OMIM®: New Home, Improved Website

KaryotypeOMIM.org is the new, official home of OMIM®, Online Mendelian Inheritance in Man®. For those unfamiliar with OMIM, it provides full-text, referenced overviews on all known mendelian disorders and over 12,000 genes. The database is updated daily and is freely available on the Web.

Health care providers value the ability to search OMIM by symptoms as well as by gene or disease names. It can offer them insight into a gene function or the clinical presentation of a disease, and can assist in making or excluding a diagnosis. And, although OMIM has a more clinical focus than many genetics databases, researchers also use the database, especially for its Gene Map and its copious links to other genetics resources.

Victor A. McKusick of Johns Hopkins University began MIM-Mandelian Inheritance in Man in the early 1960s. At first a print catalog of mendelian traits and disorders, MIM became OMIM when it went online. OMIM is still biocurated at Johns Hopkins in the McKusick-Nathans Institute of Genetic Medicine, and Johns Hopkins owns the copyright to its contents.

Most of those now familiar with OMIM know it as a database available from the National Center for Biotechnology Information (NCBI). NCBI developed OMIM for the Web and hosted it from 1995 until early this year. This year OMIM migrated to a new home, http://omim.org, hosted at the University of California Santa Cruz (UCSC) Genome Bioinformatics. What does this change mean for those who use OMIM?

Search Features

If you prefer, you can continue to search OMIM in much the same way you always have. NCBI still provides a search interface for OMIM (at http://www.ncbi.nlm.nih.gov/omim), so you don't need to change to the new search platform. But now when you click on a search result, NCBI will 'bounce' you to OMIM.org to view the entry.

You may be tempted to stick with searching on NCBI, but I think that most users will want to move to OMIM.org. The new interface is missing a few things are available on NCBI, for example, the Preview/Index and the Clipboard. But OMIM.org offers some attractive enhancements, in particular an uncluttered home page with a simple, Google-like search box. The basic search will probably suffice for most queries, but if it doesn't, there are three Advanced Search options listed on the home page: OMIM, Clinical Synopses, and OMIM Gene Map.

  • OMIM is where you'll find the helpful search filters still available under Limits at the NCBI site. This, for example, is where you can narrow your search results to genes on specific chromosomes.
  • Clinicians will like the new Clinical Synopsis filters, which allow you to limit results to affected organ systems.
  • The OMIM Gene Map isn't new, but researchers will appreciate the added search options, especially the ability to specify genomic coordinates as well as genomic location.

And, for any expert searchers (librarians) in the audience, OMIM.org offers an expansive range of search operators, e.g., proximity operators and term weight boosters. See their Search Help section for details.

Search Results

I like the OMIM's new search interface, but I really like the enhancements to the search results on OMIM.org. OMIM has three types of records, corresponding to the three types of advanced searches. I think the most useful improvements are in the OMIM entries, but we'll look briefly at the Clinical Synopsis and OMIM Gene Map pages as well.

OMIM Records

OMIM records, like the OMIM home page, appear less cluttered and easier to use. More important, though, are the enhancements to the records. The website developers have said that that the new website "emphasizes the relationship between diseases and genes", and the changes start with the record's title.

OMIM search results and records still lead with the MIM number, a unique 6 digit identifier, that is usually preceded by one of four symbols, e.g., an asterisk. The symbol indicates the type of record; in theory, this allows users to quickly distinguish between gene and phenotype records. The MIM number itself reflects the mode of inheritance; for example, records with the MIM numbers from 300,000 to 399,999 represent x-linked genes or phenotypes.

Simple things for simple people: on the new interface, when you mouse over the MIM number, a javascript note tells you what the record covers! Imagine, future generations of OMIM users will not have to remember whether a MIM number that is preceded with an asterisk indicates a gene record (it does), or which number sequences code for sex linked inheritance.

Also highlighting the relationship between genotype and phenotype, a new "Phenotype Gene Relationships" table appears just below the gene or disease names and synonyms. The table makes it easy to switch back and forth between gene records and related phenotype records.

Within the gene records, just above the Relationships Table, you'll see a link labeled Cytogenetic location, which takes you to the OMIM Gene Map. Next to the Cytogenitic location link is another new feature: a link labeled Genomic coordinates. This takes you to a map showing the gene location on the UCSC Genome Browser. As you may recall, UCSC Genome Bioinformatics now hosts OMIM.

OMIM records can be lengthy; it all depends on how much is know about a disease or a gene. For example, the record for Fabry Disease, MIM number #301500, is 38 pages, while that for Fanconi Anemia (type C), MIM number #227645, is only 5 pages. A table of contents (TOC) is essential for navigating a lengthy record, and one was available in NCBI. On the new platform, the TOC floats right so you can use it as you scroll through the text. It can also be toggled opened and closed. The default is closed, minimizing visual clutter. Open it for a quick overview of the entry and to link to selected sections.

OMIM's external links make it an information portal as well as an information source for clinicians and translational researchers. Next to the TOC you'll see new links to ICD9, ICD10 or SNOMED CT codes. Just below the TOC is the extensive collection of external links to organizations such as Gene Tests, Gene Reviews, PharmGKB and Coriell Cell Repositories. External links are now grouped in categories that can be toggled open and closed. And, the links have been expanded to include new resources such as Clinicaltrials.gov, OrphaNet and Ensembl, with more resources reportedly on the way.

All OMIM records are fully referenced. Most of the citations link to PubMed, and the new site also provides links to full-text from publishers' Web sites and Pubget. The publisher links will probably work best on-campus, where many content providers recognize Levy Library's licenses. From off-campus, try Pubget. If an article is not freely available online through Pubget, select your affiliation with Mount Sinai and then authenticate as usual to bring up our FIND IT full-text service. Of course, you can also access articles through Levy Library's E-Journals database. Just plug in the PMID and authenticate when prompted.

Clinical Synopsis

The new Clinical Synopsis result page is a simple table with phenotypic characteristics of a genetic disorder, organized by organ system. In many cases, this will be enough information to enable clinicians to rule in or out a diagnosis. To see the full OMIM record, click the MIM number at the top of the page.

OMIM Gene Map

The OMIM Gene Map is a chromosome-by-chromosome list, provided in a table format, of the genes identified in OMIM and the disorders associated with them. It can be browsed to identify traits and disorders associated with genes located near a known mutation, and that could be affected by an associated insertion or deletion process. The Gene Map provides links to genetic and phenotype MIM records, and now, on OMIM.org, it links to the UCSC Gene browser.

Want to Learn More?

OpenHelix, a provider (licensed by the Levy Library) of online training on bioinformatics and genomics resources, posted a five minute video introducing the new OMIM Web site on the OpenHelix Blog and on SciVee TV. The video is below; for more details, view the complete OpenHelix blog post at: http://blog.openhelix.eu/?p=8539. Or, check out the new OMIM webisite yourself at http://omim.org.

OpenHelix. Tip of the Week: New and Improved OMIM®. 31 May 2011. Available at: http://www.scivee.tv/node/30799 [Accessed 24 July 2011].

Archives Document of the Week: Trustees’ Information Bulletins, 1943

During the early 1940s the Director’s Office of The Mount Sinai Hospital issued a biweekly newsletter, the Trustees’ Information Bulletin, to members of the Board of Trustees. These newsletters kept the Board informed of the latest developments at the Hospital. Since these bulletins were issued during the Second World War, they contain much information on the activities of the Third General Hospital, the U.S. Army unit staffed by Mount Sinai physicians and nurses. (The Archives Document of the Week has highlighted the Third General Hospital in a previous post.) Stories in the Bulletin also paint a detailed picture of medical life on the home front, and it is a selection of these stories that we highlight today.

Trustees Information Bulletin 1943-06-17 - Air Raid Drill Trustees Information Bulletin 1943-09-14 - Metal Splinter
Left: “Blackout,” July 1943. Right: “Penicillin for Civilians,” November 1943.

Many areas of life at Mount Sinai were affected by the war. An item in the July 1943 Bulletin, above left, describes how the June meeting of the Board of Trustees was interrupted by a surprise air raid drill. The meeting was suspended so that the Trustees could take an impromptu tour of the Hospital and observe its blackout preparations. The wartime needs of the military disrupted the process of introducing new medical treatments to the civilian population; a November 1943 bulletin observes that manufacturers have not yet produced enough penicillin to meet the military’s need for this newly discovered antibiotic, so civilians will not have access for close to another year.

Even during wartime, however, medicine continued to advance. A news bulletin in the September 1943 Bulletin excerpts an article from Time magazine describing an innovative operation performed at Mount Sinai during which a surgeon used an electromagnet to remove a metal splinter from the injured eye of a riveter. “Hitherto considered too crude for such fine work,” the electromagnet became a delicate instrument of healing in the hands of a Mount Sinai surgeon.

Below: “Mount Sinai in the News,” September 1943.

Trustees Information Bulletin 1943-11-29 - Penicillin

Copies of the Trustees’ Information Bulletins from 1943 to 1945 can be found in the Mount Sinai Archives.

Litt’s D.E.R.M. Database: Drug Reactions

Litts_Derm_Database_LogoBy popular demand, the Levy Library has added a subscription to the Litt's D.E.R.M DatabaseLitt's D.E.R.M. (Drug Eruptions and Reactions Manual) is an authoritative guide to adverse drug reactions and reaction patterns.  Each drug profile includes synonyms, trade names, indications, adverse reactions, half-life, category, and drug-drug interactions. Adverse reactions include information on skin, hair, nails, cardiovascular, central nervous system, respiratory and others. Search by drug name, adverse reaction, drug class, herbals and supplements and drug company. It is also heavily referenced, with links to PubMed.  Mobile Site: In addition to the online database, we also have access to a mobile version of Litt's.  To use the mobile version, you must register for a free username and password on the Litt's website while you are on-campus.  Click Login to get started. 

Access Pediatrics

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We're pleased to announce a new addition to our online resources: McGrawHill's AccessPediatrics is now available from the Library's website.  AccessPediatrics contains a collection of core textbooks such as Rudolph's Pediatrics, Neonatology, and Current Diagnosis and Treatment: Pediatrics.  Also included are images and multimedia, core topic reviews, abstracts from OMMBID (The Online Metabolic & Molecular Bases of Inherited Disease) and clerkship review materials including over 500 test questions from the Lange PreTest and Case Files books for pediatrics clerkship review.  AccessPediatrics joins our other McGrawHill's "Access" databases: AccessMedicine, AccessSurgery, AccessAnesthesiology, and AccessEmergency Medicine. Access it from the Library's list of databases.    

Archives Document of the Week: Bill of Rights Day, 1941

The July 4th holiday is upon us, reminding Americans to pause and be grateful for the freedoms we enjoy.  In 1941, President Franklin D. Roosevelt declared December 15 "Bill of Rights Day." This was commemorating the 150th anniversary of the ratification of the Bill of Rights.  Staff of The Mount Sinai Hospital organized a show to mark the day. Shown here are the last two pages from the script. (Click on the page to enlarge the image.) 

The context of this first celebration is worth remembering.  War was raging in Europe and there was much discussion in the U.S. over whether this country should be involved. Isolationist spirit was strong, but there were many who feared the fall of democracy in Europe. Roosevelt had proclaimed December 15th to be the first Bill of Rights Day before the attack on Pearl Harbor, which took place on December 7th. That attack would settle once and for all whether America would go to war.  And so that first Bill of Rights Day – it continues to be marked each year on December 15th (see 2010 video from the National Archives) – was fraught with meaning.  Seventy years later, in the 220th year of the Bill of Rights, the words of all of our charters of freedom – the Declaration of Independence, the Constitution, and the Bill of Rights - remain relevant.

        Bill of rights page 1               Bill of rights page 2

 
Draft script from The Mount Sinai Hospital staff show for Bill of Rights Day, December 15, 1941. Click on the page for a larger image. Historian's Collection, Box 1, f.11