Tag Archives: OMIA

Video Tip of the Week: OMIA, Online Mendelian Inheritance in Animals

Many people are probably familiar with OMIM, Online Mendelian Inheritance in Man. It’s one of the oldest online collections of human genetic traits around. But many people may not be aware that OMIM inspired OMIA–Online Mendelian Inheritance in Animals.

The team from the University of Sydney that develops and curates OMIA collects information on animal traits with a specific emphasis on non-laboratory animals and comparative biology. The species range is huge. You can see traits from water buffalo and from rainbow trout, and more. The amount of detail may vary–sometimes you will find just links to papers that describe a phenotype. But there are other cases where there are not only links to the papers, but the gene features may be available in that species with information about the molecular details. Further, if there is a human trait that may be related, they will link to the OMIM pages for those.  The sample page that I used to illustrate this in the short video is Aranochomelia, and you can see these types of links and details.

You can access OMIA at the Australian site, but there is also a mirror available via NCBI.  It contains the same information, but since it is integrated with other NCBI tools you can use your mad NCBI skillz to do custom queries of all sorts with limits and structured syntax, or save queries with your MyNCBI account, and more. Visit OMIA at NCBI for that access.

This week’s tip is a 5 minute look at the ways to access OMIA and explores sample records. Check them out. I think they are going to become increasingly important as “big data” projects like 10K Genomes, and numerous other next-gen sequencing projects, bring us access to hoards of new genomes. Many of those genomes are going to have limited information that we can use to annotate the features. OMIA could really help with that.

Quick links:

OMIA (Univ. of Sydney): http://omia.angis.org.au/

OMIA at NCBI: http://www.ncbi.nlm.nih.gov/omia

OMIM: http://www.omim.org/

References:

Nicholas, F. (2003). Online Mendelian Inheritance in Animals (OMIA): a comparative knowledgebase of genetic disorders and other familial traits in non-laboratory animals Nucleic Acids Research, 31 (1), 275-277 DOI: 10.1093/nar/gkg074

Lenffer, J., Nicholas FW., Castle K., Rao A., Gregory S., Poidinger M., Mailman MD., & Ranganathan S. (2006). OMIA (Online Mendelian Inheritance in Animals): an enhanced platform and integration into the Entrez search interface at NCBI Nucleic Acids Research, 34 (90001) DOI: 10.1093/nar/gkj152

Sayers, E., Barrett, T., Benson, D., Bolton, E., Bryant, S., Canese, K., Chetvernin, V., Church, D., DiCuccio, M., Federhen, S., Feolo, M., Fingerman, I., Geer, L., Helmberg, W., Kapustin, Y., Krasnov, S., Landsman, D., Lipman, D., Lu, Z., Madden, T., Madej, T., Maglott, D., Marchler-Bauer, A., Miller, V., Karsch-Mizrachi, I., Ostell, J., Panchenko, A., Phan, L., Pruitt, K., Schuler, G., Sequeira, E., Sherry, S., Shumway, M., Sirotkin, K., Slotta, D., Souvorov, A., Starchenko, G., Tatusova, T., Wagner, L., Wang, Y., Wilbur, W., Yaschenko, E., & Ye, J. (2011). Database resources of the National Center for Biotechnology Information Nucleic Acids Research, 40 (D1) DOI: 10.1093/nar/gkr1184

Tip of the Week: New and Improved OMIM®

In the realm of bioinformatics resources, few are more venerable than OMIM®, Online Mendelian Inheritance in Man [well, originally not online, on index cards...]. For those who might be new to OMIM, it is a catalog of genes and their variations, and resulting phenotypes in human, with a more clinical perspective than some resources offer. As I was reviewing the history of OMIM for this post, I began to wonder if there even is any repository in genomics that’s been maintained on a computer framework longer. I know of an older protein analysis program that I wrote about once here–from Margaret Dayhoff and Robert Ledley. But as an ongoing repository or catalog that was stored, Victor McKusick wrote:

Mendelian Inheritance in Man has been maintained on the computer since 1964.

It was stored on a mainframe at Johns Hopkins at that time. The other one that I thought was probably close was RCSB PDB, which is described on their “about” page in this way:

The PDB was established in 1971 at Brookhaven National Laboratory and originally contained 7 structures.

It’s likely that in some form it existed on a computer system earlier than that–and may give MIM a run for the record. Bruno Strasser described 4 resources developed around the same time–1965–as the Cambridge Structural Database, MIM, Index Medicus, and Atlas of Protein Sequence and Structure.

It’s not easy to maintain and develop a resource for this long. Just this past month we learned about the risk of KEGG going away. But in bioinformatics–like biology–a resource needs to evolve or die. (Actually, I can remember in grad school that phrase was used by the chair of our department to describe what biology faculty needs to do as well.) In this week’s tip of the week, I report that OMIM is evolving, and I introduce you to the new interface.

Most people have encountered OMIM at the NCBI. But if you go over to there today, you’ll see this notice on the homepage:

This is because OMIM has a new home. It’s not clear at this time if the NCBI incarnation will be updated going forward. The OMIM team at JHU is requesting that software providers who serve links to OMIM now migrate those links to the new OMIM.org site, which the OMIM team considers to be the official site and will be the up-to-date one.

Let’s talk specifically about the evolved OMIM now: it’s entered a new century! Yay! The incredible deep collection of curated data over the decades still remains, but the new interface is very nice to use and to look at–it no longer looks like 1995 over there. There are also new handy links, and new search options, and new features still to come.

Compare this same record for the APC gene (a contributor to hereditary colon cancer) in both places:

Old OMIM at NCBI: http://www.ncbi.nlm.nih.gov/omim/611731

New OMIM at JHU: http://www.omim.org/entry/611731

I find the new page to be significantly tidier, don’t you? The links you need to other resources are still there, but you can toggle open the menus to find them now. And some of the links are to resources that weren’t available on the old page (for example, BioGPS and PharmGKB which we like very much!).  I’m also told that on appropriate pages there will be links to the DECIPHER resource.

You can still browse around the MIM map by clicking on the Advanced search for Gene Map link: http://www.omim.org/search/advanced/geneMap . I have done this on many days when I have found something intriguing in a chromosomal region and I want to see what was reported in that area and stored at OMIM.

Another feature that I think is very cool is the option to change the language with the Google Translate menu. I know it’s not perfect, but I’m finding increasingly that I want to read blog posts in other languages and I am finding it works pretty well. Making the OMIM data so easily accessible to non-English speakers is a really nice touch.

Although sometimes it is tough to transition to new software, I think this is a good sign. In addition to maintaining the excellent knowledge collection that began so long ago, a new interface means that OMIM is continuing to grow and change to meet the needs of today. And as we move forward to identify more and more genomic variations and alterations that impact human health, well-curated and deep knowledge bases like this are crucial.

Congrats to the OMIM team on the new look and new home.

Quick link to the new OMIM: http://www.omim.org/

(Bonus: did you know there’s also an Online Mendelian Inheritance in Animals OMIA? http://www.ncbi.nlm.nih.gov/omia )

Follow them on Twitter: http://twitter.com/#!/OmimOrg

References:
McKusick, V. (2006). A 60-Year Tale of Spots, Maps, and Genes Annual Review of Genomics and Human Genetics, 7 (1), 1-27 DOI: 10.1146/annurev.genom.7.080505.115749

Amberger, J., Bocchini, C., & Hamosh, A. (2011). A new face and new challenges for online mendelian inheritance in man (OMIM®) Human Mutation, 32 (5), 564-567 DOI: 10.1002/humu.21466

Strasser, B. (2009). Collecting, Comparing, and Computing Sequences: The Making of Margaret O. Dayhoff’s Atlas of Protein Sequence and Structure, 1954–1965 Journal of the History of Biology, 43 (4), 623-660 DOI: 10.1007/s10739-009-9221-0 (PDF available on his faculty web site here.)

Strasser, BJ (2006) “Collecting and Experimenting: The moral economies of biological research, 1960s-1980s.”, Preprints of the Max-Planck Institute for the History of Science, 310, 105-23.