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Found 151 result(s)

GENCODE

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GENCODE is a scientific project in genome research and part of the ENCODE (ENCyclopedia Of DNA Elements) scale-up project. The GENCODE consortium was initially formed as part of the pilot phase of the ENCODE project to identify and map all protein-coding genes within the ENCODE regions (approx. 1% of Human genome). Given the initial success of the project, GENCODE now aims to build an “Encyclopedia of genes and genes variants” by identifying all gene features in the human and mouse genome using a combination of computational analysis, manual annotation, and experimental validation, and annotating all evidence-based gene features in the entire human genome at a high accuracy.

RADAR Luke

Luonnonvarakeskuksen tutkimusaineistokuvausten hakupalvelu

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RADAR service offers the ability to search for research data descriptions of the Natural Resources Institute Finland (Luke). The service includes descriptions of research data for agriculture, forestry and food sectors, game management, fisheries and environment. The public web service aims to facilitate discovering subjects of natural resources studies. In addition to Luke's research data descriptions one can search metadata of the Finnish Environment Institute (SYKE). The interface between Luke and SYKE metadata services combines Luke's research data descriptions and SYKE's descriptions of spatial datasets and data systems into a unified search service.

RADAM database portal

RADiation DAMage database

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RADAM portal is an interface to the network of RADAM (RADiation DAMage) Databases collecting data on interactions of ions, electrons, positrons and photons with biomolecular systems, on radiobiological effects and relevant phenomena occurring at different time, spatial and energy scales in irradiated targets during and after the irradiation. This networking system has been created by the Consortium of COST Action MP1002 (Nano-IBCT: Nano-scale insights into Ion Beam Cancer Therapy) during 2011-2014 using the Virtual Atomic and Molecular Data Center (VAMDC) standards.

VectorBase

Bioinformatics Resource for Invertebrate Vectors of Human Pathogens

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VectorBase provides data on arthropod vectors of human pathogens. Sequence data, gene expression data, images, population data, and insecticide resistance data for arthropod vectors are available for download. VectorBase also offers genome browser, gene expression and microarray repository, and BLAST searches for all VectorBase genomes. VectorBase Genomes include Aedes aegypti, Anopheles gambiae, Culex quinquefasciatus, Ixodes scapularis, Pediculus humanus, Rhodnius prolixus. VectorBase is one the Bioinformatics Resource Centers (BRC) projects which is funded by National Institute of Allergy and Infectious Diseases (NAID).

Mechanism and Catalytic Site Atlas

CSA (formerly)

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M-CSA is a database of enzyme reaction mechanisms. It provides annotation on the protein, catalytic residues, cofactors, and the reaction mechanisms of hundreds of enzymes. There are two kinds of entries in M-CSA. 'Detailed mechanism' entries are more complete and show the individual chemical steps of the mechanism as schemes with electron flow arrows. 'Catalytic Site' entries annotate the catalytic residues necessary for the reaction, but do not show the mechanism. The M-CSA (Mechanism and Catalytic Site Atlas) represents a unified resource that combines the data in both MACiE and the CSA

TRAILS

Tracking Adolescents' Individual Lives Survey

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TRAILS is a prospective cohort study, which started in 2001 with population cohort and 2004 with a clinical cohort (CC). Since then, a group of 2500 young people from the Northern part of the Netherlands has been closely monitored in order to chart and explain their mental, physical, and social development. These TRAILS participants have been measured every two to three years, by means of questionnaires, interviews, and all kinds of tests. By now, we have collected information that spans the total period from preadolescence up until young adulthood. One of the main goals of TRAILS is to contribute to the knowledge of the development of emotional and behavioral problems and the (social) functioning of preadolescents into adulthood, their determinants, and underlying mechanisms.

The Health Improvement Network

THIN

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THIN is a medical data collection scheme that collects anonymised patient data from its members through the healthcare software Vision. The UK Primary Care database contains longitudinal patient records for approximately 6% of the UK Population. The anonymised data collection, which goes back to 1994, is nationally representative of the UK population.

European Variation Archive

EVA

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The European Variation Archive is an open-access database of all types of genetic variation data from all species. The EVA provides access to highly detailed, granular, raw variant data from human, with other species to follow. As of September 2017, EMBL-EBI will maintain reliable accessions for non-human genetic variation data through the European Variation Archive (EVA). NCBI's dbSNP database will continue to maintain stable identifiers for human genetic variation data only. This change will enable a more rapid turnaround for data sharing in this burgeoning field.

Cellular Phenotype database

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The Cellular Phenotype database stores data derived from high-throughput phenotypic studies and it is being developed as part of the Systems Microscopy Network of Excellence project. The aim of the Cellular Phenotype database is to provide easy access to phenotypic data and facilitate the integration of independent phenotypic studies. Through its interface, users can search for a gene of interest, or a collection of genes, and retrieve the loss-of-function phenotypes observed, in human cells, by suppressing the expression of the selected gene(s), through RNA interference (RNAi), across independent phenotypic studies. Similarly, users can search for a phenotype of interest and retrieve the RNAi reagents that have caused such phenotype and the associated target genes. Information about specific RNAi reagents can also be obtained when searching for a reagent ID.

hPSCreg

human Pluripotent Stem Cell registry

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The human pluripotent stem cell registry (hPSCreg) is a public registry and data portal for human embryonic and induced pluripotent stem cell lines (hESC and hiPSC). The Registry provides comprehensive and standardized biological and legal information as well as tools to search and compare information from multiple hPSC sources and hence addresses a translational research need. To facilitate unambiguous identification over different resources, hPSCreg automatically creates a unique standardized name (identifier) for each cell line registered. In addition to biological information, hPSCreg stores extensive data about ethical standards regarding cell sourcing and conditions for application and privacy protection. hPSCreg is the first global registry that holds both, manually validated scientific and ethical information on hPSC lines, and provides access by means of a user-friendly, mobile-ready web application.

CERIC Data Portal

CERIC Metadata Catalogue

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CERIC Data Portal allows users to consult and manage data related to experiments carried out at CERIC (Central European Research Infrastructure Consortium) partner facilities. Data made available includes scientific datasets collected during experiments, experiment proposals, samples used and publications if any. Users can search for data based on related metadata (both their own data and other peoples' public data).

WikiPathways

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WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community. WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. WikiPathways thus presents a new model for pathway databases that enhances and complements ongoing efforts, such as KEGG, Reactome and Pathway Commons. Building on the same MediaWiki software that powers Wikipedia, we added a custom graphical pathway editing tool and integrated databases covering major gene, protein, and small-molecule systems. The familiar web-based format of WikiPathways greatly reduces the barrier to participate in pathway curation. More importantly, the open, public approach of WikiPathways allows for broader participation by the entire community, ranging from students to senior experts in each field. This approach also shifts the bulk of peer review, editorial curation, and maintenance to the community.

GenomeRNAi

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GenomeRNAi is a database containing phenotypes from RNA interference (RNAi) screens in Drosophila and Homo sapiens. In addition, the database provides an updated resource of RNAi reagents and their predicted quality.

Science3D

Science 3D

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----<<<< This repository is no longer available. This record is out-dated !!!!! >>>>> ----- Science3D is an Open Access project to archive and curate scientific data and make them available to everyone interested in scientific endeavours. Science3D focusses mainly on 3D tomography data from biological samples, simply because theses object make it comparably easy to understand the concepts and techniques. The data come primarily from the imaging beamlines of the Helmholtz Center Geesthacht (HZG), which make use of the uniquely bright and coherent X-rays of the Petra3 synchrotron. Petra3 - like many other photon and neutron sources in Europe and World-wide - is a fantastic instrument to investigate the microscopic detail of matter and organisms. The experiments at photon science beamlines hence provide unique insights into all kind of scientific fields, ranging from medical applications to plasma physics. The success of these experiments demands enormous efforts of the scientists and quite some investments

B2SHARE

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B2SHARE is a user-friendly, reliable and trustworthy way for researchers, scientific communities and citizen scientists to store and share small-scale research data from diverse contexts and disciplines. B2SHARE is able to add value to your research data via (domain tailored) metadata, and assigning citable Persistent Identifiers PIDs (Handles) to ensure long-lasting access and references. B2SHARE is one of the B2 services developed via EUDAT and long tail data deposits do not cost money. Special arrangements such as branding and special metadata elements can be made on request.

BioVel

Biodiversity Virtual e-Laboratory

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<<<!!!<<< This repository is no longer available. >>>!!!>>> BioVeL is a virtual e-laboratory that supports research on biodiversity issues using large amounts of data from cross-disciplinary sources. BioVeL supports the development and use of workflows to process data. It offers the possibility to either use already made workflows or create own. BioVeL workflows are stored in MyExperiment - Biovel Group http://www.myexperiment.org/groups/643/content. They are underpinned by a range of analytical and data processing functions (generally provided as Web Services or R scripts) to support common biodiversity analysis tasks. You can find the Web Services catalogued in the BiodiversityCatalogue.

European Data Portal

EDP

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The European Data Portal harvests the metadata of Public Sector Information available on public data portals across European countries. Information regarding the provision of data and the benefits of re-using data is also included.

CATH

CATH-Gene3D

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The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in the CATH hierarchy; Class, Architecture, Topology and Homologous superfamily.

The Cancer Immunome Atlas

TCIA

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The Cancer Immunome Database (TCIA) provides results of comprehensive immunogenomic analyses of next generation sequencing data (NGS) data for 20 solid cancers from The Cancer Genome Atlas (TCGA) and other datasource. The Cancer Immunome Atlas (TCIA) was developed and is maintained at the Division of Bioinformatics (ICBI). The database can be queried for the gene expression of specific immune-related gene sets, cellular composition of immune infiltrates (characterized using gene set enrichment analyses and deconvolution), neoantigens and cancer-germline antigens, HLA types, and tumor heterogeneity (estimated from cancer cell fractions). Moreover it provides survival analyses for different types immunological parameters. TCIA will be constantly updated with new data and results.

Repositorio Institucional de la Universidad de Burgos

RIUBU

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The Institutional Repository of the University of Burgos is based on the digital collections that include the documents generated by the members of the university community in their academic activities. These are accessible via the Internet, in accordance with the University's Open Access Institutional Policy.

IMGT/3Dstructure-DB and IMGT/2Dstructure-DB

International ImMunoGeneTics information system/3Dstructure-DB and IMGT/2Dstructure-DB

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IMGT/3Dstructure-DB is the IMGT three-dimensional (3D) structure database.

European Union Open Data Portal

EU Open Data Portal

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The European Union Open Data Portal is the single point of access to a growing range of data from the institutions and other bodies of the European Union (EU). Data are free for you to use and reuse for commercial or non-commercial purposes. By providing easy and free access to data, the portal aims to promote their innovative use and unleash their economic potential. It also aims to help foster the transparency and the accountability of the institutions and other bodies of the EU. The EU Open Data Portal is managed by the Publications Office of the European Union. Implementation of the EU's open data policy is the responsibility of the Directorate-General for Communications Networks, Content and Technology of the European Commission.

Array Express

functional genomics data

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ArrayExpress is one of the major international repositories for high-throughput functional genomics data from both microarray and high-throughput sequencing studies, many of which are supported by peer-reviewed publications. Data sets are submitted directly to ArrayExpress and curated by a team of specialist biological curators. In the past (until 2018) datasets from the NCBI Gene Expression Omnibus database were imported on a weekly basis. Data is collected to MIAME and MINSEQE standards.

ProteomeXchange

PX

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The ProteomeXchange consortium has been set up to provide a single point of submission of MS proteomics data to the main existing proteomics repositories, and to encourage the data exchange between them for optimal data dissemination. Current members accepting submissions are: The PRIDE PRoteomics IDEntifications database at the European Bioinformatics Institute focusing mainly on shotgun mass spectrometry proteomics data PeptideAtlas/PASSEL focusing on SRM/MRM datasets.

Catalogue of Life

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The Catalogue of Life is the most comprehensive and authoritative global index of species currently available. It consists of a single integrated species checklist and taxonomic hierarchy. The Catalogue holds essential information on the names, relationships and distributions of over 1.8 million species. This figure continues to rise as information is compiled from diverse sources around the world.