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National Cancer Institute
Enterprise Vocabulary Services
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NCIm Version: 201706 Version 2.8 (using LexEVS 6.5)
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Help

Introduction
Search
Advanced Search
Search Results
Concept Details
Cart and Export Functionality
View Hierarchy
Sources
Known Issues
Additional Information

Introduction

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NCI Metathesaurus (NCIm) is a comprehensive biomedical terminology database, connecting 4,000,000 terms from more than 75 terminologies. It contains most public domain vocabularies from the National Library of Medicine's UMLS Metathesaurus, as well as many other biomedical vocabularies created by or of interest to NCI and its partners, including some propriety vocabularies with restrictions on their use (see NCIm Sources).

The NCIm Browser is for the retrieval of concepts from the NCI Metathesaurus, and for viewing the contents, structure, and cross mappings of individual source terminologies. It is designed for ease of use by a diverse user community. This 2.8 release uses the new LexEVS 6.4 terminology server without significant changes that would affect users. The Search box separates Name and Code search, search performance is better, and Advanced Search offers new Lucene options to search with wildcards, negation, boolean operators, and fuzzy matching. Contact Us to provide feedback and get additional help on the NCIm Browser.

This help file provides basic information about how to use the NCIm Browser effectively. It also provides pointers on how to learn more about NCIm and related resources. The following typeface font conventions are used for describing search and the browser interface:

  • Bold: Browser links, buttons, page tabs, and drop-down boxes.
  • Fixed Width: Search strings
  • Italics: Concept terms

Search

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In the Search box, enter all or part of what you are looking for, set what and how you want to search, and click the Search button. Some details:

  • Text Box: Enter the exact string of characters you want to search for.
    • Search is not case sensitive (e.g., aids will match aids, Aids, and AIDS), except for Code searches, which are case sensitive (e.g., c298 will not match C298).
    • There are no wildcard characters. All characters are matched literally (e.g., searching for Begins With NAT2* will match NAT2*5 Allele but not NAT2 Gene).
    • Do not use quotes - they will be searched for literally, as characters to be matched.
    • Searching for multiple words does not search on each word separately. To match, all words have to be found in the same order you provided. For example, if you do a Contains search on Melanoma Corneal no results will be returned, but if you search on Corneal Melanoma you get the detail page for Corneal Melanoma.
  • Match method radio buttons select how your search string will be matched.
    • Contains is the default. It will search for what you enter anywhere within a term (e.g., carcinoma will match adenocarcinoma).
    • Concept Codes will only match if they exactly match what you enter, even if you select Begins With or Contains.
    • Exact Match Only terms or codes that are identical will match.
    • Begins With can be selected to find all terms that start with the words or characters you enter.
  • Match target radio buttons select what category of concept information is searched
    • Name button is the default: Search text is matched to a concept's preferred name, synonyms, or acronyms. Unless stated otherwise, all search examples in this Help page use the default name search.
    • Code button is for searching concepts by code: Search text is matched to a concept code, or source code. The search is case-sensitive.
    • Property will match to other direct property attributes of a concept, such as definitions.
    • Relationship will return concepts that have relationships to concepts that match by name/code (e.g., an exact relationship search on toe does not return the concept toe, but does return toenail and other related concepts).
  • Source drop-down box: You can choose to limit your search to concepts with terms from a specific source. For example, if you only want to find breast cancer concepts that include terms from SNOMEDCT, you would choose SNOMEDCT from the Source box. This will return concepts with at least one SNOMDEDCT term and at least one term that matches your search criteria, even if the matching terms are not from the selected source. This search method is helpful for users looking for source coverage of a term that may be expressed differently in that source (e.g., searching for grey for source FDA will return Gray color, even though the only FDA term is the American spelling gray).
  • Source Hierarchy button: If you select a source with a concept hierarchy that can be viewed, an icon will appear to the right of the source selection box; click on the icon to view the hierarchy in a separate window.
  • Search button starts a search.
  • "?" button takes you to this Search section of the Help file.

Advanced Search

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The Advanced Search link, at the bottom right corner of the main search box, leads to a separate page. Most options and selections are the same as those described under "Search" above. The key differences are:

  • Lucene: This option allows use of Name search options not available elsewhere, including wildcards, Boolean operators, negation, and fuzzy search (click the radio button to see examples).
  • Property search offers a drop down list of all specific properties in NCIm, so that they can be selected and searched individually.
  • Relationship search offers drop down lists of broad relationship labels (RELs) and specific relationship attributes (RELAs) that can be searched on, as explained in the NCIm Relationship Attributes help file. Note that many relationships have no source-assigned RELA value. For example, searching on isa RELA value will retrieve only those specifically tagged as such and not others having only a broader PAR (Parent) REL relationship.
Advanced Search options will continue to grow in future releases.

Search Results

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Search results are displayed by concept name. (If there is only one match, the concept details page is shown directly without first listing results.) Some details:

  • All matching concepts are returned.
  • Results are listed from best match to weakest. For example, a Contains search on melanocyte returns melanocyte at the top followed by concepts with two word matches (e.g., Spindle Melanocyte), followed by concepts whose terms have more non-melanocyte content. An additional column displays the semantic type(s) assigned to each concept.
  • The match will often be to synonyms or codes only visible on the concept details page (e.g., searching Begins With melanoma will show Cutaneous Melanoma in the results list because that concept contains a synonym of Melanoma of the Skin.)
  • If there are too many results to show on one page, you can page through the results with a default of 50 per page. To change the default number, use the Show results per page drop-down menu at the bottom of the results page.
  • Click on the name to see a concept's details.

Concept Details

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Detailed information on the selected concept is grouped and shown on several related pages:

  • Tabbed information gives the concept's meaning, labels, and direct relationships:
    • Terms & Properties: Gives definitions, synonyms, abbreviations, codes, and other information.
    • Relationships: Shows how other concepts are directly related to this concept, where a source asserts that terms in those concepts are related as parents, children, or in other ways.
    • Synonym Details: For each term or abbreviation, shows its source, term type, and code.
    • By Source: Shows concept information one source at a time. NCI Thesaurus content is shown if available, otherwise the initial source is chosen alphabetically. To view concept information from a different source, select the link for that source at the top of the page. NOTE: Select the ? icon next to the Source header to view a list of the source abbreviations and full names. The Relationships section shows the specific term being pointed to by relationships from the selected source, including that term's source (sometimes different), type, and code.
    • View All: Combines all of the above information on a single page.
  • In NCIt Hierarchy: Click the button to see where the concept is found within the NCIt hierarchy as presented through NCIm concepts. Concepts are often found in several different places in the hierarchy. The focus concept will be bold, underlined, and colored red. This function only appears in concepts with NCIt content. Hierarchy displays from other sources will be provided in a later browser release.

Cart and Export Functionality

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The Cart and Export functionality is available from within the detailed Concept Page of any concept that is selected for viewing. The purpose of the Cart and Export functionality is to allow the user to collect and save one or more concepts so that they can be exported to a file. The following instructions apply to the Cart and Export functionality.

  • In order to place a concept you are viewing into the Cart, click on the Add to Cart link on the right hand side of the concept details (note that the Add to Cart link appears on all of the tabbed pages: Terms & Properties, Synonym Details, Relationships, By Source, and View All).
  • Once you have placed a concept into the Cart, a link called Cart will appear underneath the Search Box at the top of the page, next to Visited Concepts; from this point forward, this link will remain there regardless of the Metathesaurus Browser page you are on (provided that the Cart is not emptied; if the Cart is emptied, the link will disappear).
  • If you click on the Cart link, you will be taken to the Cart page:
    • The number next to the word Cart on the left indicates the number of concepts you have placed in the cart.
    • The concepts you have placed in the cart are listed by concept Name (on the left) and concept Semantic Types (on the right).
    • If you want to remove a particular concept from the Cart, check the box on the left of the concept's name and then click Remove. This will also work for removing several selected concepts at once.
  • Concepts you have accumulated on the Cart page can be exported to a file in two formats:
    • Export XML will export cart contents in XML format.
    • Export CSV (Comma Separated Values) will generate a list of cart contents in CSV format readable from Excel.

View Hierarchy

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Many sources have hierarchies of concepts, arranged from the most general at the top to the most specific at the bottom leaf nodes. Most common are "is-a" hierarchies, where child concepts are subtypes of their parent(s) (e.g., Mold is-a Fungus), but other relationships, such as "part-of", are also used by some source terminologies. The browser provides several ways of viewing hierarchies when they are available.

Click on the View NCIt Hierarchy link at the top of the page to bring up a separate window showing the NCI Thesaurus hierarchy as presented through NCIm concepts. Some details:

  • At first, only the top level nodes of the hierarchy are shown.
  • At each level, concepts are listed alphabetically by concept name.
  • Browse through the levels by clicking on the + next to each concept.
  • Click on the concept name itself to see the concept's details in the main browser window.
Source drop-down box: If you select a source with a concept hierarchy that can be viewed, an icon will appear to the right of the source selection box; click on the icon to view the hierarchy in a separate window.

Sources

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Click on the Sources link at the top of the page to bring up a separate window showing the list of sources included in the current release of NCI Metathesaurus. Sources are listed alphabetically by abbreviation, showing full source names and other details. Use restrictions are described for proprietary sources. This page is also displayed if you click on the ? icon above the source information in the Relationships, Synonym Details, and By Source tabs.

Known Issues

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This 2.8 NCIm Browser release, based on LexEVS 6.4, addresses some of the search and other enhancements made in the companion Term Browser. The Search box separates Name and Code search, search performance is better, and Advanced Search offers new Lucene options to search with wildcards, negation, boolean operators, and fuzzy matching. For the latest updates of known issues, see NCI Metathesaurus Browser 2.7 Release Notes.

Please report any bugs or suggestions using the browser's Contact Us page. Suggestions to add a new concept or make changes to an existing concept can also be made using the Suggest changes to this concept link in the upper right of all concept details pages.

Additional Information

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Additional information about NCIm and EVS can be found on the EVS Web and EVS Wiki sites.


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