tmChem: a high performance approach for chemical named entity recognition and normalization

Robert Leaman1, Chih-Hsuan Wei1, Zhiyong Lu1

  • 1National Center for Biotechnology Information, 8600 Rockville Pike, Bethesda, Maryland 20894, USA.

Summary

tmChem is a new system for recognizing chemical named entities in biomedical literature. It achieves state-of-the-art performance, matching or exceeding recognition rates for genes and diseases.

Related Concept Videos

Chemical Symbols01:09

Chemical Symbols

A chemical symbol is an abbreviation that is used to indicate an element or an atom of an element. For example, the symbol for mercury is Hg. We use the same symbol to indicate one atom of mercury (microscopic domain) or to label a container of many atoms of the element mercury (macroscopic domain).
Some symbols are derived from the common name of the element; others are abbreviations of the name in another language. Most symbols have one or two letters, but three-letter symbols have been used...
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Molecular Compounds: Formulas and Nomenclature03:10

Molecular Compounds: Formulas and Nomenclature

Molecular compounds or covalent compounds result when atoms share electrons to form covalent bonds. Since there is no electron transfer, molecular compounds do not contain ions; instead, they consist of discrete, neutral molecules. 
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Nomenclature of Aromatic Compounds with a Single Substituent01:23

Nomenclature of Aromatic Compounds with a Single Substituent

Benzene is the simplest aromatic hydrocarbon or arene. The IUPAC names for simple monosubstituted benzene derivatives are derived by adding the substituent's name as a prefix to the parent benzene. For example, halobenzene, where the halogen could be fluoro (F), chloro (Cl), bromo (Br), and iodo (I).
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Coordination Compounds and Nomenclature02:54

Coordination Compounds and Nomenclature

In most main group element compounds, the valence electrons of the isolated atoms combine to form chemical bonds that satisfy the octet rule. For instance, the four valence electrons of carbon overlap with electrons from four hydrogen atoms to form CH4. The one valence electron leaves sodium and adds to the seven valence electrons of chlorine to form the ionic formula unit NaCl (Figure 1a). Transition metals do not normally bond in this fashion. They primarily form coordinate covalent bonds, a...
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Nomenclature of Aromatic Compounds with Multiple Substituents01:11

Nomenclature of Aromatic Compounds with Multiple Substituents

When more than one substituent is present on the benzene ring, the IUPAC nomenclature depends on the number of substituents present.
For disubstituted benzene derivatives, with two groups attached to the benzene ring, three constitutional isomers are possible. For example, consider dimethyl benzene, often called xylene, where the second methyl group can be substituted at the second, third, or fourth carbon. The relative position of the substituents is represented by prefixes ortho, meta, or...
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Properties of Organometallic Compounds01:23

Properties of Organometallic Compounds

Organometallic compounds are compounds that contain a carbon–metal bond. Carbon belongs to an organyl group like alkyl, aryl, allyl, or benzyl groups. The metal can be from Group I or Group II of the periodic table, a transition metal, or a semimetal.
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