Abstract
The biodiversity informatics community has discussed aspirations and approaches for assigning globally unique identifiers (GUIDs) to biocollections for nearly a decade. During that time, and despite misgivings, the de facto standard identifier has become the “Darwin Core Triplet”, which is a concatenation of values for institution code, collection code, and catalog number associated with biocollections material. Our aim is not to rehash the challenging discussions regarding which GUID system in theory best supports the biodiversity informatics use case of discovering and linking digital data across the Internet, but how well we can link those data together at this moment, utilizing the current identifier schemes that have already been deployed. We gathered Darwin Core Triplets from a subset of VertNet records, along with vertebrate records from GenBank and the Barcode of Life Data System, in order to determine how Darwin Core Triplets are deployed “in the wild”. We asked if those triplets follow the recommended structure and whether they provide an easy and unambiguous means to track from specimen records to genetic sequence records. We show that Darwin Core Triplets are often riddled with semantic and syntactic errors when deployed and curated in practice, despite specifications about how to construct them. Our results strongly suggest that Darwin Core Triplets that have not been carefully curated are not currently serving a useful role for relinking data. We briefly consider needed next steps to overcome current limitations.
Highlights
One compelling vision for biodiversity data resources is a ‘‘cloud’’ of interconnected digital objects linked together by an expressive vocabulary describing relationships between the objects, with each object bearing a globally unique identifier that can be resolved using common Internet protocols (e.g., HTTP) (Page, 2009)
The Global Biodiversity Information Facility released a 2009 report developed by a global panel of experts whose first words are ‘‘GBIF has identified the provision of identifiers for biodiversity objects as one of the central challenges to developing a global bioinformatics infrastructure’’, a sentiment shared by others (e.g., [4])
Parentheticals give the number of unique Darwin Core (DwC) Triplets involved in the matches. doi:10.1371/journal.pone.0114069.t003
Summary
One compelling vision for biodiversity data resources is a ‘‘cloud’’ of interconnected digital objects linked together by an expressive vocabulary describing relationships between the objects, with each object bearing a globally unique identifier that can be resolved using common Internet protocols (e.g., HTTP) (Page, 2009). Humans or computers could learn something about those objects by resolving their identifiers via a URI (Uniform Resource Identifiers), which would point to the object itself or a description of the object (e.g., metadata) In this information utopia, data would be unlocked from organizational and technological silos and instead reside in a global data space [1]. In the biodiversity informatics arena, the vision of a linked and open world of data has foundered on the rocks of a set of deep challenges. No challenge is more imminently solvable, yet pernicious, than the one surrounding the provision of globally unique identifiers for the biodiversity domain This view is not that of the authors. The Global Biodiversity Information Facility released a 2009 report developed by a global panel of experts whose first words are ‘‘GBIF has identified the provision of identifiers for biodiversity objects as one of the central challenges to developing a global bioinformatics infrastructure’’, a sentiment shared by others (e.g., [4])
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