Versioned Archive and Review of Biotic Interactions and Taxon Names Found within globalbioticinteractions/vertnet hash://md5/6c194df8ddb37844f7b4f1258c81d93d

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/vertnet, has fingerprint hash://md5/6c194df8ddb37844f7b4f1258c81d93d, is 2.58GiB in size and contains 221,606 interactions with 10 unique types of associations (e.g., parasiteOf) between 8,216 primary taxa (e.g., Arthropoda) and 30,238 associated taxa (e.g., Acari). This report includes detailed summaries of interaction data, a taxonomic review from multiple catalogs, and an archived version of the dataset from which the reviews are derived.

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 :

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/vertnet 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.

Results

Tools used in this review process
tool name	version
preston	0.10.1
elton	0.15.13
nomer	0.5.17
globinizer	0.4.0
mlr	6.0.0
jq	1.6
yq	4.25.3
pandoc	3.1.6.1
duckdb	1.3.1

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

Files

Archived Dataset

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 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.parquet	species interaction claims indexed from the dataset under review in Apache Parquet 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.parquet	taxonomic names found in the dataset under review in Apache Parquet 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-col.parquet	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 Apache Parquet 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-discoverlife.parquet	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 Apache Parquet 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-gbif.parquet	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 Apache Parquet 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-itis.parquet	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 Apache Parquet 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-mdd.parquet	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 Apache Parquet 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-ncbi.parquet	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 Apache Parquet 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-pbdb.parquet	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 Apache Parquet 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-tpt.parquet	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 Apache Parquet 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-wfo.parquet	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 Apache Parquet 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-resolved-worms.parquet	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 Apache Parquet 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

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

Biotic Interactions

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/vertnet, has fingerprint hash://md5/6c194df8ddb37844f7b4f1258c81d93d, is 2.58GiB in size and contains 221,606 interactions with 10 unique types of associations (e.g., parasiteOf) between 8,216 primary taxa (e.g., Arthropoda) and 30,238 associated taxa (e.g., Acari).

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

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.

Sample of Indexed Interaction Claims
sourceTaxonName	interactionTypeName	targetTaxonName	referenceCitation
Leptotrombidium peromysci	parasiteOf	Peromyscus leucopus	https://arctos.database.museum/guid/UNCG:Para:8
Androlaelaps fahrenholzi	interactsWith	Hoplopleura hirsuta	https://arctos.database.museum/guid/UNCG:Para:114
Androlaelaps fahrenholzi	parasiteOf	Sigmodon hispidus	https://arctos.database.museum/guid/UNCG:Para:114
Hoplopleura hirsuta	interactsWith	Androlaelaps fahrenholzi	https://arctos.database.museum/guid/UNCG:Para:113

Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName	count
parasiteOf	70860
hasParasite	69537
interactsWith	40413
adjacentTo	24128
coOccursWith	9627
hasHost	4546
killedBy	2111
eats	330
eatenBy	50
visits	4

Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName	count
Arthropoda	14623
Acari	7252
Siphonaptera	6499
Peromyscus maniculatus	6186
Myodes rutilus	5969
Dipodomys merriami	5488
Peromyscus leucopus	3336
Cestoda	2938
Myodes gapperi	2575
Bombus melanopygus	2492
Nematoda	2314
Peromyscus keeni	2265
Microtus pennsylvanicus	2144
Dipodomys ordii	2133
Ochotona princeps	2115
Sorex cinereus	1913
Taenia	1869
Microtus oeconomus	1850
Phthiraptera	1811

Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName	count
Acari	10542
Siphonaptera	8977
Arthropoda	8700
Myodes rutilus	6265
Ixodida	3070
Peromyscus keeni	2852
Dipodomys merriami	2734
Phthiraptera	2662
Peromyscus maniculatus	2392
Microtus oeconomus	2290
Nematoda	2196
Sorex cinereus	2100
Chamerion angustifolium	1857
Cestoda	1600
Mastophorus dipodomis	1563
Microtus pennsylvanicus	1445
Heteromyoxyuris deserti	1432
Hoplopleura arboricola	1310
Chamerion	1294

Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName	interactionTypeName	targetTaxonName	count
Arthropoda	parasiteOf	Myodes rutilus	3275
Arthropoda	parasiteOf	Peromyscus keeni	2166
Peromyscus maniculatus	hasParasite	Siphonaptera	1832
Myodes rutilus	hasParasite	Arthropoda	1693
Arthropoda	parasiteOf	Microtus oeconomus	1626
Arthropoda	parasiteOf	Sorex cinereus	1099
Peromyscus keeni	hasParasite	Arthropoda	1083
Siphonaptera	parasiteOf	Peromyscus maniculatus	982
Dipodomys merriami	hasParasite	Mastophorus dipodomis	882
Arthropoda	parasiteOf	Sorex monticolus	867
Dipodomys merriami	hasParasite	Eimeria chobotari	858
Microtus oeconomus	hasParasite	Arthropoda	816
Myodes rutilus	hasParasite	Polyplax borealis	813
Ochotona princeps	hasParasite	Ctenophyllus armatus	765
Myodes rutilus	hasParasite	Acari	689
Dipodomys merriami	hasParasite	Pterygodermatites dipodomis	664
Polyplax borealis	parasiteOf	Myodes rutilus	663
Bombus melanopygus	adjacentTo	clover	636
Arthropoda	parasiteOf	Microtus pennsylvanicus	613

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.

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.

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

Sample of Name Alignments
providedName	relationName	resolvedCatalogName	resolvedName
Slope	NONE	col	Slope
Rock	NONE	col	Rock
Diameter rock edge	NONE	col	Diameter rock edge
Diameter mossy rock	NONE	col	Diameter mossy rock

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	9037
col	class	15
col	family	178
col	genus	833
col	infraorder	1
col	kingdom	3
col	nanorder	2
col	order	34
col	parvorder	1
col	phylum	7
col	section	1
col	species	5227
col	subclass	4
col	subfamily	5
col	subgenus	21
col	suborder	1
col	subphylum	1
col	subspecies	589
col	superfamily	14
col	superorder	2
col	tribe	2
col	unranked	1
col	variety	33
discoverlife	NA	15854
discoverlife	species	53
gbif	NA	8255
gbif	class	17
gbif	family	191
gbif	form	17
gbif	genus	964
gbif	kingdom	3
gbif	order	30
gbif	phylum	8
gbif	species	5801
gbif	subspecies	708
gbif	variety	137
itis	NA	9398
itis	class	16
itis	division	2
itis	family	169
itis	genus	717
itis	infraorder	1
itis	kingdom	3
itis	order	39
itis	phylum	8
itis	species	4778
itis	subclass	9
itis	subfamily	9
itis	subgenus	1
itis	suborder	7
itis	subphylum	3
itis	subspecies	668
itis	superfamily	7
itis	superorder	3
itis	tribe	1
itis	variety	81
mdd	NA	15906
ncbi	NA	9395
ncbi	clade	2
ncbi	class	17
ncbi	cohort	1
ncbi	family	184
ncbi	genus	865
ncbi	infraorder	3
ncbi	kingdom	2
ncbi	order	34
ncbi	phylum	8
ncbi	species	5122
ncbi	subclass	9
ncbi	subfamily	15
ncbi	subgenus	18
ncbi	suborder	6
ncbi	subphylum	2
ncbi	subspecies	213
ncbi	superfamily	15
ncbi	superorder	3
ncbi	tribe	1
ncbi	varietas	14
pbdb	NA	14489
pbdb	class	18
pbdb	family	130
pbdb	genus	339
pbdb	informal	1
pbdb	infraclass	1
pbdb	kingdom	3
pbdb	order	32
pbdb	phylum	9
pbdb	species	840
pbdb	subclass	3
pbdb	subfamily	18
pbdb	suborder	8
pbdb	subspecies	11
pbdb	subtribe	1
pbdb	superclass	1
pbdb	superfamily	9
pbdb	superorder	3
pbdb	superphylum	1
pbdb	tribe	2
pbdb	unranked clade	8
tpt	NA	14630
tpt	family	3
tpt	genus	63
tpt	order	2
tpt	species	1208
wfo	NA	13403
wfo	family	11
wfo	genus	308
wfo	phylum	1
wfo	species	2113
wfo	subsection	1
wfo	subspecies	73
wfo	variety	26
worms	NA	13530
worms	class	16
worms	family	161
worms	genus	528
worms	infraorder	1
worms	kingdom	3
worms	order	35
worms	phylum	6
worms	phylum (division)	1
worms	species	1556
worms	subclass	7
worms	subfamily	4
worms	subgenus	1
worms	suborder	5
worms	subphylum	2
worms	subspecies	47
worms	superfamily	12
worms	superorder	2
worms	variety	11

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	28972
col	HAS_ACCEPTED_NAME	11624
col	SYNONYM_OF	2882
discoverlife	NONE	43929
discoverlife	HAS_ACCEPTED_NAME	106
discoverlife	SYNONYM_OF	24
discoverlife	HOMONYM_OF	10
gbif	NONE	27768
gbif	HAS_ACCEPTED_NAME	14260
gbif	SYNONYM_OF	4887
itis	NONE	29736
itis	HAS_ACCEPTED_NAME	10876
itis	SYNONYM_OF	1656
mdd	NONE	40106
mdd	HAS_ACCEPTED_NAME	1751
mdd	SYNONYM_OF	17
ncbi	NONE	31438
ncbi	SAME_AS	11702
ncbi	SYNONYM_OF	1009
ncbi	COMMON_NAME_OF	12
pbdb	NONE	38102
pbdb	HAS_ACCEPTED_NAME	3688
pbdb	SYNONYM_OF	285
tpt	NONE	38182
tpt	HAS_ACCEPTED_NAME	3765
tpt	SYNONYM_OF	217
wfo	NONE	37495
wfo	SYNONYM_OF	1117
wfo	HAS_ACCEPTED_NAME	3754
wfo	HAS_UNCHECKED_NAME	406
worms	NONE	37319
worms	HAS_ACCEPTED_NAME	4383
worms	SYNONYM_OF	641

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)

First few lines in the review notes.
reviewDate	reviewCommentType	reviewComment
2025-08-20T20:47:57Z	note	found unresolved reference [008f0ec3-68fd-4051-b53e-13b594a29545]
2025-08-20T20:47:57Z	note	found unresolved reference [00b8b626-b09e-4bc8-a2d2-7235f7382605]
2025-08-20T20:47:57Z	note	found unresolved reference [010ee0ec-986c-4b11-a2a6-03a1b048f205]
2025-08-20T20:47:57Z	note	found unresolved reference [0295a4c0-1227-4520-b786-34793eec7e1b]

Most frequently occurring review notes, if any.
reviewComment	count
found unresolved reference [008f0ec3-68fd-4051-b53e-13b594a29545]	1
found unresolved reference [00b8b626-b09e-4bc8-a2d2-7235f7382605]	1
found unresolved reference [010ee0ec-986c-4b11-a2a6-03a1b048f205]	1
found unresolved reference [0295a4c0-1227-4520-b786-34793eec7e1b]	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.

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.

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.

Note that you have to first get the data (e.g., via elton pull globalbioticinteractions/vertnet) before being able to generate reviews (e.g., elton review globalbioticinteractions/vertnet), extract interaction claims (e.g., elton interactions globalbioticinteractions/vertnet), or list taxonomic names (e.g., elton names globalbioticinteractions/vertnet)↩︎
Disclaimer: The results in this review should be considered friendly, yet naive, notes from an unsophisticated robot. Please keep that in mind when considering the review results.↩︎
Up-to-date status of the GloBI Review Badge can be retrieved from the GloBI Review Depot ↩︎
Up-to-date status of the GloBI Index Badge can be retrieved from GloBI’s API ↩︎
At time of writing (2025-08-21) the version of the GloBI dataset index was available at https://globalbioticinteractions.org/datasets ↩︎
According to http://opendefinition.org/: “Open data is data that can be freely used, re-used and redistributed by anyone - subject only, at most, to the requirement to attribute and sharealike.”↩︎