Nima Salimi; Randi Vita

“ As biocurators, we must be able to understand scientific data and to incorporate the curation guidelines in a way that maintains the integrity of both. Open communication between the scientists and the biocurators may foster a better understanding of the difficulties encountered by the biocurator and facilitate a more standardized approach to data representation in the literature. The growing use of and contribution to various high-impact databases underscores the need to establish or refine standardized biological vocabularies and definitions. ”

“ Endeavors to achieve uniformity significantly enhance the efficiency of data curation and exchange. Such reform should eventually diffuse throughout the scientific community and be reflected in the literature.
New methodologies allow scientific data to grow at an exponential pace, creating a steady demand for reliable, consistent, and accurate databases. As bioinformatics resources continue to grow, so will the role of the biocurator in their development. The expansion of bioinformatics and its applications paints a promising future for the biocurator. ”

“ 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. ”

“ For example, all influenza epitopes present in the IEDB were recently analyzed for sequence conservancy between the different strains (unpublished data: Bui HH, Peters B, Assarsson E, Mbawuike I, Sette A, Antibody and T cell epitopes of Influenza A virus—Knowledge and opportunities) .
Communication with authors and end-users is a critical skill for the IEDB biocurator for the purposes of curation, database development, and for community outreach efforts to raise public awareness about the IEDB. We often consult with outside scientists for subject-matter expertise. ”

“ As the goal of the IEDB is to present as much information as possible without subjective interpretation, we can never presume any information, but rather we must try to capture the data exactly as presented in the reference, while maintaining the conclusions of the reference in a uniform manner. For example, if all experiments are performed with a whole cell population, but the authors attribute the response to a particular cell type without any evidence, we must capture the effector cells as the entire population. ”

“ With more experienced scientists as biocurators, an accurate and controlled vocabulary among database users and contributors can be developed and promoted. The use of a shared vocabulary increases curation speed, data consistency, and serves to connect the information contained in multiple databases. ”

“ IEDB biocurators also act as ambassadors for the database, both to raise community awareness and to collect positive and constructive feedback. We must be aware of the needs of the IEDB end-user to productively enhance the curation guidelines, database structure, and ontology. We attend national and international conferences to promote and discuss the database with both end-users and contributors. Representatives from the IEDB attended the First International Biocurator Meeting in December 2005 where curation teams representing 106 databases gathered to exchange information and ideas. ”

“ Issues as simple as assigning an effector cell type, the semantics used to describe an assay type, or even the qualitative result can lead to a great deal of discussion. Many times authors may discuss conclusions or assumptions that are not depicted in the figures. ”