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EuroPhenome and EMPReSS: online mouse phenotyping resource.

Nucleic acids research | Jan 15, 2008

EuroPhenome (http://www.europhenome.org) and EMPReSS (http://empress.har.mrc.ac.uk/) form an integrated resource to provide access to data and procedures for mouse phenotyping. EMPReSS describes 96 Standard Operating Procedures for mouse phenotyping. EuroPhenome contains data resulting from carrying out EMPReSS protocols on four inbred laboratory mouse strains. As well as web interfaces, both resources support web services to enable integration with other mouse phenotyping and functional genetics resources, and are committed to initiatives to improve integration of mouse phenotype databases. EuroPhenome will be the repository for a recently initiated effort to carry out large-scale phenotyping on a large number of knockout mouse lines (EUMODIC).

Pubmed ID: 17905814 RIS Download

Mesh terms: Animals | Databases, Factual | Internet | Mice | Mice, Inbred Strains | Phenotype | Systems Integration | User-Computer Interface

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This is a list of tools and resources that we have found mentioned in this publication.


Ensembl

A collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. The goal of Ensembl is to automatically annotate the genome, integrate this annotation with other available biological data and make the data publicly available via the web. The range of available data has also expanded to include comparative genomics, variation and regulatory data. Ensembl allows users to: upload and analyze data and save it to an Ensembl account; search for a DNA or protein sequence using BLAST or BLAT; fetch desired data from the public database, using the Perl API; download the databases via FTP in FASTA, MySQL and other formats; and mine Ensembl with BioMart and export sequences or tables in text, HTML, or Excel format. The DNA sequences and assemblies used in the Ensembl genebuild are provided by various projects around the world. Ensembl has entered into an agreement with UCSC and NCBI with regard to sequence identifiers in order to improve consistency between the data provided by different genome browsers. The site also links to the Ensembl blog with updates on new species and sequences as they are added to the database.

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ArrayExpress

Database of functional genomics experiments including gene expression where you can query and download data collected to MIAME and MINSEQE standards. It includes gene expression data from microarray and high throughput sequencing studies. Gene Expression Atlas contains a subset of curated and re-annotated Archive data which can be queried for individual gene expression under different biological conditions across experiments. The ArrayExpress Archive is one of the three international public repositories of functional genomics data supporting publications. It includes data generated by sequencing or array-based technologies. Data are submitted by users and imported directly from the NCBI Gene Expression Omnibus. The ArrayExpress Archive is closely integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute. Advanced queries provided via ontology enabled interfaces include queries based on technology and sample attributes such as disease, cell types and anatomy. The Repository contains data from over 47787 experiments comprising approximately 1361377 assays (March 2014). The majority of the data are array based, but other data types are included, including ultra high-throughput sequencing transcriptomics and epigenetic data. All the data and array designs in ArrayExpress are available for direct download in a number of different formats. Submissions are welcome.

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BioMart Project

A query-oriented data management system that can be used with any type of data and is particularly suited for providing "data mining" like searches of complex descriptive data. BioMart comes with an "out of the box" website that can be installed, configured and customized according to user requirements. Further access is provided by graphical and text based applications or programmatically using web services or API written in Perl and Java. BioMart has built-in support for query optimization and data federation and in addition can be configured to work as a DAS 1.5 Annotation server. The process of converting a data source into BioMart format is fully automated by the tools included in the package. Currently supported RDBMS platforms are MySQL, Oracle and Postgres.

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European Mouse Phenotyping Resource of Standardised Screens

Database of validated Standard Operating Procedures (SOPs) for screens to determine the phenotype of a mouse, developed by the EUMORPHIA consortium. The SOP's cover all of the main body systems including: clinical chemistry, hormonal and metabolic systems, cardiovascular, allergy and infection, renal function, sensory function, neurological and behavioral function, cancer, bone and cartilage, and respiratory function. In addition, there are generic SOPs in histology, necropsy, pathology and gene expression. EMPReSS is a platform of individual tests. These can be performed as individual tests or grouped together in sequences, recommended in the EMPReSS database, to give more information on particular phenotype. Quick List of Current Pipelines: * EUMODIC Pipeline 1 * EUMODIC Pipeline 2 * GMC Pipeline * MGP Pipeline * Additional Tests * EUMODIC Pipeline 3

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Mouse Genome Informatics

An international database for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease. Its primary mission is to facilitate the use of the mouse as a model system for understanding human biology and disease. MGI creates and maintains an integrated representation of mouse genetic, genomic, expression, and phenotype data and develops definitive reference data set and consensus data views. MGI also synthesizes comparative genomic data between the mouse and other mammals, maintains a set of links and collaborations with other bioinformatics resources, develops and supports analysis and data submission tools, and provides extensive technical support for database users. The projects contributing to this resource are: Mouse Genome Database (MGD) Project, Gene Expression Database (GXD) Project, Mouse Tumor Biology (MTB) Database Project, Gene Ontology (GO) Project at MGI, and MouseCyc Project at MGI.

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Ontology Lookup Service

Interactive and programmatic interfaces to query, browse and navigate an increasing number of biomedical ontologies and controlled vocabularies. It provides a web service interface to query multiple ontologies from a single location with a unified output format. It can integrate any ontology available in the Open Biomedical Ontology (OBO) format. The database can be queried to obtain information on a single term or to browse a complete ontology using AJAX. Auto-completion provides a user-friendly search mechanism. An AJAX-based ontology viewer is available to browse a complete ontology or subsets of it. A weekly MySQL database export file can be downloaded from the EBI public FTP directory.

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