Biodiversity Information Science and Standards : Conference Abstract
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Conference Abstract
Finding Data Gaps in the GBIF Backbone Taxonomy
expand article info John Thomas Waller ‡
‡ GBIF, Copenhagen, Denmark
Corresponding author: John Thomas Waller (jhnwllr@gmail.com)
Received: 05 Aug 2022 | Published: 23 Aug 2022
© 2022 John Waller
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation: Waller JT (2022) Finding Data Gaps in the GBIF Backbone Taxonomy. Biodiversity Information Science and Standards 6: e91312. https://doi.org/10.3897/biss.6.91312
 Open Access

Abstract

When publishers supply GBIF (Global Biodiversity Information Facility) with a dwc:scientificName, this name is sometimes not found in the GBIF taxonomic backbone. The backbone is needed to organize occurrences on GBIF. In these cases, the occurrence records get a data quality flag called taxon match higher rank. This means that GBIF was only able to match the name to a higher rank. Matching is a process whereby a name supplied by the publisher is compared to a name in the already existing in the GBIF backbone taxonomy.

At GBIF, we would always like to match the name supplied by the publisher to the lowest rank possible, so that when a user comes to GBIF looking for a certain name, they will have access to the largest amount of occurrence data possible.

The main goals of this project were:

  1. Identify the types of issues that prevent matching occurrences to the backbone that come in with an identification at species level (or below) to backbone names at that same rank.
  2. Identify the responsible actors (GBIF processing, occurrence record curators, missing checklist) who are best placed to help improve the name.

In Fig. 1, I divide unique names from occurrences supplied to GBIF from publishers that have received the taxon match higher rank flag. Here we see that GBIF is probably missing many names from Coleoptera (Beetles) and Lepidoptera (Butterflies/Moths).

Figure 1.

Unique names from occurrences supplied to GBIF from publishers that have received the taxon match higher rank flag.

  • other: means that my alogrithm could not find a good reason for this name not matching. This could be a misspelling or the name could be missing from the GBIF backbone. These are names that might reflect data gaps.
  • unmatchable name: is a catch-all group for poorly formatted or unmatchable names. (see Table 1).
  • hybrid (hybrid formula): means the name refers to a hybrid. We expect poor checklist coverage for hybrid names.
  • below species: means a name at a taxonomic rank below the species level could not be matched at that level. Usually we expect less checklist coverage for subspecies and varieties.
  • too many choices: GBIF has two or more names with different authorship (homonyms), but the publisher does not provide authorship and/or higher taxonomy, so the name cannot be matched unambiguously.
Table 1.
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Unmatchable (or hard to match) names.

name not matched reason
Mystery mystery bad name
Sonus naturalis bad name
Bambusoideae spec. subfamily name
Coleoptera indet. order name
Astarte juv. genus name with life stage
Gen. sp. bad name
Astarte sp. BIOUG14667-B01 family with id
Phoneutria depilata (Strand 1909) sp. reval. species name with remark
Anisoptera Unknown Dragonfly Species infra-order name with remarks
Zygoptera suborder name
Philodromus Philodromus albidus / rufus doubtful identification (alternative)
Certhia brachydactyla/Certhia familiaris doubtful identification (alternative)
Corvus corone x C. cornix hybrid
BOLD:ADV7315 OTU (Operational Taxonomic Unit)
BOLD:ADX5419 OTU

Publishers to GBIF sometimes do not provide enough information in the dwc:scientificName for GBIF to choose between names in the backbone Fig. 2. If a publisher only supplied GBIF with "Glocianus punctiger" we would not be able to determine between the two choices, and it would get moved to the higher rank (genus Glocianus).

Figure 2.

Too many choices. Authorship is needed to decide between these entries in the backbone.

Publishers also supply GBIF with a variety of what I call unmatchable names, which are names that are impossible to match to the GBIF backbone. Sometimes these names are acceptable names, but still missing from the backbone, like missing hybrids or OTUs (Operational Taxonomic Units). Other names are simply bad names that we can’t expect to fix. Some examples below:

Table 1

It is often hard to tell if a missing name is a real data gap. To check, I randomly sampled five possibly missing names from each group from Fig. 1 to check if I could manually locate a source outside GBIF with the name.

Around 50% (44 of 86) of the possibly missing names appear to be genuinely missing from the GBIF backbone. We can therefore conservatively assume that there are thousands of missing names in the GBIF backbone. Keep in mind, however, that many missing names are missing synonyms—that is, they are not unique taxon concepts. Taking half of 50% (25%), we can make a conservative minimum missing names Table 2.

Table 2.
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Conservative minimum missing names. Based on conservative judgment, 25% of potentially missing names are genuinely absent from the GBIF backbone. Download a full table of possibly missing names from the groups above here.

group friendly name min estimated missing names
Coleoptera Beetles 26,600
Lepidoptera Butterflies 17,700
Passeriformes Bird order 4,200
Fabales Plant order 4,100
Asterales Plant order 4,000
Agaricales Mushrooms 1,600
Araneae Spiders 1,200
Rodentia Rodents 1,100
Carditida Bivalves 700
Anura Frogs 600
Carnivora Carnivores 300
Odonata Dragonflies 300
Chiroptera Bats 200
Cyatheales Ferns 100
Primates Primates 100
Neuroptera Insect order <100
Percopsiformes Fish order <100

As a data publisher, there are a few things that can be done to improve name matching to the GBIF backbone.

  • Run your dataset through the data validator
  • Match your names to the GBIF backbone before publishing using species lookup or rgbif
  • Add authorship if appropriate
  • Fill known higher-taxonomy
  • Try to avoid working name placeholders for the dwc:scientificName
  • Do not put identification qualifiers in the dwc:scientificName field but rather use the dwc:identificationQualifier field.

Keywords

taxonomic backbone, scientific name, data quality

Presenting author

John Thomas Waller

Presented at

TDWG 2022

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