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PMID: 17646325 Published · ppublish English Journal Article Research Support, N.I.H., Extramural

Manual curation is not sufficient for annotation of genomic databases.

Bioinformatics (Oxford, England) ·Vol. 23 ·No. 13 ·2007-07-01 ·Pages i41-8

Baumgartner WA, Cohen KB, Fox LM, Acquaah-Mensah G, Hunter L

Abstract

Knowledge base construction has been an area of intense activity and great importance in the growth of computational biology. However, there is little or no history of work on the subject of evaluation of knowledge bases, either with respect to their contents or with respect to the processes by which they are constructed. This article proposes the application of a metric from software engineering known as the found/fixed graph to the problem of evaluating the processes by which genomic knowledge bases are built, as well as the completeness of their contents. Well-understood patterns of change in the found/fixed graph are found to occur in two large publicly available knowledge bases. These patterns suggest that the current manual curation processes will take far too long to complete the annotations of even just the most important model organisms, and that at their current rate of production, they will never be sufficient for completing the annotation of all currently available proteomes.

MeSH Terms
Chromosome Mapping/methods Databases, Protein Documentation/methods Genomics/methods Proteins/chemistry,genetics Sequence Analysis, Protein/methods
Chemicals
Proteins
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Baumgartner William A
Center for Computational Pharmacology, University of Colorado School of Medicine, USA.
Cohen K Bretonnel
Fox Lynne M
Acquaah-Mensah George
Hunter Lawrence
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Article Info
Journal
Bioinformatics (Oxford, England)
Abbr.
Bioinformatics
ISSN
1367-4811
DOI
10.1093/bioinformatics/btm229
Published
2007-07-01
Pages
i41-8
Language
English
Region
England
NLM ID
9808944
PMCID
PMC2516305
Subset
IM
Grants
NLM NIH HHS · R01 LM008111 · United States
NLM NIH HHS · R01 LM008111-03 · United States
NLM NIH HHS · R01-LM008111 · United States
External Links
PubMed source DOI: 10.1093/bioinformatics/btm229 PMC Full Text View journal details
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