A Review of Biotic Interactions and Taxon Names Found in globalbioticinteractions/psuc-ento

by Nomer and Elton, two naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

https://github.com/globalbioticinteractions/psuc-ento/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/psuc-ento, is 9.95MiB in size and contains 12,791 interaction with 7 unique types of associations (e.g., interactsWith) between 1,695 primary taxon (e.g., Bombus impatiens) and 1,092 associated taxon (e.g., Agastache Blue Fortune). 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:

Frost Entomological Museum, Pennsylvania State University https://github.com/globalbioticinteractions/psuc-ento/archive/30b1f96619a6e9f10da18b42fb93ff22cc4f72e2.zip 2024-04-13T04:38:35.369Z 8a7fc654e7137b997ff258d3038a9c6e65747862492d4afbe4842c5126e1ebae

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/psuc-ento 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. 9.95MiB) under review 
elton pull globalbioticinteractions/psuc-ento

# generate review notes
elton review globalbioticinteractions/psuc-ento\
 > review.tsv

# export indexed interaction records
elton interactions globalbioticinteractions/psuc-ento\
 > interactions.tsv

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/psuc-ento\
 | 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/psuc-ento, is 9.95MiB in size and contains 12,791 interaction with 7 unique types of associations (e.g., interactsWith) between 1,695 primary taxon (e.g., Bombus impatiens) and 1,092 associated taxon (e.g., Agastache Blue Fortune).

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
PSUC | ENTO | http://grbio.org/cool/29fv-ztxs | PSUC_FEM_7144 | db73d8c6-4525-4e5d-b50b-2d07eaa383b4 interactsWith Prarie dog https://scan-bugs.org:443/portal/collections/individual/index.php?occid=36079106
Hybophthirus notophallus interactsWith Cape Ant Bear or Aardvark https://scan-bugs.org:443/portal/collections/individual/index.php?occid=36079107
PSUC | ENTO | http://grbio.org/cool/29fv-ztxs | PSUC_FEM_7082 | a61a4049-6127-40b6-9789-9220c144ac3d interactsWith Ovis dalli https://scan-bugs.org:443/portal/collections/individual/index.php?occid=36079108
PSUC | ENTO | http://grbio.org/cool/29fv-ztxs | PSUC_FEM_7083 | 9d7d60df-b703-4e2f-9d2d-04f36990229b interactsWith Ovis dalli https://scan-bugs.org:443/portal/collections/individual/index.php?occid=36079109
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
interactsWith 11889
adjacentTo 567
hasHost 302
eats 25
hostOf 5
visits 2
parasiteOf 1
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Bombus impatiens 944
Augochlora pura 759
Chauliognathus pensylvanicus 672
Ceratina calcerata 461
Epargyreus clarus 453
Syrphidae 400
Dermacentor variabilis 353
Apis mellifera 276
Bombus bimaculatus 263
Ixodes scapularis 218
Bombus griseocollis 207
Polites peckius 205
Chaliognathus pensylvanicus 191
Ixodes cookei 167
Atteva aurea 152
Halictus ligatus 145
Pieris rapae 142
Bombus vagans 128
Diptera 126
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
Agastache Blue Fortune 2233
Rudbeckia Herbstonne 993
Agastache Black Adder 729
Rudbeckia Triloba 603
Homo sapiens 551
Rudbeckia Goldsturm 496
Nepeta Walker’s Low 437
Rudbeckia Fulgida 379
Agastache Foeniculum 334
Canis 241
-77.702398 190
Callorhinus ursinus 178
Nepeta Faassenii 156
Nepeta Junior Walker 150
Salvia East Friesland 141
Rudbeckia Indian Summer 124
Salvia May Night 113
Salvia Caradonna 101
Solidago 79
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Chauliognathus pensylvanicus interactsWith Agastache Blue Fortune 411
Bombus impatiens interactsWith Agastache Blue Fortune 325
Ceratina calcerata interactsWith Agastache Blue Fortune 238
Dermacentor variabilis interactsWith Homo sapiens 215
Bombus impatiens interactsWith Rudbeckia Herbstonne 212
Augochlora pura interactsWith Rudbeckia Triloba 209
Epargyreus clarus interactsWith Agastache Black Adder 182
Ixodes scapularis interactsWith Homo sapiens 164
Epargyreus clarus interactsWith Agastache Blue Fortune 153
Augochlora pura interactsWith Rudbeckia Goldsturm 139
Augochlora pura interactsWith Rudbeckia Fulgida 135
Chaliognathus pensylvanicus interactsWith Agastache Blue Fortune 123
Dermacentor variabilis interactsWith Canis 121
Orthohalarachne attenuata interactsWith Callorhinus ursinus 118
Augochlora pura interactsWith Rudbeckia Herbstonne 106
Augochlora pura interactsWith Agastache Blue Fortune 105
Bombus impatiens interactsWith Agastache Black Adder 100
Chauliognathus pensylvanicus interactsWith Rudbeckia Triloba 86
Ixodes cookei interactsWith Homo sapiens 85

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 Animalia->Animalia Animalia->Animalia Animalia->Animalia Plantae Plantae Animalia->Plantae Animalia->Plantae Animalia->Plantae Fungi Fungi Animalia->Fungi
interactions Acrididae Acrididae Asteraceae Asteraceae Acrididae->Asteraceae Brassicaceae Brassicaceae Acrididae->Brassicaceae Adelgidae Adelgidae Pinaceae Pinaceae Adelgidae->Pinaceae Agelenidae Agelenidae Ichneumonidae Ichneumonidae Agelenidae->Ichneumonidae Ichneumonidae->Asteraceae Fagaceae Fagaceae Ichneumonidae->Fagaceae Erebidae Erebidae Ichneumonidae->Erebidae Agromyzidae Agromyzidae Agromyzidae->Asteraceae Alydidae Alydidae Fabaceae Fabaceae Alydidae->Fabaceae Anthomyiidae Anthomyiidae Amaryllidaceae Amaryllidaceae Anthomyiidae->Amaryllidaceae Aphalaridae Aphalaridae Cannabaceae Cannabaceae Aphalaridae->Cannabaceae Aphididae Aphididae Aphididae->Asteraceae Aphididae->Asteraceae Aphididae->Fagaceae Rosaceae Rosaceae Aphididae->Rosaceae Apidae Apidae Apidae->Asteraceae Apidae->Brassicaceae Cucurbitaceae Cucurbitaceae Apidae->Cucurbitaceae Lamiaceae Lamiaceae Apidae->Lamiaceae Araneidae Araneidae Araneidae->Asteraceae Argasidae Argasidae Hominidae Hominidae Argasidae->Hominidae Asilidae Asilidae Asilidae->Fagaceae Attelabidae Attelabidae Attelabidae->Rosaceae Attevidae Attevidae Simaroubaceae Simaroubaceae Attevidae->Simaroubaceae Braconidae Braconidae Braconidae->Asteraceae Braconidae->Fagaceae Balsaminaceae Balsaminaceae Braconidae->Balsaminaceae Tortricidae Tortricidae Braconidae->Tortricidae Tortricidae->Rosaceae Buprestidae Buprestidae Buprestidae->Fabaceae Buprestidae->Simaroubaceae Cantharidae Cantharidae Cantharidae->Asteraceae Cantharidae->Cantharidae Carabidae Carabidae Carabidae->Asteraceae Carabidae->Simaroubaceae Cerambycidae Cerambycidae Cerambycidae->Asteraceae Chalcididae Chalcididae Chalcididae->Asteraceae Chironomidae Chironomidae Chironomidae->Asteraceae Chrysomelidae Chrysomelidae Chrysomelidae->Asteraceae Chrysomelidae->Asteraceae Chrysomelidae->Brassicaceae Solanaceae Solanaceae Chrysomelidae->Solanaceae Cicadellidae Cicadellidae Cicadellidae->Asteraceae Cimicidae Cimicidae Hirundinidae Hirundinidae Cimicidae->Hirundinidae Clastopteridae Clastopteridae Clastopteridae->Asteraceae Coccidae Coccidae Oleaceae Oleaceae Coccidae->Oleaceae Magnoliaceae Magnoliaceae Coccidae->Magnoliaceae Malvaceae Malvaceae Coccidae->Malvaceae Coccinellidae Coccinellidae Coccinellidae->Asteraceae Coreidae Coreidae Coreidae->Magnoliaceae Culicidae Culicidae Sarraceniaceae Sarraceniaceae Culicidae->Sarraceniaceae Curculionidae Curculionidae Curculionidae->Asteraceae Curculionidae->Pinaceae Curculionidae->Fagaceae Curculionidae->Fagaceae Curculionidae->Rosaceae Curculionidae->Solanaceae Convolvulaceae Convolvulaceae Curculionidae->Convolvulaceae Cynipidae Cynipidae Cynipidae->Fagaceae Diaspididae Diaspididae Diaspididae->Rosaceae Diaspididae->Malvaceae Sapindaceae Sapindaceae Diaspididae->Sapindaceae Echinophthiriidae Echinophthiriidae Otariidae Otariidae Echinophthiriidae->Otariidae Phocidae Phocidae Echinophthiriidae->Phocidae Elateridae Elateridae Elateridae->Asteraceae Elateridae->Fabaceae Enderleinellidae Enderleinellidae Sciuridae Sciuridae Enderleinellidae->Sciuridae Erebidae->Fagaceae Erebidae->Sapindaceae Eriococcidae Eriococcidae Ericaceae Ericaceae Eriococcidae->Ericaceae Eumenidae Eumenidae Eumenidae->Fagaceae Figitidae Figitidae Figitidae->Malvaceae Formicidae Formicidae Formicidae->Asteraceae Formicidae->Fagaceae Formicidae->Rosaceae Membracidae Membracidae Formicidae->Membracidae Membracidae->Asteraceae Membracidae->Asteraceae Membracidae->Lamiaceae Membracidae->Formicidae Fulgoridae Fulgoridae Fulgoridae->Simaroubaceae Gelechiidae Gelechiidae Gelechiidae->Asteraceae Encyrtidae Encyrtidae Gelechiidae->Encyrtidae Gryllidae Gryllidae Gryllidae->Asteraceae Halarachnidae Halarachnidae Halarachnidae->Otariidae Halictidae Halictidae Halictidae->Asteraceae Hippoboscidae Hippoboscidae Accipitridae Accipitridae Hippoboscidae->Accipitridae Hoplopleuridae Hoplopleuridae Cricetidae Cricetidae Hoplopleuridae->Cricetidae Ixodidae Ixodidae Ixodidae->Hominidae Ixodidae->Hominidae Ixodidae->Sciuridae Ixodidae->Cricetidae Bovidae Bovidae Ixodidae->Bovidae Canidae Canidae Ixodidae->Canidae Ixodidae->Canidae Cervidae Cervidae Ixodidae->Cervidae Equidae Equidae Ixodidae->Equidae Felidae Felidae Ixodidae->Felidae Mustelidae Mustelidae Ixodidae->Mustelidae Lampyridae Lampyridae Lampyridae->Asteraceae Limacodidae Limacodidae Betulaceae Betulaceae Limacodidae->Betulaceae Linognathidae Linognathidae Linognathidae->Cervidae Lygaeidae Lygaeidae Apocynaceae Apocynaceae Lygaeidae->Apocynaceae Macrochelidae Macrochelidae Fanniidae Fanniidae Macrochelidae->Fanniidae Meloidae Meloidae Meloidae->Asteraceae Meloidae->Asteraceae Meloidae->Sapindaceae Mordellidae Mordellidae Mordellidae->Asteraceae Viburnaceae Viburnaceae Mordellidae->Viburnaceae Muscidae Muscidae Muscidae->Asteraceae Myrmeleontidae Myrmeleontidae Myrmeleontidae->Fabaceae Poaceae Poaceae Myrmeleontidae->Poaceae Nabidae Nabidae Nabidae->Fabaceae Noctuidae Noctuidae Noctuidae->Asteraceae Noctuidae->Solanaceae Nymphalidae Nymphalidae Nymphalidae->Asteraceae Nymphalidae->Fabaceae Oestridae Oestridae Oestridae->Sciuridae Ormyridae Ormyridae Ormyridae->Asteraceae Papilionidae Papilionidae Papilionidae->Asteraceae Papilionidae->Fabaceae Pedicinidae Pedicinidae Cercopithecidae Cercopithecidae Pedicinidae->Cercopithecidae Pediculidae Pediculidae Pediculidae->Hominidae Pentatomidae Pentatomidae Pentatomidae->Asteraceae Pentatomidae->Fagaceae Perilampidae Perilampidae Perilampidae->Asteraceae Phlaeothripidae Phlaeothripidae Phlaeothripidae->Fagaceae Pieridae Pieridae Pieridae->Fabaceae Pompilidae Pompilidae Pompilidae->Lamiaceae Pteromalidae Pteromalidae Pteromalidae->Asteraceae Pteromalidae->Cynipidae Pulicidae Pulicidae Pulicidae->Felidae Reduviidae Reduviidae Reduviidae->Asteraceae Reduviidae->Magnoliaceae Sarcophagidae Sarcophagidae Sarcophagidae->Asteraceae Scarabaeidae Scarabaeidae Polygonaceae Polygonaceae Scarabaeidae->Polygonaceae Scelionidae Scelionidae Scelionidae->Asteraceae Simuliidae Simuliidae Simuliidae->Hominidae Sphingidae Sphingidae Sphingidae->Asteraceae Sphingidae->Braconidae Staphylinidae Staphylinidae Staphylinidae->Asteraceae Syrphidae Syrphidae Syrphidae->Asteraceae Syrphidae->Brassicaceae Syrphidae->Malvaceae Syrphidae->Polygonaceae Tephritidae Tephritidae Annonaceae Annonaceae Tephritidae->Annonaceae Tetragnathidae Tetragnathidae Tetragnathidae->Fabaceae Tettigoniidae Tettigoniidae Tettigoniidae->Asteraceae Thripidae Thripidae Thripidae->Cucurbitaceae Thripidae->Solanaceae Thyatiridae Thyatiridae Sciaridae Sciaridae Thyatiridae->Sciaridae Tingidae Tingidae Ulmaceae Ulmaceae Tingidae->Ulmaceae Tipulidae Tipulidae Tipulidae->Cucurbitaceae Tipulidae->Balsaminaceae Trigonidiidae Trigonidiidae Trigonidiidae->Malvaceae Vespidae Vespidae Vespidae->Asteraceae Vespidae->Asteraceae Vespidae->Simaroubaceae Vespidae->Eumenidae Vespidae->Apocynaceae

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
Bracon HAS_ACCEPTED_NAME col Bracon
Celastrina HAS_ACCEPTED_NAME col Celastrina
Chrysis NONE col Chrysis
Coccus hesperidum NONE col Coccus hesperidum
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 1486
col class 1
col family 117
col genus 186
col kingdom 2
col nanorder 1
col order 19
col parvorder 1
col phylum 1
col species 668
col subfamily 2
col subgenus 9
col suborder 1
col subspecies 11
col subterclass 1
col superfamily 3
col tribe 2
col variety 4
discoverlife NA 2402
discoverlife species 88
gbif NA 1309
gbif class 1
gbif family 123
gbif form 1
gbif genus 211
gbif kingdom 3
gbif order 19
gbif phylum 1
gbif species 821
gbif subspecies 17
gbif variety 6
itis NA 1467
itis class 1
itis division 1
itis family 117
itis genus 165
itis kingdom 2
itis order 18
itis species 695
itis subclass 1
itis subfamily 4
itis suborder 6
itis subspecies 9
itis superfamily 3
itis superorder 2
itis variety 2
mdd NA 2489
ncbi NA 1542
ncbi clade 1
ncbi class 1
ncbi cohort 1
ncbi family 117
ncbi genus 184
ncbi infraorder 1
ncbi kingdom 1
ncbi order 19
ncbi species 609
ncbi subclass 1
ncbi subfamily 3
ncbi subgenus 6
ncbi suborder 3
ncbi subspecies 3
ncbi superfamily 3
ncbi superorder 1
pbdb NA 2184
pbdb class 1
pbdb family 115
pbdb genus 108
pbdb infraclass 1
pbdb infraorder 2
pbdb kingdom 2
pbdb order 20
pbdb phylum 1
pbdb species 49
pbdb subfamily 3
pbdb suborder 3
pbdb superfamily 3
pbdb tribe 1
pbdb unranked clade 3
tpt NA 2371
tpt family 8
tpt genus 15
tpt order 4
tpt species 91
wfo NA 2337
wfo family 5
wfo genus 70
wfo order 1
wfo species 74
wfo subspecies 3
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 1063
col NONE 1696
col SYNONYM_OF 249
discoverlife NONE 2712
discoverlife HAS_ACCEPTED_NAME 85
discoverlife HOMONYM_OF 6
discoverlife SYNONYM_OF 14
gbif HAS_ACCEPTED_NAME 1304
gbif SYNONYM_OF 480
gbif NONE 1508
itis HAS_ACCEPTED_NAME 1074
itis SYNONYM_OF 82
itis NONE 1676
mdd NONE 2762
mdd HAS_ACCEPTED_NAME 31
ncbi SAME_AS 1021
ncbi SYNONYM_OF 35
ncbi NONE 1755
ncbi COMMON_NAME_OF 5
pbdb HAS_ACCEPTED_NAME 333
pbdb NONE 2456
pbdb SYNONYM_OF 35
tpt NONE 2665
tpt HAS_ACCEPTED_NAME 124
tpt SYNONYM_OF 36
wfo NONE 2586
wfo HAS_ACCEPTED_NAME 197
wfo SYNONYM_OF 38
wfo HAS_UNCHECKED_NAME 10
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
2024-04-17T03:44:35Z note source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder
2024-04-17T03:44:35Z note source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder
2024-04-17T03:44:35Z note source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder
2024-04-17T03:44:35Z 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 569
found unsupported interaction type with name: [Resting on] 6
found unsupported interaction type with name: [predator of] 4
found unsupported interaction type with name: [Collected with] 4

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.