Open Mining INfrastructure for TExt and Data

Deliverables

Quality Assurance & Risk Management Plan

This deliverable comprises the Quality plan for the OpenMinTeD project. It documents the general quality policies, procedures and practices to be followed by partners throughout the duration of the project.

Interoperability Landscaping Report

A white paper to chart existing standards and specifications in the technological landscape of TDM

Platform UI Specification (26)

Description of OpenMinTeD end user functionalities and interactions. (M26)

Platform UI Specification (20)

Description of OpenMinTeD end user functionalities and interactions. (M20)

OpenMinTeD functional specifications

Functional specifications of the OpenMinTeD platform. These will be based on requirements analysis of D4.2

Platform services distributi on specification (M26)

Report that will specify how registered TDM services run on the cloud or other back end environment. (M26)

Platform release plan

A report describing the software engineering processes and artefacts to be used, and the timing of intermediate releases.

Platform Architectural Specification (26)

Architectural specification of the OpenMinTeD platform, including communication of various components. (M26)

Community Evaluation Scenarios Definition Report

Definition of concrete and detailed scenarios to form the conceptual design of community driven applications that will assist in the evaluation process

Platform UI Specification

Description of OpenMinTeD end user functionalities and interactions.

Open Calls Programme Implementation Report

Report on the mechanisms, logistics, processes, decisions and resultsof the tender calls

Platform Architectural Specification

Architectural specification of the OpenMinTeD platform, including communication of various components.

Community Driven Evaluation Methodology (indicators)

Short document that, based on community input, describes key performance indicators (and target values when available)

First Support and Training Activities Report

Report that describes the supporting and training activities of the first period.

Platform Interoperability Guidelines

Technical guidelines for infrastructure interoperability that include representations, protocols and processes. There will be sets of guidelines, each targeted to a stakeholder group.

Community Driven Evaluation Report

Report that describes the evaluation (progress and adequacy/usability) of all types of users that will be involved in the vertical use case scenarios

Final Support and Training Activities Report

Report that describes all support and training activities of the project.

Platform Interoperability Guidelines (M28)

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Open Calls Specifications

Document that describes directions/interests for calls and outlines the tender rules for participation.

Interoperability Standards and Specifications Report (20)

Interoperability specification draft for the text mining infrastructure based on the outcome of four working groups addressing language resources, resource metadata, annotations, and licensing (Month 20)

Interoperability Standards and Specifications Report

Interoperability specification draft for the text mining infrastructure based on the outcome of four working groups addressing language resources, resource metadata, annotations, and licensing.

Interoperability Standards and Specifications Report (26)

Community Requirement Analysis Report

Report that describes the distinct user community requirements, identifying the gaps and commonalities.

Requirements methodology

Methodology and plan for the requirements elicitation

Collaboration and Liaison Plan

Identification ofpossible collaborationsand liaisons, their relevance to OpenMinTeD to determine maximum exposure of OpenMinTeD and its results.

Community Driven Applications Design Report (26)

Report on the implementation of the community driven applications defined in D4.3 (M26)

Platform services distribution specification

Report that will specify how registered TDM services run on the cloud or other back end environment.

Lessons Learnt - Whitepaper from OpenMinTeD experiences

A white/position paper describing the OpenMinTeD experience, with recommendations for the way forward.

Community Driven Applications Design Report

Report on the implementation of the community driven applications defined in D4.3

Platform Architectural Specification (M20)

Architectural specification of the OpenMinTeD platform, including communication of various components. (M20)

Dissemination plan and roadmap (living document)

Presentation of the overall communication strategy of the project to determine maximum exposure of OpenMinTeD and its results

Support kit for TDM topics (30)

A set of guides, faqs, links related to various TDM topics. Related to legal, policy, technology. (M30)

Infrastructure data and service providers registration (36)

This will be an online report of all content and service providers that have registered in OpenMinTeD. (M36)

Testing methodology

Description of the methodology for testing the platform. Includes benchmarks on performance and quality.

Platform Software Documentation

On line software documentation of the platform components (relevant to the platform architecture).

On-Line Support Knowledge Base

A web based knowledge base of topics (legal, policy, technical) related to TDM.

Support kit for TDM topics (M18)

A set of guides, faqs, links related to various TDM topics. Related to legal, policy, technology. (M18)

Infrastructure Operation Report (30)

The deliverable will consist in a high-level report on the status of OpenMinTeDhardware, operation, workflows, and services. (M30)

Infrastructure Operation Report (M24)

The deliverable will consist in a high-level report on the status of OpenMinTeDhardware, operation, workflows, and services. (M24)

Application Software Documentation – updated periodically

Documentation for the community drive applications

Support kit for TDM topics (24)

A set of guides, faqs, links related to various TDM topics. Related to legal, policy, technology. (M24)

Infrastructure Operation Report (36)

The deliverable will consist in a high-level report on the status of OpenMinTeDhardware, operation, workflows, and services. (M36)

Application Software Release Report

Report on release version of community driven applications

Infrastructure data and service providers registration (30)

This will be an online report of all content and service providers that have registered in OpenMinTeD. (M30)

Software Release Report – continuously updated

A report describing intermediate software releases, and the current state of integration, testing and deployment.

Infrastructure Operation Report

The deliverable will consist in a high-level report on the status of OpenMinTeDhardware, operation, workflows, and services.

Infrastructure data and service providers registration

This will be an online report of all content and service providers that have registered in OpenMinTeD.

Infrastructure data and service providers registration (24)

This will be an online report of all content and service providers that have registered in OpenMinTeD. (M24)

Support kit for TDM topics (M10)

A set of guides, faqs, links related to various TDM topics. Related to legal, policy, technology. (M10)

Publications

EELECTION at SemEval-2017 Task 10: Ensemble of nEural Learners for kEyphrase ClassificaTION

Author(s): Steffen Eger, Erik-Lân Do Dinh, Ilia Kuznetsov, Masoud Kiaeeha, Iryna Gurevych
Published in: Proceedings of the 11th International Workshop on Semantic Evaluation (SemEval-2017), August 3rd 2017, 2017, Page(s) 942--946
Publisher: Association for Computational Linguistics

A Legal Perspective on Training Models for Natural Language Processing

Author(s): Richard Eckart de Castilho, Giulia Dore, Thomas Margoni, Penny Labropoulou, Iryna Gurevych
Published in: Proceedings of the Eleventh International Conference on Language Resources and Evaluation (LREC 2018), May 9th 2018, 2018, Page(s) 1267--1274, ISBN 979-10-95546-00-9
Publisher: European Language Resources Association (ELRA)

Incidental or influential? - Challenges in automatically detecting citation importance using publication full texts

Author(s): Pride, David; Knoth, Petr
Published in: 21st International Conference on Theory and Practise of Digital Libraries (TPDL), 2017
Publisher: Springer
DOI: 10.1007/978-3-319-67008-9_48

Incidental or influential? – A decade of using text-mining for citation function classification.

Author(s): Pride, David; Knoth, Petr
Published in: 16th International Society of Scientometrics and Informetrics Conference, 2017
Publisher: ORO

Overview of the Regulatory Network of Plant Seed Development (SeeDev) Task at the BioNLP Shared Task 2016.

Author(s): Estelle Chaix, Bertrand Dubreucq, Abdelhak Fatihi, Dialekti Valsamou, Robert Bossy, Mouhamadou Ba, Louise Delėger, Pierre Zweigenbaum, Philippe Bessières, Loïc Lepiniec, Claire Nėdellec
Published in: Proceedings of the 4th BioNLP Shared Task Workshop, 2016, Page(s) 1-11
Publisher: Association for Computational Linguistics
DOI: 10.18653/v1/W16-3001

Text mining and ontologies: new approaches to knowledge discovery of microbial diversity

Author(s): Nédellec C., Bossy R., Chaix E., Deléger L.
Published in: Proceedings of the 4th International Microbial Diversity Conference, 2017, Page(s) 221--227
Publisher: University of Bari, Italy

Text mining needs of the food microbiology research community

Author(s): Estelle Chaix, Sophie Aubin, Louise Deléger, and Claire Nédellec
Published in: 2017 EFITA WCCA Congress, 2017
Publisher: EFITA

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

Author(s): de Castilho, R. E., Ananiadou, S., Margoni, T., Peters, W. and Piperidis, S. (Eds.) (2016) Cross-Platform Text Mining and Natural Language Processing Interoperability
Published in: Proceedings of the LREC2016 conference, 2016, 2016, Page(s) 1 - 72
Publisher: European Language Resources Association

The Text and Data Mining exception in the Proposal for a Directive on Copyright in the Digital Single Market: Why it is not what EU copyright law needs

Author(s): Thomas Margoni Martin Kretschmer
Published in: EPIP 2018, Yearly, 2018, Page(s) forthcoming
Publisher: EPIP 2018

Mining Social Science Publications for Survey Variables

Author(s): Zielinski, Andrea; Mutschke, Peter
Published in: Proceedings of the Second Workshop on NLP and Computational Social ScienceVancouver, Canada, August 3, 2017, 2017, Page(s) 47-52, ISBN 978-1-945626-65-4
Publisher: Association for Computational Linguistics
DOI: 10.5281/zenodo.1299970

Towards a Gold Standard Corpus for Variable Detection and Linking in Social Science Publications

Author(s): Zielinski, Andrea; Mutschke, Peter
Published in: Proceedings of 11th International Conference on Language Resources and Evaluation (LREC), Miyazaki (Japan), 2018, 2018, ISBN 979-10-95546-00-9
Publisher: European Language Resources Association (ELRA)
DOI: 10.5281/zenodo.1299977

OpenMinTeD: A Platform Facilitating Text Mining of Scholarly Content

Author(s): Penny Labropoulou, Dimitrios Galanis, Antonis Lempesis, Mark A. Greenwood, Petr Knoth, Richard Eckart de Castilho, Stavros Sachtouris, Byron Georgantopoulos, Lucas Anastasiou, Stefania Martziou, Katerina Gkirtzou, Natalia Manola, Stelios Piperidis
Published in: Proceedings of the Eleventh International Conference on Language Resources and Evaluation (LREC 2018), May 2018, 2018, ISBN 979-10-95546-20-7
Publisher: European Language Resources Association (ELRA)

Language infrastructures in support of text mining

Author(s): Stelios Piperidis, Maria Gavrilidou, Penny Labropoulou
Published in: 5th International workshop On Mining Scientific Publications (WOSP 2016), 22-23 June 2016, 2016
Publisher: WOSP
DOI: 10.5281/zenodo.1475164

Interoperability = f(community, division of labour)

Author(s): Richard Eckart de Castilho
Published in: Proceedings of the Workshop on Cross-Platform Text Mining and Natural Language Processing Interoperability (INTEROP 2016) at LREC 2016, May 23rd 2016, 2016, Page(s) 24--28
Publisher: European Language Resources Association (ELRA)
DOI: 10.5281/zenodo.161848

Automatic Analysis of Flaws in Pre-Trained NLP Models

Author(s): Richard Eckart de Castilho
Published in: Proceedings of the Third International Workshop on Worldwide Language Service Infrastructure and Second Workshop on Open Infrastructures and Analysis Frameworks for Human Language Technologies, 12 Dec 2016, 2016, Page(s) 19--27
Publisher: WLSI-OIAF4HLT-2016 Organizing Committee

A New Corpus to Support Text Mining for the Curation of Metabolites in the ChEBI Database

Author(s): Matthew Shardlow, Nhung T.H. Nguyen, Gareth Owen, Steve Turner, Claire O’Donovan, Andrew Leach, John McNaught, Sophia Ananiadou
Published in: Proceedings of the Eleventh International Conference on Language Resources and Evaluation (2018), May 2018, 2018, ISBN 979-10-95546-00-9
Publisher: European Language Resources Association (ELRA)
DOI: 10.5281/zenodo.1468908

Evaluation of chemical and gene/protein entity recognition systems at BioCreative V.5: the CEMP and GPRO patents tracks

Author(s): Pérez-Pérez, Martin; Rabal, Obdulia; Pérez-Rodríguez, Gael; Vazquez, Miguel; Fdez-Riverola, Florentino; Oyarzabal, Julen; Valencia, Alfonso; Lourenço, Anália; Krallinger, Martin
Published in: Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 7, 2017
Publisher: CEB

Benchmarking biomedical text mining web servers at BioCreative V.5: the technical Interoperability and Performance of annotation Servers - TIPS track

Author(s): Pérez-Pérez, Martin; Pérez-Rodríguez, Gael; Blanco-Míguez, Aitor; Fdez-Riverola, Florentino; Valencia, Alfonso; Krallinger, Martin; Lourenço, Anália
Published in: Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 8, 2017
Publisher: CEB

The BioCreative V.5 evaluation workshop: tasks, organization, sessions and topics

Author(s): Martin Krallinger, Martin Pérez-Pérez, Gael Pérez-Rodríguez, Aitor Blanco-Míguez, Florentino Fdez-Riverola, Salvador Capella-Gutierrez, Anália Lourenço, Alfonso Valencia
Published in: Proceedings of the BioCreative V.5 Challenge Evaluation Workshop, 2017
Publisher: CEB

Aggregating Research Papers from Publishers’ Systems to Support Text and Data Mining: Deliberate Lack of Interoperability or Not?

Author(s): Knoth, Petr; Pontika, Nancy
Published in: Proceedings of the Workshop on Cross-Platform Text Mining and Natural Language Processing Interoperability (INTEROP 2016) at LREC 2016, May 23rd 2016, 2016, Page(s) 1-4
Publisher: European Language Resources Association (ELRA)
DOI: 10.5281/zenodo.194788

Tackling Resource Interoperability: Principles, Strategies and Models

Author(s): Wim Peters
Published in: Proceedings of the Workshop on Cross-Platform Text Mining and Natural Language Processing Interoperability (INTEROP 2016) at LREC 2016, May 23rd 2016, 2016, Page(s) 34-37
Publisher: European Language Resources Association (ELRA)

Legal Interoperability Issues in the Framework of the OpenMinTeD Project: A Methodological Overview

Author(s): Labropoulou, Penny, Piperidis, Stelios, & Margoni, Thomas
Published in: Workshop on Cross-Platform Text Mining and Natural Language Processing Interoperability (INTEROP2016), 23 May 2016, 2016
Publisher: ELRA
DOI: 10.5281/zenodo.182497

Interoperability of corpus processing work-flow engines: the case of AlvisNLP/ML in OpenMinTeD

Author(s): Mouhamadou Ba; Robert Bossy
Published in: Proceedings of the Workshop on Cross-Platform Text Mining and Natural Language Processing Interoperability (INTEROP 2016) at LREC 2016, May 23rd 2016, 2016, Page(s) 15--18
Publisher: European Language Resources Association (ELRA)
DOI: 10.5281/zenodo.200370

Classifying document types to enhance search and recommendations in digital libraries

Author(s): Charalampous, Aristotelis; Knoth, Petr
Published in: 21st International Conference on Theory and Practise of Digital Libraries (TPDL), 2, 2017
Publisher: Springer, Cham
DOI: 10.1007/978-3-319-67008-9_15

Intellectual Property and Text and Data Mining

Author(s): Thomas Margoni
Published in: HANDBOOK ON INTELLECTUAL PROPERTY RESEARCH, 2018, Page(s) Sec. 32
Publisher: OUP

Text mining tools for extracting information about microbial biodiversity in food

Author(s): Estelle Chaix, Louise Deléger, Robert Bossy, Claire Nédellec
Published in: Food Microbiology, 2018, ISSN 0740-0020
Publisher: Academic Press
DOI: 10.1016/j.fm.2018.04.011

A Text Mining Pipeline Using Active and Deep Learning for Curating Information in Computational Neuroscience

Author(s): Matthew Shardlow, Meizhi Ju, Maolin Li, Christian O'Reilly, Elisabetta Iavarone, John McNaught, Sophia Ananiadou
Published in: Neuroinformatics, 2018, ISSN 1539-2791
Publisher: Humana Press, Inc.
DOI: 10.1007/s12021-018-9404-y

Finding Convincing Arguments Using Scalable Bayesian Preference Learning

Author(s): Edwin D. Simpson, Iryna Gurevych
Published in: Transactions of the Association for Computational Linguistics, 6, 2018, Page(s) 357--371, ISSN 2307-387X
Publisher: Association for Computational Linguistics

Identification of research hypotheses and new knowledge from scientific literature

Author(s): Matthew Shardlow, Riza Batista-Navarro, Paul Thompson, Raheel Nawaz, John McNaught, Sophia Ananiadou
Published in: BMC Medical Informatics and Decision Making, 18/1, 2018, ISSN 1472-6947
Publisher: BioMed Central
DOI: 10.1186/s12911-018-0639-1

LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes

Author(s): Andres Cañada, Salvador Capella-Gutierrez, Obdulia Rabal, Julen Oyarzabal, Alfonso Valencia, Martin Krallinger
Published in: Nucleic Acids Research, 45/W1, 2017, Page(s) W484-W489, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkx462

Information Retrieval and Text Mining Technologies for Chemistry

Author(s): Martin Krallinger, Obdulia Rabal, Anália Lourenço, Julen Oyarzabal, Alfonso Valencia
Published in: Chemical Reviews, 117/12, 2017, Page(s) 7673-7761, ISSN 0009-2665
Publisher: American Chemical Society
DOI: 10.1021/acs.chemrev.6b00851

Text mining resources for the life sciences

Author(s): Piotr Przybyła, Matthew Shardlow, Sophie Aubin, Robert Bossy, Richard Eckart de Castilho, Stelios Piperidis, John McNaught, Sophia Ananiadou
Published in: Database, 2016, 2016, ISSN 1758-0463
Publisher: Oxford University Press

Analysis of the effect of sentiment analysis on extracting adverse drug reactions from tweets and forum posts

Author(s): Ioannis Korkontzelos, Azadeh Nikfarjam, Matthew Shardlow, Abeed Sarker, Sophia Ananiadou, Graciela H. Gonzalez
Published in: Journal of Biomedical Informatics, 62, 2016, Page(s) 148-158, ISSN 1532-0464
Publisher: Academic Press
DOI: 10.1016/j.jbi.2016.06.007

Frequently Asked Questions on Creative Commons & Open Access

Author(s): CREATe (UoG) OpenMinTeD
Published in: 2017
Publisher: OpenMinTeD
DOI: 10.5281/zenodo.841086

Fact Sheet on Creative Commons & Open Science

Author(s): CREATe OpenMinTeD
Published in: 2017
Publisher: CREATe
DOI: 10.5281/zenodo.840652

OpenMinTeD Executive Summary

Author(s): Androniki Pavlidou
Published in: 1, 2018
Publisher: None
DOI: 10.5281/zenodo.1404146

Why We Need a Text and Data Mining Exception (But it is Not Enough)

Author(s): Margoni, Thomas; Dore, Giulia
Published in: Proceedings of the Workshop on Cross-Platform Text Mining and Natural Language Processing Interoperability (INTEROP 2016) at LREC 2016, May 23rd 2016, 2016, Page(s) 57--59
Publisher: European Language Resources Association (ELRA)
DOI: 10.5281/zenodo.248048

Datasets

MOESM1 of Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm

Author(s): Pérez-Pérez, Martin; Pérez-Rodríguez, Gael; Blanco-Míguez, Aitor; Fdez-Riverola, Florentino; Valencia, Alfonso; Krallinger, Martin; Lourenço, Anália
Published in: figshare

MOESM3 of Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm

Author(s): Pérez-Pérez, Martin; Pérez-Rodríguez, Gael; Blanco-Míguez, Aitor; Fdez-Riverola, Florentino; Valencia, Alfonso; Krallinger, Martin; Lourenço, Anália
Published in: figshare

Additional file 9 of Identification of research hypotheses and new knowledge from scientific literature