Versioned Archive and Review of Biotic Interactions and Taxon Names Found within globalbioticinteractions/msb-para hash://md5/263dc01fb9878a15e9a5ee0660d6ba78

by Nomer, Elton and Preston, three naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

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

2025-05-21

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/msb-para, has fingerprint hash://md5/263dc01fb9878a15e9a5ee0660d6ba78, is 3.78GiB in size and contains 57,925 interaction with 4 unique types of associations (e.g., parasiteOf) between 980 primary taxa (e.g., Acari) and 33,220 associated taxon (e.g., Myodes rutilus). This report includes detailed summaries of interaction data, a taxonomic review from multiple catalogs, and an archived version of the dataset from which the reviews are derived.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:

MSB Parasite Collection (Arctos) https://ipt.vertnet.org/archive.do?r=msb_para 2025-05-17T01:48:05.443Z hash://md5/263dc01fb9878a15e9a5ee0660d6ba78

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/msb-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. 3.78GiB) under review 
elton pull globalbioticinteractions/msb-para

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

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

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/msb-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 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/msb-para, has fingerprint hash://md5/263dc01fb9878a15e9a5ee0660d6ba78, is 3.78GiB in size and contains 57,925 interaction with 4 unique types of associations (e.g., parasiteOf) between 980 primary taxa (e.g., Acari) and 33,220 associated taxon (e.g., Myodes rutilus).

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
Trichinella parasiteOf http://arctos.database.museum/guid/MSB:Host:14482 https://arctos.database.museum/guid/MSB:Para:17926
Acari parasiteOf http://arctos.database.museum/guid/MSB:Mamm:351846 https://arctos.database.museum/guid/MSB:Para:50961
Acari parasiteOf MSB:Mamm:351846 https://arctos.database.museum/guid/MSB:Para:50961
Acari parasiteOf http://arctos.database.museum/guid/MSB:Mamm:351943 https://arctos.database.museum/guid/MSB:Para:50837
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
parasiteOf 53717
coOccursWith 4131
interactsWith 50
hasParasite 27
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Acari 7009
Siphonaptera 5953
Cestoda 2823
Taenia 1869
Nematoda 1868
Toxascaris 1750
Phthiraptera 1736
Ixodida 1701
Echinococcus multilocularis 1532
Polyplax borealis 1485
Echinococcus 857
Arthropoda 844
Mastophorus dipodomis 787
Heteromyoxyuris deserti 726
Hoplopleura acanthopus 704
Uncinaria 685
Hoplopleura arboricola 665
Hoplopleura 657
Trematoda 565
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
Myodes rutilus 1631
Vulpes lagopus 722
Sorex cinereus 615
Microtus oeconomus 373
Microtus pennsylvanicus 209
Tamiasciurus hudsonicus 178
Microtus miurus 173
Urocitellus parryii 125
Myodes rufocanus 90
Sorex monticolus 90
Synaptomys borealis 84
Peromyscus keeni 74
Sorex tundrensis 61
http://arctos.database.museum/guid/MSB:Herp:107081 52
Ochotona collaris 49
Microtus xanthognathus 46
http://arctos.database.museum/guid/MSB:Herp:107086 45
http://arctos.database.museum/guid/MSB:Herp:105031 36
Myodes gapperi 27
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Polyplax borealis parasiteOf Myodes rutilus 513
Acari parasiteOf Sorex cinereus 417
Taenia parasiteOf Vulpes lagopus 227
Toxascaris parasiteOf Vulpes lagopus 217
Amalaraeus dissimilis parasiteOf Myodes rutilus 207
Echinococcus multilocularis parasiteOf Vulpes lagopus 150
Hoplopleura parasiteOf Myodes rutilus 120
Uncinaria parasiteOf Vulpes lagopus 97
Orchopeas caedens parasiteOf Tamiasciurus hudsonicus 92
Megabothris calcarifer parasiteOf Myodes rutilus 84
Cestoda parasiteOf Myodes rutilus 83
Ixodes angustus parasiteOf Sorex cinereus 80
Megabothris calcarifer parasiteOf Microtus oeconomus 78
Catallagia dacenkoi parasiteOf Myodes rutilus 77
Corrodopsylla curvata parasiteOf Sorex cinereus 77
Peromyscopsylla ostsibirica parasiteOf Microtus oeconomus 71
Hoplopleura acanthopus parasiteOf Microtus miurus 67
Oropsylla alaskensis parasiteOf Urocitellus parryii 66
Hoplopleura acanthopus parasiteOf Microtus pennsylvanicus 59

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 Plantae Plantae Plantae->Animalia
interactions Ancylostomatidae Ancylostomatidae Canidae Canidae Ancylostomatidae->Canidae Ascarididae Ascarididae Ascarididae->Canidae Felidae Felidae Ascarididae->Felidae Asteraceae Asteraceae Cricetidae Cricetidae Asteraceae->Cricetidae Cricetidae->Cricetidae Ceratophyllidae Ceratophyllidae Ceratophyllidae->Cricetidae Dipodidae Dipodidae Ceratophyllidae->Dipodidae Mustelidae Mustelidae Ceratophyllidae->Mustelidae Ochotonidae Ochotonidae Ceratophyllidae->Ochotonidae Otariidae Otariidae Ceratophyllidae->Otariidae Phocidae Phocidae Ceratophyllidae->Phocidae Sciuridae Sciuridae Ceratophyllidae->Sciuridae Soricidae Soricidae Ceratophyllidae->Soricidae Ctenophthalmidae Ctenophthalmidae Ctenophthalmidae->Cricetidae Ctenophthalmidae->Sciuridae Ctenophthalmidae->Soricidae Talpidae Talpidae Ctenophthalmidae->Talpidae Dilepididae Dilepididae Alcidae Alcidae Dilepididae->Alcidae Diphyllobothriidae Diphyllobothriidae Diphyllobothriidae->Canidae Heligmosomidae Heligmosomidae Heligmosomidae->Cricetidae Heteroxynematidae Heteroxynematidae Heteroxynematidae->Sciuridae Hoplopleuridae Hoplopleuridae Hoplopleuridae->Cricetidae Hoplopleuridae->Ochotonidae Hoplopleuridae->Sciuridae Hoplopleuridae->Soricidae Hystrichopsyllidae Hystrichopsyllidae Hystrichopsyllidae->Cricetidae Hystrichopsyllidae->Mustelidae Hystrichopsyllidae->Soricidae Hystrichopsyllidae->Talpidae Ixodidae Ixodidae Ixodidae->Cricetidae Ixodidae->Sciuridae Ixodidae->Soricidae Leiodidae Leiodidae Leiodidae->Soricidae Leptopsyllidae Leptopsyllidae Leptopsyllidae->Cricetidae Leptopsyllidae->Ochotonidae Leptopsyllidae->Sciuridae Leptopsyllidae->Soricidae Oxyuridae Oxyuridae Oxyuridae->Cricetidae Oxyuridae->Sciuridae Oxyuridae->Oxyuridae Trichuridae Trichuridae Oxyuridae->Trichuridae Trichuridae->Oxyuridae Polyplacidae Polyplacidae Polyplacidae->Cricetidae Polyplacidae->Mustelidae Polyplacidae->Ochotonidae Polyplacidae->Sciuridae Polyplacidae->Soricidae Taeniidae Taeniidae Taeniidae->Canidae Taeniidae->Felidae Taeniidae->Cricetidae Trichodectidae Trichodectidae Trichodectidae->Cricetidae Trichostrongylidae Trichostrongylidae Trichostrongylidae->Cricetidae Trombiculidae Trombiculidae Trombiculidae->Cricetidae Trombiculidae->Sciuridae

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
A25KN NONE col A25KN
A25KT NONE col A25KT
A25KU NONE col A25KU
A25KW NONE col A25KW
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 1045
col class 4
col family 54
col genus 191
col infraorder 1
col nanorder 2
col order 16
col parvorder 1
col phylum 4
col species 378
col subclass 1
col subgenus 5
col suborder 1
col subspecies 18
col superfamily 9
col unranked 1
discoverlife NA 1723
gbif NA 888
gbif class 4
gbif family 62
gbif genus 251
gbif order 12
gbif phylum 4
gbif species 480
gbif subspecies 26
itis NA 1301
itis class 4
itis family 47
itis genus 152
itis order 21
itis phylum 5
itis species 180
itis subclass 5
itis subfamily 2
itis subgenus 1
itis suborder 3
itis subspecies 5
itis superfamily 2
mdd NA 1722
ncbi NA 990
ncbi class 3
ncbi family 60
ncbi genus 224
ncbi infraorder 2
ncbi order 16
ncbi phylum 5
ncbi species 400
ncbi subclass 5
ncbi subgenus 1
ncbi suborder 4
ncbi subspecies 7
ncbi superfamily 9
pbdb NA 1624
pbdb class 4
pbdb family 10
pbdb genus 15
pbdb order 10
pbdb phylum 4
pbdb species 49
pbdb subclass 1
pbdb suborder 4
pbdb subtribe 1
pbdb superfamily 3
pbdb unranked clade 2
tpt NA 1524
tpt family 1
tpt genus 9
tpt species 188
wfo NA 1715
wfo genus 7
worms NA 1171
worms class 3
worms family 53
worms genus 187
worms infraorder 1
worms order 17
worms phylum 4
worms species 267
worms subclass 4
worms subgenus 1
worms suborder 3
worms subphylum 1
worms subspecies 2
worms superfamily 10
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 31641
col HAS_ACCEPTED_NAME 660
col SYNONYM_OF 99
discoverlife NONE 34207
gbif NONE 31487
gbif HAS_ACCEPTED_NAME 879
gbif SYNONYM_OF 144
itis NONE 31907
itis HAS_ACCEPTED_NAME 416
itis SYNONYM_OF 45
mdd NONE 32285
mdd HAS_ACCEPTED_NAME 54
ncbi NONE 33453
ncbi SAME_AS 729
ncbi SYNONYM_OF 32
pbdb NONE 32235
pbdb HAS_ACCEPTED_NAME 100
pbdb SYNONYM_OF 17
tpt NONE 32136
tpt HAS_ACCEPTED_NAME 219
tpt SYNONYM_OF 33
wfo NONE 32332
wfo SYNONYM_OF 4
wfo HAS_UNCHECKED_NAME 2
wfo HAS_ACCEPTED_NAME 3
worms NONE 31772
worms HAS_ACCEPTED_NAME 523
worms SYNONYM_OF 71
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
2025-05-21T09:56:58Z note found unresolved reference [060980]
2025-05-21T09:56:58Z note found unresolved reference [070456]
2025-05-21T09:56:58Z note found unresolved reference [077368]
2025-05-21T09:56:58Z note found unresolved reference [077679]

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 [060980] 1
found unresolved reference [070456] 1
found unresolved reference [077368] 1
found unresolved reference [077679] 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.