A Review of Biotic Interactions and Taxon Names Found in globalbioticinteractions/pu-perc

by Nomer and Elton, two naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

https://github.com/globalbioticinteractions/pu-perc/issues

2024-04-17

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/pu-perc, is 3.77MiB in size and contains 10,567 interaction with 2 unique types of associations (e.g., interactsWith) between 560 primary taxa (e.g., Acari) and 590 associated taxa (e.g., Ictidomys tridecemlineatus). 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:

Purdue Entomological Research Collection https://github.com/globalbioticinteractions/pu-perc/archive/e0909a7ca0a8df5effccb288ba64b28141e388ba.zip 2024-04-13T04:39:03.909Z 91dfb04943f379056a71f045e25806eb42163eace0d6205434190c73600e1b39

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/pu-perc 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 0.5.7
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. 3.77MiB) under review 
elton pull globalbioticinteractions/pu-perc

# generate review notes
elton review globalbioticinteractions/pu-perc\
 > review.tsv

# export indexed interaction records
elton interactions globalbioticinteractions/pu-perc\
 > interactions.tsv

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/pu-perc\
 | 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/pu-perc, is 3.77MiB in size and contains 10,567 interaction with 2 unique types of associations (e.g., interactsWith) between 560 primary taxa (e.g., Acari) and 590 associated taxa (e.g., Ictidomys tridecemlineatus).

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
Tolype velleda interactsWith Wild Cherry https://scan-bugs.org:443/portal/collections/individual/index.php?occid=27714749
Tolype velleda interactsWith Apple https://scan-bugs.org:443/portal/collections/individual/index.php?occid=27714760
Malacosoma americana interactsWith Crabapple https://scan-bugs.org:443/portal/collections/individual/index.php?occid=27714798
Malacosoma americana interactsWith Crabapple https://scan-bugs.org:443/portal/collections/individual/index.php?occid=27714808
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
interactsWith 10557
killedBy 10
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Acari 742
Oropsylla bruneri 499
Halictus ligatus 368
Halictus confusus 348
Lasioglossum imitatum 316
Andrena wilkella 290
Andrena miserabilis 276
Ctenophthalmus pseudagyrtes 233
Melissodes bimaculata 212
Aug_ella aurata 204
Lasioglossum admirandum 200
Svastra obliqua 150
Nalepella tsugafoliae 136
Haemolaelaps glasgowi 124
Orchopeas leucopus 119
Andrena imitatrix 116
Enderleinellus suturalis 115
Aug_ella persimilis 114
Bombus griseocollis 110
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
Ictidomys tridecemlineatus 568
Salix 323
Taraxacum 311
Eptesicus fuscus 272
Peromyscus leucopus 267
Salvia sage 211
Salix discolor 207
Melilotus 194
Asclepias incarnata 180
Microtus pennsylvanicus 165
Blarina brevicauda 161
Trifolium pratense 154
Helianthus annuus 153
Cotoneaster 140
Microtus ochrogaster 139
Asclepias verticillata 136
Alcea hollyhock 131
Helianthus 131
Prunus 128
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Oropsylla bruneri interactsWith Ictidomys tridecemlineatus 492
Andrena wilkella interactsWith Cotoneaster 140
Acari interactsWith Eptesicus fuscus 138
Enderleinellus suturalis interactsWith Citellus tridecemlineatus 95
Aug_ella persimilis interactsWith Salvia sage 92
Lasioglossum admirandum interactsWith Taraxacum 92
Acari interactsWith Peromyscus leucopus 91
Ctenophthalmus pseudagyrtes interactsWith Scalopus aquaticus machrinus 84
Halictus ligatus interactsWith Helianthus annuus 80
Orchopeas leucopus interactsWith Peromyscus leucopus noveboracensis 74
Halictus confusus interactsWith Asclepias verticillata 72
Lasioglossum imitatum interactsWith Anise hyssop 68
Nalepella tsugafoliae interactsWith Tsuga canadensis 66
Halictus confusus interactsWith Asclepias incarnata 64
Andrena miserabilis interactsWith Salix 64
Myodopsylla insignis interactsWith Myotis lucifugus 57
Halictus ligatus interactsWith Helianthus 56
Aug_ella aurata interactsWith Salvia sage 54
Chelostoma philadelphi interactsWith Philadelphus 50

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 Plantae Plantae Animalia->Plantae
interactions Acaridae Acaridae Vespertilionidae Vespertilionidae Acaridae->Vespertilionidae Analgidae Analgidae Alaudidae Alaudidae Analgidae->Alaudidae Corvidae Corvidae Analgidae->Corvidae Picidae Picidae Analgidae->Picidae Andrenidae Andrenidae Apiaceae Apiaceae Andrenidae->Apiaceae Apocynaceae Apocynaceae Andrenidae->Apocynaceae Asteraceae Asteraceae Andrenidae->Asteraceae Brassicaceae Brassicaceae Andrenidae->Brassicaceae Caprifoliaceae Caprifoliaceae Andrenidae->Caprifoliaceae Caryophyllaceae Caryophyllaceae Andrenidae->Caryophyllaceae Cornaceae Cornaceae Andrenidae->Cornaceae Cucurbitaceae Cucurbitaceae Andrenidae->Cucurbitaceae Euphorbiaceae Euphorbiaceae Andrenidae->Euphorbiaceae Fabaceae Fabaceae Andrenidae->Fabaceae Geraniaceae Geraniaceae Andrenidae->Geraniaceae Hydrangeaceae Hydrangeaceae Andrenidae->Hydrangeaceae Lamiaceae Lamiaceae Andrenidae->Lamiaceae Lauraceae Lauraceae Andrenidae->Lauraceae Malvaceae Malvaceae Andrenidae->Malvaceae Montiaceae Montiaceae Andrenidae->Montiaceae Paeoniaceae Paeoniaceae Andrenidae->Paeoniaceae Papaveraceae Papaveraceae Andrenidae->Papaveraceae Psilostomidae Psilostomidae Andrenidae->Psilostomidae Ranunculaceae Ranunculaceae Andrenidae->Ranunculaceae Rosaceae Rosaceae Andrenidae->Rosaceae Salicaceae Salicaceae Andrenidae->Salicaceae Sapindaceae Sapindaceae Andrenidae->Sapindaceae Viburnaceae Viburnaceae Andrenidae->Viburnaceae Apidae Apidae Apidae->Apiaceae Apidae->Apocynaceae Apidae->Asteraceae Apidae->Brassicaceae Apidae->Caryophyllaceae Apidae->Cornaceae Apidae->Cucurbitaceae Apidae->Fabaceae Apidae->Hydrangeaceae Apidae->Lamiaceae Apidae->Malvaceae Apidae->Montiaceae Apidae->Psilostomidae Apidae->Ranunculaceae Apidae->Rosaceae Apidae->Salicaceae Asparagaceae Asparagaceae Apidae->Asparagaceae Balsaminaceae Balsaminaceae Apidae->Balsaminaceae Boraginaceae Boraginaceae Apidae->Boraginaceae Celastraceae Celastraceae Apidae->Celastraceae Champiaceae Champiaceae Apidae->Champiaceae Combretaceae Combretaceae Apidae->Combretaceae Commelinaceae Commelinaceae Apidae->Commelinaceae Convolvulaceae Convolvulaceae Apidae->Convolvulaceae Goodeniaceae Goodeniaceae Apidae->Goodeniaceae Onagraceae Onagraceae Apidae->Onagraceae Plantaginaceae Plantaginaceae Apidae->Plantaginaceae Polygonaceae Polygonaceae Apidae->Polygonaceae Rubiaceae Rubiaceae Apidae->Rubiaceae Solanaceae Solanaceae Apidae->Solanaceae Verbenaceae Verbenaceae Apidae->Verbenaceae Violaceae Violaceae Apidae->Violaceae Argasidae Argasidae Argasidae->Vespertilionidae Megadermatidae Megadermatidae Argasidae->Megadermatidae Ceratophyllidae Ceratophyllidae Cricetidae Cricetidae Ceratophyllidae->Cricetidae Didelphidae Didelphidae Ceratophyllidae->Didelphidae Geomyidae Geomyidae Ceratophyllidae->Geomyidae Hirundinidae Hirundinidae Ceratophyllidae->Hirundinidae Mephitidae Mephitidae Ceratophyllidae->Mephitidae Muridae Muridae Ceratophyllidae->Muridae Procyonidae Procyonidae Ceratophyllidae->Procyonidae Sciuridae Sciuridae Ceratophyllidae->Sciuridae Soricidae Soricidae Ceratophyllidae->Soricidae Talpidae Talpidae Ceratophyllidae->Talpidae Ceratozetidae Ceratozetidae Pinaceae Pinaceae Ceratozetidae->Pinaceae Cercopidae Cercopidae Cercopidae->Geraniaceae Cheyletidae Cheyletidae Leporidae Leporidae Cheyletidae->Leporidae Colletidae Colletidae Colletidae->Apiaceae Colletidae->Apocynaceae Colletidae->Asteraceae Colletidae->Brassicaceae Colletidae->Caryophyllaceae Colletidae->Cornaceae Colletidae->Fabaceae Colletidae->Hydrangeaceae Colletidae->Lamiaceae Colletidae->Malvaceae Colletidae->Montiaceae Colletidae->Ranunculaceae Colletidae->Rosaceae Colletidae->Salicaceae Colletidae->Celastraceae Colletidae->Combretaceae Colletidae->Convolvulaceae Colletidae->Polygonaceae Anacardiaceae Anacardiaceae Colletidae->Anacardiaceae Hypericaceae Hypericaceae Colletidae->Hypericaceae Liliaceae Liliaceae Colletidae->Liliaceae Ctenophthalmidae Ctenophthalmidae Ctenophthalmidae->Cricetidae Ctenophthalmidae->Muridae Ctenophthalmidae->Sciuridae Ctenophthalmidae->Soricidae Ctenophthalmidae->Talpidae Ctenophthalmidae->Leporidae Curculionidae Curculionidae Curculionidae->Polygonaceae Demodecidae Demodecidae Hominidae Hominidae Demodecidae->Hominidae Dermanyssidae Dermanyssidae Paridae Paridae Dermanyssidae->Paridae Passeridae Passeridae Dermanyssidae->Passeridae Diaspididae Diaspididae Diaspididae->Rosaceae Digamasellidae Digamasellidae Digamasellidae->Soricidae Enderleinellidae Enderleinellidae Enderleinellidae->Sciuridae Epilohmanniidae Epilohmanniidae Vitaceae Vitaceae Epilohmanniidae->Vitaceae Eriophyidae Eriophyidae Eriophyidae->Pinaceae Haematopinidae Haematopinidae Bovidae Bovidae Haematopinidae->Bovidae Suidae Suidae Haematopinidae->Suidae Halictidae Halictidae Halictidae->Apiaceae Halictidae->Apocynaceae Halictidae->Asteraceae Halictidae->Brassicaceae Halictidae->Caprifoliaceae Halictidae->Caryophyllaceae Halictidae->Cornaceae Halictidae->Cucurbitaceae Halictidae->Fabaceae Halictidae->Hydrangeaceae Halictidae->Lamiaceae Halictidae->Malvaceae Halictidae->Montiaceae Halictidae->Paeoniaceae Halictidae->Ranunculaceae Halictidae->Rosaceae Halictidae->Salicaceae Halictidae->Sapindaceae Halictidae->Viburnaceae Halictidae->Boraginaceae Halictidae->Celastraceae Halictidae->Combretaceae Halictidae->Commelinaceae Halictidae->Convolvulaceae Halictidae->Plantaginaceae Halictidae->Polygonaceae Halictidae->Rubiaceae Halictidae->Solanaceae Halictidae->Verbenaceae Halictidae->Pinaceae Halictidae->Hypericaceae Aquifoliaceae Aquifoliaceae Halictidae->Aquifoliaceae Betulaceae Betulaceae Halictidae->Betulaceae Crassulaceae Crassulaceae Halictidae->Crassulaceae Fagaceae Fagaceae Halictidae->Fagaceae Iridaceae Iridaceae Halictidae->Iridaceae Oleaceae Oleaceae Halictidae->Oleaceae Tingidae Tingidae Halictidae->Tingidae Hoplopleuridae Hoplopleuridae Hoplopleuridae->Cricetidae Hoplopleuridae->Muridae Hoplopleuridae->Sciuridae Hystrichopsyllidae Hystrichopsyllidae Hystrichopsyllidae->Cricetidae Hystrichopsyllidae->Soricidae Ischnopsyllidae Ischnopsyllidae Ischnopsyllidae->Vespertilionidae Molossidae Molossidae Ischnopsyllidae->Molossidae Ixodidae Ixodidae Ixodidae->Cricetidae Ixodidae->Procyonidae Ixodidae->Sciuridae Ixodidae->Leporidae Laelapidae Laelapidae Laelapidae->Cricetidae Leptopsyllidae Leptopsyllidae Leptopsyllidae->Cricetidae Leptopsyllidae->Soricidae Leptopsyllidae->Leporidae Linognathidae Linognathidae Cervidae Cervidae Linognathidae->Cervidae Listrophoridae Listrophoridae Listrophoridae->Vespertilionidae Listrophoridae->Cricetidae Macrochelidae Macrochelidae Macrochelidae->Cricetidae Macrochelidae->Sciuridae Macronyssidae Macronyssidae Macronyssidae->Vespertilionidae Macronyssidae->Cricetidae Macronyssidae->Didelphidae Macronyssidae->Hirundinidae Macronyssidae->Sciuridae Macronyssidae->Hominidae Macronyssidae->Paridae Macronyssidae->Passeridae Tyrannidae Tyrannidae Macronyssidae->Tyrannidae Vireonidae Vireonidae Macronyssidae->Vireonidae Megachilidae Megachilidae Megachilidae->Apocynaceae Megachilidae->Asteraceae Megachilidae->Brassicaceae Megachilidae->Caprifoliaceae Megachilidae->Cucurbitaceae Megachilidae->Fabaceae Megachilidae->Hydrangeaceae Megachilidae->Lamiaceae Megachilidae->Ranunculaceae Megachilidae->Salicaceae Megachilidae->Asparagaceae Megachilidae->Balsaminaceae Megachilidae->Combretaceae Megachilidae->Commelinaceae Megachilidae->Convolvulaceae Megachilidae->Plantaginaceae Megachilidae->Rubiaceae Megachilidae->Verbenaceae Megachilidae->Hypericaceae Megachilidae->Liliaceae Megachilidae->Crassulaceae Megachilidae->Oleaceae Simaroubaceae Simaroubaceae Megachilidae->Simaroubaceae Myobiidae Myobiidae Myobiidae->Vespertilionidae Myobiidae->Cricetidae Myobiidae->Muridae Myobiidae->Soricidae Nymphalidae Nymphalidae Nymphalidae->Asteraceae Parasitidae Parasitidae Parasitidae->Cricetidae Philopteridae Philopteridae Odontophoridae Odontophoridae Philopteridae->Odontophoridae Phytoptidae Phytoptidae Phytoptidae->Pinaceae Podocinidae Podocinidae Podocinidae->Fagaceae Polyplacidae Polyplacidae Polyplacidae->Leporidae Psychodidae Psychodidae Psychodidae->Hominidae Pthiridae Pthiridae Pthiridae->Hominidae Pulicidae Pulicidae Pulicidae->Didelphidae Pulicidae->Muridae Pulicidae->Procyonidae Pulicidae->Sciuridae Pulicidae->Hominidae Canidae Canidae Pulicidae->Canidae Erinaceidae Erinaceidae Pulicidae->Erinaceidae Falconidae Falconidae Pulicidae->Falconidae Felidae Felidae Pulicidae->Felidae Rhinonyssidae Rhinonyssidae Rhinonyssidae->Passeridae Parulidae Parulidae Rhinonyssidae->Parulidae Spinturnicidae Spinturnicidae Spinturnicidae->Vespertilionidae Tenuipalpidae Tenuipalpidae Tenuipalpidae->Pinaceae Tenuipalpidae->Vitaceae Tenuipalpidae->Oleaceae Cactaceae Cactaceae Tenuipalpidae->Cactaceae Ericaceae Ericaceae Tenuipalpidae->Ericaceae Juglandaceae Juglandaceae Tenuipalpidae->Juglandaceae Orchidaceae Orchidaceae Tenuipalpidae->Orchidaceae Poaceae Poaceae Tenuipalpidae->Poaceae Taxaceae Taxaceae Tenuipalpidae->Taxaceae Viscaceae Viscaceae Tenuipalpidae->Viscaceae Tetranychidae Tetranychidae Tetranychidae->Caprifoliaceae Tetranychidae->Fabaceae Tetranychidae->Hydrangeaceae Tetranychidae->Malvaceae Tetranychidae->Rosaceae Tetranychidae->Salicaceae Tetranychidae->Sapindaceae Tetranychidae->Viburnaceae Tetranychidae->Asparagaceae Tetranychidae->Pinaceae Tetranychidae->Anacardiaceae Tetranychidae->Aquifoliaceae Tetranychidae->Betulaceae Tetranychidae->Fagaceae Tetranychidae->Oleaceae Tetranychidae->Ericaceae Tetranychidae->Juglandaceae Buxaceae Buxaceae Tetranychidae->Buxaceae Cupressaceae Cupressaceae Tetranychidae->Cupressaceae Margarodidae Margarodidae Tetranychidae->Margarodidae Myricaceae Myricaceae Tetranychidae->Myricaceae Oxalidaceae Oxalidaceae Tetranychidae->Oxalidaceae Rhamnaceae Rhamnaceae Tetranychidae->Rhamnaceae Rutaceae Rutaceae Tetranychidae->Rutaceae Ulmaceae Ulmaceae Tetranychidae->Ulmaceae Thripidae Thripidae Thripidae->Apocynaceae Thripidae->Fabaceae Tortricidae Tortricidae Tortricidae->Pinaceae Trombiculidae Trombiculidae Trombiculidae->Vespertilionidae Trombiculidae->Cricetidae Trombiculidae->Muridae Trombiculidae->Sciuridae Trombiculidae->Leporidae Trombiculidae->Odontophoridae Vermipsyllidae Vermipsyllidae Vermipsyllidae->Procyonidae Vermipsyllidae->Felidae

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
Brevipalpus californicus HAS_ACCEPTED_NAME col Brevipalpus californicus
Brevipalpus cardinalis HAS_ACCEPTED_NAME col Brevipalpus cardinalis
Brevipalpus essigi HAS_ACCEPTED_NAME col Brevipalpus essigi
Brevipalpus lewisi HAS_ACCEPTED_NAME col Brevipalpus lewisi
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 278
col class 2
col family 20
col genus 148
col kingdom 1
col order 8
col parvorder 1
col species 642
col subfamily 2
col subgenus 11
col suborder 2
col subspecies 27
col superfamily 2
col variety 7
discoverlife NA 923
discoverlife species 205
gbif NA 198
gbif class 2
gbif family 22
gbif form 1
gbif genus 178
gbif kingdom 1
gbif order 8
gbif species 693
gbif subspecies 35
gbif variety 14
itis NA 392
itis class 2
itis family 22
itis genus 139
itis kingdom 1
itis order 10
itis species 543
itis subclass 1
itis subfamily 2
itis suborder 2
itis subspecies 13
itis superfamily 2
itis variety 1
mdd NA 1128
ncbi NA 349
ncbi class 2
ncbi family 22
ncbi genus 161
ncbi order 8
ncbi species 565
ncbi subclass 1
ncbi subfamily 2
ncbi subgenus 1
ncbi suborder 2
ncbi subspecies 12
ncbi superfamily 2
ncbi superorder 1
ncbi varietas 1
pbdb NA 904
pbdb class 3
pbdb family 13
pbdb genus 85
pbdb infraorder 1
pbdb kingdom 1
pbdb order 9
pbdb species 108
pbdb subfamily 1
pbdb suborder 3
pbdb superfamily 2
pbdb unranked clade 1
tpt NA 839
tpt family 2
tpt genus 11
tpt order 3
tpt species 272
tpt subspecificepithet 3
wfo NA 807
wfo family 1
wfo genus 114
wfo species 206
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 833
col NONE 288
col SYNONYM_OF 182
discoverlife NONE 940
discoverlife HAS_ACCEPTED_NAME 199
discoverlife SYNONYM_OF 64
discoverlife HOMONYM_OF 13
gbif HAS_ACCEPTED_NAME 1029
gbif SYNONYM_OF 312
gbif NONE 207
itis HAS_ACCEPTED_NAME 715
itis NONE 402
itis SYNONYM_OF 58
mdd NONE 1085
mdd HAS_ACCEPTED_NAME 67
ncbi SAME_AS 758
ncbi NONE 359
ncbi SYNONYM_OF 38
ncbi COMMON_NAME_OF 2
pbdb NONE 922
pbdb SYNONYM_OF 21
pbdb HAS_ACCEPTED_NAME 229
tpt HAS_ACCEPTED_NAME 328
tpt NONE 859
tpt SYNONYM_OF 127
wfo NONE 829
wfo HAS_ACCEPTED_NAME 311
wfo SYNONYM_OF 53
wfo HAS_UNCHECKED_NAME 36
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
2024-04-17T03:45:59Z note found unsupported interaction type with name: [attacks]
2024-04-17T03:46:00Z note source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder
2024-04-17T03:46:00Z note source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder
2024-04-17T03:46:00Z 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 8
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

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.