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EVS Logo NCI Term Browser Enterprise Vocabulary Services
Terminologies Value Sets Mappings
Help

Introduction
NCI Term Browser Home Page
Terminologies Tab
     Sources
     Using the Search Box
     Search Results
     Searching Other/Multiple Versions of a Terminology
     Advanced Search
     Concept Details
     Additional Links for Individual Terminologies
     Cart and Export Functionality
Value Sets Tab
     Using the Search Box
     Concept Details
Mappings Tab
     Using the Search Box


Introduction top

NCI Enterprise Vocabulary Services (EVS) provides terminology content, tools, and services to NCI and the biomedical research community.
        
  • For browser support or suggestions, use the browser's Contact Us page.
  •         
  • For all EVS resources, services and contacts, see the EVS Web site http://evs.nci.nih.gov/.
  • NCI Term Browser provides a consistent, user-friendly tool to browse, search and retrieve all of the biomedical terminologies hosted by EVS, including both NCI Thesaurus (NCIt) and the NCI Metathesaurus (NCIm), which itself includes more than 70 terminologies. The 2.0 major release added support for value sets (flat lists of terms from one or more terminologies used for a particular coding purpose) and mappings between terminologies to support data translation and cross-reference. For information on new features and known issues, see NCI Term Browser 2.9.2 Release Notes.

    This help file provides basic information about how to use the NCI Term Browser effectively, as well as links to additional information elsewhere. 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.

    NCI Term Browser Home Page top

    In the upper left of the NCI Term Browser home page are 3 tabs: the Terminologies tab (the default tab), the Value Sets tab, and the Mappings tab:

    • The Terminologies tab allows browsing and searching within each of the NCI hosted terminologies, or within multiple terminologies.
    • The Value Sets tab allows browsing and searching within all value sets, such as the CDISC SDTM Terminology or the FDA SPL Terminology, available on the NCI server.
    • The Mappings tab allows browsing and searching within a mapping set such as the PDQ to NCIt Mapping or the NCIt to ChEBI Mapping.

    These 3 tabs will appear at the top of every Term Browser page you are on, and the tab that is highlighted indicates which section of the Term Browser you are in. The NCI Term Browser icon above the tabs always leads back to the main Terminologies home page. The Term Browser and LexEVS terminology server versions are displayed in the browser's home page banner; for more information on LexEVS, see the LexEVS Wiki Pages.

    The NCI Term Browser home page contains a Search Box in the upper right hand corner. This Search Box has different options, and will bring back different results, depending on which tab you are on in the Term Browser.

    Several links appear below the Search Box. Most appear only in certain tabs or other settings, but these appear on the home pages of all tabs:

    • Sources always appears at the left, and gives information about all terminologies and mappings including the descriptions that appear on their individual home pages.
    • Visited Concepts will appear under the Search box once you start visiting individual concept pages. It shows the concept name, terminology, and version for each concept visited, with the most recent concepts at the top.
    • Help always appears at the far right, linking to this Help page.

    Terminologies Tab top

    These terminologies normally represent each specific meaning, such as melanoma, lung, or chemotherapy, by a distinct concept with a unique, permanent code. Each concept normally provides additional information such as a preferred name, other terms and codes, definitions, and relationships with other concepts. Concepts are normally organized in parent-child hierarchies from very broad top concepts down to the most specific subcategories. All browsing and searching in this browser reflects this concept-based view of terminology. For information on other EVS browsers, file formats, and computer application access, see the EVS web site.


    Sources

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    The Terminologies tab of the NCI Term Browser home page lists the terminologies that are available: NCI Thesaurus, NCI Metathesaurus, and the rest in alphabetical order. Click on a terminology name to go to its home page, or click on a terminology's check box to include it in a search from the Terminologies tab of the NCI Term Browser home page. Both above and below the terminologies list on the Terminologies tab are four buttons:

    • All but NCIm button: Includes all terminologies except NCI Metathesaurus (NCIm); this is to search the standalone terminologies more quickly, without also searching the more than 70 terminologies in NCIm.
    • Select All button: Includes all terminologies for searching, making their check boxes checked.
    • Clear button: Unselects all terminologies and clears their check boxes.
    • Search button: Starts a search in the same way as the Search button in the search box (see below).

    Using the Search Box

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    The Search Box, in the upper right corner of the Term Browser home page and of most Term Browser pages, lets you enter all or part of what you are looking for and how you want to search for it. Some details:

    • Text Box: Enter the string of characters you want to search for.
      • Search is not case sensitive (e.g., aids will match aids, Aids, and AIDS).
      • 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.
      • Search multiple words requires that all search words be found in target terms. There are two different methods used:
        • Method 1: For Exact Match and Begins With methods, and for all Property and Relationship targets, the words must be found together in the order entered with no separation.
        • Method 2: Contains search on Name, however, now looks for those words separately. A special index makes these searches faster and more flexible than before, while still ranking best matches first. Note: The current implementation only finds matches at the start of words, not the middle or end; we plan to address this in a future release.
        For example, if you do a Contains search on Melanoma Cornea, no results will be returned, for any option covered under Method 1,but with Method 2 you will match Corneal Melanoma. Refinement of these methods is ongoing.
    • Match method radio buttons select how your search string will be matched.
      • Contains button is the default. It will search for what you enter at the start of any words in a Name search, or at the beginning or end of any words in a Property or Relationship search (e.g., adeno will match adenocarcinoma in all these searches, but carcinoma will only match it in Property or Relationship searches). For multiple word search, see description in the preceding section.
      • Exact Match Only terms or codes that are identical will match.
      • Begins With button can be selected to find all terms that start with the words or characters you enter. Codes cannot be searched this way.
      • Concept Codes will only match if they exactly match what you enter. If you select a search target of Code and then the Begins With or Contains method button, the browser will switch to the default Name search target radio button.
    • 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 button will match to other direct property attributes of a concept, such as definitions.
      • Relationship button will return concepts that have relationships to concepts that match by name/code (e.g., an exact relationship search on hand does not return the concept Hand, but does return Finger and other related concepts that have relationships that point to Hand; note that the Hand concept's Relationships tab shows relationships that point from Hand to other concepts).
    • Search button starts a search.
    • The "?" button brings you to this Search section of the Help file.

    If you are in the NCI Term Browser home page, all currently selected terminologies on the Terminologies tab will be searched. When you are in the pages of a particular terminology, only that terminology will be searched. The banner to the left of the Search box tells you which terminology environment you are in.


    Search Results

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    When a terminologies search is run, Search Results are displayed by concept preferred name. If you are searching multiple terminologies, a right-hand column displays the corresponding name of the terminology for each matching concept. If there is only one match, the concept details page is shown directly without first listing results, unless the matching concept is in the NCI Metathesaurus (because this links to the separate NCIm Browser). Some details:

    • All matching concepts are returned.
    • Results are listed from best match to weakest. For example, a Contains search on Bone returns Bone at the top, followed by concepts with two word matches (e.g., Flat Bone), followed by concepts whose terms have more non-Bone content.
    • When a terminology search is run, it looks for matches not only in the preferred name of concepts but also among the synonyms of the preferred name as listed in the concept details page. For this reason, the match will often be to synonyms or codes only visible on the concept details page (e.g., searching Begins With melanoma will show MIA in the results list because that concept contains a synonym of melanoma inhibitory activity.)
    • If there are too many 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.
    • If a concept is retired, this will be indicated by the phrase "(Retired Concept") next to the name of the concept in the Results listing.
    • Click on the preferred name to see a concept's details.
    • A Back to search results link appears in the search box when you leave the results page for other pages in the Terminologies tab; click on the link to return to that last results page. If you run a new search or switch to another main browser tab, that results page is lost and the link disappears.

    Searching Other/Multiple Versions of a Terminology

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    It is possible in some instances to search non-production or multiple versions of a particular terminology from the Terminologies tab of the Term Browser.

    • The terminologies for which this is possible will have a link to the right of them that says show other versions. Click on that link to see the non-production versions of the terminology that are available.
    • These versions, which will appear directly underneath the production version, will have a check box to the left; click on that check box and the non-production version(s) will be included in the search.

    Some details about searching other or multiple versions of a particular terminology from the Terminologies tab:

    • The Select All button will not select non-production versions of a terminology unless the show other versions link has already been clicked and the non-production version(s) are visible.
    • However, the Clear button will unselect the check box of a non-production version of a terminology even if it is hidden from view.
    • The Search Results will also indicate in parentheses under Vocabulary the terminology version the result came from.

    Advanced Search

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    The Advanced Search link, which appears under the Search Box on terminology source home pages, or Concept Details pages (see below), leads to a separate page. The options and selections are similar to those described for the Search Box, with the following key differences:

    • Lucene: This additional match method option is only available for Name targets, and allows use of Name search options not available elsewhere, including wildcards, Boolean operators, negation, and fuzzy search (click the radio button to see examples).
    • Source: Some terminologies include content from more than one contributing source. You can choose to limit search to one contributing source, or stay with the default of all, using the pull down menu.
    • Property search offers a drop-down list of all specific properties associated with the home terminology source, so that they can be selected and searched individually.
    • Relationship search offers a drop-down list of all specific relationships associated with the home terminology source, so that they can be selected and searched individually or all together. Radio buttons specify whether the search expression should match relationship source or target concepts (e.g., in the relationship [Finger] --> (Anatomic_Structure_Is_Physical_Part_Of) --> [Hand], Finger is the "source" concept and Hand is the "target").

    Concept Details

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    Detailed information on a 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.
      • Synonym Details: Shows each term or abbreviation with the corresponding term type, source, and code (for sources that have them).
      • Relationships: Shows how other concepts are directly related to this concept as parents, children, or in other ways. Note: For some sources, the browser adds inverse relationships not asserted bidirectionally in the source data file; this is often useful for informational and navigational purposes, but is sometimes confusing, and will continue to be evaluated for adjustments in future releases.
      • Mappings: Gives the mapping relationships, if any, to other vocabularies.
      • View All: Combines all of the concept details on a single page.
    • Concept specific links provide additional information and actions, some limited to sources for which they are available:
      • View in Hierarchy: Click the link to see where the concept is found within the terminology hierarchy. Concepts are often found in several different places. The focus concept will be bold, underlined, and colored red.
      • View History: Click the link to see a history of changes made to the current concept, for sources that provide concept history data.
      • View Graph: Click the link to see an interactive graphic presentation of some information available in the Relationships tab. The default displays all available relationships at once. A drop-down pick list allows choosing specific relationships for viewing.
      • Add to Cart: For information about placing concepts into the Cart (using the Add to Cart link found on the Concept Details pages) in order to Export concept information to a file, please see below.
      • Suggest Changes: This link appears in the upper right of all concept details pages of sources for which NCI can handle such requests. It goes to a special suggestion page with source and concept code filled in.

    Additional Links for Individual Terminologies

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    Extra links are added just under the Search Box for additional information available for some sources:

    • Hierarchy: Click the link to bring up a separate window showing the full terminology hierarchy. Some details:
      • At first, only the top level nodes of the hierarchy are shown.
      • At each level, concepts are listed alphabetically by concept preferred name.
      • Browse through the levels by clicking on the + next to each concept that has child concepts.
      • Click on the concept name itself to see the concept's details in the main browser window.
    • Value Sets: Click the link to bring up a separate window showing a hierarchy of the value sets defined using the terminology. Clicking on the name of a value set will bring up that value set's home page. Terminologies that do not have value sets will not have the Value Sets link (see the information on the Value Sets tab below).
    • Maps: Click the link to bring up a list of the mapping data sets of the terminology, which can then be searched. Terminologies that do not have mappings will not have the Maps link (see the information on the Mappings tab below).

    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. This is true no matter whether the concept was selected from the Terminologies tab, the Value Sets tab, or the Mappings tab of the Term Browser. 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 whose details 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, Relationships, Synonym Details, Mappings, 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 Term 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 Vocabulary (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.
    • Exporting the concepts you have accumulated in the Cart can be done 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.
      • If a concept is available in more than one version of a terminology, the user is allowed to choose between the default production version of the terminology and other available versions.

    Value Sets Tab top

    The Value Sets tab of the NCI Term Browser supports browsing and searching individual and groups of value sets, which are flat lists of member concepts intended for specific coding purposes. Value sets are available in two different views:

    • Standards View is the default view, and shows the available value sets listed by the authority responsible for their content.
      • Authorities, and value sets for each, are listed alphabetically. Some value sets are defined by combining component value sets, displayed as child entries.
      • Browse through the levels by clicking on the + next to entries having lower levels.
      • If you select one of the top-level authority entries, such as CDISC or FDA, you will go to a home page for that authority with descriptive text and a listing of value sets.
    • Terminology View shows available value sets listed by the terminologies their values come from.
      • Browse through the levels by clicking on the + next to each terminology.
      • If you select one of the top-level terminologies, you will go to the home page for that terminology.

    Both trees are compliant with Section 508 of the Rehabilitation Act. Use the Tab and the Shift-Tab keys to navigate tree nodes and use the Space bar to check or uncheck a checkbox. Hit the Enter key, when the navigation is focused on a value set name, to go to that value set's home page.

    The home page gives a brief description, and four buttons for viewing it:

    • Released File Displays the content of a value set as it appears in the file published at the NCI EVS download site.
      There are two options for exporting all of the values from the displayed set:

      • Export Excel will open or save the value set in a Excel format.
      • Export CSV (Comma Separated Values) will open or save the value set in a delimited text format.

    • Values lists all concepts contained in this value set, using the production version of each participating terminology. The listing shows:
      • Name: A descriptive name
      • Description: A plain text description of the nature of the value set
      • Concept Domain: The type of meaning represented.
      • Sources: The authority or origin of the contents.
      • Concepts: The individual concept values that comprise the value set, presented as follows:
        • The first 50 concepts of the value set are listed. Use the Show <n> results per page drop-down menu at the bottom of the page to display up to 500 concepts at once.
        • Each concept listed shows its code, name, vocabulary and namespace.
        • Select the Code link (e.g., C81209) to display the concept details. See the Terminologies Tab help section for information on the concept details display.

      There are two options for exporting all of the values from the displayed set:

      • Export XML will open or save the value set in a tagged XML format.
      • Export CSV (Comma Separated Values) will open or save the value set in a delimited text format.

    • Versions allows you to select particular versions of each terminology participating in this value set. For example, selecting the CDISC ADaM Terminology and then the Versions button will show the currently available versions of NCI Thesaurus. The version information includes:
      • Coding Scheme
      • Version
      • Tag

      The Continue button uses the selected version(s) to select the values contained in the set. See help section on Values above for information on the details contained there.

    • XML Definition opens or saves the logical definition of the value set in LexGrid XML format. This definition contains the criteria used to find the values in the value set, using concept codes, logical hierarchies, or other criteria sometimes combining multiple parts.

    Using the Search Box

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    The Search Box on either the Value Sets tab or on a particular Value Set's home page works the same way as on the Terminologies tab: the Text Box, the Match method radio buttons, and the Match target radio buttons all function the same way as with the Terminologies tab. The one exception to note is that only Name and Code match targets are supported; as elsewhere, Name is the initial default.

    Value Set search results, however, are presented differently, because matching concepts are members of one or more selected value sets, but also come from a particular terminology source. The result page indicates the search expression and selected value sets, and then presents a table of matching concepts with four columns:

    • Value Set: The value set the matching concept is in. Click on it to visit the value set's home page. Where a parent value set combines multiple child value sets, matching concepts will be listed twice, for both the parent and the child.
    • Vocabulary: The source terminology for this concept, including its version in parentheses.
    • Name: The name of the concept. Click on it to see a concept's details (the details of the concept are the same as outlined in Terminology-Concept Details, earlier in this Help).
    • Code: The code of the concept.

    Some details:

    • All matching value sets and concepts are returned.
    • If there are too many 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 page.

    The Mappings tab covers special mappings created between pairs of terminologies, showing how some or all concepts in the first (source) terminology can be mapped to one or more concepts, with the same or related meaning, in the second (target) terminology. The Mappings tab home page provides a full list of mapping data sets, but for now only allows searching one at a time. To search a mapping set, you have the choice of either

    • Searching using the list of mapping data sets (by clicking on one of the mapping set radio buttons); or
    • Searching within a particular mapping data set by clicking on its link and going to its home page (where the name of the mapping set will be prominently displayed as a banner in the upper left-hand corner of the home page).

    If you choose to go to a particular mapping set's home page, you can also choose to view the full mapping set (which will appear in a format described below for the results of a search) by clicking on the red box called View Mapping or by clicking on the link that says Mapping right underneath the Search Box. You can also export mapping contents to a file in CSV format readable from Excel by clicking on the red box called Export CSV.

    A mapping set's home page will also have a description of the mapping and, where available, links to the source of the mapping set, sites where you can download the mapping set, and other sites offering related information.


    Using the Search Box

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    Searching using the Search Box on either the Mappings tab or on a particular Mapping Set's home page works the same way as on the Terminologies tab: the Text Box, the Match method radio buttons, and the Match target radio buttons all function the same way as with the Terminologies tab. The one difference to note is that search results can come from a match to either the source or target concept in each mapping entry.

    The results of the search are quite different, however, because the search involves matched pairs of concepts from both the source and target terminologies; search hits can happen on either source or target, and what comes back are the matched pairs. In order to illustrate the nature and results of a search in the Mappings tab, we will use a PDQ to NCIt (version 201010) mapping set search for anything that contains "melanoma." A chart appears with eight columns:

    • Source: the source terminology that has been mapped to a target terminology (for a PDQ to NCIt mapping, for example, the source will always be "PDQ," since PDQ is the source terminology and NCIt is the target terminology).
    • Source Code: the concept code of a concept in a source terminology (for example, the source code CDR0000038833 of the PDQ concept "melanoma" that has been mapped to the target NCIt concept "Melanoma").
    • Source Name: the name of a concept in a source terminology (for example, the PDQ concept with the source name "melanoma" has been mapped to the NCIt concept "Melanoma").
    • REL: the relationship between the source concept and the target concept to which it has been mapped (in this case the relationship between the PDQ concept and the NCIt concept to which it has been mapped).
      • RB: indicates the source concept is broader than the target concept.
      • RN: indicates the source concept is narrower than the target concept.
      • SY: indicates the source concept and the target concept are synonymous.
      • RQ: indicates the source concept and the target concept are related and possibly synonymous.
    • Map Rank: a numerical ranking of the quality of a mapping where a "1" is considered to be the highest quality mapping and higher numbers indicate increasingly lower quality mappings (the map rank is available only for certain mapping data sets).
    • Target: the target terminology to which a source terminology has been mapped (for a PDQ to NCIt mapping, for example, the target will always be NCIt).
    • Target Code: the concept code of a target concept to which a source concept has been mapped (for example, the target code C3224 of the NCIt concept "Melanoma" to which the PDQ concept "melanoma" has been mapped).
    • Target Name: the name of a target concept to which a source concept has been mapped (for example, the NCIt concept with the target name "Melanoma" to which the PDQ concept "melanoma" has been mapped)..

    Some details regarding the results of mapping set searches:

    • All mapping matches are returned.
    • Results are listed from best match to weakest.
    • If there are too many 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 a Source Code or a Target Code to see a concept's details (the details of the concept are the same as outlined in Terminology-Concept Details, above)
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