ArctosR: An R package to interface with the Arctos Museum Database API

Resumen

Arctos is an online museum collection management database that hosts data for >5 million observational and physical records of plants, animals, and artifacts from >60 institutions worldwide. For biological specimens, these data include geographic and temporal information, detailed parts such as tissue samples, and links to related specimen records (e.g., parasites) as defined by the extended specimen concept. Although some of the data in Arctos are accessible via aggregators such as the Global Biodiversity Information Facility, information of high relevance for other research questions, such as host-parasite associations, can only be accessed using the Arctos system. These data, which are missing from aggregators, have the potential to provide rich context for large-scale biodiversity, ecological, and evolutionary research, but there is no automated way to download bulk data from Arctos. To expand access to specimen data, we developed ArctosR, an R package that enables users to query the Arctos database programmatically, download bulk data, and use those data in other R-scripted workflows. Here, we describe the package functionality and outline five use cases for ArctosR: (1) a search for georeferenced occurrences, (2) finding records of a host species that had nematodes, (3) finding tissue samples preserved in ways that are suitable for molecular exploration, (4) downloading data to explore patterns of Bergmann’s Rule, and (5) downloading data and using it in ecological niche modeling. Combined with the expanded and standardized specimen, parasite, and pathogen fields available in Arctos, ArctosR serves as a data bridge connecting biodiversity information to related biomedical investigations, enabling a more comprehensive OneHealth approach.