ZFIN serves as the zebrafish model organism database. The long term goals for ZFIN are a) to be the community database resource for the laboratory use of zebrafish, b) to develop and support integrated zebrafish genetic, genomic and developmental information, c) to maintain the definitive reference data sets of zebrafish research information, d) to link this information extensively to corresponding data in other model organism and human databases, e) to facilitate the use of zebrafish as a model for human biology and f) to serve the needs of the research community. ... [Information of the supplier]
Grid computing is regarded as one of the critical success factors in biomedical Research. The joint project MediGRID unifies well known research institutes in the area of medicine, biomedical informatics and life sciences into a consortium. Numerous associated partners from industry, healthcare and research facilities ensure a broad representation of these communities. The main goal of MediGRID is the Development of a Grid middleware integration platform enabling eScience services for biomedical life science. Therefore the consortium allocated the tasks in different modules. The four methodological modules (middleware, ontology, resource fusion and eScience) plan to incrementally develop and provide a Grid infrastructure while taking into account the need of the biomedical users. The user communities are represented in three research modules for biomedical informatics, image processing and clinical research. ... [Information of the supplier]
The JGI Genome Portal offers an interface to several bioinformatics tools for studying genomes. For each organism sequenced by JGI, a specific subset of tools is available. Throughout a subsite for a given organism, the navigation bar provides links to the tools available for that organism. [Information of the supplier, modified]
VectorBase is a web-accessible data repository for information about invertebrate vectors of human pathogens. VectorBase annotates and maintains vector genomes providing an integrated resource for the research community. Currently, VectorBase contains genome information for two organisms: Anopheles gambiae, a vector for the Plasmodium protozoan agent causing malaria, and Aedes aegypti, a vector for the flaviviral agents causing Yellow fever and Dengue fever. (Lawson, D. et al., 2007: VectorBase: a home for invertebrate vectors of human pathogens. - Nucleic Acids Research 35: D503-D505; doi:10.1093/nar/gkl960.) ... [Information of the supplier]
The HuGE Literature Finder is one component of the HuGE Navigator, an integrated, searchable knowledge base of genetic associations and related information in human genome epidemiology. In 2001, HuGENet launched the HuGE Published Literature database (HuGE Pub Lit), a continually updated and accessible knowledge base on the World Wide Web that tracks the growing published literature of human genome epidemiologic studies. HuGE Pub Lit offers a starting point for assembling articles for meta-analysis, highlighting research gaps, suggesting applied research questions, and identifying potential collaborators. HuGE Pub Lit contains links to abstracts on PubMed that meet the inclusion and exclusion criteria (see below). HuGENet research staff is responsible for extracting relevant articles from PubMed and entering them into the HuGE Pub Lit database on a weekly basis. Since June 2007, a new automatic HuGE literature screening – GAPscreener was implemented to assist the weekly HuGE literature scanning from PubMed. The sensitivity of HuGE literature screening performance can reach 97.5%. An average of 500 new articles per week is retrieved by GAPscreener. A researcher who is familiar with the eligibility criteria for human genome epidemiology then reviews each title and abstract (or in a few cases, the full text). This researcher decides whether the study will be included in the database and, if it will, assigns indexing for each article. HuGE Literature Finder is a newly-designed HuGE Pub Lit database that utilizes the Unified Medical Language System (UMLS) as an indexing mechanism. ... [Information of the supplier]
Proteases are a diverse and important group of enzymes representing >2% of the human, chimpanzee, mouse and rat genomes. This group of enzymes is implicated in numerous physiological processes. The importance of proteases is illustrated by the existence of 80 different hereditary diseases due to mutations in protease genes. Furthermore, proteases have been implicated in multiple human pathologies, including vascular diseases, rheumatoid arthritis, neurodegenerative processes, and cancer. During the last ten years, our laboratory has identified and characterized more than 60 human protease genes. Due to the importance of proteolytic enzymes in human physiology and pathology, we have recently introduced the concept of Degradome, as the complete repertoire of proteases expressed by a tissue or organism. Thanks to the recent completion of the human, chimpanzee, mouse, and rat genome sequencing projects, we were able to analyze and compare for the first time the complete protease repertoire in those mammalian organisms, as well as the complement of protease inhibitor genes. This webpage is a repository of this information, as described in The Degradome database: mammalian proteases and diseases of proteolysis Nucleic Acids Res (2008). ... [Information of the supplier]
The Fish Barcode of Life effort is creating a valuable public resource in the form of an electronic database containing DNA barcodes, images, and geospatial coordinates of examined specimens. The database contains linkages to voucher specimens, information on species distributions, nomenclature, authoritative taxonomic information, collateral natural history information and literature citations. FISH-BOL thus complements and enhances existing information resources, including FishBase and various genomics databases. ... [Information of the supplier]
Ascertaining when and where genes are expressed is of crucial importance in order to understand the physiological role of a given gene/protein and the interactions between them. In addition, the normal expression patterns can then be compared to those observed in a variety of pathological conditions to identify pathological hallmarks of gene expression. The EURExpress, an integrated project funded by the EU under the VI Framework proposes a transcriptome-wide acquisition of expression patterns chiefly by means of in situ hybridization (ISH) with non-radioactive probes and will use this data to establish a web-linked, interactive digital transcriptome atlas of embryonic mouse. The final goal of the project is to create the expression data of > 20,000 genes by RNA in situ hybridization on sagittal sections from E14.5 wild type murine embryos. This data will result in a detailed description (at a cellular level) of gene expression patterns in the developing mouse. The “transcriptome atlas” will be generated using a newly developed automated RNA in situ hybridization system. Automated scanning microscopes will collect image data, which will be electronically sent out in a digital format for annotation. The latter will be performed using a web-based “virtual” microscope and be entered in a hierarchical database specifically designed to hold large amounts of image data and display them in a user-friendly format. For a subset of genes, mainly those directly involved in human diseases, expression data will also be generated by using human and murine tissue arrays. This will offer the opportunity to compare human and mouse expression patterns in adult tissues. This project builds on a strong European concentration of skills in gene expression analysis and mouse genomics and integrates European skills, efforts, resources and information in the field of systematic gene expression analysis. All expression data generated by EURExpress will be made readily available to the scientific community via the EURExpress web-linked database, considerably advancing our knowledge of gene function and having a significant impact on the identification of gene expression markers of disease processes. ... [Information of the supplier]
In September, 2001, the National Institute of Diabetes, Digestive, and Kidney Diseases (NIDDK) convened a working group of its National Advisory Council to develop a strategic plan for Stem Cells and Developmental Biology. The working group made several recommendations, with the overall goals of providing new strategies for repairing or replacing damaged organs and generating new insights into pathologic processes underlying developmental defects and disease. There is the need for a more thorough understanding of organogenesis so that tissue degeneration and congenital malformations might be prevented and treated. The goal of GUDMAP is a fundamental description of the developing kidney and GU tract. The panel recommended that the following three objectives be combined to form the GUDMAP. a) High throughput in situ hybridization analyses to define the expression pattern of genes expressed in the developing kidney and GU tract, b) High resolution gene expression analyses to define gene expression during developmental time, the overlap in gene expression patterns, and the correlation between boundaries of gene expression and boundaries of anatomic or functional domains and c) Development of a database to house and annotate the above data and to provide rapid access of this data to the entire research community. Microarray analyses and the generation of murine strains with genetic markers are also goals of GUDMAP which serve to bolster the overall aim of defining molecular and cellular anatomy through developmental time. ... [Information of the supplier, modified]
NEMBASE is a resource for nematode transcriptome analysis, and a research tool for nematode biology, drug discovery and vaccine design. NEMBASE4 was constructed by Ben Elsworth using the PartiGene suite of tools, with assistance from James Wasmuth and Mark Blaxter. [Information of the supplier]