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      Ecological interactions in the Scratchpads virtual research environment

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          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Abstract
          Background

          The Natural History Museum, London has a number of online databases that describe interactions between species, including the HOSTS database of lepidopteran host plants ( Robinson et al. 2010) and a database of Dipterocarp Seed Predators. These databases were generally bespoke software, which has increased the technical work necessary to sustain these resources. The decision was taken to migrate these to either the Scratchpads Virtual Research Environment (VRE) ( Smith et al. 2011) or to the museum's Data Portal ( Scott et al. 2019), depending on the complexity of the existing resource, as both are being sustained by the Informatics Group at the Natural History Museum, London. Resources that can be best represented as a single table were moved to the Data Portal, while those best represented in a relational model were transferred to Scratchpads. In addition, the Phthiraptera .info Scratchpad ( Smith and Broom 2019), which already contained ecological interaction data, was migrated to the new system.

          New information

          This paper describes the implementation within the Scratchpads VRE of a new ecological interactions module that is capable of handling the needs of these projects, while at the same time is flexible to handle the needs of future projects with different data sources.

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          Uberon, an integrative multi-species anatomy ontology

          Christopher Mungall, Carlo Torniai, Georgios Gkoutos … (2012)
          We present Uberon, an integrated cross-species ontology consisting of over 6,500 classes representing a variety of anatomical entities, organized according to traditional anatomical classification criteria. The ontology represents structures in a species-neutral way and includes extensive associations to existing species-centric anatomical ontologies, allowing integration of model organism and human data. Uberon provides a necessary bridge between anatomical structures in different taxa for cross-species inference. It uses novel methods for representing taxonomic variation, and has proved to be essential for translational phenotype analyses. Uberon is available at http://uberon.org
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            A decadal view of biodiversity informatics: challenges and priorities

            Alex Hardisty, Dave Roberts, Todd Vision … (2013)
            Biodiversity informatics plays a central enabling role in the research community's efforts to address scientific conservation and sustainability issues. Great strides have been made in the past decade establishing a framework for sharing data, where taxonomy and systematics has been perceived as the most prominent discipline involved. To some extent this is inevitable, given the use of species names as the pivot around which information is organised. To address the urgent questions around conservation, land-use, environmental change, sustainability, food security and ecosystem services that are facing Governments worldwide, we need to understand how the ecosystem works. So, we need a systems approach to understanding biodiversity that moves significantly beyond taxonomy and species observations. Such an approach needs to look at the whole system to address species interactions, both with their environment and with other species. It is clear that some barriers to progress are sociological, basically persuading people to use the technological solutions that are already available. This is best addressed by developing more effective systems that deliver immediate benefit to the user, hiding the majority of the technology behind simple user interfaces. An infrastructure should be a space in which activities take place and, as such, should be effectively invisible. This community consultation paper positions the role of biodiversity informatics, for the next decade, presenting the actions needed to link the various biodiversity infrastructures invisibly and to facilitate understanding that can support both business and policy-makers. The community considers the goal in biodiversity informatics to be full integration of the biodiversity research community, including citizens’ science, through a commonly-shared, sustainable e-infrastructure across all sub-disciplines that reliably serves science and society alike.
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              Creative Commons licenses and the non-commercial condition: Implications for the re-use of biodiversity information

              Gregor Hagedorn, Daniel Mietchen, Robert A. Morris … (2011)
              Abstract The Creative Commons (CC) licenses are a suite of copyright-based licenses defining terms for the distribution and re-use of creative works. CC provides licenses for different use cases and includes open content licenses such as the Attribution license (CC BY, used by many Open Access scientific publishers) and the Attribution Share Alike license (CC BY-SA, used by Wikipedia, for example). However, the license suite also contains non-free and non-open licenses like those containing a “non-commercial” (NC) condition. Although many people identify “non-commercial” with “non-profit”, detailed analysis reveals that significant differences exist and that the license may impose some unexpected re-use limitations on works thus licensed. After providing background information on the concepts of Creative Commons licenses in general, this contribution focuses on the NC condition, its advantages, disadvantages and appropriate scope. Specifically, it contributes material towards a risk analysis for potential re-users of NC-licensed works.
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                Author and article information

                Contributors
                Edward Baker:
                ORCID: https://orcid.org/0000-0002-5887-9543
                Journal
                Journal ID (nlm-ta): Biodivers Data J
                Journal ID (iso-abbrev): Biodivers Data J
                Journal ID (publisher-id): 1
                Journal ID (index): urn:lsid:arphahub.com:pub:F9B2E808-C883-5F47-B276-6D62129E4FF4
                Journal ID (aggregator): urn:lsid:zoobank.org:pub:245B00E9-BFE5-4B4F-B76E-15C30BA74C02
                Title: Biodiversity Data Journal
                Publisher: Pensoft Publishers
                ISSN (Electronic): 1314-2828
                Publication date Collection: 2019
                Publication date (Electronic): 27 November 2019
                Volume: 7
                Electronic Location Identifier: e47043
                Affiliations
                [1 ] The Natural History Museum, London, United Kingdom The Natural History Museum London United Kingdom
                Author notes
                Corresponding author: Edward Baker ( edwbaker@ 123456gmail.com ).

                Academic editor: Anne Thessen

                Author information
                https://orcid.org/0000-0002-5887-9543
                https://orcid.org/0000-0001-6766-2840
                https://orcid.org/0000-0001-5297-7452
                Article
                Publisher ID: 47043 Publisher-manuscript ID: 10733
                DOI: 10.3897/BDJ.7.e47043
                PMC ID: 6892960
                SO-VID: fbce990a-692a-46c9-a5e6-840fda089427
                Copyright © Edward Baker, Steen Dupont, Vincent Stuart Smith
                License:

                This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                Date received : 03 October 2019
                Date accepted : 21 November 2019
                Page count
                Figures: 3, Tables: 3, References: 30
                Categories
                Subject: Software Description
                Subject: Biodiversity & Conservation
                Subject: Ecological informatics
                Subject: World

                Keywords: ecological informatics,biodiversity informatics,ecological interactions
                Data availability:
                Keywords: ecological informatics, biodiversity informatics, ecological interactions

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