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Background  The large increase in the number of scientific publications has fuelled a need for semi- and fully automated text mining approaches in order to assist in the triage process, both for individual scientists and also for larger-scale data extraction and curation into public databases. Here, we introduce a document classifier, which is able to successfully distinguish between publications that are `ChEMBL-like’ (i.e. related to small molecule drug discovery and likely to contain quantitative bioactivity data) and those that are not. The unprecedented size of the medicinal chemistry literature collection, coupled with the advantage of manual curation and mapping to chemistry and biology make the ChEMBL corpus a unique resource for text mining.    Results  The method has been implemented as a data protocol/workflow for both Pipeline Pilot (version 8.5) and KNIME (version 2.9) respectively. Both workflows and models are freely available at:  ftp://ftp.ebi.ac.uk/pub/databases/chembl/text-mining . These can be readily modified to include additional keyword constraints to further focus searches.    Conclusions  Large-scale machine learning document classification was shown to be very robust and flexible for this particular application, as illustrated in four distinct text-mining-based use cases. The models are readily available on two data workflow platforms, which we believe will allow the majority of the scientific community to apply them to their own data.    AbstractElectronic supplementary material  The online version of this article (doi:10.1186/s13321-014-0040-8) contains supplementary material, which is available to authorized users.

A document classifier for medicinal chemistry publications trained on the ChEMBL corpus