OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders

Abstract

Online Mendelian Inheritance in Man, OMIM(®), is a comprehensive, authoritative and timely research resource of curated descriptions of human genes and phenotypes and the relationships between them. The new official website for OMIM, OMIM.org (http://omim.org), was launched in January 2011. OMIM is based on the published peer-reviewed biomedical literature and is used by overlapping and diverse communities of clinicians, molecular biologists and genome scientists, as well as by students and teachers of these disciplines. Genes and phenotypes are described in separate entries and are given unique, stable six-digit identifiers (MIM numbers). OMIM entries have a structured free-text format that provides the flexibility necessary to describe the complex and nuanced relationships between genes and genetic phenotypes in an efficient manner. OMIM also has a derivative table of genes and genetic phenotypes, the Morbid Map. OMIM.org has enhanced search capabilities such as genome coordinate searching and thesaurus-enhanced search term options. Phenotypic series have been created to facilitate viewing genetic heterogeneity of phenotypes. Clinical synopsis features are enhanced with UMLS, Human Phenotype Ontology and Elements of Morphology terms and image links. All OMIM data are available for FTP download and through an API. MIMmatch is a novel outreach feature to disseminate updates and encourage collaboration.

Figure 1.

Diagram of OMIM content. Dashed lines indicate that not all genes have allelic variants; not all phenotypes are mapped; and mapped phenotypes are not necessarily part of a Phenotypic Series.

Figure 2.

OMIM entry for protein O-mannosyltransferase 1 (607423). Arrows call attention to the following: the unique MIM number 607423 with an asterisk prefix denoting a gene. Approved gene symbol obtained directly from the Human Gene Nomenclature Committee data. Cytogenetic location and Genomic coordinates obtained from NCBI. Gene–phenotype relationships table showing allelic disorders, their MIM numbers, and the phenotype mapping key. The Table of Contents (TOC) facilitates navigation within the OMIM entry, and external resource links specific for the gene are topically organized and listed below the TOC.

Figure 3.

OMIM entry muscular dystrophy-dystroglycanopathy type A1. Arrows call attention to the following: The MIM number for this entry is preceded by the prefix # denoting a phenotype that has a known molecular basis. A link for the ICD+ codes is available for this entry. The phenotype–gene relationship table shows the phenotype (with MIM number) followed by the gene (with MIM number) that is mutated in the phenotype. When available, links to OMIM's clinical synopses and phenotypic series are located in the phenotype entry. The TOC facilitates navigation within the entry, and links to external resources specific for the phenotype are available below the TOC.

Figure 4.

(A) OMIM search navigation box showing optional thesaurus terms for search terms tortuosity and cutis. Access to the clinical synopsis quick view for these entries is available from the Retrieve Corresponding Clinical Synopsis button. (B) Clinical synopsis quick view showing anatomical categories and mouse-over function to reveal detailed features. (C) Clinical synopsis of OMIM entry 614437 showing the optional display of clinical identifiers to the UMLS, SNOMED CT, HPO and EoM. A mouse-over of the EoM image link shows the image of the phenotypic feature (in this case, microcephaly). Users can search these identifiers through the OMIM.org website or through the OMIM.org API.

Figure 5.

OMIM gene map. OMIM.org provides a unique way to access gene map information from an OMIM retrieval set from the Retrieve Corresponding Gene Map button. From within the gene map retrieval set, a user can view only those entries in the map that have phenotypes by selecting the Phenotype Only Entries. A retrieval set can be downloaded as an Excel or tab-delimited file by selecting the Download As option.

Figure 6.

Allelic variants. Allelic variants are included in gene entries. The full view of the variant includes mutation details, clinical features of patients with the mutation. The Table View of the variants can be accessed from a link below the Allelic Variants heading or from the TOC. The Table View information can be downloaded as an Excel or tab-delimited file.

Figure 7.

OMIM Phenotype Series can be accessed from within phenotype entries from a link below the phenotype–gene relationship table or from the TOC. A list of disorders with a Phenotypic Series is available from the FAQ or through MIMmatch.

Figure 8.

Example of API output of an OMIM clinical synopsis. For this example, the output format is JSON and examples of the unique identifiers for UMLS, HPO identifiers are underlined. The API enables batch queries of all OMIM data and allows computational integration of data on the fly.