A Review of Biotic Interactions and Taxon Names Found in globalbioticinteractions/dmns-para hash://md5/5ffc62fde92400115f9f936b1cafa6d9

by Nomer, Elton and Preston, three naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

https://github.com/globalbioticinteractions/dmns-para/issues

2025-04-10

Abstract

Life on Earth is sustained by complex interactions between organisms and their environment. These biotic interactions can be captured in datasets and published digitally. We present a review and archiving process for such an openly accessible digital interactions dataset of known origin and discuss its outcome. The dataset under review, named globalbioticinteractions/dmns-para, has fingerprint hash://md5/5ffc62fde92400115f9f936b1cafa6d9, is 71.3MiB in size and contains 2,090 interaction with 3 unique types of associations (e.g., parasiteOf) between 64 primary taxa (e.g., Eumolpianus eumolpi) and 495 associated taxa (e.g., Tamias speciosus). This report includes detailed summaries of interaction data, a taxonomic review from multiple catalogs, and an archived version of the dataset from which the reviews are derived.

Introduction

Data Review and Archive

Data review and archiving can be a time-consuming process, especially when done manually. This review report aims to help facilitate both activities. It automates the archiving of datasets, including Darwin Core archives, and is a citable backup of a version of the dataset. Additionally, an automatic review of species interaction claims made in the dataset is generated and registered with Global Biotic Interactions (J. H. Poelen, Simons, and Mungall 2014).

This review includes summary statistics about, and observations about, the dataset under review:

DMNS Parasite collection (Arctos) http://ipt.vertnet.org:8080/ipt/archive.do?r=dmn 2025-04-04T23:39:21.331Z hash://md5/5ffc62fde92400115f9f936b1cafa6d9

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/dmns-para and inspect associated metadata files including, but not limited to, README.md, eml.xml, and/or globi.json.

Methods

The review is performed through programmatic scripts that leverage tools like Preston (Elliott et al. 2025), Elton (Kuhn, Poelen, and Leinweber 2025), Nomer (Salim and Poelen 2025), globinizer (J. Poelen, Seltmann, and Mietchen 2024) combined with third-party tools like grep, mlr, tail and head.

Tools used in this review process
tool name version
preston 0.10.1
elton 0.15.9
nomer 0.5.13
globinizer 0.4.0
mlr 6.0.0
jq 1.6
yq 4.25.3
pandoc 3.1.6.1

The review process can be described in the form of the script below 1.

# get versioned copy of the dataset (size approx. 71.3MiB) under review 
elton pull globalbioticinteractions/dmns-para

# generate review notes
elton review globalbioticinteractions/dmns-para\
 > review.tsv

# export indexed interaction records
elton interactions globalbioticinteractions/dmns-para\
 > interactions.tsv

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/dmns-para\
 | nomer append col\
 > name-alignment.tsv

or visually, in a process diagram.

review origin dataset origin elton Elton (a naive review bot) elton->origin pull (1) interactions indexed interactions elton->interactions generates (2) alignment name alignments nomer Nomer (a naive review bot) nomer->interactions extract names (3) nomer->alignment generates (5) catalog name catalog nomer->catalog uses (4)

You can find a copy of the full review script at check-data.sh. See also GitHub and Codeberg.

Results

In the following sections, the results of the review are summarized 2. Then, links to the detailed review reports are provided.

Files

The following files are produced in this review:

filename description
biblio.bib list of bibliographic reference of this review
check-dataset.sh data review workflow/process as expressed in a bash script
data.zip a versioned Preston (Elliott et al. 2025) archive of the data under review
HEAD the digital signature of the data under review
index.docx review in MS Word format
index.html review in HTML format
index.md review in Pandoc markdown format
index.pdf review in PDF format
indexed-citations.csv.gz list of distinct reference citations for reviewed species interaction claims in gzipped comma-separated values file format
indexed-citations.html.gz list of distinct reference citations for reviewed species interactions claims in gzipped html file format
indexed-citations.tsv.gz list of distinct reference citations for reviewed species interaction claims in gzipped tab-separated values format
indexed-interactions-col-family-col-family.svg network diagram showing the taxon family to taxon family interaction claims in the dataset under review as interpreted by the Catalogue of Life via Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024)
indexed-interactions-col-kingdom-col-kingdom.svg network diagram showing the taxon kingdom to taxon kingom interaction claims in the dataset under review as interpreted by the Catalogue of Life via Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024)
indexed-interactions.csv.gz species interaction claims indexed from the dataset under review in gzipped comma-separated values format
indexed-interactions.html.gz species interaction claims indexed from the dataset under review in gzipped html format
indexed-interactions.tsv.gz species interaction claims indexed from the dataset under review in gzipped tab-separated values format
indexed-interactions-sample.csv list of species interaction claims indexed from the dataset under review in gzipped comma-separated values format
indexed-interactions-sample.html first 500 species interaction claims indexed from the dataset under review in html format
indexed-interactions-sample.tsv first 500 species interaction claims indexed from the dataset under review in tab-separated values format
indexed-names.csv.gz taxonomic names indexed from the dataset under review in gzipped comma-separated values format
indexed-names.html.gz taxonomic names found in the dataset under review in gzipped html format
indexed-names.tsv.gz taxonomic names found in the dataset under review in gzipped tab-separated values format
indexed-names-resolved-col.csv.gz taxonomic names found in the dataset under review aligned with the Catalogue of Life as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped comma-separated values format
indexed-names-resolved-col.html.gz taxonomic names found in the dataset under review aligned with the Catalogue of Life as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped html format
indexed-names-resolved-col.tsv.gz taxonomic names found in the dataset under review aligned with the Catalogue of Life as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped tab-separated values format
indexed-names-resolved-discoverlife.csv.gz taxonomic names found in the dataset under review aligned with Discover Life bee species checklist as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped comma-separated values format
indexed-names-resolved-discoverlife.html.gz taxonomic names found in the dataset under review aligned with Discover Life bee species checklist as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped html format
indexed-names-resolved-discoverlife.tsv.gz taxonomic names found in the dataset under review aligned with Discover Life bee species checklist as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped tab-separated values format
indexed-names-resolved-gbif.csv.gz taxonomic names found in the dataset under review aligned with GBIF Backbone Taxonomy as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped comma-separated values format
indexed-names-resolved-gbif.html.gz taxonomic names found in the dataset under review aligned with GBIF Backbone Taxonomy as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped html format
indexed-names-resolved-gbif.tsv.gz taxonomic names found in the dataset under review aligned with GBIF Backbone Taxonomy as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped tab-separated values format
indexed-names-resolved-itis.csv.gz taxonomic names found in the dataset under review aligned with Integrated Taxonomic Information System (ITIS) as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped comma-separated values format
indexed-names-resolved-itis.html.gz taxonomic names found in the dataset under review aligned with Integrated Taxonomic Information System (ITIS) as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped html format
indexed-names-resolved-itis.tsv.gz taxonomic names found in the dataset under review aligned with Integrated Taxonomic Information System (ITIS) as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped tab-separated values format
indexed-names-resolved-mdd.csv.gz taxonomic names found in the dataset under review aligned with the Mammal Diversity Database as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped comma-separated values format
indexed-names-resolved-mdd.html.gz taxonomic names found in the dataset under review aligned with Mammal Diversity Database as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped html format
indexed-names-resolved-mdd.tsv.gz taxonomic names found in the dataset under review aligned with Mammal Diversity Database as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped tab-separated values format
indexed-names-resolved-ncbi.csv.gz taxonomic names found in the dataset under review aligned with the NCBI Taxonomy as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped comma-separated values format
indexed-names-resolved-ncbi.html.gz taxonomic names found in the dataset under review aligned with the NCBI Taxonomy as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped html format
indexed-names-resolved-ncbi.tsv.gz taxonomic names found in the dataset under review aligned with the NCBI Taxonomy as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped tab-separated values format
indexed-names-resolved-pbdb.csv.gz taxonomic names found in the dataset under review aligned with the Paleobiology Database as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped comma-separated values format
indexed-names-resolved-pbdb.html.gz taxonomic names found in the dataset under review aligned with Paleobiology Database as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped html format
indexed-names-resolved-pbdb.tsv.gz taxonomic names found in the dataset under review aligned with Paleobiology Database as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped tab-separated values format
indexed-names-resolved-tpt.csv.gz taxonomic names found in the dataset under review aligned with the Terrestrial Parasite Tracker (TPT) Taxonomic Resource as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped comma-separated values format
indexed-names-resolved-tpt.html.gz taxonomic names found in the dataset under review aligned with the Terrestrial Parasite Tracker (TPT) Taxonomic Resource as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped html format
indexed-names-resolved-tpt.tsv.gz taxonomic names found in the dataset under review aligned with the Terrestrial Parasite Tracker (TPT) Taxonomic Resource as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped tab-separated values format
indexed-names-resolved-wfo.csv.gz taxonomic names found in the dataset under review aligned with the World of Flora Online as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped comma-separated values format
indexed-names-resolved-wfo.html.gz taxonomic names found in the dataset under review aligned with the World of Flora Online as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped html format
indexed-names-resolved-wfo.tsv.gz taxonomic names found in the dataset under review aligned with the World of Flora Online as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped tab-separated values format
indexed-names-resolved-worms.csv.gz taxonomic names found in the dataset under review aligned with the World Register of Marine Species (WoRMS) as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped comma-separated values format
indexed-names-resolved-worms.html.gz taxonomic names found in the dataset under review aligned with the World Register of Marine Species (WoRMS) as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped html format
indexed-names-resolved-worms.tsv.gz taxonomic names found in the dataset under review aligned with the World Register of Marine Species (WoRMS) as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped tab-separated values format
indexed-names-sample.csv first 500 taxonomic names found in the dataset under review in comma-separated values format
indexed-names-sample.html first 500 taxonomic names found in the dataset under review in html format
indexed-names-sample.tsv first 500 taxonomic names found in the dataset under review in tab-separated values format
interaction.svg diagram summarizing the data model used to index species interaction claims
nanopub-sample.trig first 500 species interaction claims as expressed in the nanopub format (Kuhn and Dumontier 2014)
nanopub.trig.gz species interaction claims as expressed in the nanopub format (Kuhn and Dumontier 2014)
process.svg diagram summarizing the data review processing workflow
prov.nq origin of the dataset under review as expressed in rdf/nquads
review.csv.gz review notes associated with the dataset under review in gzipped comma-separated values format
review.html.gz review notes associated with the dataset under review in gzipped html format
review.tsv.gz review notes associated with the dataset under review in gzipped tab-separated values format
review-sample.csv first 500 review notes associated with the dataset under review in comma-separated values format
review-sample.html first 500 review notes associated with the dataset under review in html format
review-sample.tsv first 500 review notes associated with the dataset under review in tab-separated values format
review.svg a review badge generated as part of the dataset review process
zenodo.json metadata of this review expressed in Zenodo record metadata

Archived Dataset

Note that data.zip file in this archive contains the complete, unmodified archived dataset under review.

Biotic Interactions

model primaryTaxon Primary Taxon associatedTaxon Associated Taxon primaryOrganism Primary Organism primaryOrganism->primaryTaxon classifiedAs associatedOrganism Associated Organism primaryOrganism->associatedOrganism interactsWith associatedOrganism->associatedTaxon classifiedAs

In this review, biotic interactions (or biotic associations) are modeled as a primary (aka subject, source) organism interacting with an associate (aka object, target) organism. The dataset under review classified the primary/associate organisms with specific taxa. The primary and associate organisms The kind of interaction is documented as an interaction type.

The dataset under review, named globalbioticinteractions/dmns-para, has fingerprint hash://md5/5ffc62fde92400115f9f936b1cafa6d9, is 71.3MiB in size and contains 2,090 interaction with 3 unique types of associations (e.g., parasiteOf) between 64 primary taxa (e.g., Eumolpianus eumolpi) and 495 associated taxa (e.g., Tamias speciosus).

An exhaustive list of indexed interaction claims can be found in gzipped csv and tsv archives. To facilitate discovery, a preview of claims available in the gzipped html page at indexed-interactions.html.gz are shown below.

The exhaustive list was used to create the following data summaries below.

Sample of Indexed Interaction Claims
sourceTaxonName interactionTypeName targetTaxonName referenceCitation
Eumolpianus eumolpi parasiteOf Tamias minimus http://arctos.database.museum/guid/DMNS:Para:572
Eumolpianus eumolpi parasiteOf Tamias quadrivittatus http://arctos.database.museum/guid/DMNS:Para:684
Oxyurida parasiteOf Tamias quadrivittatus http://arctos.database.museum/guid/DMNS:Para:2210
Oxyurida hasHost Tamias quadrivittatus http://arctos.database.museum/guid/DMNS:Para:2210
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
parasiteOf 1011
hasHost 636
coOccursWith 443
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Eumolpianus eumolpi 339
Phthiraptera 322
Nematoda 298
Cestoda 191
Hoplopleura arboricola 100
Oestridae 99
Heteroxynema cucullatum 72
Rauschtineria eutamii 64
Ceratophyllus ciliatus 57
Orchopeas sexdentatus 49
Eumolpianus eutamiadis 44
Neohaematopinus pacificus 43
Siphonaptera 40
Acariformes 38
Oropsylla tuberculata 31
Anoplura 27
Ixodidae 26
Acari 22
Aetheca wagneri 21
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
Tamias speciosus 162
Tamias minimus 121
Tamias quadrivittatus 100
Bubo virginianus 70
Eumolpianus eumolpi 67
Buteo jamaicensis 51
Nematoda 51
Hoplopleura arboricola 48
Tamias minimus operarius 45
Orchopeas sexdentatus 42
Tamias umbrinus 28
Tamias alpinus 26
Tamias rufus 25
Cestoda 24
Oropsylla tuberculata 24
Colaptes auratus 22
Tamias dorsalis dorsalis 22
Turdus migratorius 21
Sylvilagus audubonii 20
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Eumolpianus eumolpi parasiteOf Tamias minimus 76
Eumolpianus eumolpi parasiteOf Tamias quadrivittatus 54
Ceratophyllus ciliatus hasHost Tamias speciosus 48
Orchopeas sexdentatus coOccursWith Orchopeas sexdentatus 42
Eumolpianus eutamiadis hasHost Tamias speciosus 41
Eumolpianus eumolpi hasHost Tamias speciosus 37
Phthiraptera parasiteOf Bubo virginianus 28
Phthiraptera parasiteOf Buteo jamaicensis 23
Cestoda parasiteOf Bubo virginianus 22
Eumolpianus eumolpi coOccursWith Eumolpianus eumolpi 20
Eumolpianus eumolpi parasiteOf Tamias minimus operarius 19
Oropsylla tuberculata coOccursWith Oropsylla tuberculata 19
Nematoda parasiteOf Buteo jamaicensis 16
Nematoda parasiteOf Accipiter striatus 15
Eumolpianus eumolpi hasHost Tamias alpinus 14
Hoplopleura arboricola coOccursWith Neohaematopinus pacificus 14
Nematoda coOccursWith Nematoda 14
Neohaematopinus pacificus coOccursWith Hoplopleura arboricola 13
Hoplopleura arboricola coOccursWith Hoplopleura arboricola 12

Interaction Networks

The figures below provide a graph view on the dataset under review. The first shows a summary network on the kingdom level, and the second shows how interactions on the family level. It is important to note that both network graphs were first aligned taxonomically using the Catalogue of Life. Please refer to the original (or verbatim) taxonomic names for a more original view on the interaction data.

interactions Animalia Animalia Animalia->Animalia Animalia->Animalia Animalia->Animalia
interactions Argasidae Argasidae Cervidae Cervidae Argasidae->Cervidae Ceratophyllidae Ceratophyllidae Ceratophyllidae->Ceratophyllidae Ctenophthalmidae Ctenophthalmidae Ceratophyllidae->Ctenophthalmidae Heteroxynematidae Heteroxynematidae Ceratophyllidae->Heteroxynematidae Hoplopleuridae Hoplopleuridae Ceratophyllidae->Hoplopleuridae Ixodidae Ixodidae Ceratophyllidae->Ixodidae Oestridae Oestridae Ceratophyllidae->Oestridae Oxyuridae Oxyuridae Ceratophyllidae->Oxyuridae Sciuridae Sciuridae Ceratophyllidae->Sciuridae Ceratophyllidae->Sciuridae Cricetidae Cricetidae Ceratophyllidae->Cricetidae Mustelidae Mustelidae Ceratophyllidae->Mustelidae Ctenophthalmidae->Ceratophyllidae Ctenophthalmidae->Ctenophthalmidae Ctenophthalmidae->Heteroxynematidae Ctenophthalmidae->Sciuridae Ctenophthalmidae->Sciuridae Heteroxynematidae->Ceratophyllidae Heteroxynematidae->Ctenophthalmidae Heteroxynematidae->Hoplopleuridae Heteroxynematidae->Oestridae Heteroxynematidae->Sciuridae Heteroxynematidae->Sciuridae Hystrichopsyllidae Hystrichopsyllidae Heteroxynematidae->Hystrichopsyllidae Hoplopleuridae->Ceratophyllidae Hoplopleuridae->Heteroxynematidae Hoplopleuridae->Hoplopleuridae Hoplopleuridae->Ixodidae Hoplopleuridae->Oestridae Hoplopleuridae->Oxyuridae Hoplopleuridae->Sciuridae Hoplopleuridae->Sciuridae Hoplopleuridae->Cricetidae Polyplacidae Polyplacidae Hoplopleuridae->Polyplacidae Ixodidae->Ceratophyllidae Ixodidae->Hoplopleuridae Ixodidae->Sciuridae Ixodidae->Sciuridae Ixodidae->Cricetidae Ixodidae->Cricetidae Geomyidae Geomyidae Ixodidae->Geomyidae Ixodidae->Geomyidae Leporidae Leporidae Ixodidae->Leporidae Ixodidae->Leporidae Canidae Canidae Ixodidae->Canidae Phalacrocoracidae Phalacrocoracidae Ixodidae->Phalacrocoracidae Procyonidae Procyonidae Ixodidae->Procyonidae Soricidae Soricidae Ixodidae->Soricidae Oestridae->Ceratophyllidae Oestridae->Heteroxynematidae Oestridae->Hoplopleuridae Oestridae->Sciuridae Oestridae->Sciuridae Oestridae->Cricetidae Oestridae->Cricetidae Oestridae->Leporidae Fringillidae Fringillidae Oestridae->Fringillidae Oxyuridae->Ceratophyllidae Oxyuridae->Hoplopleuridae Oxyuridae->Sciuridae Oxyuridae->Sciuridae Strigidae Strigidae Oxyuridae->Strigidae Hystrichopsyllidae->Heteroxynematidae Hystrichopsyllidae->Sciuridae Hippoboscidae Hippoboscidae Hippoboscidae->Cervidae Hippoboscidae->Cervidae Accipitridae Accipitridae Hippoboscidae->Accipitridae Passerellidae Passerellidae Hippoboscidae->Passerellidae Hippoboscidae->Strigidae Polyplacidae->Hoplopleuridae Polyplacidae->Sciuridae Polyplacidae->Sciuridae Polyplacidae->Cricetidae Polyplacidae->Polyplacidae Leptopsyllidae Leptopsyllidae Leptopsyllidae->Cricetidae Ochotonidae Ochotonidae Leptopsyllidae->Ochotonidae Macronyssidae Macronyssidae Hirundinidae Hirundinidae Macronyssidae->Hirundinidae Plagiorhynchidae Plagiorhynchidae Turdidae Turdidae Plagiorhynchidae->Turdidae Pulicidae Pulicidae Pulicidae->Canidae Pulicidae->Pulicidae Felidae Felidae Pulicidae->Felidae Trichodectidae Trichodectidae Trichodectidae->Geomyidae Trichodectidae->Geomyidae

You can download the indexed dataset under review at indexed-interactions.csv.gz. A tab-separated file can be found at indexed-interactions.tsv.gz

Learn more about the structure of this download at GloBI website, by opening a GitHub issue, or by sending an email.

Another way to discover the dataset under review is by searching for it on the GloBI website.

Taxonomic Alignment

As part of the review, all names are aligned against various name catalogs (e.g., col, ncbi, discoverlife, gbif, itis, wfo, mdd, tpt, pbdb, and worms). These alignments can help review name usage or aid in selecting of a suitable taxonomic name resource.

Sample of Name Alignments
providedName relationName resolvedCatalogName resolvedName
Acanthocephala HAS_ACCEPTED_NAME col Acanthocephala
Acanthocephala SYNONYM_OF col Parodia
Acari NONE col Acari
Acariformes HAS_ACCEPTED_NAME col Acariformes
Distribution of Taxonomic Ranks of Aligned Names by Catalog. Names that were not aligned with a catalog are counted as NAs. So, the total number of unaligned names for a catalog will be listed in their NA row.
resolvedCatalogName resolvedRank count
col NA 56
col class 2
col family 9
col genus 14
col infraorder 1
col nanorder 1
col order 1
col parvorder 1
col phylum 3
col species 174
col subgenus 3
col suborder 1
col subspecies 28
col superorder 1
discoverlife NA 291
gbif NA 52
gbif class 2
gbif family 9
gbif genus 18
gbif order 1
gbif phylum 3
gbif species 178
gbif subspecies 29
itis NA 77
itis class 2
itis family 9
itis genus 14
itis order 3
itis phylum 3
itis species 151
itis subclass 1
itis suborder 3
itis subspecies 28
itis superorder 1
mdd NA 290
ncbi NA 74
ncbi class 2
ncbi family 9
ncbi genus 14
ncbi infraorder 2
ncbi order 2
ncbi phylum 3
ncbi species 169
ncbi subclass 1
ncbi suborder 2
ncbi subspecies 13
ncbi superorder 1
pbdb NA 137
pbdb class 2
pbdb family 4
pbdb genus 7
pbdb infraorder 1
pbdb order 4
pbdb phylum 2
pbdb species 130
pbdb suborder 1
pbdb subspecies 1
pbdb superorder 1
pbdb unranked clade 2
tpt NA 120
tpt family 2
tpt genus 7
tpt species 161
wfo NA 289
wfo genus 1
worms NA 191
worms class 2
worms family 6
worms genus 5
worms infraorder 1
worms order 2
worms phylum 3
worms species 75
worms subclass 1
worms suborder 3
worms subspecies 1
worms superorder 1
Name relationship types per catalog. Name relationship type “NONE” means that a name was not recognized by the associated catalog. “SAME_AS” indicates either a “HAS_ACCEPTED_NAME” or “SYNONYM_OF” name relationship type. We recognize that “SYNONYM_OF” encompasses many types of nomenclatural synonymies (ICZN 1999) (e.g., junior synonym, senior synonyms).
resolvedCatalogName relationName count
col HAS_ACCEPTED_NAME 295
col SYNONYM_OF 15
col NONE 58
discoverlife NONE 585
gbif HAS_ACCEPTED_NAME 299
gbif SYNONYM_OF 24
gbif NONE 54
itis HAS_ACCEPTED_NAME 270
itis SYNONYM_OF 16
itis NONE 79
mdd NONE 271
mdd HAS_ACCEPTED_NAME 87
mdd SYNONYM_OF 1
ncbi NONE 307
ncbi SAME_AS 272
ncbi SYNONYM_OF 7
pbdb HAS_ACCEPTED_NAME 197
pbdb SYNONYM_OF 14
pbdb NONE 152
tpt NONE 143
tpt HAS_ACCEPTED_NAME 226
tpt SYNONYM_OF 18
wfo SYNONYM_OF 1
wfo NONE 358
worms HAS_ACCEPTED_NAME 123
worms NONE 231
worms SYNONYM_OF 6
List of Available Name Alignment Reports
catalog name alignment results
col associated names alignments report in gzipped html, csv, and tsv)
ncbi associated names alignments report in gzipped html, csv, and tsv)
discoverlife associated names alignments report in gzipped html, csv, and tsv)
gbif associated names alignments report in gzipped html, csv, and tsv)
itis associated names alignments report in gzipped html, csv, and tsv)
wfo associated names alignments report in gzipped html, csv, and tsv)
mdd associated names alignments report in gzipped html, csv, and tsv)
tpt associated names alignments report in gzipped html, csv, and tsv)
pbdb associated names alignments report in gzipped html, csv, and tsv)
worms associated names alignments report in gzipped html, csv, and tsv)

Additional Reviews

Elton, Nomer, and other tools may have difficulties interpreting existing species interaction datasets. Or, they may misbehave, or otherwise show unexpected behavior. As part of the review process, detailed review notes are kept that document possibly misbehaving, or confused, review bots. An sample of review notes associated with this review can be found below.

First few lines in the review notes.
reviewDate reviewCommentType reviewComment
2025-04-10T13:08:44Z note found unresolved reference [11125]
2025-04-10T13:08:44Z note found unresolved reference [11174]
2025-04-10T13:08:44Z note found unresolved reference [11433]
2025-04-10T13:08:44Z note found unresolved reference [11498]

In addition, you can find the most frequently occurring notes in the table below.

Most frequently occurring review notes, if any.
reviewComment count
found unresolved reference [11125] 1
found unresolved reference [11174] 1
found unresolved reference [11433] 1
found unresolved reference [11498] 1

For additional information on review notes, please have a look at the first 500 Review Notes in html format or the download full gzipped csv or tsv archives.

GloBI Review Badge

As part of the review, a review badge is generated. This review badge can be included in webpages to indicate the review status of the dataset under review.

review review 💬 💬

Note that if the badge is green, no review notes were generated. If the badge is yellow, the review bots may need some help with interpreting the species interaction data.

GloBI Index Badge

If the dataset under review has been registered with GloBI, and has been succesfully indexed by GloBI, the GloBI Index Status Badge will turn green. This means that the dataset under review was indexed by GloBI and is available through GloBI services and derived data products.

Picture of a GloBI Index Badge

If you’d like to keep track of reviews or index status of the dataset under review, please visit GloBI’s dataset index 5 for badge examples.

Discussion

This review and archive provides a means of creating citable versions of datasets that change frequently. This may be useful for dataset managers, including natural history collection data managers, as a backup archive of a shared Darwin Core archive. It also serves as a means of creating a trackable citation for the dataset in an automated way, while also including some information about the contents of the dataset.

This review aims to provide a perspective on the dataset to aid in understanding of species interaction claims discovered. However, it is important to note that this review does not assess the quality of the dataset. Instead, it serves as an indication of the open-ness6 and FAIRness (Wilkinson et al. 2016; Trekels et al. 2023) of the dataset: to perform this review, the data was likely openly available, Findable, Accessible, Interoperable and Reusable. The current Open-FAIR assessment is qualitative, and a more quantitative approach can be implemented with specified measurement units.

This report also showcases the reuse of machine-actionable (meta)data, something highly recommended by the FAIR Data Principles (Wilkinson et al. 2016). Making (meta)data machine-actionable enables more precise procesing by computers, enabling even naive review bots like Nomer and Elton to interpret the data effectively. This capability is crucial for not just automating the generation of reports, but also for facilitating seamless data exchanges, promoting interoperability.

Acknowledgements

We thank the many humans that created us and those who created and maintained the data, software and other intellectual resources that were used for producing this review. In addition, we are grateful for the natural resources providing the basis for these human and bot activities. Also, thanks to https://github.com/zygoballus for helping improve the layout of the review tables.

Author contributions

Nomer was responsible for name alignments. Elton carried out dataset extraction, and generated the review notes. Preston tracked, versioned, and packaged, the dataset under review.

References

Elliott, Michael, Jorrit Poelen, Icaro Alzuru, Emilio Berti, and partha04patel. 2025. “Bio-Guoda/Preston: 0.10.5.” Zenodo. https://doi.org/10.5281/zenodo.14662206.
ICZN. 1999. “International Code of Zoological Nomenclature.” The International Trust for Zoological Nomenclature, London, UK. https://www.iczn.org/the-code/the-code-online/.
Kuhn, Tobias, and Michel Dumontier. 2014. “Trusty URIs: Verifiable, Immutable, and Permanent Digital Artifacts for Linked Data.” In The Semantic Web: Trends and Challenges, edited by Valentina Presutti, Claudia d’Amato, Fabien Gandon, Mathieu d’Aquin, Steffen Staab, and Anna Tordai, 395–410. Cham: Springer International Publishing.
Kuhn, Tobias, Jorrit Poelen, and Katrin Leinweber. 2025. “Globalbioticinteractions/Elton: 0.15.1.” Zenodo. https://doi.org/10.5281/zenodo.14927734.
Poelen, Jorrit H. (ed.). 2024. “Nomer Corpus of Taxonomic Resources Hash://Sha256/ B60c0d25a16ae77b24305782017b1a270b79b5d1746f832650 F2027ba536e276 Hash://Md5/17f1363a277ee0e4ecaf1b91c665e47e.” Zenodo. https://doi.org/10.5281/zenodo.12695629.
Poelen, Jorrit H., James D. Simons, and Chris J. Mungall. 2014. “Global Biotic Interactions: An Open Infrastructure to Share and Analyze Species-Interaction Datasets.” Ecological Informatics 24 (November): 148–59. https://doi.org/10.1016/j.ecoinf.2014.08.005.
Poelen, Jorrit, Katja Seltmann, and Daniel Mietchen. 2024. “Globalbioticinteractions/Globinizer: 0.4.0.” Zenodo. https://doi.org/10.5281/zenodo.10647565.
Salim, José Augusto, and Jorrit Poelen. 2025. “Globalbioticinteractions/Nomer: 0.5.15.” Zenodo. https://doi.org/10.5281/zenodo.14893840.
Trekels, Maarten, Debora Pignatari Drucker, José Augusto Salim, Jeff Ollerton, Jorrit Poelen, Filipi Miranda Soares, Max Rünzel, Muo Kasina, Quentin Groom, and Mariano Devoto. 2023. WorldFAIR Project (D10.1) Agriculture-related pollinator data standards use cases report.” Zenodo. https://doi.org/10.5281/zenodo.8176978.
Wilkinson, Mark D., Michel Dumontier, IJsbrand Jan Aalbersberg, Gabrielle Appleton, Myles Axton, Arie Baak, Niklas Blomberg, et al. 2016. “The FAIR Guiding Principles for Scientific Data Management and Stewardship.” Scientific Data 3 (1). https://doi.org/10.1038/sdata.2016.18.