TY - JOUR
T1 - Enriched biodiversity data as a resource and service
AU - Vos, Rutger Aldo
AU - Biserkov, Jordan Valkov
AU - Balech, Bachir
AU - Beard, Niall
AU - Blissett, Matthew
AU - Brenninkmeijer, Christian
AU - van Dooren, Tom
AU - Eades, David
AU - Gosline, George
AU - Groom, Quentin John
AU - Hamann, Thomas D.
AU - Hettling, Hannes
AU - Hoehndorf, Robert
AU - Holleman, Ayco
AU - Hovenkamp, Peter
AU - Kelbert, Patricia
AU - King, David
AU - Kirkup, Don
AU - Lammers, Youri
AU - DeMeulemeester, Thibaut
AU - Mietchen, Daniel
AU - Miller, Jeremy A.
AU - Mounce, Ross
AU - Nicolson, Nicola
AU - Page, Rod
AU - Pawlik, Aleksandra
AU - Pereira, Serrano
AU - Penev, Lyubomir
AU - Richards, Kevin
AU - Sautter, Guido
AU - Shorthouse, David Peter
AU - Tähtinen, Marko
AU - Weiland, Claus
AU - Williams, Alan R.
AU - Sierra, Soraya
N1 - Publisher Copyright:
© Vos R et al.
PY - 2014
Y1 - 2014
N2 - 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.
AB - 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.
KW - Biodiversity informatics
KW - Data enrichment
KW - Hackathon
KW - Intelligent openness
KW - Linked data
KW - Open source
KW - Semantic Web
KW - Software
KW - Taxonomy
KW - Web services
UR - http://www.scopus.com/inward/record.url?scp=85018193602&partnerID=8YFLogxK
U2 - 10.3897/BDJ.2.e1125
DO - 10.3897/BDJ.2.e1125
M3 - Article
AN - SCOPUS:85018193602
SN - 1314-2836
VL - 2
JO - Biodiversity Data Journal
JF - Biodiversity Data Journal
IS - 1
M1 - e1125
ER -