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Found 12 result(s)

Human Proteinpedia

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Human Proteinpedia is a community portal for sharing and integration of human protein data. This is a joint project between Pandey at Johns Hopkins University, and Institute of Bioinformatics, Bangalore. This portal allows research laboratories around the world to contribute and maintain protein annotations. Human Protein Reference Database (HPRD) integrates data, that is deposited in Human Proteinpedia along with the existing literature curated information in the context of an individual protein. All the public data contributed to Human Proteinpedia can be queried, viewed and downloaded. Data pertaining to post-translational modifications, protein interactions, tissue expression, expression in cell lines, subcellular localization and enzyme substrate relationships may be deposited.

EcoCyc Database

EcoCyc E. coli Database

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EcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of the entire genome, and of transcriptional regulation, transporters, and metabolic pathways.

Canadian Open Neuroscience Platform Portal

CONP

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The CONP portal is a web interface for the Canadian Open Neuroscience Platform (CONP) to facilitate open science in the neuroscience community. CONP simplifies global researcher access and sharing of datasets and tools. The portal internalizes the cycle of a typical research project: starting with data acquisition, followed by processing using already existing/published tools, and ultimately publication of the obtained results including a link to the original dataset. From more information on CONP, please visit https://conp.ca

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.

IMGT/HLA Database

IPD-IMGT/HLA

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The IPD-IMGT/HLA Database provides a specialist database for sequences of the human major histocompatibility complex (MHC) and includes the official sequences named by the WHO Nomenclature Committee For Factors of the HLA System. The IPD-IMGT/HLA Database is part of the international ImMunoGeneTics project (IMGT). The database uses the 2010 naming convention for HLA alleles in all tools herein. To aid in the adoption of the new nomenclature, all search tools can be used with both the current and pre-2010 allele designations. The pre-2010 nomenclature designations are only used where older reports or outputs have been made available for download.

EMDataResource

formerly: EMDataBank

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Cryo electron microscopy enables the determination of 3D structures of macromolecular complexes and cells from 2 to 100 Å resolution. EMDataResource is the unified global portal for one-stop deposition and retrieval of 3DEM density maps, atomic models and associated metadata, and is a joint effort among investigators of the Stanford/SLAC CryoEM Facility and the Research Collaboratory for Structural Bioinformatics (RCSB) at Rutgers, in collaboration with the EMDB team at the European Bioinformatics Institute. EMDataResource also serves as a resource for news, events, software tools, data standards, and validation methods for the 3DEM community. The major goal of the EMDataResource project in the current funding period is to work with the 3DEM community to (1) establish data-validation methods that can be used in the process of structure determination, (2) define the key indicators of a well-determined structure that should accompany every deposition, and (3) implement appropriate validation procedures for maps and map-derived models into a 3DEM validation pipeline.

Ligand-Gated Ion Channel Database

LGICdb

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The Ligand-Gated Ion Channel database provides access to information about transmembrane proteins that exist under different conformations, with three primary subfamilies: the cys-loop superfamily, the ATP gated channels superfamily, and the glutamate activated cationic channels superfamily. The development of the Ligand-Gated Ion Channel database was started in 1994, as part of Le Novère's work on the phylogeny of those receptors' subunits. It grew into a serious data resource, that served the community at large. However, it is not actively maintained anymore. In addition, bioinformatics technology evolved a lot over the last two decades, so that scientists can now generate quickly customised databases from trustworthy primary data resources. Therefore, we decided to officialy freeze the data resource. The resource will not disappear, and all the information and links will stay there. But people should not consider it as an up-to-date trustable resource. For any new work, they should consider using alternative sources, such as UniProt, Ensembl, Protein Databank etc.

AnimalGenome.ORG

BioMart AnimalGenome.ORG

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This is a animal and human genome database that uses the BioMart software.

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.

The Global Proteome Machine

GPM

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The Global Proteome Machine (GPM) is a protein identification database. This data repository allows users to post and compare results. GPM's data is provided by contributors like The Informatics Factory, University of Michigan, and Pacific Northwestern National Laboratories. The GPM searchable databases are: GPMDB, pSYT, SNAP, MRM, PEPTIDE and HOT.

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.

caArray

Array Data Management System

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>>>!!!<<< caArray Retirement Announcement >>>!!!<<< The National Cancer Institute (NCI) Center for Biomedical Informatics and Information Technology (CBIIT) instance of the caArray database was retired on March 31st, 2015. All publicly-accessible caArray data and annotations will be archived and will remain available via FTP download https://wiki.nci.nih.gov/x/UYHeDQ and is also available at GEO http://www.ncbi.nlm.nih.gov/geo/ . >>>!!!<<< While NCI will not be able to provide technical support for the caArray software after the retirement, the source code is available on GitHub https://github.com/NCIP/caarray , and we encourage continued community development. Molecular Analysis of Brain Neoplasia (Rembrandt fine-00037) gene expression data has been loaded into ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3073 >>>!!!<<< caArray is an open-source, web and programmatically accessible microarray data management system that supports the annotation of microarray data using MAGE-TAB and web-based forms. Data and annotations may be kept private to the owner, shared with user-defined collaboration groups, or made public. The NCI instance of caArray hosts many cancer-related public datasets available for download.