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However, one important category of pathway \u2014 metabolic pathways \u2014 has been largely neglected.<\/jats:p>\n            <jats:p>Here we present a relatively simple method for extracting metabolic reaction information from free text that scores different permutations of assigned entities (enzymes and metabolites) within a given sentence based on the presence and location of stemmed keywords. This method extends an approach that has proved effective in the context of the extraction of protein\u2013protein interactions.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>When evaluated on a set of manually-curated metabolic pathways using standard performance criteria, our method performs surprisingly well. Precision and recall rates are comparable to those previously achieved for the well-known protein-protein interaction extraction task.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>We conclude that automated metabolic pathway construction is more tractable than has often been assumed, and that (as in the case of protein\u2013protein interaction extraction) relatively simple text-mining approaches can prove surprisingly effective. It is hoped that these results will provide an impetus to further research and act as a useful benchmark for judging the performance of more sophisticated methods that are yet to be developed.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-13-172","type":"journal-article","created":{"date-parts":[[2012,7,23]],"date-time":"2012-07-23T12:14:00Z","timestamp":1343045640000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":32,"title":["A text-mining system for extracting metabolic reactions from full-text articles"],"prefix":"10.1186","volume":"13","author":[{"given":"Jan","family":"Czarnecki","sequence":"first","affiliation":[]},{"given":"Irene","family":"Nobeli","sequence":"additional","affiliation":[]},{"given":"Adrian M","family":"Smith","sequence":"additional","affiliation":[]},{"given":"Adrian J","family":"Shepherd","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2012,7,23]]},"reference":[{"key":"5401_CR1","first-page":"1","volume-title":"Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task","author":"J Kim","year":"2009","unstructured":"Kim J, Ohta T, Pyysalo S, Kano Y, Tsujii J: Overview of BioNLP\u201909 Shared Task on Event Extraction. 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