A Standard Lexical-Terminological Resource for the Bio Domain

Quochi, Valeria; Gratta, Riccardo Del; Sassolini, Eva; Bartolini, Roberto; Monachini, Monica; Calzolari, Nicoletta

doi:10.1007/978-3-642-04235-5_28

Cited by 1 publication

(1 citation statement)

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“…Since one of the main aims of the BioLexicon is to foster semantic interoperability of systems in the biomedical community, the ISO (International Organization for Standardization) standard Lexical Markup Framework (LMF) was chosen as the reference meta-model for the structure of the BioLexicon [ 75 ]. The LMF, together with linguistic constants used for lexical description (called data categories), provides a common, flexible representation of lexical objects that allows for the encoding of detailed linguistic information.…”

Section: Methodsmentioning

confidence: 99%

The BioLexicon: a large-scale terminological resource for biomedical text mining

et al. 2011

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BackgroundDue to the rapidly expanding body of biomedical literature, biologists require increasingly sophisticated and efficient systems to help them to search for relevant information. Such systems should account for the multiple written variants used to represent biomedical concepts, and allow the user to search for specific pieces of knowledge (or events) involving these concepts, e.g., protein-protein interactions. Such functionality requires access to detailed information about words used in the biomedical literature. Existing databases and ontologies often have a specific focus and are oriented towards human use. Consequently, biological knowledge is dispersed amongst many resources, which often do not attempt to account for the large and frequently changing set of variants that appear in the literature. Additionally, such resources typically do not provide information about how terms relate to each other in texts to describe events.ResultsThis article provides an overview of the design, construction and evaluation of a large-scale lexical and conceptual resource for the biomedical domain, the BioLexicon. The resource can be exploited by text mining tools at several levels, e.g., part-of-speech tagging, recognition of biomedical entities, and the extraction of events in which they are involved. As such, the BioLexicon must account for real usage of words in biomedical texts. In particular, the BioLexicon gathers together different types of terms from several existing data resources into a single, unified repository, and augments them with new term variants automatically extracted from biomedical literature. Extraction of events is facilitated through the inclusion of biologically pertinent verbs (around which events are typically organized) together with information about typical patterns of grammatical and semantic behaviour, which are acquired from domain-specific texts. In order to foster interoperability, the BioLexicon is modelled using the Lexical Markup Framework, an ISO standard.ConclusionsThe BioLexicon contains over 2.2 M lexical entries and over 1.8 M terminological variants, as well as over 3.3 M semantic relations, including over 2 M synonymy relations. Its exploitation can benefit both application developers and users. We demonstrate some such benefits by describing integration of the resource into a number of different tools, and evaluating improvements in performance that this can bring.

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Section: Methodsmentioning

confidence: 99%