Help
Introduction
Search
Advanced Search
Search Results
Concept Details
Cart and Export Functionality
View Hierarchy
Sources
Known Issues
Additional Information
NCI Metathesaurus (NCIm) is a comprehensive biomedical terminology database, connecting
6,700,000 terms from over 85 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 2.17 release uses the new LexEVS 6.5.5 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
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.
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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 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.
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.
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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.
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The concepts you have placed in the cart are listed by concept Name (on the left) and concept Semantic Types (on the right).
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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.
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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.
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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.
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.
This 2.17 NCIm Browser release, based on LexEVS 6.5.5,
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 2.17 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 about NCIm and EVS can be found on the
EVS Web and
EVS Wiki
sites.