A Review of Biotic Interactions and Taxon Names Found in globalbioticinteractions/msu-msuc

by Nomer and Elton, two naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

https://github.com/globalbioticinteractions/msu-msuc/issues

2024-04-29

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/msu-msuc, is 20.6MiB in size and contains 7,879 interaction with 6 unique types of associations (e.g., interactsWith) between 1,381 primary taxon (e.g., Orchopeas howardi) and 1,648 associated taxon (e.g., S. niger rufiventer). 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:

The Albert J. Cook Arthropod Research Collection https://github.com/globalbioticinteractions/msu-msuc/archive/38960906380443bd8108c9e44aeff4590d8d0b50.zip 2024-04-20T03:15:32.225Z f1c1de76413bece7cc53a4838049b46eb17177960faebba685833f43f8a3adcf

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/msu-msuc 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 0.13.2
nomer 0.5.8
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. 20.6MiB) under review 
elton pull globalbioticinteractions/msu-msuc

# generate review notes
elton review globalbioticinteractions/msu-msuc\
 > review.tsv

# export indexed interaction records
elton interactions globalbioticinteractions/msu-msuc\
 > interactions.tsv

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/msu-msuc\
 | 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/msu-msuc, is 20.6MiB in size and contains 7,879 interaction with 6 unique types of associations (e.g., interactsWith) between 1,381 primary taxon (e.g., Orchopeas howardi) and 1,648 associated taxon (e.g., S. niger rufiventer).

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
Amphipyra pyramidoides adjacentTo wild grape in sand dunes https://scan-bugs.org:443/portal/collections/individual/index.php?occid=16773622
Noctuidae adjacentTo scrub oak https://scan-bugs.org:443/portal/collections/individual/index.php?occid=16773824
Noctuidae adjacentTo scrub oak https://scan-bugs.org:443/portal/collections/individual/index.php?occid=16773827
Simyra insularis adjacentTo cattail https://scan-bugs.org:443/portal/collections/individual/index.php?occid=16775527
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
interactsWith 7070
adjacentTo 710
hasHost 95
eats 14
visits 1
killedBy 1
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Orchopeas howardi 485
Macrochelidae 174
Pyralidae 122
Noctuidae 108
Megachile inermis 106
Tortricidae 103
Phthiraptera 89
Hoplopleura hesperomydis 88
Coptotriche citrinipennella 75
Euphyes vestris metacomet 74
Malacosoma californicum 73
Dermanyssidae 69
Hemileuca maia 66
Phyllonorycter 59
Lophocampa maculata 53
Geometridae 53
Megachile gemula 51
Bucculatrix ainsliella 49
Gracillaria syringella 48
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
S. niger rufiventer 293
Quercus 289
Necrophorus pustulatus 175
S. carolinensis 134
Quercus rubra 121
Quercus alba 97
Salix 94
Juglans nigra 81
on 80
Populus tremuloides 76
Prunus 70
mildweed 67
Quercus bicolor 64
Silpha surinamensis 61
Ostrya virginiana 60
Prunus serotina 59
chicken 52
Quercus ellipsoidalis 50
Acer saccharum 50
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Orchopeas howardi interactsWith S. niger rufiventer 258
Macrochelidae interactsWith Necrophorus pustulatus 141
Orchopeas howardi interactsWith S. carolinensis 134
Euphyes vestris metacomet adjacentTo mildweed 67
Pyralidae interactsWith Juglans nigra 54
Gracillaria syringella interactsWith Syringa vulgaris 48
Phyllonorycter interactsWith Populus tremuloides 40
Anisota consularis interactsWith Q. alba 39
Dorsipes balli interactsWith Carabus taedatus 38
Bucculatrix ainsliella interactsWith Quercus rubra 36
Hoplopleura hesperomydis interactsWith Peromyscus leucopus (Rafinesque) Female 35
Orchopeas howardi hasHost S. niger rufiventer 34
Phyllonorycter restrictella interactsWith Fagus grandifolia 33
Cameraria bethunella interactsWith Quercus rubra 32
Macrochelidae interactsWith Silpha surinamensis 29
Orchopeas howardi interactsWith s. niger rufiventer 28
Endothenia hebesana interactsWith Gentiana andrewsii 28
Acaridae interactsWith Silpha surinamensis 28
Megachile sculpturalis interactsWith Styphnolobium japonicum 28

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 Animalia->Plantae Animalia->Plantae Fungi Fungi Animalia->Fungi Plantae->Plantae Fungi->Plantae
interactions Acanthopteroctetidae Acanthopteroctetidae Rhamnaceae Rhamnaceae Acanthopteroctetidae->Rhamnaceae Acaridae Acaridae Staphylinidae Staphylinidae Acaridae->Staphylinidae Andrenidae Andrenidae Asteraceae Asteraceae Andrenidae->Asteraceae Ericaceae Ericaceae Andrenidae->Ericaceae Fabaceae Fabaceae Andrenidae->Fabaceae Rosaceae Rosaceae Andrenidae->Rosaceae Salicaceae Salicaceae Andrenidae->Salicaceae Apocynaceae Apocynaceae Rosaceae->Apocynaceae Aphididae Aphididae Aphididae->Asteraceae Aphididae->Salicaceae Araceae Araceae Aphididae->Araceae Cornaceae Cornaceae Aphididae->Cornaceae Aphididae->Cornaceae Apiaceae Apiaceae Aphididae->Apiaceae Aphididae->Apocynaceae Dennstaedtiaceae Dennstaedtiaceae Aphididae->Dennstaedtiaceae Fagaceae Fagaceae Apocynaceae->Fagaceae Sapindaceae Sapindaceae Apocynaceae->Sapindaceae Argyresthiidae Argyresthiidae Cupressaceae Cupressaceae Argyresthiidae->Cupressaceae Attevidae Attevidae Simaroubaceae Simaroubaceae Attevidae->Simaroubaceae Blastobasidae Blastobasidae Anacardiaceae Anacardiaceae Blastobasidae->Anacardiaceae Juglandaceae Juglandaceae Blastobasidae->Juglandaceae Bucculatricidae Bucculatricidae Bucculatricidae->Fagaceae Amaranthaceae Amaranthaceae Bucculatricidae->Amaranthaceae Cerambycidae Cerambycidae Cerambycidae->Sapindaceae Myrtaceae Myrtaceae Cerambycidae->Myrtaceae Ceratophyllidae Ceratophyllidae Sciuridae Sciuridae Ceratophyllidae->Sciuridae Ceratophyllidae->Sciuridae Canidae Canidae Ceratophyllidae->Canidae Cricetidae Cricetidae Ceratophyllidae->Cricetidae Chernetidae Chernetidae Chernetidae->Cricetidae Erebidae Erebidae Chernetidae->Erebidae Erebidae->Asteraceae Erebidae->Ericaceae Erebidae->Fabaceae Erebidae->Rosaceae Erebidae->Salicaceae Erebidae->Apocynaceae Erebidae->Fagaceae Erebidae->Sapindaceae Erebidae->Anacardiaceae Erebidae->Juglandaceae Erebidae->Amaranthaceae Betulaceae Betulaceae Erebidae->Betulaceae Malvaceae Malvaceae Erebidae->Malvaceae Pinaceae Pinaceae Erebidae->Pinaceae Ulmaceae Ulmaceae Erebidae->Ulmaceae Ranunculaceae Ranunculaceae Erebidae->Ranunculaceae Erebidae->Ranunculaceae Hamamelidaceae Hamamelidaceae Erebidae->Hamamelidaceae Laetiporaceae Laetiporaceae Erebidae->Laetiporaceae Myricaceae Myricaceae Erebidae->Myricaceae Oleaceae Oleaceae Erebidae->Oleaceae Plantaginaceae Plantaginaceae Erebidae->Plantaginaceae Polygonaceae Polygonaceae Erebidae->Polygonaceae Rubiaceae Rubiaceae Erebidae->Rubiaceae Viburnaceae Viburnaceae Erebidae->Viburnaceae Vitaceae Vitaceae Erebidae->Vitaceae Chthoniidae Chthoniidae Chthoniidae->Cricetidae Coleophoridae Coleophoridae Coleophoridae->Rosaceae Coleophoridae->Salicaceae Coleophoridae->Betulaceae Elaeagnaceae Elaeagnaceae Coleophoridae->Elaeagnaceae Coleophoridae->Malvaceae Coleophoridae->Pinaceae Tingidae Tingidae Coleophoridae->Tingidae Coleophoridae->Ulmaceae Colpocephalidae Colpocephalidae Accipitridae Accipitridae Colpocephalidae->Accipitridae Cosmopterigidae Cosmopterigidae Cosmopterigidae->Rosaceae Typhaceae Typhaceae Cosmopterigidae->Typhaceae Cossidae Cossidae Cossidae->Fagaceae Cossidae->Pinaceae Penaeidae Penaeidae Cossidae->Penaeidae Crambidae Crambidae Crambidae->Fabaceae Crambidae->Apiaceae Crambidae->Apocynaceae Crambidae->Malvaceae Cyperaceae Cyperaceae Crambidae->Cyperaceae Eumenidae Eumenidae Crambidae->Eumenidae Poaceae Poaceae Crambidae->Poaceae Scrophulariaceae Scrophulariaceae Crambidae->Scrophulariaceae Ctenophthalmidae Ctenophthalmidae Talpidae Talpidae Ctenophthalmidae->Talpidae Muridae Muridae Ctenophthalmidae->Muridae Curculionidae Curculionidae Curculionidae->Pinaceae Curculionidae->Pinaceae Euphorbiaceae Euphorbiaceae Curculionidae->Euphorbiaceae Depressariidae Depressariidae Depressariidae->Apiaceae Depressariidae->Fagaceae Dermanyssidae Dermanyssidae Dermanyssidae->Dermanyssidae Mimidae Mimidae Dermanyssidae->Mimidae Passeridae Passeridae Dermanyssidae->Passeridae Turdidae Turdidae Dermanyssidae->Turdidae Discourellidae Discourellidae Trogidae Trogidae Discourellidae->Trogidae Doidae Doidae Doidae->Euphorbiaceae Drepanidae Drepanidae Drepanidae->Cornaceae Elachistidae Elachistidae Elachistidae->Malvaceae Erythraeidae Erythraeidae Sphagnaceae Sphagnaceae Erythraeidae->Sphagnaceae Gelechiidae Gelechiidae Gelechiidae->Rhamnaceae Gelechiidae->Asteraceae Gelechiidae->Ericaceae Gelechiidae->Fabaceae Gelechiidae->Rosaceae Gelechiidae->Salicaceae Gelechiidae->Fagaceae Gelechiidae->Sapindaceae Gelechiidae->Cupressaceae Gelechiidae->Anacardiaceae Gelechiidae->Amaranthaceae Gelechiidae->Betulaceae Gelechiidae->Pinaceae Gelechiidae->Hamamelidaceae Gelechiidae->Gelechiidae Cistaceae Cistaceae Gelechiidae->Cistaceae Combretaceae Combretaceae Gelechiidae->Combretaceae Lamiaceae Lamiaceae Gelechiidae->Lamiaceae Geometridae Geometridae Geometridae->Asteraceae Geometridae->Fabaceae Geometridae->Rosaceae Geometridae->Salicaceae Geometridae->Fagaceae Geometridae->Sapindaceae Geometridae->Juglandaceae Geometridae->Betulaceae Geometridae->Malvaceae Geometridae->Pinaceae Geometridae->Tingidae Geometridae->Ulmaceae Geometridae->Oleaceae Geometridae->Vitaceae Passifloraceae Passifloraceae Geometridae->Passifloraceae Pteromalidae Pteromalidae Geometridae->Pteromalidae Gracillariidae Gracillariidae Gracillariidae->Asteraceae Gracillariidae->Ericaceae Gracillariidae->Fabaceae Gracillariidae->Rosaceae Gracillariidae->Salicaceae Gracillariidae->Fagaceae Gracillariidae->Sapindaceae Gracillariidae->Anacardiaceae Gracillariidae->Juglandaceae Gracillariidae->Betulaceae Gracillariidae->Malvaceae Gracillariidae->Ulmaceae Gracillariidae->Hamamelidaceae Gracillariidae->Myricaceae Gracillariidae->Oleaceae Gracillariidae->Vitaceae Cannabaceae Cannabaceae Gracillariidae->Cannabaceae Caprifoliaceae Caprifoliaceae Gracillariidae->Caprifoliaceae Grossulariaceae Grossulariaceae Gracillariidae->Grossulariaceae Thymelaeaceae Thymelaeaceae Gracillariidae->Thymelaeaceae Heliodinidae Heliodinidae Nyctaginaceae Nyctaginaceae Heliodinidae->Nyctaginaceae Onagraceae Onagraceae Heliodinidae->Onagraceae Heliozelidae Heliozelidae Heliozelidae->Cornaceae Hesperiidae Hesperiidae Hesperiidae->Fabaceae Hesperiidae->Rosaceae Hesperiidae->Fagaceae Hesperiidae->Amaranthaceae Hesperiidae->Amaranthaceae Hesperiidae->Poaceae Hesperiidae->Ranunculaceae Cannaceae Cannaceae Hesperiidae->Cannaceae Hippoboscidae Hippoboscidae Strigidae Strigidae Hippoboscidae->Strigidae Histiostomatidae Histiostomatidae Histiostomatidae->Staphylinidae Ichneumonidae Ichneumonidae Pieridae Pieridae Ichneumonidae->Pieridae Saturniidae Saturniidae Ichneumonidae->Saturniidae Brassicaceae Brassicaceae Pieridae->Brassicaceae Psilostomidae Psilostomidae Pieridae->Psilostomidae Saturniidae->Fabaceae Saturniidae->Rosaceae Saturniidae->Salicaceae Saturniidae->Fagaceae Saturniidae->Betulaceae Saturniidae->Pinaceae Saturniidae->Euphorbiaceae Saturniidae->Rubiaceae Lauraceae Lauraceae Saturniidae->Lauraceae Magnoliaceae Magnoliaceae Saturniidae->Magnoliaceae Menyanthaceae Menyanthaceae Saturniidae->Menyanthaceae Incurvariidae Incurvariidae Incurvariidae->Rosaceae Incurvariidae->Pinaceae Ischnopsyllidae Ischnopsyllidae Vespertilionidae Vespertilionidae Ischnopsyllidae->Vespertilionidae Ixodidae Ixodidae Leporidae Leporidae Ixodidae->Leporidae Lasiocampidae Lasiocampidae Lasiocampidae->Rhamnaceae Lasiocampidae->Rosaceae Lasiocampidae->Fagaceae Lasiocampidae->Sapindaceae Lasiocampidae->Hamamelidaceae Leptopsyllidae Leptopsyllidae Leptopsyllidae->Muridae Liacaridae Liacaridae Liacaridae->Turdidae Limacodidae Limacodidae Limacodidae->Fabaceae Limacodidae->Rosaceae Limacodidae->Fagaceae Limacodidae->Sapindaceae Limacodidae->Anacardiaceae Limacodidae->Betulaceae Limacodidae->Malvaceae Limacodidae->Ulmaceae Linognathidae Linognathidae Linognathidae->Canidae Lycaenidae Lycaenidae Lycaenidae->Fabaceae Lycaenidae->Rosaceae Lycaenidae->Salicaceae Lycaenidae->Apocynaceae Lycaenidae->Fagaceae Lycaenidae->Viburnaceae Smilacaceae Smilacaceae Lycaenidae->Smilacaceae Lyonetiidae Lyonetiidae Lyonetiidae->Fabaceae Macrochelidae Macrochelidae Macrochelidae->Staphylinidae Macrochelidae->Sphagnaceae Megachilidae Megachilidae Megachilidae->Asteraceae Megachilidae->Fabaceae Megachilidae->Rosaceae Megachilidae->Apocynaceae Megachilidae->Lamiaceae Megachilidae->Caprifoliaceae Megachilidae->Onagraceae Megachilidae->Brassicaceae Campanulaceae Campanulaceae Megachilidae->Campanulaceae Verbenaceae Verbenaceae Megachilidae->Verbenaceae Megalopygidae Megalopygidae Megalopygidae->Fabaceae Megalopygidae->Rosaceae Menoponidae Menoponidae Apodidae Apodidae Menoponidae->Apodidae Momphidae Momphidae Momphidae->Onagraceae Neilonellidae Neilonellidae Neilonellidae->Rhamnaceae Neilonellidae->Fagaceae Neilonellidae->Sapindaceae Nepticulidae Nepticulidae Nepticulidae->Rhamnaceae Nepticulidae->Rosaceae Nepticulidae->Salicaceae Nepticulidae->Fagaceae Nepticulidae->Sapindaceae Nepticulidae->Ulmaceae Noctuidae Noctuidae Noctuidae->Asteraceae Noctuidae->Asteraceae Noctuidae->Fabaceae Noctuidae->Rosaceae Noctuidae->Salicaceae Noctuidae->Cornaceae Noctuidae->Apiaceae Noctuidae->Apocynaceae Noctuidae->Fagaceae Noctuidae->Sapindaceae Noctuidae->Cupressaceae Noctuidae->Juglandaceae Noctuidae->Amaranthaceae Noctuidae->Malvaceae Noctuidae->Pinaceae Noctuidae->Tingidae Noctuidae->Ulmaceae Noctuidae->Typhaceae Noctuidae->Poaceae Noctuidae->Oleaceae Noctuidae->Plantaginaceae Noctuidae->Polygonaceae Noctuidae->Viburnaceae Noctuidae->Vitaceae Noctuidae->Combretaceae Noctuidae->Lamiaceae Noctuidae->Cannabaceae Noctuidae->Onagraceae Asparagaceae Asparagaceae Noctuidae->Asparagaceae Eremiaphilidae Eremiaphilidae Noctuidae->Eremiaphilidae Metacapnodiaceae Metacapnodiaceae Noctuidae->Metacapnodiaceae Polemoniaceae Polemoniaceae Noctuidae->Polemoniaceae Primulaceae Primulaceae Noctuidae->Primulaceae Sarraceniaceae Sarraceniaceae Noctuidae->Sarraceniaceae Saururaceae Saururaceae Noctuidae->Saururaceae Solanaceae Solanaceae Noctuidae->Solanaceae Nolidae Nolidae Nolidae->Fagaceae Notodontidae Notodontidae Notodontidae->Rosaceae Notodontidae->Salicaceae Notodontidae->Fagaceae Notodontidae->Anacardiaceae Notodontidae->Juglandaceae Notodontidae->Malvaceae Crassulaceae Crassulaceae Notodontidae->Crassulaceae Nymphalidae Nymphalidae Nymphalidae->Rhamnaceae Nymphalidae->Asteraceae Nymphalidae->Rosaceae Nymphalidae->Salicaceae Nymphalidae->Apocynaceae Nymphalidae->Fagaceae Nymphalidae->Betulaceae Nymphalidae->Ulmaceae Nymphalidae->Cyperaceae Nymphalidae->Oleaceae Nymphalidae->Sphagnaceae Nymphalidae->Passifloraceae Nymphalidae->Cannabaceae Nymphalidae->Grossulariaceae Nymphalidae->Metacapnodiaceae Orobanchaceae Orobanchaceae Nymphalidae->Orobanchaceae Urticaceae Urticaceae Nymphalidae->Urticaceae Oecophoridae Oecophoridae Oecophoridae->Rhamnaceae Oecophoridae->Fagaceae Oecophoridae->Anacardiaceae Oecophoridae->Ulmaceae Oecophoridae->Ranunculaceae Orchidaceae Orchidaceae Orchidaceae->Asteraceae Orchidaceae->Rosaceae Papilionidae Papilionidae Papilionidae->Rosaceae Papilionidae->Apiaceae Papilionidae->Oleaceae Papilionidae->Lauraceae Papilionidae->Lauraceae Aristolochiaceae Aristolochiaceae Papilionidae->Aristolochiaceae Rutaceae Rutaceae Papilionidae->Rutaceae Philopteridae Philopteridae Philopteridae->Accipitridae Columbidae Columbidae Philopteridae->Columbidae Phasianidae Phasianidae Philopteridae->Phasianidae Plutellidae Plutellidae Plutellidae->Rosaceae Plutellidae->Caprifoliaceae Plutellidae->Brassicaceae Celastraceae Celastraceae Plutellidae->Celastraceae Prodoxidae Prodoxidae Prodoxidae->Asparagaceae Pterophoridae Pterophoridae Pterophoridae->Rhamnaceae Pterophoridae->Asteraceae Pterophoridae->Rosaceae Pterophoridae->Vitaceae Convolvulaceae Convolvulaceae Pterophoridae->Convolvulaceae Geraniaceae Geraniaceae Pterophoridae->Geraniaceae Pulicidae Pulicidae Pulicidae->Canidae Pulicidae->Muridae Dipodidae Dipodidae Pulicidae->Dipodidae Pyralidae Pyralidae Pyralidae->Rhamnaceae Pyralidae->Rosaceae Pyralidae->Cornaceae Pyralidae->Apiaceae Pyralidae->Fagaceae Pyralidae->Sapindaceae Pyralidae->Anacardiaceae Pyralidae->Juglandaceae Pyralidae->Typhaceae Pyralidae->Poaceae Pyralidae->Scrophulariaceae Pyralidae->Combretaceae Pyralidae->Megachilidae Pyralidae->Convolvulaceae Apidae Apidae Pyralidae->Apidae Raphignathidae Raphignathidae Raphignathidae->Turdidae Reduviidae Reduviidae Reduviidae->Nymphalidae Rhinotermitidae Rhinotermitidae Rhinotermitidae->Fagaceae Rhopalopsyllidae Rhopalopsyllidae Rhopalopsyllidae->Cricetidae Riodinidae Riodinidae Riodinidae->Asteraceae Scythrididae Scythrididae Scythrididae->Asteraceae Sesiidae Sesiidae Sesiidae->Rosaceae Sesiidae->Salicaceae Sesiidae->Malvaceae Sesiidae->Pinaceae Sesiidae->Viburnaceae Sesiidae->Vitaceae Sesiidae->Onagraceae Boraginaceae Boraginaceae Sesiidae->Boraginaceae Sphingidae Sphingidae Sphingidae->Asteraceae Sphingidae->Rosaceae Sphingidae->Salicaceae Sphingidae->Juglandaceae Sphingidae->Malvaceae Sphingidae->Oleaceae Sphingidae->Viburnaceae Sphingidae->Vitaceae Sphingidae->Caprifoliaceae Sphingidae->Onagraceae Sphingidae->Brassicaceae Sphingidae->Polemoniaceae Sphingidae->Solanaceae Bignoniaceae Bignoniaceae Sphingidae->Bignoniaceae Carabidae Carabidae Sphingidae->Carabidae Caryophyllaceae Caryophyllaceae Sphingidae->Caryophyllaceae Stereocaulaceae Stereocaulaceae Melastomataceae Melastomataceae Stereocaulaceae->Melastomataceae Stigmaeidae Stigmaeidae Stigmaeidae->Sphagnaceae Stratiomyidae Stratiomyidae Stratiomyidae->Ulmaceae Termitidae Termitidae Burseraceae Burseraceae Termitidae->Burseraceae Tischeriidae Tischeriidae Tischeriidae->Asteraceae Tischeriidae->Rosaceae Tischeriidae->Fagaceae Tortricidae Tortricidae Tortricidae->Rhamnaceae Tortricidae->Asteraceae Tortricidae->Fabaceae Tortricidae->Rosaceae Tortricidae->Salicaceae Tortricidae->Cornaceae Tortricidae->Fagaceae Tortricidae->Sapindaceae Tortricidae->Anacardiaceae Tortricidae->Juglandaceae Tortricidae->Betulaceae Tortricidae->Malvaceae Tortricidae->Pinaceae Tortricidae->Typhaceae Tortricidae->Ranunculaceae Tortricidae->Viburnaceae Tortricidae->Vitaceae Tortricidae->Lamiaceae Bunocotylidae Bunocotylidae Tortricidae->Bunocotylidae Araliaceae Araliaceae Tortricidae->Araliaceae Gentianaceae Gentianaceae Tortricidae->Gentianaceae Yponomeutidae Yponomeutidae Yponomeutidae->Rosaceae Yponomeutidae->Fagaceae Yponomeutidae->Sapindaceae Yponomeutidae->Juglandaceae Yponomeutidae->Betulaceae Yponomeutidae->Oleaceae Yponomeutidae->Nyctaginaceae Yponomeutidae->Celastraceae Zygaenidae Zygaenidae Zygaenidae->Rosaceae Zygaenidae->Vitaceae

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, and pbdb). 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
Acronicta HAS_ACCEPTED_NAME col Acronicta
Acyrthosiphon pisum SYNONYM_OF col Acyrthosiphon primulae
Acyrthosiphon pisum HAS_ACCEPTED_NAME col Acyrthosiphon pisum
Acyrthosiphon pisum SYNONYM_OF col Acyrthosiphon pisum pisum
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 1147
col family 84
col genus 252
col kingdom 1
col nanorder 1
col order 4
col parvorder 1
col section 1
col species 1196
col subclass 1
col subfamily 13
col subgenus 10
col suborder 1
col subspecies 42
col superfamily 1
col superorder 2
col tribe 1
col variety 8
discoverlife NA 2709
discoverlife species 20
gbif NA 1031
gbif class 1
gbif family 95
gbif genus 274
gbif kingdom 1
gbif order 4
gbif species 1288
gbif subspecies 59
gbif variety 13
itis NA 1503
itis family 81
itis genus 208
itis kingdom 1
itis order 5
itis species 855
itis subclass 1
itis subfamily 17
itis suborder 2
itis subspecies 45
itis superfamily 1
itis superorder 2
itis variety 9
mdd NA 2728
ncbi NA 1206
ncbi class 1
ncbi family 85
ncbi genus 239
ncbi order 5
ncbi species 1154
ncbi subfamily 14
ncbi subgenus 5
ncbi suborder 2
ncbi subspecies 19
ncbi superfamily 1
ncbi superorder 2
ncbi varietas 1
pbdb NA 2436
pbdb class 1
pbdb family 57
pbdb genus 130
pbdb kingdom 1
pbdb order 6
pbdb species 86
pbdb subfamily 9
pbdb suborder 2
pbdb superfamily 1
pbdb superorder 2
pbdb unranked clade 1
tpt NA 2564
tpt family 5
tpt genus 24
tpt species 135
wfo NA 2287
wfo family 3
wfo genus 141
wfo phylum 1
wfo species 291
wfo subspecies 6
wfo variety 4
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 1617
col SYNONYM_OF 367
col NONE 1348
discoverlife NONE 3025
discoverlife HAS_ACCEPTED_NAME 20
discoverlife SYNONYM_OF 5
discoverlife HOMONYM_OF 3
gbif HAS_ACCEPTED_NAME 1911
gbif SYNONYM_OF 562
gbif NONE 1217
itis HAS_ACCEPTED_NAME 1231
itis SYNONYM_OF 133
itis NONE 1708
mdd NONE 2993
mdd HAS_ACCEPTED_NAME 43
ncbi SAME_AS 1539
ncbi NONE 1419
ncbi SYNONYM_OF 71
ncbi COMMON_NAME_OF 39
pbdb NONE 2667
pbdb HAS_ACCEPTED_NAME 370
pbdb SYNONYM_OF 20
tpt NONE 2862
tpt HAS_ACCEPTED_NAME 171
tpt SYNONYM_OF 66
wfo NONE 2513
wfo SYNONYM_OF 111
wfo HAS_ACCEPTED_NAME 480
wfo HAS_UNCHECKED_NAME 65
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)

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
2024-04-29T03:42:31Z note date [0000-01-01T00:00:00Z] occurred in the first century AD
2024-04-29T03:42:31Z note date [0000-01-01T00:00:00Z] occurred in the first century AD
2024-04-29T03:42:31Z note source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder
2024-04-29T03:42:32Z note found unsupported interaction type with name: [reared ex Caenothus herbaceous recv]

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

Most frequently occurring review notes, if any.
reviewComment count
source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder 138
found unsupported interaction type with name: [reared ex Cercis Canadensis LOT] 5
date [0000-01-01T00:00:00Z] occurred in the first century AD 4
found unsupported interaction type with name: [Andropogon] 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 (2024-04-29) 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.