PubMed · 15688594
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Alexander Pertsemlidis, Harold R Garner. Text comparison based on dynamic programming.. https://doi.org/10.1109/memb.2004.1378640
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In the past year, DDBJ (http://www.ddbj.nig.ac.jp) collected and released 1,956,826 entries or 1,741,313,111 bases. The released data include approximately 90,000 ESTs and cDNAs of Macaca fascicularis, and 280 million bases of mouse GSS. In addition to the data collection, we have indexed the submitted data to the International Nucleotide Sequence Database Collaboration (INSDC, http://www.insdc.org) to classify the entries into research projects behind data submissions. They are expected to be useful to the data submitters and users for enhancing the data submission, retrieval and systematic data analyses at INSDC. The results of indexing also allow one to grasp research projects in life sciences that promoted and produced the DNA sequences submitted to INSDC.
The available tools for searching literature in the field of Molecular Epidemiology are largely unsatisfactory. To identify major problems in retrieving information on this discipline, we comment here on the results of a literature search on cytogenetic biomarkers in children exposed to environmental pollutants. The search, done on the PubMed/MedLine database, was based on a strategy combining descriptors listed in the PubMed Medical Subject Headings (MeSH) Thesaurus and other available tools (free text or phrase search tools). 178 articles were retrieved by searching the period from January 1, 1980 to November 30, 2004. Only 2 of the 178 articles were indexed by the MeSH term "Epidemiology, molecular" (introduced in 1994) and 30 of 178 by the MeSH term "Biological markers" (introduced in 1989). The case of chromosome aberration (CA) was emblematic of the problem: 44 of 78 articles (56.4%) were not pertinent to the search. The reasons for this poor performance are reported and discussed. Authors and indexers may be able to improve the efficiency of article retrieval in the field of molecular epidemiology by using relevant terms in the title and abstract. This may suggest appropriate MeSH terms to the indexers for the indexing process. As regards the difficulty in identifying population studies using CA, the introduction of a specific MeSH term for chromosome aberrations when used as a biomarker would improve the search process.
Web servers at the National Library of Medicine (NLM) displayed images of ten skin lesions to practicing dermatologists and provided an online form for capturing text they used to describe the pictures. The terms were submitted to the UMLS Metathesaurus (Meta). Concepts retrieved, their semantic types, definitions and synonyms, were returned to each subject in a second web-based form. Subjects rated the concepts against their own descriptive terms. They submitted 825 terms, 346 of which were unique and 300 mapped to UMLS concepts. The dermatologists rated 295 concepts as 'Exact Match' and they accomplished both tasks in about 30 min.