A Review of Biotic Interactions and Taxon Names Found in globalbioticinteractions/mcz hash://md5/f0dd4a24369d5fd0104b440fb8d7465a

by Nomer, Elton and Preston, three naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

https://github.com/globalbioticinteractions/mcz/issues

2025-04-11

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/mcz, has fingerprint hash://md5/f0dd4a24369d5fd0104b440fb8d7465a, is 3.26GiB in size and contains 9,957 interaction with 9 unique types of associations (e.g., interactsWith) between 1,990 primary taxon (e.g., Gasterosteus aculeatus Linnaeus, 1758) and 2,863 associated taxon (e.g., ground). This report includes detailed summaries of interaction data, a taxonomic review from multiple catalogs, and an archived version of the dataset from which the reviews are derived.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:

Museum of Comparative Zoology, Harvard University - Version 162.465 http://digir.mcz.harvard.edu/ipt/archive.do?r=mczbase 2025-04-05T01:17:56.929Z hash://md5/f0dd4a24369d5fd0104b440fb8d7465a

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/mcz 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. 3.26GiB) under review 
elton pull globalbioticinteractions/mcz

# generate review notes
elton review globalbioticinteractions/mcz\
 > review.tsv

# export indexed interaction records
elton interactions globalbioticinteractions/mcz\
 > interactions.tsv

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/mcz\
 | 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/mcz, has fingerprint hash://md5/f0dd4a24369d5fd0104b440fb8d7465a, is 3.26GiB in size and contains 9,957 interaction with 9 unique types of associations (e.g., interactsWith) between 1,990 primary taxon (e.g., Gasterosteus aculeatus Linnaeus, 1758) and 2,863 associated taxon (e.g., ground).

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
Lithobates catesbeianus (Shaw, 1802) eats MCZ:Herp:R-200746 http://mczbase.mcz.harvard.edu/guid/MCZ:Herp:A-109076
Lithobates catesbeianus (Shaw, 1802) eats MCZ:Herp:R-200745 http://mczbase.mcz.harvard.edu/guid/MCZ:Herp:A-109076
Pyxicephalus adspersus interactsWith duplicates of MCZ-A-20225 - 20228 are given new catalog numbers MCZ-A-154068 - 154070 02OCT2023 Tsuyoshi Takahashi http://mczbase.mcz.harvard.edu/guid/MCZ:Herp:A-20227
Lissotriton vulgaris vulgaris (Linnaeus, 1758) interactsWith Ichthyosaura alpestris alpestris (Laurenti, 1768) http://mczbase.mcz.harvard.edu/guid/MCZ:Herp:A-4724
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
interactsWith 5743
adjacentTo 2701
hasHost 764
parasiteOf 690
eats 31
hasParasite 10
visits 9
eatenBy 8
killedBy 1
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Gasterosteus aculeatus Linnaeus, 1758 1032
Perdita sp. Smith, 1853 536
Xylocopa darwini Cockerell, 1926 482
Camallanus Railliet & Henry, 1915 338
Subdoluseps bowringii (Günther, 1864) (Günther, 1864) 311
Symbion americanus Obst, Funch & Kristensen, 2006 208
Camponotus sp. Mayr, 1861 197
Pheidole sp. Westwood, 1839 184
Cephalochlamys Blanchard, 1908 169
Eutropis multifasciata multifasciata (Kuhl, 1820) 114
Andrena hirticincta Provancher, 1888 102
Hepialidae Stephens, 1829 94
Bdelloura candida (Girard, 1850) 65
Andrena sp. Fabricius 1775 63
Pontoniinae 60
Formicidae Latreille, 1809 57
Pheidole Westwood, 1839 54
Hylaeus modestus Say, 1837 54
Globicephala melaena (Traill, 1809) 49
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
ground 437
Mites 228
Ceanothus 176
Stylopized 172
Heterotheca 141
ex rotten log 131
Solidago 119
Ophiocordyceps 94
ex dead twig 89
under 88
low vegetation 86
Mentzelia 83
Haplopappus 80
tree 60
gilled mushrooms 56
vegetation 49
Chamaesaracha 46
trout 44
Trout 44
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Xylocopa darwini Cockerell, 1926 interactsWith Mites 167
Perdita sp. Smith, 1853 interactsWith Heterotheca 136
Hepialidae Stephens, 1829 interactsWith Ophiocordyceps 94
Andrena hirticincta Provancher, 1888 interactsWith Stylopized 90
Perdita sp. Smith, 1853 interactsWith Mentzelia 83
Perdita sp. Smith, 1853 interactsWith Haplopappus 77
Perdita sp. Smith, 1853 interactsWith Chamaesaracha 46
Camponotus sp. Mayr, 1861 adjacentTo ground 45
Gasterosteus aculeatus Linnaeus, 1758 interactsWith trout 44
Gasterosteus aculeatus Linnaeus, 1758 interactsWith Trout 44
Globicephala melaena (Traill, 1809) interactsWith Globicephala melaena (Traill, 1809) 40
Lapethus newtoni Slipinski adjacentTo gilled mushrooms 40
Pseudopanurgus pauper (Cresson, 1878) interactsWith Ceanothus 40
Gasterosteus aculeatus Linnaeus, 1758 interactsWith sculpin 39
Trigona ceophloei Schwarz hasHost Ex stomach of Ceoploeus lineatus 38
Perdita sp. Smith, 1853 interactsWith Solidago 38
Xylocopa darwini Cockerell, 1926 interactsWith mites 38
Crematogaster laeviuscula Mayr, 1870 adjacentTo cotton wood tree 37
Gasterosteus aculeatus Linnaeus, 1758 interactsWith Salmonids 35

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 Plantae Plantae Animalia->Plantae Animalia->Plantae
interactions Andrenidae Andrenidae Salicaceae Salicaceae Andrenidae->Salicaceae Apidae Apidae Asteraceae Asteraceae Apidae->Asteraceae Polygonaceae Polygonaceae Apidae->Polygonaceae Chrysogorgiidae Chrysogorgiidae Cladorhizidae Cladorhizidae Chrysogorgiidae->Cladorhizidae Cladorhizidae->Chrysogorgiidae Delphinidae Delphinidae Delphinidae->Delphinidae Eulimidae Eulimidae Cucumariidae Cucumariidae Eulimidae->Cucumariidae Eulophidae Eulophidae Fabaceae Fabaceae Eulophidae->Fabaceae Gonyleptidae Gonyleptidae Araucariaceae Araucariaceae Gonyleptidae->Araucariaceae Metridiidae Metridiidae Microcionidae Microcionidae Metridiidae->Microcionidae Neopilionidae Neopilionidae Neopilionidae->Neopilionidae Salticidae Salticidae Pinaceae Pinaceae Salticidae->Pinaceae Thomisidae Thomisidae Apiaceae Apiaceae Thomisidae->Apiaceae Tretodictyidae Tretodictyidae Tretodictyidae->Tretodictyidae

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
Triungulin NONE col Triungulin
Pungitius HAS_ACCEPTED_NAME col Pungitius
Salmonids NONE col Salmonids
High plants NONE col High plants
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 1581
col class 5
col family 65
col genus 377
col infraspecific name 1
col kingdom 1
col order 6
col phylum 2
col section 1
col species 1494
col subfamily 5
col subgenus 6
col suborder 1
col subspecies 53
col tribe 1
col variety 7
discoverlife NA 3239
discoverlife species 351
gbif NA 1315
gbif class 5
gbif family 69
gbif genus 418
gbif kingdom 2
gbif order 6
gbif phylum 2
gbif species 1717
gbif subspecies 65
gbif variety 12
itis NA 1792
itis class 5
itis family 64
itis genus 352
itis kingdom 1
itis order 6
itis phylum 2
itis species 1301
itis subclass 1
itis subfamily 4
itis suborder 1
itis subspecies 50
itis tribe 1
itis variety 12
mdd NA 3589
ncbi NA 1920
ncbi class 6
ncbi family 62
ncbi genus 369
ncbi infraorder 1
ncbi order 6
ncbi phylum 2
ncbi species 1200
ncbi subfamily 4
ncbi subgenus 10
ncbi subspecies 17
ncbi tribe 1
ncbi varietas 2
pbdb NA 3191
pbdb class 7
pbdb family 55
pbdb genus 214
pbdb informal 1
pbdb kingdom 1
pbdb order 6
pbdb phylum 2
pbdb species 110
pbdb subclass 1
pbdb subfamily 2
pbdb suborder 1
pbdb tribe 1
pbdb unranked clade 1
tpt NA 3532
tpt genus 3
tpt species 54
wfo NA 3250
wfo family 4
wfo genus 130
wfo phylum 1
wfo species 194
wfo subspecies 5
wfo variety 8
worms NA 2872
worms class 5
worms family 54
worms genus 239
worms kingdom 1
worms order 6
worms phylum 2
worms species 403
worms subclass 1
worms subfamily 2
worms subgenus 1
worms suborder 1
worms subspecies 4
worms variety 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 NONE 2665
col HAS_ACCEPTED_NAME 1965
col SYNONYM_OF 406
discoverlife NONE 4445
discoverlife HAS_ACCEPTED_NAME 331
discoverlife SYNONYM_OF 114
discoverlife HOMONYM_OF 24
gbif NONE 2390
gbif HAS_ACCEPTED_NAME 2456
gbif SYNONYM_OF 609
itis NONE 2880
itis HAS_ACCEPTED_NAME 1792
itis SYNONYM_OF 152
mdd NONE 4758
mdd HAS_ACCEPTED_NAME 15
ncbi NONE 3029
ncbi SAME_AS 1717
ncbi SYNONYM_OF 76
ncbi COMMON_NAME_OF 3
pbdb NONE 4309
pbdb HAS_ACCEPTED_NAME 462
pbdb SYNONYM_OF 40
tpt NONE 4710
tpt HAS_ACCEPTED_NAME 65
tpt SYNONYM_OF 1
wfo NONE 4400
wfo SYNONYM_OF 100
wfo HAS_ACCEPTED_NAME 312
wfo HAS_UNCHECKED_NAME 55
worms NONE 3995
worms HAS_ACCEPTED_NAME 745
worms SYNONYM_OF 130
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
2025-04-11T12:48:38Z note found unresolved reference [MCZ:Cryo:14052]
2025-04-11T12:48:38Z note found unresolved reference [MCZ:Cryo:14068]
2025-04-11T12:48:38Z note found unresolved reference [MCZ:Cryo:14075]
2025-04-11T12:48:38Z note found unresolved reference [MCZ:Cryo:14076]

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 [MCZ:Cryo:14052] 1
found unresolved reference [MCZ:Cryo:14068] 1
found unresolved reference [MCZ:Cryo:14075] 1
found unresolved reference [MCZ:Cryo:14076] 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

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