Getting More out of Biomedical Documents with GATE's Full Lifecycle Open Source Text Analytics.

This software article describes the GATE family of open source text analysis tools and processes. GATE is one of the most widely used systems of its type with yearly download rates of tens of thousands and many active users in both academic and industrial contexts. In this paper we report three examples of GATE-based systems operating in the life sciences and in medicine. First, in genome-wide association studies which have contributed to discovery of a head and neck cancer mutation association. Second, medical records analysis which has significantly increased the statistical power of treatment/ outcome models in the UK’s largest psychiatric patient cohort. Third, richer constructs in drug-related searching. We also explore the ways in which the GATE family supports the various stages of the lifecycle present in our examples. We conclude that the deployment of text mining for document abstraction or rich search and navigation is best thought of as a process, and that with the right computational tools and data collection strategies this process can be made defined and repeatable. The GATE research programme is now 20 years old and has grown from its roots as a specialist development tool for text processing to become a rather comprehensive ecosystem, bringing together software developers, language engineers and research staff from diverse fields. GATE now has a strong claim to cover a uniquely wide range of the lifecycle of text analysis systems. It forms a focal point for the integration and reuse of advances that have been made by many people (the majority outside of the authors’ own group) who work in text processing for biomedicine and other areas. GATE is available online ,1. under GNU open source licences and runs on all major operating systems. Support is available from an active user and developer community and also on a commercial basis

Statistical analysis plan for the Head Position in Stroke Trial (HeadPoST): An international cluster cross-over randomized trial

Background There is evidence to indicate that the lying flat head position increases cerebral blood flow and oxygenation in patients with acute ischemic stroke, but how these physiological effects translate into clinical outcomes is uncertain. The Head Position in Stroke Trial aims to determine the comparative effectiveness of lying flat (0°) compared to sitting up (≥30°) head positioning, initiated within 24 h of hospital admission for patients with acute stroke. Design An international, pragmatic, cluster-randomized, crossover, open, blinded outcome assessed clinical trial. Each hospital with an established acute stroke unit (cluster) site was required to recruit up to 140 consecutive cases of acute stroke (one phase of head positioning before immediately crossing over to the other phase of head positioning), including both acute ischemic stroke and intracerebral hemorrhage, in each randomized head position as a 'business as usual' policy. Objective To outline in detail the predetermined statistical analysis plan for the study. Methods All accumulated data will be reviewed and formally assessed. Information regarding baseline characteristics of patients, their process of care and management will be outlined, and for each item, statistically relevant descriptive elements will be described. For the trial outcomes, the most appropriate statistical comparisons are described. Results A statistical analysis plan was developed that is transparent, verifiable, and predetermined before completion of data collection. Conclusions We developed a predetermined statistical analysis plan for Head Position in Stroke Trial to avoid analysis bias arising from prior knowledge of the findings, in order to reliably quantify the benefits and harms of lying flat versus sitting up early after the onset of acute stroke. Trial registration ClinicalTrials.gov identifier NCT02162017; ANZCTR identifier ACTRN12614000483651

Language Engineering Tools for Collaborative Corpus Annotation

this paper we will present the new collaborative corpus annotation facilities, recently developed as part of the GATE language engineering tools and infrastructure. These facilities have been used to build OLLIE -- a client-server application that allows users to use the collaborative corpus annotation facilities in their own Web browse

Merging and ranking answers in the Semantic Web: the wisdom of crowds

In this paper we propose algorithms for combining and ranking answers from distributed heterogeneous data sources in the context of a multi-ontology Question Answering task. Our proposal includes a merging algorithm that aggregates, combines and filters ontology-based search results and three different ranking algorithms that sort the final answers according to different criteria such as popularity, confidence and semantic interpretation of results. An experimental evaluation on a large scale corpus indicates improvements in the quality of the search results with respect to a scenario where the merging and ranking algorithms were not applied. These collective methods for merging and ranking allow to answer questions that are distributed across ontologies, while at the same time, they can filter irrelevant answers, fuse similar answers together, and elicit the most accurate answer(s) to a question

GATE : an architecture for development of robust HLT applications

In this paper we present GATE, a framework and graphical development environment which enables users to develop and deploy language engineering components and resources in a robust fashion. The GATE architecture has enabled us not only to develop a number of successful applications for various language processing tasks (such as Information Extraction), but also to build and annotate corpora and carry out evaluations on the applications generated. The framework can be used to develop applications and resources in multiple languages, based on its thorough Unicode support

Variabilité des quasi-espèces du virus de l'hépatite C après transplantation hépatique pour cirrhose virale C (Mise en place de la technique d'étude par séquençage après clonage.)

STRASBOURG-Medecine (674822101) / SudocPARIS-BIUM (751062103) / SudocSudocFranceF

A unicode-based environment for creation and use of language resources.

GATE is a Unicode-aware architecture, development environment and framework for building systems that process human language. It is often thought that the character sets problem has been solved by the arrival of the Unicode standard. This standard is an important advance, but in practice the ability to process text in a large number of the World's languages is still limited. This paper describes work done in the context of the GATE project that makes use of Unicode and plugs some of the gaps for language processing R&D