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