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Found 9 result(s)

FAIRDOMHub

The SEEK datafiles

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The FAIRDOMHub is built upon the SEEK software suite, which is an open source web platform for sharing scientific research assets, processes and outcomes. FAIRDOM (Web Site) will establish a support and service network for European Systems Biology. It will serve projects in standardizing, managing and disseminating data and models in a FAIR manner: Findable, Accessible, Interoperable and Reusable. FAIRDOM is an initiative to develop a community, and establish an internationally sustained Data and Model Management service to the European Systems Biology community. FAIRDOM is a joint action of ERA-Net EraSysAPP and European Research Infrastructure ISBE.

Journal of Cell Biology - JCB DataViewer

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>>>!!!<<< Data originally published in the JCB DataViewer has been moved BioStudies. Please note that while the majority of data were moved, some authors opted to remove their data completely. >>>!!!<<< Migrated data can be found at https://www.ebi.ac.uk/biostudies/JCB/studies. Screen data are available in the Image Data Resource repository. http://idr.openmicroscopy.org/webclient/?experimenter=-1 >>>!!!<<< The DataViewer was decommissioned in 2018 as the journal evolved to an all-encompassing archive policy towards original source data and as new data repositories that go beyond archiving data and allow investigators to make new connections between datasets, potentially driving discovery, emerged. JCB authors are encouraged to make available all datasets included in the manuscript from the date of online publication either in a publicly available database or as supplemental materials hosted on the journal website. We recommend that our authors store and share their data in appropriate publicly available databases based on data type and/or community standard. >>>!!!<<<

SABIO-RK

System for the Analysis of Biochemical Pathways - Reaction Kinetics

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The SABIO-RK is a web-based application based on the SABIO relational database that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. It aims to support modellers in the setting-up of models of biochemical networks, but it is also useful for experimentalists or researchers with interest in biochemical reactions and their kinetics. All the data are manually curated and annotated by biological experts, supported by automated consistency checks.

Datanator

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Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms.

Barcode of Life Data Systems

BOLD Systems

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The Barcode of Life Data Systems (BOLD) provides DNA barcode data. BOLD's online workbench supports data validation, annotation, and publication for specimen, distributional, and molecular data. The platform consists of four main modules: a data portal, a database of barcode clusters, an educational portal, and a data collection workbench. BOLD is the go-to site for DNA-based identification. As the central informatics platform for DNA barcoding, BOLD plays a crucial role in assimilating and organizing data gathered by the international barcode research community. Two iBOL (International Barcode of Life) Working Groups are supporting the ongoing development of BOLD.

Small Molecule Pathway Database

formerly: PathBank

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The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Accompanying data includes detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram.

MetaCyc

Metabolic Pathway Database

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MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway. MetaCyc applications include: Online encyclopedia of metabolism, Prediction of metabolic pathways in sequenced genomes, Support metabolic engineering via enzyme database, Metabolite database aids. metabolomics research.

PeptideAtlas

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The PeptideAtlas validates expressed proteins to provide eukaryotic genome data. Peptide Atlas provides data to advance biological discoveries in humans. The PeptideAtlas accepts proteomic data from high-throughput processes and encourages data submission.

Global Genome Biodiversity Network

DNA Bank Network (formerly)

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The DNA Bank Network was established in spring 2007 and was funded until 2011 by the German Research Foundation (DFG). The network was initiated by GBIF Germany (Global Biodiversity Information Facility). It offers a worldwide unique concept. DNA bank databases of all partners are linked and are accessible via a central web portal, providing DNA samples of complementary collections (microorganisms, protists, plants, algae, fungi and animals). The DNA Bank Network was one of the founders of the Global Genome Biodiversity Network (GGBN) and is fully merged with GGBN today. GGBN agreed on using the data model proposed by the DNA Bank Network. The Botanic Garden and Botanical Museum Berlin-Dahlem (BGBM) hosts the technical secretariat of GGBN and its virtual infrastructure. The main focus of the DNA Bank Network is to enhance taxonomic, systematic, genetic, conservation and evolutionary studies by providing: • high quality, long-term storage of DNA material on which molecular studies have been performed, so that results can be verified, extended, and complemented, • complete on-line documentation of each sample, including the provenance of the original material, the place of voucher deposit, information about DNA quality and extraction methodology, digital images of vouchers and links to published molecular data if available.