2006 TheBiocurator

• (Salimi & Vita, 2006) ⇒ Nima Salimi, Randi Vita. (2006). “The Biocurator: Connecting and Enhancing Scientific Data.” In: PLoS Computational Biology, 2(10).

Subject Headings: Biocuration Task, Biocurator.

Quotes

• From Impressionism and Pop Art to phosphorylation sites and interacting atom pairs, the realm of curation has been expanded. The recent growth of bioinformatics, driven by exponentially growing data, advanced computing techniques, and increased funding from private and governmental organizations, has created the need for novel strategies to adequately capture, store, and analyze the multitude of data present in the scientific literature. To meet this challenge, the number and scope of scientific databases has soared in recent years, creating a new profession, the biocurator. Indeed, the present emphasis on expanding computational resources, capable of managing and analyzing complex biological data, presents an ever-growing demand for biocurators capable of interpreting the increasingly complex scientific literature and extracting relevant data in an efficient, yet consistent, manner.
• The Immune Epitope Database and Analysis Resource (IEDB) at http://www.immuneepitope.org [1,2] was established to capture, house, and analyze complex immune-epitope–related data extracted from the scientific literature by a team of specialized biocurators. Our experiences as IEDB biocurators are presented here to provide insight into the role of the biocurator and the challenges of literature-based curation of complex scientific data.
• Despite the use of our extensive Curation Manual, there are difficult situations that inherently arise during curation. We often encounter inconsistent terminologies in the literature that present formidable challenges to our consistent interpretation of the data. Scientists frequently use highly diverse and controversial nomenclature, for example, in the naming of MHC molecules. The methods used to perform an experiment may be somewhat obscure or contradictory. The conclusions drawn by the authors may be difficult to represent based upon the limitations of the database fields and our curation guidelines. Newly created assay types may require interpretation and assignment to a particular assay group. Thus, valuable meetings involving the curation team and the EC are held weekly to discuss novel issues arising in curation and to review specific references. While every effort is made to address such problems using our established guidelines, novel challenges are often dealt with on a reference-by-reference basis. The solution is then translated into a generalized guideline that can be consistently applied to similar occurrences in the future.

References

1 Peters, B; Sidney, J; Bourne, P; Huynh-Hoa, B; Buus, S, et al. The immune epitope database and analysis resource: From vision to blueprint. PLoS Biol. 2005;3(3):379–381. doi:10.1371/journal.pbio.0030091. Available: http://biology.plosjournals.org/archive/1545–7885/3/3/pdf/10.1371_journal.pbio.0030091-L.pdf.

2 Peters, B; Sidney, J; Bourne, P; Huynh-Hoa, B; Buus, S, et al. The design and implementation of the immune epitope database and analysis resource. Immunogenetics. 2005;57:326–336.

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	Author	volume	Date Value	title	type	journal	titleUrl	doi	note	year
2006 TheBiocurator	Nima Salimi Randi Vita			The Biocurator: Connecting and Enhancing Scientific Data			http://dx.doi.org/10.1371/journal.pcbi.0020125	10.1371/journal.pcbi.0020125