A Review of Biotic Interactions and Taxon Names Found in globalbioticinteractions/fmnh

by Nomer and Elton, two naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

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

2024-11-18

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/fmnh, is 1.12GiB in size and contains 129,051 interaction with 8 unique types of associations (e.g., adjacentTo) between 22,406 primary taxon (e.g., Trichobius joblingi Wenzel, 1966) and 33,977 associated taxon (e.g., Carollia perspicillata). 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:

Field Museum of Natural History (Botany) Bryophyte Collection - Version 11.9 https://fmipt.fieldmuseum.org/ipt/archive.do?r=fmnh_bryophyte 2024-11-16T01:25:33.267Z 318f6e1904be7e0a8d13598f5e1cf5d2145322d946354170ee4faf24e1c297e2 Field Museum of Natural History (Botany) Fungi Collection - Version 4.14 https://fmipt.fieldmuseum.org/ipt/archive.do?r=fmnh_fungi 2024-11-16T01:25:33.267Z 318f6e1904be7e0a8d13598f5e1cf5d2145322d946354170ee4faf24e1c297e2 Field Museum of Natural History (Botany) Lichen Collection - Version 2.15 https://fmipt.fieldmuseum.org/ipt/archive.do?r=fmnh_lichens 2024-11-16T01:25:33.267Z 318f6e1904be7e0a8d13598f5e1cf5d2145322d946354170ee4faf24e1c297e2 Field Museum of Natural History (Botany) Pteridophyte Collection - Version 2.9 https://fmipt.fieldmuseum.org/ipt/archive.do?r=fmnh_pteridophytes 2024-11-16T01:25:33.267Z 318f6e1904be7e0a8d13598f5e1cf5d2145322d946354170ee4faf24e1c297e2 Field Museum of Natural History (Botany) Seed Plant Collection - Version 11.16 https://fmipt.fieldmuseum.org/ipt/archive.do?r=fmnh_seedplants 2024-11-16T01:25:33.267Z 318f6e1904be7e0a8d13598f5e1cf5d2145322d946354170ee4faf24e1c297e2 Field Museum of Natural History (Zoology) Bird Collection - Version 14.22 https://fmipt.fieldmuseum.org/ipt/archive.do?r=fm_birds 2024-11-16T01:25:33.267Z 318f6e1904be7e0a8d13598f5e1cf5d2145322d946354170ee4faf24e1c297e2 Field Museum of Natural History (Zoology) Insect, Arachnid and Myriapod Collection - Version 12.62 https://fmipt.fieldmuseum.org/ipt/archive.do?r=fmnh_insects 2024-11-16T01:25:33.267Z 318f6e1904be7e0a8d13598f5e1cf5d2145322d946354170ee4faf24e1c297e2 Field Museum of Natural History (Zoology) Invertebrate Collection - Version 18.44 https://fmipt.fieldmuseum.org/ipt/archive.do?r=fmnh_invertebrates 2024-11-16T01:25:33.267Z 318f6e1904be7e0a8d13598f5e1cf5d2145322d946354170ee4faf24e1c297e2

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/fmnh 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, Elton, Nomer combined with third-party tools like grep, mlr, tail and head.

Tools used in this review process
tool name version
elton 0.13.9
nomer 0.5.13
mlr 6.0.0
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. 1.12GiB) under review 
elton pull globalbioticinteractions/fmnh

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

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

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/fmnh\
 | 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/fmnh, is 1.12GiB in size and contains 129,051 interaction with 8 unique types of associations (e.g., adjacentTo) between 22,406 primary taxon (e.g., Trichobius joblingi Wenzel, 1966) and 33,977 associated taxon (e.g., Carollia perspicillata).

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
Octopodidae eatenBy Thunnus Field Museum of Natural History (Zoology) Invertebrate Collection - Version 18.44. Accessed at https://fmipt.fieldmuseum.org/ipt/archive.do?r=fmnh_invertebrates on 18 Nov 2024.
Drymaeus jonasi (L. Pfeiffer) adjacentTo pine roots bde9145a-fe74-43b7-a1c2-9c4b107e31af
Achatinella abbreviata L. A. Reeve, 1850 adjacentTo lehua 7c18d673-e28c-48ed-a51a-cfae439f34c3
Utterbackia imbecillis (Say, 1829) adjacentTo bank at very edge of water f13607e5-c23e-4c28-84d2-9245d0c29c20
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
adjacentTo 92436
ectoparasiteOf 34987
interactsWith 891
parasiteOf 564
hasHost 175
eats 11
hostOf 2
eatenBy 1
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Trichobius joblingi Wenzel, 1966 2639
Marchantiophyta Stotler & Crand.-Stotl. 1516
Megistopoda aranea (Coquillétt, 1899) 1287
Megistopoda proxima (Séguy, 1926) 1162
Trichobius parasiticus Gervais, 1844 1012
Strebla guajiro (Garcia & Casal, 1965) 1000
Strebla wiedemanni Kolenati, 1856 946
Aspidoptera phyllostomatis (Perty, 1833) 820
Speiseria ambigua Kessel, 1925 779
Fungus indet. 730
Aspidoptera falcata Wenzel, 1976 720
Hippoboscoidea 609
Paratrichobius longicrus (Miranda Ribeiro, 1907) 597
Trichobius costalimai Guimarães, 1938 573
Nycterophilia coxata Ferris, 1916 543
Usnea Dill. ex Adans. 516
Ixodida Leach, 1815 505
Trichobius dugesii Townsend, 1891 492
Trichobioides perspicillatus (Pessoa & Galvao, 1937) 422
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
Carollia perspicillata 2692
Artibeus jamaicensis 1740
Desmodus rotundus 1564
Sturnira lilium 1527
ground 1398
tree 1221
rocks 1175
Phyllostomus discolor 1123
log 1003
dead wood 831
Pteronotus parnellii 792
soil 791
Carollia brevicauda 776
trees 682
Carollia perspicillata azteca 649
beach 638
leaf litter 638
Glossophaga soricina 629
Artiodactyla 618
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Trichobius joblingi Wenzel, 1966 ectoparasiteOf Carollia perspicillata 1377
Megistopoda proxima (Séguy, 1926) ectoparasiteOf Sturnira lilium 906
Megistopoda aranea (Coquillétt, 1899) ectoparasiteOf Artibeus jamaicensis 793
Trichobius parasiticus Gervais, 1844 ectoparasiteOf Desmodus rotundus 775
Strebla wiedemanni Kolenati, 1856 ectoparasiteOf Desmodus rotundus 697
Strebla guajiro (Garcia & Casal, 1965) ectoparasiteOf Carollia perspicillata 570
Aspidoptera falcata Wenzel, 1976 ectoparasiteOf Sturnira lilium 520
Aspidoptera phyllostomatis (Perty, 1833) ectoparasiteOf Artibeus jamaicensis 504
Trichobius costalimai Guimarães, 1938 ectoparasiteOf Phyllostomus discolor 454
Speiseria ambigua Kessel, 1925 ectoparasiteOf Carollia perspicillata 366
Paratrichobius longicrus (Miranda Ribeiro, 1907) ectoparasiteOf Artibeus lituratus 351
Trichobioides perspicillatus (Pessoa & Galvao, 1937) ectoparasiteOf Phyllostomus discolor 340
Trichobius joblingi Wenzel, 1966 ectoparasiteOf Carollia perspicillata azteca 317
Trichobius caecus Edwards, 1918 ectoparasiteOf Pteronotus parnellii 292
Strebla hertigi Wenzel, 1966 ectoparasiteOf Phyllostomus discolor 284
Nycterophilia coxata Ferris, 1916 ectoparasiteOf Leptonycteris curasoae 272
Trichobius dugesii Townsend, 1891 ectoparasiteOf Glossophaga soricina 259
Trichobius joblingi Wenzel, 1966 ectoparasiteOf Carollia brevicauda 256
Trichobius longipes (Rudow, 1871) ectoparasiteOf Phyllostomus hastatus 244

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 Animalia->Animalia Animalia->Animalia Plantae Plantae Animalia->Plantae Animalia->Plantae Fungi Fungi Animalia->Fungi Chromista Chromista Animalia->Chromista Plantae->Animalia Plantae->Plantae Fungi->Plantae Fungi->Fungi
interactions Ancistronidae Ancistronidae Gruidae Gruidae Ancistronidae->Gruidae Armadillidae Armadillidae Pandanaceae Pandanaceae Armadillidae->Pandanaceae Atheliaceae Atheliaceae Celastraceae Celastraceae Atheliaceae->Celastraceae Fagaceae Fagaceae Atheliaceae->Fagaceae Malvaceae Malvaceae Atheliaceae->Malvaceae Auriculariaceae Auriculariaceae Platanaceae Platanaceae Auriculariaceae->Platanaceae Viburnaceae Viburnaceae Auriculariaceae->Viburnaceae Boletaceae Boletaceae Boletaceae->Fagaceae Boopiidae Boopiidae Canidae Canidae Boopiidae->Canidae Macropodidae Macropodidae Boopiidae->Macropodidae Brassicaceae Brassicaceae Betulaceae Betulaceae Brassicaceae->Betulaceae Calymperaceae Calymperaceae Arecaceae Arecaceae Calymperaceae->Arecaceae Ceratophyllidae Ceratophyllidae Cricetidae Cricetidae Ceratophyllidae->Cricetidae Geomyidae Geomyidae Ceratophyllidae->Geomyidae Heteromyidae Heteromyidae Ceratophyllidae->Heteromyidae Mustelidae Mustelidae Ceratophyllidae->Mustelidae Ochotonidae Ochotonidae Ceratophyllidae->Ochotonidae Phalacrocoracidae Phalacrocoracidae Ceratophyllidae->Phalacrocoracidae Sciuridae Sciuridae Ceratophyllidae->Sciuridae Soricidae Soricidae Ceratophyllidae->Soricidae Cerrenaceae Cerrenaceae Cerrenaceae->Fagaceae Cerrenaceae->Betulaceae Sapindaceae Sapindaceae Cerrenaceae->Sapindaceae Coleosporiaceae Coleosporiaceae Asteraceae Asteraceae Coleosporiaceae->Asteraceae Ericaceae Ericaceae Coleosporiaceae->Ericaceae Colpocephalidae Colpocephalidae Ardeidae Ardeidae Colpocephalidae->Ardeidae Cariamidae Cariamidae Colpocephalidae->Cariamidae Cathartidae Cathartidae Colpocephalidae->Cathartidae Ciconiidae Ciconiidae Colpocephalidae->Ciconiidae Corticiaceae Corticiaceae Corticiaceae->Fagaceae Corticiaceae->Betulaceae Corticiaceae->Arecaceae Corticiaceae->Sapindaceae Cronartiaceae Cronartiaceae Grossulariaceae Grossulariaceae Cronartiaceae->Grossulariaceae Pinaceae Pinaceae Cronartiaceae->Pinaceae Ctenophthalmidae Ctenophthalmidae Ctenophthalmidae->Cricetidae Ctenophthalmidae->Heteromyidae Ctenophthalmidae->Soricidae Dacrymycetaceae Dacrymycetaceae Lauraceae Lauraceae Dacrymycetaceae->Lauraceae Diaporthaceae Diaporthaceae Urticaceae Urticaceae Diaporthaceae->Urticaceae Eocronartiaceae Eocronartiaceae Climaciaceae Climaciaceae Eocronartiaceae->Climaciaceae Erysiphaceae Erysiphaceae Erysiphaceae->Asteraceae Eunicidae Eunicidae Meandrinidae Meandrinidae Eunicidae->Meandrinidae Exobasidiaceae Exobasidiaceae Exobasidiaceae->Ericaceae Filobasidiaceae Filobasidiaceae Omphalotaceae Omphalotaceae Filobasidiaceae->Omphalotaceae Fomitopsidaceae Fomitopsidaceae Fomitopsidaceae->Pinaceae Frullaniaceae Frullaniaceae Altingiaceae Altingiaceae Frullaniaceae->Altingiaceae Primulaceae Primulaceae Frullaniaceae->Primulaceae Rosaceae Rosaceae Frullaniaceae->Rosaceae Glomosporiaceae Glomosporiaceae Amaranthaceae Amaranthaceae Glomosporiaceae->Amaranthaceae Graphidaceae Graphidaceae Graphidaceae->Arecaceae Apocynaceae Apocynaceae Graphidaceae->Apocynaceae Gymnosporangiaceae Gymnosporangiaceae Gymnosporangiaceae->Rosaceae Gyropidae Gyropidae Aotidae Aotidae Gyropidae->Aotidae Echimyidae Echimyidae Gyropidae->Echimyidae Octodontidae Octodontidae Gyropidae->Octodontidae Hippoboscidae Hippoboscidae Bovidae Bovidae Hippoboscidae->Bovidae Corvidae Corvidae Hippoboscidae->Corvidae Hipposideridae Hipposideridae Hippoboscidae->Hipposideridae Miniopteridae Miniopteridae Hippoboscidae->Miniopteridae Passerellidae Passerellidae Hippoboscidae->Passerellidae Pteropodidae Pteropodidae Hippoboscidae->Pteropodidae Rhinolophidae Rhinolophidae Hippoboscidae->Rhinolophidae Vespertilionidae Vespertilionidae Hippoboscidae->Vespertilionidae Hipponicidae Hipponicidae Haliotidae Haliotidae Hipponicidae->Haliotidae Hyaloriaceae Hyaloriaceae Hyaloriaceae->Malvaceae Hyaloscyphaceae Hyaloscyphaceae Poaceae Poaceae Hyaloscyphaceae->Poaceae Hydnaceae Hydnaceae Hydnaceae->Pinaceae Hygrophoraceae Hygrophoraceae Hygrophoraceae->Fagaceae Hygrophoraceae->Pinaceae Araliaceae Araliaceae Hygrophoraceae->Araliaceae Hymenochaetaceae Hymenochaetaceae Hymenochaetaceae->Fagaceae Hymenochaetaceae->Viburnaceae Hymenochaetaceae->Betulaceae Hymenochaetaceae->Sapindaceae Hymenochaetaceae->Ericaceae Hymenochaetaceae->Pinaceae Hymenochaetaceae->Rosaceae Cupressaceae Cupressaceae Hymenochaetaceae->Cupressaceae Salicaceae Salicaceae Hymenochaetaceae->Salicaceae Hyphodermataceae Hyphodermataceae Hyphodermataceae->Fagaceae Hyphodermataceae->Malvaceae Hyphodermataceae->Betulaceae Hyphodontiaceae Hyphodontiaceae Hyphodontiaceae->Fagaceae Hyphodontiaceae->Betulaceae Hyphodontiaceae->Rosaceae Moraceae Moraceae Hyphodontiaceae->Moraceae Hypoxylaceae Hypoxylaceae Hypoxylaceae->Fagaceae Hypoxylaceae->Rosaceae Hystrichopsyllidae Hystrichopsyllidae Hystrichopsyllidae->Cricetidae Hystrichopsyllidae->Sciuridae Hystrichopsyllidae->Soricidae Hystrichopsyllidae->Passerellidae Talpidae Talpidae Hystrichopsyllidae->Talpidae Irpicaceae Irpicaceae Irpicaceae->Fagaceae Irpicaceae->Pinaceae Nyssaceae Nyssaceae Irpicaceae->Nyssaceae Ischnopsyllidae Ischnopsyllidae Ischnopsyllidae->Vespertilionidae Lepidoziaceae Lepidoziaceae Nothofagaceae Nothofagaceae Lepidoziaceae->Nothofagaceae Leptopsyllidae Leptopsyllidae Leptopsyllidae->Cricetidae Meliolaceae Meliolaceae Meliolaceae->Ericaceae Menoponidae Menoponidae Falconidae Falconidae Menoponidae->Falconidae Phasianidae Phasianidae Menoponidae->Phasianidae Sturnidae Sturnidae Menoponidae->Sturnidae Turnicidae Turnicidae Menoponidae->Turnicidae Meruliaceae Meruliaceae Meruliaceae->Fagaceae Meruliaceae->Betulaceae Meruliaceae->Sapindaceae Meruliaceae->Pinaceae Meruliaceae->Salicaceae Magnoliaceae Magnoliaceae Meruliaceae->Magnoliaceae Micropeltidaceae Micropeltidaceae Micropeltidaceae->Pinaceae Microthyriaceae Microthyriaceae Microthyriaceae->Pinaceae Mycosphaerellaceae Mycosphaerellaceae Cucurbitaceae Cucurbitaceae Mycosphaerellaceae->Cucurbitaceae Mycosyringaceae Mycosyringaceae Vitaceae Vitaceae Mycosyringaceae->Vitaceae Naididae Naididae Lepisosteidae Lepisosteidae Naididae->Lepisosteidae Octopodidae Octopodidae Scombridae Scombridae Octopodidae->Scombridae Oxyporaceae Oxyporaceae Oxyporaceae->Sapindaceae Phanerochaetaceae Phanerochaetaceae Phanerochaetaceae->Fagaceae Phanerochaetaceae->Betulaceae Phanerochaetaceae->Pinaceae Phanerochaetaceae->Salicaceae Phanerochaetaceae->Magnoliaceae Crossosomataceae Crossosomataceae Phanerochaetaceae->Crossosomataceae Philopteridae Philopteridae Philopteridae->Cariamidae Philopteridae->Falconidae Philopteridae->Phasianidae Accipitridae Accipitridae Philopteridae->Accipitridae Columbidae Columbidae Philopteridae->Columbidae Scolopacidae Scolopacidae Philopteridae->Scolopacidae Tinamidae Tinamidae Philopteridae->Tinamidae Phragmidiaceae Phragmidiaceae Phragmidiaceae->Rosaceae Physalacriaceae Physalacriaceae Physalacriaceae->Malvaceae Physalacriaceae->Magnoliaceae Physciaceae Physciaceae Physciaceae->Sapindaceae Polyporaceae Polyporaceae Polyporaceae->Fagaceae Polyporaceae->Betulaceae Polyporaceae->Pinaceae Polyporaceae->Salicaceae Polyporaceae->Nothofagaceae Ulmaceae Ulmaceae Polyporaceae->Ulmaceae Porinaceae Porinaceae Porinaceae->Lauraceae Pseudomenoponidae Pseudomenoponidae Rallidae Rallidae Pseudomenoponidae->Rallidae Pucciniaceae Pucciniaceae Pucciniaceae->Asteraceae Berberidaceae Berberidaceae Pucciniaceae->Berberidaceae Cyperaceae Cyperaceae Pucciniaceae->Cyperaceae Hydrophyllaceae Hydrophyllaceae Pucciniaceae->Hydrophyllaceae Ranunculaceae Ranunculaceae Pucciniaceae->Ranunculaceae Pulicidae Pulicidae Pulicidae->Canidae Pulicidae->Cricetidae Pulicidae->Vespertilionidae Felidae Felidae Pulicidae->Felidae Leporidae Leporidae Pulicidae->Leporidae Mephitidae Mephitidae Pulicidae->Mephitidae Punctulariaceae Punctulariaceae Punctulariaceae->Malvaceae Raveneliaceae Raveneliaceae Raveneliaceae->Rosaceae Rhopalopsyllidae Rhopalopsyllidae Rhopalopsyllidae->Cricetidae Rhopalopsyllidae->Heteromyidae Rhopalopsyllidae->Leporidae Caviidae Caviidae Rhopalopsyllidae->Caviidae Didelphidae Didelphidae Rhopalopsyllidae->Didelphidae Saxifragaceae Saxifragaceae Saxifragaceae->Pteropodidae Schizoporaceae Schizoporaceae Schizoporaceae->Fagaceae Anacardiaceae Anacardiaceae Schizoporaceae->Anacardiaceae Sebacinaceae Sebacinaceae Sebacinaceae->Rosaceae Sebacinaceae->Polyporaceae Steccherinaceae Steccherinaceae Steccherinaceae->Fagaceae Steccherinaceae->Viburnaceae Succineidae Succineidae Typhaceae Typhaceae Succineidae->Typhaceae Syrphidae Syrphidae Gleicheniaceae Gleicheniaceae Syrphidae->Gleicheniaceae Thelephoraceae Thelephoraceae Thelephoraceae->Fagaceae Thelephoraceae->Malvaceae Tremellaceae Tremellaceae Tremellaceae->Fagaceae

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
Tall NONE col Tall
Ft peat over sand NONE col Ft peat over sand
Cm diam trunk bog pine NONE col Cm diam trunk bog pine
Diam trunk NONE col Diam trunk
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 23737
col class 23
col family 156
col form 3
col genus 1961
col gigaclass 1
col infraorder 3
col kingdom 3
col order 50
col parvorder 1
col phylum 18
col section 1
col species 21019
col subclass 6
col subfamily 5
col subgenus 46
col suborder 4
col subspecies 882
col superclass 1
col superfamily 4
col tribe 1
col variety 223
discoverlife NA 47801
gbif NA 21541
gbif class 25
gbif family 170
gbif form 29
gbif genus 2052
gbif kingdom 4
gbif order 49
gbif phylum 19
gbif species 22946
gbif subspecies 1095
gbif variety 470
itis NA 37629
itis class 24
itis division 8
itis family 160
itis genus 1340
itis infraorder 2
itis kingdom 3
itis order 56
itis phylum 13
itis species 7953
itis subclass 9
itis subfamily 6
itis subgenus 5
itis suborder 4
itis subphylum 2
itis subspecies 392
itis superclass 1
itis superfamily 3
itis variety 217
mdd NA 47800
ncbi NA 32284
ncbi clade 8
ncbi class 23
ncbi family 157
ncbi forma 1
ncbi forma specialis 2
ncbi genus 1861
ncbi infraorder 4
ncbi kingdom 2
ncbi order 54
ncbi phylum 14
ncbi section 1
ncbi species 13133
ncbi subclass 10
ncbi subfamily 7
ncbi subgenus 9
ncbi suborder 3
ncbi subphylum 1
ncbi subspecies 191
ncbi subtribe 1
ncbi superclass 1
ncbi superfamily 5
ncbi tribe 3
ncbi varietas 37
pbdb NA 45841
pbdb class 28
pbdb family 126
pbdb genus 694
pbdb informal 2
pbdb infraorder 3
pbdb kingdom 3
pbdb order 52
pbdb phylum 18
pbdb species 1005
pbdb subclass 8
pbdb subfamily 8
pbdb subgenus 2
pbdb suborder 6
pbdb subspecies 3
pbdb superclass 1
pbdb superfamily 4
pbdb superorder 3
pbdb superphylum 2
pbdb tribe 2
pbdb unranked clade 10
tpt NA 46608
tpt family 3
tpt genus 129
tpt order 2
tpt species 1058
wfo NA 39233
wfo family 39
wfo form 3
wfo genus 927
wfo phylum 1
wfo section 1
wfo species 7323
wfo subsection 1
wfo subspecies 227
wfo tribe 1
wfo variety 187
worms NA 42510
worms class 24
worms family 138
worms genus 933
worms gigaclass 1
worms infraclass 1
worms infraorder 3
worms kingdom 3
worms order 52
worms phylum 11
worms phylum (division) 7
worms species 3934
worms subclass 8
worms subfamily 2
worms suborder 4
worms subphylum 2
worms subspecies 170
worms superclass 1
worms superfamily 4
worms variety 53
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 30955
col HAS_ACCEPTED_NAME 18882
col SYNONYM_OF 12238
discoverlife NONE 58190
gbif NONE 28638
gbif HAS_ACCEPTED_NAME 24675
gbif SYNONYM_OF 16964
itis NONE 45312
itis HAS_ACCEPTED_NAME 10142
itis SYNONYM_OF 3145
mdd NONE 57347
mdd SYNONYM_OF 31
mdd HAS_ACCEPTED_NAME 737
ncbi NONE 39870
ncbi SAME_AS 15705
ncbi SYNONYM_OF 2737
ncbi COMMON_NAME_OF 7
pbdb NONE 55148
pbdb HAS_ACCEPTED_NAME 2869
pbdb SYNONYM_OF 246
tpt NONE 56879
tpt SYNONYM_OF 103
tpt HAS_ACCEPTED_NAME 1207
wfo NONE 46940
wfo HAS_ACCEPTED_NAME 7954
wfo SYNONYM_OF 4271
wfo HAS_UNCHECKED_NAME 1612
worms NONE 51896
worms HAS_ACCEPTED_NAME 5846
worms SYNONYM_OF 1421
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
2024-11-18T02:03:28Z note found unresolved reference [c8bdd05a-1fad-44c3-96fa-367fb96ec0de]
2024-11-18T02:03:28Z note found unresolved reference [https://arctos.database.museum/guid/CHAS:Bird:18783]
2024-11-18T02:03:28Z note found unresolved reference [https://arctos.database.museum/guid/CHAS:Bird:18830]
2024-11-18T02:03:28Z note found unresolved reference [https://arctos.database.museum/guid/CHAS:Bird:8302]

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

Most frequently occurring review notes, if any.
reviewComment count
found unresolved reference [c8bdd05a-1fad-44c3-96fa-367fb96ec0de] 1
found unresolved reference [https://arctos.database.museum/guid/CHAS:Bird:18783] 1
found unresolved reference [https://arctos.database.museum/guid/CHAS:Bird:18830] 1
found unresolved reference [https://arctos.database.museum/guid/CHAS:Bird:8302] 1

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 (2024-11-18) 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.

Author contributions

Nomer was responsible for name alignments. Elton carried out dataset extraction, and generated the review notes.

References

ICZN. 1999. “International Code of Zoological Nomenclature.” The International Trust for Zoological Nomenclature, London, UK. https://www.iczn.org/the-code/the-code-online/.
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.
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.