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Link to original content: http://dx.doi.org/10.1038/nbt0910-897
The FEBS Letters/BioCreative II.5 experiment: making biological information accessible | Nature Biotechnology
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The FEBS Letters/BioCreative II.5 experiment: making biological information accessible

Nature Biotechnology volume 28, pages 897–899 (2010)Cite this article

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To the Editor:

Current publications lack structured representations of the entities and relationships they report on. As a consequence, information retrieval is hampered and much of the scientific literature is poorly accessible unless it is organized in domain-specific databases by expert curation1. However, manual curation is a slow process and databases lag behind, failing to cover much of the published information. The combined effort of the IMEx group deals with only ∼20% of the estimated 10,000 protein interaction articles published yearly (Supplementary Methods). To explore new publication strategies, the FEBS Letters experiment asked authors to supply structured annotations for their publications that were linked to databases with the intervention of professional bio-curators2. The BioCreative II.5 challenge then compared these annotations provided by authors and curators to automated systems3. Combining these two efforts has generated the first quantitative data to support the debate on ways to supplement publications with structured information.

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Figure 1: Evaluation results.

References

  1. Seringhaus, M.R. & Gerstein, M.B. BMC Bioinformatics 8, 17 (2007).

    Article  Google Scholar 

  2. Ceol, A., Chatr-Aryamontri, A., Licata, L. & Cesareni, G. FEBS Lett. 582, 1171–1177 (2008).

    Article  CAS  Google Scholar 

  3. Leitner, F. et al. IEEE/ACM Trans. Comput. Biol. Bioinformatics 7, 385–399 (2010).

    Article  CAS  Google Scholar 

  4. Orchard, S. et al. Nat. Biotechnol. 25, 894–898 (2007).

    Article  CAS  Google Scholar 

  5. Gerstein, M., Seringhaus, M. & Fields, S. Nature 447, 142 (2007).

    Article  CAS  Google Scholar 

  6. Hahn, U., Wermter, J., Blasczyk, R. & Horn, P. Nature 448, 130 (2007).

    Article  CAS  Google Scholar 

  7. Chatr-aryamontri, A. et al. Nucleic Acids Res. 35, D572–D574 (2007).

    Article  CAS  Google Scholar 

  8. Leitner, F. & Valencia, A. FEBS Lett. 582, 1178–1181 (2008).

    Article  CAS  Google Scholar 

  9. Aloy, P. & Russell, R.B. Nat. Rev. Mol. Cell Biol. 7, 188–197 (2006).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The authors acknowledge the BioCreative II.5 participants. G.C. thanks P. McCabe, F. Wieland, G. Superti-Furga, F. Goni, I. Mowbray and A. Klinkenberg for their support. L. Salwinski participated in the inter-annotator agreement study. The work on BioCreative was supported by the European Commission FP6 NoEs ENFIN LSHG-CT-2005-518254 and EMBRACE LSG-CT-2004-512092, and by grants BIO2007-66855 from the Spanish Ministerio de Ciencia e Innovación and by the Spanish National Bioinformatics Institute (http://www.inab.org/). The work on the MINT database is supported by FEBS, AIRC and Telethon grants. The participation of L.H. and S.A.M. in BioCreative II.5 was funded by US National Science Foundation grant IIS-0844419.

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Authors and Affiliations

  1. Structural and Computational Biology Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain

    Florian Leitner, Martin Krallinger & Alfonso Valencia

  2. Department of Biology, University of Rome Tor Vergata, Rome, Italy

    Andrew Chatr-aryamontri, Arnaud Ceol, Luana Licata & Gianni Cesareni

  3. The MITRE Corporation, Bedford, Massachusetts, USA

    Scott A Mardis & Lynette Hirschman

  4. Research Institute 'Fondazione Santa Lucia,' Rome, Italy, and IRCSS Santa Lucia, Rome, Italy

    Gianni Cesareni

Authors
  1. Florian Leitner
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  2. Andrew Chatr-aryamontri
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  8. Gianni Cesareni
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  9. Alfonso Valencia
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Corresponding authors

Correspondence to Gianni Cesareni or Alfonso Valencia.

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Supplementary information

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Supplementary Methods, Results, Discussion and List of Participants (PDF 3881 kb)

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Leitner, F., Chatr-aryamontri, A., Mardis, S. et al. The FEBS Letters/BioCreative II.5 experiment: making biological information accessible. Nat Biotechnol 28, 897–899 (2010). https://doi.org/10.1038/nbt0910-897

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