Dictionary-based named entity recognition

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The document describes Lars Juhl Jensen's dictionary-based approach to named entity recognition. It involves compiling a comprehensive dictionary of biological and biomedical terms from various sources, including genes, proteins, species, diseases, pathways and more. The dictionary is expanded to include synonyms, abbreviations, prefixes/suffixes and plural forms. Ambiguity is handled by either allowing, disallowing or disambiguating terms. The named entity recognition is performed in two rounds to identify species/organisms and genes/proteins with flexible matching. The approach achieves around 85% precision and 75% recall.

Science

Lars Juhl Jensen
Dictionary-based
named entity recognition

Hoffmann & Valencia, Nature Genetics, 2004www.ihop-net.org

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The voltage across the plasma membrane which emanates due to the presence of different ion channels/transporters with specific ion selectivity and permeability is known as membrane.[1] It is the main biophysical indication in non-excitable cells controlling some essential cellular activities, such as proliferation and differentiation. Hence, the plurality of different ion channels/transporters indicated on various cells is finely tailored toward maintaining the membrane potential

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Single Nucleotide Polymorphism (SNP) Polymorphism is a generic term that means 'many shapes‘. It is the ability to appsear in different form . A single nucleotide polymorphism (SNP) is a DNA sequence variation occurring when a single nucleotide - A, T, C, or G - in the genome differs between members of a species (or between paired chromosomes in an individual). For example, two sequenced DNA fragments from different individuals, AAGCCTA to AAGCTTA, contain a difference in a single nucleotide. For a variation to be considered a SNP, it must occur in at least 1% of the population. CHARACTERISTICS OF SNP • In human beings, 99.9 percent bases are same. • Remaining 0.1 percent makes a person unique. • Different attributes / characteristics / traits • How a person looks, diseases he or she develops. These variations can be:  Harmless (change in phenotype)  Harmful (diabetes, cancer, heart disease, Huntington's disease, and hemophilia )  Latent (variations found in coding and regulatory regions, are not harmful on their own, and the change in each gene only becomes apparent under certain conditions e.g. susceptibility to lung cancer) TYPES OF SNP NON-CODING REGION A segment of DNA that does comprise a gene and thus does not code for a protein . CODING REGION Regions of DNA/RNA sequences that code for proteins Synonymous A SNP in which both forms lead to the same polypeptide sequence is termed synonymous (sometimes called a silent mutation). Non synonymous If a different polypeptide sequence is produced they are non synonymous . A non synonymous change may either be missense or nonsense, where a missense change results in a different amino acid, while a nonsense change results in a premature stop codon. SNP Applications • Gene discovery and mapping • Association-based candidate polymorphism testing • Diagnostics/risk profiling • Response prediction • Homogeneity testing/study design • Gene function identification

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