Journal Article

Enriched biodiversity data as a resource and service

Hamann, Thomas, Biserkov, Jordan, Kelbert, Patricia, Holleman, Ayco, Gosline, George, Sautter, Guido, Hovenkamp, Peter, Williams, Alan, Vos, Rutger, Balech, Bachir, Groom, Quentin, Miller, Jeremy, Hoehndorf, Robert, Page, Rod, Beard, Niall, Weiland, Claus, van Dooren, Tom, Kirkup, Don, Mounce, Ross, Brenninkmeijer, Christian, Blissett, Matthew, Sierra, Soraya, Hettling, Hannes, Nicolson, Nicola, Richards, Kevin, Mietchen, Daniel, DeMeulemeester, Thibaut, Penev, Lyubomir, Pawlik, Aleksandra, Pereira, Serrano, King, David, Tähtinen, Marko, Shorthouse, David, Eades, David, Lammers, Youri

2014

Overview

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.

• Publisher: Pensoft Publishers
• Subject: Belgium / Biodiversity / Biodiversity informatics / Bioinformatics / Bulgaria / Canada / Collaboration / Computer programs / computer software / Data Analysis & Modelling / Data collection / Data enrichment / Data processing / Finland / Geographic information systems / Germany / Hackathon / humans / Identification keys / Informatics / Information processing / Integration / Intelligent openness / Interfaces / Internet / Interoperability / Italy / Linked data / natural history / Netherlands / New Zealand / Open source / prototypes / provenance / Semantic Web / Software / spatial data / stakeholders / Taxonomy / Web services