLS Meta in addition to some proprietary vocabularies. Some vocabularies are strictly for NON-COMMERCIAL USE ONLY/by permission and others are made available subject to license restrictions. Can read full license agreement..  

## NCI Metathesaurus:Basic Navigation

**About: View helpful information**
**Browse: Browse the NCI Thesaurus**
**Copyright: View license and copyright**
**New Term: Request that a new term be added**
**Sources: View a list of included vocabularies and license restrictions**
**User’s Guide: View the NCI Metaphrase User Guide**

**Two Search Options:**
**Basic**
**Advanced**

**Notes:**
Links to left:
Click About 
Browse – Loads Java applet for browsing (only) the thesaurus portion of the Meta (don’t open takes forever!) - Note You cannot browse the entire NCI Metathesaurus – only the NCI Thesaurus portion. 
Copyright – View license and copyright information
New Term – Can Suggest a new term.
Sources – View included vocabularies. Click. NCI Local Sources and Sub-Sources shown in red 
 User’s Guide his (hover) launches the NCI Metaphrase User Guide.

Two Search Options: Basic & Advanced
Some instruction in small text

Local = sources that NCI creates and maintains
Sub-source = sources NCI has licensed

## NCI Metathesaurus:Browse the NCI Thesaurus from within the Metathesaurus

## NCI Metathesaurus:Basic Search

**Enter the word or phrase for which you would like to search**
**Use a period ( . ) as the wildcard.**
**The search engine uses lexical matching and ranking**
- It looks for terms that have the words or the word bases in common with what you have typed.
- It orders the results based on the strength of the lexical match.

**Notes:**
Can Enter the word or phrase for which you would like to search
Type gene.
Use a period ( . ) as the wildcard. Does not assume wildcard
Hit Enter
The search engine uses lexical matching and ranking, so it looks for terms that have the words or the word bases in common with what you have typed. 
It orders the results based on the strength of the lexical match.
See variety of results beginning w/ gene 

See small print if slow.

Lexical = Pertaining to how the characters in source code are translated into tokens that the compiler can understand
Lexical matching = searches for one or more authoritative terms that share ‘significant’ lexemes (word bases). Ex.,  lots of hits for ‘mole’ but all very different meanings.

## NCI Metathesaurus:Advanced Search

**Limit your results by selecting**
**a single vocabulary.**

**Enter search term,**
**phrase, or code.**

**Limit the **
**number of**
**results**
**returned.**

**Search defaults**
**to String. Click**
**Code or CUI  to**
**change setting.**

**Limit your results **
**to the best lexical **
**matches (Short)**
**or show all by **
**lexical match **
**ranking (Score).**

**Notes:**
Click Advanced
Here can... enter search term, phrase, or code
Limit # results returned
Can limit search to a source. This is particularly useful for more general terms to speed the time.
The default is by string but can search by code or CUI
Short return ONLY results w/ best lexical match, score will show ALL results ranked by lexical match

to see, change max to 100, search Gene, short than score

## NCI Metathesaurus:Search Tips

**Do not worry about capitalization.**
- The search engine is not case-sensitive
**Leave out special characters and punctuation marks.**
- The search engine will ignore them (except for wildcards).
**Omit small words - such as “a”, “the”, “and”, “of”, “for”, “with”, etc.**
- The search engine will ignore them.
**Limit your search to one source vocabulary at a time when searching by code or by general terms like “cancer” or “disease.”**
- Doing so will speed your search.
**Be aware of spelling.**
- The search engine has spell-check built in, but misspelled words may slow processing as the system checks for possible interpretations of what you meant.

**Notes:**
>The search engine ignore small words like the, special characters and punctuation marks (except for wildcards), case, word order largely ignored but order of result might vary
Type GeEn
For example – enter protiase and will still find.
The search engine has spell-check built in, but misspelled words may slow processing, since the system checks for possible interpretations of what you meant.
Spell check does not apply when searching for code so need exact #

## NCI Metathesaurus:Search Results...

**NCI Metathesaurus:****Search Results...**

**Click on the links to view **
**concept details and evaluate **
**the potential matches. **

**The semantic type **
**indicates what sort **
**of thing potential **
**matches are. **

**Notes:**
Look at results
Left is concept
Right column is the semantic type of each search result. 
If doesn’t exist can Click New Term or Suggest New Term
Open protease.

## NCI Metathesaurus:Search Results

**NCI Metathesaurus:****Search Results**

**Notes:**
Point out Links at top.  Takes to spot on screen
Click Open NCI Hierarchy, then| View Hierarchy Location
Shows this term in hierarchy
Scroll to Protease.
	point out parent/children, e.g., hydrolase
Clicking one opens in metathesauras
Minimize
See in meta.  

If Slow – mention to use back and forward 

## NCI Metathesaurus:Evaluating Your Search Results

**Definition(s) listed by source**
**Synonyms**
**Sources **
**Concepts More General Than (Parents)**
**Concepts More Specific Than (Children)**
**Related concepts**
- Medications
- Procedures
- Laboratory
- Diagnosis

**Links to related concepts and **
**to research articles on PubMed**

## NCI Metathesaurus:Use Case

**NCI Metathesaurus:****Use Case**

-     **Search     Term**

-      **Vocabularies associated with term**

## NCI Metathesaurus:Common Pitfalls to Avoid...

**Common Pitfall:**
**My search is taking a long time to run.**
**Tips and Techniques:**
**Are you using the Advanced Search?**
- The more parameters you can enter, the quicker your search will be.
**Are you searching all vocabularies?**
- Limiting your search to one vocabulary will limit how much data the search engine must go through.
**Have you double-checked your spelling?**
- The Metathesaurus will spell-check your search term, which could add to the time if there are multiple possibilities.

**Notes:**
Questions?
>What if search is taking a long time to run. Try using Advanced Search. The more parameters you can enter, the quicker your search will be.
Try Limiting your search to one vocabulary – it will limit how much data the search engine must go through. 

Let’s say you’re trying to search by code but am receiving No Matches, you must select a source to search by code.

(Can anyone recommend how to improve search speed?  If word is general (cancer), limit serach to once source vocabulary, or adjust max results.)

## NCI Metathesaurus:Common Pitfalls to Avoid

**Common Pitfall: **
**I am trying to search by code but I am receiving “No Matches” or “Invalid Source” instead of the term.**
**Tips and Techniques:**
**Are you using Advanced Search?**
- Basic Search looks for words and word bases related to what you entered.
**Did you click on the radio button next to Code?**
- You must select Code for the search engine to specifically look for code.
**Are you searching the correct source?**
- Make sure you have selected the correct vocabulary or “All.”
**Did you enter the full code exactly as it should appear?**
- Wildcard and spell check do not work on codes.

## NCI Metathesaurus:Suggesting a New Term...

**NCI Metathesaurus:****Suggesting a New Term...**

**If you cannot find the concept for **
**which you are looking, you can **
**request the addition of a new term.**

## NCI Metathesaurus:Suggesting a New Term

**NCI Metathesaurus:****Suggesting a New Term**

**New Term Name: **
***Defaults to search term***

**Nearest concept: **
***Lists search results***** **

**caDSR Type**

**Description, definition **
**and reason for request**

**Name and contact information**

**Submit for Review**

## NCI Metathesaurus:Lesson 3 Review

**Now that you have successfully completed this lesson, you should be able to:**
- Access the NCI Metathesaurus.
- Browse the NCI Metathesaurus.
- Use the NCI Metathesaurus to search for terms.
- Evaluate search results to identify the best match.
**Any Questions?**

## Lesson 4: EVS in Practice

**In this lesson, you will learn how to:**
- Access EVS from the CDE Browser.
- Distinguish between the NCI Thesaurus and the NCI Metathesaurus to choose the best tool for the task at hand.
- Use EVS as a resource in choosing Common Data Elements (CDEs) and permissible values.

**Notes:**
Apply what learned. Access EVS via CDE Browser and use EVS as resource in choosing b/t CDEs
(close meta and launch CDE)

## EVS in Practice:Accessing EVS from the CDE Browser...

**EVS in Practice:****Accessing EVS from the CDE Browser...**

**NCI Metathesaurus**

**NCI Thesaurus**

**Notes:**
Search for anything containing *biomarker*  Enter.  From CDE Browser, can access meta and thes. 
(slow – familiar w/ CDE so know but if don’t already know, * is wildcard.  
Scroll to Collected Blood Infusion Reaction (last CTEP) to launch Data Element Details 

## EVS in Practice:Accessing EVS from the CDE Browser...

**EVS in Practice:****Accessing EVS from the CDE Browser...**

**The Data Element **
**Concept and **
**Permissible Values **
**tabs may provide **
**direct links to **
**corresponding **
**concepts in the **
**NCI Thesaurus.**

**Notes:**
Click DEC Tab. The Data Element Concept and Permissible Values tabs provide you with direct links to the corresponding concepts in the NCI Thesaurus.
Scroll Down
Recall that CDE composed of DEC which consists of Object Class and Property, and a Value Domain.
(read object class concept and property concept) – collected blood is concatenation of 2 terms
Property concept has a code that’s from meta as indicated by CL and source shows us also)

Can link to NCI Thesaurus or Meta by clicking on these concept codes for object class and property concept because all object classes and property concepts in caDSR are linked to one or more concepts in the EVS terminology server. 
.

## EVS in Practice:Accessing EVS from the CDE Browser...

**EVS in Practice:****Accessing EVS from the CDE Browser...**

**From the Data Element Concept tab, you can link directly to the NCI Thesaurus by clicking on the concept codes for the object class and property concepts.**

## EVS in Practice:Accessing EVS from the CDE Browser

**EVS in Practice:****Accessing EVS from the CDE Browser**

**If permissible values are enumerated – that is, a specific pick list of values is provided, the value meaning concept codes (when available) will link directly to the corresponding code in the NCI Thesaurus.**

**Notes:**
Same communication exists between permissible values and EVS...
Click permissible Value tab and scroll to ‘value meaning concept codes’ – If permissible values are enumerated – that is, a specific pick list of values is provided like ‘yes’ or ‘no’, the value meaning concept codes will link directly to the corresponding code in the NCI Thesaurus or meta (see CL so meta, click, it does.  Click Back button.

Let’s say you want to evaluate a CDE for quality of reuse, say on a form or UML model...
Check:
 2201987  (Biomarker Results Type)
 2406662  (Biomarker Test Result Percentage Number)
5477   (Biomarker Value)

(7th, 9th, 12th)
compare CDEs

## EVS in Practice:Use Case...

**EVS in Practice:****Use Case...**

- 	**Compare 2 or more CDEs**

- 	**Evaluate CUIs associated with CDEs**

**Notes:**
Look @ quality of administered components that comprise these CDEs.
Look similar w/ slight variation.  All Qualified and released.  (Scroll) First has substantial definition. Middle - not great, bad def, no concept codes and draft new.  So remove. First DEC code has 2 codes so concatenation of terms (biomarker and testing), the last of which looks like a meta CUI. The 2nd has thesaurus code. Can tell thes by C-----.  Meta are CO or CL or C followed by some letter------

How know which to use?   Use one w/ thes code.  Click code.

1)  NCI thes code is invariant; they will never change/are guaranteed to be stable over time.    2) Thesaurus also provides a concept history facility to track changes made to a concept over time.
 --Whereas Metathesaurus codes, while are derived from the NLM’s UMLS, do not provide concept history, don’t guaranteed long-term stability.  Remember that meta represents mapping across several vocabulary sources.
 --Therefore thes codes are suitable for use in assigning database codes to this concept, and for retrieving data/coding. 

## EVS in Practice:Use Case

**	****By entering a term, you can see who it’s both owned and used by**

## EVS in Practice:Thesaurus or Metathesaurus?

| NCI Thesaurus
http://nciterms.nci.nih.gov | NCI Metathesaurus
http://ncimeta.nci.nih.gov |
| --- | --- |
| Stand-alone reference terminology | Relational: Links to multiple terminologies |
| One definition for (cancer) research | One or more definitions from multiple sources |
| Designed for annotation and database coding to facilitate data analysis and retrieval | Designed for mapping cancer terms across terminologies throughout the cancer research community to facilitate integration  |

**Notes:**
Questions on metathesaurus?

...
Meta – larger........ Designed for term mapping and document indexing across vocabularies
distinctions...read slide

## EVS in Practice:Searches: Thesaurus vs. Metathesaurus

|  | NCI Thesaurus
http://nciterms.nci.nih.gov | NCI Metathesaurus
http://ncimeta.nci.nih.gov |
| --- | --- | --- |
| Wildcard | Asterisk ( * ) | Period ( . ) |
| Wildcard rule | Quick Search assumes wildcard at end unless “Exact match” is selected. | Does not assume a wildcard. Wildcard must be entered.  |

**Notes:**

Also, Benefits of Thes
Free (public domain/open source - NCI reference terminology)
Editable real-time
Terms are Treed
Maintained

## EVS in Practice:Lesson 4 Review

**Now that you have successfully completed this lesson, you should be able to:**
- Access EVS from the CDE Browser
- Use EVS as a resource in choosing Common Data Elements (CDEs) and permissible values
- Distinguish between the NCI Thesaurus and the NCI Metathesaurus to choose the best tool for the task at hand
**Any Questions?**

## Session Review

**Now that you have successfully completed this session, you should be able to:**
- Explain the importance of standard vocabularies
- Describe the EVS initiative, components, and functionality
- Distinguish between the NCI Thesaurus and the NCI Metathesaurus to choose the best tool for the task at hand
- Access, browse, and search the NCI Thesaurus and NCI Metathesaurus
- Evaluate search results to identify the best match.
- Use EVS as a resource in choosing Common Data Elements (CDEs) and permissible values

## Session Review: Questions?

**Any questions about anything we have covered?**
- Lesson 1: Introduction to Enterprise Vocabulary Services (EVS)
- Lesson 2: The NCI Thesaurus
- Lesson 3: The NCI Metathesaurus
- Lesson 4: EVS in Practice

## Recommended Resources

**NCI Thesaurus**
- NCI Terminology Browser Guide
- _[http://nciterms.nci.nih.gov/NCIBrowser/docs/help/NCITerminologyBrowserGuide.html](http://nciterms.nci.nih.gov/NCIBrowser/docs/help/NCITerminologyBrowserGuide.html)_** **
**NCI Metathesaurus**
- NCI Metaphrase Guide
- _[http://ncimeta.nci.nih.gov/Metaphrase/NCIMetaphraseUserGuideV1.02Final.pdf](http://ncimeta.nci.nih.gov/Metaphrase/NCIMetaphraseUserGuideV1.02Final.pdf)_

## NCI Thesaurus:NCICB Application Support

**Live Support: Monday – Friday 8 am – 8 pm Eastern Time**
- Telephone support is available Monday to Friday, 8 am – 8 pm Eastern Time, excluding government holidays.
- You may leave a message, send an email or submit a support request via the Web at any time.
- Specify the browser and tool (Thesaurus or Metathesaurus) you were using, the terminology you were viewing, and the error message you received
**Email: ncicb@pop.nci.nih.gov**
**Phone: 301-451-4384**
**Toll-free: 888-478-4423**
**Web: **_[http://](http://ncicb.nci.nih.gov/NCICB/support)__[ncicb.nci.nih.gov](http://ncicb.nci.nih.gov/NCICB/support)__[/NCICB/support](http://ncicb.nci.nih.gov/NCICB/support)_** **