Abstract
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.
Highlights
A venerable tradition in taxonomy is compiling and publishing lists of scientific names, whether in printed form or as online databases (Michel 2016)
The International Plant Names Index (IPNI) curators have added a link to the corresponding page in the Biodiversity Heritage Library (BHL) and, for some recently added records, the IPNI web site may give the Digital Object Identifiers (DOIs) for a publication, but the majority of IPNI records are not linked to a digital identifier for the publication associated with each name
Some simple queries include finding the DOIs for publications of new names in a given genus, such as Begonia : select Id, Full_name_without_family_and_authors, doi from ipni where Genus="Begonia" and doi is not null; JSTOR has digitised many botanical journals, so for some taxa such as the genus Tiquilia, it is an excellent source of taxonomic literature: select Id, Full_name_without_family_and_authors, doi from ipni where genus='Tiquilia' and jstor is not null; the primary goal of the name-to-literature mapping is to find digital versions of the descriptions for each species, the datasette enables queries that might address other questions
Summary
A venerable tradition in taxonomy is compiling and publishing lists of scientific names, whether in printed form or as online databases (Michel 2016). If the lists include bibliographic information, these lists can serve as search indices to the taxonomic literature. This functionality is often hampered by the use of cryptic citations and a mismatch between the granularity sought by taxonomists (often page-level) and that used by researchers when citing sources. Each taxonomic name would be linked to a detailed bibliographic record of where that name was published and that publication would be available in digital form, as would any subsequent taxonomic revisions (Agosti and Egloff 2009, Page 2016c). There are detailed databases of names that cite the primary literature, but typically these citations are text strings, not actionable digital identifiers
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