Infrastructure for Semantic Annotation in the Genomics Domain

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

Cross-Platform Text Mining and Natural Language Processing Interoperability - Proceedings of the LREC2016 conference

No abstract available

Cross-Platform Text Mining and Natural Language Processing Interoperability - Proceedings of the LREC2016 conference

No abstract available

An ontology for CoNLL-RDF: formal data structures for TSV formats in language technology

In language technology and language sciences, tab-separated values (TSV) represent a frequently used formalism to represent linguistically annotated natural language, often addressed as "CoNLL formats". A large number of such formats do exist, but although they share a number of common features, they are not interoperable, as different pieces of information are encoded differently in these dialects. CoNLL-RDF refers to a programming library and the associated data model that has been introduced to facilitate processing and transforming such TSV formats in a serialization-independent way. CoNLL-RDF represents CoNLL data, by means of RDF graphs and SPARQL update operations, but so far, without machine-readable semantics, with annotation properties created dynamically on the basis of a user-defined mapping from columns to labels. Current applications of CoNLL-RDF include linking between corpora and dictionaries [Mambrini and Passarotti, 2019] and knowledge graphs [Tamper et al., 2018], syntactic parsing of historical languages [Chiarcos et al., 2018; Chiarcos et al., 2018], the consolidation of syntactic and semantic annotations [Chiarcos and Fäth, 2019], a bridge between RDF corpora and a traditional corpus query language [Ionov et al., 2020], and language contact studies [Chiarcos et al., 2018]. We describe a novel extension of CoNLL-RDF, introducing a formal data model, formalized as an ontology. The ontology is a basis for linking RDF corpora with other Semantic Web resources, but more importantly, its application for transformation between different TSV formats is a major step for providing interoperability between CoNLL formats

Report on the 2015 NSF Workshop on Unified Annotation Tooling

On March 30 & 31, 2015, an international group of twenty-three researchers with expertise in linguistic annotation convened in Sunny Isles Beach, Florida to discuss problems with and potential solutions for the state of linguistic annotation tooling. The participants comprised 14 researchers from the U.S. and 9 from outside the U.S., with 7 countries and 4 continents represented, and hailed from fields and specialties including computational linguistics, artificial intelligence, speech processing, multi-modal data processing, clinical & medical natural language processing, linguistics, documentary linguistics, sign-language linguistics, corpus linguistics, and the digital humanities. The motivating problem of the workshop was the balkanization of annotation tooling, namely, that even though linguistic annotation requires sophisticated tool support to efficiently generate high-quality data, the landscape of tools for the field is fractured, incompatible, inconsistent, and lacks key capabilities. The overall goal of the workshop was to chart the way forward, centering on five key questions: (1) What are the problems with current tool landscape? (2) What are the possible benefits of solving some or all of these problems? (3) What capabilities are most needed? (4) How should we go about implementing these capabilities? And, (5) How should we ensure longevity and sustainability of the solution? I surveyed the participants before their arrival, which provided significant raw material for ideas, and the workshop discussion itself resulted in identification of ten specific classes of problems, five sets of most-needed capabilities. Importantly, we identified annotation project managers in computational linguistics as the key recipients and users of any solution, thereby succinctly addressing questions about the scope and audience of potential solutions. We discussed management and sustainability of potential solutions at length. The participants agreed on sixteen recommendations for future work. This technical report contains a detailed discussion of all these topics, a point-by-point review of the discussion in the workshop as it unfolded, detailed information on the participants and their expertise, and the summarized data from the surveys

Fintan - Flexible, Integrated Transformation and Annotation eNgineering

We introduce the Flexible and Integrated Transformation and Annotation eNgeneering (Fintan) platform for converting heterogeneous linguistic resources to RDF. With its modular architecture, workflow management and visualization features, Fintan facilitates the development of complex transformation pipelines by integrating generic RDF converters and augmenting them with extended graph processing capabilities: Existing converters can be easily deployed to the system by means of an ontological data structure which renders their properties and the dependencies between transformation steps. Development of subsequent graph transformation steps for resource transformation, annotation engineering or entity linking is further facilitated by a novel visual rendering of SPARQL queries. A graphical workflow manager allows to easily manage the converter modules and combine them to new transformation pipelines. Employing the stream-based graph processing approach first implemented with CoNLL-RDF, we address common challenges and scalability issues when transforming resources and showcase the performance of Fintan by means of a purely graph-based transformation of the Universal Morphology data to RDF

When linguistics meets web technologies. Recent advances in modelling linguistic linked data

This article provides an up-to-date and comprehensive survey of models (including vocabularies, taxonomies and ontologies) used for representing linguistic linked data (LLD). It focuses on the latest developments in the area and both builds upon and complements previous works covering similar territory. The article begins with an overview of recent trends which have had an impact on linked data models and vocabularies, such as the growing influence of the FAIR guidelines, the funding of several major projects in which LLD is a key component, and the increasing importance of the relationship of the digital humanities with LLD. Next, we give an overview of some of the most well known vocabularies and models in LLD. After this we look at some of the latest developments in community standards and initiatives such as OntoLex-Lemon as well as recent work which has been in carried out in corpora and annotation and LLD including a discussion of the LLD metadata vocabularies META-SHARE and lime and language identifiers. In the following part of the paper we look at work which has been realised in a number of recent projects and which has a significant impact on LLD vocabularies and models

Using the European Language Grid as a consumer

This chapter describes the European Language Grid cloud platform from the point of view of a consumer who wishes to access language resources or make use of language technology tools and services. Three aspects are discussed: 1. the webbased user interface (UI) for casual and non-technical users, 2. the underlying REST APIs that drive the UI but can also be called directly by third parties to integrate ELG functionality in their own tools, and 3. the Python Software Development Kit (SDK) that we have developed to simplify access to these APIs from Python code. The chapter concludes with a preview of the upcoming payment module that will enable the sale of commercial LT services and resources through ELG, and a discussion of how ELG compares and relates to other similar platforms and initiatives