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

by Nomer and Elton, two naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

https://github.com/globalbioticinteractions/uhim/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/uhim, is 13.6MiB in size and contains 24,850 interaction with 4 unique types of associations (e.g., interactsWith) between 2,255 primary taxon (e.g., Lygaeidae) and 3,241 associated taxon (e.g., rocks). 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 Hawaii Insect Museum https://github.com/globalbioticinteractions/uhim/archive/53fa790309e48f25685e41ded78ce6a51bafde76.zip 2024-11-16T12:27:18.615Z d4bd19d501a1ae6cbbcafb34a9236b9239f3e5f6a9f226f6b240c922ea87f4ed

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/uhim 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. 13.6MiB) under review 
elton pull globalbioticinteractions/uhim

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

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

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/uhim\
 | 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/uhim, is 13.6MiB in size and contains 24,850 interaction with 4 unique types of associations (e.g., interactsWith) between 2,255 primary taxon (e.g., Lygaeidae) and 3,241 associated taxon (e.g., rocks).

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
Nezara viridula adjacentTo Dodonea viscosa https://scan-bugs.org:443/portal/collections/individual/index.php?occid=13121416
Nezara viridula adjacentTo Dodonea viscosa https://scan-bugs.org:443/portal/collections/individual/index.php?occid=13121417
Nezara viridula adjacentTo Dodonea viscosa https://scan-bugs.org:443/portal/collections/individual/index.php?occid=13121419
Nezara viridula adjacentTo Dodonea viscosa https://scan-bugs.org:443/portal/collections/individual/index.php?occid=13121420
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
interactsWith 13990
hasHost 6170
adjacentTo 4654
eats 38
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Lygaeidae 778
Miridae and/or Anthocoridae 708
Nysius coenosulus 442
Braconidae 440
Canaceoides 435
Canacidae 408
Liriomyza sativae 332
Trupanea cratericola 331
Ephydridae 318
Liriomyza brassicae 297
Nysius nemorivagus 275
Pycnoderes quadrimaculatus 261
Miridae/Anthocoridae 244
Scatella cilipes 234
Scatella warreni 227
Corythucha marmorata 226
Trupanea arboreae 224
Dolichopodidae 209
Scaptomyza caliginosa 195
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
rocks 797
rocks in stream 511
wet rocks 496
Raillardia 310
sweet potato 255
cabbage 254
silversword 248
Acacia koa 245
Irish potato 230
eggplant 224
Carica papaya 218
corn 209
ex. Metrosideros polymorpha 191
Morning glory flowers 174
ex stream 162
beans 160
ex Metrosideros 152
chinese cabbage 144
tomato 141
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Canacidae adjacentTo rocks 316
Canaceoides adjacentTo wet rocks 210
Trupanea cratericola interactsWith silversword 209
Pycnoderes quadrimaculatus interactsWith pole bean 141
Nysius coenosulus interactsWith Raillardia 140
Canaceoides adjacentTo rocks in stream 139
Nysius nemorivagus interactsWith chinese cabbage 139
Geometridae interactsWith Acacia koa 137
Braconidae interactsWith Bactrocera spp (Tephritidae) 136
Ephydridae adjacentTo rocks in stream 131
Scaptomyza caliginosa interactsWith Morning glory flowers 124
Corythucha marmorata hasHost ex cockle bur 121
Euscepes postfasciatus interactsWith sweet potato 115
Scatella cilipes adjacentTo rocks 109
Murgantia histrionica interactsWith broccoli 107
Scatella warreni adjacentTo rocks in stream 99
Callosobruchus maculatus hasHost ex cowpea 98
Braconidae interactsWith Psidium guajava 97
Scatella cilipes hasHost ex Stream 97

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 Plantae Plantae Animalia->Plantae Animalia->Plantae Animalia->Plantae Animalia->Plantae Fungi Fungi Fungi->Animalia Fungi->Plantae
interactions Agaonidae Agaonidae Moraceae Moraceae Agaonidae->Moraceae Agromyzidae Agromyzidae Asteraceae Asteraceae Agromyzidae->Asteraceae Agromyzidae->Asteraceae Asparagaceae Asparagaceae Agromyzidae->Asparagaceae Brassicaceae Brassicaceae Agromyzidae->Brassicaceae Cleomaceae Cleomaceae Agromyzidae->Cleomaceae Ephydridae Ephydridae Agromyzidae->Ephydridae Ericaceae Ericaceae Agromyzidae->Ericaceae Fabaceae Fabaceae Agromyzidae->Fabaceae Goodeniaceae Goodeniaceae Agromyzidae->Goodeniaceae Margarodidae Margarodidae Agromyzidae->Margarodidae Plantaginaceae Plantaginaceae Agromyzidae->Plantaginaceae Poaceae Poaceae Agromyzidae->Poaceae Rosaceae Rosaceae Agromyzidae->Rosaceae Sapindaceae Sapindaceae Agromyzidae->Sapindaceae Sapotaceae Sapotaceae Agromyzidae->Sapotaceae Scrophulariaceae Scrophulariaceae Agromyzidae->Scrophulariaceae Solanaceae Solanaceae Agromyzidae->Solanaceae Verbenaceae Verbenaceae Agromyzidae->Verbenaceae Ephydridae->Fabaceae Ephydridae->Goodeniaceae Ephydridae->Poaceae Rubiaceae Rubiaceae Ephydridae->Rubiaceae Aizoaceae Aizoaceae Ephydridae->Aizoaceae Anisolabididae Anisolabididae Caricaceae Caricaceae Anisolabididae->Caricaceae Anobiidae Anobiidae Anobiidae->Asteraceae Anobiidae->Scrophulariaceae Bovidae Bovidae Anobiidae->Bovidae Euphorbiaceae Euphorbiaceae Anobiidae->Euphorbiaceae Hydrangeaceae Hydrangeaceae Anobiidae->Hydrangeaceae Phyllanthaceae Phyllanthaceae Anobiidae->Phyllanthaceae Primulaceae Primulaceae Anobiidae->Primulaceae Anobiidae->Rubiaceae Urticaceae Urticaceae Anobiidae->Urticaceae Anthomyiidae Anthomyiidae Anthomyiidae->Fabaceae Anthomyiidae->Caricaceae Anthribidae Anthribidae Anthribidae->Asteraceae Anthribidae->Ericaceae Anthribidae->Fabaceae Anthribidae->Urticaceae Anthribidae->Urticaceae Passifloraceae Passifloraceae Anthribidae->Passifloraceae Apidae Apidae Apidae->Asteraceae Apidae->Asteraceae Asteiidae Asteiidae Asteiidae->Fabaceae Asteiidae->Fabaceae Asteiidae->Rosaceae Asteiidae->Bovidae Asteiidae->Euphorbiaceae Campanulaceae Campanulaceae Asteiidae->Campanulaceae Malvaceae Malvaceae Asteiidae->Malvaceae Amaranthaceae Amaranthaceae Asteiidae->Amaranthaceae Aquifoliaceae Aquifoliaceae Asteiidae->Aquifoliaceae Araliaceae Araliaceae Asteiidae->Araliaceae Nyctaginaceae Nyctaginaceae Asteiidae->Nyctaginaceae Theaceae Theaceae Asteiidae->Theaceae Veneridae Veneridae Asteiidae->Veneridae Belidae Belidae Belidae->Hydrangeaceae Belidae->Primulaceae Bombyliidae Bombyliidae Eumenidae Eumenidae Bombyliidae->Eumenidae Eumenidae->Fabaceae Eumenidae->Caricaceae Eumenidae->Malvaceae Bostrichidae Bostrichidae Bostrichidae->Sapindaceae Braconidae Braconidae Braconidae->Asteraceae Braconidae->Fabaceae Braconidae->Scrophulariaceae Braconidae->Verbenaceae Braconidae->Caricaceae Braconidae->Hydrangeaceae Braconidae->Rubiaceae Braconidae->Campanulaceae Anacardiaceae Anacardiaceae Braconidae->Anacardiaceae Aphididae Aphididae Braconidae->Aphididae Cucurbitaceae Cucurbitaceae Braconidae->Cucurbitaceae Gleicheniaceae Gleicheniaceae Braconidae->Gleicheniaceae Myrtaceae Myrtaceae Braconidae->Myrtaceae Piperaceae Piperaceae Braconidae->Piperaceae Rutaceae Rutaceae Braconidae->Rutaceae Bucculatricidae Bucculatricidae Bucculatricidae->Malvaceae Buprestidae Buprestidae Buprestidae->Fabaceae Calliphoridae Calliphoridae Calliphoridae->Asteraceae Carabidae Carabidae Carabidae->Aquifoliaceae Carabidae->Gleicheniaceae Carabidae->Myrtaceae Achatinidae Achatinidae Carabidae->Achatinidae Asteliaceae Asteliaceae Carabidae->Asteliaceae Cibotiaceae Cibotiaceae Carabidae->Cibotiaceae Pandanaceae Pandanaceae Carabidae->Pandanaceae Carposinidae Carposinidae Carposinidae->Ericaceae Carposinidae->Sapotaceae Cecidomyiidae Cecidomyiidae Cecidomyiidae->Asteraceae Cecidomyiidae->Rubiaceae Hypericaceae Hypericaceae Cecidomyiidae->Hypericaceae Cerambycidae Cerambycidae Cerambycidae->Fabaceae Cerambycidae->Fabaceae Cerambycidae->Sapindaceae Cerambycidae->Solanaceae Cerambycidae->Caricaceae Cerambycidae->Euphorbiaceae Cerambycidae->Malvaceae Cerambycidae->Amaranthaceae Cerambycidae->Myrtaceae Apocynaceae Apocynaceae Cerambycidae->Apocynaceae Erebidae Erebidae Cerambycidae->Erebidae Ceraphronidae Ceraphronidae Ceraphronidae->Poaceae Chalcididae Chalcididae Chalcididae->Asteraceae Chalcididae->Poaceae Asilidae Asilidae Chalcididae->Asilidae Chrysomelidae Chrysomelidae Chalcididae->Chrysomelidae Chrysomelidae->Myrtaceae Chloropidae Chloropidae Chloropidae->Asteraceae Chloropidae->Goodeniaceae Chloropidae->Passifloraceae Chloropidae->Apocynaceae Chloropidae->Apocynaceae Chrysopidae Chrysopidae Chrysopidae->Fabaceae Chrysopidae->Sapotaceae Chrysopidae->Pandanaceae Cicadellidae Cicadellidae Cicadellidae->Asteraceae Cicadellidae->Ericaceae Cicadellidae->Fabaceae Cicadellidae->Poaceae Cicadellidae->Poaceae Cicadellidae->Poaceae Cicadellidae->Solanaceae Cicadellidae->Verbenaceae Cicadellidae->Bovidae Cicadellidae->Hydrangeaceae Cicadellidae->Rubiaceae Cicadellidae->Urticaceae Cicadellidae->Amaranthaceae Not assigned Not assigned Cicadellidae->Not assigned Oleaceae Oleaceae Cicadellidae->Oleaceae Tamaricaceae Tamaricaceae Cicadellidae->Tamaricaceae Cixiidae Cixiidae Cixiidae->Asteraceae Cixiidae->Ericaceae Cixiidae->Goodeniaceae Cixiidae->Rosaceae Cixiidae->Scrophulariaceae Cixiidae->Caricaceae Cixiidae->Primulaceae Cixiidae->Rubiaceae Cixiidae->Malvaceae Cixiidae->Theaceae Cixiidae->Myrtaceae Cixiidae->Cibotiaceae Cixiidae->Oleaceae Aspleniaceae Aspleniaceae Cixiidae->Aspleniaceae Rhamnaceae Rhamnaceae Cixiidae->Rhamnaceae Salicaceae Salicaceae Cixiidae->Salicaceae Cleridae Cleridae Cleridae->Solanaceae Coccinellidae Coccinellidae Coccinellidae->Asparagaceae Coccinellidae->Fabaceae Coccinellidae->Scrophulariaceae Coccinellidae->Caricaceae Coccinellidae->Malvaceae Coccinellidae->Amaranthaceae Coccinellidae->Myrtaceae Coccinellidae->Apocynaceae Coccinellidae->Not assigned Pittosporaceae Pittosporaceae Coccinellidae->Pittosporaceae Santalaceae Santalaceae Coccinellidae->Santalaceae Coenagrionidae Coenagrionidae Coenagrionidae->Asteraceae Coenagrionidae->Asteliaceae Coenagrionidae->Pandanaceae Araceae Araceae Coenagrionidae->Araceae Convolvulaceae Convolvulaceae Coenagrionidae->Convolvulaceae Colletidae Colletidae Colletidae->Asteraceae Colletidae->Ericaceae Colletidae->Euphorbiaceae Colletidae->Rubiaceae Colletidae->Rubiaceae Crabronidae Crabronidae Crabronidae->Scrophulariaceae Crabronidae->Malvaceae Crabronidae->Convolvulaceae Portulacaceae Portulacaceae Crabronidae->Portulacaceae Crabronidae->Portulacaceae Crambidae Crambidae Crambidae->Asteraceae Crambidae->Rubiaceae Crambidae->Amaranthaceae Crambidae->Asilidae Cyperaceae Cyperaceae Crambidae->Cyperaceae Hydrobiidae Hydrobiidae Crambidae->Hydrobiidae Curculionidae Curculionidae Curculionidae->Asteraceae Curculionidae->Asparagaceae Curculionidae->Fabaceae Curculionidae->Goodeniaceae Curculionidae->Sapindaceae Curculionidae->Sapotaceae Curculionidae->Scrophulariaceae Curculionidae->Solanaceae Curculionidae->Solanaceae Curculionidae->Caricaceae Curculionidae->Euphorbiaceae Curculionidae->Malvaceae Curculionidae->Araliaceae Curculionidae->Cibotiaceae Curculionidae->Apocynaceae Annonaceae Annonaceae Curculionidae->Annonaceae Arecaceae Arecaceae Curculionidae->Arecaceae Bignoniaceae Bignoniaceae Curculionidae->Bignoniaceae Burseraceae Burseraceae Curculionidae->Burseraceae Ebenaceae Ebenaceae Curculionidae->Ebenaceae Lecythidaceae Lecythidaceae Curculionidae->Lecythidaceae Malpighiaceae Malpighiaceae Curculionidae->Malpighiaceae Muricidae Muricidae Curculionidae->Muricidae Orchidaceae Orchidaceae Curculionidae->Orchidaceae Delphacidae Delphacidae Delphacidae->Asteraceae Delphacidae->Poaceae Delphacidae->Poaceae Delphacidae->Scrophulariaceae Delphacidae->Euphorbiaceae Delphacidae->Rubiaceae Delphacidae->Urticaceae Delphacidae->Campanulaceae Delphacidae->Cyperaceae Gunneraceae Gunneraceae Delphacidae->Gunneraceae Dermestidae Dermestidae Dermestidae->Myrtaceae Dolichopodidae Dolichopodidae Dolichopodidae->Fabaceae Dolichopodidae->Poaceae Dolichopodidae->Hydrangeaceae Dolichopodidae->Araliaceae Dolichopodidae->Araliaceae Dolichopodidae->Myrtaceae Drosophilidae Drosophilidae Drosophilidae->Asteraceae Drosophilidae->Ericaceae Drosophilidae->Ericaceae Drosophilidae->Fabaceae Drosophilidae->Fabaceae Drosophilidae->Sapotaceae Drosophilidae->Bovidae Drosophilidae->Euphorbiaceae Drosophilidae->Hydrangeaceae Drosophilidae->Rubiaceae Drosophilidae->Urticaceae Drosophilidae->Urticaceae Drosophilidae->Passifloraceae Drosophilidae->Campanulaceae Drosophilidae->Campanulaceae Drosophilidae->Amaranthaceae Drosophilidae->Aquifoliaceae Drosophilidae->Araliaceae Drosophilidae->Araliaceae Drosophilidae->Nyctaginaceae Drosophilidae->Nyctaginaceae Drosophilidae->Theaceae Drosophilidae->Myrtaceae Drosophilidae->Rutaceae Drosophilidae->Pandanaceae Drosophilidae->Pandanaceae Drosophilidae->Asilidae Drosophilidae->Convolvulaceae Cyaneidae Cyaneidae Drosophilidae->Cyaneidae Gesneriaceae Gesneriaceae Drosophilidae->Gesneriaceae Drosophilidae->Gesneriaceae Myricaceae Myricaceae Drosophilidae->Myricaceae Blechnaceae Blechnaceae Drosophilidae->Blechnaceae Caryophyllaceae Caryophyllaceae Drosophilidae->Caryophyllaceae Dryopteridaceae Dryopteridaceae Drosophilidae->Dryopteridaceae Dryinidae Dryinidae Dryinidae->Myrtaceae Dryophthoridae Dryophthoridae Dryophthoridae->Asteraceae Dryophthoridae->Fabaceae Dryophthoridae->Goodeniaceae Dryophthoridae->Urticaceae Dryophthoridae->Campanulaceae Dryophthoridae->Aquifoliaceae Dryophthoridae->Araliaceae Dryophthoridae->Theaceae Dryophthoridae->Myrtaceae Dryophthoridae->Cibotiaceae Teiidae Teiidae Dryophthoridae->Teiidae Elateridae Elateridae Elateridae->Myrtaceae Elateridae->Cibotiaceae Elateridae->Pandanaceae Encyrtidae Encyrtidae Encyrtidae->Fabaceae Encyrtidae->Fabaceae Encyrtidae->Poaceae Encyrtidae->Poaceae Encyrtidae->Malvaceae Encyrtidae->Myrtaceae Encyrtidae->Apocynaceae Encyrtidae->Santalaceae Encyrtidae->Convolvulaceae Lamiaceae Lamiaceae Encyrtidae->Lamiaceae Pseudococcidae Pseudococcidae Encyrtidae->Pseudococcidae Eulophidae Eulophidae Eulophidae->Asteraceae Eulophidae->Cleomaceae Eulophidae->Ericaceae Eulophidae->Fabaceae Eulophidae->Poaceae Eulophidae->Verbenaceae Eulophidae->Euphorbiaceae Eulophidae->Rubiaceae Eulophidae->Urticaceae Eulophidae->Urticaceae Eulophidae->Malvaceae Eulophidae->Amaranthaceae Eulophidae->Araliaceae Eulophidae->Veneridae Eulophidae->Myrtaceae Eulophidae->Not assigned Eulophidae->Oleaceae Eulophidae->Santalaceae Blattidae Blattidae Eulophidae->Blattidae Formicidae Formicidae Formicidae->Caricaceae Formicidae->Rubiaceae Formicidae->Myrtaceae Formicidae->Pseudococcidae Melastomataceae Melastomataceae Formicidae->Melastomataceae Geometridae Geometridae Geometridae->Ericaceae Geometridae->Fabaceae Geometridae->Sapindaceae Geometridae->Phyllanthaceae Geometridae->Rubiaceae Geometridae->Myrtaceae Geometridae->Pandanaceae Gracillariidae Gracillariidae Gracillariidae->Portulacaceae Hemerobiidae Hemerobiidae Hemerobiidae->Ericaceae Hemerobiidae->Fabaceae Hemerobiidae->Caricaceae Hemerobiidae->Oleaceae Hydrophilidae Hydrophilidae Hydrophilidae->Asilidae Ichneumonidae Ichneumonidae Ichneumonidae->Asteraceae Ichneumonidae->Ericaceae Ichneumonidae->Ericaceae Ichneumonidae->Fabaceae Ichneumonidae->Goodeniaceae Ichneumonidae->Euphorbiaceae Ichneumonidae->Urticaceae Ichneumonidae->Amaranthaceae Ichneumonidae->Myrtaceae Ichneumonidae->Cibotiaceae Ichneumonidae->Crambidae Araneidae Araneidae Ichneumonidae->Araneidae Plutellidae Plutellidae Ichneumonidae->Plutellidae Proteaceae Proteaceae Ichneumonidae->Proteaceae Syrphidae Syrphidae Ichneumonidae->Syrphidae Tortricidae Tortricidae Ichneumonidae->Tortricidae Tortricidae->Fabaceae Tortricidae->Urticaceae Tortricidae->Santalaceae Tortricidae->Proteaceae Jacobsoniidae Jacobsoniidae Jacobsoniidae->Urticaceae Latridiidae Latridiidae Latridiidae->Amaranthaceae Leucospidae Leucospidae Leucospidae->Euphorbiaceae Libellulidae Libellulidae Libellulidae->Araceae Lycaenidae Lycaenidae Lycaenidae->Fabaceae Lycaenidae->Verbenaceae Lycaenidae->Portulacaceae Lygaeidae Lygaeidae Lygaeidae->Asteraceae Lygaeidae->Asteraceae Lygaeidae->Ericaceae Lygaeidae->Ericaceae Lygaeidae->Fabaceae Lygaeidae->Fabaceae Lygaeidae->Poaceae Lygaeidae->Scrophulariaceae Lygaeidae->Scrophulariaceae Lygaeidae->Solanaceae Lygaeidae->Caricaceae Lygaeidae->Euphorbiaceae Lygaeidae->Rubiaceae Lygaeidae->Amaranthaceae Lygaeidae->Amaranthaceae Lygaeidae->Araliaceae Lygaeidae->Veneridae Lygaeidae->Myrtaceae Lygaeidae->Not assigned Lygaeidae->Portulacaceae Acanthaceae Acanthaceae Lygaeidae->Acanthaceae Lygaeidae->Acanthaceae Geraniaceae Geraniaceae Lygaeidae->Geraniaceae Mantidae Mantidae Mantidae->Poaceae Megachilidae Megachilidae Megachilidae->Fabaceae Membracidae Membracidae Membracidae->Proteaceae Miridae Miridae Miridae->Asteraceae Miridae->Asteraceae Miridae->Ericaceae Miridae->Fabaceae Miridae->Fabaceae Miridae->Rosaceae Miridae->Scrophulariaceae Miridae->Solanaceae Miridae->Caricaceae Miridae->Euphorbiaceae Miridae->Euphorbiaceae Miridae->Hydrangeaceae Miridae->Rubiaceae Miridae->Passifloraceae Miridae->Campanulaceae Miridae->Amaranthaceae Miridae->Cibotiaceae Miridae->Oleaceae Miridae->Convolvulaceae Miridae->Portulacaceae Athyriaceae Athyriaceae Miridae->Athyriaceae Nothofagaceae Nothofagaceae Miridae->Nothofagaceae Muscidae Muscidae Muscidae->Asteraceae Muscidae->Ericaceae Muscidae->Fabaceae Muscidae->Goodeniaceae Muscidae->Phyllanthaceae Muscidae->Campanulaceae Muscidae->Rutaceae Muscidae->Gesneriaceae Nabidae Nabidae Nabidae->Ericaceae Nabidae->Fabaceae Nabidae->Sapindaceae Nabidae->Cibotiaceae Nitidulidae Nitidulidae Nitidulidae->Ericaceae Nitidulidae->Caricaceae Nitidulidae->Bovidae Nitidulidae->Rubiaceae Noctuidae Noctuidae Noctuidae->Asteraceae Noctuidae->Asteraceae Noctuidae->Asparagaceae Noctuidae->Fabaceae Noctuidae->Caricaceae Desmanthidae Desmanthidae Noctuidae->Desmanthidae Notodontidae Notodontidae Notodontidae->Passifloraceae Nymphalidae Nymphalidae Nymphalidae->Urticaceae Macrothricidae Macrothricidae Nymphalidae->Macrothricidae Pentatomidae Pentatomidae Pentatomidae->Ericaceae Pentatomidae->Fabaceae Pentatomidae->Rubiaceae Pentatomidae->Araliaceae Pentatomidae->Myrtaceae Polleniidae Polleniidae Polleniidae->Asteraceae Psathyrellaceae Psathyrellaceae Psathyrellaceae->Teiidae Pseudocaeciliidae Pseudocaeciliidae Pseudocaeciliidae->Ericaceae Pseudocaeciliidae->Fabaceae Pseudocaeciliidae->Sapindaceae Pseudocaeciliidae->Scrophulariaceae Pseudocaeciliidae->Primulaceae Pseudocaeciliidae->Amaranthaceae Pseudocaeciliidae->Myrtaceae Pseudocaeciliidae->Rutaceae Pseudocaeciliidae->Geraniaceae Penaeidae Penaeidae Pseudocaeciliidae->Penaeidae Pterophoridae Pterophoridae Pterophoridae->Verbenaceae Reduviidae Reduviidae Reduviidae->Scrophulariaceae Reduviidae->Caricaceae Reduviidae->Passifloraceae Rhopalidae Rhopalidae Rhopalidae->Asteraceae Scoliidae Scoliidae Scoliidae->Asteraceae Signiphoridae Signiphoridae Signiphoridae->Myricaceae Eriococcidae Eriococcidae Signiphoridae->Eriococcidae Sphingidae Sphingidae Sphingidae->Rubiaceae Sphingidae->Apocynaceae Sphingidae->Bignoniaceae Dioscoreaceae Dioscoreaceae Sphingidae->Dioscoreaceae Staphylinidae Staphylinidae Staphylinidae->Goodeniaceae Staphylinidae->Sapindaceae Staphylinidae->Caricaceae Staphylinidae->Campanulaceae Tenebrionidae Tenebrionidae Tenebrionidae->Myrtaceae Tephritidae Tephritidae Tephritidae->Asteraceae Tephritidae->Asteraceae Tephritidae->Ericaceae Tephritidae->Ericaceae Tephritidae->Verbenaceae Tephritidae->Euphorbiaceae Tephritidae->Rubiaceae Tephritidae->Oleaceae Tephritidae->Penaeidae Tephritidae->Tephritidae Tettigoniidae Tettigoniidae Tettigoniidae->Caricaceae Tingidae Tingidae Tingidae->Asteraceae Tingidae->Verbenaceae Tingidae->Passifloraceae Trigonidiidae Trigonidiidae Trigonidiidae->Myrtaceae Venturiaceae Venturiaceae Venturiaceae->Asteraceae Venturiaceae->Fabaceae Venturiaceae->Amaranthaceae Vespidae Vespidae Vespidae->Asteraceae Vespidae->Amaranthaceae

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
Diomus HAS_ACCEPTED_NAME col Diomus
Anobiidae HAS_ACCEPTED_NAME col Anobiidae
Banza parvula HAS_ACCEPTED_NAME col Banza parvula
Anthribidae HAS_ACCEPTED_NAME col Anthribidae
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 2569
col class 1
col family 85
col genus 355
col gigaclass 1
col infraspecific name 2
col kingdom 2
col order 1
col section 1
col species 1337
col subclass 1
col subgenus 4
col subspecies 15
col tribe 3
col variety 4
discoverlife NA 4353
discoverlife species 18
gbif NA 2228
gbif class 2
gbif family 94
gbif form 1
gbif genus 382
gbif kingdom 3
gbif order 1
gbif species 1637
gbif subspecies 39
gbif variety 3
itis NA 2810
itis class 1
itis family 85
itis genus 301
itis kingdom 2
itis order 1
itis species 1131
itis subclass 1
itis subfamily 3
itis subspecies 29
itis superclass 1
itis tribe 2
itis variety 5
mdd NA 4370
ncbi NA 3105
ncbi class 2
ncbi family 85
ncbi genus 324
ncbi kingdom 1
ncbi order 1
ncbi section 1
ncbi species 832
ncbi species group 1
ncbi subfamily 3
ncbi subgenus 13
ncbi suborder 1
ncbi subspecies 6
ncbi superclass 1
ncbi tribe 1
ncbi varietas 2
pbdb NA 4087
pbdb class 4
pbdb family 85
pbdb genus 174
pbdb informal 1
pbdb kingdom 2
pbdb order 1
pbdb species 14
pbdb subfamily 1
pbdb superclass 1
pbdb tribe 2
pbdb unranked clade 2
tpt NA 4366
tpt genus 4
wfo NA 3957
wfo family 6
wfo genus 202
wfo species 197
wfo subspecies 6
wfo variety 3
worms NA 3874
worms class 2
worms family 75
worms genus 199
worms gigaclass 1
worms kingdom 2
worms order 1
worms species 214
worms subspecies 2
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 2123
col NONE 3200
col SYNONYM_OF 761
discoverlife NONE 5478
discoverlife HAS_ACCEPTED_NAME 17
discoverlife SYNONYM_OF 3
gbif HAS_ACCEPTED_NAME 2694
gbif SYNONYM_OF 999
gbif NONE 2839
itis HAS_ACCEPTED_NAME 1886
itis NONE 3471
itis SYNONYM_OF 216
mdd NONE 5480
ncbi SAME_AS 1672
ncbi NONE 3778
ncbi SYNONYM_OF 95
ncbi COMMON_NAME_OF 16
pbdb NONE 4975
pbdb SYNONYM_OF 34
pbdb HAS_ACCEPTED_NAME 514
tpt NONE 5469
tpt HAS_ACCEPTED_NAME 11
wfo NONE 4680
wfo HAS_ACCEPTED_NAME 700
wfo HAS_UNCHECKED_NAME 25
wfo SYNONYM_OF 150
worms HAS_ACCEPTED_NAME 752
worms NONE 4718
worms SYNONYM_OF 77
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
2024-11-18T07:59:24Z note found unsupported interaction type with name: [Sapindus Island]
2024-11-18T07:59:25Z note source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder
2024-11-18T07:59:25Z note source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder
2024-11-18T07:59:25Z note source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder

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 513
found unsupported interaction type with name: [Marsh] 21
found unsupported interaction type with name: [Pomegranate ex] 9
found unsupported interaction type with name: [coll.] 8

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.