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genecard数据库里面涵盖的数据库

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发表于 2017-3-23 11:41:37 | 显示全部楼层 |阅读模式
genecard本身不产生数据,就是了解各种公开的数据库的API,做一个整合。
他们的重点是,大而且全,用户友好型,界面美观。
他们涵盖的数据库有下面这些:
GeneCards Sources and External Links
The information presented in GeneCards is extracted from or linked to the following databases:
  • Addgene The non profit plasmid repository: Addgene provides a non-profit plasmid repository, and is dedicated to helping scientists around the world share high-quality plasmids
  • Abcam: Abcam: maker and commercial supplier of primary and secondary antibodies, biochemicals, proteins, peptides, lysates, immunoassays and other kits
  • AceView: AceView offers an integrated view of the human and nematode genes as reconstructed by mRNA and EST alignments
  • antibodies-online: antibodies-online, a marketplace for research reagents, offers >1 million research antibodies, ELISA kits, proteins and related products from over 150 suppliers
  • ApexBio - An Apoptosis and Epigenetics Company: ApexBio provides peptides and lab reagents for biological research
  • Atlas: ATLAS of Genetics and Cytogenetics in Oncology and Haematology
  • BioGPS: BioGPS is a service from the Genomics Institute of Novartis Research Foundation which provides an integrated portal which displays gene-centric annotation, including "annotation" based on reference gene expression data sets
  • BitterDB: BitterDB provides several ways to investigate the bitter world: search for bitter compounds by different criteria, search for bitter molecules with structure similar to a query compound, blast bitter receptors and more.
  • Blocks: BLOCKS is a database of Blocks multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins
  • Blood Group Antigen Gene Mutation Database: BGMUT is the Blood Group Antigen Gene Mutation Database of variations in the genes that encode antigens of blood group systems
  • BRCA Exchange: The BRCA Exchange aims to advance our understanding of the genetic basis of breast cancer, ovarian cancer and other diseases by pooling data on BRCA1/2 genetic variants and corresponding clinical data from around the world.
  • Cell Signaling Technology: CST (Cell Signaling Technology) provides discovery tools for cell signaling research, including information about pathways and phosphorylation sites
  • Centers for Disease Control and Prevention: The Centers for Disease Control and Prevention (CDC) contains information about various diseases and health conditions.
  • CGAP SAGE: CGAP (The Cancer Genome Anatomy Project) determines the gene expression profiles of normal, precancer, and cancer cells,leading eventually to improved detection, diagnosis, and treatment for the patient
  • ClinicalTrials.gov: ClinicalTrials.gov is a registry and results database of federally and privately supported clinical trials conducted in the United States and around the world.
  • ClinVar: ClinVar archives and aggregates information about relationships among variation and human health
  • Cloud-Clone Corp.: Cloud-Clone Corp.: produces ELISA Kits and other relevant life sciences reagents covering a full range of fields.
  • COMPARTMENTS Subcellular localization database: COMPARTMENTS Subcellular localization database integrates evidence on protein subcellular localization from manually curated literature, high-throughput screens, automatic text mining, and sequence-based prediction methods
  • Cyagen Biosciences Inc.: Cyagen Biosciences Inc. is a contract research organization and cell culture product manufacturer, a leader in custom animal models and molecular biology tools.
  • Data Mining of Enzymes: Data Mining of Enzymes (DME): a Web service that provides Specific Peptides for arbitrary proteins, determining from its sequence whether a protein is an enzyme and what the enzyme's EC classification is
  • Database of Genetic Variants: The Database of Genomic Variants (DGV) provides a comprehensive summary of structural variation in the human genome
  • Disease Ontology: Disease Ontology provides a hierarchical open source ontology for the integration of biomedical data that is associated with human disease.
  • diseasecard: Diseasecard is an information retrieval tool for accessing and integrating genetic and medical information for health applications.
  • DrugBank: The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information
  • eBioscience: eBioscience, an Affymetrix company, leads in immunology and oncology flow cytometry reagents, and offers large selections of antibodies, ELISAs and proteins for Life Science research and diagnostics
  • EMD MILLIPORE: EMD Millipore offers a broad range of Life Science tools, technologies, and services, and creates personalized solutions to industry challenges to assure scientific success
  • ENCODE: The ENCODE (Encyclopedia of DNA Elements) Consortium is an international collaboration of research groups with the goal to build a comprehensive list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active.
  • Ensembl: Ensembl: a software system producing and maintaining automatic annotation on eukaryotic genomes, which provides identification of known human genes in the genome sequence, prediction of additional genes with supporting evidence, and ortholog predictions based on duplication aware phylogenetic trees
  • Ensembl Pan Taxonomic Compara: Ensembl pan taxonomic compara: A broad view of homologous relationships across representative genomes from all significant clades represented in Ensembl and EnsemblGenomes
  • Enzo Life Sciences: Enzo Life Sciences incorporates BIOMOL, a supplier of specialty biochemicals, with applications in signal transduction, lipid research, apoptosis,neuroscience and drug discovery
  • ESI BIO: ESI BIO provides human embryonic stemcell lines and human embryonic progenitor cells
  • euGenes: euGenes: Genomic Information for Eukaryotic Organisms Database for more details on similar genes in other organisms
  • FANTOM5 Human Transcribed Enhancer Atlas: A database describing enhancer regions defined by CAGE tags in the FANTOM5 project.
  • FlyBase: a database of the Drosophila genome.
  • fRNAdb: A comprehensive non-coding RNA sequence database
  • GENATLAS: Genatlas: a catalog of genes, markers and phenotypes with many links to major data sources. GeneCards offers the short description of the gene that often contains interesting, concise information about its cellular functions and/or role in diseases
  • GenBank: the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences.
  • Gene Ontology: GO, the Gene Ontology, is a dynamic controlled vocabulary that can be applied to all organisms even as knowledge of gene and protein roles in cells is accumulating and changing
  • Gene Wiki: Gene Wiki is a project that facilitates transferring information on human genes to Wikipedia article stubs with the goal of promoting collaboration and expansion of the articles
  • GeneAnnot: Annotation of high-density oligunocleotide arrays at the Weizmann Institute of Science, with links to Affymetrix probe-sets.
  • GeneCards: GeneCards is a searchable, integrative database that provides comprehensive, user-friendly information on all annotated and predicted human genes
  • GeneGo (Thomson Reuters Life Sciences Research): GeneGo (Thomson Reuters) Maps are interactive pathways with consensus knowledge on signaling and metabolism involved in human biology and diseases
  • GeneLoc: GeneLoc (formerly The Unified DataBase (UDB)) integrates information on the human genome, with emphasis on mapping information. Mapped DNA segments, classified by categories (such as genes, EST clusters and STSs mapped by various methods) are presented on a Megabase-scale integrated map, with further links to relevant databases
  • GeneReviews: GeneReviews are expert-authored, peer-reviewed disease descriptions presented in a standardized format and focused on clinically relevant and medically actionable information on the diagnosis, management, and genetic counseling of patients and families with specific inherited conditions.
  • GENETests: GeneTests (formerly GeneClinics): a clinical information resource relating genetic testing to the diagnosis, management, and genetic counseling of individuals and families with specific inherited disorders
  • GeneTex: GeneTex provides GeneCards with antibodies and recombinant proteins, and strives to serve and accelerate life science research by creating essential biomedical reagents where quality can be found in every vial
  • Genetic Association Database: The Genetic Association Database (GAD) is an archive of human genetic association studies of complex diseases and disorders
  • Genetic Testing Registry: The Genetic Testing Registry (GTR) provides a central location for voluntary submission of genetic test information by providers. The scope includes the test's purpose, methodology, validity, evidence of the test's usefulness, and laboratory contacts and credentials.
  • Genetics Home Reference: Genetics Home Reference provides consumer-friendly information about the effects of genetic variations on human health.
  • Genome Annotation for Alternative Splicing: A new EST clustering method that produces gene models based on genomic alignment of mRNA and ESTs
  • GenomeRNAi: Genome RNAi is a database containing phenotypes from RNA interference (RNAi) screens in Drosophila and Homo sapiens. In addition, the database provides an updated resource of RNAi reagents and their predicted quality
  • GenScript: GenScript is a biology clinical research organization focusing exclusively on early drug discovery and development services
  • HomoloGene: HomoloGene: a resource of curated and calculated orthologs for genes as represented by UniGene or by annotation of genomic sequences
  • HORDE: HORDE is the Human Olfactory Receptor Data Explorer at the Weizmann Institute of Science
  • Horizon: Horizon is a fully integrated life science company that provides enabling products, services and research programs to clients engaged at every stage of the healthcare continuum from sequence to treatment.
  • HUGE: HUGE: the Database of Human Unidentified Gene-Encoded Large Proteins
  • Hugo Gene Nomenclature Committee: HUGO Gene Nomenclature Committee (HGNC) is the central clearinghouse for assigning gene names
  • Human Cytochrome P450 Allele Nomenclature Database: The Human Cytochrome P450 Allele Nomenclature Database is a database of CYP alleles and their associated effects
  • Human Gene Damage Index: The gene damage index (GDI) is the accumulated mutational damage of each human gene in healthy human population, based on the 1000 Genomes Project database (Phase 3) gene variations of healthy individuals and of the CADD score for calculating impact.
  • Human Gene Mutation Database: HGMD (Human Gene Mutation Database): information about disease-causing mutations in genes. GeneCards presents a link to specific entries in this database whenever they can be found
  • Human Genome Epidemiology Navigator: The HUman Genome Epidemiology Navigator: An integrated, searchable knowledge base of genetic associations and human genome epidemiology
  • Human Metabolome Database: HMDB (The Human Metabolome Database) is an electronic database containing detailed information about small molecule metabolites found in the human body
  • Human-Invitational Database: HInv-DB: H-Invitational Database (H-InvDB) is an integrated database of curated annotations of human genes and transcripts
  • Hypergeometric Optimization of Motif Enrichment: Hypergeometric Optimization of Motif EnRichment is a suite of tools for Motif Discovery and next-gen sequencing analysis
  • Illumina Human BodyMap: Illumina Human BodyMap: RNA obtained from 16 normal human tissues was sequenced and mapped to genes via their transcripts
  • ImMunoGeneTics Information System: ImMunoGeneTics Information System (IMGT): a high-quality integrated information system specialising in Immunoglobulins (IG), T cell receptors (TR) and Major Histocompatibility Complex (MHC) molecules of all vertebrate species
  • IntAct: IntAct: IntAct provides a freely available, open source database system and analysis tools for protein interaction data. All interactions are derived from literature curation or direct user submissions and are freely available
  • Integrated Interactions Database: IID (Integrated Interaction Database) is an on-line database of known and predicted eukaryotic protein-protein interactions, in 30 tissues of model organisms and humans.
  • International Union of Basic and Clinical Pharmacology: The IUPHAR: Guide to Pharmocology provides a searchable database with quantitative information on drug targets and the prescription medicines and experimental drugs that act on them
  • International Union of Biochemistry and Molecular Biology: IUBMB: The International Union of Biochemistry and Molecular Biology - the Nomenclature Committee
  • InterPro: InterPro: a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences
  • Invitrogen by Thermo Fisher Scientific: Thermo Fisher Scientific provides analytical instruments, laboratory equipment, software, services, consumables and reagents
  • KEGG, Kyoto Encyclopedia of Genes and Genomes: Kyoto Encyclopedia of Genes and Genomes (KEGG) provides pathway information
  • Leiden Muscular Dystrophy: Leiden Muscular Dystrophy pages are specifically designed for scientists performing research and/or diagnosis in Duchenne and Duchenne-like muscular dystrophies
  • LifeMap Sciences: LifeMap: a web based discovery platform aiding research and product development efforts in the stem cells field
  • Locus Specific Mutation Databases: LSDB: The Human Genome Variation Society's Locus Specific Mutation Databases
  • MalaCards: MalaCards: an integrated database of human maladies and their annotations, modeled on the architecture and richness of GeneCards, and leveraging GeneDecks and GeneNote
  • Medical Subject Headings: MeSH is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity.
  • MedlinePlus: Medlineplus contains health information from the National Library of Medicine.
  • miRBase: miRBase is the new home for microRNA data, incorporating the database and gene naming roles previously provided by the miRNA Registry, and including the new miRBase Target database
  • miRTarBase: miRTarBase is a database that curates experimentally validated microRNA-target interactions
  • Molecular INTeraction database: MINT (Molecular Interactions Database) focuses on experimentally verified protein interactions with special emphasis on proteomes from mammalian organisms, consists of entries mined in the scientific literature by curators
  • MOPED: Model Organism Protein Expression Database (frozen)
  • Mouse Genome Informatics: MGI (Mouse Genome Informatics, formerly MGD) provides a comprehensive source of information on the experimental genetics of the laboratory mouse; it includes information on mouse markers, mammalian homologies, probes and clones. GeneCards presents links to mammalian homology pages, the name of the mouse gene, its location (in centiMorgan), phenotypic alleles, and links to the entries for the mouse gene
  • National Institute of Neurological Disorders and Stroke: The National Institute of Neurological Disorders and Stroke (NINDS) conducts and supports research on brain and nervous system disorders.
  • NCBI: National Center for Biotechnology Information creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information
  • NCBI BioSystems Database: The NCBI BioSystems Database provides integrated access to biological systems and their component genes, proteins, and small molecules, as well as literature describing those biosystems and other related data throughout Entrez
  • NCBI Bookshelf: The NCBI Bookshelf provides free online access to books and documents in life science and healthcare.
  • NCBI Entrez Gene: EntrezGene at NCBI provides a single query interface to curated sequence and descriptive information about genetic loci
  • NCBI Reference Sequence Database: RefSeq: NCBI Reference Sequence Database A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
  • NCBI-PubMed: PubMed: NLM's search service to access the 9 million citations in MEDLINE and Pre-MEDLINE (with links to participating on-line journals), and other related databases
  • NEXTPROT: neXtProt offers seamless integration of human protein data
  • NIH Rare Diseases: The Office of Rare Diseases Research (ORDR) at the National Institutes of Health (NIH) coordinates research and information on rare diseases.
  • NONCODE: NONCODE is a database of all kinds of noncoding RNAs (except tRNAs and rRNAs)
  • Novoseek: Novoseek extracts knowledge from biological databases and text repositories, enabling users to uncover the knowledge hidden within these data sources
  • Novus Biologicals: Novus Biologicals provides the biological research community with a mechanism for commercializing unique biological materials
  • Nuclear Receptor Signaling Atlas: The mission of NURSA is to accrue, develop, and communicate information that advances our understanding of the roles of nuclear receptors (NRs) in human diseases and conditions in which NRs play an integral role.
  • OCA: OCA a browser-database for protein structure/function
  • Online Mendelian Inheritance in Man: OMIM (Online Mendelian Inheritance in Man): a catalog of human genes and genetic disorders with a lot of information about many different aspects (medical and genetic).GeneCards presents a list of diseases listed as allelic variants in the respective entry for the gene, synonyms for the gene, and a link to the OMIM database entry
  • OriGene: OriGene is a world-wide supplier of authentic full-length CDNA clones in a standard expression vector
  • Orphanet: Orphanet is the reference portal for information on rare diseases and orphan drugs, for all audiences. Orphanet's aim is to help improve the diagnosis, care and treatment of patients with rare diseases.
  • PathCards: PathCards is an integrated database of human pathways and their annotations. Human pathways were clustered into SuperPaths based on gene content similarity. Each PathCards provides information on one SuperPath which represent one or more human pathways. 1073 SuperPath entries, consolidated from 12 sources
  • PaxDb: Protein Abundance Across Organisms: PaxDb is a database of protein abundances across organisms
  • Pharmacogenomics Knowledge Base: The PharmGKB is an integrated resource about how variation in human genes leads to variation in our response to drugs
  • PhosphoSitePlus: PhosphoSitePlus from CST is a curated, sequence-oriented protein database dedicated to in vivo phosphorylation sites
  • ProSci Inc: With over 18,000 completed Custom Antibody projects and 18 years of experience, ProSci specializes in custom polyclonal, monoclonal, and single domain antibody development and production using its own USDA and NIH accredited animal facilities.
  • ProSpec: ProSpec, a biotechnology company, specializes in production of bacterial-derived recombinant proteins
  • ProteomicsDB: ProteomicsDB is dedicated to expedite the identification of the human proteome and its use across the scientific community.
  • Proteopedia: Proteopedia is a project that provides structural and functional knowledge about protein, RNA, DNA, and other macromolecules, and their assemblies and interactions with small molecules, in a manner that is relevant and broadly accessible to students and scientists
  • ProtoNet: ProtoNet at the Hebrew University of Jerusalem provides global classification of the proteins into hierarchical clusters
  • Pseudogene.org: Pseudogene.org, a project of the Gerstein Lab at Yale University, provides information on pseudogenes and intergenic analyses
  • Qiagen: Qiagen provides sample and assay technologies
  • R&D Systems: R&D Systems:a specialty manufacturer of biological products with two operating divisions: Biotechnology and Hematology
  • Reactome, a curated pathway database: Reactome is an open-source, open access, manually curated and peer-reviewed pathway database
  • Residual Variation Intolerance Score: RVIS (Residual Variation Intolerance Score) is a gene-based score intended to help in the interpretation of human sequence data. The intolerance score in its current form is based upon allele frequency data as represented in whole exome sequence data from the NHLBI-ESP6500 data set.
  • RNA Database: RNAdb (RNA Database) is a database for RNA genes annotations
  • Saccharomyces Genome Database: (Saccharomyces Genome Database) is a scientific database of the molecularbiology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast
  • Santa Cruz Biotechnology, (SCBT): Santa Cruz Biotechnology, SCBT, is a leading producer of antibodies, RNAi, CRISPR KO/Activation products, biochemicals and labware for research applications.
  • SIGnaling Network Open Resource: SIGNOR, the SIGnaling Network Open Resource, organizes and stores signaling information published in the scientific literature in a structured format.
  • SIMAP: SIMAP is a database containing the similarity space formed by all amino-acid sequences from public databases and completely sequenced genomes
  • Sino Biological: Sino Biological offers cost-effective premium quality services and reagents for life science research and biological product development
  • SNP Database: SNP Database at NCBI provides information on Single Nucleotide Polymorphisms
  • SNPedia: SNPedia is a wiki investigating human genetics. It shares information about the effects of variations in DNA, citing peer-reviewed scientific publications.
  • SOURCE: SOURCE (The Stanford Online Universal Resource for Clones and ESTs) compiles information from several publicly accessible databases, including UniGene, dbEST, UniprotKB/Swiss-Prot, GeneMap99, GeneCardsand EntrezGene
  • SPIRE: Systematic Protein Investigative Research Environment, proteomics analysis pipeline (frozen)
  • STRING: STRING is a database of known and predicted protein-protein interactions
  • SwitchGear Genomics: SwitchGear Genomics identifies functional elements in the human genome and develops this genomic content into novel high-throughput cell-based functional assays
  • Taconic Biosciences: Taconic Biosciences aims to create a difference in human health by providing the best, most relevant mouse and rat models to researchers in the life science community.
  • The Alternative Splicing Database: The Alternative Splicing Database (ASD) maintains a database of alternative splice events and the resultant isoform splice patterns of genes from human, and other model species
  • The Drug Gene Interaction Database: The Drug-Gene Interaction Database is a web resource that consolidates disparate data sources describing drug-gene interactions and gene druggability
  • The Genotype-Tissue Expression project: The Genotype-Tissue Expression project (GTEx) is providing a comprehensive atlas of gene expression and regulation across multiple human tissues.
  • The Human Phenotype Ontology: The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease.
  • The MaxQuant DataBase: MaxQB is a database that stores and displays collections of large proteomics projects and allows joint analysis and comparison
  • The University of Copenhagen DISEASES: The University of Copenhagen DISEASES database provides disease-gene associations mined from literature
  • Tocris Bioscience: Tocris Bioscience is a leading supplier of high performance life science reagents, peptides and antibodies, with customers in virtually all of the world's major pharmaceutical companies, universities and research institutes
  • TreeFam: TreeFam contains gene phylogenetic trees
  • Tumor Gene Family of Databases: The Tumor Gene Database (TGDB) contains information about genes that are targets for cancer-causing mutations
  • UCSC Golden Path: UCSC Golden Path: the University of California at Santa Cruz Human Draft Genomic Assembly
  • Undiagnosed Diseases Network: The Undiagnosed Diseases Network (UDN) is a research study that is funded by the National Institutes of Health Common Fund. Its purpose is to bring together clinical and research experts from across the United States to solve the most challenging medical mysteries using advanced technologies.
  • Unified Medical Language System: The UMLS integrates and distributes key terminology, classification and coding standards, and associated resources to promote creation of more effective and interoperable biomedical information systems and services, including electronic health records.
  • UniGene: UniGene: an experimental system for automatically partitioning GenBank sequences into a non-redundant set of gene-oriented clusters. GeneCards extracts from UniGene the cluster (Hs.) number, gene symbol or title, GenBank accession, EST's clone identifier and library ID
  • UniProtKB/Swiss-Prot: UniprotKB/Swiss-Prot stores information about proteins (the sequence, some notes about cellular functions, and many other useful data, as well as links to related sites on the web). GeneCards extracts from Swiss-Prot the name of the product(s) of the gene and data about the cellular functions, similarities, involvement in diseases, and links to other databases related to the gene product(s)
  • UniProtKB/TrEMBL: UniprotKB/TrEMBL: a computer-annotated supplement of Swiss-Prot that contains all the translations of EMBL nucleotide sequence entries not yet integrated in Swiss-Prot. GeneCards extracts from TrEMBL the name of the product(s) of the gene and data about the cellular functions, similarities, involvement in diseases, and links to other databases related to the gene product(s)
  • USFDA Approved Drugs: The Food and Drug Administration (FDA or USFDA) is a federal agency of the United States Department of Health and Human Services. The FDA is responsible for protecting and promoting public health through the regulation and supervision of food safety, tobacco products, dietary supplements, prescription and over-the-counter pharmaceutical drugs (medications), vaccines, biopharmaceuticals, blood transfusions, medical devices, electromagnetic radiation emitting devices (ERED), cosmetics, animal foods & feed and veterinary products.
  • Vector BioLabs: Vector BioLabs provides gene delivery products & services using many viral platforms, including recombinant adenoviruses, adeno-associated virus (AAV) and lentivirus
  • VectorBuilder: The VectorBuilder platform, powered by Cyagen, allows researchers to custom design and order their own vectors online.
  • ViGene Biosciences Inc: ViGene Biosciences Inc is a genomics tool company that develops cutting-edge, next generation life science research reagents to support high throughput drug discovery and functional genomics.
  • VISTA Enhancer Browser: A resource for experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice.
  • WormBase: WormBase, the genome and biology of C.elegans

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