PubMed Nucleotide Protein Genome Structure PopSet Taxonomy OMIM

OMIM Help Revised July 7, 2005

This help document provides tips for searching OMIM in Entrez, along with sample searches. The OMIM FAQs provide additional information about the database and related questions. The Entrez Help in Bookshelf provides additional details about the search system and the other Entrez databases.
  1. Overview
  2. Three Levels of Search Complexity  (quick start tutorial)
  3. Search Fields
  4. Search Tips
  5. Search Results
  6. How To Print
  7. Sample Searches
  8. How To Make WWW Links to OMIM

Overview back to top

Scope back to top

Online Mendelian Inheritance in Man (OMIM) is a catalog of human genes and genetic disorders, with links to literature references, sequence records, maps, and related databases. It is based on the book, Mendelian Inheritance in Man. The online version is updated daily. The OMIM FAQs provide additional information about the book and the online database.

Main Features back to top

While preserving the functions of the earlier OMIM search system, the Entrez system provides the following new functions:

  • search at any one of three levels: basic, advanced, or complex Boolean.

  • browse the index of a field to see the available terms, and the number of entries that contain each term, using the Index function.

  • build your query one step at a time using the Preview function.

  • restrict a search by criteria such as search field, chromosome number, or record type (such as records which describe allelic variants) using Limits.

  • combine the results of two or more searches with Boolean AND, OR, NOT logic using History.

  • select and display multiple records at once, choosing from a number of Display Formats.

  • store selected records from multiple searches in the Clipboard.

  • take advantage of Entrez's integration and cross-referencing to find related records in other Entrez databases using the various Display Formats

Sample Questions back to top

Examples of questions that can be answered with OMIM in Entrez
  1. What human genes are related to hypertension? Which of those genes are on chromosome 17? (strategy)

  2. List the OMIM entries that describe genes on chromosome 10. (strategy)

  3. List the OMIM entries that contain information about allelic variants. (strategy)

  4. Retrieve the OMIM record for the cystic fibrosis transmembrane conductance regulator (CFTR), and link to related protein sequence records via Entrez. (strategy)

  5. Find the OMIM record for the p53 tumor protein, and link out to related information in Entrez Gene and the p53 Mutation Database. (strategy)

The "strategy" links lead to the Sample Searches section of this document.

Three Levels of Search Complexity back to top

This section briefly introduces the three levels of search complexity, showing how you can retrieve records for cancer-related genes that have been mapped to chromosome 11 and have an autosomal dominant mode of inheritance in Basic, Advanced, or Complex Boolean search mode. Additional details about each search level are provided in subsequent sections.
  • Basic

    Enter one or more search terms into the text box without specifying search fields, other limits, or Boolean operators.  For example, enter: 
    cancer 11 autosomal dominant
  • Advanced

    Control your search to a greater degree by using the "Limits," "Index," and "History" options. These enable you to select search fields or other limits, view the index of a field, or combine components of your search in various ways.

    For example, you can search for each term individually, limiting it to the desired search field, and then use "History" to combine the searches: 
    Step 1:
Enter:  cancer
Select Limits option under the text box.
Activate check box for Title to select that field.
Activate check box for Chromosome 11
Press Go.

Once the search results are shown,
deactivate the Limits check box
in the grey header bar and press Clear
in order to begin a new search.

Step 2:
Enter:  autosomal dominant
Select Limits option under the text box.
Activate check box for Clinical Synopsis
to select that field.
Press Go.

Step 3:
Select the History option
Enter:  #1 AND #2
(Your search numbers might be different from
those above.  Use the numbers of your actual
searches that you want to combine.)
    Compare the search results with the Basic search.
  • Complex Boolean

    As a shortcut to the steps shown under Advanced Search, above, you can use a command language that includes terms, field qualifiers in square brackets [], and Boolean operators. For example, enter:

    cancer[titl] AND 11[chrom] AND autosomal dominant[clin]
    These results should be identical to the Advanced search. The main advantage is that you can insert your complete search into the Entrez query box in a single step.

    If you want to broaden your search to include various synonyms, you can enter a search such as:

    (cancer[titl] OR neoplas*[titl] OR tumor[titl]) AND
autosomal dominant[clin] AND 11[chrom]

1.  Basic Search back to top

The default OMIM search is set to the Basic mode. Simply enter one or more terms in the text box and click on 'go.'

Example A:     Basic Search

  • To retrieve OMIM records that contain the term "allergic," simply enter the term into the search box at the top of the page: 
         allergic
  • Press "Go" to see the titles of the documents retrieved.
It is possible that the index contains similar terms which have variations in spelling, and which were therefore not retrieved by this search. To see the other terms that are available, you can use the Index function, described in the next example.

If multiple terms are entered, they will be combined with a Boolean AND by default. For example, a search for kinase receptor will be interpreted as kinase AND receptor. To force Entrez to search multiple words as a phrase, enclose the words in double quotes (e.g., "kinase receptor"). In addition, you can change the Boolean operator by explicitly including the desired operator in the search box (e.g., "kinase NOT receptor"). Additional information on Boolean operators is below.

Note that Entrez automatically recognizes some multiple terms as a phrase (e.g., cystic fibrosis), and therefore searches for them as a phrase, whether or not they are enclosed in double quotes.

Entrez will search All Fields by default. Since the search terms can appear in any field of the record, you might retrieve some irrelevant hits -- i.e., records that briefly mention the search term, but do not have it as a main topic. If you want the search term to be a stronger focus of the record, you can Limit your search to a field such as Title Word.

Entrez sometimes recognizes a term that belongs to a specific search field and it will use that field. E.g., if an author name is entered in the format lastname i or lastname ii, Entrez will automatically search the correct field.

Click on the Details folder tab on the search results page to see exactly how Entrez executed your search. You can also manually edit your search in the Details dialog box. (See Entrez Help in Bookshelf for more information on the Details folder tab.)

2.  Advanced Options back to top

Advanced options provide more control over your search by allowing you to:
  • select search fields using the Limits or Preview/Index function
  • browse the Index of a field to select one or more terms of interest, and to see the number of records that contain each term
  • preview the quantity of records retrieved by a search before viewing the actual search results
  • limit search results to desired subsets using the Limits function
  • combine the results of two or more searches with Boolean AND, OR, NOT logic using History
  • store selected records from multiple searches in the Clipboard

Preview/Index back to top

The Preview/Index page allows you to do several things:

  1. Preview button -

    • at the top of page -

      shows only the number of documents retrieved by a search, without listing the titles of the retrieved records. This allows you to quickly evaluate your search strategy and modify it if necessary to increase or decrease the number of retrieved documents before viewing the actual search results.

      You can modify your query by either (a) editing the search shown in the text box at the top of the page, and then hitting "Preview" to glance at the search result numbers, or hitting "Go" to view the titles of the retrieved records; or (b) using the text box, field selection pop-up menu, and Preview button in the middle of the page, as described below.

    • in the middle of the page -

      adds a new term to your query, in the search field you have selected, and shows the new number of records retrieved.

      If you simply hit the Preview button after entering a term into the search box in the middle of the page, your term will be combined the rest of your search using a Boolean AND. To select a different Boolean operator, hit the OR or NOT buttons after entering your term, then hit the "Preview" button.

      Because you remain on the query page after you hit the "Preview" button, rather than on the page the displays the actual search retrieval, you can continue to build your query one step at a time, and evaluate your search strategy and results at each step.

      You can select a different search field and/or browse that field's index at each step.

      Once you are satisfied with your search, you can display the documents retrieved by clicking on the number in the "Result" column.

  2. Index button -

    Shows the index of the selected field, allowing you to:

    • browse an alphabetical list of terms in the index,
    • see the number of documents, shown in parentheses, that contain each term
    • select one or more terms from the index and add them to your search.

    Simply select the search field of interest from the pop-up menu (which by default is set to All Fields), enter a term of interest in the search box beside it, and press the Index button.

    If you do not enter a search term, pressing the "Index" button will take you to the top of the index for that search field. You can then use the "Down" button to scroll through the index.

    Once you are browsing the index, you can select one or more terms for inclusion in your query.

    • If you select a single term from the index, use the AND, OR, or NOT button to include that term in your search.

    • If you select two or more terms, they will be be combined together with a Boolean OR. Then use the AND, OR, or NOT button to include that set of terms in your search.

    The method by which you select multiple terms varies with the type of computer. For example:

    • Unix - use the left mouse button to select one or more terms by simply clicking on each term of interest.
    • PC - use the left mouse button to select the first term of interest, and the shift key + left mouse button to select the last item in a range, or the control key + left mouse button to select multiple items that are not in a range.
    • Mac - use the mouse button to select the first term of interest, and the shift key + mouse button to select the last item in a range, or the apple key + left mouse button to select multiple items that are not in a range.

Example B:     Browsing the Index  

In example A, above, you did a basic search to retrieve OMIM records that contain the term allergic. However, it is possible that the index contains similar terms which have variations in spelling, and which were therefore not retrieved by the search.

To broaden your retrieval, you can browse the index to select additional terms of interest, and to see the number of records that contain each term:
  • Select the Preview/Index option beneath the search box.

  • Type the following term into the search box in the middle of the page, beside the search field pop up menu: 
         allergic
  • For this example, leave the search field set to the default All Fields.

  • Press the Index button to browse the index of that field.

  • Select one or more terms of interest. (Information on how to select multiple terms is given above.) For example, select the terms:

    allergic
    allergies
    allergy

    The system will group the terms together with a Boolean OR. That is, it will look for records that contain
    allergic OR allergies OR allergy.

  • Press the Preview button to see the total number of records found.

    Note:  If you already have some terms in the query box at the top of the page, pressing the Preview button will add the new group of terms to the rest of your query using a Boolean AND. To use a different Boolean operator, use the AND, OR, or NOT buttons.

    For example, if the term "allergic" already appears in the search box at the top of the page, you just need include the new terms "allergies" and "allergy" in your search. Select those terms from the scrolling index and press the OR button (which add both terms to the first part of your query using a Boolean OR). Then use the Preview or Go button at the top of the page to execute the search.

If you would now like to limit your search by some criterion such as chromosome number, see the next example under Limits.


Limits back to top

The Limits function allows you to limit the search to:

You can also use the Limits function on its own, and not just to limit an existing query. For example, you can begin a new search on the Limits page and simply check the box for chromosome 21 to see all the genes and disorders described in OMIM which have been mapped to that chromsosome.

Caution:  Once you select a particular limit and execute the search, notice that a check mark appears beside the Limits option in the grey header bar. As long as that box remains checked, the limit will apply to subsequent searches. Therefore, remember to deactivate the Limits check box if you do not want to use that limit for the next part of your search.

Example C:     Using Limits  

In example B, above, you retrieved records that contained the terms:  allergic OR allergies OR allergy

  • If you would now like to limit your search by a criterion such as chromosome number, select the Limits option beneath the search box.

  • Activate the check boxes for chromosomes 3, 7, and X.

  • Press the Go button to see the subset of records that describe genes or disorders that have been mapped to those chromosomes.

After you finish, remember to deactivate the Limits check box in the grey header bar if you want do not want to use that limit for the next part of your search.

The next example, under History, shows how to do another search for records that contain the term immunodeficiency (and other spelling variations), and then combine the results of both searches.


Search Fields on the Limits page include the following:

  • Title
  • MIM Number
  • Allelic Variants
  • Text
  • References
  • Clinical Synopsis
  • Gene Map Disorder
  • Contributors
The complete list of Search Fields can be accessed through the pop-up menu on the Preview/Index page.

Chromosome number:

Check the box(es) for the chromosome number(s) of interest.

If no boxes are checked, the system will search all OMIM records (both mapped and unmapped).

If you select multiple chromosomes, the system will retrieve records that are on any of those chromosomes.

To retrieve entries that do not have a location on the OMIM Gene Map, check unknown.

If you want to retrieve records that have been mapped to a specific cytogenetic band, search the Gene Map field using the pop-up search field menu on the Preview/Index page.

If desired, you can retrieve "Only records with" certain attributes, such as:

  • Allelic Variants
  • Clinical Synopsis
  • Gene Map Locus
The Limits page presents check boxes for the most commonly used attributes. To view a complete list of attributes, you can use the Index function to browse the index of the Properties field.

MIM Number Prefixes include the following.  See OMIM FAQs for additional information about each symbol.
* gene with known sequence
+ gene with known sequence and phenotype
# phenotype description, molecular basis known
% mendelian phenotype or locus, molecular basis unknown
no prefix other, mainly phenotypes with suspected mendelian basis

Recently added or updated records can be retrieved by limiting to those created or modified in the past:

  • 1 week
  • 1 month
  • 2 months
  • 3 months
  • 6 months
  • 1 year
Or, you can enter an explicit range of modification or creation dates, using the format YYYY/MM/DD (month and day are optional).

History back to top

The History provides a record of the searches performed during a search session and allow you to:

  1. quickly retrieve the results from previous searches

  2. combine two or more searches using AND, OR, NOT Boolean operators

  3. revise an earlier search
Histories are database-specific. The search history for an Entrez database expires after one hour of inactivity.

Boolean operators should be in upper case. The OR and NOT operators are also available, and parentheses can be used to nest the search.

Example D:     Using History to Combine Searches

In example C, above, you searched for records that contained the terms allergic OR allergies OR allergy and then limited the retrieval to genes or disorders on chromosomes 3, 7, and X.
  • If you are also interested in records that contain the term immunodeficiency, you can add that term to your search in several ways. One way is to do a new search for that term, and then use History function to combine the searches. For example:

  • Clear the search box and deactivate the limits check box (if it is activated) to begin a new search.

  • Enter the term:

         immunodef*

    Since the term might appear as several variations (e.g., immunodeficiency, immunodeficient, immunodeficiencies), you can truncate the term to search for its stem.

    Use the asterisk as a wildcard to represent zero or more characters, so the search will retrieve any records containing that word stem.

  • Press the Go button.

  • Select the History option to see a list of the searches you have done.

  • You can combine the searches of interest by typing their search numbers (preceded by a pound # sign) and the desired Boolean operators (AND, OR, or NOT, in upper case). For example, enter the following into the search box:

         #3 AND #4

    Note:  Your actual search numbers might be different from those above. Use the numbers of your actual searches that you want to combine. You can also retrieve the records that do not contain the term "immunodef*" by entering the search:  #3 NOT #4

The next example, under Complex Boolean Searches, shows a shortcut to doing the search. Using a command line, you can do all these steps with a single query.


Clipboard back to top

The Clipboard function is a temporary place where search results can be saved by users. Clipboards are database specific and can store up to 500 records. Items will be lost after one hour of inactivity.

The Clipboard is useful, for example, to collect selected records from several different searches into a single file.

For example, an Entrez OMIM search for "huntington" in All Fields retrieves 72 documents. If you would like to store records 1, 2, 3, 9, 16 from that search in your clipboard, activate the checkboxes beside those records and click on the "Add to Clipboard" button. Then, if you do another search, you can add selected records from that search into the clipboard as well.

3.  Complex Boolean Searches back to top

You can enter your search in command language, indicating field qualifiers in square brackets [].  The general syntax is:
     term[field] BOOLEAN term[field] BOOLEAN term[field]
For example:
      cancer[titl] AND 11[chrom] AND autosomal dominant[clin]
If no field qualifier is indicated for a term, All Fields will be assumed. The Search Fields section of this document provides a brief description of each field and its corresponding abbreviation.

It is not necessary to include a space between the search term and the field qualifier, although spaces must surround the Boolean operator.

The Boolean operators, AND, OR, NOT, should be written in upper case. Boolean operators are normally processed from left to right. If you want the operators to be processed out of order, use parentheses for nesting. In that case, Booleans within parentheses will be processed first, and then the remaining Booleans will be processed from left to right. For example:
  • diabetes AND  insipidus OR renal
    retrieves entries that contain the two terms "diabetes" and "insipidus," OR entries that contain the single term "renal"
  • diabetes AND  (insipidus OR  renal)
    retrieves entries that contain the term "diabetes," plus either of the terms "insipidus" OR "renal".

Entrez Help in Bookshelf contains additional detail on writing advanced search statements.

Example E:     Complex Boolean Searches

This example shows a shortcut for example D, above, which combined a search for records that contain the terms allergic OR allergies OR allergy and are on chromosomes 3, 7, or X, with a search for records that contain the word stem immunodef*

  • Type (or copy and paste) the following command into the search box at the top of the page:

    (allergic[All] OR allergies[All] OR allergy[All]) AND (3[chr] OR 7[chr] OR X[chr]) AND immunodef*[all]

  • Press the Go button

Search Fields back to top

Search Field Description Qualifier
All Fields Contains all terms from all searchable database fields in the database.  (search tips) [ALL]
Allelic Variant Describes a subset of disease-producing mutations.  (search tips) [AV] or
[VAR]
Chromosome The chromosome onto which a gene or disorder has been mapped, as reported in the OMIM Gene or Morbid Map.  (search tips) [CH] or
[CHR]
Clinical Synopsis Clinical features of a disorder and the mode of inheritance (e.g., autosomal dominant, autosomal recessive, x-linked), if known. [CS] or
[CLIN]
Contributor Contributor to an OMIM record. Names are in the format of lastname followed by one or more initials (with no periods), e.g., Smith AB   (search tips) [AU] or
[CTRB]
Creation Date The date on which an OMIM record was created, in the format YYYY/MM/DD.  (search tips) [CD] or
[CDAT]
EC/RN Number Number assigned by the Enzyme Commission or Chemical Abstract Service (CAS) to designate a particular enzyme or chemical, respectively.  (search tips) [EC] or
[ECNO]
Editor Editor of OMIM record. Names are in the format of lastname followed by one or more initials (with no periods), e.g., Smith AB   (search tips) [ED] or
[EDTR]
Filter Primarily used to retrieve subsets of records that contain crosslinks to other Entrez databases, and LinkOuts to external (non-Entrez) resources. (search tips)

There is a separate LinkOut site which provides more detail about that service. 		[FI] or
[FILT]
Gene Map Cytogenetic map location represented in the OMIM Gene Map.  (search tips) [GM] or
[MAP]
Gene Map Disorder Text words appearing in the Disorder column of the OMIM Gene Map. [DIS] or
[DI]
Gene Name The official gene symbol, and alternate gene symbols, associated with a record. Currently limited to gene symbols present on the OMIM Gene Map. All gene symbols represented in OMIM (mapped or unmapped) can be searched in the Title Word field, described below.  (search tips)

 [GN] or
[GENE]
MIM Number For information on the numbering system, see the OMIM FAQs.  (search tips) [ID] or
[MIM]
Modification date Date on which the record was last modified, in the format YYYY/MM/DD.  (search tips) [MD] or
[MDAT]
Modification History All dates on which an OMIM record was updated, in the format YYYY/MM/DD.  (search tips) [MDH] or
[HIST]
Properties An index containing various properties of OMIM records, identifying those which have attributes such as Allelic Variants, Clinical Synopsis, or Gene Map locus.

The most commonly used attributes are presented as check boxes on the Limits page.

To see a complete list of attributes, you can browse the index of the Properties field by use the Index option. 		[PR] or
[PROP]
Reference Contains author names and title words from the articles cited in an OMIM entry.
Names are in the format of lastname followed by one or more initials (with no periods), e.g., Smith AB   (search tips) 		[RE] or
[REF]
Text Word Contains terms from the main text-containing section of a record, which begins under the title of a record and ends above the Allelic Variants section (if present), or above the References section (if no Allelic Variants are described).  (search tips)
 [TXT] or
[WORD]
Title Word Words in title of an OMIM record. Includes words in the primary title, alternative titles, and included titles.  (general search tips; gene name search tips) [TI] or
[TITL]

Search Tips back to top

General Search Tips back to top

Truncation

You can use truncation to retrieve records that contain a word stem. For instance, Example D, above, searches for records that contain the word stem "immunodef*" by using an asterisk as a wildcard to represent zero or more characters. Entrez Help in Bookshelf contains additional detail on truncation.

Browsing the index of a search field

If a term might be present in various spellings, it is often helpful to browse the index of a search field to see the variations that exist. You can do that with the Index function, as shown in Example B, above, which finds the terms "allergic," "allergies," and "allergy" in the index, and selects all three terms for inclusion in a search.

Broadening a search

If your search retrieves too few documents, you can broaden your search:
  • truncate your search term, as described above, to search for records that contain the word stem and variations in the ending
  • browse the index, as described above, to find variations in spelling and alternative terms. If you select multiple terms from the index, they will be grouped together using a Boolean OR. Therefore, your search is broadened to retrieve records that contain any one of the terms.
  • search for synonyms or related terms (e.g., stomach OR intestinal OR gastrointestinal)
  • search for an abbreviation OR its full spelling (e.g., CF OR cystic fibrosis)

Narrowing a search

If your search retrieves too many documents, you can narrow your search:
  • limit your search to a specific field, using Limits (e.g., a search for "brain" in All Fields retrieves over 2000 documents. Limiting the search to the Title Field narrows the retrieval to less than 100. Because the search term appears in the title, rather than anywhere in the record, the brain is a more central topic in those records.
  • add one or more terms to your query to make it more specific. (e.g., if you still prefer to look for "brain" in All Fields, another way you can narrow the query is to search for another term of interest: brain AND receptor)

Searching by MIM Number back to top

When you search by MIM number, the first returned entry is an exact match, and the other entries refer to this number. If you want to retrieve only the exact match, use the "MIM Number" checkbox on the Limits page.

Searching for an Author's Name back to top

The Contributor, Editor, Reference fields contain author names in the format of lastname followed by one or more initials (with no periods), e.g., Smith AB

If no initials are entered in a search, the system will retrieve all authors with the specified last name.

To retrieve OMIM records that cite articles written by a particular author (or contain words from the titles of those articles) use the Reference field.

Searching by Date back to top

The date fields include creation date, modification date, modification history.

When searching any date field, enter the date in the format YYYY/MM/DD. Year is mandatory but month and date are optional.

Map Locations back to top

Search by Chromosome Number

To retrieve records from a specific chromosome(s), you can check the chromosomes of interest on the Limits page, or you can search the Chromosome field using the pop-up search field menu on the Preview/Index page. Note that the Chromosome field contains only chromosome numbers, not cytogenetic locations. To search for a specific cytogenetic location, use the Gene Map Field, discussed below.

Not all OMIM entries have been placed on the OMIM Gene Map. To see those that do, use the Limits function to retrieve "Only records with gene map locus." To retrieve records that do not yet have a map location, check "unknown" under "Chromosome" on the Limits page.

Search by Cytogenetic Location

To retrieve records that contain information on cytogenetic location, search the Gene Map Field. You can select that field from the pop-up menu on the Preview/Index page, or by using the [map] field specifier.

For example, a search for 17q11[map] will retrieve the OMIM records containing genes that have been mapped to that cytogenetic band. Only records that contain the exact search string will be retrieved. A search for 17q11[map] will not retrieve records with an OMIM Gene Map location of 17pter-q11.

You can browse the OMIM Gene Map directly. Enter gene symbol, chromosomal location, or disorder keyword to search for, e.g. "CYP1","5", "1pter", "Xq", or "alzheimer". Capitalize X and Y to search for those chromosomes. You can specify as few characters as you like. OMIM will go to the first location that starts with the characters you give. The "Find Next" button can then be used to find subsequent instances of the term.

The OMIM Gene Map displays 20 entries at a time. You can move up or down the map, also 20 entries at a time. The OMIM Gene Map is a single file that lists genes from 1pter through 22qter, followed by Xpter through Yqter. If a gene has been localized only to a chromosome number, rather than to a specific cytogenetic band, that entry is usually shown at the end of the genes on that chromosome.

Allelic Variants back to top

You can search the Allelic Variants field for phenotype (e.g., deafness) or affected amino acids (e.g., use the abbreviation "asn," without the quotes, for asparagine).

Allelic variants are given a 10 digit number: the 6-digit number of the parent locus followed by a decimal point and a unique 4-digit variant number.

Note that for most genes, only selected mutations are included as specific subentries. Criteria for inclusion include: the first mutation to be discovered, high population frequency, distinctive phenotype, historic significance, unusual mechanism of mutation, unusual pathogenetic mechanism, and distinctive inheritance (e.g., dominant with some mutations, recessive with other mutations in the same gene).

Most of the allelic variants represent disease-producing mutations. A few polymorphisms are included, many of which show a positive statistical correlation with particular common disorders.

EC/RN Numbers back to top

If you are searching All Fields, you must include periods in the number (e.g., 1.1.1.1).

If you search the EC/RN Number field directly, you can enter the number with either periods or spaces separating the digits (e.g., either  1.1.1.1  or  1 1 1 1  will work).

You can search the EC/RN Number field directly by using the [ECNO] field specifier after your search term (e.g., 1.1.1.1[ecno] ), or by selecting that field from the pop-up menu on the Preview/Index page.

Using Filters back to top

The Filter Field is primarily used to retrieve subsets of records that contain crosslinks to other Entrez databases, and LinkOuts to external (non-Entrez) resources.

For example, to retrieve OMIM records that have:

links to other Entrez databases:
  • enter omim gene[filter] to retrieve OMIM records that have links to the Entrez Gene database
  • enter omim protein[filter] to retrieve OMIM records that have links to the Entrez Proteins database
  • enter omim structure[filter] to retrieve OMIM records that have links to the Entrez Structures database
  • (use the Index function on the Preview/Index page to browse the index of the Filter field and view the other Entrez databases to which OMIM links)
external links from certain LinkOut providers (denoted by the prefix "loprov"), for example:
  • enter loprovhgmdb[filt] to retrieve the subset of records which contains links that have been provided by the Cardiff Human Gene Mutation Database (HGMD)
Note:  There is a separate LinkOut site that provides more details about that service.
To see a complete list of Filter options, you can browse the index of the Filter field by using the Index function on the Preview/Index page.

Gene Names back to top

You can search for gene symbols, or the full spelling of a gene, in the Title Word field. For example, you can search for either CFTR or cystic fibrosis transmembrane conductance regulator in the Title Word field to retrieve OMIM entry 602421.

The Gene Name field can also be used to search for gene symbols, but it does not include full spellings. Also, it currently contains only the subset of gene symbols that have been placed on the OMIM Gene Map, as well as the DSegment numbers (e.g., D10S105e) that are in the Symbol column of the OMIM Gene Map.

All symbols represented in OMIM (mapped or unmapped) can be searched in the Title Word field.

Retrieving subsets of OMIM records with certain attributes back to top

You can use the Limits page or the Properties Field to retrieve OMIM records that have certain attributes, such as Allelic Variants, Clinical Synopsis, or a Gene Map locus.

The most commonly used attributes are presented as check boxes on the Limits page.

To see a complete list of attributes, you can browse the index of the Properties field by using the Index option.

Using My NCBI to customize OMIM features, save searches, and more back to top

My NCBI, originally known as "Cubby", allows you to customize various features of Entrez. Many of these features are selected and saved separately for each Entrez database. For example, in OMIM as well as in other Entrez databases, you can:

  • customize the display for Entrez search results
    • save your preferences for the Filter tabs that you would like to see by default in the search results display
    • set your LinkOut preferences
  • save search strategies
    • receive automatic e-mail updates for saved searches

Additional information on how to use My NCBI is provided on the sign in page, help document, and in a tutorial.

Search Results back to top

Sort Order back to top

What logic is used to order the entries returned by a search?

There are 18 fields by which the database entries are indexed. They can be seen in the drop-down list in the center of the Preview/Index page.

Search results are sorted depending on where (in which field), and how many times the word or phrase appears in the entry. Each appearance of the word contributes a number of points to the score used for sorting. Some fields are valued more than others:

  • title word field is preferred most: 200 points per appearance
  • clinical synopsis and gene map disorder: 10 points per appearance
  • text word and allelic variants: 3 points per appearance
  • reference (Authors and titles of citations): 1 point per appearance

For simplicity, the described scheme does not include numerical terms like MIM numbers, genemap loci, etc. They also have their own fields and scores.

Additional factors that affect the score include field specifiers, Boolean operators, and the presence of a search term in a list of important phrases:

  • if you explicitly specify search fields with [brackets] or via 'Limits' page, only appearances in those fields would add to the score

  • in queries with the Boolean operators 'AND,' 'OR,' the scores are added for each term; scores for terms after 'NOT' are ignored

  • if a multiple-word search term (e.g., mental retardation) is present in a list of important phrases, the search system retrieves records that contain an exact match to the phrase. If the search term is not present in the phrase list, the system automatically inserts a Boolean AND between the terms (e.g., mental AND retardation) and looks for those individual terms anywhere in the record, in any order. This affects the number of documents retrieved by a search as well as their sort order.

    In the example used above, mental retardation actually does appear in the phrase list and retrieves 971 documents (as of June 2001). On the other hand, if you tried a Boolean search for mental AND retardation, the system would retrieve 984 documents and their sort order would be different.

    On the contrary, a query for alpha beta would be treated as alpha AND beta (which retrieves 1121 items), not as the phrase "alpha beta." This is because "alpha beta" is not listed as an important phrase for Entrez. (Note: You can force the search system to treat multiple words as a phrase, regardless of whether they appear in the list of important phrases, by enclosing them in quotes. For example, you can search for "alpha beta" to retrieve the 14 items containing that phrase.)

Display Formats back to top

The Display button on the search results page allows you to:
  • view one or more OMIM records in a variety of formats
  • view related records from OMIM, other Entrez databases
  • view external links that are associated with the OMIM entries of interest
Display formats can be selected from the pop-up menu and include the choices listed in the following table.

The DOPT Value in the first two sections of the table shows the text string that can be included in a URL when making WWW links to OMIM. The third section of the table, "Related Entrez Records," does not contain DOPT values. Instead, if you want to make WWW links to Nucleotide, Protein, Structure, or Genomes records that are associated with an OMIM record, you can use URL format #4 described under How To Make WWW Links to OMIM. How to make links to PubMed from OMIM is documented in #5.

Format Description DOPT Value
OMIM record formats
Titles MIM Number, Title, and Gene Map Locus (if available) DocSum
Detailed The text of the main OMIM entry, including MIM number, Title, and the various sections of descriptive information that are available for a gene. The main entry includes descriptions of Allelic Variants (disease-producing mutations), if available, but does not include Clinical Synopsis. If a Clinical Synopsis is available for a disorder, it is displayed separately from the main entry (see below).

Note: There are two ways to display a record in Detailed format, starting from a search results page:
  1. click on the MIM number of interest,  or
  2. check the box beside the entry of interest, select "Detailed" from the pop-up menu beside the "Display" button, and press "Display."
The first method will display a customized blue sidebar for an entry, showing its table of contents, as well as curated links that lead to additional information in other resources. The second method can be used to display one or more records, and will display the general OMIM sidebar. 		Detailed
Clinical Synopsis Clinical features of a disorder and the mode of inheritance (e.g., autosomal dominant, autosomal recessive, x-linked), if known. Synopsis
Allelic Variants Lists the titles of allelic variants that are described for a particular gene. Clicking on the title of a variant takes you to the text of the OMIM record, where you can use the sidebar to jump down to the allelic variants section and view the detailed descriptions. (More information on allelic variants is provided in a separate document.) Variants
ASN.1 Abstract Syntax Notation format, an International Standards Organization (ISO) data representation format designed for computer readability. (See the ASN.1 summary document for additional detail.) ASN.1
Links to Resources External to Entrez
LinkOut Related entries from other (non-Entrez) NCBI databases, and related resources maintained by external organizations.
There is a separate LinkOut site that provides more detail about that service. 		ExternalLink
Related Entrez Records (Subset)
The records retrieved by these display options correspond to the choices in the Links menu. Not all are documented specifically here.
Related Entries Other OMIM records that are cited in the text of an OMIM entry. no dopt value;
use URL format #4, below
PubMed (cited) Links References cited in an OMIM entry. omim_pubmed_cited;
use URL format #5, below
PubMed (calculated) Links Includes references calculated as being related via text to an OMIM entry (from the Light bulb links) and those cited in the OMIM entry . omim_pubmed_calculated;
use URL format #4, below
Protein Links Protein sequence records that are associated with the publications referenced in the OMIM record. no dopt value;
use URL format #4, below
Nucleotide Links Nucleotide sequence records that are cited in the publications referenced in the OMIM record. no dopt value;
use URL format #4, below
Structure Links Protein structures that are associated with the publications referenced in the OMIM record. no dopt value;
use URL format #4, below
Genome Links Human chromosomes that are mentioned in the OMIM record. (See additional detail below.) no dopt value;
use URL format #4, below

Links to Related Information back to top

Each OMIM record can be linked to a variety of related resources. There are two general categories of links:
  1. Links menu

    The Links menu appears above the title of a record, to the right of its MIM number. It lists various Entrez databases that have information related to OMIM record being displayed. The menu can include Related Entries (in OMIM), PubMed, Protein, Nucleotide, Structure, and Genome.

  2. Sidebar links

    Links also appear in the customized blue sidebar of an entry, beneath its table of contents. The customized blue sidebar is shown when an entry is viewed in Detailed format by clicking on its MIM number in the search results page.

    There are two subsets of curated links:  (1) Entrez Gene-associated links, such as the RefSeq, GenBank, Protein, and UniGene records associated with the Entrez Gene entry that corresponds to the OMIM record; and (2) LinkOut links to other resources, such as Locus-specific databases known to be related to the MIM record.

Additional information about each category of links is provided below.

Links Menu back to top

Related Entries - other OMIM records that are cited in the text of an OMIM entry.

PubMed (cited) - links to PubMed records for the references cited in an OMIM entry.
PubMed (calculated) - links to PubMed records for the references calculated as Light bulb links . This also includes the references cited in the OMIM entry, so the PubMed (cited) set is a subset of PubMed (calculated).

Protein - links to sequence records associated with the references cited in the OMIM record.

Nucleotide - links to sequence records associated with the references cited in the OMIM record.

Structure - links to protein structures associated with the references cited in the OMIM record.

Genome - links to human chromosomes that are mentioned in the OMIM record. The Genome link will of course lead to the chromosome onto which a gene has been mapped (if a location is known), but it might also lead to other chromosomes that are discussed in the entry.
For example, OMIM #219700 for cystic fibrosis (CF) mentions chromosome 7 as the map location for the CFTR gene, and chromosome 13 as a possible map location that was investigated and ultimately rejected in the history of the study of cystic fibrosis. Therefore, the Genome link retrieves both of the chromosomes.

The link for each chromosome leads to the Entrez Map Viewer and displays three of the approximately 20 human maps that are available in that viewer. On that map display, you can search for the location of the gene of interest (e.g., CFTR on chromosome 7) to see its position and to zoom into more detailed views of that region. You can also use the "Display Settings" option to add or remove maps, display rulers for the maps, etc. Please refer to the Map Viewer Help documentation for more information.
The Light bulb at the end of a paragraph retrieves up to 30 records in PubMed for which the text most closely matches the text of that paragraph. The records are found with the Entrez PubMed neighboring function, which uses a word weight algorithm to identify database records that contain similar terminology. The PubMed (calculated) links include all the light bulb links in an OMIM record and the cited ones. In contrast, the PubMed (cited) links (described above) lead to PubMed records for the references directly cited in an OMIM record.

Sidebar Links back to top

Entrez Gene-associated Links back to top

When viewing an individual OMIM record in Detailed format, a customized blue sidebar presents a table of contents for that record, followed by links to associated resources for that record, such as the OMIM Gene Map.

If the OMIM record discusses a gene, its customized blue sidebar also links to the associated Entrez Gene entry. Entrez Gene is a resource that provides a central hub of sequence and descriptive information for genetic loci in a wide range of organisms, including human.

OMIM records that discuss phenotypes are also associated with Entrez Gene entries. If a phenotype is associated with more than one gene, the OMIM record will link to all of the associated genes. For example, the OMIM entry for colorectal cancer (MIM #114500) links to the Entrez Gene records for all of the human genes that OMIM editors have found to be associated with colon cancer, based on their review of the literature.

When the customized blue sidebar includes Entrez Gene, it also shows one or more colored buttons for database records associated with the Entrez Gene entry(ies). These can include:

HUGO Human Gene Nomenclature
RefSeq (Reference Sequence) mRNA
GenBank
Protein
UniGene

The button leads to GenBank records associated with the corresponding Entrez Gene entry. Those were selected by the Entrez Gene curators as representative nucleotide sequences for the gene. In contrast, the "Nucleotide" link provided in the "Links" popup menu (upper right corner of the OMIM record) leads to sequence records cited by the articles referenced in the OMIM record. There is often overlap between the two groups.

Similarly, the button leads to protein records associated with the corresponding Entrez Gene entry. Those were also selected by the Entrez Gene curators as representative sequences for the gene; the records can be from RefSeq, GenPept or other protein databases. In contrast, the "Protein" link provided in the "Links" popup menu (upper right corner of the OMIM record) leads to sequence records cited by the articles referenced in the OMIM record. There is often overlap between the two groups.

LinkOut Links back to top

LinkOut leads to related entries in other (non-Entrez) NCBI databases, and to related resources maintained by external organizations. The LinkOut home page provides more detail about that service.

The LinkOut link is shown in all Display Formats except Titles. It appears in the Links menu to the right of the MIM number.

If an OMIM record is displayed in Detailed format, grey buttons in the sidebar provide quick access to the subset of LinkOut links, such as locus-specific mutation databases, the Human Gene Mutation Database (HGMD), and the Coriell Cell Repositories.

How To Print back to top

Before printing an OMIM record, it is helpful to display the entry without the blue sidebar and grey header bar.  To do that:
  • display the entry in Detailed format.
  • click on the MIM number in the Detailed view. That will open a new window showing the MIM entry without the blue sidebar.
  • from here, you can select the "File/Print" option from your browser's menu bar.
Please note that printing is a function of your WWW browser, rather than a function of the Entrez search tool. Therefore, if you experience problems with your browser's printing function, or you need assistance configuring your WWW browser and printer, please contact your local system administrator.

Sample Searches back to top

1.  What human genes are related to hypertension? Which of those genes are on chromosome 17? back to top

  • enter: hypertension in the search box
  • select Limits
  • check the box for chromosome 17
  • press Go
Note that some of the records retrieved will mention hypertension as part of the text of an entry, rather than in the title. That is because Entrez searches All Fields of a record by default. If you would like to limit retrieval only to records that contain the term hypertension in the Title Word field, check the "Search in Field" box for "Title" on the Limits page, in addition to checking the box for Chromosome 17.

2.  List the OMIM entries that describe genes on chromosome 10. back to top

This search can be done in one of three ways:
  1. Use the Limits page:

    • From the OMIM home page, select the Limits option under the search box.
    • check the box for chromosome 10.
    • Press Go.

    OR

  2. Enter the search as a command:

    • On the OMIM home page, enter the following in the search box:
      10[chr]
    • Press Go.

    OR

  3. Use the Preview/Index page:

    • From the OMIM home page, select the Preview/Index option under the search box.
    • Select Chromosome from the pop-up search field menu in the middle of the page.
    • Enter 10 in the search box beside the pop-up search field menu.
    • Press Preview.
    • Click on the number in the "Result" column to view a title listing of the records.

3.  List the OMIM entries that contain information about allelic variants. back to top

This search can be done in one of three ways:
  1. Use the Limits page:

    • From the OMIM home page, select the Limits option under the search box.
    • check the box for "Only Records With" Allelic Variants.
    • Press Go.

    OR

  2. Use the Preview/Index page:

    • From the OMIM home page, select the Preview/Index option under the search box.
    • Select Properties from the pop-up search field menu in the middle of the page.
    • Enter allelic variants in the search box beside the pop-up search field menu.
    • Press Preview.
    • Click on the number in the "Result" column to view a title listing of the records.

    OR

  3. Enter the search as a command:

    • On the OMIM home page, enter the following in the search box:
      allelic variants[prop]
    • Press Go.

4.  Retrieve the OMIM record for the cystic fibrosis transmembrane conductance regulator (CFTR), and link to related protein sequence records in Entrez. back to top

  • enter CFTR in the search box
    (or enter the full spelling, whichever you prefer)
  • Click on the MIM number 602421 to display the record
  • Select Protein from the Links pop-up menu in the upper right corner of the record (or select Protein Links from the Display pop-up menu above the upper left of the record)

Note that Entrez will link only to protein sequence records associated with the publications cited in the OMIM record. This is also true for links to nucleotide sequences and protein structures. Once you have retrieved the associated sequence or structure records, you can then follow the 'related sequences' or 'related structures' links in those databases to browse further.

Protein records can also be retrieved by pressing the button in the blue sidebar. See the section on Entrez Gene-Associated Links for more information about the similarities and differences between the protein records retrieved by that button compared to the Links menu of an OMIM record.

5.  Find the OMIM record for the p53 tumor protein, and linkout to related information in Entrez Gene and the p53 Mutation Database. back to top

  • Enter p53 in the search box
  • Press Go
  • Click on the MIM number 191170 to display the record
  • Follow the Entrez Gene link in the blue sidebar to display the corresponding gene record
  • Follow the LinkOut link for p53 in the blue sidebar to access the mutation database for that gene
  • To view the additional LinkOuts to related resources, select LinkOut from the Display pop-up menu near the top of the OMIM record
There is a separate LinkOut site that provides more detail about that service.

How To Make WWW Links to OMIM back to top

From Your Site to OMIM back to top

The tips and examples below are for linking to the OMIM database in Entrez. Additional information on making WWW links to various Entrez databases is provided in Linking to PubMed and other Entrez databases.

URL Format back to top

To create a link from your WWW document that:

1)  displays a specific OMIM record:

http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=MIMNumber

The URL above displays the OMIM record in the default detailed format. A command (cmd) option can be added to the end of the URL to specify alternative display formats, such as plain (plain text, not html) or ASN.1 format:

http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=MIMNumber&cmd=plain
http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=MIMNumber&cmd=asn.1

2)  retrieves two or more specific OMIM records:

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&
db=OMIM&dopt=DocSum&list_uids=MIMNumber,MIMNumber

3)  searches for a given term or terms:

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&
db=omim&term=Term.&doptcmdl=Format

Term can include multiple words and Boolean operators, as shown in example #3, below. As noted in the section on Complex Boolean Searches, Boolean operators must be written in upper case and are processed from left to right, unless parentheses are used for nesting.

4)  links to associated records in other Entrez databases (except PubMed)

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Link&
db=TargetDatabase&dbFrom=OMIM&from_uid=MIMNumber&from_uid=MIMNumber
TargetDatabase can include:   Gene, Nucleotide, Protein, Genome, UniSTS or Structure. As noted in the third section of the Display Formats table, links to Nucleotide, Protein and Genome database exist only when they contain records directly associated with the publications cited in the OMIM record. For example, if an OMIM record cites a specific journal article, Entrez will provide a link to the PubMed (cited) record for the article. If that article reports the accession number of a nucleotide sequence record, Entrez will also create a link from the OMIM (and PubMed) record to the GenBank sequence record.

5)  links to associated records in PubMed

cited:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Display&
db=omim&dopt=omim_pubmed_cited&from_uid=MIMNumber&from_uid=MIMNumber
calculated:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Display&
db=omim&dopt=omim_pubmed_calculated&from_uid=MIMNumber&from_uid=MIMNumber
In the examples below, note that spaces have been replaced with plus (+) characters, as HTML convention requires. The OMIM database can be written in upper or lower case.  The sample URLs below contain line breaks for readability, but should of course be written on a single line.

Examples back to top

1)  Display the entry with MIM number 602421.

http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=602421

The URL above displays the OMIM record in the default detailed format. A command (cmd) option can be added to the end of the URL to specify alternative display formats, such as plain (plain text, not html) or ASN.1 format, below:

http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=602421&cmd=plain
http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=602421&cmd=asn.1
2)  Retrieve the two entries with MIM numbers 250250 and 100070.

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&
db=OMIM&dopt=DocSum&list_uids=250250,100070
3)  Search for entries containing given terms:

a)  Search for entries containing the term "tourette" in any field.

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&
db=omim&term=tourette

b)  Search for entries containing the terms "estrogen" and "receptor" in the title only.

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&
db=omim&term=estrogen[title]+receptor[title]

c)  Search for entries containing the terms "hunter" or "hurler" in any field, but only those that have been modified in the past 30 days

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&
db=omim&term=(hunter+OR+hurler)&orig_db=omim&filters=on&pmfilter_MDatLimit=30+Days

4)  Retrieve the Gene links associated with MIM numbers 250250 and 100070.

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Link&db=gene&dbFrom=omim&from_uid=250250&from_uid=100070
5)  Retrieve the PubMed links associated with MIM numbers 250250 and 100070.

From OMIM to Your Site back to top

LinkOut back to top

LinkOut is a registry service that allows you to create links from records in Entrez databases, including OMIM, to resources on your web site. The goal is to facilitate access to relevant online resources beyond the Entrez system in order to extend, clarify, or supplement information found in the Entrez databases.

Participation in LinkOut requires the submission of files that include information such as your URL, resource name, and brief description of your web site. Links can be made to specific Entrez records by providing a list of identifiers for those records, or to a set of Entrez records that are found by a Boolean query. Further information on how to participate in LinkOut, including specifications for the required files, is accessible from the LinkOut page.

Once the links are made, Entrez users can see the links to your site by following the LinkOut option for an Entrez record of interest. The users can also select which external links are visible in their searches, through the My NCBI service (sign in, help document, tutorial).

Questions or Comments?
Write to the NCBI Service Desk