Community Next Steps for Making Globally Unique Identifiers Work for Biocollections Data

Abstract

Biodiversity data is being digitized and made available online at a rapidly increasing rate but current practices typically do not preserve linkages between these data, which impedes interoperation, provenance tracking, and assembly of larger datasets. For data associated with biocollections, the biodiversity community has long recognized that an essential part of establishing and preserving linkages is to apply globally unique identifiers at the point when data are generated in the field and to persist these identifiers downstream, but this is seldom implemented in practice. There has neither been coalescence towards one single identifier solution (as in some other domains), nor even a set of recommended best practices and standards to support multiple identifier schemes sharing consistent responses. In order to further progress towards a broader community consensus, a group of biocollections and informatics experts assembled in Stockholm in October 2014 to discuss community next steps to overcome current roadblocks. The workshop participants divided into four groups focusing on: identifier practice in current field biocollections; identifier application for legacy biocollections; identifiers as applied to biodiversity data records as they are published and made available in semantically marked-up publications; and cross-cutting identifier solutions that bridge across these domains. The main outcome was consensus on key issues, including recognition of differences between legacy and new biocollections processes, the need for identifier metadata profiles that can report information on identifier persistence missions, and the unambiguous indication of the type of object associated with the identifier. Current identifier characteristics are also summarized, and an overview of available schemes and practices is provided.

DNA barcoding and taxonomy: dark taxa and dark texts

“…The biodiversity informatics community has yet to standardise identifiers for specimens, despite numerous efforts [17], consequently there may be little apparent overlap between specimen identifiers in different databases [16]. As an example, despite the limited sharing of data between BOLD and GBIF, there are already barcoded specimens in GBIF.…”

The potential of using sets of specimens to handle species concepts

“…Recent increases in the rate of specimen digitisation in natural history museums (e.g. [6]), combined with persistent identifiers for these specimens [7] allows for robust species concepts defined by a collection (set) of specimens. This paper experiments with using mathematical set notation (rather than the terminology used by [8]) to define operations on groups of specimens that may be considered equivalent to taxonomic and nomenclatural acts.…”

20 Years of Persistent Identifiers – Which Systems are Here to Stay?

“…After two months without a central resolving system, a resolver has been made available at http://www.lsid.info. However, the discussion is ongoing and significant parts of the biodiversity informatics community recommend switching from LSID to cool URI (Guralnick et al 2015). Using Google Scholar as a search engine we estimated that about 14,000 LSIDs have been used in the scientific literature.…”