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.
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Overview |
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Scope |
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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 |
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While preserving the functions of the earlier OMIM search system,
the Entrez system provides the following new functions:
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Sample Questions |
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Examples of questions that can be answered with OMIM in Entrez
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Three Levels of Search Complexity |
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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.
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1. Basic Search |
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The default OMIM search is set to the Basic mode. Simply enter one or more terms in the text box and click on 'go.' |
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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 |
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Advanced options provide more control over your search by allowing you to:
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Preview/Index |
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The Preview/Index page allows you to do several things:
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Limits |
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The Limits function allows you to limit the search to:
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Search Fields on the Limits page include the following:
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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:
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MIM Number Prefixes include the following. See OMIM FAQs for additional information about each symbol. | ||||||||||||
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Recently added or updated records can be retrieved by limiting to those created or modified in the past:
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History |
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The History provides a record of the searches performed during a
search session and allow you to:
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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. |
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Clipboard |
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3. Complex Boolean Searches |
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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:
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Search Fields |
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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 |
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General Search Tips |
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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:
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Narrowing a search
If your search retrieves too many documents, you can narrow your search:
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Searching by MIM Number |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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:
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 |
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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 |
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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 |
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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:
Additional information on how to use My NCBI is provided on the sign in page, help document, and in a tutorial. |
Search Results |
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Sort Order |
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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:
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:
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Display Formats |
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The Display button on the search results page allows you to:
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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:
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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 |
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Each OMIM record can be linked to a variety of related resources. There are two general categories of links:
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Links Menu |
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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. |
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 |
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Entrez Gene-associated Links |
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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 |
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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 |
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Before printing an OMIM record, it is helpful to display the entry without the blue sidebar and grey header bar. To do that:
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Sample Searches |
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1. What human genes are related to hypertension? Which of those genes are on chromosome 17? |
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2. List the OMIM entries that describe genes on chromosome 10. |
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This search can be done in one of three ways:
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3. List the OMIM entries that contain information about allelic variants. |
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This search can be done in one of three ways:
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4. Retrieve the OMIM record for the cystic fibrosis transmembrane conductance regulator (CFTR), and link to related protein sequence records in Entrez. |
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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. |
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How To Make WWW Links to OMIM |
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From Your Site to OMIM |
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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 |
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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 2) retrieves two or more specific OMIM records: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve& 3) searches for a given term or terms: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&
4) links to associated records in other Entrez databases (except PubMed) http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Link& 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: calculated: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 |
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1) Display the entry with MIM number 602421.
http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=6024212) Retrieve the two entries with MIM numbers 250250 and 100070. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&3) Search for entries containing given terms: a) Search for entries containing the term "tourette" in any field.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=1000705) Retrieve the PubMed links associated with MIM numbers 250250 and 100070. |
From OMIM to Your Site |
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LinkOut |
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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 |