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.

IMPORTANCE Compared with the treatment of physical conditions, the quality of care of mental health disorders remains poor and the rate of improvement in treatment is slow, a primary reason being the lack of objective and systematic methods for measuring the delivery of psychotherapy. OBJECTIVE To use a deep learning model applied to a large-scale clinical data set of cognitive behavioral therapy (CBT) session transcripts to generate a quantifiable measure of treatment delivered and to determine the association between the quantity of each aspect of therapy delivered and clinical outcomes. DESIGN, SETTING, AND PARTICIPANTS All data were obtained from patients receiving internet-enabled CBT for the treatment of a mental health disorder between June 2012 and March 2018 in England. Cognitive behavioral therapy was delivered in a secure online therapy room via instant synchronous messaging. The initial sample comprised a total of 17 572 patients (90 934 therapy session transcripts). Patients self-referred or were referred by a primary health care worker directly to the service. EXPOSURES All patients received National Institute for Heath and Care Excellence-approved disorder-specific CBT treatment protocols delivered by a qualified CBT therapist. MAIN OUTCOMES AND MEASURES Clinical outcomes were measured in terms of reliable improvement in patient symptoms and treatment engagement. Reliable improvement was calculated based on 2 severity measures: Patient Health Questionnaire (PHQ-9) and Generalized Anxiety Disorder 7-item scale (GAD-7), corresponding to depressive and anxiety symptoms respectively, completed by the patient at initial assessment and before every therapy session. RESULTS Treatment sessions from a total of 14 899 patients (10 882 women) aged between 18 and 94 years (median age, 34.8 years) were included in the final analysis. We trained a deep learning model to automatically categorize therapist utterances into 1 or more of 24 feature categories. The trained model was applied to our data set to obtain quantifiable measures of each feature of treatment delivered. A logistic regression revealed that increased quantities of a number of session features, including change methods (cognitive and behavioral techniques used in CBT), were associated with greater odds of reliable improvement in patient symptoms (odds ratio, 1.11; 95% CI, 1.06-1.17) and patient engagement (odds ratio, 1.20, 95% CI, 1.12-1.27). The quantity of nontherapy-related content was associated with reduced odds of symptom improvement (odds ratio, 0.89; 95% CI, 0.85-0.92) and patient engagement (odds ratio, 0.88, 95% CI, 0.84-0.92). CONCLUSIONS AND RELEVANCE This work demonstrates an association between clinical outcomes in psychotherapy and the content of therapist utterances. These findings support the principle that CBT change methods help produce improvements in patients' presenting symptoms. The application of deep learning to large clinical data sets can provide valuable insights into psychotherapy, informing the development of new tre...

In this paper we present recent work on GATE, a widely-used framework and graphical development environment for creating and deploying Language Engineering components and resources in a robust fashion. The GATE architecture has facilitated the development of a number of successful applications for various language processing tasks (such as Information Extraction, dialogue and summarisation), the building and annotation of corpora and the quantitative evaluations of LE applications. The focus of this paper is on recent developments in response to new challenges in Language Engineering: Semantic Web, integration with Information Retrieval and data mining, and the need for machine learning support.

Abstract. This paper presents a controlled language for ontology editing and a software implementation, based partly on standard NLP tools, for processing that language and manipulating an ontology. The input sentences are analysed deterministically and compositionally with respect to a given ontology, which the software consults in order to interpret the input's semantics; this allows the user to learn fewer syntactic structures since some of them can be used to refer to either classes or instances, for example. A repeated-measures, task-based evaluation has been carried out in comparison with a well-known ontology editor; our software received favourable results for basic tasks. The paper also discusses work in progress and future plans for developing this language and tool.

This paper presents GATE Teamware-an open-source, web-based, collaborative text annotation framework. It enables users to carry out complex corpus annotation projects, involving distributed annotator teams. Different user roles are provided (annotator, manager, administrator) with customisable user interface functionalities, in order to support the complex workflows and user interactions that occur in corpus annotation projects. Documents may be pre-processed automatically, so that human annotators can begin with text that has already been pre-annotated and thus making them more efficient. The user interface is simple to learn, aimed at non-experts, and runs in an ordinary web browser, without need of additional software installation. GATE Teamware has been evaluated through the creation of several gold standard corpora and internal projects, as well as through external evaluation in commercial and EU text annotation projects. It is