1. Accessing EVS via BioPortal Course Number:1030 Intended Audience: caDSR Users and Metadata Consumers Duration:Self-Paced

2. Session Details: Accessing EVS via BioPortal Prerequisites Course 1000: Introduction to caCORE and caDSR Course 1010: Introduction to ISO/IEC 11179 Course 1020: Using the CDE Browser and UML Model Browser All course materials are available through the caBIG Learning Management System (LMS) http://ncicbtraining.nci.nih.gov Register for courses Take quiz to receive credit for each course

3. Session Details: Accessing EVS via BioPortal Session Outline Course Learning Objectives Lesson 1: Introduction to EVS Lesson 2: Introduction to BioPortal Lesson 3: The NCI Thesaurus Lesson 4: The NCI Metathesaurus Lesson 5: EVS in Practice

4. Session Details: Accessing EVS via BioPortal Learning Objectives Upon successful completion of this session, you will be able to: Explain the importance of standard vocabularies Describe the EVS components and functionality Distinguish between the NCI Thesaurus and the NCI Metathesaurus to choose the best tool for the task at hand Discuss LexBIG and how it interacts with BioPortal Access, browse, and search the NCI Thesaurus and NCI Metathesaurus via BioPortal Use EVS as a resource in evaluating Common Data Elements (CDEs) Request a new term to EVS

5. Lesson 1: Introduction to EVS In this lesson, you will learn how to: Explain the importance of standard vocabularies Describe EVS Identify EVS components and functionality

6. Lesson 1: Introduction to EVS Importance of Standard Vocabularies Standard vocabularies help to ensure we attach the same meaning to what is being communicated. Answers to questions depend upon the different perspectives in an audience Consider the question “Why Are We Here?” and some possible different interpretations: Why do we need this training? Why am I in this particular room (virtual or physical)? Why do we exist? When you develop, collect and/or analyze data, results are inconclusive if each person is referring to something different.

7. Lesson 1: Introduction to EVS Context is Important Semantics- What do you MEAN ??? 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 Concepts can mean many different things in different contexts.

8. Lesson 1: Introduction to EVS Why is Standard Vocabulary Necessary? Facilitates translational research Accelerate information sharing Accelerate discovery Supports the integration of diverse data systems throughout the cancer research community Ensures validity of cross study data comparison and analysis Improves evaluation efficiency, safety, and efficacy Improves the links between healthcare delivery system and clinical research trials Increases accuracy and speed of data collection Increases patient safety Decreases approval time for safe and effective treatments

9. Lesson 1: Introduction to EVS What Is EVS? NCI Enterprise Vocabulary Services (EVS): provides resources and services to meet NCI needs for standard vocabularies facilitates the standardization of terminology and information systems across the Institute and the larger biomedical community service of the Center for Biomedical Informatics and Information Technology (CBIIT) key component of the cancer Common Ontologic Resource Environment (caCORE) and the cancer Biomedical Informatics Grid (caBIG®)

10. Lesson 1: Introduction to EVS 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

11. Lesson 1: Introduction to EVS Elements of EVS NCI Thesaurus Stand-alone reference terminology One definition for cancer research Designed for annotation and database coding to facilitate data analysis and retrieval NCI Metathesaurus Relational: Links to multiple terminologies One or more definitions from multiple sources Designed for mapping cancer terms across terminologies throughout the cancer research community to facilitate integration

12. Lesson 1: Introduction to EVS EVS- NCI Thesaurus NCI Thesaurus Designed for application development: database coding, searching, and data mining NCI reference terminology (public domain, open source) 34,000 concepts structured into 20 taxonomic trees covering agents, anatomy, biological processes, diseases, genes, gene products, and techniques/equipment terminology-like vocabulary that includes broad coverage of the cancer domain Combines terms from numerous cancer research related domains, and provides a way to integrate or link these kinds of information together through semantic relationships.

13. Lesson 1: Introduction to EVS EVS- NCI Metathesaurus NCI Metathesaurus Designed for term mapping and document indexing across vocabularies Allows you to see the relationship between the vocabularies Based on description logic Uses Lexical Matching 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

14. Lesson 1: Introduction to EVS What Is A Concept? EVS contains concepts which help us establish semantics or determine what is meant. A concept is more comprehensive than a dictionary term. Dictionary- contains alphabetical listing of terms and their associated definitions EVS- contains concepts that contain metadata that aid in conveying meaning

15. Lesson 1: Introduction to EVS Concept Details In EVS each concept is represented by metadata: 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 Roles -Relationships with other concepts Taxonomy / Hierarchy Superconcepts= Parent (More General Concepts) Subconcepts = Children (More Specific Concepts)

16. Lesson 1: Introduction to EVS How Is EVS Kept Up to Date? Recommendations from users Content Drivers Subject Matter Experts Terminology Modelers (PhDs, MDs, DPharms) Software Developers Operations and Maintenance Outside Reviewers: Contracts: e.g., College of American Pathology Formal collaborations: FDA, VA, CDC, caBIG Cancer Centers Informal collaborations: Standards Groups, Federal Agencies, Professional Societies, Universities

17. Lesson 1: Introduction to EVS How Can EVS Help You? Check and compare different terminology definitions Find synonyms Determine relationships to other concepts/terms Identify and evaluate potential options when curating new Metadata Example: adding terms to permissible value lists Provide links to related research publications

18. Lesson 1: Introduction to EVS Review What are the 2 major components of EVS? A.NCI Thesaurus B.BioPortal C.NCI Metathesaurus D.caDSR Match the concept with its hierarchical relationship Concept Relationship Blood Pressure Subconcept/ Child Systolic Blood PressureSuperconcept/Parent ____________is designed for mapping cancer terms across terminologies throughout the cancer research community to facilitate integration. A.NCI Thesaurus B.NCI Metathesaurus

19. Lesson 1: Introduction to EVS Answers What are the 2 major components of EVS? Answer: A. NCI Thesaurus and C. NCI Metathesaurus Match the concept with its hierarchical relationship Concept Relationship Blood PressureSubconcept/ Child Systolic Blood PressureSuperconcept/Parent ____________is designed for mapping cancer terms across terminologies throughout the cancer research community to facilitate integration. Answer: B. NCI Metathesaurus

20. Lesson 2: Introduction to BioPortal In this lesson you will learn how to: Define BioPortal List the sources of help available in BioPortal Demonstrate the basic functions of BioPortal Submit a new term request to EVS

21. Lesson 2: Introduction to BioPortal What is LexBIG? Open source public domain terminology server Developed by the Mayo Clinic as part of the caBIG® Program Provides a robust, scalable, open-source implementation of EVS- compliant vocabulary services Utilizes standard tools for load and distribution of vocabulary content Includes, but is not limited to, support of standardized representations such as the UMLS Rich Release Format (RRF), OWL (Web terminology Language), and Open Biomedical Ontologies (OBO)

22. Lesson 2: Introduction to BioPortal What is BioPortal? A terminology browser Source of content is LexBIG Provides access to the NCI Thesaurus, the NCI Metathesaurus and other select and publicly accessible biomedical terminologies hosted at the NCI Allows users to browse, search, download, or visualize terminology data Accessible on the web at http://bioportal.nci.nih.govhttp://bioportal.nci.nih.gov

23. Lesson 2: Introduction to BioPortal BioPortal Homepage http://bioportal.nci.nih.gov Library Statistics

24. Lesson 2: Introduction to BioPortal Action Icons Download Enables you to download the current version of an ontology in its native format. This function is not supported for all terminologies. Visualize Enables you to view the ontology in tree and graph views. This function is not available for the NCI Metathesaurus. Search Switches to the Quick Search page Action Icons for Performing Different Functions

25. Lesson 2: Introduction to BioPortal Sources of Help Help Menu: User’s Guide- opens the NCI BioPortal User’s Guide Online Help- opens a help system in which you can search and browse topics in the Online User’s Guide Known Issues- enables you to view a list of issues DO THIS FIRST! Help Icon: opens the Online User’s Guide to a specific topic Help Menu BioPortal Homepage Help Menu Help Icon

26. Lesson 2: Introduction to BioPortal Quick Links NCI Quick Links Menu- Provides links to related resource sites EVS Home NCI OC Home NCIVB Home NCI Home NIH Home HHS Home USA Home Quick Links Quick Links Menu on BioPortal Homepage

27. Lesson 2: Introduction to BioPortal 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://ncicb.nci.nih.gov/NCICB/support/http://ncicb.nci.nih.gov/NCICB/support/

28. Lesson 2: Introduction to BioPortal Basic Functions of BioPortal- Browse Browse Page with List of Terminologies Browse Tab

29. Lesson 2: Introduction to BioPortal Project Information Page NCI Thesaurus Project Information Page Visualize Search Return to Ontologies

30. Lesson 2: Introduction to BioPortal Basic Functions of BioPortal- Search Quick Search Page Search Tab

31. Lesson 2: Introduction to BioPortal New Term Request Link If you cannot find the term you are looking for, BioPortal provides a link from which you can submit a New Term Request for consideration by EVS staff. New Term Request

32. Lesson 2: Introduction to BioPortal Submitting a New Term Request New Term Request Page

33. Lesson 2: Introduction to BioPortal Review What are the sources of help available in the BioPortal Browser? A.NCICB Application Support B.NCI BioPortal User’s Guide C.NCI Homepage D.All of the above What are the two basic functions of BioPortal? A.Coding B.Browse C.Data Repository D.Search Match each Action Icon with its correct action: Download Search Visualize

34. Lesson 2: Introduction to BioPortal Answers What are the sources of help available in the BioPortal Browser? Answer: D) All of the above - NCICB Application Support, NCI BioPortal User’s Guide, and the NCI Homepage are all sources of help available in BioPortal. What are the two basic functions of BioPortal? Answer: B) Browse and D) Search Match each Action Icon with its correct action: Download Search Visualize

35. Lesson 3: The NCI Thesaurus (NCIt) 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

36. Lesson 3: The NCI Thesaurus Accessing the NCI Thesaurus BioPortal - http://bioportal.nci.nih.govhttp://bioportal.nci.nih.gov CDE Browser CDE Curation Tool Through APIs Note: The BioPortal Terminology Browser is optimized for: Mac: Safari/Safari 1.2/Safari 2.X PC/Mac/Unix: Firefox 1.5, 2.X PC: Internet Explorer: 6.X, 7.X

37. Lesson 3: The NCI Thesaurus Visualizing the NCI Thesaurus 2 ways to Visualize the NCI Thesaurus: 1.From the Terminologies page, click the Visualize icon located in the Action column on the right 2.From the Project Detail page, click the Visualize button under the terminology title Both of these methods display a Tree View of the NCI Thesaurus. Terminologies Page Project Detail Page Visualize Icon Visualize Button

38. Lesson 3: The NCI Thesaurus Visualizing the NCI Thesaurus Tree View for the NCI Thesaurus

39. Lesson 3: The NCI Thesaurus Types of Graph Views 1.Local Neighborhood (the default) Displays a class with a subclass one level below Shows ALL of the direct associations for the selected class 2.Hierarchy to Root (Subclass Only) Displays the selected class and any subclass relationships at the associated top node

40. Lesson 3: The NCI Thesaurus Local Neighborhood Graph View Local Neighborhood Graph View Class Subclass Concept Information

41. Lesson 3: The NCI Thesaurus Hierarchy to Root Graph Views Class Subclass Hierarchy to Root Graph View

42. Lesson 3: The NCI Thesaurus Initiating a Quick Search Methods: Select the Search icon next to the NCI Thesaurus on the Terminologies page Select the button On the NCI Thesaurus Project Information page Terminologies Page NCIt Project Information Page Search Icon

43. Lesson 3: The NCI Thesaurus Quick Search Page Features Search Features: Scope- Class/Type Name or ID (default), Attributes, or both Type- Parameters include Exact, Contains, or Sounds Like Check Include Obsolete Classes/Types to include retired classes NCI Thesaurus Quick Search Page Runs Results Clears Search Text Field Features

44. Lesson 3: The NCI Thesaurus Quick Search Results Separate tabs for viewing the Class/Type Names or ID and Attributes. Instances of the word are highlighted Select the Visualize icon to view the tree and graph view Class ID- Thesaurus Concept Unique Identifier (CUI) Metastasis Search Results Tree and Graph View Return to Search Results

45. Lesson 3: The NCI Thesaurus Detailed Search Results Detailed Search Results Search Results Page Individual Concept Details Visualize Tree and Graph View

46. Lesson 3: The NCI Thesaurus Search Results- Attributes Tab Attributes Tab Search Results Visualize Icon Search Term

47. Lesson 3: The NCI Thesaurus Advanced Search Advanced Search Page An Advanced Search may be selected any time the Search tab is enabled. Properties Drop Down Menu Roles Drop Down Menu Associations Drop Down Menu Search Parameters

48. Lesson 3: The NCI Thesaurus Advanced Search Advance Search Results Page Show/ Hide All Details Show Individual Detail ID or NCIt CUI Visualize Icon

49. Lesson 3: The NCI Thesaurus Evaluating Search Results Does this term match what I’m looking for? Check the Name and ID- Concepts from the NCIt will have a ID or Concept Unique Identifier starting with “C” followd by 5 numbers Examine the attributes- definitions, alternate definitions, Preferred Name, Semantic Type Relationships to other concepts (Roles) Note Super or Sub-concepts (parent & children)

50. Lesson 3: The NCI Thesaurus Review 1.Which of the following is NOT a way to access the NCI Thesaurus? A.BioPortal B.CDE Curation Tool C.CDE Browser D.Semantic Integration Workbench (SIW) 2.Advanced Search allows you to refine your search by: A.Roles B.Associations C.Properties D.All of the Above

51. Lesson 3: The NCI Thesaurus Answers 1.Which of the following is NOT a way to access the NCI Thesaurus? A.BioPortal B.CDE Curation Tool C.CDE Browser D.Semantic Integration Workbench (SIW) 2.Advanced Search allows you to refine your search by: A.Roles B.Associations C.Properties D.All of the Above

52. Lesson 4: The NCI Metathesaurus In this lesson you will lean how to: Access the NCI Metathesaurus Use the NCI Metathesaurus to search for terms Evaluate search results to identify the best match

53. Lesson 4: The NCI Metathesaurus Accessing the NCI Metathesaurus BioPortal- http://bioportal.nci.nih.govhttp://bioportal.nci.nih.gov CDE Browser CDE Curation Tool Through APIs

54. Lesson 4: The NCI Metathesaurus Project Information Page NCI Metathesaurus Project Information Page List of Terminologies Disabled Icons: Download and Visualize Visualize Not Enabled

55. Lesson 4: The NCI Metathesaurus Quick Search License Agreement The NCI Metathesaurus cannot be included in an Advanced Search. Once a term is entered on the Quick Search screen, you must agree to a License Agreement. NCI Metathesaurus License Agreement Quick Search Page with NCI Metathesaurus Selected Search Parameters

56. Lesson 4: The NCI Metathesaurus Search Results The NCI Metathesaurus search results have the same features and functions as the NCI Thesaurus. Number of Search Results NCI Metathesaurus Search Results NCI Metathesaurus CUIs

57. Lesson 4: The NCI Metathesaurus Quick Search Results Class/Type Name and Id Attributes: Definitions textualPresentation Semantic_Type NCI Metathesaurus Search Results Visualize Search Result Note: No Tree and Graph Views Available in the NCI Metathesaurus

58. Lesson 4: The NCI Metathesaurus Search Tips If you are not getting the results you are looking for try: Double check your spelling- if you are not getting the search results that you want and are not sure of spelling try selecting the Sounds Like radio button If you entered a specific concept code or ID and are getting no results- make sure Class/Type Name or ID box is checked or make sure you have the correct code and not a caDSR Public ID or some other database code If you are getting too few or no results- make sure the Exact radio button is not selected or select the Attributes button to include synonyms

59. Lesson 4: The NCI Metathesaurus Reivew 1.True or False: The NCI Metathesaurus Concept Unique Identifiers (CUIs) follow the same format as the CUIs from the NCI Thesaurus. 2.If you do not know how to spell a term that you want to search for, what button should you make sure is checked on the search page? A.Attributes B.Sounds Like C.Includes Obsolete Classes/ Types 3.What THREE features are available for the NCI Thesaurus and NOT for the NCI Metathesaurus? A.Browse B.Advanced Search C.Quick Search D.Tree/ Graph Views

60. Lesson 4: The NCI Metathesaurus Answers 1.True or False: The NCI Metathesaurus Concept Unique Identifiers (CUIs) DO NOT follow the same format as the CUIs from the NCI Thesaurus. The NCI Thesaurus CUI format will always start with “C” followed by 5 numbers. The Metathesaurus CUI format is not as consistent. It starts with a “C” and is followed by a longer number. 2.If you do not know how to spell a term that you want to search for, what button should you make sure is checked on the search page? A.Attributes B.Sounds Like C.Includes Obsolete Classes/ Types 3.What THREE features are available for the NCI Thesaurus and NOT for the NCI Metathesaurus? A.Browse B.Advanced Search C.Quick Search D.Tree/ Graph Views

61. Lesson 5: 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 for the task at hand Use EVS as a resource in choosing Common Data Elements (CDEs) and Permissible Values

62. Lesson 5: EVS In Practice CDE Browser Direct Links to EVS CDE Browser Home Page https://cdebrowser.nci.nih.gov NCI Thesaurus Link NCI Metathesaurus Link

63. Lesson 5: EVS In Practice EVS to BioPortal via CDE Browser From the CDE Browser NCI Metathesaurus Link you are taken to the NCI Metathesaurus Project Information Page From the CDE Browser NCI Terminology Server Link you are taken to the List of Terminologies in BioPortal

64. Lesson 5: EVS in Practice Access EVS from the CDE Browser Data Element Details The Data Element Concept and Permissible Values tabs may provide direct links to corresponding concepts in the NCI Thesaurus CDE Browser Search Page CDE Browser Search Results Data Element Details Page

65. Lesson 5: EVS in Practice Concepts, CDEs and the caDSR Data Element Concept Object ClassProperty Value Domain Data Element Gene Identifier Java.Lang.Long Identifier Java.Lang.Long Gene Representation Term Number C16612C25364C25337 C16612 C25364 C25337 ItemConcept Code GeneC16612 IdentifierC25364 NumberC25337 caDSR EVS

66. Lesson 5: EVS in Practice Concept Codes Provide EVS Links Data Elements Concept Tab Links to EVS Tree and Graph View of NCIt

67. Lesson 5: EVS in Practice Permissible Values Tab to EVS Permissible Values Tab Links to EVS If Permissible Values are enumerated, the value meaning concept code will link directly to the corresponding concept in EVS.

68. Lesson 5: EVS in Practice Compare CDEs Selecting the correct concepts to convey meaning is essential. Evaluate CDEs for quality or reuse by comparing CDEs using the CDE Browser. CDE Browser Search Results Compare CDE Function Note Workflow and Registration Status

69. Lesson 5: EVS in Practice Evaluating CDEs CDEs Compared Evaluate Concept Unique Identifiers Associated with the CDEs Compare CDE Results

70. Lesson 5: EVS in Practice NCI Thesaurus vs. NCI Metathesaurus The NCI Thesaurus code is invariant codes will never change guaranteed to be stable over time NCI Metathesaurus codes are derived from the NLM’s UMLS do not provide a concept history and do not guarantee long-term stability NCI Thesaurus codes are more suitable for assigning database codes to concepts

71. Lesson 5: EVS in Practice Review 1.The NCI Thesaurus can be accessed from the CDE Browser by all of the following EXCEPT: A.Selecting a NCIt CUI from the Data Elements Concept tab B.Directly from the homepage by selecting NCI Terminology Server link C.Selecting a NCIt CUI from the Permissible Values tab D.Selecting the CUI CL00078344 from the Permissible Values tab 2.What are the reasons that NCI Thesaurus codes and not Metathesaurus should be utilized? A.The NCI Thesaurus code is invariant B.NCI Thesaurus codes are more suitable for assigning database codes to concepts C.NCI Metathesaurus codes are derived from the NLM’s UMLS D.All of the above

72. Lesson 5: EVS in Practice Answers 1.The NCI Thesaurus can be accessed from the CDE Browser by all of the following EXCEPT: A.Selecting a NCIt CUI from the Data Elements Concept tab B.Directly from the homepage by selecting NCI Terminology Server link C.Selecting a NCIt CUI from the Permissible Values tab D.Selecting the CUI CL00078344 from the Permissible Values tab 2.What are the reasons that NCI Thesaurus codes and not Metathesaurus should be utilized? A.The NCI Thesaurus code is invariant B.NCI Thesaurus codes are more suitable for assigning database codes to concepts C.NCI Metathesaurus codes are derived from the NLM’s UMLS D.All of the above

73. 1030 Course Recap Now that you have successfully completed this course you should be able to: Explain the importance of standard vocabularies Describe the EVS components and functionality Distinguish between the NCI Thesaurus and the NCI Metathesaurus to choose the best tool for the task at hand Discuss LexBIG and how it interacts with BioPortal Access, browse, and search the NCI Thesaurus and NCI Metathesaurus via BioPortal Use EVS as a resource in evaluating Common Data Elements (CDEs) Request a new term to EVS

74. 1030 Quiz In order to obtain credit for this course please complete the associated quiz located in the LMS under your 1030 Course Registration materials. Link to be provided once quiz loaded to the LMS

75. Contact Information Contacts: Jennifer Brush, Jamie Keller, Beck Angeles, Lori Thompson jbrush@scenpro.com jkeller@scenpro.com bangeles@scenpro.com lthompson@scenpro.com NCI CBIIT Liaison: Dianne Reeves reevesd@mail.nih.gov NCI CBIIT Application Support ncicb@pop.nci.nih.gov BioPortal Homepage https://bioportal.nci.nih.gov caCORE Training Wiki https://wiki.nci.nih.gov/x/OAFy