Representation and Encoding of Heterogeneous Data in a Web Based Research Environment for Manuscript and Textual Studies

This paper describes the general architecture of a digital research environment for manuscript and textual studies (particularly those pertaining to ancient Greek and Byzantine texts), and it discusses some questions of data representation and encoding in the framework of such an online research platform. The platform is being developed by the project Teuchos. Zentrum für Handschriften- und Textforschung, established in 2007 by the Institut für Griechische und Lateinische Philologie (Universität Hamburg) in cooperation with the Aristoteles-Archiv (Freie Universität Berlin). Teuchos is a long-term infrastructural project of the Universität Hamburg. It is currently in its three-year initial phase which is being co-funded by the German Research Foundation (DFG) through the "Thematic Information Networks" scheme within the "Scientific Library Services and Information Systems" programme. We introduce the main object types to be handled by our system and describe the overall functionality of the online platform. The paper focuses on the representations of two main object types: manuscripts as textual witnesses and watermarks, with an emphasis on the former. Since the adequate encoding of different layers of structure of a transmitted text is particularly relevant to optimising users' choices of navigating both digital images of the containing manuscripts and trancriptions of the text contained, this topic is discussed in some detail. We introduce the formal data model and the corresponding encoding for the object types discussed. The project encodes textual data in XML, aiming for TEI conformance where possible. Since no accepted XML model exists for the encoding of metadata within a watermark collection, we briefly explain how we chose to model the objects to accomodate the collections the project is making accessible

Enroller: an experiment in aggregating resources

This chapter describes a collaborative project between e-scientists and humanists working to create an online repository of linguistic data sets and tools. Corpora, dictionaries, and a thesaurus are brought together to enable a new method of research. It combines our most advanced knowledge in both computing and linguistic research techniques

The TXM Portal Software giving access to Old French Manuscripts Online

Texte intégral en ligne : http://www.lrec-conf.org/proceedings/lrec2012/workshops/13.ProceedingsCultHeritage.pdfInternational audiencehttp://www.lrec-conf.org/proceedings/lrec2012/workshops/13.ProceedingsCultHeritage.pdf This paper presents the new TXM software platform giving online access to Old French Text Manuscripts images and tagged transcriptions for concordancing and text mining. This platform is able to import medieval sources encoded in XML according to the TEI Guidelines for linking manuscript images to transcriptions, encode several diplomatic levels of transcription including abbreviations and word level corrections. It includes a sophisticated tokenizer able to deal with TEI tags at different levels of linguistic hierarchy. Words are tagged on the fly during the import process using IMS TreeTagger tool with a specific language model. Synoptic editions displaying side by side manuscript images and text transcriptions are automatically produced during the import process. Texts are organized in a corpus with their own metadata (title, author, date, genre, etc.) and several word properties indexes are produced for the CQP search engine to allow efficient word patterns search to build different type of frequency lists or concordances. For syntactically annotated texts, special indexes are produced for the Tiger Search engine to allow efficient syntactic concordances building. The platform has also been tested on classical Latin, ancient Greek, Old Slavonic and Old Hieroglyphic Egyptian corpora (including various types of encoding and annotations)

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

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

Introduction (to Special Issue on Tibetan Natural Language Processing)

This introduction surveys research on Tibetan NLP, both in China and in the West, as well as contextualizing the articles contained in the special issue

Design of a Controlled Language for Critical Infrastructures Protection

We describe a project for the construction of controlled language for critical infrastructures protection (CIP). This project originates from the need to coordinate and categorize the communications on CIP at the European level. These communications can be physically represented by official documents, reports on incidents, informal communications and plain e-mail. We explore the application of traditional library science tools for the construction of controlled languages in order to achieve our goal. Our starting point is an analogous work done during the sixties in the field of nuclear science known as the Euratom Thesaurus.JRC.G.6-Security technology assessmen

Named Entity Recognition for early-modern textual sources: a review of capabilities and challenges with strategies for the future

Purpose: By mapping-out the capabilities, challenges and limitations of named-entity recognition (NER), this article aims to synthesise the state of the art of NER in the context of the early modern research field and to inform discussions about the kind of resources, methods and directions that may be pursued to enrich the application of the technique going forward. // Design/methodology/approach: Through an extensive literature review, this article maps out the current capabilities, challenges and limitations of NER and establishes the state of the art of the technique in the context of the early modern, digitally augmented research field. It also presents a new case study of NER research undertaken by Enlightenment Architectures: Sir Hans Sloane's Catalogues of his Collections (2016–2021), a Leverhulme funded research project and collaboration between the British Museum and University College London, with contributing expertise from the British Library and the Natural History Museum. // Findings: Currently, it is not possible to benchmark the capabilities of NER as applied to documents of the early modern period. The authors also draw attention to the situated nature of authority files, and current conceptualisations of NER, leading them to the conclusion that more robust reporting and critical analysis of NER approaches and findings is required. // Research limitations/implications: This article examines NER as applied to early modern textual sources, which are mostly studied by Humanists. As addressed in this article, detailed reporting of NER processes and outcomes is not necessarily valued by the disciplines of the Humanities, with the result that it can be difficult to locate relevant data and metrics in project outputs. The authors have tried to mitigate this by contacting projects discussed in this paper directly, to further verify the details they report here. // Practical implications: The authors suggest that a forum is needed where tools are evaluated according to community standards. Within the wider NER community, the MUC and ConLL corpora are used for such experimental set-ups and are accompanied by a conference series, and may be seen as a useful model for this. The ultimate nature of such a forum must be discussed with the whole research community of the early modern domain. // Social implications: NER is an algorithmic intervention that transforms data according to certain rules-, patterns- or training data and ultimately affects how the authors interpret the results. The creation, use and promotion of algorithmic technologies like NER is not a neutral process, and neither is their output A more critical understanding of the role and impact of NER on early modern documents and research and focalization of some of the data- and human-centric aspects of NER routines that are currently overlooked are called for in this paper. // Originality/value: This article presents a state of the art snapshot of NER, its applications and potential, in the context of early modern research. It also seeks to inform discussions about the kinds of resources, methods and directions that may be pursued to enrich the application of NER going forward. It draws attention to the situated nature of authority files, and current conceptualisations of NER, and concludes that more robust reporting of NER approaches and findings are urgently required. The Appendix sets out a comprehensive summary of digital tools and resources surveyed in this article