The paper introduces a framework for representation and acquisition of knowledge emerging from large samples of textual data. We utilise a tensor-based, distributional representation of simple statements extracted from text, and show how one can use the representation to infer emergent knowledge patterns from the textual data in an unsupervised manner. Examples of the patterns we investigate in the paper are implicit term relationships or conjunctive IF-THEN rules. To evaluate the practical relevance of our approach, we apply it to annotation of life science articles with terms from MeSH (a controlled biomedical vocabulary and thesaurus).
Regarding the application of our framework to annotation of biomedical articles, a body of more or less recent works like @cite_8 , @cite_9 , @cite_5 , @cite_14 or @cite_0 exists (the second, third and fifth of the approaches are either used or considered for use as a support service for the professional annotators of the articles on PubMed, a biomedical literature repository). The state of the art methods, however, often require at least an indirect input from human users before they can produce annotations of new articles automatically. For instance, @cite_9 and @cite_0 require a large corpus of previously annotated articles for learning and ranking possible annotations of new resources. Other methods like @cite_5 require rather sophisticated tuning (e.g., experimenting with parameter settings or with the processing pipeline composition) for optimum performance on new data. This is not the case of our approach, as it can work in a purely unsupervised manner off-the-shelf.
@cite_14 @cite_8 @cite_9 @cite_0 @cite_5
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Motivation: The abundance of biomedical literature has attracted significant interest in novel methods to automatically extract biomedical relations from the literature. Until recently, most research was focused on extracting binary relations such as protein–protein interactions and drug–disease relations. However, these binary relations cannot fully represent the original biomedical data. Therefore, there is a need for methods that can extract fine-grained and complex relations known as biomedical events. Results: In this article we propose a novel method to extract biomedical events from text. Our method consists of two phases. In the first phase, training data are mapped into structured representations. Based on that, templates are used to extract rules automatically. In the second phase, extraction methods are developed to process the obtained rules. When evaluated against the Genia event extraction abstract and full-text test datasets (Task 1), we obtain results with F-scores of 52.34 and 53.34, respectively, which are comparable to the state-of-the-art systems. Furthermore, our system achieves superior performance in terms of computational efficiency. Availability: Our source code is available for academic use at http: dl.dropbox.com u 10256952 BioEvent.zip Contact: [email protected] A significant portion of biomedical literature is represented in a manner that makes it difficult for consumers to find or aggregate content through a computational query. One approach to facilitate reuse of the scientific literature is to structure this information as linked data using standardized web technologies. In this paper we present the second version of Biotea, a semantic, linked data version of the open-access subset of PubMed Central that has been enhanced with specialized annotation pipelines that uses existing infrastructure from the National Center for Biomedical Ontology. We expose our models, services, software and datasets. Our infrastructure enables manual and semi-automatic annotation, resulting data are represented as RDF-based linked data and can be readily queried using the SPARQL query language. We illustrate the utility of our system with several use cases. Our datasets, methods and techniques are available at http: biotea.github.io. Objective: The amount of new discoveries (as published in the scientific literature) in the biomedical area is growing at an exponential rate. This growth makes it very difficult to filter the most relevant results, and thus the extraction of the core information becomes very expensive. Therefore, there is a growing interest in text processing approaches that can deliver selected information from scientific publications, which can limit the amount of human intervention normally needed to gather those results. Materials and methods: This paper presents and evaluates an approach aimed at automating the process of extracting functional relations (e.g. interactions between genes and proteins) from scientific literature in the biomedical domain. The approach, using a novel dependency-based parser, is based on a complete syntactic analysis of the corpus. Results: We have implemented a state-of-the-art text mining system for biomedical literature, based on a deep-linguistic, full-parsing approach. The results are validated on two different corpora: the manually annotated genomics information access (GENIA) corpus and the automatically annotated arabidopsis thaliana circadian rhythms (ATCR) corpus. Conclusion: We show how a deep-linguistic approach (contrary to common belief) can be used in a real world text mining application, offering high-precision relation extraction, while at the same time retaining a sufficient recall. The volume of biomedical literature has experienced explosive growth in recent years. This is reflected in the corresponding increase in the size of MEDLINE^(R), the largest bibliographic database of biomedical citations. Indexers at the US National Library of Medicine (NLM) need efficient tools to help them accommodate the ensuing workload. After reviewing issues in the automatic assignment of Medical Subject Headings (MeSH^(R) terms) to biomedical text, we focus more specifically on the new subheading attachment feature for NLM's Medical Text Indexer (MTI). Natural Language Processing, statistical, and machine learning methods of producing automatic MeSH main heading subheading pair recommendations were assessed independently and combined. The best combination achieves 48 precision and 30 recall. After validation by NLM indexers, a suitable combination of the methods presented in this paper was integrated into MTI as a subheading attachment feature producing MeSH indexing recommendations compliant with current state-of-the-art indexing practice.