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  • Open Access English
    Authors: 
    Partzsch, Henriette;
    Publisher: Universidad Nacional de Educacion a Distancia
    Country: United Kingdom

    ‘Salvage’ evokes complex dynamics of loss, recovery and value, in such contexts\ud as waste management or shipwreck and maritime law. Similar dynamics, often\ud triggered by a collective or individual experience of a void or an absence, motivate\ud and inform much research into the history of women’s writing. The present article\ud explores, from the point of view of literary studies, the effects of understanding\ud research into the history of women’s writing as a salvage operation. This metaphor\ud bestows on the material studied the ambiguous status of remains. While\ud hindering the full integration of women’ s writing in more traditional accounts of\ud the literary past, the understanding of surviving material as remains can become\ud the starting point for constructing new, inclusive approaches to literary history.\ud This reframing of the problem is possible thanks to recent developments in the\ud Humanities, with an increasing interest in models and theories that allow us\ud to better understand complex and dynamic phenomena. In order to illustrate\ud the possibilities of this approach, the article draws on a brief analysis of nineteenth-century Spanish fashion magazines.

  • Publication . Part of book or chapter of book . 2017
    Open Access English
    Authors: 
    Hughes, Lorna;
    Publisher: Sapienza Università Editrice
    Country: United Kingdom

    No abstract available.

  • Open Access English
    Authors: 
    Magdalena Matysek; Stephanie Evers; Marshall K. Samuel; Sofie Sjögersten;
    Publisher: Springer Verlag
    Country: United Kingdom

    AbstractTropical peatlands are currently being rapidly cleared and drained for the establishment of oil palm plantations, which threatens their globally significant carbon sequestration capacity. Large-scale land conversion of tropical peatlands is important in the context of greenhouse gas emission factors and sustainable land management. At present, quantification of carbon dioxide losses from tropical peatlands is limited by our understanding of the relative contribution of heterotrophic and autotrophic respiration to net peat surface CO2 emissions. In this study we separated heterotrophic and autotrophic components of peat CO2 losses from two oil palm plantations (one established in ‘2000’ and the other in 1978, then replanted in ‘2006’) using chamber-based emissions sampling along a transect from the rooting to non-rooting zones on a peatland in Selangor, Peninsular Malaysia over the course of 3 months (June–August, 2014). Collar CO2 measurements were compared with soil temperature and moisture at site and also accompanied by depth profiles assessing peat C and bulk density. The soil respiration decreased exponentially with distance from the palm trunks with the sharpest decline found for the plantation with the younger palms with overall fluxes of 1341 and 988 mg CO2 m−2 h−1, respectively, at the 2000 and 2006 plantations, respectively. The mean heterotrophic flux was 909 ± SE 136 and 716 ± SE 201 mg m−2 h−1 at the 2000 and 2006 plantations, respectively. Autotrophic emissions adjacent to the palm trunks were 845 ± SE 135 and 1558 ± SE 341 mg m−2 h−1 at the 2000 and 2006 plantations, respectively. Heterotrophic CO2 flux was positively related to peat soil moisture, but not temperature. Total peat C stocks were 60 kg m−2 (down to 1 m depth) and did not vary among plantations of different ages but SOC concentrations declined significantly with depth at both plantations but the decline was sharper in the second generation 2006 plantation. The CO2 flux values reported in this study suggest a potential for very high carbon (C) loss from drained tropical peats during the dry season. This is particularly concerning given that more intense dry periods related to climate change are predicted for SE Asia. Taken together, this study highlights the need for careful management of tropical peatlands, and the vulnerability of their carbon storage capability under conditions of drainage.

  • Open Access English
    Authors: 
    Bridgette Wessels; Rachel Finn; Peter Linde; Paolo Mazzetti; Stefano Nativi; Susan Riley; Rod Smallwood; Mark J. Taylor; Victoria Tsoukala; Kush Wadhwa; +1 more
    Countries: Italy, Sweden, Netherlands
    Project: EC | APARSEN (269977), EC | RECODE (321463), EC | OPENAIRE (246686), EC | ETTIS (285593), EC | DRIVER II (212147)

    This paper explores key issues in the development of open access to research data. The use of digital means for developing, storing and manipulating data is creating a focus on ‘data-driven science’. One aspect of this focus is the development of ‘open access’ to research data. Open access to research data refers to the way in which various types of data are openly available to public and private stakeholders, user communities and citizens. Open access to research data, however, involves more than simply providing easier and wider access to data for potential user groups. The development of open access requires attention to the ways data are considered in different areas of research. We identify how open access is being unevenly developed across the research environment and the consequences this has in terms of generating data gaps. Data gaps refer to the way data becomes detached from published conclusions. To address these issues, we examine four main areas in developing open access to research data: stakeholder roles and values; technological requirements for managing and sharing data; legal and ethical regulations and procedures; institutional roles and policy frameworks. We conclude that problems of variability and consistency across the open access ecosystem need to be addressed within and between these areas to ensure that risks surrounding a data gap are managed in open access. 11 authors. Missing: Sally Wyatt

  • Open Access English
    Authors: 
    Terras, Melissa; Baker, James; Hetherington, James; Beavan, David; Welsh, Anne; O'Neill, Helen; Finley, Will; Duke-Williams, Oliver; Farquhar, Adam;
    Publisher: Oxford University Press
    Country: United Kingdom

    Although there has been a drive in the cultural heritage sector to provide large-scale, open data sets for researchers, we have not seen a commensurate rise in humanities researchers undertaking complex analysis of these data sets for their own research purposes. This article reports on a pilot project at University College London, working in collaboration with the British Library, to scope out how best high-performance computing facilities can be used to facilitate the needs of researchers in the humanities. Using institutional data-processing frameworks routinely used to support scientific research, we assisted four humanities researchers in analysing 60,000 digitized books, and we present two resulting case studies here. This research allowed us to identify infrastructural and procedural barriers and make recommendations on resource allocation to best support non-computational researchers in undertaking ‘big data’ research. We recommend that research software engineer capacity can be most efficiently deployed in maintaining and supporting data sets, while librarians can provide an essential service in running initial, routine queries for humanities scholars. At present there are too many technical hurdles for most individuals in the humanities to consider analysing at scale these increasingly available open data sets, and by building on existing frameworks of support from research computing and library services, we can best support humanities scholars in developing methods and approaches to take advantage of these research opportunities.

  • Open Access English
    Authors: 
    Anneke Zuiderwijk; Keith G. Jeffery; Marijn Janssen;
    Publisher: JeDEM
    Country: Netherlands

    Public and private organizations increasingly release their data to gain benefits such as transparency and economic growth. The use of these open data can be supported and stimulated by providing considerable metadata (data about the data), including discovery, contextual and detailed metadata. In this paper we argue that metadata are key enablers for the effective use of Linked Open Data (LOD). We illustrate the potential of metadata by 1) presenting an overview of advantages and disadvantages of metadata derived from literature, 2) presenting metadata requirements for LOD architectures derived from literature, workshops and a questionnaire, 3) describing a LOD metadata architecture that meets the requirements and 4) showing examples of the application of this architecture in the ENGAGE project. The paper shows that using metadata with the appropriate metadata architecture can yield considerable benefits for LOD publication and use, including improving find ability, accessibility, storing, preservation, analysing, comparing, reproducing, finding inconsistencies, correct interpretation, visualizing, linking data, assessing and ranking the quality of data and avoiding unnecessary duplication of data. The Common European Research Information Format (CERIF) can be used to build the metadata architecture and achieve the advantages.

  • Publication . Other literature type . Article . 2016
    Open Access English
    Authors: 
    Birgit Schmidt; Astrid Orth; Gwen Franck; Iryna Kuchma; Petr Knoth; Jose Carvalho;
    Countries: Portugal, Germany
    Project: EC | FOSTER (612425)

    Open science refers to all things open in research and scholarly communication: from publications and research data to code, models and methods as well as quality evaluation based on open peer review. However, getting started with implementing open science might not be as straightforward for all stakeholders. For example, what do research funders expect in terms of open access to publications and/or research data? Where and how to publish research data? How to ensure that research results are reproducible? These are all legitimate questions and, in particular, early career researchers may benefit from additional guidance and training. In this paper we review the activities of the European-funded FOSTER project which organized and supported a wide range of targeted trainings for open science, based on face-to-face events and on a growing suite of e-learning courses. This article reviews the approach and experiences gained from the first two years of the project. The FOSTER project has received funding from the European Union’s Seventh Framework Programme for research, technological development and demonstration under grant agreement no 612425. The authors gratefully acknowledge the contributions of all project partners to the design and implementation of the FOSTER project.

  • Open Access English
    Authors: 
    Barker, Elton; Isaksen, Leif; Rabinowitz, Nick; Bouzarovski, Stefan; Pelling, Chris;
    Publisher: Institute of Classical Studies, University of London

    Involving the collaboration of researchers from Classics, Geography and Archaeological Computing, and supported by funding from the AHRC, HESTIA (the Herodotus Encoded Space-Text-Imaging Archive) aims to enrich contemporary discussions of space by developing an innovative methodology for the study of an ancient narrative, Herodotus’s Histories. Using the latest digital technology in combination with close textual study, we investigate the geographical concepts through which Herodotus describes the conflict between Greeks and Persians. Our findings nuance the customary topographical vision of an east versus west polarity by drawing attention to the topological network culture that criss-crosses the two, and develop the means of bringing that world to a mass audience via the internet. In this paper we discuss three main aspects to the project: the data capture of place-names in Herodotus; their visualization and dissemination using the web-mapping technologies of GIS, Google Earth and Timemap; and the interrogation of the relationships that Herodotus draws between different geographical concepts using the digital resources at our disposal. Our concern will be to set out in some detail the digital basis to our methodology and the technologies that we have been exploiting, as well as the problems that we have encountered, in the hope of contributing not only to a more complex picture of space in Herodotus but also to a basis for future digital projects across the Humanities that spatially visualize large text-based corpora. With this in mind we end with a brief discussion of some of the ways in which this study is being developed, with assistance from research grants from the Google Digital Humanities Awards Program and JISC.

  • Publication . Article . Preprint . 2018
    Open Access English
    Authors: 
    Nadia Boukhelifa; Michael Bryant; Natasa Bulatovic; Ivan Čukić; Jean-Daniel Fekete; Milica Knežević; Jörg Lehmann; David I. Stuart; Carsten Thiel;
    Publisher: HAL CCSD
    Countries: France, United Kingdom
    Project: EC | CENDARI (284432)

    International audience; The CENDARI infrastructure is a research-supporting platform designed to provide tools for transnational historical research, focusing on two topics: medieval culture and World War I. It exposes to the end users modern Web-based tools relying on a sophisticated infrastructure to collect, enrich, annotate, and search through large document corpora. Supporting researchers in their daily work is a novel concern for infrastructures. We describe how we gathered requirements through multiple methods to understand historians' needs and derive an abstract workflow to support them. We then outline the tools that we have built, tying their technical descriptions to the user requirements. The main tools are the note-taking environment and its faceted search capabilities; the data integration platform including the Data API, supporting semantic enrichment through entity recognition; and the environment supporting the software development processes throughout the project to keep both technical partners and researchers in the loop. The outcomes are technical together with new resources developed and gathered, and the research workflow that has been described and documented.

  • Open Access English
    Authors: 
    Raheel Nawaz; Paul Thompson; Sophia Ananiadou;
    Publisher: BMC
    Country: United Kingdom
    Project: UKRI | From data to knowledge / ... (BB/F006039/1)

    Abstract Background Negation occurs frequently in scientific literature, especially in biomedical literature. It has previously been reported that around 13% of sentences found in biomedical research articles contain negation. Historically, the main motivation for identifying negated events has been to ensure their exclusion from lists of extracted interactions. However, recently, there has been a growing interest in negative results, which has resulted in negation detection being identified as a key challenge in biomedical relation extraction. In this article, we focus on the problem of identifying negated bio-events, given gold standard event annotations. Results We have conducted a detailed analysis of three open access bio-event corpora containing negation information (i.e., GENIA Event, BioInfer and BioNLP’09 ST), and have identified the main types of negated bio-events. We have analysed the key aspects of a machine learning solution to the problem of detecting negated events, including selection of negation cues, feature engineering and the choice of learning algorithm. Combining the best solutions for each aspect of the problem, we propose a novel framework for the identification of negated bio-events. We have evaluated our system on each of the three open access corpora mentioned above. The performance of the system significantly surpasses the best results previously reported on the BioNLP’09 ST corpus, and achieves even better results on the GENIA Event and BioInfer corpora, both of which contain more varied and complex events. Conclusions Recently, in the field of biomedical text mining, the development and enhancement of event-based systems has received significant interest. The ability to identify negated events is a key performance element for these systems. We have conducted the first detailed study on the analysis and identification of negated bio-events. Our proposed framework can be integrated with state-of-the-art event extraction systems. The resulting systems will be able to extract bio-events with attached polarities from textual documents, which can serve as the foundation for more elaborate systems that are able to detect mutually contradicting bio-events.

search
Include:
18 Research products, page 1 of 2
  • Open Access English
    Authors: 
    Partzsch, Henriette;
    Publisher: Universidad Nacional de Educacion a Distancia
    Country: United Kingdom

    ‘Salvage’ evokes complex dynamics of loss, recovery and value, in such contexts\ud as waste management or shipwreck and maritime law. Similar dynamics, often\ud triggered by a collective or individual experience of a void or an absence, motivate\ud and inform much research into the history of women’s writing. The present article\ud explores, from the point of view of literary studies, the effects of understanding\ud research into the history of women’s writing as a salvage operation. This metaphor\ud bestows on the material studied the ambiguous status of remains. While\ud hindering the full integration of women’ s writing in more traditional accounts of\ud the literary past, the understanding of surviving material as remains can become\ud the starting point for constructing new, inclusive approaches to literary history.\ud This reframing of the problem is possible thanks to recent developments in the\ud Humanities, with an increasing interest in models and theories that allow us\ud to better understand complex and dynamic phenomena. In order to illustrate\ud the possibilities of this approach, the article draws on a brief analysis of nineteenth-century Spanish fashion magazines.

  • Publication . Part of book or chapter of book . 2017
    Open Access English
    Authors: 
    Hughes, Lorna;
    Publisher: Sapienza Università Editrice
    Country: United Kingdom

    No abstract available.

  • Open Access English
    Authors: 
    Magdalena Matysek; Stephanie Evers; Marshall K. Samuel; Sofie Sjögersten;
    Publisher: Springer Verlag
    Country: United Kingdom

    AbstractTropical peatlands are currently being rapidly cleared and drained for the establishment of oil palm plantations, which threatens their globally significant carbon sequestration capacity. Large-scale land conversion of tropical peatlands is important in the context of greenhouse gas emission factors and sustainable land management. At present, quantification of carbon dioxide losses from tropical peatlands is limited by our understanding of the relative contribution of heterotrophic and autotrophic respiration to net peat surface CO2 emissions. In this study we separated heterotrophic and autotrophic components of peat CO2 losses from two oil palm plantations (one established in ‘2000’ and the other in 1978, then replanted in ‘2006’) using chamber-based emissions sampling along a transect from the rooting to non-rooting zones on a peatland in Selangor, Peninsular Malaysia over the course of 3 months (June–August, 2014). Collar CO2 measurements were compared with soil temperature and moisture at site and also accompanied by depth profiles assessing peat C and bulk density. The soil respiration decreased exponentially with distance from the palm trunks with the sharpest decline found for the plantation with the younger palms with overall fluxes of 1341 and 988 mg CO2 m−2 h−1, respectively, at the 2000 and 2006 plantations, respectively. The mean heterotrophic flux was 909 ± SE 136 and 716 ± SE 201 mg m−2 h−1 at the 2000 and 2006 plantations, respectively. Autotrophic emissions adjacent to the palm trunks were 845 ± SE 135 and 1558 ± SE 341 mg m−2 h−1 at the 2000 and 2006 plantations, respectively. Heterotrophic CO2 flux was positively related to peat soil moisture, but not temperature. Total peat C stocks were 60 kg m−2 (down to 1 m depth) and did not vary among plantations of different ages but SOC concentrations declined significantly with depth at both plantations but the decline was sharper in the second generation 2006 plantation. The CO2 flux values reported in this study suggest a potential for very high carbon (C) loss from drained tropical peats during the dry season. This is particularly concerning given that more intense dry periods related to climate change are predicted for SE Asia. Taken together, this study highlights the need for careful management of tropical peatlands, and the vulnerability of their carbon storage capability under conditions of drainage.

  • Open Access English
    Authors: 
    Bridgette Wessels; Rachel Finn; Peter Linde; Paolo Mazzetti; Stefano Nativi; Susan Riley; Rod Smallwood; Mark J. Taylor; Victoria Tsoukala; Kush Wadhwa; +1 more
    Countries: Italy, Sweden, Netherlands
    Project: EC | APARSEN (269977), EC | RECODE (321463), EC | OPENAIRE (246686), EC | ETTIS (285593), EC | DRIVER II (212147)

    This paper explores key issues in the development of open access to research data. The use of digital means for developing, storing and manipulating data is creating a focus on ‘data-driven science’. One aspect of this focus is the development of ‘open access’ to research data. Open access to research data refers to the way in which various types of data are openly available to public and private stakeholders, user communities and citizens. Open access to research data, however, involves more than simply providing easier and wider access to data for potential user groups. The development of open access requires attention to the ways data are considered in different areas of research. We identify how open access is being unevenly developed across the research environment and the consequences this has in terms of generating data gaps. Data gaps refer to the way data becomes detached from published conclusions. To address these issues, we examine four main areas in developing open access to research data: stakeholder roles and values; technological requirements for managing and sharing data; legal and ethical regulations and procedures; institutional roles and policy frameworks. We conclude that problems of variability and consistency across the open access ecosystem need to be addressed within and between these areas to ensure that risks surrounding a data gap are managed in open access. 11 authors. Missing: Sally Wyatt

  • Open Access English
    Authors: 
    Terras, Melissa; Baker, James; Hetherington, James; Beavan, David; Welsh, Anne; O'Neill, Helen; Finley, Will; Duke-Williams, Oliver; Farquhar, Adam;
    Publisher: Oxford University Press
    Country: United Kingdom

    Although there has been a drive in the cultural heritage sector to provide large-scale, open data sets for researchers, we have not seen a commensurate rise in humanities researchers undertaking complex analysis of these data sets for their own research purposes. This article reports on a pilot project at University College London, working in collaboration with the British Library, to scope out how best high-performance computing facilities can be used to facilitate the needs of researchers in the humanities. Using institutional data-processing frameworks routinely used to support scientific research, we assisted four humanities researchers in analysing 60,000 digitized books, and we present two resulting case studies here. This research allowed us to identify infrastructural and procedural barriers and make recommendations on resource allocation to best support non-computational researchers in undertaking ‘big data’ research. We recommend that research software engineer capacity can be most efficiently deployed in maintaining and supporting data sets, while librarians can provide an essential service in running initial, routine queries for humanities scholars. At present there are too many technical hurdles for most individuals in the humanities to consider analysing at scale these increasingly available open data sets, and by building on existing frameworks of support from research computing and library services, we can best support humanities scholars in developing methods and approaches to take advantage of these research opportunities.

  • Open Access English
    Authors: 
    Anneke Zuiderwijk; Keith G. Jeffery; Marijn Janssen;
    Publisher: JeDEM
    Country: Netherlands

    Public and private organizations increasingly release their data to gain benefits such as transparency and economic growth. The use of these open data can be supported and stimulated by providing considerable metadata (data about the data), including discovery, contextual and detailed metadata. In this paper we argue that metadata are key enablers for the effective use of Linked Open Data (LOD). We illustrate the potential of metadata by 1) presenting an overview of advantages and disadvantages of metadata derived from literature, 2) presenting metadata requirements for LOD architectures derived from literature, workshops and a questionnaire, 3) describing a LOD metadata architecture that meets the requirements and 4) showing examples of the application of this architecture in the ENGAGE project. The paper shows that using metadata with the appropriate metadata architecture can yield considerable benefits for LOD publication and use, including improving find ability, accessibility, storing, preservation, analysing, comparing, reproducing, finding inconsistencies, correct interpretation, visualizing, linking data, assessing and ranking the quality of data and avoiding unnecessary duplication of data. The Common European Research Information Format (CERIF) can be used to build the metadata architecture and achieve the advantages.

  • Publication . Other literature type . Article . 2016
    Open Access English
    Authors: 
    Birgit Schmidt; Astrid Orth; Gwen Franck; Iryna Kuchma; Petr Knoth; Jose Carvalho;
    Countries: Portugal, Germany
    Project: EC | FOSTER (612425)

    Open science refers to all things open in research and scholarly communication: from publications and research data to code, models and methods as well as quality evaluation based on open peer review. However, getting started with implementing open science might not be as straightforward for all stakeholders. For example, what do research funders expect in terms of open access to publications and/or research data? Where and how to publish research data? How to ensure that research results are reproducible? These are all legitimate questions and, in particular, early career researchers may benefit from additional guidance and training. In this paper we review the activities of the European-funded FOSTER project which organized and supported a wide range of targeted trainings for open science, based on face-to-face events and on a growing suite of e-learning courses. This article reviews the approach and experiences gained from the first two years of the project. The FOSTER project has received funding from the European Union’s Seventh Framework Programme for research, technological development and demonstration under grant agreement no 612425. The authors gratefully acknowledge the contributions of all project partners to the design and implementation of the FOSTER project.

  • Open Access English
    Authors: 
    Barker, Elton; Isaksen, Leif; Rabinowitz, Nick; Bouzarovski, Stefan; Pelling, Chris;
    Publisher: Institute of Classical Studies, University of London

    Involving the collaboration of researchers from Classics, Geography and Archaeological Computing, and supported by funding from the AHRC, HESTIA (the Herodotus Encoded Space-Text-Imaging Archive) aims to enrich contemporary discussions of space by developing an innovative methodology for the study of an ancient narrative, Herodotus’s Histories. Using the latest digital technology in combination with close textual study, we investigate the geographical concepts through which Herodotus describes the conflict between Greeks and Persians. Our findings nuance the customary topographical vision of an east versus west polarity by drawing attention to the topological network culture that criss-crosses the two, and develop the means of bringing that world to a mass audience via the internet. In this paper we discuss three main aspects to the project: the data capture of place-names in Herodotus; their visualization and dissemination using the web-mapping technologies of GIS, Google Earth and Timemap; and the interrogation of the relationships that Herodotus draws between different geographical concepts using the digital resources at our disposal. Our concern will be to set out in some detail the digital basis to our methodology and the technologies that we have been exploiting, as well as the problems that we have encountered, in the hope of contributing not only to a more complex picture of space in Herodotus but also to a basis for future digital projects across the Humanities that spatially visualize large text-based corpora. With this in mind we end with a brief discussion of some of the ways in which this study is being developed, with assistance from research grants from the Google Digital Humanities Awards Program and JISC.

  • Publication . Article . Preprint . 2018
    Open Access English
    Authors: 
    Nadia Boukhelifa; Michael Bryant; Natasa Bulatovic; Ivan Čukić; Jean-Daniel Fekete; Milica Knežević; Jörg Lehmann; David I. Stuart; Carsten Thiel;
    Publisher: HAL CCSD
    Countries: France, United Kingdom
    Project: EC | CENDARI (284432)

    International audience; The CENDARI infrastructure is a research-supporting platform designed to provide tools for transnational historical research, focusing on two topics: medieval culture and World War I. It exposes to the end users modern Web-based tools relying on a sophisticated infrastructure to collect, enrich, annotate, and search through large document corpora. Supporting researchers in their daily work is a novel concern for infrastructures. We describe how we gathered requirements through multiple methods to understand historians' needs and derive an abstract workflow to support them. We then outline the tools that we have built, tying their technical descriptions to the user requirements. The main tools are the note-taking environment and its faceted search capabilities; the data integration platform including the Data API, supporting semantic enrichment through entity recognition; and the environment supporting the software development processes throughout the project to keep both technical partners and researchers in the loop. The outcomes are technical together with new resources developed and gathered, and the research workflow that has been described and documented.

  • Open Access English
    Authors: 
    Raheel Nawaz; Paul Thompson; Sophia Ananiadou;
    Publisher: BMC
    Country: United Kingdom
    Project: UKRI | From data to knowledge / ... (BB/F006039/1)

    Abstract Background Negation occurs frequently in scientific literature, especially in biomedical literature. It has previously been reported that around 13% of sentences found in biomedical research articles contain negation. Historically, the main motivation for identifying negated events has been to ensure their exclusion from lists of extracted interactions. However, recently, there has been a growing interest in negative results, which has resulted in negation detection being identified as a key challenge in biomedical relation extraction. In this article, we focus on the problem of identifying negated bio-events, given gold standard event annotations. Results We have conducted a detailed analysis of three open access bio-event corpora containing negation information (i.e., GENIA Event, BioInfer and BioNLP’09 ST), and have identified the main types of negated bio-events. We have analysed the key aspects of a machine learning solution to the problem of detecting negated events, including selection of negation cues, feature engineering and the choice of learning algorithm. Combining the best solutions for each aspect of the problem, we propose a novel framework for the identification of negated bio-events. We have evaluated our system on each of the three open access corpora mentioned above. The performance of the system significantly surpasses the best results previously reported on the BioNLP’09 ST corpus, and achieves even better results on the GENIA Event and BioInfer corpora, both of which contain more varied and complex events. Conclusions Recently, in the field of biomedical text mining, the development and enhancement of event-based systems has received significant interest. The ability to identify negated events is a key performance element for these systems. We have conducted the first detailed study on the analysis and identification of negated bio-events. Our proposed framework can be integrated with state-of-the-art event extraction systems. The resulting systems will be able to extract bio-events with attached polarities from textual documents, which can serve as the foundation for more elaborate systems that are able to detect mutually contradicting bio-events.

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