Towards ease of building legos in assessing ehealth language technologies

A RESTful laboratory for data and software

Hanna Suominen, Karl Kreiner, Mike Wu, Leif Hanlen

Research output: A Conference proceeding or a Chapter in BookConference contribution

Abstract

More and more scientific literature, care guidelines, health records, social media, and other textual eHealth information are electronically available. Language technologies provide a way to analyse these documents for the benefit of both individuals and populations. In order to catalyse the development of eHealth language technologies, we propose a virtual laboratory with a standardised platform for easy building and assessment of the systems from the "lego" bricks of shared data, resources, and software. Our aim is to address specific needs in eHealth: governance and sharing of private data; provenance and sharing of resources and software; systematic benchmarking and quality control of systems and their components; and collaboration of eHealth language technology developers and users across healthcare services, academia, industry, and government. The Epicure virtual laboratory is intended to be used for software and re-source evaluation and development as well as for data analysis if data subjects' privacy is ensured. Epicure is a meta-framework in the sense of abstracting over existing frameworks. Its five roles for clients are data or resource provider, ap-plication assembler, application user, software developer, and system administrator. We have implemented Epicure based on publicly available software. Its control layer is a Glassfish JavaEE server, providing a RESTful (REpresentational State Transfer) application programming interface; web interface for accessing and installing third-party platforms; and easy operation via standard web commands. After proper user authentication and authorisation of incoming requests, it builds applications, analyses data and assesses outcomes by orchestrating storage and execution layers. The storage layer of Epicure uses a CouchDB-based repository for centralised storage of data, resources, and software. It enables controlling document access on the level of documents; tracking all changes; recording these revisions; storing all analysis outcomes; and associating the outcomes with the data, resources and software used in their generation. The execution layer of Epicure provides a runtime environment for executing data analysis tasks and installing third party platforms. It invokes tools as simple commands. A tool must be specify its input format, output formats, parameters, and their possible values as a file and be executable on a command line. Tools do not need to be installed within Epicure itself but instead be accessed via a network interface and wrapper, which provides access from Epicure to this re-mote service.

Original languageEnglish
Title of host publication2012 Cross Language Evaluation Forum Conference, CLEF 2012
Subtitle of host publicationCEUR Workshop Proceedings
EditorsJ. Karlgren, C. Womser-Hacker, N. Ferro, P. Forner
Place of PublicationRome, Italy
PublisherCEUR Workshop Proceedings
Pages1-5
Number of pages5
Volume1178
Publication statusPublished - 17 Sep 2012
Externally publishedYes

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Interfaces (computer)
Data privacy
Benchmarking
Brick
Health care
Application programming interfaces (API)
Authentication
Quality control
Servers
Industry

Cite this

Suominen, H., Kreiner, K., Wu, M., & Hanlen, L. (2012). Towards ease of building legos in assessing ehealth language technologies: A RESTful laboratory for data and software. In J. Karlgren, C. Womser-Hacker, N. Ferro, & P. Forner (Eds.), 2012 Cross Language Evaluation Forum Conference, CLEF 2012: CEUR Workshop Proceedings (Vol. 1178, pp. 1-5). Rome, Italy: CEUR Workshop Proceedings. CEUR Workshop Proceedings
Suominen, Hanna ; Kreiner, Karl ; Wu, Mike ; Hanlen, Leif. / Towards ease of building legos in assessing ehealth language technologies : A RESTful laboratory for data and software. 2012 Cross Language Evaluation Forum Conference, CLEF 2012: CEUR Workshop Proceedings. editor / J. Karlgren ; C. Womser-Hacker ; N. Ferro ; P. Forner. Vol. 1178 Rome, Italy : CEUR Workshop Proceedings, 2012. pp. 1-5 (CEUR Workshop Proceedings).
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title = "Towards ease of building legos in assessing ehealth language technologies: A RESTful laboratory for data and software",
abstract = "More and more scientific literature, care guidelines, health records, social media, and other textual eHealth information are electronically available. Language technologies provide a way to analyse these documents for the benefit of both individuals and populations. In order to catalyse the development of eHealth language technologies, we propose a virtual laboratory with a standardised platform for easy building and assessment of the systems from the {"}lego{"} bricks of shared data, resources, and software. Our aim is to address specific needs in eHealth: governance and sharing of private data; provenance and sharing of resources and software; systematic benchmarking and quality control of systems and their components; and collaboration of eHealth language technology developers and users across healthcare services, academia, industry, and government. The Epicure virtual laboratory is intended to be used for software and re-source evaluation and development as well as for data analysis if data subjects' privacy is ensured. Epicure is a meta-framework in the sense of abstracting over existing frameworks. Its five roles for clients are data or resource provider, ap-plication assembler, application user, software developer, and system administrator. We have implemented Epicure based on publicly available software. Its control layer is a Glassfish JavaEE server, providing a RESTful (REpresentational State Transfer) application programming interface; web interface for accessing and installing third-party platforms; and easy operation via standard web commands. After proper user authentication and authorisation of incoming requests, it builds applications, analyses data and assesses outcomes by orchestrating storage and execution layers. The storage layer of Epicure uses a CouchDB-based repository for centralised storage of data, resources, and software. It enables controlling document access on the level of documents; tracking all changes; recording these revisions; storing all analysis outcomes; and associating the outcomes with the data, resources and software used in their generation. The execution layer of Epicure provides a runtime environment for executing data analysis tasks and installing third party platforms. It invokes tools as simple commands. A tool must be specify its input format, output formats, parameters, and their possible values as a file and be executable on a command line. Tools do not need to be installed within Epicure itself but instead be accessed via a network interface and wrapper, which provides access from Epicure to this re-mote service.",
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Suominen, H, Kreiner, K, Wu, M & Hanlen, L 2012, Towards ease of building legos in assessing ehealth language technologies: A RESTful laboratory for data and software. in J Karlgren, C Womser-Hacker, N Ferro & P Forner (eds), 2012 Cross Language Evaluation Forum Conference, CLEF 2012: CEUR Workshop Proceedings. vol. 1178, CEUR Workshop Proceedings, Rome, Italy, CEUR Workshop Proceedings, pp. 1-5.

Towards ease of building legos in assessing ehealth language technologies : A RESTful laboratory for data and software. / Suominen, Hanna; Kreiner, Karl; Wu, Mike; Hanlen, Leif.

2012 Cross Language Evaluation Forum Conference, CLEF 2012: CEUR Workshop Proceedings. ed. / J. Karlgren; C. Womser-Hacker; N. Ferro; P. Forner. Vol. 1178 Rome, Italy : CEUR Workshop Proceedings, 2012. p. 1-5 (CEUR Workshop Proceedings).

Research output: A Conference proceeding or a Chapter in BookConference contribution

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Suominen H, Kreiner K, Wu M, Hanlen L. Towards ease of building legos in assessing ehealth language technologies: A RESTful laboratory for data and software. In Karlgren J, Womser-Hacker C, Ferro N, Forner P, editors, 2012 Cross Language Evaluation Forum Conference, CLEF 2012: CEUR Workshop Proceedings. Vol. 1178. Rome, Italy: CEUR Workshop Proceedings. 2012. p. 1-5. (CEUR Workshop Proceedings).