DOI: 10.5061/dryad.3160r
title: Data from: Challenges with using names to link digital biodiversity information

description: The need for a names-based cyber-infrastructure for digital biology is
 based on the argument that scientific names serve as a standardized
 metadata system that has been used consistently and near universally for
 250 years. As we move towards data-centric biology, name-strings can be
 called on to discover, index, manage, and analyze accessible digital
 biodiversity information from multiple sources. Known impediments to the
 use of scientific names as metadata include synonyms, homonyms,
 mis-spellings, and the use of other strings as identifiers. We here
 compare the name-strings in GenBank, Catalogue of Life (CoL), and the
 Dryad Digital Repository (DRYAD) to assess the effectiveness of the
 current names-management toolkit developed by Global Names to achieve
 interoperability among distributed data sources. New tools that have been
 used here include Parser (to break name-strings into component parts and
 to promote the use of canonical versions of the names), a modified
 TaxaMatch fuzzy-matcher (to help manage typographical, transliteration,
 and OCR errors), and Cross-Mapper (to make comparisons among data sets).
 The data sources include scientific names at multiple ranks; vernacular
 (common) names; acronyms; strain identifiers and other surrogates
 including idiosyncratic abbreviations and concatenations. About 40% of the
 name-strings in GenBank are scientific names representing about 400,000
 species or infraspecies and their synonyms. Of the formally-named terminal
 taxa (species and lower taxa) represented, about 82% have a match in CoL.
 Using a subset of content in DRYAD, about 45% of the identifiers are names
 of species and infraspecies, and of these only about a third have a match
 in CoL. With simple processing, the extent of matching between DRYAD and
 CoL can be improved to over 90%. The findings confirm the necessity for
 name-processing tools and the value of scientific names as a mechanism to
 interconnect distributed data, and identify specific areas of improvement
 for taxonomic data sources. Some areas of diversity (bacteria and viruses)
 are not well represented by conventional scientific names, and they and
 other forms of strings (acronyms, identifiers, and other surrogates) that
 are used instead of names need to be managed in reconciliation services
 (mapping alternative name-strings for the same taxon together). On-line
 resolution services will bring older scientific names up to date or
 convert surrogate name-strings to scientific names should such names
 exist. Examples are given of many of the aberrant forms of ‘names’ that
 make their way into these databases. The occurrence of scientific names
 with incorrect authors, such as chresonyms within synonymy lists, is a
 quality-control issue in need of attention. We propose a future-proofing
 solution that will empower stakeholders to take advantage of the
 name-based infrastructure at little cost. This proposed infrastructure
 includes a standardized system that adopts or creates UUIDs for
 name-strings, software that can identify name-strings in sources and apply
 the UUIDs, reconciliation and resolution services to manage the
 name-strings, and an annotation environment for quality control by users
 of name-strings.
description: Tab delimited file of
 data used in and described in the Patterson et al Challenges paper in
 Biodiversity Data Journal (2016)Data produced as a
 result of mapping of GenBank and DRYAD content against Catalogue of Life
 and subsequent reclassification as described in the 'Challenges'
 paper. For full details see publication ('The Challenges
 Paper'). Tab delimited format. Fields: Serial Number (as provided by
 FileMaker software); Input Name (name-string as obtained from source); GN
 UUID (UUID as created by Global Names as described in the challenges
 paper); Canonical version (canonical form of name-string as formed by
 Global Names software); GenBank (indicates if name-string was in the
 GenBank download); Dryad Original (indicates if the name-string was in the
 original downloads from DRYAD; DRYAD Preprocessed (indicates if the
 name-string was in the DRYAD compilation after pre-processing); Scientific
 Name (indicates if the name-string is a scientific name); Terminal Taxon
 (indicates if the name-string refers to a species or subordinate taxon);
 GNXM (classification of matches as formed by Global Names Cross Mapper,
 details in full publication); GN Matched Name (name-string that Global
 Names Cross Mapper matched to); GN Matched Canonical Form (canonical form
 of name-string that Global Names Cross Mapper matched to); Input Rank
 (rank assigned to name-string by data source); GNXM Matched Rank (rank
 inferred by Global Names Cross Mapper); GNXM Matched Edit Distance (edit
 distances as described in associated paper for fuzzy matches found by
 Global Names Cross Mapper); GNXM Matched Score (confidence measure as
 described in associated paper for matches found by Global Names Cross
 Mapper); and Final Annotation (final classification made as a result of
 the analyses of this paper, and as described in the
 paper).Patterson_et_al_Challenges_with_Names_data_file_160430.tab