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Enriched biodiversity data as a resource and service

Abstract. Background: Recent years have seen a surge in projects that produce large volumes of structured, machine-readable biodiversity data. To make these data amenable to processing by generic, open source “data enrichment” workflows, they are increasingly being represented in a variety of standa...

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Autores principales: Vos, Rutger Aldo, Biserkov, Jordan Valkov, Balech, Bachir, Beard, Niall, Blissett, Matthew, Brenninkmeijer, Christian, van Dooren, Tom, Eades, David, Gosline, George, Groom, Quentin John, Hamann, Thomas D., Hettling, Hannes, Hoehndorf, Robert, Holleman, Ayco, Hovenkamp, Peter, Kelbert, Patricia, King, David, Kirkup, Don, Lammers, Youri, DeMeulemeester, Thibaut, Mietchen, Daniel, Miller, Jeremy A., Mounce, Ross, Nicolson, Nicola, Page, Rod, Pawlik, Aleksandra, Pereira, Serrano, Penev, Lyubomir, Richards, Kevin, Sautter, Guido, Shorthouse, David Peter, Tähtinen, Marko, Weiland, Claus, Williams, Alan R., Sierra, Soraya
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Pensoft Publishers 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4092319/
https://www.ncbi.nlm.nih.gov/pubmed/25057255
http://dx.doi.org/10.3897/BDJ.2.e1125
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author Vos, Rutger Aldo
Biserkov, Jordan Valkov
Balech, Bachir
Beard, Niall
Blissett, Matthew
Brenninkmeijer, Christian
van Dooren, Tom
Eades, David
Gosline, George
Groom, Quentin John
Hamann, Thomas D.
Hettling, Hannes
Hoehndorf, Robert
Holleman, Ayco
Hovenkamp, Peter
Kelbert, Patricia
King, David
Kirkup, Don
Lammers, Youri
DeMeulemeester, Thibaut
Mietchen, Daniel
Miller, Jeremy A.
Mounce, Ross
Nicolson, Nicola
Page, Rod
Pawlik, Aleksandra
Pereira, Serrano
Penev, Lyubomir
Richards, Kevin
Sautter, Guido
Shorthouse, David Peter
Tähtinen, Marko
Weiland, Claus
Williams, Alan R.
Sierra, Soraya
author_facet Vos, Rutger Aldo
Biserkov, Jordan Valkov
Balech, Bachir
Beard, Niall
Blissett, Matthew
Brenninkmeijer, Christian
van Dooren, Tom
Eades, David
Gosline, George
Groom, Quentin John
Hamann, Thomas D.
Hettling, Hannes
Hoehndorf, Robert
Holleman, Ayco
Hovenkamp, Peter
Kelbert, Patricia
King, David
Kirkup, Don
Lammers, Youri
DeMeulemeester, Thibaut
Mietchen, Daniel
Miller, Jeremy A.
Mounce, Ross
Nicolson, Nicola
Page, Rod
Pawlik, Aleksandra
Pereira, Serrano
Penev, Lyubomir
Richards, Kevin
Sautter, Guido
Shorthouse, David Peter
Tähtinen, Marko
Weiland, Claus
Williams, Alan R.
Sierra, Soraya
author_sort Vos, Rutger Aldo
collection PubMed
description Abstract. Background: Recent years have seen a surge in projects that produce large volumes of structured, machine-readable biodiversity data. To make these data amenable to processing by generic, open source “data enrichment” workflows, they are increasingly being represented in a variety of standards-compliant interchange formats. Here, we report on an initiative in which software developers and taxonomists came together to address the challenges and highlight the opportunities in the enrichment of such biodiversity data by engaging in intensive, collaborative software development: The Biodiversity Data Enrichment Hackathon. Results: The hackathon brought together 37 participants (including developers and taxonomists, i.e. scientific professionals that gather, identify, name and classify species) from 10 countries: Belgium, Bulgaria, Canada, Finland, Germany, Italy, the Netherlands, New Zealand, the UK, and the US. The participants brought expertise in processing structured data, text mining, development of ontologies, digital identification keys, geographic information systems, niche modeling, natural language processing, provenance annotation, semantic integration, taxonomic name resolution, web service interfaces, workflow tools and visualisation. Most use cases and exemplar data were provided by taxonomists. One goal of the meeting was to facilitate re-use and enhancement of biodiversity knowledge by a broad range of stakeholders, such as taxonomists, systematists, ecologists, niche modelers, informaticians and ontologists. The suggested use cases resulted in nine breakout groups addressing three main themes: i) mobilising heritage biodiversity knowledge; ii) formalising and linking concepts; and iii) addressing interoperability between service platforms. Another goal was to further foster a community of experts in biodiversity informatics and to build human links between research projects and institutions, in response to recent calls to further such integration in this research domain. Conclusions: Beyond deriving prototype solutions for each use case, areas of inadequacy were discussed and are being pursued further. It was striking how many possible applications for biodiversity data there were and how quickly solutions could be put together when the normal constraints to collaboration were broken down for a week. Conversely, mobilising biodiversity knowledge from their silos in heritage literature and natural history collections will continue to require formalisation of the concepts (and the links between them) that define the research domain, as well as increased interoperability between the software platforms that operate on these concepts.
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spelling pubmed-40923192014-07-23 Enriched biodiversity data as a resource and service Vos, Rutger Aldo Biserkov, Jordan Valkov Balech, Bachir Beard, Niall Blissett, Matthew Brenninkmeijer, Christian van Dooren, Tom Eades, David Gosline, George Groom, Quentin John Hamann, Thomas D. Hettling, Hannes Hoehndorf, Robert Holleman, Ayco Hovenkamp, Peter Kelbert, Patricia King, David Kirkup, Don Lammers, Youri DeMeulemeester, Thibaut Mietchen, Daniel Miller, Jeremy A. Mounce, Ross Nicolson, Nicola Page, Rod Pawlik, Aleksandra Pereira, Serrano Penev, Lyubomir Richards, Kevin Sautter, Guido Shorthouse, David Peter Tähtinen, Marko Weiland, Claus Williams, Alan R. Sierra, Soraya Biodivers Data J General Research Article Abstract. Background: Recent years have seen a surge in projects that produce large volumes of structured, machine-readable biodiversity data. To make these data amenable to processing by generic, open source “data enrichment” workflows, they are increasingly being represented in a variety of standards-compliant interchange formats. Here, we report on an initiative in which software developers and taxonomists came together to address the challenges and highlight the opportunities in the enrichment of such biodiversity data by engaging in intensive, collaborative software development: The Biodiversity Data Enrichment Hackathon. Results: The hackathon brought together 37 participants (including developers and taxonomists, i.e. scientific professionals that gather, identify, name and classify species) from 10 countries: Belgium, Bulgaria, Canada, Finland, Germany, Italy, the Netherlands, New Zealand, the UK, and the US. The participants brought expertise in processing structured data, text mining, development of ontologies, digital identification keys, geographic information systems, niche modeling, natural language processing, provenance annotation, semantic integration, taxonomic name resolution, web service interfaces, workflow tools and visualisation. Most use cases and exemplar data were provided by taxonomists. One goal of the meeting was to facilitate re-use and enhancement of biodiversity knowledge by a broad range of stakeholders, such as taxonomists, systematists, ecologists, niche modelers, informaticians and ontologists. The suggested use cases resulted in nine breakout groups addressing three main themes: i) mobilising heritage biodiversity knowledge; ii) formalising and linking concepts; and iii) addressing interoperability between service platforms. Another goal was to further foster a community of experts in biodiversity informatics and to build human links between research projects and institutions, in response to recent calls to further such integration in this research domain. Conclusions: Beyond deriving prototype solutions for each use case, areas of inadequacy were discussed and are being pursued further. It was striking how many possible applications for biodiversity data there were and how quickly solutions could be put together when the normal constraints to collaboration were broken down for a week. Conversely, mobilising biodiversity knowledge from their silos in heritage literature and natural history collections will continue to require formalisation of the concepts (and the links between them) that define the research domain, as well as increased interoperability between the software platforms that operate on these concepts. Pensoft Publishers 2014-06-16 /pmc/articles/PMC4092319/ /pubmed/25057255 http://dx.doi.org/10.3897/BDJ.2.e1125 Text en Rutger Aldo Vos, Jordan Valkov Biserkov, Bachir Balech, Niall Beard, Matthew Blissett, Christian Brenninkmeijer, Tom van Dooren, David Eades, George Gosline, Quentin John Groom, Thomas D. Hamann, Hannes Hettling, Robert Hoehndorf, Ayco Holleman, Peter Hovenkamp, Patricia Kelbert, David King, Don Kirkup, Youri Lammers, Thibaut DeMeulemeester, Daniel Mietchen, Jeremy A. Miller, Ross Mounce, Nicola Nicolson, Rod Page, Aleksandra Pawlik, Serrano Pereira, Lyubomir Penev, Kevin Richards, Guido Sautter, David Peter Shorthouse, Marko Tähtinen, Claus Weiland, Alan R. Williams, Soraya Sierra http://creativecommons.org/licenses/by/4.0 This is an open access article distributed under the terms of the Creative Commons Attribution License 4.0 (CC-BY), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle General Research Article
Vos, Rutger Aldo
Biserkov, Jordan Valkov
Balech, Bachir
Beard, Niall
Blissett, Matthew
Brenninkmeijer, Christian
van Dooren, Tom
Eades, David
Gosline, George
Groom, Quentin John
Hamann, Thomas D.
Hettling, Hannes
Hoehndorf, Robert
Holleman, Ayco
Hovenkamp, Peter
Kelbert, Patricia
King, David
Kirkup, Don
Lammers, Youri
DeMeulemeester, Thibaut
Mietchen, Daniel
Miller, Jeremy A.
Mounce, Ross
Nicolson, Nicola
Page, Rod
Pawlik, Aleksandra
Pereira, Serrano
Penev, Lyubomir
Richards, Kevin
Sautter, Guido
Shorthouse, David Peter
Tähtinen, Marko
Weiland, Claus
Williams, Alan R.
Sierra, Soraya
Enriched biodiversity data as a resource and service
title Enriched biodiversity data as a resource and service
title_full Enriched biodiversity data as a resource and service
title_fullStr Enriched biodiversity data as a resource and service
title_full_unstemmed Enriched biodiversity data as a resource and service
title_short Enriched biodiversity data as a resource and service
title_sort enriched biodiversity data as a resource and service
topic General Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4092319/
https://www.ncbi.nlm.nih.gov/pubmed/25057255
http://dx.doi.org/10.3897/BDJ.2.e1125
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