Global biotic interactions: An open infrastructure to share and analyze species-interaction datasets

Poelen, Jorrit; Simons, J.D.; Mungall, Chris

doi:10.1016/j.ecoinf.2014.08.005

Cited by 225 publications

(190 citation statements)

References 29 publications

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“…However, only three TraitBank data partners, Environments-EOL [28], Global Biotic Interaction [36], and Polytraits [14] fall into this category. Most of the resources we aggregate are not "born semantic," i.e., the data come to us with labels, some metadata, and sometimes an associated article explaining the rationale and methods of the study.…”

Section: Semantic Annotationmentioning

confidence: 99%

“…The TraitBank data search interface has so far been accessed over 5,000 times, and more than 1,500 data packages have been downloaded. Also, papers citing TraitBank as a data source are starting to appear in the literature (e.g., [1,4,8,28,36,37,44]). Future development efforts will focus on improving TraitBank's utility for research by improving the search interface, exposing the data in more advanced machinereadable formats, employing standardized data quality descriptors, replacing provisional EOL terms with community-managed terms, and exploring the best use of reasoning within the EOL-TraitBank framework.…”

Section: Impact On Semantic Community Data Providers and Research Comentioning

confidence: 99%

“…To promote progress in the aggregation of comprehensive data sets of particular interest to scientists and the public, EOL has funded projects like GloBi (Global Biotic Interactions) [36] and Environments-EOL [28]. For these communities and other ongoing projects like Polytraits and OBIS, TraitBank provides a live platform for distribution and re-use that exposes their data to broader audiences and promotes significant community curation.…”

Section: Impact On Semantic Community Data Providers and Research Comentioning

confidence: 99%

“…Some new terms are therefore created through Term Genie, 34 a post-composition tool that formally constructs composite attributes by combining classes from PATO and GO or UBERON. For example, secondary xylem volumetric density 35 (i.e., wood density) and cell shape 36 are attributes from TraitBank data sets that have been added to OBA.…”

Section: Semantic Annotationmentioning

confidence: 99%

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TraitBank: Practical semantics for organism attribute data

Parr

Schulz

Hammock

et al. 2016

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Abstract. Encyclopedia of Life (EOL) has developed TraitBank (http://eol.org/traitbank), a new repository for organism attribute (trait) data. TraitBank aggregates, manages and serves attribute data for organisms across the tree of life, including life history characteristics, habitats, distributions, ecological relationships and other data types. We describe how TraitBank ingests and manages these data in a way that leverages EOL's existing infrastructure and semantic annotations to facilitate reasoning across the TraitBank corpus and interoperability with other resources. We also discuss TraitBank's impact on users and collaborators and the challenges and benefits of our lightweight, scalable approach to the integration of biodiversity data.

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Section: Semantic Annotationmentioning

confidence: 99%

Section: Impact On Semantic Community Data Providers and Research Comentioning

confidence: 99%

Section: Impact On Semantic Community Data Providers and Research Comentioning

confidence: 99%

Section: Semantic Annotationmentioning

confidence: 99%

See 2 more Smart Citations

TraitBank: Practical semantics for organism attribute data

Parr

Schulz

Hammock

et al. 2016

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“…(e.g. Kattge et al 2011;Kissling et al 2014;Naeem and Bunker 2009) (Poelen, Simons, and Mungall 2014), but the limited availability of data for modelling species interactions across large spatial scales remains a challenge (e.g. Blois et al 2013;Kissling et al 2012;Morales-Castilla et al 2015;Wisz et al 2013).…”

Section: Scientific Content and Workhops Of Globis-bmentioning

confidence: 99%

Towards global interoperability for supporting biodiversity research on essential biodiversity variables (EBVs)

et al. 2015

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General rightsIt is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons). Disclaimer/Complaints regulationsIf you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: http://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible. Essential biodiversity variables (EBVs) have been proposed by the Group on Earth Observations Biodiversity Observation Network (GEO BON) to identify a minimum set of essential measurements that are required for studying, monitoring and reporting biodiversity and ecosystem change. Despite the initial conceptualisation, however, the practical implementation of EBVs remains challenging. There is much discussion about the concept and implementation of EBVs: which variables are meaningful; which data are needed and available; at which spatial, temporal and topical scales can EBVs be calculated; and how sensitive are EBVs to variations in underlying data? To advance scientific progress in implementing EBVs we propose that both scientists and research infrastructure operators need to cooperate globally to serve and process the essential large datasets for calculating EBVs. We introduce GLOBIS-B (GLOBal Infrastructures for Supporting Biodiversity research), a global cooperation funded by the Horizon 2020 research and innovation framework programme of the European Commission. The main aim of GLOBIS-B is to bring together biodiversity scientists, global research infrastructure operators and legal interoperability experts to identify the research needs and infrastructure services underpinning the concept of EBVs. The project will facilitate the multi-lateral cooperation of biodiversity research infrastructures worldwide and identify the required primary data, analysis tools, methodologies and legal and technical bottlenecks to develop an agenda for research and infrastructure development to compute EBVs. This requires development of standards, protocols and workflows that are 'self-documenting' and openly shared to allow the discovery and analysis of data across large spatial extents and different temporal resolutions. The interoperability of existing biodiversity research infrastructures will be crucial for integrating the necessary biodiversity data to calculate EBVs, and to advance our ability to assess progress towards the Aichi targets for 2020 of the Convention on Biological Diversity (CBD).

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Herbarium data: Global biodiversity and societal botanical needs for novel research

et al. 2018

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Building on centuries of research based on herbarium specimens gathered through time and around the globe, a new era of discovery, synthesis, and prediction using digitized collections data has begun. This paper provides an overview of how aggregated, open access botanical and associated biological, environmental, and ecological data sets, from genes to the ecosystem, can be used to document the impacts of global change on communities, organisms, and society; predict future impacts; and help to drive the remediation of change. Advocacy for botanical collections and their expansion is needed, including ongoing digitization and online publishing. The addition of non‐traditional digitized data fields, user annotation capability, and born‐digital field data collection enables the rapid access of rich, digitally available data sets for research, education, informed decision‐making, and other scholarly and creative activities. Researchers are receiving enormous benefits from data aggregators including the Global Biodiversity Information Facility (GBIF), Integrated Digitized Biocollections (iDigBio), the Atlas of Living Australia (ALA), and the Biodiversity Heritage Library (BHL), but effective collaboration around data infrastructures is needed when working with large and disparate data sets. Tools for data discovery, visualization, analysis, and skills training are increasingly important for inspiring novel research that improves the intrinsic value of physical and digital botanical collections.

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Global biotic interactions: An open infrastructure to share and analyze species-interaction datasets

Cited by 225 publications

References 29 publications

TraitBank: Practical semantics for organism attribute data

TraitBank: Practical semantics for organism attribute data

Towards global interoperability for supporting biodiversity research on essential biodiversity variables (EBVs)

Herbarium data: Global biodiversity and societal botanical needs for novel research

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