Abstract
Paleobiologists and paleoecologists interested in studying biodiversity dynamics over broad spatial and temporal scales have built multiple community-curated data resources, each emphasizing a particular spatial domain, timescale, or taxonomic group(s). This multiplicity of data resources is understandable, given the enormous diversity of life across Earth's history, but creates a barrier to achieving a truly global understanding of the diversity and distribution of life across time. Here we present the Earth Life Consortium Application Programming Interface (ELC API), a lightweight data service designed to search and retrieve fossil occurrence and taxonomic information from across multiple paleobiological resources. Key endpoints include Occurrences (returns spatiotemporal locations of fossils for selected taxa), Locales (returns information about sites with fossil data), References (returns bibliographic information), and Taxonomy (returns names of subtaxa associated with selected taxa). Data objects are returned as JSON or CSV format. The ELC API supports tectonic-driven shifts in geographic position back to 580 Ma using services from Macrostrat and GPlates. The ELC API has been implemented first for the Paleobiology Database and Neotoma Paleoecology Database, with a test extension to the Strategic Environmental Archaeology Database. The ELC API is designed to be readily extensible to other paleobiological data resources, with all endpoints fully documented and following open-source standards (e.g., Swagger, OGC). The broader goal is to help build an interlinked and federated ecosystem of paleobiological and paleoenvironmental data resources, which together provide paleobiologists, macroecologists, biogeographers, and other interested scientists with full coverage of the diversity and distribution of life across time.
Highlights
Study of the patterns and processes governing the diversity of life on earth at long timescales and broad spatial scales requires the assembly of many individual fossil occurrences into larger, open, community-curated data resources (CCDRs; Williams et al 2018a) such as the Paleobiology Database (PBDB), the Neotoma Paleoecology Database, and others (Uhen et al 2013)
Design and development of the Earth Life Consortium Application Programming Interface (ELC API) followed a user-centered and “API first” development process, that emphasizes careful consideration of how to robustly represent and access information before application development. This approach consists of the following steps: 1) Developers and paleobiologists from the Neotoma and PBDB teams met to review the data models of the existing data resources and native APIs, identify semantic commonalities, and points of divergence
The paleobiological data and knowledge gathered by CCDRs such as Neotoma and the PBDB represents decades to centuries of accumulated data and knowledge and hundreds of millions of dollars of scientific investment
Summary
Study of the patterns and processes governing the diversity of life on earth at long timescales and broad spatial scales requires the assembly of many individual fossil occurrences into larger, open, community-curated data resources (CCDRs; Williams et al 2018a) such as the Paleobiology Database (PBDB), the Neotoma Paleoecology Database, and others (Uhen et al 2013). Large paleodata syntheses are used to understand how contemporary ecological systems are shaped by historical legacies of slowacting processes (e.g., Whittaker et al 2001, Jablonski 2008), test the ecological forecasting models used to project and prepare for the impacts of 21st-century climate change (e.g., Veloz et al 2012, Blois et al 2013), assess the patterns and causes of abrupt ecological and environmental change (Williams et al 2010, Shanahan et al 2015, Shuman et al 2019), constrain phylogenetic models of species divergence and rates of evolution (Muller & Reisz 2005), assess the novelty of contemporary ecosystems relative to historic or deeper-time baselines (Jackson & Williams 2004, Radeloff 2015), and understand the fundamental processes that generate, maintain, and rebuild biodiversity (Crame 2001, Jablonski et al 2013) These open paleodata resources make paleobiological data accessible to scientists from allied disciplines, powering the generation of convergent research.
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