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Roderic D. M. Page
University of Glasgow
Phylogenetic treeComputer scienceBiologyPhylogeneticsZoology
127Publications
44H-index
16.2kCitations
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#1Roderic D. M. Page (Glas.: University of Glasgow)H-Index: 44
Taxonomic names remain fundamental to linking biodiversity data, but information on these names resides in separate silos. Despite often making their contents available in RDF, records in these taxonomic databases are rarely linked to identifiers in external databases, such as DOIs for publications, or ORCIDs for people. This paper explores how author names in publication databases such as CrossRef and ORCID can be reconciled with author names in a taxonomic database using existing vocabularies ...
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#1David ShorthouseH-Index: 6
#2Roderic D. M. PageH-Index: 44
1 CitationsSource
#1Quentin GroomH-Index: 20
Last. Elspeth HastonH-Index: 11
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The concept of building a network of relationships between entities, a knowledge graph, is one of the most effective methods to understand the relations between data. By organizing data, we facilitate the discovery of complex patterns not otherwise evident in the raw data. Each datum at the nodes of a knowledge graph needs a persistent identifier (PID) to reference it unambiguously. In the biodiversity knowledge graph, people are key elements (Page 2016). They collect and identify specimens, the...
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#1Roderic D. M. PageH-Index: 44
The taxonomic literature is one of the largest resources of information on biodiversity, both current and in the past. Unlike many scientific disciplines this literature remains perpetually relevant as successive taxonomic work builds upon those earlier foundations. Projects such as the Biodiversity Heritage Library (BHL) have greatly increased access to that literature, as have numerous independent digitisation efforts by museums, herbaria, and publishers. But the focus of this access has been ...
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#1Roderic D. M. PageH-Index: 44
This talk explores the role Wikidata (Vrandecic and Krotzsch 2014) might play in the task of assembling biodiversity information into a single, richly annotated and cross linked structure known as the biodiversity knowledge graph (Page 2016). Initially conceived as a language-independent data store of facts derived from the Wikipedia, Wikidata has morphed into a global knowledge graph, complete with a user friendly interface for data entry and a powerful implementation of the SPARQL query langua...
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#1Joel SachsH-Index: 2
#2Roderic D. M. PageH-Index: 44
Last. Zacchaeus ComsponH-Index: 1
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Knowledge graphs have the potential to unite disconnected digitized biodiversity data, and there are a number of efforts underway to build biodiversity knowledge graphs. More generally, the recent popularity of knowledge graphs, driven in part by the advent and success of the Google Knowledge Graph, has breathed life into the ongoing development of semantic web infrastructure and prototypes in the biodiversity informatics community. We describe a one week training event and hackathon that focuse...
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Enormous quantities of biodiversity data are being made available online, but much of this data remains isolated in silos. One approach to breaking these silos is to map local, often database-specific identifiers to shared global identifiers. This mapping can then be used to construct a knowledge graph, where entities such as taxa, publications, people, places, specimens, sequences, and institutions are all part of a single, shared knowledge space. Motivated by the 2018 GBIF Ebbe Nielsen Challen...
2 CitationsSource
#1Roderic D. M. Page (Glas.: University of Glasgow)H-Index: 44
Many nucleotide sequences in the publicly available genomics databases lack spatial information, such as the latitude and longitude coordinates for the locality where the sample for sequencing was taken. In this note I discuss several approaches to geocoding sequence records. The first method uses the Global Biodiversity Information Facility (GBIF: https://gbif.org) as a gazetter. The availability of a simple full text search across GBIF data makes it possible to rapidly geocode locality informa...
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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. Datasette...
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Both classical taxonomy and DNA barcoding are engaged in the task of digitizing the living world. Much of the taxonomic literature remains undigitized. The rise of open access publishing this century and the freeing of older literature from the shackles of copyright have greatly increased the online availability of taxonomic descriptions, but much of the literature of the mid- to late-twentieth century remains offline (‘dark texts’). DNA barcoding is generating a wealth of computable data that i...
22 CitationsSource
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