Kanehisa M., Goto S., Sato Y., Furumichi M., Tanabe M. KEGG for integration and interpretation of large-scale molecular data sets. Computer tools are there to manipulate the biological data, update, delete, insert, etc. Opin. Many secondary databases are applied to the protein sequences rather than nucleotide sequences and a few examples are given in the next steps. BMC Bioinformatics 15, 110 (2014), Sievers, F., Wilm, A., Dineen, D.G., et al. They help researchers find relevant biological data by making it available in a format that is readable on a computer. Biol. Giardine B., Borg J., Viennas E., Pavlidis C., Moradkhani K., Joly P., et al. President of the EASE, Development Editor of Reproductive BioMedicine Online Journal, Editor and Researcher at the National Astronomical Observatories, Chinese Academy of Sciences, Chair & Professor, Department of Physiology and Pathophysiology, Peking University Health Science Center. Opin. : New and continuing developments at PROSITE. Pathway commons, a web resource for biological pathway data. Yang Z., Yang J., Liu W., Wu L., Xing L., Wang Y., et al. The New Trend of Data Journals. The primary function of human DNA databases includes establishment of the reference genome (e.g., NCBI RefSeq [8]), profiling of human genetic variation (e.g., dbSNP [13]), association of genotype with phenotype (e.g., EGA [14]), and identification of human microbiome metagenomes (e.g., IMG/HMP [15]). Zhang Z., Zhu W., Luo J. In this section we will discuss two different types of public databases and the mechanisms that they use to describe data consistently. Biological databases are complex, heterogeneous, dynamic, and yet inconsistent. Rhodes D.R., Yu J., Shanker K., Deshpande N., Varambally R., Ghosh D., et al. document.getElementById( "ak_js_1" ).setAttribute( "value", ( new Date() ).getTime() ); Planning your research is very important to obtain desirable results. Find out more about saving to your Kindle. : SMART: A Web-based tool for the study of genetically mobile domains. 28, 231234 (2000), Morris, G.M., Huey, R., Lindstrom, W., et al. 20, 243248 (2013), Liwo, A., Lee, J., Ripoll, D.R., et al. Method of the Year 2022: long-read sequencing. Bioinformatics Databases, Software, and Tools with Uses - The Biology Notes Bioinformatics 14, 892893 (1998), Bystroff, C., Thorsson, V., Baker, D.: HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins. A database is a computerized archive used to store and organize data in such a way that information can be retrieved easily via a variety of search criteria. 40, D84D90 (2012), Gaudet, P., Fey, P., Basu, S., et al. According to a report of 2014 Molecular Biology Database Collection in the journal Nucleic Acids Research, there are a sum of 1552 databases that are publicly accessible online [1]. Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations. Rev. As human-related databases continue to grow not only in count but also in volume, challenges are ahead in big data storage, processing, exchange and curation. page Primary and secondary databases . Yang J.H., Li J.H., Jiang S., Zhou H., Qu L.H. As database classification based on data type is informative and straightforward, we assign one major category to each database, albeit one database may correspond to multiple categories. Gray K.A., Yates B., Seal R.L., Wright M.W., Bruford E.A. http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=lncBase/index, http://bioinfo.life.hust.edu.cn/lncRNASNP, http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index, http://www.grenoble.prabi.fr/obiwarehouse/unipathway, http://www.disgenet.org/web/DisGeNET/v2.1, http://www.ncbi.nlm.nih.gov/genbank/statistics, A deep catalog of human genetic variation, Database of single nucleotide polymorphisms, Genomic information for eukaryotic organisms, Transcription factor binding profile database, Polymorphism in miRNAs and their Target Sites, Database of transcriptional regulation of lncRNA and miRNA genes, Human-transcriptome DataBase for Alternative Splicing, Database of differentially-expressed genes after lncRNA knockdown or overexpression, Experimentally-validated miRNAtarget interactions, Rigorously Annotated Database of A-to-I RNA editing, International database of ncRNA sequences, Database of human H/ACA and C/D box snoRNAs, Experimentally-validated miRNA:gene interactions, Compendium ofProteinLysineModifications, EukaryoticKinase andPhosphataseDatabase, Protein sequence analysis and classification, Database of proteolytic enzymes, their substrates, and inhibitors, Database of comparative protein structure models, Protein ANalysis THrough Evolutionary Relationships, Protein Data Bank for 3D structures of biological macromolecules, Database of conserved protein families and domains, Genetic polymorphisms that influence protein phosphorylation, Database of protein domains, families and functional sites, Database of phylogenetic trees of animal species, Universal PBM Resource for Oligonucleotide Binding Evaluation, Ubiquitin and Ubiquitin-like Conjugation Database, Database of functional genomics experiments, Portal for querying and organizing gene annotation resources, Multi-Omics Profiling Expression Database, Tissue-specific Gene Expression and Regulation, Unified resource for Human transcriptomics research, Curated and peer-reviewed pathway database, Database for gene dysregulation in Alzheimers disease, Gene expression-based Outcome for Breast cancer Online, A comprehensive resource for the comparison and interrogation of genome-wide association studies, Human genetic variants identified by genome-wide association studies, Database of DNA methylation and gene expression in human cancer, Database of human DNA Methylation and cancer, Database for miRNA deregulation in human disease, Polymorphisms and mutations in human mitochondrial DNA, Curated resource of SNP-trait associations, Connections associated with type 2 diabetes, Database of biomedical literature from MEDLINE. : JPred: a consensus secondary structure prediction server. 28, 4144 (2000), Barker, W.C., Garavelli, J.S., Haft, D.H., et al. : Computational inference of homologous gene structures in the human genome. Biological databases are developed for diverse purposes, encompass various types of data at heterogeneous coverage and are curated at different levels with different methods, so that there are accordingly several different criteria applicable to database classification. RefSeq: an update on mammalian reference sequences. Techno India College of Technology, Durgapur, West Bengal, India, Professional Colleges (SRMGPC), Shri Ramswaroop Memorial Group of, Lucknow, Uttar Pradesh, India, Faculty of Computers & Information, Cairo University, Giza, Egypt, 2016 Springer International Publishing Switzerland, Kumari, A., Kanchan, S., Sinha, R.P., Kesheri, M. (2016). Nucleic Acids Res. Finn R.D., Mistry J., Schuster-Bockler B., Griffiths-Jones S., Hollich V., Lassmann T., et al. Describing data and metadata consistently. Secondary databases are called so because they contain the analysis results of the sequences in the primary sources. Nucleic Acids Res. The four examples of biological databases are: (1) Nucleotide Sequence Databases (2) Protein Sequence Databases (3) Macromolecular Databases and (4) Other Databases. Springer, New York (2003), CrossRef (PDF) Bioinformatics Database Resources - ResearchGate : Secondary and tertiary structure prediction of proteins: a bioinformatic approach. BMC Syst. Caspi R., Altman T., Billington R., Dreher K., Foerster H., Fulcher C.A., et al. The information in these databases is based on the original data from primary databases. Secondary databases comprise data derived from analysing entries in primary databases. : CMAP: complement map database. The main purpose of databases is to enable easy handling and retrieval of information through multiple search features (Garcia-Molina et al. The development of databases to handle the vast amount of molecular biological data is thus a fundamental task of bioinformatics. Computational, statistical, and computer programming techniques have been used for computer simulation analyses of biological queries. Using the proper tools, existing databases can be used to establish new data, e.g., predicting protein structure by artificial intelligence. Received 2015 Jan 1; Revised 2015 Jan 16; Accepted 2015 Jan 16. Examples include: Composite databases contain a variety of primary databases, which eliminates the need to search each one separately. HHS Vulnerability Disclosure, Help PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways. It involves the creation and application of computational tools, algorithms, and databases for storing, retrieving, managing, and analysing biological data. Jones P., Cote R.G., Cho S.Y., Klie S., Martens L., Quinn A.F., et al. Liu X., Yu X., Zack D.J., Zhu H., Qian J. TiGER: a database for tissue-specific gene expression and regulation. please confirm that you agree to abide by our usage policies. 5, pp. : Protein structure predictionby global optimization of a potential energy function. Find out more about saving content to Google Drive. GWASdb: a database for human genetic variants identified by genome-wide association studies. : Ab initio gene finding in Drosophila genomic DNA. Therefore, an increasing number of human RNA databases have been built for deciphering ncRNAs (e.g., GENCODE [17]), in particular lncRNAs that attract the rising interest (e.g., LncRNAWiki [10]), and characterizing their functions and interactions (e.g., RNAcentral [18]). Toward this end, there are two well-known cancer projects, viz., The Cancer Genome Atlas (TCGA) [32] and International Cancer Genome Consortium (ICGC) [33]. CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China. Enago Academy - Learn. Ensembl 2014. Biological Process. Chem. Nat. The Protein Information Resource. Appl. 2.1 Introduction to Databases Database is a computerized resource where data is structured in a way that makes it easy to add, access, and update it. Brooksbank C., Bergman M.T., Apweiler R., Birney E., Thornton J. An enhanced MITOMAP with a global mtDNA mutational phylogeny. : HMMER web server: interactive sequence similarity searching. Bethesda, MD 20894, Web Policies : Jalview version 2-a multiple sequence alignment editor and analysis workbench. Wishart D.S., Jewison T., Guo A.C., Wilson M., Knox C., Liu Y., et al. : PANTHER: a library of protein families and subfamilies indexed by function. Primary databases contain raw data as archival repository such as the NCBI Sequence Read Archive (SRA) [7], whereas secondary or derivative databases contain curated information as added value, e.g., NCBI RefSeq [8]. 541569. Biol. Sai Lakshmi S., Agrawal S. piRNABank: a web resource on classified and clustered Piwi-interacting RNAs. Start your subscription for just 29.99 19.99. Control 12(1), 3340, Boeckmann, B., Bairoch, A., Apweiler, R., et al. Primary: databases comprising of data generated experimentally like nucleotide sequences and 3D structures are identified as primary databases. 1. Bioinformatics Databases - Bioinformatics - Research Subject Guides at On the other hand, specialized databases contain specific types of data or data from specific organisms. 42(D1), D490D495 (2014), Bowes, J.B., Snyder, K.A., Segerdell, E., et al. . Genet. Specialized databases are databases that are designed to serve a specific research interest. Open Tree arrow-right-1 Primary and secondary databases Describing data consistently Minimum information standards Controlled vocabularies Open Tree arrow-right-1 Non-hierarchical list Taxonomy Thesaurus Using ontologies to provide controlled vocabularies Gene Ontology Through the . Volders P.J., Helsens K., Wang X., Menten B., Martens L., Gevaert K., et al. TCGA, founded in 2006 by the National Cancer Institute and National Human Genome Research Institute at the National Institutes of Health, aims to collect a wide diversity of omics data (including exome, SNP, mRNA, miRNA, and methylation) for more than 20 different types of human cancer (http://cancergenome.nih.gov). The data are given accession numbers when they are entered into the database. Nucleic Acids Res. Takeda J., Suzuki Y., Sakate R., Sato Y., Gojobori T., Imanishi T., et al. With the explosive growth of biological data, there is an increasing number of biological databases that have been developed in aid of human-related research. Bringing biocuration to China. PLoS ONE 5, e9490 (2010), Kumar, S., Tamura, K., Nei, M.: MEGA: molecular evolutionary genetics analysis software for microcomputers. Gong J., Liu W., Zhang J., Miao X., Guo A.Y. J. Mol. Methods 11, 9499 (2014), Schultz, J., Copley, R.R., Doerks, T., et al. Biological Databases for Human Research - PMC - National Center for The European nucleotide archive. Nucleic Acids Res. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Amberger J.S., Bocchini C.A., Schiettecatte F., Scott A.F., Hamosh A. OMIM.org: online mendelian inheritance in man (OMIM(R)), an online catalog of human genes and genetic disorders. The RNAcentral Consortium RNAcentral: an international database of ncRNA sequences. English Editing Enago.com | Enago.jp | Enago.cn | Enago.co.kr. J. Mol. BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. 40, D48D53 (2012), Kinjo, A.R., Suzuki, H., Yamashita, R., et al. Nucleic Acids Res. Nucleic Acids Res. The purpose of constructing protein databases includes collection of universal proteins (e.g., UniProt [22]), identification of protein families and domains (e.g., Pfam [23]), reconstruction of phylogenetic trees (e.g., TreeFam [24]), and profiling of protein structures (e.g., PDB [25]). J. Mol. Cerami E.G., Gross B.E., Demir E., Rodchenkov I., Babur O., Anwar N., et al. Then enter the name part However, over the time, database became a preferable term. Mitchell A., Chang H.Y., Daugherty L., Fraser M., Hunter S., Lopez R., et al. : Entrez: making use of its power. Rfam 11.0: 10 years of RNA families. One of them uses the generic names of the drugs . Cancer Genome Atlas Research Network, Weinstein J.N., Collisson E.A., Mills G.B., Shaw K.R., Ozenberger B.A., et al. Secondary databases - FutureLearn The Human Gene Mutation Database (HGMD) and its exploitation in the fields of personalized genomics and molecular evolution. Secondary Databases - Definition, Types, Examples, Uses - Microbiology Note

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