A Review of Biotic Interactions and Taxon Names Found in EMTuckerLabUMMZ/ummzi

by Nomer and Elton, two naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

https://github.com/EMTuckerLabUMMZ/ummzi/issues

2024-04-29

Abstract

Life on Earth is sustained by complex interactions between organisms and their environment. These biotic interactions can be captured in datasets and published digitally. We present a review process of such an openly accessible digital interactions dataset of known origin, and discuss its outcome. The dataset under review, named EMTuckerLabUMMZ/ummzi, is 211MiB in size and contains 93,376 interaction with 1 unique type of association (e.g., hasHost) between 766 primary taxa (e.g., Acari) and 12,548 associated taxon (e.g., Acrocephalus arundinaceus). 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 Michigan Museum of Zoology Insect Division. Full Database Export 2020-11-20 provided by Erika Tucker and Barry Oconner. https://github.com/EMTuckerLabUMMZ/ummzi/archive/6731357a377e9c2748fc931faa2ff3dc0ce3ea7a.zip 2024-04-19T22:40:07.362Z 2c8c0ec09c6b0509882ad2d98a8a1ee1d1ea870c3ab2e7d69a0486f2e4643b01

For additional metadata related to this dataset, please visit https://github.com/EMTuckerLabUMMZ/ummzi 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.  211MiB) under review 
elton pull EMTuckerLabUMMZ/ummzi

# generate review notes
elton review EMTuckerLabUMMZ/ummzi\
 > review.tsv

# export indexed interaction records
elton interactions EMTuckerLabUMMZ/ummzi\
 > interactions.tsv

# export names and align them with the Catalogue of Life using Nomer 
elton names EMTuckerLabUMMZ/ummzi\
 | 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 EMTuckerLabUMMZ/ummzi, is 211MiB in size and contains 93,376 interaction with 1 unique type of association (e.g., hasHost) between 766 primary taxa (e.g., Acari) and 12,548 associated taxon (e.g., Acrocephalus arundinaceus).

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
Acari hasHost Scarabaeidae doi:10.15468/tmxd7n
Acari hasHost Dermestes maculatus doi:10.15468/tmxd7n
Acari hasHost Anthidium undulatiforme doi:10.15468/tmxd7n
Acari hasHost Anthidium flavomaculatum doi:10.15468/tmxd7n
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
hasHost 94489
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Acari 57444
Arthropoda 9457
Proctophyllodes 3237
Proterothrix 1004
Proctophyllodes polyxenus 944
Pterodectes 645
Bombus 634
Amerodectes 584
Trouessartia trouessarti 558
Hymenoptera 487
Proctophyllodes spini 478
Trouessartia lonchurae 406
Trouessartia trouessartii 363
Ceratina 355
Nycteridocaulus 354
Proctophyllodes cotyledon 304
Apis 293
Proctophyllodes egglestoni 273
Proctophyllodes hylocichlae 249
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
Acrocephalus arundinaceus 1340
Hirundo rustica 1101
Turdus migratorius 494
Spinus tristis 448
Lophuromys aquilus 424
Myotis velifer 416
Emberiza rutila 375
Geospiza fuliginosa 368
Praomys taitae 350
Quiscalus quiscula 350
Bombycilla cedrorum 336
Haemorhous mexicanus 334
Pheucticus ludovicianus 330
Seiurus aurocapilla 294
Solidago 256
Centaurea stoebe 256
Lonchura leucogastra 252
Junco hyemalis 249
Chilocorus cacti 239
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Acari hasHost Hirundo rustica 867
Trouessartia trouessarti hasHost Acrocephalus arundinaceus 515
Acari hasHost Acrocephalus arundinaceus 421
Acari hasHost Myotis velifer 416
Acari hasHost Lophuromys aquilus 387
Acari hasHost Geospiza fuliginosa 368
Acari hasHost Praomys taitae 350
Trouessartia trouessartii hasHost Acrocephalus arundinaceus 349
Proctophyllodes hasHost Turdus migratorius 336
Proctophyllodes spini hasHost Spinus tristis 308
Acari hasHost Emberiza rutila 288
Acari hasHost Chilocorus cacti 239
Proctophyllodes ampelidis hasHost Bombycilla cedrorum 234
Proctophyllodes hasHost Haemorhous mexicanus 204
Acari hasHost Microgale cowani 169
Acari hasHost Zosterops erythropleurus 166
Proctophyllodes polyxenus hasHost Junco hyemalis 162
Acari hasHost Microtus pennsylvanicus 159
Acari hasHost Turdus migratorius 158

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->Animalia Plantae->Plantae
interactions Ampulicidae Ampulicidae Asteraceae Asteraceae Ampulicidae->Asteraceae Asteraceae->Asteraceae Brassicaceae Brassicaceae Asteraceae->Brassicaceae Lamiaceae Lamiaceae Asteraceae->Lamiaceae Psilostomidae Psilostomidae Asteraceae->Psilostomidae Rosaceae Rosaceae Asteraceae->Rosaceae Boraginaceae Boraginaceae Asteraceae->Boraginaceae Andrenidae Andrenidae Andrenidae->Asteraceae Apocynaceae Apocynaceae Andrenidae->Apocynaceae Asparagaceae Asparagaceae Andrenidae->Asparagaceae Andrenidae->Brassicaceae Caprifoliaceae Caprifoliaceae Andrenidae->Caprifoliaceae Cornaceae Cornaceae Andrenidae->Cornaceae Cupressaceae Cupressaceae Andrenidae->Cupressaceae Elaeagnaceae Elaeagnaceae Andrenidae->Elaeagnaceae Ericaceae Ericaceae Andrenidae->Ericaceae Fabaceae Fabaceae Andrenidae->Fabaceae Geraniaceae Geraniaceae Andrenidae->Geraniaceae Hydrangeaceae Hydrangeaceae Andrenidae->Hydrangeaceae Hypericaceae Hypericaceae Andrenidae->Hypericaceae Iridaceae Iridaceae Andrenidae->Iridaceae Andrenidae->Lamiaceae Metacapnodiaceae Metacapnodiaceae Andrenidae->Metacapnodiaceae Montiaceae Montiaceae Andrenidae->Montiaceae Polygalaceae Polygalaceae Andrenidae->Polygalaceae Andrenidae->Psilostomidae Ranunculaceae Ranunculaceae Andrenidae->Ranunculaceae Rhamnaceae Rhamnaceae Andrenidae->Rhamnaceae Andrenidae->Rosaceae Rubiaceae Rubiaceae Andrenidae->Rubiaceae Salicaceae Salicaceae Andrenidae->Salicaceae Sapindaceae Sapindaceae Andrenidae->Sapindaceae Viburnaceae Viburnaceae Andrenidae->Viburnaceae Apidae Apidae Apidae->Asteraceae Apidae->Apocynaceae Apidae->Asparagaceae Apidae->Brassicaceae Apidae->Caprifoliaceae Apidae->Elaeagnaceae Apidae->Ericaceae Apidae->Fabaceae Apidae->Geraniaceae Apidae->Hydrangeaceae Apidae->Hypericaceae Apidae->Iridaceae Apidae->Lamiaceae Apidae->Metacapnodiaceae Apidae->Montiaceae Apidae->Psilostomidae Apidae->Ranunculaceae Apidae->Rosaceae Apidae->Rubiaceae Apidae->Salicaceae Apidae->Sapindaceae Apiaceae Apiaceae Apidae->Apiaceae Balsaminaceae Balsaminaceae Apidae->Balsaminaceae Apidae->Boraginaceae Caryophyllaceae Caryophyllaceae Apidae->Caryophyllaceae Lythraceae Lythraceae Apidae->Lythraceae Onagraceae Onagraceae Apidae->Onagraceae Plantaginaceae Plantaginaceae Apidae->Plantaginaceae Polygonaceae Polygonaceae Apidae->Polygonaceae Scrophulariaceae Scrophulariaceae Apidae->Scrophulariaceae Violaceae Violaceae Apidae->Violaceae Braconidae Braconidae Braconidae->Brassicaceae Braconidae->Boraginaceae Aphididae Aphididae Braconidae->Aphididae Coleophoridae Coleophoridae Braconidae->Coleophoridae Ceratophyllidae Ceratophyllidae Aplodontiidae Aplodontiidae Ceratophyllidae->Aplodontiidae Castoridae Castoridae Ceratophyllidae->Castoridae Cricetidae Cricetidae Ceratophyllidae->Cricetidae Dipodidae Dipodidae Ceratophyllidae->Dipodidae Geomyidae Geomyidae Ceratophyllidae->Geomyidae Hirundinidae Hirundinidae Ceratophyllidae->Hirundinidae Leporidae Leporidae Ceratophyllidae->Leporidae Mephitidae Mephitidae Ceratophyllidae->Mephitidae Mustelidae Mustelidae Ceratophyllidae->Mustelidae Passerellidae Passerellidae Ceratophyllidae->Passerellidae Procyonidae Procyonidae Ceratophyllidae->Procyonidae Sciuridae Sciuridae Ceratophyllidae->Sciuridae Troglodytidae Troglodytidae Ceratophyllidae->Troglodytidae Chrysididae Chrysididae Chrysididae->Asteraceae Chrysididae->Rosaceae Chrysididae->Apiaceae Colletidae Colletidae Colletidae->Asteraceae Colletidae->Apocynaceae Colletidae->Brassicaceae Colletidae->Cupressaceae Colletidae->Ericaceae Colletidae->Fabaceae Colletidae->Hydrangeaceae Colletidae->Hypericaceae Colletidae->Lamiaceae Colletidae->Ranunculaceae Colletidae->Rhamnaceae Colletidae->Rosaceae Colletidae->Rubiaceae Colletidae->Salicaceae Colletidae->Sapindaceae Colletidae->Apiaceae Colletidae->Boraginaceae Amaryllidaceae Amaryllidaceae Colletidae->Amaryllidaceae Euphorbiaceae Euphorbiaceae Colletidae->Euphorbiaceae Solanaceae Solanaceae Colletidae->Solanaceae Crabronidae Crabronidae Crabronidae->Asteraceae Crabronidae->Brassicaceae Crabronidae->Hypericaceae Crabronidae->Lamiaceae Crabronidae->Apiaceae Crabronidae->Plantaginaceae Ctenophthalmidae Ctenophthalmidae Ctenophthalmidae->Aplodontiidae Ctenophthalmidae->Castoridae Ctenophthalmidae->Cricetidae Ctenophthalmidae->Dipodidae Ctenophthalmidae->Mustelidae Ctenophthalmidae->Sciuridae Soricidae Soricidae Ctenophthalmidae->Soricidae Enderleinellidae Enderleinellidae Enderleinellidae->Sciuridae Eumenidae Eumenidae Eumenidae->Asteraceae Eumenidae->Brassicaceae Eumenidae->Fabaceae Eumenidae->Hypericaceae Eumenidae->Lamiaceae Eumenidae->Rosaceae Eumenidae->Apiaceae Formicidae Formicidae Formicidae->Asteraceae Formicidae->Brassicaceae Formicidae->Lamiaceae Formicidae->Rosaceae Formicidae->Apiaceae Formicidae->Boraginaceae Halictidae Halictidae Halictidae->Asteraceae Halictidae->Apocynaceae Halictidae->Asparagaceae Halictidae->Brassicaceae Halictidae->Caprifoliaceae Halictidae->Cupressaceae Halictidae->Elaeagnaceae Halictidae->Ericaceae Halictidae->Fabaceae Halictidae->Geraniaceae Halictidae->Hypericaceae Halictidae->Iridaceae Halictidae->Lamiaceae Halictidae->Metacapnodiaceae Halictidae->Polygalaceae Halictidae->Ranunculaceae Halictidae->Rhamnaceae Halictidae->Rosaceae Halictidae->Rubiaceae Halictidae->Salicaceae Halictidae->Sapindaceae Halictidae->Viburnaceae Halictidae->Apiaceae Halictidae->Boraginaceae Halictidae->Onagraceae Halictidae->Plantaginaceae Halictidae->Polygonaceae Halictidae->Scrophulariaceae Halictidae->Violaceae Halictidae->Euphorbiaceae Oxalidaceae Oxalidaceae Halictidae->Oxalidaceae Hystrichopsyllidae Hystrichopsyllidae Hystrichopsyllidae->Aplodontiidae Hystrichopsyllidae->Cricetidae Hystrichopsyllidae->Soricidae Ichneumonidae Ichneumonidae Ichneumonidae->Asteraceae Ichneumonidae->Brassicaceae Ichneumonidae->Lamiaceae Ichneumonidae->Rosaceae Ichneumonidae->Apiaceae Ischnopsyllidae Ischnopsyllidae Pteropodidae Pteropodidae Ischnopsyllidae->Pteropodidae Vespertilionidae Vespertilionidae Ischnopsyllidae->Vespertilionidae Laelapidae Laelapidae Laelapidae->Apidae Laelapidae->Castoridae Laelapidae->Cricetidae Acrididae Acrididae Laelapidae->Acrididae Didelphidae Didelphidae Laelapidae->Didelphidae Lucanidae Lucanidae Laelapidae->Lucanidae Passalidae Passalidae Laelapidae->Passalidae Scarabaeidae Scarabaeidae Laelapidae->Scarabaeidae Leptopsyllidae Leptopsyllidae Leptopsyllidae->Cricetidae Megachilidae Megachilidae Megachilidae->Asteraceae Megachilidae->Apocynaceae Megachilidae->Caprifoliaceae Megachilidae->Ericaceae Megachilidae->Fabaceae Megachilidae->Hypericaceae Megachilidae->Lamiaceae Megachilidae->Montiaceae Megachilidae->Psilostomidae Megachilidae->Rosaceae Megachilidae->Rubiaceae Megachilidae->Onagraceae Megachilidae->Plantaginaceae Megachilidae->Violaceae Anacardiaceae Anacardiaceae Megachilidae->Anacardiaceae Poaceae Poaceae Megachilidae->Poaceae Verbenaceae Verbenaceae Megachilidae->Verbenaceae Pompilidae Pompilidae Pompilidae->Asteraceae Pompilidae->Brassicaceae Pompilidae->Apiaceae Proctotrupidae Proctotrupidae Proctotrupidae->Psilostomidae Pteromalidae Pteromalidae Pteromalidae->Lamiaceae Pteromalidae->Coleophoridae Tortricidae Tortricidae Pteromalidae->Tortricidae Pulicidae Pulicidae Pulicidae->Cricetidae Pulicidae->Leporidae Pulicidae->Mephitidae Pulicidae->Procyonidae Pulicidae->Sciuridae Canidae Canidae Pulicidae->Canidae Felidae Felidae Pulicidae->Felidae Hominidae Hominidae Pulicidae->Hominidae Muridae Muridae Pulicidae->Muridae Rhopalopsyllidae Rhopalopsyllidae Rhopalopsyllidae->Cricetidae Rhopalopsyllidae->Didelphidae Sphecidae Sphecidae Sphecidae->Asteraceae Sphecidae->Apiaceae Stephanocircidae Stephanocircidae Stephanocircidae->Cricetidae Caenolestidae Caenolestidae Stephanocircidae->Caenolestidae Tenthredinidae Tenthredinidae Tenthredinidae->Asteraceae Tenthredinidae->Brassicaceae Tenthredinidae->Caprifoliaceae Tenthredinidae->Rosaceae Tiphiidae Tiphiidae Tiphiidae->Apiaceae Trouessartiidae Trouessartiidae Trouessartiidae->Passerellidae Monarchidae Monarchidae Trouessartiidae->Monarchidae Vermipsyllidae Vermipsyllidae Vermipsyllidae->Salicaceae Vermipsyllidae->Procyonidae Vermipsyllidae->Didelphidae Vermipsyllidae->Canidae Vespidae Vespidae Vespidae->Asteraceae Vespidae->Lamiaceae Vespidae->Rosaceae Vespidae->Apiaceae Vespidae->Balsaminaceae Vespidae->Boraginaceae Vespidae->Lythraceae Vespidae->Plantaginaceae Vespidae->Polygonaceae

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
reserved by Klimov for Brazilian trp NONE col reserved by Klimov for Brazilian trp
Abditomys latidens HAS_ACCEPTED_NAME col Abditomys latidens
Abeillia abeillei HAS_ACCEPTED_NAME col Abeillia abeillei
Abies alba HAS_ACCEPTED_NAME col Abies alba
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 2955
col class 6
col family 150
col genus 543
col infraorder 1
col order 23
col phylum 3
col species 7641
col subfamily 2
col subgenus 29
col subspecies 1317
col superfamily 1
col tribe 3
col variety 8
discoverlife NA 11644
discoverlife species 973
gbif NA 2311
gbif class 6
gbif family 157
gbif form 11
gbif genus 636
gbif order 23
gbif phylum 3
gbif species 8127
gbif subspecies 1393
gbif variety 18
itis NA 3661
itis class 5
itis division 2
itis family 149
itis genus 468
itis order 25
itis phylum 1
itis species 7032
itis subclass 1
itis subfamily 3
itis subspecies 1263
itis superfamily 2
itis superorder 1
itis tribe 2
itis variety 4
mdd NA 12616
ncbi NA 4579
ncbi class 5
ncbi cohort 1
ncbi family 146
ncbi genus 562
ncbi order 25
ncbi phylum 3
ncbi species 6869
ncbi subclass 1
ncbi subfamily 6
ncbi subgenus 28
ncbi subspecies 413
ncbi superfamily 1
ncbi tribe 2
ncbi varietas 2
pbdb NA 10480
pbdb class 7
pbdb family 141
pbdb genus 316
pbdb infraclass 1
pbdb infraorder 1
pbdb order 27
pbdb phylum 1
pbdb species 1631
pbdb subclass 1
pbdb subfamily 5
pbdb suborder 2
pbdb subspecies 7
pbdb superfamily 1
pbdb tribe 2
pbdb unranked clade 4
tpt NA 7625
tpt family 24
tpt genus 162
tpt order 2
tpt species 4803
wfo NA 12123
wfo family 16
wfo genus 109
wfo species 362
wfo subspecies 12
wfo variety 4
Name relationship types per catalog. Name relationship type “NONE” means that a name was not recognized by the associated catalog. “SAME_AS” indicates either a “HAS_ACCEPTED_NAME” or “SYNONYM_OF” name relationship type. We recognize that “SYNONYM_OF” encompasses many types of nomenclatural synonymies (ICZN 1999) (e.g., junior synonym, senior synonyms).
resolvedCatalogName relationName count
col NONE 3167
col HAS_ACCEPTED_NAME 11015
col SYNONYM_OF 1665
discoverlife NONE 14331
discoverlife SYNONYM_OF 290
discoverlife HAS_ACCEPTED_NAME 939
discoverlife HOMONYM_OF 56
gbif NONE 2471
gbif HAS_ACCEPTED_NAME 12310
gbif SYNONYM_OF 2499
itis NONE 3933
itis HAS_ACCEPTED_NAME 10252
itis SYNONYM_OF 1256
mdd NONE 14271
mdd HAS_ACCEPTED_NAME 1084
ncbi NONE 5046
ncbi SAME_AS 9528
ncbi SYNONYM_OF 943
pbdb NONE 12192
pbdb HAS_ACCEPTED_NAME 3015
pbdb SYNONYM_OF 203
tpt NONE 9038
tpt HAS_ACCEPTED_NAME 6277
tpt SYNONYM_OF 112
wfo NONE 14786
wfo HAS_ACCEPTED_NAME 523
wfo SYNONYM_OF 108
wfo HAS_UNCHECKED_NAME 101
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
2024-04-28T22:46:52Z note target taxon name missing
2024-04-28T22:46:52Z note target taxon name missing
2024-04-28T22:46:52Z note target taxon name missing
2024-04-28T22:46:52Z note target taxon name missing

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

Most frequently occurring review notes, if any.
reviewComment count
target taxon name missing 367307
target taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder 255
source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder 29

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

GloBI Review Badge

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

review review 💬 💬

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

GloBI Index Badge

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

Picture of a GloBI Index Badge

If you’d like to keep track of reviews or index status of the dataset under review, please visit [GloBI’s dataset index ^[At time of writing (2024-04-29) the version of the GloBI dataset index was available at https://globalbioticinteractions.org/datasets for badge examples.

Discussion

This review aims to provide a perspective on the dataset to aid in understanding of species interaction claims discovered. However, it is important to note that this review does not assess the quality of the dataset. Instead, it serves as an indication of the open-ness5 and FAIRness (Wilkinson et al. 2016; Trekels et al. 2023) of the dataset: to perform this review, the data was likely openly available, Findable, Accessible, Interoperable and Reusable. The current Open-FAIR assessment is qualitative, and a more quantitative approach can be implemented with specified measurement units.

This report also showcases the reuse of machine-actionable (meta)data, something highly recommended by the FAIR Data Principles (Wilkinson et al. 2016). Making (meta)data machine-actionable enables more precise procesing by computers, enabling even naive review bots like Nomer and Elton to interpret the data effectively. This capability is crucial for not just automating the generation of reports, but also for facilitating seamless data exchanges, promoting interoperability.

Acknowledgements

We thank the many humans that created us and those who created and maintained the data, software and other intellectual resources that were used for producing this review. In addition, we are grateful for the natural resources providing the basis for these human and bot activities.

Author contributions

Nomer was responsible for name alignments. Elton carried out dataset extraction, and generated the review notes.

References

ICZN. 1999. “International Code of Zoological Nomenclature.” The International Trust for Zoological Nomenclature, London, UK. https://www.iczn.org/the-code/the-code-online/.
Poelen, Jorrit H., James D. Simons, and Chris J. Mungall. 2014. “Global Biotic Interactions: An Open Infrastructure to Share and Analyze Species-Interaction Datasets.” Ecological Informatics 24 (November): 148–59. https://doi.org/10.1016/j.ecoinf.2014.08.005.
Trekels, Maarten, Debora Pignatari Drucker, José Augusto Salim, Jeff Ollerton, Jorrit Poelen, Filipi Miranda Soares, Max Rünzel, Muo Kasina, Quentin Groom, and Mariano Devoto. 2023. “WorldFAIR Project (D10.1) Agriculture-related pollinator data standards use cases report.” Zenodo. https://doi.org/10.5281/zenodo.8176978.
Wilkinson, Mark D., Michel Dumontier, IJsbrand Jan Aalbersberg, Gabrielle Appleton, Myles Axton, Arie Baak, Niklas Blomberg, et al. 2016. “The FAIR Guiding Principles for Scientific Data Management and Stewardship.” Scientific Data 3 (1). https://doi.org/10.1038/sdata.2016.18.