258 research outputs found

    Infrastructure for Semantic Annotation in the Genomics Domain

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    We describe a novel super-infrastructure for biomedical text mining which incorporates an end-to-end pipeline for the collection, annotation, storage, retrieval and analysis of biomedical and life sciences literature, combining NLP and corpus linguistics methods. The infrastructure permits extreme-scale research on the open access PubMed Central archive. It combines an updatable Gene Ontology Semantic Tagger (GOST) for entity identification and semantic markup in the literature, with a NLP pipeline scheduler (Buster) to collect and process the corpus, and a bespoke columnar corpus database (LexiDB) for indexing. The corpus database is distributed to permit fast indexing, and provides a simple web front-end with corpus linguistics methods for sub-corpus comparison and retrieval. GOST is also connected as a service in the Language Application (LAPPS) Grid, in which context it is interoperable with other NLP tools and data in the Grid and can be combined with them in more complex workflows. In a literature based discovery setting, we have created an annotated corpus of 9,776 papers with 5,481,543 words

    A text-mining system for extracting metabolic reactions from full-text articles

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    Background: Increasingly biological text mining research is focusing on the extraction of complex relationships relevant to the construction and curation of biological networks and pathways. However, one important category of pathway—metabolic pathways—has been largely neglected. Here we present a relatively simple method for extracting metabolic reaction information from free text that scores different permutations of assigned entities (enzymes and metabolites) within a given sentence based on the presence and location of stemmed keywords. This method extends an approach that has proved effective in the context of the extraction of protein–protein interactions. Results: When evaluated on a set of manually-curated metabolic pathways using standard performance criteria, our method performs surprisingly well. Precision and recall rates are comparable to those previously achieved for the well-known protein-protein interaction extraction task. Conclusions: We conclude that automated metabolic pathway construction is more tractable than has often been assumed, and that (as in the case of protein–protein interaction extraction) relatively simple text-mining approaches can prove surprisingly effective. It is hoped that these results will provide an impetus to further research and act as a useful benchmark for judging the performance of more sophisticated methods that are yet to be developed

    Domain-sensitive Temporal Tagging for Event-centric Information Retrieval

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    Temporal and geographic information is of major importance in virtually all contexts. Thus, it also occurs frequently in many types of text documents in the form of temporal and geographic expressions. Often, those are used to refer to something that was, is, or will be happening at some specific time and some specific place – in other words, temporal and geographic expressions are often used to refer to events. However, so far, event-related information needs are not well served by standard information retrieval approaches, which motivates the topic of this thesis: event-centric information retrieval. An important characteristic of temporal and geographic expressions – and thus of two components of events – is that they can be normalized so that their meaning is unambiguous and can be placed on a timeline or pinpointed on a map. In many research areas in which natural language processing is involved, e.g., in information retrieval, document summarization, and question answering, applications can highly benefit from having access to normalized information instead of only the words as they occur in documents. In this thesis, we present several frameworks for searching and exploring document collections with respect to occurring temporal, geographic, and event information. While we rely on an existing tool for extracting and normalizing geographic expressions, we study the task of temporal tagging, i.e., the extraction and normalization of temporal expressions. A crucial issue is that so far most research on temporal tagging dealt with English news-style documents. However, temporal expressions have to be handled in different ways depending on the domain of the documents from which they are extracted. Since we do not want to limit our research to one domain and one language, we develop the multilingual, cross-domain temporal tagger HeidelTime. It is the only publicly available temporal tagger for several languages and easy to extend to further languages. In addition, it achieves state-of-the-art evaluation results for all addressed domains and languages, and lays the foundations for all further contributions developed in this thesis. To achieve our goal of exploiting temporal and geographic expressions for event-centric information retrieval from a variety of text documents, we introduce the concept of spatio-temporal events and several concepts to "compute" with temporal, geographic, and event information. These concepts are used to develop a spatio-temporal ranking approach, which does not only consider textual, temporal, and geographic query parts but also two different types of proximity information. Furthermore, we adapt the spatio-temporal search idea by presenting a framework to directly search for events. Additionally, several map-based exploration frameworks are introduced that allow a new way of exploring event information latently contained in huge document collections. Finally, an event-centric document similarity model is developed that calculates document similarity on multilingual corpora solely based on extracted and normalized event information

    TIDA: A spanish EHR semantic search engine

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    Electronic Health Records (EHR) and the constant adoption of Information Technologies in healthcare have dramatically increased the amount of unstructured data stored. The extraction of key information from this data will bring better caregivers decisions and an improvement in patients? treatments. With more than 495 million people talking Spanish, the need to adapt algorithms and technologies used in EHR knowledge extraction in English speaking countries, leads to the development of different frameworks. Thus, we present TIDA, a Spanish EHR semantic search engine, to give support to Spanish speaking medical centers and hospitals to convert pure raw data into information understandable for cognitive systems. This paper presents the results of TIDA?s Spanish EHR free-text treatment component with the adaptation of negation and context detection algorithms applied in a semantic search engine with a database with more than 30,000 clinical notes

    Information Extraction from Text for Improving Research on Small Molecules and Histone Modifications

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    The cumulative number of publications, in particular in the life sciences, requires efficient methods for the automated extraction of information and semantic information retrieval. The recognition and identification of information-carrying units in text – concept denominations and named entities – relevant to a certain domain is a fundamental step. The focus of this thesis lies on the recognition of chemical entities and the new biological named entity type histone modifications, which are both important in the field of drug discovery. As the emergence of new research fields as well as the discovery and generation of novel entities goes along with the coinage of new terms, the perpetual adaptation of respective named entity recognition approaches to new domains is an important step for information extraction. Two methodologies have been investigated in this concern: the state-of-the-art machine learning method, Conditional Random Fields (CRF), and an approximate string search method based on dictionaries. Recognition methods that rely on dictionaries are strongly dependent on the availability of entity terminology collections as well as on its quality. In the case of chemical entities the terminology is distributed over more than 7 publicly available data sources. The join of entries and accompanied terminology from selected resources enables the generation of a new dictionary comprising chemical named entities. Combined with the automatic processing of respective terminology – the dictionary curation – the recognition performance reached an F1 measure of 0.54. That is an improvement by 29 % in comparison to the raw dictionary. The highest recall was achieved for the class of TRIVIAL-names with 0.79. The recognition and identification of chemical named entities provides a prerequisite for the extraction of related pharmacological relevant information from literature data. Therefore, lexico-syntactic patterns were defined that support the automated extraction of hypernymic phrases comprising pharmacological function terminology related to chemical compounds. It was shown that 29-50 % of the automatically extracted terms can be proposed for novel functional annotation of chemical entities provided by the reference database DrugBank. Furthermore, they are a basis for building up concept hierarchies and ontologies or for extending existing ones. Successively, the pharmacological function and biological activity concepts obtained from text were included into a novel descriptor for chemical compounds. Its successful application for the prediction of pharmacological function of molecules and the extension of chemical classification schemes, such as the the Anatomical Therapeutic Chemical (ATC), is demonstrated. In contrast to chemical entities, no comprehensive terminology resource has been available for histone modifications. Thus, histone modification concept terminology was primary recognized in text via CRFs with a F1 measure of 0.86. Subsequent, linguistic variants of extracted histone modification terms were mapped to standard representations that were organized into a newly assembled histone modification hierarchy. The mapping was accomplished by a novel developed term mapping approach described in the thesis. The combination of term recognition and term variant resolution builds up a new procedure for the assembly of novel terminology collections. It supports the generation of a term list that is applicable in dictionary-based methods. For the recognition of histone modification in text it could be shown that the named entity recognition method based on dictionaries is superior to the used machine learning approach. In conclusion, the present thesis provides techniques which enable an enhanced utilization of textual data, hence, supporting research in epigenomics and drug discovery

    Semantic text mining support for lignocellulose research

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    Biofuels produced from biomass are considered to be promising sustainable alternatives to fossil fuels. The conversion of lignocellulose into fermentable sugars for biofuels production requires the use of enzyme cocktails that can efficiently and economically hydrolyze lignocellulosic biomass. As many fungi naturally break down lignocellulose, the identification and characterization of the enzymes involved is a key challenge in the research and development of biomass-derived products and fuels. One approach to meeting this challenge is to mine the rapidly-expanding repertoire of microbial genomes for enzymes with the appropriate catalytic properties. Semantic technologies, including natural language processing, ontologies, semantic Web services and Web-based collaboration tools, promise to support users in handling complex data, thereby facilitating knowledge-intensive tasks. An ongoing challenge is to select the appropriate technologies and combine them in a coherent system that brings measurable improvements to the users. We present our ongoing development of a semantic infrastructure in support of genomics-based lignocellulose research. Part of this effort is the automated curation of knowledge from information on fungal enzymes that is available in the literature and genome resources. Working closely with fungal biology researchers who manually curate the existing literature, we developed ontological natural language processing pipelines integrated in a Web-based interface to assist them in two main tasks: mining the literature for relevant knowledge, and at the same time providing rich and semantically linked information

    D6.1: Technologies and Tools for Lexical Acquisition

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    This report describes the technologies and tools to be used for Lexical Acquisition in PANACEA. It includes descriptions of existing technologies and tools which can be built on and improved within PANACEA, as well as of new technologies and tools to be developed and integrated in PANACEA platform. The report also specifies the Lexical Resources to be produced. Four main areas of lexical acquisition are included: Subcategorization frames (SCFs), Selectional Preferences (SPs), Lexical-semantic Classes (LCs), for both nouns and verbs, and Multi-Word Expressions (MWEs)
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