Encyclopedia of Database Systems

2018 Edition
| Editors: Ling Liu, M. Tamer Özsu

Biological Metadata Management

  • Zoé LacroixEmail author
  • Cartik R. Kothari
  • Peter Mork
  • Mark D. Wilkinson
  • Sarah Cohen-Boulakia
Reference work entry
DOI: https://doi.org/10.1007/978-1-4614-8265-9_628


Metadata characterize biological resources by core information including a name, a description of its input and its output (parameters or format), its address, and various additional properties. Resources are organized with respect to metadata that characterize their content (for data sources), their semantics (in terms of ontological classes and relationships), their characteristics (syntactical properties), their performance (with metrics and benchmarks), their quality (curation, reliability, trust), etc.

Historical Background

Digital resources for the Life Sciences include a variety of data sources and applications whose number increases dramatically every year [4]. Although this rich and valuable offering provides scientists with multiple options to implement and execute their scientific protocols (i.e., pipelines, dataflows, workflows), selecting the resources suitable for implementing each scientific step remains a difficult task. Scientific protocols are typically...

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Recommended Reading

  1. 1.
    Brazama A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Holstege FCP, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M. Minimum information about a microarray experiment (MIAME) – toward standards for microarray data. Nat Genet. 2001;29(4):365–71.CrossRefGoogle Scholar
  2. 2.
    Cohen-Boulakia S, Davidson S, Froidevaux C, Lacroix Z, Vidal ME. Path-based systems to guide scientists in the maze of biological resources. J Bioinform Comput Biol. 2006;4(5):1069–95.CrossRefGoogle Scholar
  3. 3.
    Cohen-Boulakia S, Biton O, Davidson S, Froidevaux C. BioGuideSRS: querying multiple sources with a user-centric perspective. Bioinformatics. 2007;23(10):1301–3.CrossRefGoogle Scholar
  4. 4.
    Galperin MY. The molecular biology database collection: 2007 update. Nucleic Acids Res. 2007;35(Database issue): D3–4.CrossRefGoogle Scholar
  5. 5.
    Lacroix Z, Raschid L, Eckman B. Techniques for optimization of queries on integrated biological resources. J Bioinform Comput Biol. 2004;2(2):375–411.CrossRefGoogle Scholar
  6. 6.
    Orchard S, Salwinski L, Kerrien S, Montecchi-Palazzi L, Oesterheld M, Stmpflen V, Ceol A, Chatr-aryamontri A, Armstrong J, Woollard P, Salama JJ, Moore S, Wojcik J, Bader GD, Vidal M, Cusick ME, Gerstein M, Gavin AC, Superti-Furga G, Greenblatt J, Bader J, Uetz P, Tyers M, Legrain P, Fields S, Mulder N, Gilson M, Niepmann M, Burgoon L, De Las Rivas J, Prieto C, Perreau VM, Hogue C, Mewes HW, Apweiler R, Xenarios I, Eisenberg D, Cesareni G, Hermjakob H. The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol. 2007;25(8):894–8.CrossRefGoogle Scholar
  7. 7.
    Taylor CF, Paton NW, Lilley KS, Binz PA, Julian RK, Jones AR, Zhu W, Apweiler R, Aebersold R, Deutsch EW, Dunn MJ, Heck AJR, Leitner A, Macht M, Mann M, Martens L, Neubert TA, Patterson SD, Ping P, Seymour SL, Souda P, Tsugita A, Vandekerckhove J, Vondriska TM, Whitelegge JP, Wilkins MR, Xenarios I, Yates JR, Hermjakob H. The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol. 2007;25(8):887–93.CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Zoé Lacroix
    • 1
    Email author
  • Cartik R. Kothari
    • 2
  • Peter Mork
    • 3
  • Mark D. Wilkinson
    • 4
  • Sarah Cohen-Boulakia
    • 5
  1. 1.Arizona State UniversityTempeUSA
  2. 2.Biomedical InformaticsOhio State University, College of MedicineColumbusUSA
  3. 3.The MITRE CorporationMcLeanUSA
  4. 4.University of British ColumbiaVancouverCanada
  5. 5.University Paris-SudOrsay CedexFrance

Section editors and affiliations

  • Louiqa Raschid
    • 1
  1. 1.Robert H. Smith School of BusinessUniversity of MarylandCollege ParkUSA