Other Biological Databases

  • Divya Mishra
  • Vivek Kumar Chaturvedi
  • V. P. Snijesh
  • Noor Ahmad Shaik
  • M. P. Singh


The remarkable progress made in genomics, proteomics, metabolomics, and microarray gene expression methods has led to exponential rise in the amount of biological data available to scientific community. This huge raw data requires storage, annotation, accurate analysis, and visualization. Hence, there is a growing demand to develop diverse computational databases, which can submit, store, edit, and update the large-scale data. In this context, the rapid emergence of computational informatics has greatly assisted us in developing databases which deal with heterogeneous data covering molecular sequence, structure, localization, and biological relevance. Moreover, computational databases also allow the user to execute custom queries and provide integrated views and evaluation of distinct kinds of datasets. In this chapter we brief about protein identification database and some other important biological databases and their classification into different categories.


Protein identification database Other biological databases Specialized database 


  1. Apweiler R, Bairoch A, Wu CH (2004) Protein sequence databases. J Adv Protein Chem 8(1):76–80Google Scholar
  2. Aranda B, Achuthan P, Alam-Faruque Y, Armean I, Bridge A, Derow C, Feuermann M, Ghanbarian AT et al (2009) The IntAct molecular interaction database in. Nucleic Acids Res 38:525–531Google Scholar
  3. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. J Nat Genet 25(1):25–29Google Scholar
  4. Camon E, Magrane M, Barrell D, Lee V, Dimmer E, Maslen J, Binns D, Harte N, Lopez R, Apweiler R (2004) The gene ontology annotation (goa) database: sharing knowledge in uniprot with gene ontology. Nucleic Acids Res 32:262–266Google Scholar
  5. Chistine H, Jaen CS, Luisa T, Pierre AB, Amos B, Denis FH, Ron DA (2000) The 1999 SWISS-2DPAGE database updates. Nucleic Acids Res 28(1):286–288Google Scholar
  6. Corpet F, Gouzy J, Kahn D (1999) Recent improvements of the ProDom database of protein domain families. Nucleic Acids Res 27(1):263–267PubMedPubMedCentralGoogle Scholar
  7. De Matos P, Dekker A, Ennis M, Hastings J, Haug K, Turner S, Steinbeck C (2010) ChEBI: a chemistry ontology and database. J Cheminform 2:6Google Scholar
  8. Degtyarenko K, De Matos P, Ennis M, Hastings J, Zbinden M, McNaught A, Alcántara R, Darsow M, Guedj M, Ashburner M (2007) ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res 36:344–350Google Scholar
  9. Engel SR (2009) Using Model Organism Databases (MODs). Curr Protoc Essential Lab Tech 1:1–17Google Scholar
  10. Evelyn C, Michele M, Daniel B, Vivian L, Emily D, John M, David B, Nicola H, Rodrigo L, Rolf A (2004) The gene ontology annotation (GOA) databases: sharing knowledge in Uniprot with gene ontology. Nucleic Acids Res 32:262–266Google Scholar
  11. Fleischmann A, Darsow M, Degtyarenko K, Fleischmann W, Boyce S, Axelsen KB, Bairoch A, Schomburg D, Tipton KF, Apweiler R (2004) IntEnz: the integrated relational databases. Nucleic Acids Res 32:434–437Google Scholar
  12. Hermjakob H, Montecchi-Palazzi L, Lewington C, Mudali S, Kerrien S, Orchard S, Vingron M, Roechert B, Roepstorff P, Valencia A, Margalit H (2004) IntAct: an open source molecular interaction database. Nucleic Acids Res 32:452–455Google Scholar
  13. Hoogland C, Sanchez JC, Tonella L, Bairoch A, Hochstrasser DF, Appel RD (1999) The SWISS-2DPAGE database: what has changed during the last year. Nucleic Acids Res 27:289–291PubMedPubMedCentralGoogle Scholar
  14. Jones P, Côté RG, Martens L, Quinn AF, Taylor CF, Derache W, Hermjakob H, Apweiler R (2006) PRIDE: a public repository of protein and peptide identifications for the proteomics community. Nucleic Acids Res 34:659–663Google Scholar
  15. Jones P, Cote RG, Cho SY, Klie S, Martens L, Quinn AF, Thorneycroft D, Hermjakob H (2007) PRIDE: new developments and new datasets. Nucleic Acids Res 36:878–883Google Scholar
  16. Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K (2016) KEGG: new perspectives on genomes, pathways, disease and drugs. Nucleic Acids Res 45:353–361Google Scholar
  17. Majumdar I, Kinch LN, Grishin NV (2009) A database of domain definitions for proteins with complex interdomain geometry. PLoS One 4:5084Google Scholar
  18. McHugh L, Arthur JW (2008) Computational methods for protein identification from mass spectrometry data. PLoS Comput Biol 4:12Google Scholar
  19. Périer RC, Junier T, Bucher P (1998) The eukaryotic promoter database EPD. Nucleic Acids Res 26(1):353–357Google Scholar
  20. Whitfield EJ, Pruess M, Apweiler R (2006) Bioinformatics database infrastructure for biotechnology research. J Biotechnol 124(4):629–639PubMedGoogle Scholar
  21. Wingender E, Chen X, Hehl R, Karas H, Liebich I, Matys V, Meinhardt T, Prüß M, Reuter I, Schacherer F (2000) TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Res 28(1):316–319PubMedPubMedCentralGoogle Scholar
  22. Wishart DS, Knox C, Guo AC, Cheng D, Shrivastava S, Tzur D, Gautam B, Hassanali M (2007) DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res 36:901–906Google Scholar
  23. Zanzoni A, Montecchi-Palazzi L, Quondam M, Ausiello G, Helmer-Citterich M, Cesareni G (2002) MINT: a Molecular INTeraction database. FEBS Lett 513(1):135–140PubMedGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Divya Mishra
    • 1
  • Vivek Kumar Chaturvedi
    • 2
  • V. P. Snijesh
    • 3
  • Noor Ahmad Shaik
    • 4
  • M. P. Singh
    • 2
  1. 1.Centre of BioinformaticsUniversity of AllahabadAllahabadIndia
  2. 2.Centre of BiotechnologyUniversity of AllahabadAllahabadIndia
  3. 3.Innov4Sight Health and Biomedical System Private LimitedBangaloreIndia
  4. 4.Department of Genetic Medicine, Faculty of MedicineKing Abdulaziz UniversityJeddahSaudi Arabia

Personalised recommendations