A Review of Biotic Interactions and Taxon Names Found in globalbioticinteractions/ucsb-izc

by Nomer and Elton, two naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

https://github.com/globalbioticinteractions/ucsb-izc/issues

2024-04-22

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/ucsb-izc, is 6.01MiB in size and contains 2,028 interaction with 8 unique types of associations (e.g., interactsWith) between 381 primary taxa (e.g., Apis mellifera) and 397 associated taxa (e.g., Lupinus bicolor). 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 California Santa Barbara Invertebrate Zoology Collection https://github.com/globalbioticinteractions/ucsb-izc/archive/42a422d5369aafe3a41c6b4d4c9f905fe2a74b2f.zip 2024-04-20T04:41:42.358Z 6d5c8c051a264b07a767631b35d2208dfaac509ab332921a4394d06d5b726af3

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/ucsb-izc 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. 6.01MiB) under review 
elton pull globalbioticinteractions/ucsb-izc

# generate review notes
elton review globalbioticinteractions/ucsb-izc\
 > review.tsv

# export indexed interaction records
elton interactions globalbioticinteractions/ucsb-izc\
 > interactions.tsv

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/ucsb-izc\
 | 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/ucsb-izc, is 6.01MiB in size and contains 2,028 interaction with 8 unique types of associations (e.g., interactsWith) between 381 primary taxa (e.g., Apis mellifera) and 397 associated taxa (e.g., Lupinus bicolor).

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
Lasioglossum interactsWith inside flower of Eschscholzia californica UCSB-IZC00038170 https://ecdysis.org/collections/individual/index.php?occid=881445
Diptera adjacentTo flower of Mimulus auranticus UCSB-IZC00038207 https://ecdysis.org/collections/individual/index.php?occid=881446
Diptera adjacentTo flower of Mimulus auranticus UCSB-IZC00038169 https://ecdysis.org/collections/individual/index.php?occid=881447
Diptera adjacentTo flower of Eschscholzia californica UCSB-IZC00038248 https://ecdysis.org/collections/individual/index.php?occid=881448
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
interactsWith 1465
adjacentTo 341
visits 151
visitsFlowersOf 44
hasHost 18
hostOf 4
eats 3
coOccursWith 2
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Apis mellifera 105
Linepithema humile 87
Araneidae 74
Cicadellidae 71
Lasioglossum 61
Solenopsis 46
Augochlorella pomoniella 41
Hemiptera 39
Heleomyzidae 39
Ceratina acantha 35
Temnothorax andrei 35
Bombus vosnesenskii 34
Halictus tripartitus 32
Agapostemon texanus 28
Aphididae 27
Lygus 26
Syrphidae 26
Lasioglossum (Evylaeus) 23
Anthomyiidae 21
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
Lupinus bicolor 282
Lupinus nipomensis 99
Quercus agrifolia 96
Venegasia carpesioides 63
Erigonium 59
Arctostaphylos 49
Marrubium 46
Populus 42
Brassica 40
Salix 39
Encelia californica 36
Foeniculum 36
Atriplex lentiformis 32
Cupressus macrocarpa 31
Lupinus succulentus 26
Convolvulus arvensis 26
Heteromeles arbutifolia 25
Salvia mellifera 24
Baccharis pilularis 21
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Cicadellidae interactsWith Lupinus bicolor 52
Solenopsis interactsWith Quercus agrifolia 32
Heleomyzidae interactsWith Lupinus bicolor 30
Lasioglossum interactsWith Venegasia carpesioides 30
Linepithema humile interactsWith Populus 29
Lygus interactsWith Lupinus bicolor 24
Linepithema humile interactsWith Salix 24
Aphididae interactsWith Lupinus bicolor 22
Hemiptera interactsWith Lupinus bicolor 21
Apis mellifera interactsWith Arctostaphylos 19
Temnothorax andrei interactsWith Quercus agrifolia 17
Apis mellifera interactsWith Marrubium 16
Closterocoris amoenus adjacentTo Lupinus nipomensis 15
Apis mellifera interactsWith Erigonium 15
Syrphidae interactsWith Lupinus bicolor 14
Andrena principalis interactsWith Arctostaphylos 13
Thrips adjacentTo Lupinus nipomensis 13
Camponotus clarithorax interactsWith Quercus agrifolia 13
Apis mellifera interactsWith Brassica 13

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 Animalia->Plantae Animalia->Plantae Animalia->Plantae Plantae->Animalia Plantae->Plantae Plantae->Plantae Plantae->Plantae Fungi Fungi Fungi->Plantae
interactions Acrididae Acrididae Fabaceae Fabaceae Acrididae->Fabaceae Acrididae->Fabaceae Poaceae Poaceae Acrididae->Poaceae Lamiaceae Lamiaceae Acrididae->Lamiaceae Scrophulariaceae Scrophulariaceae Acrididae->Scrophulariaceae Agaonidae Agaonidae Moraceae Moraceae Agaonidae->Moraceae Agromyzidae Agromyzidae Agromyzidae->Fabaceae Aleyrodidae Aleyrodidae Aleyrodidae->Fabaceae Andrenidae Andrenidae Andrenidae->Lamiaceae Rhamnaceae Rhamnaceae Andrenidae->Rhamnaceae Andrenidae->Rhamnaceae Asteraceae Asteraceae Andrenidae->Asteraceae Andrenidae->Asteraceae Brassicaceae Brassicaceae Andrenidae->Brassicaceae Andrenidae->Brassicaceae Convolvulaceae Convolvulaceae Andrenidae->Convolvulaceae Ericaceae Ericaceae Andrenidae->Ericaceae Andrenidae->Ericaceae Andrenidae->Ericaceae Rosaceae Rosaceae Andrenidae->Rosaceae Ranunculaceae Ranunculaceae Andrenidae->Ranunculaceae Asteraceae->Lamiaceae Asteraceae->Asteraceae Asteraceae->Asteraceae Linyphiidae Linyphiidae Asteraceae->Linyphiidae Anthocoridae Anthocoridae Anthocoridae->Fabaceae Anthocoridae->Fabaceae Anthomyiidae Anthomyiidae Anthomyiidae->Fabaceae Anthomyiidae->Fabaceae Anthomyiidae->Fabaceae Anthomyiidae->Fabaceae Anthomyiidae->Lamiaceae Anthomyiidae->Brassicaceae Apiaceae Apiaceae Anthomyiidae->Apiaceae Aphididae Aphididae Aphididae->Fabaceae Aphididae->Fabaceae Aphididae->Asteraceae Aphididae->Asteraceae Aphididae->Asteraceae Apidae Apidae Apidae->Fabaceae Apidae->Fabaceae Apidae->Lamiaceae Apidae->Lamiaceae Apidae->Lamiaceae Apidae->Scrophulariaceae Apidae->Asteraceae Apidae->Asteraceae Apidae->Asteraceae Apidae->Brassicaceae Apidae->Convolvulaceae Apidae->Convolvulaceae Apidae->Ericaceae Apidae->Rosaceae Apidae->Rosaceae Apidae->Apiaceae Onagraceae Onagraceae Apidae->Onagraceae Apidae->Onagraceae Polygonaceae Polygonaceae Apidae->Polygonaceae Apidae->Polygonaceae Cucurbitaceae Cucurbitaceae Apidae->Cucurbitaceae Papaveraceae Papaveraceae Apidae->Papaveraceae Apidae->Papaveraceae Phrymaceae Phrymaceae Apidae->Phrymaceae Solanaceae Solanaceae Apidae->Solanaceae Verbenaceae Verbenaceae Apidae->Verbenaceae Anacardiaceae Anacardiaceae Apidae->Anacardiaceae Tropaeolaceae Tropaeolaceae Apidae->Tropaeolaceae Hydrophyllaceae Hydrophyllaceae Apidae->Hydrophyllaceae Araneidae Araneidae Araneidae->Fabaceae Araneidae->Asteraceae Araneidae->Rosaceae Araneidae->Anacardiaceae Asparagaceae Asparagaceae Araneidae->Asparagaceae Cactaceae Cactaceae Araneidae->Cactaceae Fagaceae Fagaceae Araneidae->Fagaceae Malvaceae Malvaceae Araneidae->Malvaceae Orobanchaceae Orobanchaceae Araneidae->Orobanchaceae Asilidae Asilidae Asilidae->Fabaceae Asilidae->Fabaceae Asilidae->Fabaceae Asilidae->Fabaceae Asilidae->Lamiaceae Attelabidae Attelabidae Attelabidae->Rosaceae Bibionidae Bibionidae Bibionidae->Fabaceae Bombyliidae Bombyliidae Bombyliidae->Lamiaceae Bombyliidae->Asteraceae Bombyliidae->Ericaceae Bombyliidae->Rosaceae Bombyliidae->Apiaceae Bostrichidae Bostrichidae Bostrichidae->Asteraceae Bostrichidae->Asteraceae Braconidae Braconidae Braconidae->Fabaceae Buprestidae Buprestidae Buprestidae->Asteraceae Buprestidae->Asteraceae Lauraceae Lauraceae Buprestidae->Lauraceae Calliphoridae Calliphoridae Calliphoridae->Brassicaceae Calliphoridae->Ericaceae Canacidae Canacidae Canacidae->Fabaceae Canacidae->Polygonaceae Iridaceae Iridaceae Canacidae->Iridaceae Viburnaceae Viburnaceae Canacidae->Viburnaceae Cecidomyiidae Cecidomyiidae Cecidomyiidae->Fabaceae Cerambycidae Cerambycidae Cerambycidae->Asteraceae Cerambycidae->Brassicaceae Chalcididae Chalcididae Chalcididae->Fabaceae Chironomidae Chironomidae Chironomidae->Fabaceae Chironomidae->Asteraceae Chloropidae Chloropidae Chloropidae->Fabaceae Chloropidae->Poaceae Chloropidae->Asteraceae Chloropidae->Iridaceae Amaranthaceae Amaranthaceae Chloropidae->Amaranthaceae Salicaceae Salicaceae Chloropidae->Salicaceae Chrysomelidae Chrysomelidae Chrysomelidae->Poaceae Chrysomelidae->Asteraceae Chrysomelidae->Polygonaceae Chrysomelidae->Solanaceae Chrysomelidae->Lauraceae Chrysomelidae->Amaranthaceae Liliaceae Liliaceae Chrysomelidae->Liliaceae Chrysopidae Chrysopidae Chrysopidae->Poaceae Chrysopidae->Asteraceae Chrysopidae->Brassicaceae Chrysopidae->Apiaceae Chrysopidae->Lauraceae Cicadellidae Cicadellidae Cicadellidae->Fabaceae Cicadellidae->Fabaceae Cicadellidae->Poaceae Cicadellidae->Asteraceae Cicadellidae->Asteraceae Cicadellidae->Fagaceae Cicadellidae->Amaranthaceae Cicadidae Cicadidae Cicadidae->Fabaceae Coccinellidae Coccinellidae Coccinellidae->Lamiaceae Coccinellidae->Asteraceae Coccinellidae->Asteraceae Coccinellidae->Brassicaceae Coccinellidae->Rosaceae Coccinellidae->Apiaceae Coccinellidae->Papaveraceae Coenagrionidae Coenagrionidae Coenagrionidae->Brassicaceae Coenagrionidae->Polygonaceae Coenagrionidae->Amaranthaceae Colletidae Colletidae Colletidae->Lamiaceae Colletidae->Lamiaceae Colletidae->Asteraceae Colletidae->Brassicaceae Colletidae->Convolvulaceae Colletidae->Convolvulaceae Colletidae->Rosaceae Colletidae->Rosaceae Colletidae->Rosaceae Colletidae->Apiaceae Colletidae->Polygonaceae Colletidae->Anacardiaceae Coniopterygidae Coniopterygidae Coniopterygidae->Fagaceae Conopidae Conopidae Conopidae->Brassicaceae Coreidae Coreidae Coreidae->Poaceae Coreidae->Asteraceae Coreidae->Asteraceae Crabronidae Crabronidae Crabronidae->Fabaceae Crabronidae->Lamiaceae Crabronidae->Asteraceae Crabronidae->Rosaceae Crabronidae->Polygonaceae Curculionidae Curculionidae Curculionidae->Fabaceae Curculionidae->Fabaceae Curculionidae->Poaceae Curculionidae->Brassicaceae Curculionidae->Amaranthaceae Pinaceae Pinaceae Curculionidae->Pinaceae Dictyopharidae Dictyopharidae Dictyopharidae->Papaveraceae Dictyopharidae->Papaveraceae Dolichopodidae Dolichopodidae Dolichopodidae->Fabaceae Elateridae Elateridae Elateridae->Rosaceae Endomychidae Endomychidae Endomychidae->Fabaceae Endomychidae->Fabaceae Ephydridae Ephydridae Ephydridae->Amaranthaceae Eucnemidae Eucnemidae Eucnemidae->Fabaceae Eulophidae Eulophidae Eulophidae->Amaranthaceae Eupelmidae Eupelmidae Eupelmidae->Polygonaceae Eurytomidae Eurytomidae Eurytomidae->Fabaceae Fanniidae Fanniidae Fanniidae->Fabaceae Fanniidae->Brassicaceae Forficulidae Forficulidae Forficulidae->Fabaceae Forficulidae->Brassicaceae Forficulidae->Papaveraceae Formicidae Formicidae Formicidae->Fabaceae Formicidae->Fabaceae Formicidae->Lamiaceae Formicidae->Asteraceae Formicidae->Brassicaceae Formicidae->Polygonaceae Formicidae->Fagaceae Formicidae->Lauraceae Formicidae->Amaranthaceae Formicidae->Salicaceae Formicidae->Formicidae Arecaceae Arecaceae Formicidae->Arecaceae Cupressaceae Cupressaceae Formicidae->Cupressaceae Loasaceae Loasaceae Formicidae->Loasaceae Montiaceae Montiaceae Formicidae->Montiaceae Fulgoridae Fulgoridae Fulgoridae->Fabaceae Gryllidae Gryllidae Gryllidae->Fabaceae Halictidae Halictidae Halictidae->Fabaceae Halictidae->Fabaceae Halictidae->Poaceae Halictidae->Lamiaceae Halictidae->Lamiaceae Halictidae->Asteraceae Halictidae->Asteraceae Halictidae->Asteraceae Halictidae->Brassicaceae Halictidae->Brassicaceae Halictidae->Convolvulaceae Halictidae->Convolvulaceae Halictidae->Convolvulaceae Halictidae->Rosaceae Halictidae->Apiaceae Halictidae->Polygonaceae Halictidae->Papaveraceae Halictidae->Papaveraceae Halictidae->Papaveraceae Halictidae->Anacardiaceae Halictidae->Tropaeolaceae Heleomyzidae Heleomyzidae Heleomyzidae->Fabaceae Heleomyzidae->Fabaceae Heleomyzidae->Fabaceae Heleomyzidae->Asteraceae Heleomyzidae->Viburnaceae Hemerobiidae Hemerobiidae Hemerobiidae->Fagaceae Herpotrichiellaceae Herpotrichiellaceae Herpotrichiellaceae->Asteraceae Herpotrichiellaceae->Polygonaceae Hesperiidae Hesperiidae Hesperiidae->Polygonaceae Ichneumonidae Ichneumonidae Ichneumonidae->Fabaceae Ichneumonidae->Asteraceae Issidae Issidae Issidae->Fabaceae Largidae Largidae Largidae->Poaceae Largidae->Asteraceae Largidae->Onagraceae Largidae->Iridaceae Largidae->Amaranthaceae Lauxaniidae Lauxaniidae Lauxaniidae->Fabaceae Lauxaniidae->Asteraceae Lauxaniidae->Amaranthaceae Lycaenidae Lycaenidae Lycaenidae->Fabaceae Lycaenidae->Poaceae Lycaenidae->Brassicaceae Lycaenidae->Brassicaceae Lycaenidae->Rosaceae Lygaeidae Lygaeidae Apocynaceae Apocynaceae Lygaeidae->Apocynaceae Masaridae Masaridae Masaridae->Fabaceae Megachilidae Megachilidae Megachilidae->Lamiaceae Megachilidae->Lamiaceae Megachilidae->Asteraceae Megachilidae->Asteraceae Meinertellidae Meinertellidae Meinertellidae->Poaceae Membracidae Membracidae Membracidae->Fabaceae Membracidae->Fabaceae Membracidae->Poaceae Membracidae->Asteraceae Membracidae->Fagaceae Membracidae->Cupressaceae Miridae Miridae Miridae->Fabaceae Miridae->Fabaceae Miridae->Fabaceae Miridae->Fabaceae Miridae->Lamiaceae Miridae->Asteraceae Miridae->Asteraceae Miridae->Asteraceae Mordellidae Mordellidae Mordellidae->Fabaceae Muscidae Muscidae Muscidae->Fabaceae Muscidae->Fabaceae Muscidae->Fabaceae Muscidae->Poaceae Muscidae->Asteraceae Nabidae Nabidae Nabidae->Fabaceae Notodontidae Notodontidae Notodontidae->Fabaceae Notodontidae->Fagaceae Nymphalidae Nymphalidae Nymphalidae->Malvaceae Pentatomidae Pentatomidae Pentatomidae->Fabaceae Pieridae Pieridae Pieridae->Brassicaceae Pipunculidae Pipunculidae Pipunculidae->Onagraceae Pompilidae Pompilidae Pompilidae->Fabaceae Psyllidae Psyllidae Psyllidae->Fabaceae Pteromalidae Pteromalidae Pteromalidae->Fabaceae Pteromalidae->Amaranthaceae Pulicidae Pulicidae Canidae Canidae Pulicidae->Canidae Pyralidae Pyralidae Pyralidae->Fabaceae Reduviidae Reduviidae Reduviidae->Fabaceae Reduviidae->Asteraceae Reduviidae->Papaveraceae Rhopalidae Rhopalidae Rhopalidae->Fabaceae Sarcophagidae Sarcophagidae Muridae Muridae Sarcophagidae->Muridae Saxifragaceae Saxifragaceae Saxifragaceae->Fabaceae Saxifragaceae->Asteraceae Saxifragaceae->Convolvulaceae Saxifragaceae->Rosaceae Saxifragaceae->Papaveraceae Saxifragaceae->Phrymaceae Scarabaeidae Scarabaeidae Scarabaeidae->Lamiaceae Scarabaeidae->Moraceae Schizopodidae Schizopodidae Schizopodidae->Fabaceae Sciaridae Sciaridae Sciaridae->Fabaceae Sepsidae Sepsidae Sepsidae->Asteraceae Sepsidae->Brassicaceae Sphecidae Sphecidae Sphecidae->Poaceae Sphecidae->Asteraceae Sphecidae->Rosaceae Sphecidae->Polygonaceae Sphingidae Sphingidae Sphingidae->Brassicaceae Sphingidae->Brassicaceae Staphylinidae Staphylinidae Staphylinidae->Fabaceae Staphylinidae->Fabaceae Staphylinidae->Poaceae Staphylinidae->Asteraceae Staphylinidae->Anacardiaceae Staphylinidae->Fagaceae Stratiomyidae Stratiomyidae Stratiomyidae->Brassicaceae Syrphidae Syrphidae Syrphidae->Fabaceae Syrphidae->Lamiaceae Syrphidae->Asteraceae Syrphidae->Brassicaceae Syrphidae->Brassicaceae Syrphidae->Ericaceae Syrphidae->Apiaceae Syrphidae->Papaveraceae Syrphidae->Hydrophyllaceae Syrphidae->Amaranthaceae Syrphidae->Montiaceae Tachinidae Tachinidae Tachinidae->Asteraceae Tachinidae->Brassicaceae Tephritidae Tephritidae Tephritidae->Fabaceae Tephritidae->Asteraceae Tephritidae->Asteraceae Tephritidae->Ericaceae Tettigoniidae Tettigoniidae Tettigoniidae->Fabaceae Tettigoniidae->Polygonaceae Tettigoniidae->Apocynaceae Therevidae Therevidae Therevidae->Fabaceae Therevidae->Apiaceae Therevidae->Viburnaceae Thripidae Thripidae Thripidae->Fabaceae Tipulidae Tipulidae Tipulidae->Fabaceae Tropiduchidae Tropiduchidae Tropiduchidae->Asteraceae Tropiduchidae->Polygonaceae Tropiduchidae->Amaranthaceae Vespidae Vespidae Vespidae->Lamiaceae Vespidae->Asteraceae Vespidae->Asteraceae Vespidae->Apiaceae

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
Distichlis spicata HAS_ACCEPTED_NAME col Distichlis spicata
Cryptonevra nigritarsis HAS_ACCEPTED_NAME col Cryptonevra nigritarsis
Eulonchus HAS_ACCEPTED_NAME col Eulonchus
Meromyza HAS_ACCEPTED_NAME col Meromyza
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 267
col class 1
col family 103
col genus 110
col kingdom 1
col order 12
col species 218
col subfamily 9
col subgenus 3
col suborder 1
col subspecies 8
col subtribe 1
col superfamily 4
col tribe 2
col variety 1
discoverlife NA 668
discoverlife species 62
gbif NA 241
gbif class 1
gbif family 106
gbif genus 127
gbif kingdom 1
gbif order 12
gbif species 240
gbif subspecies 16
gbif variety 6
itis NA 247
itis class 1
itis family 103
itis genus 99
itis infraorder 2
itis kingdom 1
itis order 12
itis species 229
itis subclass 1
itis subfamily 10
itis suborder 6
itis subspecies 13
itis superfamily 4
itis superorder 1
itis variety 1
mdd NA 729
ncbi NA 263
ncbi class 1
ncbi cohort 1
ncbi family 104
ncbi genus 110
ncbi infraorder 2
ncbi order 12
ncbi species 210
ncbi subclass 1
ncbi subfamily 16
ncbi subgenus 8
ncbi suborder 2
ncbi subspecies 3
ncbi superfamily 6
ncbi varietas 1
pbdb NA 518
pbdb class 2
pbdb family 104
pbdb genus 56
pbdb infraclass 1
pbdb infraorder 1
pbdb kingdom 1
pbdb order 13
pbdb species 10
pbdb subfamily 15
pbdb suborder 3
pbdb superfamily 6
pbdb unranked clade 3
tpt NA 725
tpt genus 1
tpt species 3
wfo NA 581
wfo family 1
wfo genus 44
wfo phylum 1
wfo species 101
wfo subspecies 2
wfo 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 505
col SYNONYM_OF 66
col NONE 281
discoverlife NONE 724
discoverlife SYNONYM_OF 23
discoverlife HAS_ACCEPTED_NAME 59
discoverlife HOMONYM_OF 2
gbif HAS_ACCEPTED_NAME 621
gbif SYNONYM_OF 127
gbif NONE 255
itis HAS_ACCEPTED_NAME 504
itis NONE 260
itis SYNONYM_OF 32
mdd NONE 782
mdd HAS_ACCEPTED_NAME 1
ncbi SAME_AS 511
ncbi SYNONYM_OF 18
ncbi NONE 280
ncbi COMMON_NAME_OF 2
pbdb NONE 549
pbdb HAS_ACCEPTED_NAME 240
pbdb SYNONYM_OF 15
tpt NONE 777
tpt HAS_ACCEPTED_NAME 6
wfo HAS_ACCEPTED_NAME 161
wfo NONE 615
wfo SYNONYM_OF 24
wfo HAS_UNCHECKED_NAME 8
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
2024-04-22T07:22:26Z note source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder
2024-04-22T07:22:26Z note source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder
2024-04-22T07:22:27Z note source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder
2024-04-22T07:22:28Z note found unsupported interaction type with name: [11]

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 13
found unsupported interaction type with name: [11] 3
found unsupported interaction type with name: [Hovering over] 3
found unsupported interaction type with name: [attacks] 1

For addition information on review notes, please have a look at the first 500 Review Notes or the download full csv or tsv archives.

GloBI Review Badge

As part of the review, a review badge is generated. This review badge can be included in webpages to indicate the review status of the dataset under review.

review review 💬 💬

Note that if the badge is green, no review notes were generated. If the badge is yellow, the review bots may need some help with interpreting the species interaction data.

GloBI Index Badge

If the dataset under review has been registered with GloBI, and has been succesfully indexed by GloBI, the GloBI Index Status Badge will turn green. This means that the dataset under review was indexed by GloBI and is available through GloBI services and derived data products.

Picture of a GloBI Index Badge

If you’d like to keep track of reviews or index status of the dataset under review, please visit GloBI’s dataset index 5 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-ness6 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

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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.
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