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Found 59 result(s)

HUGO Gene Nomenclature Committee

HGNC

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The HUGO Gene Nomenclature Committee (HGNC) assigned unique gene symbols and names to over 35,000 human loci, of which around 19,000 are protein coding. This curated online repository of HGNC-approved gene nomenclature and associated resources includes links to genomic, proteomic and phenotypic information, as well as dedicated gene family pages.

WorldWide Antimalarial Resistance Network

WWARN

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The WorldWide Antimalarial Resistance Network (WWARN) is a collaborative platform generating innovative resources and reliable evidence to inform the malaria community on the factors affecting the efficacy of antimalarial medicines. Access to data is provided through diverse Tools and Resources: WWARN Explorer, Molecular Surveyor K13 Methodology, Molecular Surveyor pfmdr1 & pfcrt, Molecular Surveyor dhfr & dhps.

FlyReactome

a curated knowledgebase of drosophila melanogaster pathways

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<<<!!!<<< This repository is no longer available. This record is out dated >>>!!!>>>- eir fields, maintained by the FlyReactome staff.

EMBL-EBI

European Molecular Biology Laboratory - European Bioinformatics Institute

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The European Bioinformatics Institute (EBI) has a long-standing mission to collect, organise and make available databases for biomolecular science. It makes available a collection of databases along with tools to search, download and analyse their content. These databases include DNA and protein sequences and structures, genome annotation, gene expression information, molecular interactions and pathways. Connected to these are linking and descriptive data resources such as protein motifs, ontologies and many others. In many of these efforts, the EBI is a European node in global data-sharing agreements involving, for example, the USA and Japan.

ORDA - The University of Sheffield Research Data Catalogue and Repository

Discover research from The University of Sheffield

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The figshare service for the University of Sheffield allows researchers to store, share and publish research data. It helps the research data to be accessible by storing Metadata alongside datasets. Additionally, every uploaded item receives a Digital Object identifier (DOI), which allows the data to be citable and sustainable. If there are any ethical or copyright concerns about publishing a certain dataset, it is possible to publish the metadata associated with the dataset to help discoverability while sharing the data itself via a private channel through manual approval.

The Monarch Initiative

Monarch Initiative

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As with most biomedical databases, the first step is to identify relevant data from the research community. The Monarch Initiative is focused primarily on phenotype-related resources. We bring in data associated with those phenotypes so that our users can begin to make connections among other biological entities of interest. We import data from a variety of data sources. With many resources integrated into a single database, we can join across the various data sources to produce integrated views. We have started with the big players including ClinVar and OMIM, but are equally interested in boutique databases. You can learn more about the sources of data that populate our system from our data sources page https://monarchinitiative.org/about/sources.

MGnify

formerly: EBI Metagenomics

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MGnify (formerly: EBI Metagenomics) offers an automated pipeline for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis.

Ensembl Metazoa

e!EnsemblMetazoa

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Ensembl Metazoa is a genome-centric portal for metazoan species of scientific interest.

Ensembl Plants

e!EnsemblPlants

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EnsemblPlants is a genome-centric portal for plant species. Ensembl Plants is developed in coordination with other plant genomics and bioinformatics groups via the EBI's role in the transPLANT consortium.

Natural History Museum, Data Portal

Explore and download the Natural History Museum’s research and collections data

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The Museum is committed to open access and open science, and has launched the Data Portal to make its research and collections datasets available online. It allows anyone to explore, download and reuse the data for their own research. Our natural history collection is one of the most important in the world, documenting 4.5 billion years of life, the Earth and the solar system. Almost all animal, plant, mineral and fossil groups are represented. These datasets will increase exponentially. Under the Museum's ambitious digital collections programme we aim to have 20 million specimens digitised in the next five years.

Virtual Fly Brain

VFB

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Virtual Fly Brain (VFB) - an interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the Drosophila melanogaster CNS.

Environmental Information Data Centre

EIDC

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The Environmental Information Data Centre (EIDC) is part of the Natural Environment Research Council's (NERC) Environmental Data Service and is hosted by the UK Centre for Ecology & Hydrology (UKCEH). We manage nationally-important datasets concerned with the terrestrial and freshwater sciences.

University of Manchester figshare

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The University selected figshare as a general purpose research data repository to enable researchers to share research data, facilitate open research practices and meet the evolving requirements of research funders and academic publishers. This is a public-facing platform for researchers to share their data and build, over time, a comprehensive representation of the research done at the University across all faculties and disciplines.

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

UK Polar Data Centre

UK PDC

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The UK Polar Data Centre (UK PDC) is the focal point for Arctic and Antarctic environmental data management in the UK. Part of the Natural Environmental Research Council’s (NERC) network of environmental data centres and based at the British Antarctic Survey, it coordinates the management of polar data from UK-funded research and supports researchers in complying with national and international data legislation and policy.

History of Marine Animal Populations

HMAP Data Pages

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<<<!!!<<< The data are no longer accessible. >>>!!!>>>

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.

International HapMap Project

国际人类基因组单体型图计划

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<<<!!!<<< OFFLINE >>>!!!>>> A recent computer security audit has revealed security flaws in the legacy HapMap site that require NCBI to take it down immediately. We regret the inconvenience, but we are required to do this. That said, NCBI was planning to decommission this site in the near future anyway (although not quite so suddenly), as the 1,000 genomes (1KG) project has established itself as a research standard for population genetics and genomics. NCBI has observed a decline in usage of the HapMap dataset and website with its available resources over the past five years and it has come to the end of its useful life. The International HapMap Project is a multi-country effort to identify and catalog genetic similarities and differences in human beings. Using the information in the HapMap, researchers will be able to find genes that affect health, disease, and individual responses to medications and environmental factors. The Project is a collaboration among scientists and funding agencies from Japan, the United Kingdom, Canada, China, Nigeria, and the United States. All of the information generated by the Project will be released into the public domain. The goal of the International HapMap Project is to compare the genetic sequences of different individuals to identify chromosomal regions where genetic variants are shared. By making this information freely available, the Project will help biomedical researchers find genes involved in disease and responses to therapeutic drugs. In the initial phase of the Project, genetic data are being gathered from four populations with African, Asian, and European ancestry. Ongoing interactions with members of these populations are addressing potential ethical issues and providing valuable experience in conducting research with identified populations. Public and private organizations in six countries are participating in the International HapMap Project. Data generated by the Project can be downloaded with minimal constraints. The Project officially started with a meeting in October 2002 (https://www.genome.gov/10005336/) and is expected to take about three years.

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.

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.

Pfam Protein Families

Pfam

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The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). !!! Powering down the Pfam website On October 5th, redirecting the traffic from Pfam (pfam.xfam.org) to InterPro (www.ebi.ac.uk/interpro) will start. The Pfam website will be available at legacy.pfam.xfam.org until January 2023, when it will be decommissioned. You can read more about the sunset period in the blog post (https://xfam.wordpress.com/2022/08/04/pfam-website-decommission/). !!!

Open Research Data Online

ORDO

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The figshare service for The Open University was launched in 2016 and allows researchers to store, share and publish research data. It helps the research data to be accessible by storing metadata alongside datasets. Additionally, every uploaded item receives a Digital Object Identifier (DOI), which allows the data to be citable and sustainable. If there are any ethical or copyright concerns about publishing a certain dataset, it is possible to publish the metadata associated with the dataset to help discoverability while sharing the data itself via a private channel through manual approval.

Edinburgh DataShare

DataShare

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Edinburgh DataShare is a digital repository of research data produced at the University of Edinburgh, hosted by the Research Data Service in Information Services. Edinburgh University researchers who have produced research data associated with an existing or forthcoming publication, or which has potential use for other researchers, are invited to upload their dataset for sharing and safekeeping. A persistent identifier and suggested citation will be provided.

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