D4.1. Technologies and tools for corpus creation, normalization and annotation

The objectives of the Corpus Acquisition and Annotation (CAA) subsystem are the acquisition and processing of monolingual and bilingual language resources (LRs) required in the PANACEA context. Therefore, the CAA subsystem includes: i) a Corpus Acquisition Component (CAC) for extracting monolingual and bilingual data from the web, ii) a component for cleanup and normalization (CNC) of these data and iii) a text processing component (TPC) which consists of NLP tools including modules for sentence splitting, POS tagging, lemmatization, parsing and named entity recognition

Exploring subdomain variation in biomedical language.

BACKGROUND: Applications of Natural Language Processing (NLP) technology to biomedical texts have generated significant interest in recent years. In this paper we identify and investigate the phenomenon of linguistic subdomain variation within the biomedical domain, i.e., the extent to which different subject areas of biomedicine are characterised by different linguistic behaviour. While variation at a coarser domain level such as between newswire and biomedical text is well-studied and known to affect the portability of NLP systems, we are the first to conduct an extensive investigation into more fine-grained levels of variation. RESULTS: Using the large OpenPMC text corpus, which spans the many subdomains of biomedicine, we investigate variation across a number of lexical, syntactic, semantic and discourse-related dimensions. These dimensions are chosen for their relevance to the performance of NLP systems. We use clustering techniques to analyse commonalities and distinctions among the subdomains. CONCLUSIONS: We find that while patterns of inter-subdomain variation differ somewhat from one feature set to another, robust clusters can be identified that correspond to intuitive distinctions such as that between clinical and laboratory subjects. In particular, subdomains relating to genetics and molecular biology, which are the most common sources of material for training and evaluating biomedical NLP tools, are not representative of all biomedical subdomains. We conclude that an awareness of subdomain variation is important when considering the practical use of language processing applications by biomedical researchers

A Dependency Parsing Approach to Biomedical Text Mining

Biomedical research is currently facing a new type of challenge: an excess of information, both in terms of raw data from experiments and in the number of scientific publications describing their results. Mirroring the focus on data mining techniques to address the issues of structured data, there has recently been great interest in the development and application of text mining techniques to make more effective use of the knowledge contained in biomedical scientific publications, accessible only in the form of natural human language. This thesis describes research done in the broader scope of projects aiming to develop methods, tools and techniques for text mining tasks in general and for the biomedical domain in particular. The work described here involves more specifically the goal of extracting information from statements concerning relations of biomedical entities, such as protein-protein interactions. The approach taken is one using full parsing—syntactic analysis of the entire structure of sentences—and machine learning, aiming to develop reliable methods that can further be generalized to apply also to other domains. The five papers at the core of this thesis describe research on a number of distinct but related topics in text mining. In the first of these studies, we assessed the applicability of two popular general English parsers to biomedical text mining and, finding their performance limited, identified several specific challenges to accurate parsing of domain text. In a follow-up study focusing on parsing issues related to specialized domain terminology, we evaluated three lexical adaptation methods. We found that the accurate resolution of unknown words can considerably improve parsing performance and introduced a domain-adapted parser that reduced the error rate of theoriginal by 10% while also roughly halving parsing time. To establish the relative merits of parsers that differ in the applied formalisms and the representation given to their syntactic analyses, we have also developed evaluation methodology, considering different approaches to establishing comparable dependency-based evaluation results. We introduced a methodology for creating highly accurate conversions between different parse representations, demonstrating the feasibility of unification of idiverse syntactic schemes under a shared, application-oriented representation. In addition to allowing formalism-neutral evaluation, we argue that such unification can also increase the value of parsers for domain text mining. As a further step in this direction, we analysed the characteristics of publicly available biomedical corpora annotated for protein-protein interactions and created tools for converting them into a shared form, thus contributing also to the unification of text mining resources. The introduced unified corpora allowed us to perform a task-oriented comparative evaluation of biomedical text mining corpora. This evaluation established clear limits on the comparability of results for text mining methods evaluated on different resources, prompting further efforts toward standardization. To support this and other research, we have also designed and annotated BioInfer, the first domain corpus of its size combining annotation of syntax and biomedical entities with a detailed annotation of their relationships. The corpus represents a major design and development effort of the research group, with manual annotation that identifies over 6000 entities, 2500 relationships and 28,000 syntactic dependencies in 1100 sentences. In addition to combining these key annotations for a single set of sentences, BioInfer was also the first domain resource to introduce a representation of entity relations that is supported by ontologies and able to capture complex, structured relationships. Part I of this thesis presents a summary of this research in the broader context of a text mining system, and Part II contains reprints of the five included publications.Siirretty Doriast

D6.2 Integrated Final Version of the Components for Lexical Acquisition

The PANACEA project has addressed one of the most critical bottlenecks that threaten the development of technologies to support multilingualism in Europe, and to process the huge quantity of multilingual data produced annually. Any attempt at automated language processing, particularly Machine Translation (MT), depends on the availability of language-specific resources. Such Language Resources (LR) contain information about the language\u27s lexicon, i.e. the words of the language and the characteristics of their use. In Natural Language Processing (NLP), LRs contribute information about the syntactic and semantic behaviour of words - i.e. their grammar and their meaning - which inform downstream applications such as MT. To date, many LRs have been generated by hand, requiring significant manual labour from linguistic experts. However, proceeding manually, it is impossible to supply LRs for every possible pair of European languages, textual domain, and genre, which are needed by MT developers. Moreover, an LR for a given language can never be considered complete nor final because of the characteristics of natural language, which continually undergoes changes, especially spurred on by the emergence of new knowledge domains and new technologies. PANACEA has addressed this challenge by building a factory of LRs that progressively automates the stages involved in the acquisition, production, updating and maintenance of LRs required by MT systems. The existence of such a factory will significantly cut down the cost, time and human effort required to build LRs. WP6 has addressed the lexical acquisition component of the LR factory, that is, the techniques for automated extraction of key lexical information from texts, and the automatic collation of lexical information into LRs in a standardized format. The goal of WP6 has been to take existing techniques capable of acquiring syntactic and semantic information from corpus data, improving upon them, adapting and applying them to multiple languages, and turning them into powerful and flexible techniques capable of supporting massive applications. One focus for improving the scalability and portability of lexical acquisition techniques has been to extend exiting techniques with more powerful, less "supervised" methods. In NLP, the amount of supervision refers to the amount of manual annotation which must be applied to a text corpus before machine learning or other techniques are applied to the data to compile a lexicon. More manual annotation means more accurate training data, and thus a more accurate LR. However, given that it is impractical from a cost and time perspective to manually annotate the vast amounts of data required for multilingual MT across domains, it is important to develop techniques which can learn from corpora with less supervision. Less supervised methods are capable of supporting both large-scale acquisition and efficient domain adaptation, even in the domains where data is scarce. Another focus of lexical acquisition in PANACEA has been the need of LR users to tune the accuracy level of LRs. Some applications may require increased precision, or accuracy, where the application requires a high degree of confidence in the lexical information used. At other times a greater level of coverage may be required, with information about more words at the expense of some degree of accuracy. Lexical acquisition in PANACEA has investigated confidence thresholds for lexical acquisition to ensure that the ultimate users of LRs can generate lexical data from the PANACEA factory at the desired level of accuracy

Datasets for generic relation extraction

A vast amount of usable electronic data is in the form of unstructured text. The relation extraction task aims to identify useful information in text (e.g. PersonW works for OrganisationX, GeneY encodes ProteinZ) and recode it in a format such as a relational database or RDF triplestore that can be more effectively used for querying and automated reasoning. A number of resources have been developed for training and evaluating automatic systems for relation extraction in different domains. However, comparative evaluation is impeded by the fact that these corpora use different markup formats and notions of what constitutes a relation. We describe the preparation of corpora for comparative evaluation of relation extraction across domains based on the publicly available ACE 2004, ACE 2005 and BioInfer data sets. We present a common document type using token standoff and including detailed linguistic markup, while maintaining all information in the original annotation. The subsequent reannotation process normalises the two data sets so that they comply with a notion of relation that is intuitive, simple and informed by the semantic web. For the ACE data, we describe an automatic process that automatically converts many relations involving nested, nominal entity mentions to relations involving non-nested, named or pronominal entity mentions. For example, the first entity is mapped from 'one' to 'Amidu Berry' in the membership relation described in 'Amidu Berry, one half of PBS'. Moreover, we describe a comparably reannotated version of the BioInfer corpus that flattens nested relations, maps part-whole to part-part relations and maps n-ary to binary relations. Finally, we summarise experiments that compare approaches to generic relation extraction, a knowledge discovery task that uses minimally supervised techniques to achieve maximally portable extractors. These experiments illustrate the utility of the corpora.39 page(s