title: Text mining resources for the life sciences.
abstract: Text mining is a powerful technology for quickly distilling key information from vast quantities of biomedical literature. However, to harness this power the researcher must be well versed in the availability, suitability, adaptability, interoperability and comparative accuracy of current text mining resources. In this survey, we give an overview of the text mining resources that exist in the life sciences to help researchers, especially those employed in biocuration, to engage with text mining in their own work. We categorize the various resources under three sections: Content Discovery looks at where and how to find biomedical publications for text mining; Knowledge Encoding describes the formats used to represent the different levels of information associated with content that enable text mining, including those formats used to carry such information between processes; Tools and Services gives an overview of workflow management systems that can be used to rapidly configure and compare domain- and task-specific processes, via access to a wide range of pre-built tools. We also provide links to relevant repositories in each section to enable the reader to find resources relevant to their own area of interest. Throughout this work we give a special focus to resources that are interoperable-those that have the crucial ability to share information, enabling smooth integration and reusability.
authors.affiliation: National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester, UK matthew.shardlow@manchester.ac.uk.
authors.forename: Piotr
authors.initials: P
authors.lastname: Przybyła
authors.affiliation: National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester, UK matthew.shardlow@manchester.ac.uk.
authors.forename: Matthew
authors.initials: M
authors.lastname: Shardlow
authors.affiliation: Institut National de la Recherche Agronomique, Jouy-en-Josas, France.
authors.forename: Sophie
authors.initials: S
authors.lastname: Aubin
authors.affiliation: Institut National de la Recherche Agronomique, Jouy-en-Josas, France.
authors.forename: Robert
authors.initials: R
authors.lastname: Bossy
authors.affiliation: Ubiquitous Knowledge Processing Lab, Technische Universität Darmstadt, Darmstadt, Germany and.
authors.forename: Richard
authors.initials: R
authors.lastname: Eckart de Castilho
authors.affiliation: Institute for Language and Speech Processing, Athena Research Center, Athens, Greece.
authors.forename: Stelios
authors.initials: S
authors.lastname: Piperidis
authors.affiliation: National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester, UK.
authors.forename: John
authors.initials: J
authors.lastname: McNaught
authors.affiliation: National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester, UK.
authors.forename: Sophia
authors.initials: S
authors.lastname: Ananiadou
mesh_terms: D057225:Data Mining / Q000379:methods*; D016208:Databases, Factual; D006801:Humans