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Found 25 result(s)
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Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of 'small molecular entities'. The term 'molecular entity' encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms (either deliberately, as for drugs, or unintentionally', as for chemicals in the environment). The qualifier 'small' implies the exclusion of entities directly encoded by the genome, and thus as a rule nucleic acids, proteins and peptides derived from proteins by cleavage are not included.
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The Database of Protein Disorder (DisProt) is a curated database that provides information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part. DisProt is a community resource annotating protein sequences for intrinsically disorder regions from the literature.
It classifies intrinsic disorder based on experimental methods and three ontologies for molecular function, transition and binding partner.
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STRING is a database of known and predicted protein interactions.
The interactions include direct (physical) and indirect (functional) associations; they are derived from four sources:
- Genomic Context
- High-throughput Experiments
- (Conserved) Coexpression
- Previous Knowledge
STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable.
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The BioProject database is a searcheable collection of complete and incomplete (in-progress) large-scale molecular projects including genome sequencing and assembly, transcriptome, metagenomic, annotation, expression and mapping projects. BioProject provides a central point to link to all data associated with a project in the NCBI molecular and literature databases.
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The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database accepts submissions via an online tool, or in a simple tab-delimited format. It also enables authors to submit supplementary information and link to it from the publication.
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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.
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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.
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>>>>!!!!<<<< AspGD data are being integrated into FungiDB. Please click here for additional details http://fungidb.org/ . Discussion of how to maximize the value of FungiDB for the Aspergillus research community will be a major topic at the upcoming AsperFest12 meeting at Asilomar (March 16-17, 2015). >>>>!!!!<<<< AspGD is an organized collection of genetic and molecular biological information about the filamentous fungi of the genus Aspergillus. Among its many species, the genus contains an excellent model organism (A. nidulans, or its teleomorph Emericella nidulans), an important pathogen of the immunocompromised (A. fumigatus), an agriculturally important toxin producer (A. flavus), and two species used in industrial processes (A. niger and A. oryzae). AspGD contains information about genes and proteins of multiple Aspergillus species; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; gene, protein, and chromosome sequence information; tools for analysis and comparison of sequences; and links to literature information; as well as a multispecies comparative genomics browser tool (Sybil) for exploration of orthology and synteny across multiple sequenced Aspergillus species.
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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).
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The Antimicrobial Peptide Database (APD) was originally created by a graduate student, Zhe Wang, as his master's thesis in the laboratory of Dr. Guangshun Wang. The project was initiated in 2002 and the first version of the database was open to the public in August 2003. It contained 525 peptide entries, which can be searched in multiple ways, including APD ID, peptide name, amino acid sequence, original location, PDB ID, structure, methods for structural determination, peptide length, charge, hydrophobic content, antibacterial, antifungal, antiviral, anticancer, and hemolytic activity. Some results of this bioinformatics tool were reported in the 2004 database paper. The peptide data stored in the APD were gleaned from the literature (PubMed, PDB, Google, and Swiss-Prot) manually in over a decade.
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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.
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KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies
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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.
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The mission of the GO Consortium is to develop a comprehensive, computational model of biological systems, ranging from the molecular to the organism level, across the multiplicity of species in the tree of life.
The Gene Ontology (GO) knowledgebase is the world’s largest source of information on the functions of genes. This knowledge is both human-readable and machine-readable, and is a foundation for computational analysis of large-scale molecular biology and genetics experiments in biomedical research.
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Giardia lamblia is a significant, environmentally transmitted, human pathogen and an amitochondriate protist. It is a major contributor to the enormous worldwide burden of human diarrheal diseases, yet the basic biology of this parasite is not well understood. No virulence factor has been identified. The Giardia lamblia genome contains only 12 million base pairs distributed onto five chromosomes. Its analysis promises to provide insights about the origins of nuclear genome organization, the metabolic pathways used by parasitic protists, and the cellular biology of host interaction and avoidance of host immune systems.
Since the divergence of Giardia lamblia lies close to the transition between eukaryotes and prokaryotes in universal ribosomal RNA phylogenies, it is a valuable, if not unique, model for gaining basic insights into genetic innovations that led to formation of eukaryotic cells. In evolutionary terms, the divergence of this organism is at least twice as ancient as the common ancestor for yeast and man. A detailed study of its genome will provide insights into an early evolutionary stage of eukaryotic chromosome organization as well as other aspects of the prokaryotic / eukaryotic divergence.
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The Coronavirus Antiviral Research Database is designed to expedite the development of SARS-CoV-2 antiviral therapy. It will benefit global coronavirus drug development efforts by (1) promoting uniform reporting of experimental results to facilitate comparisons between different candidate antiviral compounds; (2) identifying gaps in coronavirus antiviral drug development research; (3) helping scientists, clinical investigators, public health officials, and funding agencies prioritize the most promising compounds and repurposed drugs for further development; (4) providing an objective, evidenced-based, source of information for the public; and (5) creating a hub for the exchange of ideas among coronavirus researchers whose feedback is sought and welcomed. By comprehensively reviewing all published laboratory, animal model, and clinical data on potential coronavirus therapies, the Database makes it unlikely that promising treatment approaches will be overlooked. In addition, by making it possible to compare the underlying data associated with competing treatment strategies, stakeholders will be better positioned to prioritize the most promising anti-coronavirus compounds for further development.
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The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. The UniProt databases are the UniProt Knowledgebase (UniProtKB), the UniProt Reference Clusters (UniRef), and the UniProt Archive (UniParc).
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TriTrypDB is an integrated genomic and functional genomic database for pathogens of the family Trypanosomatidae, including organisms in both Leishmania and Trypanosoma genera. TriTrypDB and its continued development are possible through the collaborative efforts between EuPathDB, GeneDB and colleagues at the Seattle Biomedical Research Institute (SBRI).
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The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography.
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Patients-derived tumor xenograft (PDX) mouse models are an important oncology research platform to study tumor evolution, drug response and personalised medicine approaches.
We have expanded to organoids and cell lines and are now called CancerModels.Org
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GNPS is a web-based mass spectrometry ecosystem that aims to be an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. GNPS aids in identification and discovery throughout the entire life cycle of data; from initial data acquisition/analysis to post publication.
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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.
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The Life Science Database Archive maintains and stores the datasets generated by life scientists in Japan in a long-term and stable state as national public goods. The Archive makes it easier for many people to search datasets by metadata (description of datasets) in a unified format, and to access and download the datasets with clear terms of use.
In addition, the Archive provides datasets in forms friendly to different types of users in public and private institutions, and thereby supports further contribution of each research to life science.
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The GWAS Catalog is an open access repository of all human genome wide association studies. It is considered the “go-to” resource for genetic evidence of associations between common genetic variation and diseases or phenotypes, is accessed by scientists, clinicians and other users worldwide, and is integrated with numerous other resources. Association data and metadata are identified and extracted from the scientific literature by expert data curators. Submissions of full genome wide summary data can be made directly by authors, either before or after journal publication.
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This is CSDB version 1 merged from Bacterial (BCSDB) and Plant&Fungal (PFCSDB) databases. This database aims at provision of structural, bibliographic, taxonomic, NMR spectroscopic and other information on glycan and glycoconjugate structures of prokaryotic, plant and fungal origin. It has been merged from the Bacterial and Plant&Fungal Carbohydrate Structure Databases (BCSDB+PFCSDB). The key points of this service are:
High coverage. The coverage for bacteria (up to 2016) and archaea (up to 2016) is above 80%. Similar coverage for plants and fungi is expected in the future. The database is close to complete up to 1998 for plants, and up to 2006 for fungi.
Data quality. High data quality is achieved by manual curation using original publications which is assisted by multiple automatic procedures for error control. Errors present in publications are reported and corrected, when possible. Data from other databases are verified on import.
Detailed annotations. Structural data are supplied with extended bibliography, assigned NMR spectra, taxon identification including strains and serogroups, and other information if available in the original publication.
Services. CSDB serves as a platform for a number of computational services tuned for glycobiology, such as NMR simulation, automated structure elucidation, taxon clustering, 3D molecular modeling, statistical processing of data etc.
Integration. CSDB is cross-linked to other glycoinformatics projects and NCBI databases. The data are exportable in various formats, including most widespread encoding schemes and records using GlycoRDF ontology.
Free web access. Users can access the database for free via its web interface (see Help).
The main source of data is retrospective literature analysis. About 20% of data were imported from CCSD (Carbbank, University of Georgia, Athens; structures published before 1996) with subsequent manual curation and approval. The current coverage is displayed in red on the top of the left menu. The time lag between the publication of new data and their deposition into CSDB is ca. 1 year.
In the scope of bacterial carbohydrates, CSDB covers nearly all structures of this origin published up to 2016. Prokaryotic, plant and fungal means that a glycan was found in the organism(s) belonging to these taxonomic domains or was obtained by modification of those found in them. Carbohydrate means a structure composed of any residues linked by glycosidic, ester, amidic, ketal, phospho- or sulpho-diester bonds in which at least one residue is a sugar or its derivative.
- Current projects
- EOSC FAIR-IMPACT
- re3data COREF
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To the extent possible under law,
re3data.org
has waived all copyright and related or neighboring rights to
the database entries of re3data.org.
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Except where otherwise noted, content on this site is licensed under a
Creative Commons Attribution 4.0 International License
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- Cite this service: re3data.org - Registry of Research Data Repositories. https://doi.org/10.17616/R3D last accessed: 2024-04-24
