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<h2 id="technical-basis-and-theoretical-concepts">Technical basis and theoretical concepts</h2> <p><a href="/facts/Relational_database/pEKGmJLy">Relational database</a> concepts of <a href="/facts/Computer_science/lN3pEyPz">computer science</a> and <a href="/facts/Information_retrieval/MFSmpeNw">Information retrieval</a> concepts of <a href="/facts/Digital_library/aBCP81In">digital libraries</a> are important for understanding biological databases. Biological database design, development, and long-term management is a core area of the discipline of <a href="/facts/Bioinformatics/D5x2L8ee">bioinformatics</a>.<a class="footnote-ref" id="fnref:2" href="#fn:2"><sup>2</sup></a> Data contents include gene sequences, textual descriptions, attributes and <a href="/facts/Ontology_(information_science)/SQlhl6lp">ontology</a> classifications, citations, and tabular data. These are often described as semi-<a href="/facts/Structured_data/j1YyzpJ3">structured data</a>, and can be represented as tables, key delimited records, and <a href="/facts/XML/clNgUfWk">XML</a> structures. </p> <h2 id="access">Access</h2> <p>Most biological databases are available through web sites that organise data such that users can browse through the data online. In addition the underlying data is usually available for download in a variety of formats. <a href="/facts/Biological_data/y6rI6UFS">Biological data</a> comes in many formats. These formats include text, sequence data, protein structure and links. Each of these can be found from certain sources, for example: </p> <ul><li>Text formats are provided by <a href="/facts/PubMed/JlHAvMHt">PubMed</a> and <a href="/facts/OMIM/PkW3zCCU">OMIM</a>.</li> <li>Sequence data is provided by <a href="/facts/GenBank/XyMcrktE">GenBank</a>, in terms of DNA, and <a href="/facts/UniProt/lfDDHjAl">UniProt</a>, in terms of protein.</li> <li>Protein structures are provided by <a href="/facts/Protein_Data_Bank/oUhq4ABD">PDB</a>, <a href="/facts/Structural_Classification_of_Proteins/4uz6VcF7">SCOP</a>, and <a href="/facts/CATH/n5mBVu02">CATH</a>.</li></ul> <h2 id="problems-and-challenges">Problems and challenges</h2> <p>Biological knowledge is distributed among countless databases. This sometimes makes it difficult to ensure the consistency of information, e.g. when different names are used for the same species or different data formats. As a consequence, inter-operability is a constant challenge for information exchange. For instance, if a DNA sequence database stores the DNA sequence along the name of a species, a name change of that species may break the links to other databases which may use a different name. <a href="/facts/Integrative_bioinformatics/ALAf5RPu">Integrative bioinformatics</a> is one field attempting to tackle this problem by providing unified access. One solution is how biological databases <a href="/facts/Cross-reference/Fe1Bwq7c">cross-reference</a> to other databases with <a href="/facts/Accession_number_(bioinformatics)/dFgIX9VE">accession numbers</a> to link their related knowledge together (e.g. so that the accession number stays the same even if a species name changes). Redundancy is another problem, as many databases must store the same information, e.g. <a href="/facts/Protein_structure_database/GxthxCoC">protein structure databases</a> also contain the sequence of the proteins they cover, their sequence, and their bibliographic information. </p> <h2 id="model-organism-databases">Model-organism databases</h2> <p class="note">Main article: <a href="/facts/Model_organism_database/jwfXHn56">Model organism database</a></p> <p>Species-specific databases are available for some species, mainly those that are often used in research (<a href="/facts/Model_organism/vNv6q4yb"><i>model organisms</i></a>). For example, EcoCyc is an <i>E. coli</i> database. Other popular <a href="/facts/Model_organism_databases/jwfXHn56">model organism databases</a> include <a href="/facts/Mouse_Genome_Informatics/cRF3seoe">Mouse Genome Informatics</a> for the <a href="/facts/Laboratory_mouse/jhVnpjg7">laboratory mouse</a>, <i>Mus musculus</i>, the <a href="/facts/Rat_Genome_Database/WwTceYDc">Rat Genome Database</a> for <i>Rattus</i>, <a href="/facts/ZFIN/l02rFhFJ">ZFIN</a> for <i>Danio Rerio</i> (zebrafish), <a href="/facts/PomBase/Huc0nvHQ">PomBase</a><a class="footnote-ref" id="fnref:3" href="#fn:3"><sup>3</sup></a> for the fission yeast <i>Schizosaccharomyces pombe</i>, <a href="/facts/FlyBase/23EKKvl3">FlyBase</a> for <i>Drosophila</i>, <a href="/facts/WormBase/vUkJdykd">WormBase</a> for the nematodes <i><a href="/facts/Caenorhabditis_elegans/XJVJzPn2">Caenorhabditis elegans</a></i> and <i><a href="/facts/Caenorhabditis_briggsae/UIpMhtzr">Caenorhabditis briggsae</a></i>, and <a href="/facts/Xenbase/c2EFotmu">Xenbase</a> for <i><a href="/facts/Xenopus_tropicalis/uoS2ALeT">Xenopus tropicalis</a></i> and <i><a href="/facts/Xenopus_laevis/khG1KPrd">Xenopus laevis</a></i> frogs. </p> <h2 id="biodiversity-and-species-databases">Biodiversity and species databases</h2> <p>Numerous databases attempt to document the diversity of life on earth. A prominent example is the <a href="/facts/Catalogue_of_Life/MzzX0VRf">Catalogue of Life</a>, first created in 2001 by Species 2000 and the Integrated Taxonomic Information System.<a class="footnote-ref" id="fnref:4" href="#fn:4"><sup>4</sup></a> The Catalogue of Life is a collaborative project that aims to document taxonomic categorization of all currently accepted species in the world.<a class="footnote-ref" id="fnref:5" href="#fn:5"><sup>5</sup></a> The Catalogue of Life provides a consolidated and consistent database for researchers and policymakers to reference. The Catalogue of Life curates up-to-date datasets from other sources such as Conifer Database, <a href="/facts/International_Committee_on_Taxonomy_of_Viruses/M71khRCo">ICTV</a> MSL (for viruses), and LepIndex (for butterflies and moths). In total, the Catalogue of Life draws from 165 databases as of May 2022.<a class="footnote-ref" id="fnref:6" href="#fn:6"><sup>6</sup></a> Operational costs of the Catalogue of Life are paid for by the <a href="/facts/Global_Biodiversity_Information_Facility/oalM9el2">Global Biodiversity Information Facility</a>, the <a href="/facts/Illinois_Natural_History_Survey/tApp5zrL">Illinois Natural History Survey</a>, the <a href="/facts/Naturalis_Biodiversity_Center/WU6mPHj9">Naturalis Biodiversity Center</a>, and the <a href="/facts/Smithsonian_Institution/pqC74ta9">Smithsonian Institution</a>.<a class="footnote-ref" id="fnref:7" href="#fn:7"><sup>7</sup></a> </p><p>Some biological databases also document geographical distribution of different species. Shuang Dai et al. created a new multi-source database to document spatial/geographical distribution of 1,371 bird species in China, as existing databases had been severely lacking in spatial distribution data for many species.<a class="footnote-ref" id="fnref:8" href="#fn:8"><sup>8</sup></a> Sources for this new database included books, literature, GPS tracking, and online webpage data. The new database displayed taxonomy, distribution, species info, and data sources for each species. After completion of the bird spatial distribution database, it was discovered that 61% of known species in China were found to be distributed in regions beyond where they were previously known.<a class="footnote-ref" id="fnref:9" href="#fn:9"><sup>9</sup></a> </p> <h2 id="medical-databases">Medical databases</h2> <p>Medical databases are a special case of biomedical data resource and can range from bibliographies, such as <a href="/facts/PubMed/JlHAvMHt">PubMed</a>, to image databases for the development of AI based diagnostic software. For instance, one such image database was developed with the goal of aiding in the development of wound monitoring algorithms.<a class="footnote-ref" id="fnref:10" href="#fn:10"><sup>10</sup></a> Over 188 multi-modal image sets were curated from 79 patient visits, consisting of photographs, thermal images, and 3D mesh depth maps. Wound outlines were manually drawn and added to the photo datasets.<a class="footnote-ref" id="fnref:11" href="#fn:11"><sup>11</sup></a> The database was made publicly available in the form of a program called WoundsDB, downloadable from the Chronic Wound Database website. </p> <h2 id="nucleic-acids-researchdatabase-issue"><i>Nucleic Acids Research</i> Database Issue</h2> <p>An important resource for finding biological databases is a special yearly issue of the journal <i><a href="/facts/Nucleic_Acids_Research/0e1akdxA">Nucleic Acids Research</a></i> (NAR). The Database Issue of NAR is freely available, and categorizes many of the public biological databases. A companion database to the issue called the Online Molecular Biology Database Collection lists 1,380 online databases.<a class="footnote-ref" id="fnref:12" href="#fn:12"><sup>12</sup></a> Other collections of databases exist such as MetaBase and the Bioinformatics Links Collection.<a class="footnote-ref" id="fnref:13" href="#fn:13"><sup>13</sup></a><a class="footnote-ref" id="fnref:14" href="#fn:14"><sup>14</sup></a> </p> <h2 id="see-also">See also</h2> <ul><li><a href="/facts/Biobank/cQEQqdcl">Biobank</a></li> <li><a href="/facts/Biological_data/y6rI6UFS">Biological data</a></li> <li><a href="/facts/Chemical_database/AvlsG1nv">Chemical database</a></li> <li><a href="/facts/Death_Domain_database/xvGYTwm0">Death Domain database</a></li> <li><a href="/facts/European_Bioinformatics_Institute/g1GsqPXd">European Bioinformatics Institute</a></li> <li><a href="/facts/Gene_Disease_Database/fbdpIG4P">Gene Disease Database</a></li> <li><a href="/facts/Integrative_bioinformatics/ALAf5RPu">Integrative bioinformatics</a></li> <li><a href="/facts/List_of_biological_databases/z1o0kcKt">List of biological databases</a></li> <li><a href="/facts/Model_organism_databases/jwfXHn56">Model organism databases</a></li> <li><a href="/facts/National_Center_for_Biotechnology_Information/6Xj5wCbu">NCBI</a></li> <li><a href="/facts/PubMed/JlHAvMHt">PubMed</a> (a database of biomedical literature)</li></ul> <h2 id="external-links">External links</h2> <ul><li><a href="https://web.archive.org/web/20060112045100/http://www.oxfordjournals.org/nar/database/c">Interactive list of biological databases</a>, classified by categories, from <a href="/facts/Nucleic_Acids_Research/0e1akdxA">Nucleic Acids Research</a>, 2010</li> <li><a href="https://web.archive.org/web/20191202045455/http://www.biodbs.info/">DBD: Database of Biological Databases</a></li> <li><a href="http://www.Biosharing.org">Biosharing</a> (a database of biological databases)</li> <li><a href="https://chronicwounddatabase.eu/">Chronic Wounds Database</a> WoundsDB</li> <li><a href="https://www.catalogueoflife.org/">Catalogue of Life</a> Catalogue of Life</li></ul> <h2 id="references">References</h2> <ol> <li id="fn:1"><p>Altman RB (March 2004). "Building successful biological databases". Brief. Bioinformatics. 5 (1): 4–5. doi:10.1093/bib/5.1.4. PMID 15153301. <a href="https://doi.org/10.1093%2Fbib%2F5.1.4" target="_blank">https://doi.org/10.1093%2Fbib%2F5.1.4</a> <a href="#fnref:1" class="footnote-back-ref">↩</a></p></li> <li id="fn:2"><p>Bourne P (August 2005). "Will a biological database be different from a biological journal?". PLOS Comput. Biol. 1 (3): 179–81. Bibcode:2005PLSCB...1...34B. doi:10.1371/journal.pcbi.0010034. PMC 1193993. PMID 16158097. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1193993" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1193993</a> <a href="#fnref:2" class="footnote-back-ref">↩</a></p></li> <li id="fn:3"><p>Rutherford KM, Lera-Ramírez M, Wood V (May 2024). "PomBase: a Global Core Biodata Resource—growth, collaboration, and sustainability". Genetics. 227 (1). doi:10.1093/genetics/iyae007. PMC 11075564. PMID 38376816. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11075564" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11075564</a> <a href="#fnref:3" class="footnote-back-ref">↩</a></p></li> <li id="fn:4"><p>Jones, Andrew C. (2011). "Identifying and Relating Biological Concepts in the Catalogue of Life". Journal of Biomedical Semantics. 2 (1): 7. doi:10.1186/2041-1480-2-7. PMC 3245425. PMID 22004596. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245425" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245425</a> <a href="#fnref:4" class="footnote-back-ref">↩</a></p></li> <li id="fn:5"><p>Catalogue of Life (2001). "What is Catalogue of Life?". Our Mission. Species 2000. Archived from the original on 2022-05-05. Retrieved 2022-05-05. <a href="https://www.catalogueoflife.org/about/catalogueoflife#our-mission." target="_blank">https://www.catalogueoflife.org/about/catalogueoflife#our-mission.</a> <a href="#fnref:5" class="footnote-back-ref">↩</a></p></li> <li id="fn:6"><p>Catalogue of Life (2001). "Source Datasets". Species 2000. Archived from the original on 2022-05-14. Retrieved 2022-05-05. <a href="https://www.catalogueoflife.org/data/source-datasets" target="_blank">https://www.catalogueoflife.org/data/source-datasets</a> <a href="#fnref:6" class="footnote-back-ref">↩</a></p></li> <li id="fn:7"><p>Catalogue of Life (2001). "Funding". Species 2000. Archived from the original on 2022-05-05. Retrieved 2022-05-05. <a href="https://www.catalogueoflife.org/about/funding" target="_blank">https://www.catalogueoflife.org/about/funding</a> <a href="#fnref:7" class="footnote-back-ref">↩</a></p></li> <li id="fn:8"><p>Dai, Shuang (2019). "A Spatialized Digital Database for All Bird Species in China". Science China Life Sciences. 62 (5): 661–667. doi:10.1007/s11427-018-9419-2. PMID 30900164. S2CID 84845653. Retrieved 2022-05-05. <a href="https://doi.org/10.1007/s11427-018-9419-2" target="_blank">https://doi.org/10.1007/s11427-018-9419-2</a> <a href="#fnref:8" class="footnote-back-ref">↩</a></p></li> <li id="fn:9"><p>Dai, Shuang (2019). "A Spatialized Digital Database for All Bird Species in China". Science China Life Sciences. 62 (5): 661–667. doi:10.1007/s11427-018-9419-2. PMID 30900164. S2CID 84845653. Retrieved 2022-05-05. <a href="https://doi.org/10.1007/s11427-018-9419-2" target="_blank">https://doi.org/10.1007/s11427-018-9419-2</a> <a href="#fnref:9" class="footnote-back-ref">↩</a></p></li> <li id="fn:10"><p>Kręcichwost, Michał (2021). "Chronic Wounds Multimodal Image Database". Computerized Medical Imaging and Graphics. 88: 101844. doi:10.1016/j.compmedimag.2020.101844. PMID 33477091. S2CID 231676950. Retrieved 2022-05-05. <a href="https://doi.org/10.1016/j.compmedimag.2020.101844" target="_blank">https://doi.org/10.1016/j.compmedimag.2020.101844</a> <a href="#fnref:10" class="footnote-back-ref">↩</a></p></li> <li id="fn:11"><p>"Chronic Wound Database". WoundsDB. Silesian University of Technology. 2020. Retrieved 2022-05-05. <a href="https://chronicwounddatabase.eu/" target="_blank">https://chronicwounddatabase.eu/</a> <a href="#fnref:11" class="footnote-back-ref">↩</a></p></li> <li id="fn:12"><p>Galperin MY; Fernández-Suárez XM (January 2012). "The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection". Nucleic Acids Res. 40 (Database issue): D1–8. doi:10.1093/nar/gkr1196. PMC 3245068. PMID 22144685. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245068" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245068</a> <a href="#fnref:12" class="footnote-back-ref">↩</a></p></li> <li id="fn:13"><p>Bolser DM; Chibon PY; Palopoli N; et al. (January 2012). "MetaBase--the wiki-database of biological databases". Nucleic Acids Res. 40 (Database issue): D1250–4. doi:10.1093/nar/gkr1099. PMC 3245051. PMID 22139927. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245051" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245051</a> <a href="#fnref:13" class="footnote-back-ref">↩</a></p></li> <li id="fn:14"><p>Brazas MD; Yim DS; Yamada JT; Ouellette BF (July 2011). "The 2011 Bioinformatics Links Directory update: more resources, tools and databases and features to empower the bioinformatics community". Nucleic Acids Res. 39 (Web Server issue): W3–7. doi:10.1093/nar/gkr514. PMC 3125814. PMID 21715385. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125814" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125814</a> <a href="#fnref:14" class="footnote-back-ref">↩</a></p></li> </ol>