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Global Biodata Coalition
The Global Biodata Coalition is an organization promoting biocuration and fostering support of research funders for the sustainability of biological data resources. Global Core Biodata Resources (GCBRs) The organization maintains a list of resources, representing "critical components for ensuring the reproducibility and integrity of life sciences research." As of 2023, the list includes the following organizations: * Alliance of Genome Resources * BacDive * BAR: Bio-Analytic Resource for Plant Biology * Bgee * BRENDA * Catalogue of Life (COL) * CATH database * Cellosaurus * ChEBI * ChEMBL * CIViC: Clinical Interpretation of Variants in Cancer * Clinical Genome Resource (ClinGen) * DNA Data Bank of Japan (DDBJ Center) * EcoCyc * Ensembl * Europe PMC * European Nucleotide Archive (ENA) * FlyBase * GENCODE * Gene Ontology (GO) * Global Biodiversity Information Facility (GBIF) * Genome Aggregation Database (gnomAD) * Genome Sequence Archive (GSA) * NHGRI-EBI Catalog o ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bgee
Bgee is a biological database, database maintained by the SIB Swiss Institute of Bioinformatics and the University of Lausanne for retrieval and comparison of gene expression patterns from RNA-Seq, scRNA-Seq, DNA_microarray, Microarray, In situ hybridization and Expressed sequence tag, EST studies, across multiple animal species. Bgee provides an intuitive answer to the question ''where is a gene expressed?'' and supports research in cancer and agriculture, as well as evolutionary biology. Bgee is based exclusively on curated, healthy Wild type, wild-type, expression data (i.e., no Gene knockout, gene knock-out, no treatment, no disease), to provide a comparable reference of healthy wild-type gene expression. Bgee produces calls of presence/absence of expression, and of differential over-/under-expression, integrated along with information of gene Sequence homology#Orthology, orthology, and of Homology (biology), homology between Organ (biology), organs. This allows comparisons o ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Biocuration
Biocuration is the field of life sciences dedicated to organizing biomedical data, information and knowledge into structured formats, such as spreadsheets, tables and knowledge graphs. The biocuration of biomedical knowledge is made possible by the cooperative work of biocurators, software developers and bioinformaticians and is at the base of the work of biological databases. Biocuration as a profession A biocurator is a professional scientist who curates, collects, annotates, and validates information that is disseminated by biological and model organism databases. It is a new profession, with the first mentions in the scientific literature dating of 2006 in the context of the work in databases like the Immune Epitope Database and Analysis Resource. Biocurators usually are PhD-level with a mix of experiences in wet lab and computational representations of knowledge (e.g. via ontologies). The role of a biocurator encompasses quality control of primary biological research dat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
European Nucleotide Archive
The European Nucleotide Archive (ENA) is a repository providing free and unrestricted access to annotated nucleic acid sequence, DNA and RNA sequences. It also stores complementary information such as experimental procedures, details of Genome project#Genome assembly, sequence assembly and other metadata related to genome project, sequencing projects. The archive is composed of three main databases: the Sequence Read Archive, the Trace Archive and the EMBL Nucleotide Sequence Database (also known as EMBL-bank). The ENA is produced and maintained by the European Bioinformatics Institute and is a member of the International Nucleotide Sequence Database Collaboration (INSDC) along with the DNA Data Bank of Japan and GenBank. The ENA has grown out of the EMBL Data Library which was released in 1982 as the first internationally supported resource for nucleotide sequence data. As of early 2012, the ENA and other INSDC member databases each contained complete genomes of 5,682 organisms ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
List Of Prokaryotic Names With Standing In Nomenclature
List of Prokaryotic names with Standing in Nomenclature (LPSN) is an online database that maintains information on the naming and taxonomy of prokaryotes, following the taxonomy requirements and rulings of the International Code of Nomenclature of Prokaryotes. The database was curated from 1997 to June 2013 by Jean P. Euzéby. From July 2013 to January 2020, LPSN was curated by Aidan C. Parte. In February 2020, a new version of LPSN was published as a service of the Leibniz Institute DSMZ, thereby also integrating the Prokaryotic Nomenclature Up-to-date service and since 2022 LPSN is interconnected with the Type (Strain) Genome Server (TYGS), DSMZ's high-throughput platform for accurate genome-based taxonomy. See also * Code of Nomenclature of Prokaryotes Described from Sequence Data References External links List of Prokaryotic names with Standing in Nomenclature [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
LIPID MAPS
LIPID MAPS (Lipid Metabolites and Pathways Strategy) is a web portal designed to be a gateway to Lipidomics resources. The resource has spearheaded a classification of biological lipids, dividing them into eight general categories. LIPID MAPS provides standardised methodologies for mass spectrometry analysis of lipids, e.g. LIPID MAPS has been cited as evidence of a growing appreciation of the study of lipid metabolism and the rapid development and standardisation of the lipidomics field Key LIPID MAPS resources include: * LIPID MAPS Structure Database (LMSD) - a database of structures and annotations of biologically relevant lipids, containing over 49000 different lipids. The paper describing this resource has, according to PubMed, been cited more than 200 times. * LIPID MAPS In-Silico Structure Database (LMISSD) - a database of computationally predicted lipids generated by expansion of headgroups for commonly occurring lipid classes * LIPID MAPS Gene/Proteome Database (LMPD) - ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Guide To Pharmacology
The IUPHAR/BPS Guide to PHARMACOLOGY is an open-access website, acting as a portal to information on the biological targets of licensed drugs and other small molecules. The Guide to PHARMACOLOGY (with GtoPdb being the standard abbreviation) is developed as a joint venture between the International Union of Basic and Clinical Pharmacology (IUPHAR) and the British Pharmacological Society (BPS). This replaces and expands upon the original 2009 IUPHAR Database (standard abbreviation IUPHAR-DB). The Guide to PHARMACOLOGY aims to provide a concise overview of all pharmacological targets, accessible to all members of the scientific and clinical communities and the interested public, with links to details on a selected set of targets. The information featured includes pharmacological data, target, and gene nomenclature, as well as curated chemical information for ligands. Overviews and commentaries on each target family are included, with links to key references. Background and developme ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
InterPro
InterPro is a database of protein families, protein domains and functional sites in which identifiable features found in known proteins can be applied to new protein sequences in order to functionally characterise them. The contents of InterPro consist of diagnostic signatures and the proteins that they significantly match. The signatures consist of models (simple types, such as regular expressions or more complex ones, such as Hidden Markov models) which describe protein families, domains or sites. Unknown sequences are searched to create homology models. Each of the member databases of InterPro contributes towards a different niche, from very high-level, structure-based classifications ( SUPERFAMILY and CATH-Gene3D) through to quite specific sub-family classifications ( PRINTS and PANTHER). InterPro's intention is to provide a one-stop-shop for protein classification, where all the signatures produced by the different member databases are placed into entries within the Inte ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
International Molecular Exchange Consortium
The International Molecular Exchange Consortium (IMEx) is a group of the major public providers of molecular interaction data to provide a single, non-redundant set of molecular interactions. Data is captured using a detailed curation model and made available in the PSI-MI standard formats. Participating databases include DIP, IntAct, the Molecular Interaction Database (MINT), MatrixDB, InnateDB, IID, HPIDB, UCL Cardiovascular Gene Annotation, MBInfo, Molecular Connections and UniProt. The group collates the interaction data and prevents duplicate entries in the various databases. The IMEx consortium also supports and contributes to the development of the HUPO-PSI Psi, PSI or Ψ may refer to: Alphabetic letters * Psi (Greek) (Ψ or ψ), the twenty-third letter of the Greek alphabet * Psi (Cyrillic), letter of the early Cyrillic alphabet, adopted from Greek Arts and entertainment * "Psi" as an abbreviat ...-MI XML format, which is now widely implemented. External reference ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Human Protein Atlas
The Human Protein Atlas (HPA) is a Swedish-based program started in 2003 with the aim to map all the human proteins in cells, tissues and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics and systems biology. All the data in the knowledge resource is open access to allow scientists both in academia and industry to freely access the data for exploration of the human proteome. In June 2023, version 23 was launched where a new Interaction section was introduced containing human protein-protein interaction networks for more than 11,000 genes that will add new aspects in terms of protein function. The resource now includes twelve separate sections with complementary information about all human proteins. All data has been updated on the approximately 5 million individual web pages. The Human Protein Atlas program has already contributed to several thousands of publications in the field of human ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Disease Ontology
The Disease Ontology (DO) is a formal ontology of human disease. ThDisease Ontology projectis hosted at thInstitute for Genome Sciencesat the University of Maryland School of Medicine. The Disease Ontology project was initially developed in 2003 at Northwestern University to address the need for a purpose-built ontology that covers the full spectrum of disease concepts annotated within biomedical repositories within an ontological framework that is extensible to meet community needs. The Disease Ontology is an OBO ( Open Biomedical Ontologies) Foundry ontology. Disease Ontology Identifiers (DOIDs) consist of the prefix DOID: followed by number, for example, Alzheimer's disease has the stable identifieDOID:10652 DO is cross-referenced in several resources such as UniProt. Example term The Disease Ontology entry for motor neuron disease in OBO format is given below, showing the links to other classification schemes, including ICD-9, ICD-10, MeSH, SNOMED and UMLS. :id: DOID:231 :n ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
HUGO Gene Nomenclature Committee
The HUGO Gene Nomenclature Committee (HGNC) is a committee of the Human Genome Organisation (HUGO) that sets the standards for human gene nomenclature. The HGNC approves a ''unique'' and ''meaningful'' name for every known human gene, based on a query of experts. In addition to the name, which is usually 1 to 10 words long, the HGNC also assigns a symbol (a short group of characters) to every gene. As with an SI symbol, a gene symbol is like an abbreviation but is more than that, being a second unique name that can stand on its own just as much as substitute for the longer name. It may not necessarily "stand for" the initials of the name, although many gene symbols do reflect that origin. Purpose Full gene names, and especially gene abbreviations and symbols, are often not specific to a single gene. A marked example is CAP which can refer to any of 6 different genes (BRD4'', CAP1'', HACD1'', LNPEP'', SERPINB6'', and SORBS1''). The HGNC short gene names, or gene symbols, unlik ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
GWAS Catalog
The GWAS catalog is a free online database that compiles data of genome-wide association studies (GWAS), summarizing unstructured data from different literature sources into accessible high quality data. It was created by the National Human Genome Research Institute (NHGRI) in 2008 and have become a collaborative project between the NHGRI and the European Bioinformatics Institute (EBI) since 2010. As of September 2018, it has included 71,673 SNP–trait associations in 3,567 publications. A GWAS identifies genetic loci associated with common traits and disease through the analysis of categorized variants across the genome and the catalog provides information from all published GWAS results that meet its criteria. The catalog contains publication information, study groups information (origin, size) and SNP-disease association information (including SNP identifier, P-value, gene and risk allele). Over the years, the GWAS catalog has enhanced its data release frequency by adding fe ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
