Searching Online Mendelian Inheritance in Man (OMIM) Over the Internet Protocol
OMIM database is a catalog of human genes and genetic disorders authored and edited by Dr. Victor A. McKusick and his colleagues at Johns Hopkins and elsewhere, and developed for the World Wide Web by NCBI, the National Center for Biotechnology Information. The database contains textual information and references. It also contains copious links to MEDLINE and sequence records in the Entrez system, and links to additional related resources at NCBI and elsewhere.
OMIM may be accessed directly from the NCBI home page (http://www.ncbi.nlm.nih.gov) by clicking on the OMIM link in the blue bar at the top of the page.
I will describe to you on how to access the Web site and enter search terms to retrieve OMIM records. I then briefly review the format of an OMIM record and guide the user through the numerous hyperlinks that are available.
**Note that "synuclein" will be the term used as an example throughout this protocol.**
Performing an OMIM search
1. Open the browser and go to the NCBI home page (http://www.ncbi.nlm.nih.gov).
2. Change the search pull-down from GenBank to OMIM. Enter the search term or terms into the text box, which may be coupled by Boolean operators such as "AND," "OR," or "NOT." Each search term can, in turn, be qualified so that it is compared only to particular parts of the OMIM record. Once you have entered the search terms, submit the search by pressing the Go button, or by hitting Enter on the keyboard.
3. Select the OMIM entry of interest by clicking on the corresponding OMIM accession number. For this example, access the detailed OMIM entry for alpha-synuclein by clicking on the hyperlinked accession number (*163890).
4. Select how to view the OMIM entry. The pull-down menu beside the Display button will allow the user to change between views; once the desired view is selected from the pull-down menu, the user should then click Display. The default display is Detailed. Each of the options, but not all options will be available for each OMIM entry. The user will immediately notice that there is some redundancy built into the OMIM interface, in that certain pieces of information can be found in more than one way. A complete description of the detailed OMIM record can be found.
5. From the detailed view of the entry, click on the Gene map locus 4q21 link that appears beneath the alternate titles and symbols near the top of the OMIM record (or on the hyperlink marked Gene Map in the navigation bar on the left-hand side of the page). The OMIM Gene Map presents the cytogenetic locations of the genes described in OMIM having a published map location. The list begins at the p telomere of chromosome 1 and continues through to the q telomere of chromosome 22. This is then followed by the genes found on the X and Y chromosomes. The header at the top of the table gives the details of the gene range displayed in the chart, as well as the cytogenetic range displayed in the chart. For display purposes, the genes are shown in groups of 20. When the gene shares the same cytogenetic location as another gene, they are sorted by primary symbol. When there is only a chromosomal location and no cytogenetic band location, the gene is listed at the end of the chromosome. In this case, the table begins with the SNCA gene, and its cytogenetic location is listed as 4q21. The table will always begin with the gene from which the OMIM gene map was accessed.
6. From the OMIM Gene Map page, one can link to the OMIM Morbid map by clicking on the link at the top of the page. The basic feature that differentiates the Morbid Map from the Gene Map is that the Morbid Map presents all listed genes in alphabetical rather than chromosomal order. OMIM hyperlinks available to the left of an OMIM record
7. Return to the page showing the Display view for the synuclein entry by clicking the back button twice from the Morbid Map page. In the left-hand frame, there are multiple hyperlinks that allow the user to easily navigate through the detailed OMIM record. Specifically, the links take users to the Description, Cloning, Gene Function, Mapping, Molecular Genetics, Animal Model, Allelic Variants, References, Contributors, Creation Date, and Edit History sections of the record. A View List link just beneath the Allelic Variants link takes users to a list of allelic variants, rather than a detailed description of the variants.
8. The Gene map link offers users another route to the OMIM gene map
9. Beneath the Gene map link is a hyperlink labeled LocusLink. Clicking on this link brings the user to the relevant LocusLink page on the NCBI Web site. LocusLink provides a single query interface to various types of information regarding a given genetic locus, such as phenotypes, map locations, and homologies to other genes. The LocusLink search space currently includes information from humans, mice, rats, fruit flies, and zebrafish.
10. Return to the page showing the Display view for the synuclein entry.
11. At the bottom of the left-hand frame, there is a hyperlink labeled LinkOut. Clicking on this link brings the user to the LinkOut resources . LinkOut is an NCBI utility that is designed to provide users direct connections to a wide variety of relevant external online resources, including full-text publications, biological databases, consumer health information, research tools, and more. The resulting links are grouped into three categories: medical, molecular biology databases, and "other."
a. Medical databases:
NCBI's Genes and Diseases. NCBI's Genes and Diseases database is an extremely useful database for physicians, researchers and scientists alike. This database is part of an ongoing effort to map and characterize diseases caused by the mutation in one gene or a result of mutations in several genes such as asthma and diabetes. The Genes and Disease site linked to from the SNCA entry in OMIM is made up of two sections. The first section of note is located in the large middle panel containing an overview of the disease. The second section, on the left, contains additional links to information on SNCA and Parkinson's Disease. The most relevant source of information from a clinical standpoint is found in the Information subsection, towards the bottom of the left-hand sidebar. This section includes links to general information for clinicians, physicians and patients. It also includes the Medline Plus feature which when selected provides a link to the Clinical Trials page.
b. Molecular biology databases:
Genome Database. The Genome Database (GDB) is the official central repository for genomic mapping data resulting from the Human Genome Initiative. The Human Genome Initiative is a worldwide research effort to analyze the structure of human DNA and determine the location and sequence of the human genes. In support of this project, GDB stores and curates data generated worldwide by those researchers engaged in the mapping effort of the Human Genome Project (HGP). The Synuclein link to GDB displays all the information stored from GDB on SNCA (not shown). The information displayed comprises alternate gene symbols, the cytogenetic location of the gene and the resource used to map it, nucleic acid links for the SNCA gene, protein links for the SNCA gene, related amplimers and clones, polymorphisms, clones, phenotype and homology links, and additional external links.
Cardiff Human Gene Mutation Database. The Cardiff Human Gene Mutation Database (HGMD) site represents an attempt to collate known published gene lesions responsible for human inherited diseases into a comprehensive reference source. The Cardiff Human Gene Mutation Database provides information of practical diagnostic importance to researchers and diagnosticians in human molecular genetics, physicians interested in a particular inherited condition in a given patient or family, and genetic counselors. For SNCA, the database documents two nonsense mutations, which contribute to Parkinson disease. The Web site also offers hyperlinks to mutation maps, the cDNA native sequence, and the SNCA entries in the genome database (GDB), GenAtlas, and OMIM.
c. Other databases:
Jackson Laboratory Mouse Genome Database. The Jackson Laboratory Mouse Genome Database includes data on gene characterization and nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data. The Mouse Genome Database provides chromosomal location, alternate names, polymorphism information, and mammalian homologies of the gene in the OMIM database.