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      APIs: A Common Interface for the Global Biodiversity Informatics Community

      Biodiversity Information Science and Standards

      Pensoft Publishers

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          Abstract

          Web APIs (Application Programming Interfaces) facilitate the exchange of resources (data) between two functionally independent entities across a common programmatic interface. In more general terms, Web APIs can connect almost anything to the world wide web. Unlike traditional software, APIs are not compiled, installed, or run. Instead, data are read (or consumed in API speak) through a web-based transaction, where a client makes a request and a server responds. Web APIs can be loosely grouped into two categories within the scope of biodiversity informatics, based on purpose. First, Product APIs deliver data products to end-users. Examples include the Global Biodiversity Information Facility (GBIF) and iNaturalist APIs. Designed and built to solve specific problems, web-based Service APIs are the second type and the focus of this presentation (referred to as Service APIs). Their primary function is to provide on-demand support to existing programmatic processes. Examples of this type include Elasticsearch Suggester API and geolocation, a service that delivers geographic locations from spatial input (latitude and longitude coordinates) (Pejic et al. 2010).Many challenges lie ahead for biodiversity informatics and the sharing of global biodiversity data (e.g., Blair et al. 2020). Service-driven, standardized web-based Service APIs that adhere to best practices within the scope of biodiversity informatics can provide the transformational change needed to address many of these issues. This presentation will highlight several critical areas of interest in the biodiversity data community, describing how Service APIs can address each individually. The main topics include:standardized vocabularies,interoperability of heterogeneous data sources anddata quality assessment and remediation.Fundamentally, the value of any innovative technical solution can be measured by the extent of community adoption. In the context of Service APIs, adoption takes two primary forms:financial and temporal investment in the construction of clients that utilize Service APIs andwillingness of the community to integrate Service APIs into their own systems and workflows.To achieve this, Service APIs must be simple, easy to use, pragmatic, and designed with all major stakeholder groups in mind, including users, providers, aggregators, and architects (Anderson et al. 2020Anderson et al. 2020; this study). Unfortunately, many innovative and promising technical solutions have fallen short not because of an inability to solve problems (Verner et al. 2008), rather, they were difficult to use, built in isolation, and/or designed without effective communication with stakeholders. Fortunately, projects such as Darwin Core (Wieczorek et al. 2012), the Integrated Publishing Toolkit (Robertson et al. 2014), and Megadetector (Microsoft 2021) provide the blueprint for successful community adoption of a technological solution within the biodiversity community. The final section of this presentation will examine the often overlooked non-technical aspects of this technical endeavor. Within this context, specifically how following these models can broaden community engagement and bridge the knowledge gap between the major stakeholders, resulting in the successful implementation of Service APIs.

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          The GBIF Integrated Publishing Toolkit: Facilitating the Efficient Publishing of Biodiversity Data on the Internet

          The planet is experiencing an ongoing global biodiversity crisis. Measuring the magnitude and rate of change more effectively requires access to organized, easily discoverable, and digitally-formatted biodiversity data, both legacy and new, from across the globe. Assembling this coherent digital representation of biodiversity requires the integration of data that have historically been analog, dispersed, and heterogeneous. The Integrated Publishing Toolkit (IPT) is a software package developed to support biodiversity dataset publication in a common format. The IPT’s two primary functions are to 1) encode existing species occurrence datasets and checklists, such as records from natural history collections or observations, in the Darwin Core standard to enhance interoperability of data, and 2) publish and archive data and metadata for broad use in a Darwin Core Archive, a set of files following a standard format. Here we discuss the key need for the IPT, how it has developed in response to community input, and how it continues to evolve to streamline and enhance the interoperability, discoverability, and mobilization of new data types beyond basic Darwin Core records. We close with a discussion how IPT has impacted the biodiversity research community, how it enhances data publishing in more traditional journal venues, along with new features implemented in the latest version of the IPT, and future plans for more enhancements.
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            Darwin Core: An Evolving Community-Developed Biodiversity Data Standard

            Biodiversity data derive from myriad sources stored in various formats on many distinct hardware and software platforms. An essential step towards understanding global patterns of biodiversity is to provide a standardized view of these heterogeneous data sources to improve interoperability. Fundamental to this advance are definitions of common terms. This paper describes the evolution and development of Darwin Core, a data standard for publishing and integrating biodiversity information. We focus on the categories of terms that define the standard, differences between simple and relational Darwin Core, how the standard has been implemented, and the community processes that are essential for maintenance and growth of the standard. We present case-study extensions of the Darwin Core into new research communities, including metagenomics and genetic resources. We close by showing how Darwin Core records are integrated to create new knowledge products documenting species distributions and changes due to environmental perturbations.
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                Author and article information

                Contributors
                Journal
                Biodiversity Information Science and Standards
                BISS
                Pensoft Publishers
                2535-0897
                September 16 2021
                September 16 2021
                : 5
                Article
                10.3897/biss.5.75267
                © 2021

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