Chemlist
From the scientific community, a lot of effort has been spent on the correct identification of gene and protein names in text, while less effort has been spent on the correct identification of chemical names. Dictionary-based term identification has the power to recognize the diverse representation of chemical information in the literature and map the chemicals to their database identifiers. We developed a dictionary for the identification of small molecules and drugs in text, combining information from UMLS, MeSH, ChEBI, DrugBank, KEGG, HMDB, and ChemIDplus. Rule-based term filtering, manual check of highly frequent terms, and disambiguation rules were applied. We tested the combined dictionary and the dictionaries derived from the individual resources on an annotated corpus, and conclude the following: (1) each of the different processing steps increase precision with a minor loss of recall; (2) the overall performance of the combined dictionary is acceptable (precision 0.67, recall 0.40 (0.80 for trivial names); (3) the combined dictionary performed better than the dictionary in the chemical recognizer OSCAR3; (4) the performance of a dictionary based on ChemIDplus alone is comparable to the performance of the combined dictionary.
The Chemlist dictionary is available in Simple Knowledge Organisation Systems (SKOS) format.
List of database identifier names:
CHID = ChemIDplus
CHEB = ChEBI
CAS = CAS number
PUBC = PubChem compound
PUBS = PubChem substance
INCH = InChI code
DRUG = DrugBank
HMBD = Human Metabolome Database
KEGG = KEGG compound
KEGD = KEGG drug
MESH = Medical Subject Headings (and supplemental records)
Citing Chemlist
If you have used Chemlist in your study, please cite:
A Dictionary to Identify Small Molecules and Drugs in Free Text.
Hettne KM, Stierum RH, Schuemie MJ, Hendriksen PJ, Schijvenaars BJ, van Mulligen EM, Kleinjans J, Kors JA.
Bioinformatics. 2009 Sep 16. [Epub ahead of print]