Integrated resources

The EMMA strain search outcomes are enriched by phenotypic annotations from external resouces. A brief summary list as well as a source linkage for each annotation is provided as part of the search result. The INFRAFRONTIER bibliography and INFRAFRONTIER's rare disease related pages also integrate data from external resources, as stated below.

Mouse Genome Informatics (MGI)

MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease.

INFRAFRONTIER utilizes MGI data to highlight their annotated disease models in our strain search. Manually validated genetic background matches are shown for each mouse strain in the result list. Moreover, phenotype annotations from MGI are displayed where the allele and/or gene matches the corresponding mouse strain.

International Mouse Phenotype Consortium (IMPC)

The IMPC is a federation of phenotyping projects to carry out systemic phenotyping of mouse lines for each of the approximately 20.000 protein-coding genes in the mammalian genome in order to create an encyclopaedia of mammalian gene function. Systematic broad-based phenotyping is performed by each IMPC center using standardized procedures found within the International Mouse Phenotyping Resource of Standardised Screens (IMPReSS) resource. Gene-to-phenotype associations are made by a versioned statistical analysis with all data freely available.

INFRAFRONTIER incorporates IMPC phenotype annotations to provide rich information for mice available at our repository where the allele and/or gene matches the corresponding mouse strain.

Disease Ontology (DO)

The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts.

We use DO to enable browsing, visualisation and linking of MGI curated mouse disease models in the INFRAFRONTIER search and result interface.

Ensembl

Ensembl is a joint project between EMBL-EBI and the Wellcome Trust Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes.

We utilize this datasource to identify human orthologoue genes matching our mouse strains. This information is used to map existing mouse genes to human rare diseases displayed in the INFRAFRONTIER rare disease landing page.

PubMed

PubMed is a free search engine accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine (NLM) at the National Institutes of Health maintains the database as part of the Entrez system of information retrieval.

Publication data contains information on title, author, abstract, publication date etc.. This information is displayed in the INFRAFRONTIER public strain search and the INFRAFRONTIER bibliography.

 MeSH is the National Library of Medicine's controlled vocabulary thesaurus, used for indexing articles for the MEDLINE/PubMed database. Each article citation is associated with a set of MeSH terms that describe the content of the citation.

 MeSH terms are extracted from the PubMed service to display them on the INFRAFRONTIER bibliography. Additionally, the information is used on the EMMA Mutant Submission Form to capture information about scientific interest of the submitted strain in a structured way.

Orphanet

Orphanet is a European website providing information about orphan drugs and rare diseases. It contains content both for physicians and for patients. Its administrative office is in Paris and its official medical journal is the Orphanet Journal of Rare Diseases published on their behalf by BioMed Central.

INFRAFRONTIER extracts Orphanet data via the EBI ontology lookup service (see below). First the human orthologous gene is identified via Ensembl and then the EMMA strain carrying a mutation in the corresponding gene is mapped to the human rare disease. The content is displayed on the bibliography and on INFRAFRONTIER's rare disease related resources.

EBI ontology  lookup service (EBI OLS)

The EBI OLS is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions. Ontologies can be browsed through the website as well as programmatically via the OLS API.