 | | Databases & Portals Biological Sciences
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| | AGRIS (agris.fao.org/agris-search/index.do) International System for Agricultural Science and Technology providing access to bibliographic information on agricultural science and technology. AGRIS started in 1974 by the Food and Agriculture Organization (FAO) of the United Nations, to serve users from both developed and developing countries, to enable access to available knowledge in agriculture, science and technology. AGRIS facilitates access to publications, journal articles, monographs, book chapters, and grey literature - including unpublished science and technical reports, theses, dissertations and conference papers. |
| | AgroZoo (agrozoo.ru) ► Russian agricultural databases. |
| | Allen Brain Atlas (www.brain-map.org) Allen Institute Portal. Contains transcriptomic atlases for mouse and man. |
| | Australian Plant Image Index (anbg.gov.au/photo/index.html) ► The Australian National Botanic Gardens (ANBG) has for many years been building up a collection of photographs and illustrations of Australia's native plants. Originally these were photos taken on field collecting trips to supplement the herbarium specimens and data associated with the living plants. In recent years many other photographers have contributed to the Index. The aim of the project is to have a good quality coloured slide or born-digital image of every Australian native plant represented in the Australian Plant Image Index. |
| | Avibase (avibase.bsc-eoc.org/avibase.jsp) ► Avibase is an online database that organizes bird taxonomic and distribution data globally. At its core, the database relies on the notion of taxonomic concepts rather than taxonomic names. The rationale and the methodology for this were explained in a paper published in ZooKeys (Lepage et al., 2014). This web site offers checklists for over 20,000 geographic regions of the world, species pages with taxonomic information and synonyms, and tools for observers to maintain their own sightings and obtain reports (e.g. map showing countries or eBird hotspots with the number of target species that are missing from one of their life list). Avibase incorporates taxonomic data from the major taxonomic publishers (Clements's checklist, HBW/Birdlife, IOC Checklist and Howard and Moore) and other regional sources (e.g. all editions of the AOU checklist since 1886). Taxonomic concepts in over 230 different taxonomic sources have been mapped and cross-referenced to Avibase concepts. Avibase has been created and maintained by Denis Lepage, Senior Director, Data Science and Technology at Birds Canada. |
| | BioCyc (https://biocyc.org/)The BioCyc collection of Pathway/Genome Databases (PGDBs) provides a reference on the genomes, metabolic pathways, and (in some cases) regulatory networks of thousands of sequenced organisms. The EcoCyc and MetaCyc databases are freely available to all users because their curation is supported by NIH funding. Also free is the database for the cyanobacterium Arthrospira platensis NIES-39 as an example of a Tier 3 database. The other BioCyc databases are available via subscription, which supports their curation. |
| | The Biodiversity Heritage Library (www.biodiversitylibrary.org)The Biodiversity Heritage Library improves research methodology by collaboratively making biodiversity literature openly available to the world as part of a global biodiversity community. |
| | BioModels (www.ebi.ac.uk/biomodels/) ► BioModels is a repository of mathematical models of biological and biomedical systems. It hosts a vast selection of existing literature-based physiologically and pharmaceutically relevant mechanistic models in standard formats. The mission is to provide the systems modelling community with reproducible, high-quality, freely-accessible models published in the scientific literature. |
| | BOLD (v4.boldsystems.org/)The Barcode of Life Data System (BOLD) is an online workbench and database that supports the assembly and use of DNA barcode data. BOLD is a cloud-based data storage and analysis platform developed at the Centre for Biodiversity Genomics in Canada. It consists of four main modules, a data portal, an educational portal, a registry of BINs (putative species), and a data collection and analysis workbench. |
| | Bookshelf (www.ncbi.nlm.nih.gov) An electronic library for books in medicine and biological science supported by National Center of Biotechnological Information (NCBI, USA). |
| | Brenda (brenda-enzymes.info) ►BRENDA is the most comprehensive information repository on enzymes and enzyme ligand data. The BRENDA enzyme information system has developed into an elaborate system of enzyme and enzyme-ligand information obtained from different sources, combined with flexible query systems and evaluation tools. BRENDA has been developed and is maintained by the Institute of Biochemistry and Bioinformatics at the Technical University of Braunschweig, Germany. Data on enzyme function are extracted manually from primary literature, and are complemented by text and data mining, data integration, and prediction algorithms. |
| | Cancer GeneticsWeb (www.cancerindex.org/geneweb)The site provides comprehensive links to reliable information about genes, their associated proteins, and genetic mutations associated with cancer and related disorders. Each gene page includes links to major genetic databases. |
| | Catalogue of Life (www.catalogueoflife.org) Catalogue of Life includes all species of live nature that are recorded by the professionals. |
| | CBS-KNAW culture collection (wi.knaw.nl)The CBS-KNAW culture collection is the largest one in the world with more 100.000 strains of fungi (including yeasts) and bacteria. |
| | ChEBI (ebi.ac.uk/chebi/) ► Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds. The term ‘molecular entity’ refers to 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. |
| | Complete Work of Charles Darwin Online (darwin-online.org.uk)Free-access Darwin works that have been prepared by a historian of science Dr. John van Wyhe. |
| | ConsensusPathDB (darwin-online.org.uk)ConsensusPathDB is a meta-database that integrates different types of functional interactions from heterogeneous interaction data resources. Physical protein interactions, metabolic and signaling reactions and gene regulatory interactions are integrated in a seamless functional association network that simultaneously describes multiple functional aspects of genes, proteins, complexes, metabolites, etc. With 155 432 human, 194 480 yeast and 13 648 mouse complex functional interactions (originating from 18 databases on human and eight databases on yeast and mouse interactions each), ConsensusPathDB currently constitutes the most comprehensive publicly available interaction repository for these species. The Web interface at http://cpdb.molgen.mpg.de offers different ways of utilizing these integrated interaction data, in particular with tools for visualization, analysis and interpretation of high-throughput expression data in the light of functional interactions and biological pathways. |
| | eBird (ebird.org)eBird is among the world’s largest biodiversity-related science projects, with more than 100 million bird sightings contributed each year by eBirders around the world. A collaborative enterprise with hundreds of partner organizations, thousands of regional experts, and hundreds of thousands of users, eBird is managed by the Cornell Lab of Ornithology. |
| | Ensembl (http://www.ensembl.org/index.html)Ensembl is a genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. Ensembl annotates genes, computes multiple alignments, predicts regulatory function and collects disease data. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor for all supported species. |
| | EURExpress (www.eurexpress.org/ee)EURExpress is a Transcriptome Atlas Database for Mouse Embryo (European Community Project). |
| | European Bioinformatics Institute (www.ebi.ac.uk) Portal of European Bioinformatics Institute that is a subsidiary of the European Molecular Biology Lab (EMBL). It offers an information on biological experiments and gives an access to several molecular data bases. |
| | ExPASy (www.expasy.org) Portal of SIB Bioinformatics Resource that gives an access to DBs and resource on various fields of biological sciences including proteomics, genomics, phylogeny, system biology, population genetics, transcriptomics etc. |
| | Fungal databases - nomenclature and species banks (www.mycobank.org/) Fungal Databases that are supported by International Mycology Association. |
| | Fungal Genetics Stock Center (www.fgsc.net) Open Repository Database on Fungal Genetics. |
| | GBIF (Global Biodiversity Information Facility) (www.gbif.org) GBIF—the Global Biodiversity Information Facility - is an international network and research infrastructure funded by the world's governments and aimed at providing anyone, anywhere, open access to data about all types of life on Earth. It is the largest biodiversity database in the world with records of hundreds of millions of occurrences of over 1.7 million species, ranging from bacteria to blue whales. Institutions from over 50 countries contribute species occurrence and related data to the open-access platform, which make possible regional or global-scale analyses of data ranging from global distributions to invasive species and climate change impacts. |
| | GBIF.ru (gbif.ru/) ► Russian site focused on open access biodiversity information. Among various materials on biodiversity in Russia, presented is the information on the Global Biodiversity Information Facility (GBIF) and biodiversity portals all over the world, as well as related events, such as conferences and conference proceedings. |
| | GEISHA (geisha.arizona.edu/geisha/) ►GEISHA is the online repository of in situ hybridization and corresponding metadata for genes expressed in the chicken embryo during the first six days of development. GEISHA is a public resource funded by the National Institutes of Health, USA. |
| | GenAtlas (genatlas.medecine.univ-paris5.fr) A specialized data base on gene structure, expression and function, gene mutations. It offers to search by specific gene or phenotype. Reference information search is available. |
| | Global Registry of Scientific Collections (grbio.org) This registry of scientific collections builds on GRSciColl, a comprehensive, community-curated clearinghouse of collections information originally developed by Consortium of the Barcode of Life (CBOL). |
| | Hudsen (hudsen.org/) ► The HUDSEN Atlas is a three-dimensional (3D) spatial framework for studying gene expression in the developing human brain. |
| | IntAct Molecular Interaction Database (ebi.ac.uk/intact/) ► IntAct provides an open source database and toolkit for the storage, presentation and analysis of protein interactions. The web interface provides both textual and graphical representations of protein interactions, and allows exploring interaction networks in the context of the GO annotations of the interacting proteins. A web service allows direct computational access to retrieve interaction networks in XML format. IntAct currently contains about 2200 binary and complex interactions imported from the literature and curated in collaboration with the Swiss‐Prot team. |
| | ITIS (itis.gov/) ► Integrated Taxonomic Information System. Here you will find authoritative taxonomic information on plants, animals, fungi, and microbes of North America and the world. The project is a partnership of U.S., Canadian, and Mexican agencies (ITIS-North America); other organizations; and taxonomic specialists. ITIS is also a partner of Species 2000 and the Global Biodiversity Information Facility (GBIF). The ITIS and Species 2000 Catalogue of Life (CoL) partnership is proud to provide the taxonomic backbone to the Encyclopedia of Life (EOL). |
| | KEGG: Kyoto Encyclopedia of Genes and Genomes (www.genome.jp)A knowledge base for systematic analysis of gene functions, linking genomic information with higher order functional information. It 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. A vast library of information gathered from fully sequenced genomes, genes, proteins, pathways, and chemical compounds pertaining to over a hundred different species of both prokaryotes and eukaryotes. |
| | Learn. Genetics (learn.genetics.utah.edu) The website from the Genetic Science Learning Center at the University of Utah contains a massive amount of information on genetics. There are detailed explorations of transcription and translation, heredity and traits, and cells. Each topic page has links to other topic pages for review and for further information. There are also four virtual labs: DNA extraction, gel electrophoresis, PCR, and DNA microarrays. In addition to basic genetics, the site also has some segments on topics such as epigenetics, the science of addiction, genetic disorders, and pharmacogenomics. There are also useful links to other Internet sites, including one linking to a list of videos and images of actual cells. |
| | MedBioWorld (www.medbioworld.com/index.php) A portal that provides information on medicine and biotechnology. |
| | MetaCyc Metabolic Pathway Database (metacyc.org) ►A curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2937 pathways from 3295 different organisms 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. |
| | MINT (mint.bio.uniroma2.it) ►MINT, the Molecular INTeraction database, focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. MINT is designed to store data on functional interactions between proteins. Beyond cataloguing binary complexes, MINT was conceived to store other types of functional interactions, including enzymatic modifications of one of the partners. |
| | miRBase (mirbase.org/) ► A searchable database of published miRNA sequences and annotation. Each entry represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence. Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download. miRBase also provides a confidential gene-naming service, assigning official miRNA names to novel genes before their publication. |
| | MycoBank (mycobank.org) ► MycoBank is an on-line database aimed as a service to the mycological and scientific community by documenting mycological nomenclatural novelties (new names and combinations) and associated data, for example descriptions and illustrations. Pairwise sequence alignments and polyphasic identifications of fungi and yeasts against curated references databases are proposed. |
| | NAR Database Summary Paper Category List
(www.oxfordjournals.org/nar/database/c)A catalogue of biological data bases of a broad scope that is published by Nucleic Acids Research (NAR) Journal. |
| | NCBI databases (ncbi.nlm.nih.gov)Databases of the National Center for Biotechnology Information contain information on biomedicine and genomics |
| | NetPath (netpath.org) ► NetPath is a manually curated resource of signal transduction pathways in humans. It is a collaborative effort between the PandeyLab at Johns Hopkins University and the Institute of Bioinformatics. The initial set of 10 cancer signaling pathways were developed in collaboration with the Computational Biology Center at Memorial Sloan-Kettering Cancer Center and with Gary Bader's lab at the University of Toronto for the Cancer Cell Map. |
| | OneZoom tree of life explorer (onezoom.org/) ►OneZoom is the only tool where you can explore the complete tree of all known life, over two million species, on one page. An interactive map of the evolutionary links between all living things known to science. Everything that is alive, or has ever been alive has a place somewhere on the complete tree of life. Each leaf represents a different species and the branches show how they are evolved from common ancestors over billions of years. |
| | Pathbase (pathbase.net/) ► A web accessible database of histopathological images of laboratory mice, developed as a resource for the coding and archiving of data derived from the analysis of mutant or genetically engineered mice and their background strains. The metadata for the images, which allows retrieval and interoperability with other databases, is derived from a series of orthogonal ontologies and controlled vocabularies. Lesions are described according to the Pathbase pathology ontology developed by the Pathbase European Consortium, and available here or on the BioPortal website. |
| | Pathway Commons (pathwaycommons.org) ► An integrated resource of publicly available information about biological pathways including biochemical reactions, assembly of biomolecular complexes, transport and catalysis events and physical interactions involving proteins, DNA, RNA, and small molecules. Data is collected from multiple providers in standard formats, including the Biological Pathway Exchange language and the Proteomics Standards Initiative Molecular Interactions format, and then integrated. Pathway Commons provides biologists with tools to search this comprehensive resource, a download site offering integrated bulk sets of pathway, reusable software libraries for working with pathway information in several programming languages and a web service for programmatically querying the entire dataset. |
| | Plantarium (plantarium.ru/) ► The site features an extensive amount of information related to plants and lichens of Russia and neighbouring countries, including a species identification guide. |
| | Plants For A Future (www.pfaf.org/user/plantsearch.aspx)Plants For A Future (PFAF) data base that includes about 7000 plant species |
| | Protein Information Resource (www-nbrf.georgetown.edu)PIR is an integrated public bioinformatics resource to support genomic, proteomic and systems biology research and scientific studies.copy (mirror) of the database. |
| | RCSB Protein Data Bank (www.rcsb.org)The Protein Data Bank (PDB) was established as the first open access digital data resource in all of biology and medicine. It is today a leading global resource for experimental data central to scientific discovery. Through an internet information portal and downloadable data archive, the PDB provides access to 3D structure data for large biological molecule. |
| | REACTOME (reactome.org) ►REACTOME is an open-source, open access, manually curated and peer-reviewed pathway database. The goal is to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge to support basic and clinical research, genome analysis, modeling, systems biology and education. Founded in 2003. |
| | REBASE (rebase.neb.com/rebase/rebase.html) The database on restriction ferments. |
| | SDAP - Structural Database of Allergenic Proteins (fermi.utmb.edu/SDAP/) ► SDAP - Structural Database of Allergenic Proteins - is a Web server that integrates a database of allergenic proteins with various computational tools that can assist structural biology studies related to allergens. SDAP is an important tool in the investigation of the cross-reactivity between known allergens, in testing the FAO/WHO allergenicity rules for new proteins, and in predicting the IgE-binding potential of genetically modified food proteins. Using this Internet service through a browser, it is possible to retrieve information related to an allergen from the most common protein sequence and structure databases (SwissProt, PIR, NCBI, PDB), to find sequence and structural neighbors for an allergen, and to search for the presence of an epitope other the whole collection of allergens. |
| | SIGNOR (signor.uniroma2.it) ► The SIGnaling Network Open Resource organizes and stores in a structured format signaling information published in the scientific literature. The captured information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow. The entire network can be freely downloaded and used to support logic modeling or to interpret high content datasets. The core of this project is a collection of more than 11000 manually-annotated causal relationships between proteins that participate in signal transduction. Each relationship is linked to the literature reporting the experimental evidence. In addition each node is annotated with the chemical inhibitors that modulate its activity. The signaling information is mapped to the human proteome even if the experimental evidence is based on experiments on mammalian model organisms.. |
| | SMPDB (smpdb.ca/) ► SMPDB, Small Molecule Pathway Database is an interactive, visual database containing more than 30 000 small molecule pathways found in humans only. The majority of these pathways are not found in any other pathway database. SMPDB is designed specifically to support pathway elucidation and pathway discovery in metabolomics, transcriptomics, proteomics and systems biology. It is able to do so, in part, by providing exquisitely detailed, fully searchable, hyperlinked diagrams of human metabolic pathways, metabolic disease pathways, metabolite signaling pathways and drug-action pathways. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein complex cofactors, protein complex locations, metabolite locations, chemical structures and protein complex quaternary structures. Each small molecule is hyperlinked to detailed descriptions contained in the HMDB or DrugBank and each protein complex or enzyme complex is hyperlinked to UniProt. All SMPDB pathways are accompanied with detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram. The database is easily browsed and supports full text, sequence and chemical structure searching. Users may query SMPDB with lists of metabolite names, drug names, genes/protein complex names, SwissProt IDs, GenBank IDs, Affymetrix IDs or Agilent microarray IDs. These queries will produce lists of matching pathways and highlight the matching molecules on each of the pathway diagrams. Gene, metabolite and protein complex concentration data can also be visualized through SMPDB's mapping interface. |
| | SPIKE (cs.tau.ac.il/~spike) SPIKE, Signaling Pathways Integrated Knowledge Engine, is a database of highly curated human signaling pathways with an associated interactive software tool. Users can view and download individual pathway maps and browse the entire database from this website, or launch a map viewer tool that allows dynamic visualization of the database and save networks in XGMML format that can be viewed in all generic XGMML viewers. |
| | The UCSC Genome Browser (genome.ucsc.edu/) ►The UCSC Genome Browser. the website has grown to include a broad collection of vertebrate and model organism assemblies and annotations, along with a large suite of tools for viewing, analyzing and downloading data. For more than two decades, the UCSC Genome Browser database has provided high-quality genomics data visualization and genome annotations to the research community. Apart from incorporating data from researchers and consortia, the Browser also provides tools available for users to view and compare their own data with ease. Custom tracks allow users to quickly view a dataset, and track hubs allow users to extensively organize their data and share it privately using a URL. |
| | UniProt (www.uniprot.org) The Universal Protein Resource (UniProt) is UniProt Knowledgebase data bases (UniProtKB), the UniProt Reference Clusters (UniRef), and the UniProt Archive (UniParc). It is one of the most comprehensive information directories on proteins and its functions. |
| | Unknome (unknome.mrc-lmb.cam.ac.uk/) ► The database provides all protein clusters that contain at least 1 protein from humans or any of 11 model organisms. The clusters can be ranked by knownness, and the user can modify this list so as to include only those proteins that are present in a particular combination of species, such as human plus a preferred model organism. For each protein family, the interface shows the orthologs in its cluster and how the knownness of the cluster has changed over time. These design principles maximise the versatility and power of the Unknome database as a tool for researchers from different biomedical fields. |
| | Whole Mouse Catalog (wmc.rodentia.com)The catalogue of Internet resources of particular interest to scientific researchers using mice or rats in their work. |
| | WikiPathway (www.wikipathways.org/)WikiPathways is a database of biological pathways maintained by and for the scientific 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. 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. |
| | World Flora Online (www.worldfloraonline.org)The World Flora Online is an open-access, Web-based compendium of the world’s plant species. It will be a collaborative, international project, building upon existing knowledge and published floras, checklists and revisions but will also require the collection and generation of new information on poorly know plant groups and plants in unexplored regions |
| | World-Wide Virtual Library: Botany (www.ou.edu/cas/botany-micro/www-vl)A virtual library on plant biology (agriculture, ecology, biotechnology, gardening, forestry etc) |
| | zoomet.ru (zoomet.ru/) An electronic biological library containing Russian books and articles. |
