In addition to the FAQs below, an OMIM Help document provides tips for searching OMIM in Entrez, along with sample searches.

General Information about OMIM

1. What is OMIM?
2. What is the difference between OMIM and the book, Mendelian Inheritance in Man?
3. What does "Mendelian inheritance" mean?
4. What numbering system is used in the OMIM database?
5. Symbols: What do the symbols preceding a MIM number represent?
   (asterisk (*), number (#), plus (+), percent (%), caret (^))
6. What is the OMIM Gene Map?
7. What is the OMIM Morbid Map?
8. Symbols: What do brackets [ ], braces { }, a question mark (?), and the numbers (1)(2)(3) mean in the Disorder column of the Gene Map and Morbid Map?
9. Can I suggest the addition of a reference to an OMIM record, or make other comments?
10. How should I cite OMIM?

1. How many records does OMIM currently contain?
2. Is there a list of all the genetic diseases represented in the OMIM database?
3. How many inherited diseases have a known sequence associated with them?
4. How many inherited diseases have a known phenotype but no corresponding sequence data?
5. Does OMIM contain information on chromosomal aberrations?
6. How many human diseases are caused by genetic mutations or chromosomal aberrations?
7. What other NCBI resources contain information related to the human genome?

1. How can I improve my search strategy?
2. Sort order of search results: what logic is used to order the entries returned by a search?
3. Nucleotide and protein links: why do the nucleotide or protein links at the top of an OMIM record sometimes lead to unrelated genes?
4. What is the best way to print an OMIM entry?
5. What search tips can I use if I don't know the exact name or spelling of a syndrome?
6. Is it possible to search the OMIM Gene Map by cytogenetic map location?
7. Can I save my OMIM search strategies and receive automatic e-mail updates of search results?

1. Somone I know has been diagnosed with a genetic disease. Where can I get information on the disease?
2. Where can I go to get genetic testing?
3. I am interested in a gene or disease. Can NCBI help me with reference and research questions?

1. Can I download OMIM?
2. How can I uncompress the omim.txt.Z file?
3. Database structure:  is OMIM maintained in a relational database?

1. How is OMIM funded?

An asterisk (*) before an entry number indicates a gene of known sequence.

A number symbol (#) before an entry number indicates that it is a descriptive entry, usually of a phenotype, and does not represent a unique locus. The reason for the use of the #-sign is given in the first paragraph of the entry. Discussion of any gene(s) related to the phenotype resides in another entry(ies) as described in the first paragraph.

A plus sign (+) before an entry number indicates that the entry contains the description of a gene of known sequence and a phenotype.

A percent sign (%) before an entry number indicates that the entry describes a confirmed mendelian phenotype or phenotypic locus for which the underlying molecular basis is not known.

No symbol before an entry number generally indicates a description of a phenotype for which the mendelian basis, although suspected, has not been clearly established or that the separateness of this phenotype from that in another entry is unclear.

A caret symbol (^) before an entry number means the entry no longer exists because it was removed from the database or moved to another entry as indicated.

See also the description of symbols used in the disorder column of the OMIM Gene Map and Morbid Map.

The OMIM Gene Map presents the cytogenetic locations of genes that are described in OMIM. It is a single file, presented in tabular format, listing genes from the p telomere of chromosome 1 through the q telomere of chromosome 22, followed by genes on the X and Y chromosomes (also in ptel to qtel order). Not all OMIM entries are represented in the Gene Map, but only those for which a cytogenetic location has been published in the cited references. The OMIM Gene Map is available on the web and as an FTP'able file.

The web version of the OMIM Gene Map can be searched by gene symbol (e.g., "SOD1"), chromosomal location (e.g., "5", "1pter", "Xq" ), or by disorder keyword (e.g., "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.

The FTP file is available at ftp://ftp.ncbi.nih.gov/repository/OMIM/genemap. An explanation of the symbols and columns in that file is given in the genemap.key. Much of that information also applies to the web display of the OMIM Gene Map. The symbols used in the disorder column of the map are also explained below. (Additional information about FTP files is provided under "Can I download OMIM?")

The OMIM Gene Map data have been included in the Genes_Cytogenetic map of the Entrez Map Viewer, which presents a graphical display of various cytogenetic, genetic linkage, sequence, radiation hybrid, and other maps. When viewing a chromosome, use the "Display Settings" option to select the Genes_Cytogenetic map. The Map Viewer Help document provides additional information about how to use the viewer.

The OMIM Morbid Map is an alphabetical list of diseases described in OMIM and their corresponding cytogenetic locations. The OMIM Morbid Map is available on the web and as an FTP'able file.

The web version of the OMIM Morbid Map can be searched by gene symbol (e.g., "SOD1"), chromosomal location (e.g., "1pter", "Xq" ), or by disorder keyword (e.g., "alzheimer"). You must capitalize "X" and "Y" to search for those chromosomes. You can also search for a number, such as "5". However, that number might appear in a column other than Location. The search system will take you to the first instance of your search term in the file, and will display the 20 entries in that region of the file. You can then scroll up and down the file 20 entries at a time. (As is true for the OMIM Gene Map, the Morbid Map is a single file.) Or, you can use the "Find Next" button to jump to the next instance of the search term.

The FTP file is available at ftp://ftp.ncbi.nih.gov/repository/OMIM/morbidmap. The symbols used in the disorder column of the map are explained below. (Additional information about FTP files is provided under "Can I download OMIM?")

A Morbid Map is displayed graphically in the Entrez Map Viewer, showing the disease genes in positional order. When viewing a chromosome, use the "Display Settings" option to select the Morbid map. The Map Viewer Help document provides additional information about how to use the viewer.

Certain "nondiseases," mainly genetic variations that lead to apparently abnormal laboratory test values (e.g., dysalbuminemic euthyroidal hyperthyroxinemia), are included in brackets, "[ ]".

Braces, "{ }", indicate examples of mutations that lead to universal susceptibility to a specific infection (diphtheria, polio), to frequent resistance to a specific infection (vivax malaria), protection from nicotine addiction, as well as some other susceptibilities.

A question mark, "?", before the disease name is the equivalent of L (in limbo) for mapping status.

The number in parentheses after the name of each disorder indicates whether the mutation was positioned by mapping the wildtype gene (1), by mapping the disease phenotype itself (2), or by both approaches (3). The last "3", includes mapping of the wildtype gene combined with demonstration of a mutation in that gene in association with the disorder.

The genemap.key file on the FTP site contains additional information about the OMIM Gene Map. Although it was written to describe the contents of the genemap FTP file (ftp://ftp.ncbi.nih.gov/repository/OMIM/genemap), much of that information also applies to the web display of the OMIM Gene Map.

If you have comments about an OMIM record, please send them to the NCBI Service Desk and your message will be forwarded to the OMIM editorial staff for consideration.

If you are suggesting the addition of a reference to an OMIM record, please include the MIM number of the entry and the complete bibliographic citation of the reference (author(s), article title, journal name, volume, page numbers, and year). Please note that the editors of OMIM attempt to include the essential references for a particular topic, not necessarily everything that has been published. Additionally, a neighboring feature has been applied to OMIM that links additional, relevant articles from PubMed to each entry, thereby ensuring that all relevant articles are easily retrievable.

To cite MIM or OMIM in a journal article or on-line publication, please use the following conventions:

Citing the printed version of MIM:

McKusick, V.A.: Mendelian Inheritance in Man. A Catalog of Human Genes and Genetic Disorders. Baltimore: Johns Hopkins University Press, 1998 (12th edition).

Citing OMIM as a whole:

Online Mendelian Inheritance in Man, OMIM (TM). McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University (Baltimore, MD) and National Center for Biotechnology Information, National Library of Medicine (Bethesda, MD), {date of download}. World Wide Web URL: http://www.ncbi.nlm.nih.gov/omim/

Citing a specific entry in OMIM:

(Note! Many times it is most appropriate to cite the actual journal article for the data of interest.)

Online Mendelian Inheritance in Man, OMIM (TM). Johns Hopkins University, Baltimore, MD. MIM Number: {MIM number}: {Date last edited}: . World Wide Web URL: http://www.ncbi.nlm.nih.gov/omim/

Citing an OMIM entry for personal communication:

{Authors};{Date}. Personal Communication in OMIM (TM) Online Mendelian Inheritance in Man. MIM Number: {MIM number} Johns Hopkins University, Baltimore, MD. World Wide Web URL: http://www.ncbi.nlm.nih.gov/omim/

No, there is no comprehensive list of all the genetic diseases in OMIM. You can search OMIM by disease name to see if a disease of interest is in the database. Many diseases are known by several synonyms. OMIM will automatically map search terms to cover multiple ways of referring to the same anomaly. The OMIM Help document provides additional information about searching.

In lieu of a comprehensive list, there are two search strategies you can use in OMIM to retrieve subsets of records that (1) are associated with a phenotype, or (2) have a clinical synopsis:

1. To retrieve OMIM records associated with a phenotype:
• use the Limits page to retrieve MIM records whose numbers have prefixes of +, #, and %, as well as those that have no prefix (none). (The meaning of each prefix is described in the FAQ on symbols.)
• simply check the box for each of those prefixes on the Limits page and press the Go button. It is not necessary to enter a query in the text box
• the records retrieved will be those that have a phenotype. Many, but not necessarily all, of the phenotypes are diseases.
• Note: the prefixes are also listed in the Properties field, which can be browsed using the Index function on the Preview/Index page.


2. To retrieve OMIM records that have a clinical synopsis:
• on the Limits page, under the Only Records with header, simply check the box for Clinical Synopsis under the . (Deactivate the check boxes for the prefixes noted above if your only search criterion is the presence of a clinical synopsis.) Then press the Go button. It is not necessary to enter a query in the text box.
• note that a clinical synopsis is not necessarily available for every disease-related OMIM record. However, it is available for many of them, so it is a way of retrieving a large number of disease-related OMIM records in a single step.

If desired, use the History page to combine the retrieval from the two sample searches above in order to retrieve the subset of OMIM records that have both a phenotype and a clinical synopsis.

The OMIM database does not track this number specifically. In addition, the number of cloned (i.e., sequenced) genes for human genetic disorders depends on how "disorder" and "clone" are defined (e.g., full length, partial).

However, there are two subsets of OMIM records that are related to the question and might be of interest:

1. records that describe GENES of known sequence and phenotype;
   these have MIM numbers that begin with the plus sign (+) prefix.
2. records that describe PHENOTYPES that have a known molecular basis;
   these have MIM numbers that begin with the pound sign (#) prefix.

To see the number of records whose MIM number has either prefix, you can (a) see the OMIM statistics page, or (b) activate the check box for the prefix of interest on the OMIM Limits page and press the Go button. Both approaches display the number of records in each subset and enable you to retrieve the records.

The OMIM database does not track this number specifically. However, OMIM uses the percent sign (%) prefix for records that describe a "mendelian phenotype or locus, molecular basis unknown". To see the number of records whose MIM number has that prefix, you can either (a) see the OMIM statistics page, or (b) activate the check box for that prefix on the OMIM Limits page and press the Go button. Both approaches display the number of records in the subset and enable you to retrieve the records.

Entrez Gene also enables you to retrieve human genes for which (a) we have no sequence data, or (b) for which only a phenotype is known. To do this, follow the search strategies below. However, there is no way to currently limit Entrez Gene searches to only disease genes.

• to retrieve human genes for which we do not yet have sequence data:

  human[orgn] NOT gene_nucleotide[filter]

  That will retrieve database records for human genes that do not have links to nucleotide sequence records. Specifically, the search retrieves all human gene records and then uses the Filter field (discussed in the OMIM help document) to exclude the subset of Gene records that have links to nucleotide sequences.
  
  
• to retrieve human genes for which only a phenotype is known:

  human[orgn] AND phenotype_only[Properties]

  That will retrieve a similar number of records to an OMIM search that uses the Limits page to retrieve records whose MIM numbers start with the percent (%) prefix. While there is likely to be a great deal of overlap between the lists of genes retrieved by both approaches, there might also be some differences.
  
  
• to retrieve human genes for which only a phenotype is known and which have links to OMIM records:

  human[orgn] AND phenotype_only[Properties] AND gene_omim[filter]

No, although there are a few exceptions.

OMIM contains records about human genes and genetic disorders that are inherited in a Mendelian manner. Genetic conditions that are due to a chromosomal aberration, such as monosomy or trisomy, generally do not have entries in OMIM. There are a couple of chromosome aberrations (Trisomy 21 and cri-du-chat) which have been given an entry in OMIM for historic or other reasons; however, monosomy or trisomy of any chromosome would not normally be included in the database.

For information on chromosomal aberrations, see Schinzel, Albert: Catalog of Unbalanced Chromosomal Aberrations in Man. de Gruyter, 1984.

In addition, a genome-wide map of chromosomal breakpoints in human cancer, by Drs. Mitelman, Mertens, and Johansson is available on the NCBI web site. It is a hypertext version of a recent special issue of Nature Genetics, Vol. 15(Spec. No.):417-74 (April 1997). The Mitelman Breakpoint Map is also displayed graphically in the Entrez Map Viewer. When viewing a chromosome, use the "Display Settings" option to select the Mitelman Breakpoint Map. The Map Viewer Help document provides additional information about how to use the viewer.

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 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.

Disease names often are known by many synonyms. OMIM will automatically map search terms to cover multiples ways of referring to the same anomaly. For example, a search for "Diabetes Mellitus Type I" in the Title field will retrieve the same record as a search for "Juvenile-Onset Diabetes."

If you are unsure of a gene or disease name, you can browse an alphabetical list of gene symbols and disease names that appear in the Title field of OMIM records. The OMIM help document provides additional information on using the Index function.

If you want to retrieve records that contain a particular word stem, but have various endings, you can truncate the term and use an asterisk (*) as a wild card. The OMIM help document provides additional information on truncation.

You might also find it helpful to consult a resource such as Jablonski's Dictionary of Syndromes & Eponymic Diseases, 2nd ed., by Stanley Jablonski (Malabar, FL.: Krieger Pub. Co., 1991).

Yes. The OMIM Gene Map can be searched by gene symbol (e.g., "SOD1"), chromosomal location (e.g., "5", "1pter", "Xq" ), or by disorder keyword (e.g., "alzheimer"). You must capitalize "X" and "Y" to search for those chromosomes.

Note that the OMIM Gene Map is a single file. It is presented in tabular format and lists genes from the p telomere of chromosome 1 through the q telomere of chromosome 22, followed by genes on the X and Y chromosomes (also in ptel to qtel order). The search system will take you to the first instance of your search term in the file, and will display the 20 entries in that region of the file. You can then scroll up and down the file 20 entries at a time.

The OMIM Gene Map data have been included in the Genes_Cytogenetic map of the Entrez Map Viewer, which presents a graphical display of various cytogenetic, genetic linkage, sequence, radiation hybrid, and other maps. When viewing a chromosome, use the "Display Settings" option to select the Genes_Cytogenetic map. The Map Viewer Help document provides additional information about how to use the viewer.

Yes, you can use the "My NCBI" tool in Entrez to do both. Originally known as "Cubby", My NCBI 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.

You can search various NCBI resources for information. Some resources you might find helpful are OMIM, PubMed, Entrez Gene, and Genes and Disease. The NCBI Resource Guide provides a brief description of each one, as well as a number of other human genome resources.

However, please note that NCBI cannot respond to questions regarding personal medical or genetic problems. In addition to contacting your personal physician or hospital medical genetics clinic, we suggest that you contact the following organizations:

Genetic Alliance
35 Wisconsin Circle, Suite 440
Chevy Chase, MD 20815-7015
Tel: 1-800-336-GENE or 301-652-5553
Fax: 301-654-0170
E-mail: info@geneticalliance.org
http://www.geneticalliance.org

National Organization for Rare Disorders (NORD)
PO Box 1968
Danbury, CT 06813-1968
Tel: 1-800-999-6673 or 203-744-0100
E-Mail: orphan@rarediseases.org
http://www.rarediseases.org

Additionally, the National Library of Medicine's (NLM) Genetics Home Reference provides consumer information about genetic conditions and the genes or chromosomes responsible for those conditions. Another consumer health website at NLM, MEDLINEplus, provides carefully selected health information resources geared toward the general public. While MEDLINEplus covers a broad range of health topics, it does contain information on some genetic disorders.

NCBI cannot respond to questions regarding personal medical or genetic problems. We urge you to contact your personal physician or a medical genetics clinic for questions about genetic testing. You might also find the GeneTests^TM web site helpful. It is a directory of DNA diagnostic laboratories, containing information on DNA diagnostic and research tests and the laboratories that run them. The database was developed and is maintained by Roberta A. Pagon, MD, at the Children's Hospital and Medical Center in Seattle, Washington. Please see the GeneTests^TM web site for more information and to register for its use.

When appropriate, OMIM records link directly to the GeneTests web site. The link is shown for appropriate records on an OMIM search results page and in the upper right corner of individual OMIM records. (For example, see the GeneTests link in OMIM #114500, for colorectal cancer.)

NCBI does not provide a reference service. However, anyone is welcome to use our databases to do his or her own research on a topic. A number of resources that you might find helpful are listed under the question about obtaining information on genetic diseases.

• The complete text of OMIM, compressed (omim.txt.Z)
• The OMIM Gene Map (genemap)
• The OMIM Gene Map key (genemap.key) - explains the symbols and columns in the genemap file
• The OMIM Morbid Map (morbidmap)
• The OMIM Gene Table - available in the /Omim/Index/ directory of the NCBI Web site, rather than on the ftp site; alphabetical list of gene symbols and their corresponding MIM numbers