Towards the bibliography of life

Ten years and a million links: building a global taxonomic library connecting persistent identifiers for names, publications and people

A major gap in the biodiversity knowledge graph is a connection between taxonomic names and the taxonomic literature. While both names and publications often have persistent identifiers (PIDs), such as Life Science Identifiers (LSIDs) or Digital Object Identifiers (DOIs), LSIDs for names are rarely linked to DOIs for publications. This article describes efforts to make those connections across three large taxonomic databases: Index Fungorum, International Plant Names Index (IPNI) and the Index of Organism Names (ION). Over a million names have been matched to DOIs or other persistent identifiers for taxonomic publications. This represents approximately 36% of names for which publication data are available. The mappings between LSIDs and publication PIDs are made available through ChecklistBank. Applications of this mapping are discussed, including a web app to locate the citation of a taxonomic name and a knowledge graph that uses data on researcher ORCID ids to connect taxonomic names and publications to authors of those names.

Wikidata and the bibliography of life

Biological taxonomy rests on a long tail of publications spanning nearly three centuries. Not only is this literature vital to resolving disputes about taxonomy and nomenclature, for many species it represents a key source-indeed sometimes the only source-of information about that species. Unlike other disciplines such as biomedicine, the taxonomic community lacks a centralised, curated literature database (the "bibliography of life"). This article argues that Wikidata can be that database as it has flexible and sophisticated models of bibliographic information, and an active community of people and programs ("bots") adding, editing, and curating that information.

Liberating links between datasets using lightweight data publishing: an example using plant names and the taxonomic literature

Constructing a biodiversity knowledge graph will require making millions of cross links between diversity entities in different datasets. Researchers trying to bootstrap the growth of the biodiversity knowledge graph by constructing databases of links between these entities lack obvious ways to publish these sets of links. One appealing and lightweight approach is to create a "datasette", a database that is wrapped together with a simple web server that enables users to query the data. Datasettes can be packaged into Docker containers and hosted online with minimal effort. This approach is illustrated using a dataset of links between globally unique identifiers for plant taxonomic namesand identifiers for the taxonomic articles that published those names.