A Review of Biotic Interactions and Taxon Names Found in globalbioticinteractions/ummz-ummzi hash://md5/0045c3c4e8d81a2c718dc1f16c21e8db

by Nomer, Elton and Preston, three naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

https://github.com/globalbioticinteractions/ummz-ummzi/issues

2025-04-01

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 process of such an openly accessible digital interactions dataset of known origin, and discuss its outcome. The dataset under review, named globalbioticinteractions/ummz-ummzi, has fingerprint hash://md5/0045c3c4e8d81a2c718dc1f16c21e8db, is 36.1MiB in size and contains 54,786 interaction with 2 unique types of associations (e.g., interactsWith) between 1,889 primary taxon (e.g., Proctophyllodes) and 4,218 associated taxon (e.g., Mammalia Chiroptera Vespertilionidae Myotis velifer). The report includes detailed summaries of interactions data as well as a taxonomic review from multiple catalogs.

Introduction

Data Review

Data review can be a time consuming process, especially when done manually. This review report aims to help facilitate data review of species interaction claims made in datasets registered with Global Biotic Interactions (Poelen, Simons, and Mungall 2014). The review includes summary statistics of, and observations about, the dataset under review:

University of Michigan Museum of Zoology, Division of Insects https://github.com/globalbioticinteractions/ummz-ummzi/archive/0f20ed99288f6668fb894b69b98c01658c08debe.zip 2025-03-29T05:50:30.790Z hash://md5/0045c3c4e8d81a2c718dc1f16c21e8db

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/ummz-ummzi 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) 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
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. 36.1MiB) under review 
elton pull globalbioticinteractions/ummz-ummzi

# generate review notes
elton review globalbioticinteractions/ummz-ummzi\
 > review.tsv

# export indexed interaction records
elton interactions globalbioticinteractions/ummz-ummzi\
 > interactions.tsv

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/ummz-ummzi\
 | 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 recent copy of the full review script at check-data.sh.

Results

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

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/ummz-ummzi, has fingerprint hash://md5/0045c3c4e8d81a2c718dc1f16c21e8db, is 36.1MiB in size and contains 54,786 interaction with 2 unique types of associations (e.g., interactsWith) between 1,889 primary taxon (e.g., Proctophyllodes) and 4,218 associated taxon (e.g., Mammalia Chiroptera Vespertilionidae Myotis velifer).

An exhaustive list of indexed interaction claims can be found in csv and tsv archives. To facilitate discovery, the first 500 claims available on the html page at indexed-interactions.html are shown below.

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

Sample of Indexed Interaction Claims
sourceTaxonName interactionTypeName targetTaxonName referenceCitation
Agathis pumila interactsWith Coleophoridae Coleophora laricella 53814451-56ee-4222-a6a0-ea61b4789e2c
Agathis pumila interactsWith Coleophoridae Coleophora laricella afab9dee-1270-4793-8e89-16b1ef20c24e
Agathis pumila interactsWith Coleophoridae Coleophora laricella caed85f4-b30c-45b9-ae01-4bb8765a878d
Agathis pumila interactsWith Coleophoridae Coleophora laricella a3cbebba-acae-4b91-9487-9a7d74042b9b
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
interactsWith 54785
adjacentTo 1
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Proctophyllodes 3206
Chiroptoglyphus americanus 1641
Macronyssus crosbyi 1553
Proterothrix 1170
Proctophyllodes polyxenus 925
Macronyssus unidens 882
Acari 671
Pterodectes 625
Freyana anatina 597
Trouessartia trouessarti 552
Amerodectes 498
Alloptellus coniventris 489
Freyana largifolia 486
Prolistrophorus bidentatus 478
Proctophyllodes spini 471
Eustathia cultrifera 457
Freyana nyrocae 441
Trouessartia lonchurae 411
Pterolichus obtusus 392
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
Mammalia Chiroptera Vespertilionidae Myotis velifer 3929
Aves Passeriformes Acrocephalidae Acrocephalus arundinaceus 800
Aves Passeriformes Icteridae Quiscalus quiscula 438
Aves Suliformes Fregatidae Fregata ariel ariel 437
Aves Passeriformes Turdidae Turdus migratorius 363
Aves Galliformes Phasianidae Gallus gallus domesticus 359
Aves Passeriformes Fringillidae Spinus tristis 345
Aves Passeriformes Cardinalidae Pheucticus ludovicianus 309
Aves Passeriformes Parulidae Seiurus aurocapilla 297
Salix 271
Aves Apodiformes Apodidae Chaetura pelagica 267
Aves Apodiformes Apodidae Apus apus apus 267
Aves Passeriformes Fringillidae Haemorhous mexicanus 263
Aves Passeriformes Bombycillidae Bombycilla cedrorum 253
Mammalia Rodentia Cricetidae Akodon aerosus 244
Aves Strigiformes Strigidae Bubo virginianus 223
Apodiformes Apodidae Collocalia C. esculenta 220
Mammalia Didelphimorphia Didelphidae Metachirus nudicaudatus 215
Charadrius vociferus 207
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Macronyssus crosbyi interactsWith Mammalia Chiroptera Vespertilionidae Myotis velifer 1544
Chiroptoglyphus americanus interactsWith Mammalia Chiroptera Vespertilionidae Myotis velifer 1530
Macronyssus unidens interactsWith Mammalia Chiroptera Vespertilionidae Myotis velifer 855
Trouessartia trouessarti interactsWith Aves Passeriformes Acrocephalidae Acrocephalus arundinaceus 441
Trouessartia trouessartii interactsWith Aves Passeriformes Acrocephalidae Acrocephalus arundinaceus 348
Pterolichus obtusus interactsWith Aves Galliformes Phasianidae Gallus gallus domesticus 346
Proctophyllodes interactsWith Aves Passeriformes Turdidae Turdus migratorius 336
Proctophyllodes spini interactsWith Aves Passeriformes Fringillidae Spinus tristis 308
Prolistrophorus bidentatus interactsWith Mammalia Rodentia Cricetidae Akodon aerosus 244
Alloptellus coniventris interactsWith Aves Suliformes Fregatidae Fregata ariel ariel 243
Proctophyllodes ampelidis interactsWith Aves Passeriformes Bombycillidae Bombycilla cedrorum 239
Eustathia cultrifera interactsWith Aves Apodiformes Apodidae Apus apus apus 228
Echineustathia tricapitosetosa interactsWith Aves Apodiformes Apodidae Chaetura pelagica 208
Proctophyllodes interactsWith Aves Passeriformes Fringillidae Haemorhous mexicanus 204
Prolistrophorus bidentatus interactsWith Mammalia Rodentia Cricetidae Akodon torques 170
Metachiroecius brasiliensis interactsWith Mammalia Didelphimorphia Didelphidae Metachirus nudicaudatus 170
Proctophyllodes polyxenus interactsWith Aves Passeriformes Passerellidae Junco hyemalis 162
Plicatalloptes fregatae interactsWith Aves Suliformes Fregatidae Fregata ariel ariel 160
Kramerella interactsWith Aves Strigiformes Strigidae Bubo virginianus 153

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 Plantae Plantae Animalia->Plantae Animalia->Plantae Fungi Fungi Animalia->Fungi Plantae->Plantae
interactions Andrenidae Andrenidae Anacardiaceae Anacardiaceae Andrenidae->Anacardiaceae Apiaceae Apiaceae Andrenidae->Apiaceae Apocynaceae Apocynaceae Andrenidae->Apocynaceae Aquifoliaceae Aquifoliaceae Andrenidae->Aquifoliaceae Asparagaceae Asparagaceae Andrenidae->Asparagaceae Asteraceae Asteraceae Andrenidae->Asteraceae Brassicaceae Brassicaceae Andrenidae->Brassicaceae Caprifoliaceae Caprifoliaceae Andrenidae->Caprifoliaceae Caryophyllaceae Caryophyllaceae Andrenidae->Caryophyllaceae Cornaceae Cornaceae Andrenidae->Cornaceae Cupressaceae Cupressaceae Andrenidae->Cupressaceae Elaeagnaceae Elaeagnaceae Andrenidae->Elaeagnaceae Ericaceae Ericaceae Andrenidae->Ericaceae Fabaceae Fabaceae Andrenidae->Fabaceae Gentianaceae Gentianaceae Andrenidae->Gentianaceae Geraniaceae Geraniaceae Andrenidae->Geraniaceae Grossulariaceae Grossulariaceae Andrenidae->Grossulariaceae Hydrangeaceae Hydrangeaceae Andrenidae->Hydrangeaceae Hydrophyllaceae Hydrophyllaceae Andrenidae->Hydrophyllaceae Hypericaceae Hypericaceae Andrenidae->Hypericaceae Lamiaceae Lamiaceae Andrenidae->Lamiaceae Limnanthaceae Limnanthaceae Andrenidae->Limnanthaceae Melanthiaceae Melanthiaceae Andrenidae->Melanthiaceae Metacapnodiaceae Metacapnodiaceae Andrenidae->Metacapnodiaceae Montiaceae Montiaceae Andrenidae->Montiaceae Namaceae Namaceae Andrenidae->Namaceae Nesomyidae Nesomyidae Andrenidae->Nesomyidae Papaveraceae Papaveraceae Andrenidae->Papaveraceae Polemoniaceae Polemoniaceae Andrenidae->Polemoniaceae Polygalaceae Polygalaceae Andrenidae->Polygalaceae Polygonaceae Polygonaceae Andrenidae->Polygonaceae Ranunculaceae Ranunculaceae Andrenidae->Ranunculaceae Rhamnaceae Rhamnaceae Andrenidae->Rhamnaceae Rosaceae Rosaceae Andrenidae->Rosaceae Rubiaceae Rubiaceae Andrenidae->Rubiaceae Salicaceae Salicaceae Andrenidae->Salicaceae Sapindaceae Sapindaceae Andrenidae->Sapindaceae Viburnaceae Viburnaceae Andrenidae->Viburnaceae Asteraceae->Ranunculaceae Apidae Apidae Apidae->Apocynaceae Apidae->Aquifoliaceae Apidae->Asteraceae Apidae->Brassicaceae Apidae->Caprifoliaceae Apidae->Cornaceae Apidae->Elaeagnaceae Apidae->Ericaceae Apidae->Fabaceae Apidae->Gentianaceae Apidae->Grossulariaceae Apidae->Hydrangeaceae Apidae->Hydrophyllaceae Apidae->Hypericaceae Apidae->Lamiaceae Apidae->Metacapnodiaceae Apidae->Montiaceae Apidae->Namaceae Apidae->Ranunculaceae Apidae->Rosaceae Apidae->Rubiaceae Apidae->Salicaceae Apidae->Sapindaceae Boraginaceae Boraginaceae Apidae->Boraginaceae Bromeliaceae Bromeliaceae Apidae->Bromeliaceae Bunocotylidae Bunocotylidae Apidae->Bunocotylidae Cleomaceae Cleomaceae Apidae->Cleomaceae Clethraceae Clethraceae Apidae->Clethraceae Cucurbitaceae Cucurbitaceae Apidae->Cucurbitaceae Lythraceae Lythraceae Apidae->Lythraceae Malvaceae Malvaceae Apidae->Malvaceae Nyctaginaceae Nyctaginaceae Apidae->Nyctaginaceae Onagraceae Onagraceae Apidae->Onagraceae Pinaceae Pinaceae Apidae->Pinaceae Plantaginaceae Plantaginaceae Apidae->Plantaginaceae Sarraceniaceae Sarraceniaceae Apidae->Sarraceniaceae Smilacaceae Smilacaceae Apidae->Smilacaceae Apionacaridae Apionacaridae Apodidae Apodidae Apionacaridae->Apodidae Rallidae Rallidae Apionacaridae->Rallidae Argasidae Argasidae Pteropodidae Pteropodidae Argasidae->Pteropodidae Colletidae Colletidae Colletidae->Apiaceae Colletidae->Apocynaceae Colletidae->Aquifoliaceae Colletidae->Asteraceae Colletidae->Brassicaceae Colletidae->Cupressaceae Colletidae->Ericaceae Colletidae->Fabaceae Colletidae->Hydrangeaceae Colletidae->Hypericaceae Colletidae->Lamiaceae Colletidae->Polygonaceae Colletidae->Ranunculaceae Colletidae->Rhamnaceae Colletidae->Rosaceae Colletidae->Rubiaceae Colletidae->Salicaceae Colletidae->Sapindaceae Colletidae->Boraginaceae Amaryllidaceae Amaryllidaceae Colletidae->Amaryllidaceae Euphorbiaceae Euphorbiaceae Colletidae->Euphorbiaceae Psilostomidae Psilostomidae Colletidae->Psilostomidae Saxifragaceae Saxifragaceae Colletidae->Saxifragaceae Solanaceae Solanaceae Colletidae->Solanaceae Dermanyssidae Dermanyssidae Cricetidae Cricetidae Dermanyssidae->Cricetidae Hirundinidae Hirundinidae Dermanyssidae->Hirundinidae Muridae Muridae Dermanyssidae->Muridae Paridae Paridae Dermanyssidae->Paridae Passeridae Passeridae Dermanyssidae->Passeridae Picidae Picidae Dermanyssidae->Picidae Troglodytidae Troglodytidae Dermanyssidae->Troglodytidae Turdidae Turdidae Dermanyssidae->Turdidae Halictidae Halictidae Halictidae->Apiaceae Halictidae->Apocynaceae Halictidae->Asparagaceae Halictidae->Asteraceae Halictidae->Brassicaceae Halictidae->Caprifoliaceae Halictidae->Cupressaceae Halictidae->Ericaceae Halictidae->Fabaceae Halictidae->Hydrophyllaceae Halictidae->Hypericaceae Halictidae->Lamiaceae Halictidae->Metacapnodiaceae Halictidae->Polygalaceae Halictidae->Polygonaceae Halictidae->Ranunculaceae Halictidae->Rhamnaceae Halictidae->Rosaceae Halictidae->Rosaceae Halictidae->Rubiaceae Halictidae->Salicaceae Halictidae->Sapindaceae Halictidae->Viburnaceae Halictidae->Onagraceae Halictidae->Plantaginaceae Halictidae->Euphorbiaceae Oxalidaceae Oxalidaceae Halictidae->Oxalidaceae Scrophulariaceae Scrophulariaceae Halictidae->Scrophulariaceae Verbenaceae Verbenaceae Halictidae->Verbenaceae Violaceae Violaceae Halictidae->Violaceae Hoplopleuridae Hoplopleuridae Hoplopleuridae->Cricetidae Ixodidae Ixodidae Ixodidae->Cricetidae Ixodidae->Muridae Ixodidae->Troglodytidae Ixodidae->Turdidae Caenolestidae Caenolestidae Ixodidae->Caenolestidae Canidae Canidae Ixodidae->Canidae Cardinalidae Cardinalidae Ixodidae->Cardinalidae Castoridae Castoridae Ixodidae->Castoridae Cuculidae Cuculidae Ixodidae->Cuculidae Dasyproctidae Dasyproctidae Ixodidae->Dasyproctidae Didelphidae Didelphidae Ixodidae->Didelphidae Dipodidae Dipodidae Ixodidae->Dipodidae Hominidae Hominidae Ixodidae->Hominidae Lacertidae Lacertidae Ixodidae->Lacertidae Leporidae Leporidae Ixodidae->Leporidae Mephitidae Mephitidae Ixodidae->Mephitidae Mustelidae Mustelidae Ixodidae->Mustelidae Passerellidae Passerellidae Ixodidae->Passerellidae Sciuridae Sciuridae Ixodidae->Sciuridae Soricidae Soricidae Ixodidae->Soricidae Leeuwenhoekiidae Leeuwenhoekiidae Leeuwenhoekiidae->Cricetidae Leeuwenhoekiidae->Didelphidae Crotaphytidae Crotaphytidae Leeuwenhoekiidae->Crotaphytidae Echimyidae Echimyidae Leeuwenhoekiidae->Echimyidae Phrynosomatidae Phrynosomatidae Leeuwenhoekiidae->Phrynosomatidae Macronyssidae Macronyssidae Macronyssidae->Cricetidae Macronyssidae->Hirundinidae Macronyssidae->Muridae Macronyssidae->Paridae Macronyssidae->Passeridae Macronyssidae->Picidae Macronyssidae->Troglodytidae Macronyssidae->Turdidae Macronyssidae->Cardinalidae Macronyssidae->Didelphidae Macronyssidae->Dipodidae Macronyssidae->Passerellidae Macronyssidae->Echimyidae Accipitridae Accipitridae Macronyssidae->Accipitridae Agamidae Agamidae Macronyssidae->Agamidae Anguidae Anguidae Macronyssidae->Anguidae Corvidae Corvidae Macronyssidae->Corvidae Erinaceidae Erinaceidae Macronyssidae->Erinaceidae Fringillidae Fringillidae Macronyssidae->Fringillidae Icteridae Icteridae Macronyssidae->Icteridae Mimidae Mimidae Macronyssidae->Mimidae Molossidae Molossidae Macronyssidae->Molossidae Motacillidae Motacillidae Macronyssidae->Motacillidae Parulidae Parulidae Macronyssidae->Parulidae Phalacrocoracidae Phalacrocoracidae Macronyssidae->Phalacrocoracidae Phasianidae Phasianidae Macronyssidae->Phasianidae Phyllostomidae Phyllostomidae Macronyssidae->Phyllostomidae Psittacidae Psittacidae Macronyssidae->Psittacidae Regulidae Regulidae Macronyssidae->Regulidae Remizidae Remizidae Macronyssidae->Remizidae Strigidae Strigidae Macronyssidae->Strigidae Sturnidae Sturnidae Macronyssidae->Sturnidae Thamnophilidae Thamnophilidae Macronyssidae->Thamnophilidae Thraupidae Thraupidae Macronyssidae->Thraupidae Tyrannidae Tyrannidae Macronyssidae->Tyrannidae Viperidae Viperidae Macronyssidae->Viperidae Megachilidae Megachilidae Megachilidae->Anacardiaceae Megachilidae->Apocynaceae Megachilidae->Asteraceae Megachilidae->Caprifoliaceae Megachilidae->Cornaceae Megachilidae->Ericaceae Megachilidae->Fabaceae Megachilidae->Hydrophyllaceae Megachilidae->Hypericaceae Megachilidae->Lamiaceae Megachilidae->Limnanthaceae Megachilidae->Montiaceae Megachilidae->Ranunculaceae Megachilidae->Rhamnaceae Megachilidae->Rosaceae Megachilidae->Rubiaceae Megachilidae->Lythraceae Megachilidae->Malvaceae Megachilidae->Onagraceae Megachilidae->Plantaginaceae Megachilidae->Psilostomidae Megachilidae->Verbenaceae Megachilidae->Violaceae Cactaceae Cactaceae Megachilidae->Cactaceae Phaseolidae Phaseolidae Megachilidae->Phaseolidae Poaceae Poaceae Megachilidae->Poaceae Tamaricaceae Tamaricaceae Megachilidae->Tamaricaceae Psorergatidae Psorergatidae Psorergatidae->Cricetidae Psorergatidae->Muridae Psorergatidae->Mustelidae Psorergatidae->Sciuridae Psorergatidae->Soricidae Psorergatidae->Molossidae Psorergatidae->Phyllostomidae Bathyergidae Bathyergidae Psorergatidae->Bathyergidae Bovidae Bovidae Psorergatidae->Bovidae Emballonuridae Emballonuridae Psorergatidae->Emballonuridae Gliridae Gliridae Psorergatidae->Gliridae Talpidae Talpidae Psorergatidae->Talpidae Vespertilionidae Vespertilionidae Psorergatidae->Vespertilionidae Spinturnicidae Spinturnicidae Spinturnicidae->Molossidae Spinturnicidae->Phyllostomidae Spinturnicidae->Vespertilionidae Miniopteridae Miniopteridae Spinturnicidae->Miniopteridae Myzopodidae Myzopodidae Spinturnicidae->Myzopodidae Syringophilidae Syringophilidae Syringophilidae->Apodidae Syringophilidae->Rallidae Syringophilidae->Hirundinidae Syringophilidae->Passeridae Syringophilidae->Picidae Syringophilidae->Turdidae Syringophilidae->Cardinalidae Syringophilidae->Passerellidae Syringophilidae->Corvidae Syringophilidae->Fringillidae Syringophilidae->Icteridae Syringophilidae->Mimidae Syringophilidae->Motacillidae Syringophilidae->Parulidae Syringophilidae->Psittacidae Syringophilidae->Thraupidae Anatidae Anatidae Syringophilidae->Anatidae Bombycillidae Bombycillidae Syringophilidae->Bombycillidae Charadriidae Charadriidae Syringophilidae->Charadriidae Laridae Laridae Syringophilidae->Laridae Odontophoridae Odontophoridae Syringophilidae->Odontophoridae Phoenicopteridae Phoenicopteridae Syringophilidae->Phoenicopteridae Phylloscopidae Phylloscopidae Syringophilidae->Phylloscopidae Pteroclididae Pteroclididae Syringophilidae->Pteroclididae Scolopacidae Scolopacidae Syringophilidae->Scolopacidae Trombiculidae Trombiculidae Trombiculidae->Salicaceae Trombiculidae->Pteropodidae Trombiculidae->Cricetidae Trombiculidae->Muridae Trombiculidae->Picidae Trombiculidae->Caenolestidae Trombiculidae->Cuculidae Trombiculidae->Didelphidae Trombiculidae->Dipodidae Trombiculidae->Passerellidae Trombiculidae->Sciuridae Trombiculidae->Soricidae Trombiculidae->Crotaphytidae Trombiculidae->Phrynosomatidae Trombiculidae->Icteridae Trombiculidae->Phyllostomidae Trombiculidae->Strigidae Trombiculidae->Emballonuridae Trombiculidae->Vespertilionidae Trombiculidae->Scolopacidae Dicaeidae Dicaeidae Trombiculidae->Dicaeidae Fagaceae Fagaceae Trombiculidae->Fagaceae Gecarcinidae Gecarcinidae Trombiculidae->Gecarcinidae Heteromyidae Heteromyidae Trombiculidae->Heteromyidae Hipposideridae Hipposideridae Trombiculidae->Hipposideridae Pachycephalidae Pachycephalidae Trombiculidae->Pachycephalidae Phaethontidae Phaethontidae Trombiculidae->Phaethontidae Rhinolophidae Rhinolophidae Trombiculidae->Rhinolophidae Scincidae Scincidae Trombiculidae->Scincidae

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

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
Acanthonyssus HAS_ACCEPTED_NAME col Acanthonyssus
Acanthonyssus dentipes HAS_ACCEPTED_NAME col Acanthonyssus dentipes
Acanthonyssus proechimys HAS_ACCEPTED_NAME col Acanthonyssus proechimys
Acari NONE col Acari
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 1320
col class 6
col family 26
col genus 171
col kingdom 1
col order 29
col parvorder 1
col phylum 2
col species 1231
col subgenus 11
col subspecies 38
col variety 5
discoverlife NA 2509
discoverlife species 308
gbif NA 937
gbif class 6
gbif family 28
gbif genus 279
gbif kingdom 1
gbif order 29
gbif phylum 2
gbif species 1501
gbif subspecies 56
gbif variety 12
itis NA 1460
itis class 7
itis division 1
itis family 24
itis genus 153
itis kingdom 1
itis order 30
itis phylum 1
itis species 1111
itis subclass 1
itis subgenus 1
itis subspecies 22
itis variety 6
mdd NA 2816
ncbi NA 1475
ncbi clade 1
ncbi class 6
ncbi family 24
ncbi genus 197
ncbi kingdom 1
ncbi order 29
ncbi phylum 2
ncbi species 1066
ncbi subclass 1
ncbi subfamily 2
ncbi subgenus 3
ncbi subspecies 11
ncbi varietas 2
pbdb NA 2453
pbdb class 7
pbdb family 15
pbdb genus 60
pbdb kingdom 1
pbdb order 30
pbdb phylum 1
pbdb species 248
pbdb subclass 1
pbdb superorder 1
pbdb unranked clade 6
tpt NA 1261
tpt family 10
tpt genus 24
tpt order 24
tpt species 1497
wfo NA 2528
wfo family 2
wfo genus 87
wfo order 2
wfo species 191
wfo subspecies 14
wfo variety 4
worms NA 2432
worms class 4
worms family 16
worms genus 78
worms kingdom 1
worms order 26
worms phylum 1
worms phylum (division) 1
worms species 254
worms subclass 2
worms subspecies 3
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 HAS_ACCEPTED_NAME 4709
col NONE 1337
col SYNONYM_OF 236
discoverlife NONE 5805
discoverlife HAS_ACCEPTED_NAME 301
discoverlife SYNONYM_OF 99
discoverlife HOMONYM_OF 23
gbif HAS_ACCEPTED_NAME 5390
gbif NONE 946
gbif SYNONYM_OF 440
itis HAS_ACCEPTED_NAME 4549
itis SYNONYM_OF 111
itis NONE 1482
mdd NONE 5965
mdd HAS_ACCEPTED_NAME 142
mdd SYNONYM_OF 6
ncbi NONE 1504
ncbi SAME_AS 4560
ncbi SYNONYM_OF 63
pbdb NONE 2489
pbdb SYNONYM_OF 10105
pbdb HAS_ACCEPTED_NAME 3615
tpt NONE 4160
tpt HAS_ACCEPTED_NAME 1851
tpt SYNONYM_OF 406
wfo NONE 5804
wfo HAS_ACCEPTED_NAME 275
wfo HAS_UNCHECKED_NAME 84
wfo SYNONYM_OF 83
worms NONE 2484
worms HAS_ACCEPTED_NAME 3626
worms SYNONYM_OF 59
List of Available Name Alignment Reports
catalog name alignment results
col associated names alignments (first 500, full csv/tsv)
ncbi associated names alignments (first 500, full csv/tsv)
discoverlife associated names alignments (first 500, full csv/tsv)
gbif associated names alignments (first 500, full csv/tsv)
itis associated names alignments (first 500, full csv/tsv)
wfo associated names alignments (first 500, full csv/tsv)
mdd associated names alignments (first 500, full csv/tsv)
tpt associated names alignments (first 500, full csv/tsv)
pbdb associated names alignments (first 500, full csv/tsv)
worms associated names alignments (first 500, full csv/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
2025-04-01T18:45:27Z note source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder
2025-04-01T18:45:27Z note source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder
2025-04-01T18:45:33Z note issue handling date range [1962-01-01/1961-01-01]: The end instant must be greater than the start instant
2025-04-01T18:45:33Z note issue handling date range [1962-01-01/1961-01-01]: The end instant must be greater than the start instant

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

Most frequently occurring review notes, if any.
reviewComment count
issue handling date range [1971-10/1971-03]: The end instant must be greater than the start instant 140
issue handling date range [1972-10/1972-03]: The end instant must be greater than the start instant 12
issue handling date range [1920-12-01/1920-08-16]: The end instant must be greater than the start instant 6
issue handling date range [1944-06-09/1944-06-03]: The end instant must be greater than the start instant 4

For addition information on review notes, please have a look at the first 500 Review Notes or the download full 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 ^[At time of writing (2025-04-01) the version of the GloBI dataset index was available at https://globalbioticinteractions.org/datasets for badge examples.

Discussion

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-ness5 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, Jorrit Poelen, and Katrin Leinweber. 2025. “Globalbioticinteractions/Elton: 0.15.1.” Zenodo. https://doi.org/10.5281/zenodo.14927734.
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.
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.