Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Minimum information about a bioactive entity (MIABE)

Abstract

Bioactive molecules such as drugs, pesticides and food additives are produced in large numbers by many commercial and academic groups around the world. Enormous quantities of data are generated on the biological properties and quality of these molecules. Access to such data — both on licensed and commercially available compounds, and also on those that fail during development — is crucial for understanding how improved molecules could be developed. For example, computational analysis of aggregated data on molecules that are investigated in drug discovery programmes has led to a greater understanding of the properties of successful drugs. However, the information required to perform these analyses is rarely published, and when it is made available it is often missing crucial data or is in a format that is inappropriate for efficient data-mining. Here, we propose a solution: the definition of reporting guidelines for bioactive entities — the Minimum Information About a Bioactive Entity (MIABE) — which has been developed by representatives of pharmaceutical companies, data resource providers and academic groups.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

References

  1. 1

    Hopkins, A. L. & Groom, C. R. The druggable genome. Nature Rev. Drug Discov. 1, 727–730 (2002).

    CAS  Article  Google Scholar 

  2. 2

    Hajduk, P. J., Huth, J. R., & Tse, C. Predicting protein druggability. Drug Discov. Today 10, 1675–1682 (2005).

    CAS  Article  Google Scholar 

  3. 3

    Schmidtke, P. & Barril, X. Understanding and predicting druggability. A high-throughput method for detection of drug binding sites. J. Med. Chem. 53, 5858–5867 (2010).

    CAS  Article  Google Scholar 

  4. 4

    Halgren, T. A. Identifying and characterizing binding sites and assessing druggability. J. Chem. Inf. Model. 49, 377–389 (2009).

    CAS  Article  Google Scholar 

  5. 5

    Zhang, Z. & Grigorov, M. G. Similarity networks of protein binding sites. Proteins 62, 470–478 (2006).

    CAS  Article  Google Scholar 

  6. 6

    Overington, J. P., Al-Lazikani, B. & Hopkins, A. L. How many drug targets are there? Nature Rev. Drug Discov. 5, 993–996 (2006).

    CAS  Article  Google Scholar 

  7. 7

    The UniProt Consortium. Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res. 39, D214–D219 (2010).

  8. 8

    Berriman, M. et al. The genome of the blood fluke Schistosoma mansoni. Nature 460, 352–358 (2009).

    CAS  Article  Google Scholar 

  9. 9

    Brazma, A. et al. Minimum information about a microarray experiment (MIAME) — toward standards for microarray data. Nature Genet. 29, 365–371 (2001).

    CAS  Article  Google Scholar 

  10. 10

    Degtyarenko, K. et al. ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res. 36, D344–D350 (2008).

    CAS  Article  Google Scholar 

  11. 11

    Sayers, E. W. et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 39, D38–D51 (2011).

    CAS  Article  Google Scholar 

  12. 12

    Seiler, K. P. et al. ChemBank: a small-molecule screening and cheminformatics resource database. Nucleic Acids Res. 36, D351–D359 (2008).

    CAS  Article  Google Scholar 

  13. 13

    Pederson, F., de Brujin, J., Munn, S. & van Leeuwen, K. Assessment of additional testing needs under REACH. Effects of (Q)SAR, risk based testing and voluntary industry activity. European Commission report EUR 20863 (2003).

  14. 14

    Vizcaino, J. A., Martens, L., Hermjakob, H., Julian, R. K. & Paton, N. W. The PSI formal document process and its implementation on the PSI website. Proteomics 7, 2355–2357 (2007).

    CAS  Article  Google Scholar 

  15. 15

    Yeung, B. K. et al. Spirotetrahydro β-carbolines (spiroindolones): a new class of potent and orally efficacious compounds for the treatment of malaria. J. Med. Chem. 53, 5155–5164 (2010).

    CAS  Article  Google Scholar 

  16. 16

    Kerrien, S. et al. Broadening the horizon — level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol. 5, 44 (2007).

    Article  Google Scholar 

  17. 17

    Aranda, B. et al. PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nature Methods 8, 528–529 (2011).

    CAS  Article  Google Scholar 

  18. 18

    Croft, D. et al. Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res. 39, D691–D697 (2011).

    CAS  Article  Google Scholar 

  19. 19

    Taylor, C. F. et al. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nature Biotech. 26, 889–896 (2008).

    CAS  Article  Google Scholar 

  20. 20

    Orchard, S. et al. The minimum information required for reporting a molecular interaction experiment (MIMIx). Nature Biotech. 25, 894–898 (2007).

    CAS  Article  Google Scholar 

  21. 21

    Bourbeillon, J. et al. Minimum Information about a protein affinity reagent (MIAPAR). Nature Biotech. 28, 650–653 (2010).

    CAS  Article  Google Scholar 

  22. 22

    Schuffenhauer, A. et al. An ontology for pharmaceutical ligands and its application for in silico screening and library design. J. Chem. Inf. Comput. Sci. 42, 947–955 (2002).

    CAS  Article  Google Scholar 

  23. 23

    Qi, D. et al. An ontology for description of drug discovery investigations. J. Integr. Bioinform. 25 Mar 2010 (doi:10.2390/biecoll-jib-2010-126).

  24. 24

    Weininger, D. SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. J. Chem. Inf. Comput. Sci. 28, 31–36 (1988).

    CAS  Article  Google Scholar 

  25. 25

    Stein, S. E., Heller, S. R. & Tchekhovskoi, D. An open standard for chemical structure representation: the IUPAC chemical identifier. Proceedings of the 2003 International Chemical Information Conference (Nîmes), Infonortics, 131–143 (2003).

  26. 26

    Inglese, J., Shamu, C. E. & Guy, R. K. Reporting data from high-throughput screening of small-molecule libraries. Nature Chem. Biol. 3, 438–441 (2007).

    CAS  Article  Google Scholar 

  27. 27

    Gene Ontology Consortium. The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res. 38, D331–D335 (2010).

Download references

Acknowledgements

This work has, in part, been funded by the European Commission under the Proteomics Standards Initiative and International Molecular Exchange (PSIMEx), contract number FP7-HEALTH-2007-223411.

Author information

Affiliations

Authors

Corresponding author

Correspondence to Sandra Orchard.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary information Table S1

Sample MIABE file exemplifying data extracted from PMID: 20568778 (PDF 423 kb)

Supplementary information Table S2

Binding affinity to human ERG (XML 45 kb)

Related links

Related links

FURTHER INFORMATION

ChEMBL database

ChEMBL-og website

Cytoscape

Disease Ontology Community Wiki

EBI Industry Programme

EU-Openscreen project

HUPO Proteomics Standards Initiative website

HUPO PSI-MI XML 2.5 documentation

InchI Trust

Innovative Medicines Initiative

IUPAC website

MIACA

MIACA homepage

MIBBI Foundry

MIBBI portal

MIBBI website

MIMIx guidelines

Molecular Interactions workgroup

Molecular Libraries Program

Ontology Lookup Service

Open Biological and Biomedical Ontologies

PSICQUIC web service

STRENDA guidelines

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Orchard, S., Al-Lazikani, B., Bryant, S. et al. Minimum information about a bioactive entity (MIABE). Nat Rev Drug Discov 10, 661–669 (2011). https://doi.org/10.1038/nrd3503

Download citation

Further reading

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing