A Review of Biotic Interactions and Taxon Names Found in globalbioticinteractions/ucm-ucmc

by Nomer and Elton, two naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

https://github.com/globalbioticinteractions/ucm-ucmc/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/ucm-ucmc, is 5.69MiB in size and contains 9,592 interaction with 2 unique types of associations (e.g., interactsWith) between 889 primary taxa (e.g., Lasioglossum) and 451 associated taxa (e.g., Penstemon degeneri). 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 Colorado Museum of Natural History Entomology Collection https://github.com/globalbioticinteractions/ucm-ucmc/archive/60530dcc82d33c9675a4026ad60dc40bea8f2a91.zip 2024-11-16T12:25:18.505Z 9d8d9fe4018eff3a20ab33e4dfc6495b8c5a1460c2d672b1b299fb71c7dc945a

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/ucm-ucmc 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. 5.69MiB) under review 
elton pull globalbioticinteractions/ucm-ucmc

# generate review notes
elton review globalbioticinteractions/ucm-ucmc\
 > review.tsv

# export indexed interaction records
elton interactions globalbioticinteractions/ucm-ucmc\
 > interactions.tsv

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/ucm-ucmc\
 | 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/ucm-ucmc, is 5.69MiB in size and contains 9,592 interaction with 2 unique types of associations (e.g., interactsWith) between 889 primary taxa (e.g., Lasioglossum) and 451 associated taxa (e.g., Penstemon degeneri).

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
Cerceris frontata interactsWith Eriogonum effusum https://scan-bugs.org:443/portal/collections/individual/index.php?occid=16983520
Philanthus crabroniformis interactsWith Geranium fremontii https://scan-bugs.org:443/portal/collections/individual/index.php?occid=16983545
Halictus avalonensis interactsWith Anthemis https://scan-bugs.org:443/portal/collections/individual/index.php?occid=29534362
Melanoplus yarrowii interactsWith Citrus https://scan-bugs.org:443/portal/collections/individual/index.php?occid=29534363
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
interactsWith 9540
adjacentTo 52
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Lasioglossum 411
Andrena 387
Bombus huntii 330
Bombus centralis 253
Bombus rufocinctus 191
Bombus appositus 165
Halictus tripartitus 141
Paratiphia 137
Bombus fervidus 134
Bombus pensylvanicus 133
Bombus flavifrons 125
Dendroctonus ponderosae 124
Bombus sylvicola 108
Bombus nevadensis 103
Bombus bifarius 102
Bombus morrisoni 83
Eurygaster 74
Augochlorella aurata 74
Osmia 72
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
Penstemon degeneri 566
Salix 488
Tamarix 400
Chrysothamnus 369
Melilotus 367
Asclepias 342
Helianthus 306
Pinus ponderosa 301
Solidago 300
Grindelia 174
Clematis ligusticifolia 139
Cardaria 114
Rhus trilobata 110
Erigeron 102
Cleome 101
Heterotheca villosa 98
Eriogonum effusum 93
Prunus virginiana 91
Astragalus 89
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Andrena interactsWith Salix 211
Paratiphia interactsWith Tamarix 123
Bombus centralis interactsWith Penstemon degeneri 119
Lasioglossum interactsWith Salix 115
Bombus huntii interactsWith Chrysothamnus 84
Eurygaster interactsWith Poa 74
Bombus huntii interactsWith Penstemon degeneri 64
Dendroctonus ponderosae interactsWith Pinus ponderosa 57
Dendroctonus pseudotsugae interactsWith Pseudotsuga menziesii 57
Blepharida rhois interactsWith Rhus trilobata 55
Kleidocerys interactsWith Betula papyrifera 50
Smicronyx sordidus interactsWith Helianthus 50
Ips plastographus maritimus interactsWith Pinus radiata 50
Bembix pallidipicta interactsWith Asclepias 48
Deraeocoris interactsWith Pinus ponderosa 47
Gymnetron tetrum interactsWith Verbascum 44
Bombus appositus interactsWith Delphinium barbeyi 43
Dendroctonus ponderosae interactsWith Pinus contorta 40
Andrena interactsWith Prunus virginiana 39

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 Fungi Fungi Animalia->Fungi Plantae Plantae Animalia->Plantae Plantae->Plantae
interactions Acrididae Acrididae Anacardiaceae Anacardiaceae Acrididae->Anacardiaceae Asteraceae Asteraceae Acrididae->Asteraceae Berberidaceae Berberidaceae Acrididae->Berberidaceae Eremiaphilidae Eremiaphilidae Acrididae->Eremiaphilidae Euphorbiaceae Euphorbiaceae Acrididae->Euphorbiaceae Fabaceae Fabaceae Acrididae->Fabaceae Grossulariaceae Grossulariaceae Acrididae->Grossulariaceae Pinaceae Pinaceae Acrididae->Pinaceae Poaceae Poaceae Acrididae->Poaceae Rosaceae Rosaceae Acrididae->Rosaceae Rutaceae Rutaceae Acrididae->Rutaceae Asteraceae->Asteraceae Asteraceae->Fabaceae Asteraceae->Rosaceae Crassulaceae Crassulaceae Asteraceae->Crassulaceae Salicaceae Salicaceae Asteraceae->Salicaceae Geraniaceae Geraniaceae Asteraceae->Geraniaceae Champiaceae Champiaceae Asteraceae->Champiaceae Plantaginaceae Plantaginaceae Asteraceae->Plantaginaceae Poaceae->Asteraceae Poaceae->Fabaceae Poaceae->Rosaceae Cleomaceae Cleomaceae Poaceae->Cleomaceae Polygonaceae Polygonaceae Poaceae->Polygonaceae Poaceae->Salicaceae Poaceae->Geraniaceae Hydrophyllaceae Hydrophyllaceae Poaceae->Hydrophyllaceae Alydidae Alydidae Alydidae->Anacardiaceae Alydidae->Asteraceae Alydidae->Fabaceae Andrenidae Andrenidae Andrenidae->Anacardiaceae Andrenidae->Asteraceae Andrenidae->Berberidaceae Andrenidae->Fabaceae Andrenidae->Grossulariaceae Andrenidae->Poaceae Andrenidae->Rosaceae Apiaceae Apiaceae Andrenidae->Apiaceae Asparagaceae Asparagaceae Andrenidae->Asparagaceae Brassicaceae Brassicaceae Andrenidae->Brassicaceae Cactaceae Cactaceae Andrenidae->Cactaceae Caryophyllaceae Caryophyllaceae Andrenidae->Caryophyllaceae Andrenidae->Cleomaceae Andrenidae->Crassulaceae Cupressaceae Cupressaceae Andrenidae->Cupressaceae Ericaceae Ericaceae Andrenidae->Ericaceae Lamiaceae Lamiaceae Andrenidae->Lamiaceae Loasaceae Loasaceae Andrenidae->Loasaceae Montiaceae Montiaceae Andrenidae->Montiaceae Andrenidae->Polygonaceae Andrenidae->Salicaceae Tamaricaceae Tamaricaceae Andrenidae->Tamaricaceae Verbenaceae Verbenaceae Andrenidae->Verbenaceae Apiaceae->Fabaceae Apiaceae->Salicaceae Apiaceae->Geraniaceae Aphididae Aphididae Aphididae->Ericaceae Apidae Apidae Apidae->Anacardiaceae Apidae->Asteraceae Apidae->Berberidaceae Apidae->Euphorbiaceae Apidae->Fabaceae Apidae->Grossulariaceae Apidae->Pinaceae Apidae->Poaceae Apidae->Rosaceae Apidae->Apiaceae Apidae->Asparagaceae Apidae->Brassicaceae Apidae->Cactaceae Apidae->Caryophyllaceae Apidae->Cleomaceae Apidae->Crassulaceae Apidae->Cupressaceae Apidae->Ericaceae Apidae->Lamiaceae Apidae->Loasaceae Apidae->Polygonaceae Apidae->Salicaceae Apidae->Tamaricaceae Apidae->Geraniaceae Amaryllidaceae Amaryllidaceae Apidae->Amaryllidaceae Apocynaceae Apocynaceae Apidae->Apocynaceae Boraginaceae Boraginaceae Apidae->Boraginaceae Campanulaceae Campanulaceae Apidae->Campanulaceae Caprifoliaceae Caprifoliaceae Apidae->Caprifoliaceae Apidae->Champiaceae Combretaceae Combretaceae Apidae->Combretaceae Convolvulaceae Convolvulaceae Apidae->Convolvulaceae Cucurbitaceae Cucurbitaceae Apidae->Cucurbitaceae Cyprididae Cyprididae Apidae->Cyprididae Fringillidae Fringillidae Apidae->Fringillidae Gentianaceae Gentianaceae Apidae->Gentianaceae Hydrangeaceae Hydrangeaceae Apidae->Hydrangeaceae Apidae->Hydrophyllaceae Hypericaceae Hypericaceae Apidae->Hypericaceae Iridaceae Iridaceae Apidae->Iridaceae Liliaceae Liliaceae Apidae->Liliaceae Linaceae Linaceae Apidae->Linaceae Malvaceae Malvaceae Apidae->Malvaceae Onagraceae Onagraceae Apidae->Onagraceae Orobanchaceae Orobanchaceae Apidae->Orobanchaceae Papaveraceae Papaveraceae Apidae->Papaveraceae Apidae->Plantaginaceae Polemoniaceae Polemoniaceae Apidae->Polemoniaceae Psilostomidae Psilostomidae Apidae->Psilostomidae Ranunculaceae Ranunculaceae Apidae->Ranunculaceae Saxifragaceae Saxifragaceae Apidae->Saxifragaceae Scrophulariaceae Scrophulariaceae Apidae->Scrophulariaceae Solanaceae Solanaceae Apidae->Solanaceae Zygophyllaceae Zygophyllaceae Apidae->Zygophyllaceae Attelabidae Attelabidae Attelabidae->Anacardiaceae Attelabidae->Rosaceae Berytidae Berytidae Berytidae->Euphorbiaceae Berytidae->Brassicaceae Berytidae->Polygonaceae Berytidae->Hydrophyllaceae Bostrichidae Bostrichidae Juglandaceae Juglandaceae Bostrichidae->Juglandaceae Braconidae Braconidae Braconidae->Anacardiaceae Braconidae->Asteraceae Braconidae->Fabaceae Braconidae->Geraniaceae Buprestidae Buprestidae Buprestidae->Asteraceae Buprestidae->Fabaceae Buprestidae->Grossulariaceae Buprestidae->Rosaceae Buprestidae->Salicaceae Buprestidae->Geraniaceae Buprestidae->Malvaceae Buprestidae->Onagraceae Buprestidae->Scrophulariaceae Namaceae Namaceae Buprestidae->Namaceae Carabidae Carabidae Carabidae->Asteraceae Carabidae->Fabaceae Carabidae->Rosaceae Carabidae->Brassicaceae Carabidae->Salicaceae Carabidae->Ranunculaceae Carabidae->Solanaceae Cecidomyiidae Cecidomyiidae Cecidomyiidae->Asteraceae Cerambycidae Cerambycidae Cerambycidae->Asteraceae Cerambycidae->Apiaceae Cerambycidae->Cactaceae Cerambycidae->Apocynaceae Chrysomelidae Chrysomelidae Chrysomelidae->Asteraceae Chrysomelidae->Euphorbiaceae Chrysomelidae->Fabaceae Chrysomelidae->Poaceae Chrysomelidae->Rosaceae Chrysomelidae->Brassicaceae Chrysomelidae->Polygonaceae Chrysomelidae->Salicaceae Chrysomelidae->Solanaceae Cordiaceae Cordiaceae Chrysomelidae->Cordiaceae Musaceae Musaceae Chrysomelidae->Musaceae Chrysopidae Chrysopidae Chrysopidae->Asteraceae Chrysopidae->Tamaricaceae Chrysopidae->Apocynaceae Chrysopidae->Caprifoliaceae Cicadellidae Cicadellidae Cicadellidae->Asteraceae Cicadellidae->Fabaceae Cicadellidae->Poaceae Cicadidae Cicadidae Cicadidae->Asteraceae Cicadidae->Rosaceae Cicadidae->Apocynaceae Cleridae Cleridae Cleridae->Fabaceae Coccinellidae Coccinellidae Coccinellidae->Pinaceae Coccinellidae->Cupressaceae Coccinellidae->Scrophulariaceae Colletidae Colletidae Colletidae->Anacardiaceae Colletidae->Asteraceae Colletidae->Euphorbiaceae Colletidae->Fabaceae Colletidae->Grossulariaceae Colletidae->Rosaceae Colletidae->Apiaceae Colletidae->Brassicaceae Colletidae->Polygonaceae Colletidae->Salicaceae Colletidae->Tamaricaceae Colletidae->Geraniaceae Colletidae->Apocynaceae Colletidae->Boraginaceae Colletidae->Champiaceae Colletidae->Convolvulaceae Colletidae->Gentianaceae Colletidae->Hydrophyllaceae Colletidae->Iridaceae Colletidae->Liliaceae Colletidae->Plantaginaceae Colletidae->Scrophulariaceae Vitaceae Vitaceae Colletidae->Vitaceae Coreidae Coreidae Coreidae->Cactaceae Corydalidae Corydalidae Corydalidae->Asteraceae Crabronidae Crabronidae Crabronidae->Asteraceae Crabronidae->Euphorbiaceae Crabronidae->Fabaceae Crabronidae->Rosaceae Crabronidae->Apiaceae Crabronidae->Brassicaceae Crabronidae->Cleomaceae Crabronidae->Loasaceae Crabronidae->Polygonaceae Crabronidae->Salicaceae Crabronidae->Tamaricaceae Crabronidae->Geraniaceae Crabronidae->Apocynaceae Crabronidae->Boraginaceae Crabronidae->Caprifoliaceae Crabronidae->Hydrophyllaceae Crabronidae->Plantaginaceae Crabronidae->Ranunculaceae Crabronidae->Scrophulariaceae Crabronidae->Solanaceae Rhamnaceae Rhamnaceae Crabronidae->Rhamnaceae Curculionidae Curculionidae Curculionidae->Asteraceae Curculionidae->Euphorbiaceae Curculionidae->Fabaceae Curculionidae->Pinaceae Curculionidae->Rosaceae Curculionidae->Brassicaceae Curculionidae->Cleomaceae Curculionidae->Salicaceae Curculionidae->Apocynaceae Curculionidae->Campanulaceae Curculionidae->Scrophulariaceae Sarcobataceae Sarcobataceae Curculionidae->Sarcobataceae Tingidae Tingidae Curculionidae->Tingidae Tingidae->Asteraceae Tingidae->Fabaceae Tingidae->Caprifoliaceae Tingidae->Cyprididae Dermestidae Dermestidae Dermestidae->Tamaricaceae Dryophthoridae Dryophthoridae Dryophthoridae->Brassicaceae Dryophthoridae->Ranunculaceae Erebidae Erebidae Erebidae->Asteraceae Eumenidae Eumenidae Eumenidae->Anacardiaceae Eumenidae->Asteraceae Eumenidae->Euphorbiaceae Eumenidae->Fabaceae Eumenidae->Grossulariaceae Eumenidae->Pinaceae Eumenidae->Rosaceae Eumenidae->Apiaceae Eumenidae->Brassicaceae Eumenidae->Crassulaceae Eumenidae->Cupressaceae Eumenidae->Lamiaceae Eumenidae->Polygonaceae Eumenidae->Salicaceae Eumenidae->Tamaricaceae Eumenidae->Geraniaceae Eumenidae->Apocynaceae Eumenidae->Caprifoliaceae Eumenidae->Malvaceae Eumenidae->Papaveraceae Eumenidae->Plantaginaceae Eumenidae->Ranunculaceae Eumenidae->Scrophulariaceae Formicidae Formicidae Formicidae->Asteraceae Formicidae->Euphorbiaceae Formicidae->Fabaceae Formicidae->Grossulariaceae Formicidae->Rosaceae Formicidae->Brassicaceae Formicidae->Cactaceae Formicidae->Ericaceae Formicidae->Loasaceae Formicidae->Salicaceae Formicidae->Tamaricaceae Formicidae->Apocynaceae Formicidae->Campanulaceae Formicidae->Papaveraceae Cladoniaceae Cladoniaceae Formicidae->Cladoniaceae Geocoridae Geocoridae Geocoridae->Asteraceae Geocoridae->Brassicaceae Gryllidae Gryllidae Gryllidae->Asteraceae Halictidae Halictidae Halictidae->Anacardiaceae Halictidae->Asteraceae Halictidae->Berberidaceae Halictidae->Eremiaphilidae Halictidae->Euphorbiaceae Halictidae->Fabaceae Halictidae->Grossulariaceae Halictidae->Rosaceae Halictidae->Apiaceae Halictidae->Asparagaceae Halictidae->Brassicaceae Halictidae->Cactaceae Halictidae->Caryophyllaceae Halictidae->Crassulaceae Halictidae->Lamiaceae Halictidae->Montiaceae Halictidae->Polygonaceae Halictidae->Salicaceae Halictidae->Tamaricaceae Halictidae->Verbenaceae Halictidae->Amaryllidaceae Halictidae->Apocynaceae Halictidae->Boraginaceae Halictidae->Campanulaceae Halictidae->Caprifoliaceae Halictidae->Champiaceae Halictidae->Convolvulaceae Halictidae->Gentianaceae Halictidae->Hydrophyllaceae Halictidae->Hypericaceae Halictidae->Liliaceae Halictidae->Linaceae Halictidae->Malvaceae Halictidae->Onagraceae Halictidae->Orobanchaceae Halictidae->Papaveraceae Halictidae->Plantaginaceae Halictidae->Psilostomidae Halictidae->Ranunculaceae Halictidae->Scrophulariaceae Oxalidaceae Oxalidaceae Halictidae->Oxalidaceae Lampyridae Lampyridae Lampyridae->Asteraceae Lampyridae->Rosaceae Lampyridae->Brassicaceae Lampyridae->Salicaceae Lampyridae->Apocynaceae Lampyridae->Combretaceae Lampyridae->Ranunculaceae Lasiocampidae Lasiocampidae Lasiocampidae->Salicaceae Lygaeidae Lygaeidae Lygaeidae->Asteraceae Lygaeidae->Euphorbiaceae Lygaeidae->Fabaceae Lygaeidae->Rosaceae Lygaeidae->Apiaceae Lygaeidae->Brassicaceae Lygaeidae->Caryophyllaceae Lygaeidae->Geraniaceae Lygaeidae->Apocynaceae Lygaeidae->Malvaceae Betulaceae Betulaceae Lygaeidae->Betulaceae Masaridae Masaridae Masaridae->Fabaceae Masaridae->Cleomaceae Masaridae->Hydrophyllaceae Megachilidae Megachilidae Megachilidae->Asteraceae Megachilidae->Eremiaphilidae Megachilidae->Fabaceae Megachilidae->Grossulariaceae Megachilidae->Rosaceae Megachilidae->Asparagaceae Megachilidae->Brassicaceae Megachilidae->Cactaceae Megachilidae->Cleomaceae Megachilidae->Crassulaceae Megachilidae->Ericaceae Megachilidae->Salicaceae Megachilidae->Tamaricaceae Megachilidae->Geraniaceae Megachilidae->Boraginaceae Megachilidae->Campanulaceae Megachilidae->Champiaceae Megachilidae->Convolvulaceae Megachilidae->Hydrophyllaceae Megachilidae->Liliaceae Megachilidae->Onagraceae Megachilidae->Papaveraceae Megachilidae->Plantaginaceae Megachilidae->Psilostomidae Miridae Miridae Miridae->Anacardiaceae Miridae->Asteraceae Miridae->Fabaceae Miridae->Pinaceae Miridae->Rosaceae Miridae->Apiaceae Miridae->Brassicaceae Miridae->Geraniaceae Miridae->Combretaceae Miridae->Ranunculaceae Myrmeleontidae Myrmeleontidae Myrmeleontidae->Asteraceae Myrmeleontidae->Tamaricaceae Nabidae Nabidae Nabidae->Asteraceae Nabidae->Malvaceae Nemestrinidae Nemestrinidae Nemestrinidae->Asteraceae Nemestrinidae->Apocynaceae Nitidulidae Nitidulidae Nitidulidae->Asteraceae Nitidulidae->Fabaceae Nitidulidae->Pinaceae Nitidulidae->Asparagaceae Nitidulidae->Cactaceae Nitidulidae->Tamaricaceae Nitidulidae->Liliaceae Noctuidae Noctuidae Noctuidae->Asteraceae Pentatomidae Pentatomidae Pentatomidae->Asteraceae Pentatomidae->Euphorbiaceae Pentatomidae->Fabaceae Pentatomidae->Rosaceae Pentatomidae->Brassicaceae Pentatomidae->Salicaceae Pentatomidae->Tamaricaceae Pentatomidae->Apocynaceae Pentatomidae->Ranunculaceae Pentatomidae->Scrophulariaceae Phalacridae Phalacridae Phalacridae->Apiaceae Pompilidae Pompilidae Pompilidae->Asteraceae Pompilidae->Euphorbiaceae Pompilidae->Fabaceae Pompilidae->Grossulariaceae Pompilidae->Rosaceae Pompilidae->Apiaceae Pompilidae->Brassicaceae Pompilidae->Cleomaceae Pompilidae->Polygonaceae Pompilidae->Salicaceae Pompilidae->Tamaricaceae Pompilidae->Apocynaceae Pompilidae->Caprifoliaceae Pompilidae->Malvaceae Pompilidae->Ranunculaceae Pompilidae->Solanaceae Pompilidae->Rhamnaceae Melanthiaceae Melanthiaceae Pompilidae->Melanthiaceae Raphidiidae Raphidiidae Raphidiidae->Fabaceae Raphidiidae->Rosaceae Raphidiidae->Brassicaceae Raphidiidae->Papaveraceae Reduviidae Reduviidae Reduviidae->Fabaceae Reduviidae->Pinaceae Reduviidae->Cleomaceae Reduviidae->Salicaceae Reduviidae->Tamaricaceae Reduviidae->Ranunculaceae Reduviidae->Sarcobataceae Rhopalidae Rhopalidae Rhopalidae->Asteraceae Rhopalidae->Fabaceae Rhopalidae->Rosaceae Rhopalidae->Brassicaceae Rhopalidae->Salicaceae Rhyparochromidae Rhyparochromidae Rhyparochromidae->Asteraceae Rhyparochromidae->Rosaceae Rhyparochromidae->Tamaricaceae Scarabaeidae Scarabaeidae Scarabaeidae->Asteraceae Scarabaeidae->Pinaceae Scarabaeidae->Rosaceae Scarabaeidae->Cleomaceae Scarabaeidae->Salicaceae Scarabaeidae->Tamaricaceae Scarabaeidae->Geraniaceae Scarabaeidae->Ranunculaceae Scutelleridae Scutelleridae Scutelleridae->Poaceae Sialidae Sialidae Sialidae->Rosaceae Sphecidae Sphecidae Sphecidae->Anacardiaceae Sphecidae->Asteraceae Sphecidae->Euphorbiaceae Sphecidae->Fabaceae Sphecidae->Grossulariaceae Sphecidae->Rosaceae Sphecidae->Apiaceae Sphecidae->Brassicaceae Sphecidae->Cactaceae Sphecidae->Cleomaceae Sphecidae->Crassulaceae Sphecidae->Polygonaceae Sphecidae->Salicaceae Sphecidae->Tamaricaceae Sphecidae->Geraniaceae Sphecidae->Apocynaceae Sphecidae->Boraginaceae Sphecidae->Campanulaceae Sphecidae->Caprifoliaceae Sphecidae->Hydrophyllaceae Sphecidae->Malvaceae Sphecidae->Onagraceae Sphecidae->Orobanchaceae Sphecidae->Plantaginaceae Sphecidae->Polemoniaceae Sphecidae->Ranunculaceae Sphecidae->Sarcobataceae Sphingidae Sphingidae Sphingidae->Rosaceae Staphylinidae Staphylinidae Staphylinidae->Asteraceae Stratiomyidae Stratiomyidae Stratiomyidae->Fabaceae Stratiomyidae->Cactaceae Syrphidae Syrphidae Syrphidae->Anacardiaceae Syrphidae->Fabaceae Syrphidae->Brassicaceae Syrphidae->Cleomaceae Syrphidae->Salicaceae Tachinidae Tachinidae Tachinidae->Fabaceae Thyreocoridae Thyreocoridae Thyreocoridae->Fabaceae Thyreocoridae->Scrophulariaceae Tiphiidae Tiphiidae Tiphiidae->Asteraceae Tiphiidae->Euphorbiaceae Tiphiidae->Apiaceae Tiphiidae->Polygonaceae Tiphiidae->Apocynaceae Trogidae Trogidae Trogidae->Apocynaceae Vespidae Vespidae Vespidae->Anacardiaceae Vespidae->Asteraceae Vespidae->Fabaceae Vespidae->Grossulariaceae Vespidae->Rosaceae Vespidae->Apiaceae Vespidae->Brassicaceae Vespidae->Cupressaceae Vespidae->Lamiaceae Vespidae->Polygonaceae Vespidae->Salicaceae Vespidae->Tamaricaceae Vespidae->Geraniaceae Vespidae->Apocynaceae Vespidae->Caprifoliaceae Vespidae->Gentianaceae Vespidae->Plantaginaceae Celastraceae Celastraceae Vespidae->Celastraceae

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
Agulla adnixa HAS_ACCEPTED_NAME col Agulla adnixa
Agulla adnixa SYNONYM_OF col Agulla adnixa
Agulla astuta SYNONYM_OF col Agulla astuta
Agulla astuta HAS_ACCEPTED_NAME col Agulla astuta
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 177
col family 13
col genus 294
col species 801
col subfamily 2
col subgenus 7
col subspecies 60
col variety 8
discoverlife NA 1164
discoverlife species 176
gbif NA 88
gbif family 14
gbif genus 306
gbif species 866
gbif subspecies 74
gbif variety 13
itis NA 232
itis family 13
itis genus 290
itis species 764
itis subfamily 2
itis subspecies 27
itis variety 12
mdd NA 1340
ncbi NA 371
ncbi family 13
ncbi genus 295
ncbi species 643
ncbi subfamily 2
ncbi subgenus 12
ncbi subspecies 13
ncbi tribe 1
ncbi varietas 1
pbdb NA 1152
pbdb family 14
pbdb genus 149
pbdb species 23
pbdb subfamily 1
pbdb tribe 1
tpt NA 1338
tpt genus 2
wfo NA 924
wfo family 13
wfo genus 157
wfo species 235
wfo subspecies 7
wfo tribe 1
wfo variety 8
worms NA 1114
worms family 13
worms genus 132
worms species 75
worms subspecies 2
worms tribe 1
worms 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 1093
col SYNONYM_OF 222
col NONE 177
discoverlife NONE 1164
discoverlife HAS_ACCEPTED_NAME 169
discoverlife SYNONYM_OF 56
discoverlife HOMONYM_OF 13
gbif HAS_ACCEPTED_NAME 1340
gbif SYNONYM_OF 355
gbif NONE 88
itis HAS_ACCEPTED_NAME 1040
itis NONE 232
itis SYNONYM_OF 110
mdd NONE 1340
ncbi SAME_AS 946
ncbi NONE 371
ncbi SYNONYM_OF 47
pbdb NONE 1152
pbdb HAS_ACCEPTED_NAME 187
pbdb SYNONYM_OF 7
tpt NONE 1338
tpt HAS_ACCEPTED_NAME 2
wfo NONE 924
wfo HAS_ACCEPTED_NAME 361
wfo HAS_UNCHECKED_NAME 39
wfo SYNONYM_OF 90
worms NONE 1114
worms HAS_ACCEPTED_NAME 226
worms SYNONYM_OF 39
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
2024-11-18T07:52:42Z summary https://github.com/globalbioticinteractions/ucm-ucmc/archive/60530dcc82d33c9675a4026ad60dc40bea8f2a91.zip
2024-11-18T07:52:42Z summary 9592 interaction(s)
2024-11-18T07:52:42Z summary 0 note(s)
2024-11-18T07:52:42Z summary 10537 info(s)

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

: Most frequently occurring review notes, if any.

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.