A Review of Biotic Interactions and Taxon Names Found in globalbioticinteractions/cas-ent

by Nomer and Elton, two naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

https://github.com/globalbioticinteractions/cas-ent/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 globalbioticinteractions/cas-ent, is 12.2MiB in size and contains 17,317 interaction with 4 unique types of associations (e.g., interactsWith) between 2,018 primary taxon (e.g., Euaresta aequalis) and 2,014 associated taxon (e.g., Pseudotsuga menziesii). 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:

CAS Entomology (ENT) - Version 6.274 http://ipt.calacademy.org:8080/archive.do?r=ent 2024-04-19T23:12:36.247Z 2bbe613531729edaa0f57e775e9e0acbaf853ff743bd26af09167ef80fdcd201 CAS Entomology Type (TYPE) - Version 1.233 http://ipt.calacademy.org:8080/archive.do?r=type 2024-04-19T23:12:36.247Z 2bbe613531729edaa0f57e775e9e0acbaf853ff743bd26af09167ef80fdcd201

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/cas-ent 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. 12.2MiB) under review 
elton pull globalbioticinteractions/cas-ent

# generate review notes
elton review globalbioticinteractions/cas-ent\
 > review.tsv

# export indexed interaction records
elton interactions globalbioticinteractions/cas-ent\
 > interactions.tsv

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/cas-ent\
 | 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/cas-ent, is 12.2MiB in size and contains 17,317 interaction with 4 unique types of associations (e.g., interactsWith) between 2,018 primary taxon (e.g., Euaresta aequalis) and 2,014 associated taxon (e.g., Pseudotsuga menziesii).

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
Physocyclus globosus (Taczanowski, 1874) adjacentTo cave wall in web urn:catalog:CAS:ENT:9069617
Strophiona laeta (LeConte, 1857) adjacentTo Quercus dumosa urn:catalog:CAS:ENT:8383067
Strophiona laeta (LeConte, 1857) adjacentTo Quercus dumosa urn:catalog:CAS:ENT:8383083
Brachysomida californica (LeConte, 1851) adjacentTo Potentilla sp. urn:catalog:CAS:ENT:8384162
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
interactsWith 10762
adjacentTo 6218
hasHost 352
eats 1
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Euaresta aequalis 332
Anthaxia Eschscholtz, 1829 298
Neoclytus conjunctus (LeConte, 1857) 268
Callidium antennatus ssp. hesperum 254
Callidium antennatum ssp. hesperum 239
Omus californicus ssp. californicus 230
Phymatodes nitidus LeConte, 1874 204
Campiglossa genalis 183
Acmaeodera holsteni White, 1939 180
Phymatodes Mulsant, 1839 170
Anthaxia pseudotsugae Chamberlin 130
Copidosoma 125
Xylotrechus nauticus (Mannerheim, 1843) 122
Tephritis californica Doane, 1899 119
Trupanea californica 118
Chimoptesis chrysopyla Powell, 1964 108
Neoclytus balteatus LeConte, 1873 107
Phymatodes decussatus ssp. decussatus 104
Euarestoides acutangulus (Thomson, 1869) 104
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
Pseudotsuga menziesii 954
Eucalyptus 368
Xanthium canadense 329
Adenostoma fasciculatum 307
Nothofagus 304
Pinus ponderosa 270
Sequoia sempervirens 260
Chrysothamnus sp. 260
Ceanothus 220
Quercus kelloggii 196
juniper 194
snow at night 186
Baccharis pilularis 185
Quercus 182
Casaurina 174
Quercus dumosa 170
Artemisia tridentata 162
Quercus agrifolia 159
Pinus sabiniana 150
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Euaresta aequalis interactsWith Xanthium canadense 326
Acmaeodera holsteni White, 1939 adjacentTo Adenostoma fasciculatum 142
Callidium antennatus ssp. hesperum interactsWith Pseudotsuga menziesii 136
Callidium antennatum ssp. hesperum interactsWith Pseudotsuga menziesii 124
Omus californicus ssp. californicus interactsWith O. sequoiarum laevis 121
Neoclytus conjunctus (LeConte, 1857) adjacentTo madrone 120
Phymatodes Mulsant, 1839 interactsWith Pseudotsuga menziesii 113
Tephritis californica Doane, 1899 interactsWith Baccharis pilularis 105
Anthaxia pseudotsugae Chamberlin interactsWith Pseudotsuga menziesii 102
Trupanea californica interactsWith Gnaphalium chilense 99
Anthaxia retifer LeConte, 1860 adjacentTo Notholithocarpus densiflorum 93
Andricus bakkeri adjacentTo Quercus dumosa 86
Holopleura marginata LeConte, 1873 interactsWith Pseudotsuga menziesii 80
Phymatodes maculicollis LeConte, 1878 adjacentTo Pseudotsuga menziesii 79
Campiglossa genalis interactsWith Senecio jacobaea 77
Nebria turmaduodecima Kavanaugh, 1981 adjacentTo snow at night 75
Aciurina maculata interactsWith Chrysothamnus sp. 73
Neoclytus balteatus LeConte, 1873 interactsWith Ceanothus thyrsiflorus 70
Nebria spatulata ssp. sierrae adjacentTo snow at night 69

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
interactions Acrididae Acrididae Myrtaceae Myrtaceae Acrididae->Myrtaceae Acropsopilionidae Acropsopilionidae Araucariaceae Araucariaceae Acropsopilionidae->Araucariaceae Aleyrodidae Aleyrodidae Fagaceae Fagaceae Aleyrodidae->Fagaceae Aphididae Aphididae Aphididae->Fagaceae Amaryllidaceae Amaryllidaceae Aphididae->Amaryllidaceae Apiaceae Apiaceae Aphididae->Apiaceae Asteraceae Asteraceae Aphididae->Asteraceae Betulaceae Betulaceae Aphididae->Betulaceae Fabaceae Fabaceae Aphididae->Fabaceae Poaceae Poaceae Aphididae->Poaceae Rosaceae Rosaceae Aphididae->Rosaceae Sapindaceae Sapindaceae Aphididae->Sapindaceae Apidae Apidae Apidae->Apiaceae Apidae->Apiaceae Apidae->Asteraceae Apidae->Asteraceae Apidae->Fabaceae Apidae->Rosaceae Onagraceae Onagraceae Apidae->Onagraceae Apidae->Onagraceae Polygonaceae Polygonaceae Apidae->Polygonaceae Apidae->Polygonaceae Apocynaceae Apocynaceae Apidae->Apocynaceae Boraginaceae Boraginaceae Apidae->Boraginaceae Convolvulaceae Convolvulaceae Apidae->Convolvulaceae Ericaceae Ericaceae Apidae->Ericaceae Rhamnaceae Rhamnaceae Apidae->Rhamnaceae Ascidae Ascidae Muridae Muridae Ascidae->Muridae Asilidae Asilidae Asilidae->Rosaceae Asilidae->Onagraceae Asilidae->Polygonaceae Grossulariaceae Grossulariaceae Asilidae->Grossulariaceae Plantaginaceae Plantaginaceae Asilidae->Plantaginaceae Verbenaceae Verbenaceae Asilidae->Verbenaceae Bombyliidae Bombyliidae Bombyliidae->Fagaceae Bombyliidae->Asteraceae Buprestidae Buprestidae Buprestidae->Polygonaceae Buprestidae->Rhamnaceae Ephedraceae Ephedraceae Buprestidae->Ephedraceae Buprestidae->Ephedraceae Malvaceae Malvaceae Buprestidae->Malvaceae Buprestidae->Malvaceae Pinaceae Pinaceae Buprestidae->Pinaceae Campodeidae Campodeidae Campodeidae->Fagaceae Campodeidae->Rhamnaceae Cupressaceae Cupressaceae Campodeidae->Cupressaceae Cerambycidae Cerambycidae Cerambycidae->Pinaceae Cerococcidae Cerococcidae Cerococcidae->Fagaceae Chrysididae Chrysididae Chrysididae->Polygonaceae Chrysididae->Polygonaceae Chrysididae->Rhamnaceae Chrysididae->Pinaceae Chrysididae->Pinaceae Chrysididae->Cupressaceae Brassicaceae Brassicaceae Chrysididae->Brassicaceae Chrysopidae Chrysopidae Chrysopidae->Fabaceae Coccidae Coccidae Coccidae->Asteraceae Coccidae->Poaceae Coccidae->Rosaceae Coccidae->Pinaceae Amaranthaceae Amaranthaceae Coccidae->Amaranthaceae Celastraceae Celastraceae Coccidae->Celastraceae Moraceae Moraceae Coccidae->Moraceae Coenagrionidae Coenagrionidae Coenagrionidae->Polygonaceae Crabronidae Crabronidae Crabronidae->Fagaceae Crabronidae->Asteraceae Crabronidae->Asteraceae Crabronidae->Rosaceae Culicidae Culicidae Culicidae->Myrtaceae Culicidae->Fagaceae Culicidae->Asteraceae Culicidae->Betulaceae Culicidae->Boraginaceae Culicidae->Malvaceae Culicidae->Pinaceae Culicidae->Cupressaceae Culicidae->Culicidae Cephalotaxaceae Cephalotaxaceae Culicidae->Cephalotaxaceae Gentianaceae Gentianaceae Culicidae->Gentianaceae Pandanaceae Pandanaceae Culicidae->Pandanaceae Salicaceae Salicaceae Culicidae->Salicaceae Cynipidae Cynipidae Cynipidae->Fagaceae Dactylopiidae Dactylopiidae Cactaceae Cactaceae Dactylopiidae->Cactaceae Diaspididae Diaspididae Diaspididae->Fagaceae Diaspididae->Poaceae Diaspididae->Rosaceae Diaspididae->Sapindaceae Diaspididae->Ericaceae Diaspididae->Rhamnaceae Diaspididae->Pinaceae Diaspididae->Cupressaceae Diaspididae->Salicaceae Araliaceae Araliaceae Diaspididae->Araliaceae Diaspididae->Araliaceae Lauraceae Lauraceae Diaspididae->Lauraceae Arecaceae Arecaceae Diaspididae->Arecaceae Cycadaceae Cycadaceae Diaspididae->Cycadaceae Juglandaceae Juglandaceae Diaspididae->Juglandaceae Orchidaceae Orchidaceae Diaspididae->Orchidaceae Pittosporaceae Pittosporaceae Diaspididae->Pittosporaceae Tamaricaceae Tamaricaceae Diaspididae->Tamaricaceae Theaceae Theaceae Diaspididae->Theaceae Vitaceae Vitaceae Diaspididae->Vitaceae Encyrtidae Encyrtidae Encyrtidae->Myrtaceae Encyrtidae->Fagaceae Encyrtidae->Fagaceae Encyrtidae->Aphididae Encyrtidae->Apiaceae Encyrtidae->Asteraceae Encyrtidae->Asteraceae Encyrtidae->Fabaceae Encyrtidae->Rosaceae Encyrtidae->Rhamnaceae Encyrtidae->Pinaceae Encyrtidae->Pinaceae Encyrtidae->Coccidae Encyrtidae->Coccidae Encyrtidae->Salicaceae Encyrtidae->Lauraceae Encyrtidae->Lauraceae Pseudococcidae Pseudococcidae Encyrtidae->Pseudococcidae Chamaemyiidae Chamaemyiidae Encyrtidae->Chamaemyiidae Coreidae Coreidae Encyrtidae->Coreidae Eriococcidae Eriococcidae Encyrtidae->Eriococcidae Noctuidae Noctuidae Encyrtidae->Noctuidae Notodontidae Notodontidae Encyrtidae->Notodontidae Pseudococcidae->Fagaceae Pseudococcidae->Rosaceae Pseudococcidae->Cupressaceae Hypericaceae Hypericaceae Pseudococcidae->Hypericaceae Phrymaceae Phrymaceae Pseudococcidae->Phrymaceae Eriococcidae->Fagaceae Eriococcidae->Rosaceae Ulmaceae Ulmaceae Eriococcidae->Ulmaceae Noctuidae->Asteraceae Eurytomidae Eurytomidae Anacardiaceae Anacardiaceae Eurytomidae->Anacardiaceae Fulgoridae Fulgoridae Fulgoridae->Cactaceae Fulgoridae->Anacardiaceae Hippoboscidae Hippoboscidae Malaconotidae Malaconotidae Hippoboscidae->Malaconotidae Histiostomatidae Histiostomatidae Carabidae Carabidae Histiostomatidae->Carabidae Ichneumonidae Ichneumonidae Ichneumonidae->Fagaceae Inocelliidae Inocelliidae Inocelliidae->Pinaceae Ixodidae Ixodidae Canidae Canidae Ixodidae->Canidae Lecanodiaspididae Lecanodiaspididae Lecanodiaspididae->Rosaceae Lecanodiaspididae->Anacardiaceae Mydidae Mydidae Mydidae->Polygonaceae Mydidae->Boraginaceae Mydidae->Rhamnaceae Mythicomyiidae Mythicomyiidae Mythicomyiidae->Asteraceae Mythicomyiidae->Asteraceae Mythicomyiidae->Salicaceae Oonopidae Oonopidae Combretaceae Combretaceae Oonopidae->Combretaceae Philopteridae Philopteridae Laridae Laridae Philopteridae->Laridae Megapodiidae Megapodiidae Philopteridae->Megapodiidae Sturnidae Sturnidae Philopteridae->Sturnidae Tinamidae Tinamidae Philopteridae->Tinamidae Pompilidae Pompilidae Pompilidae->Anacardiaceae Pulicidae Pulicidae Pulicidae->Canidae Suidae Suidae Pulicidae->Suidae Raphidiidae Raphidiidae Raphidiidae->Fagaceae Raphidiidae->Fagaceae Raphidiidae->Asteraceae Raphidiidae->Asteraceae Raphidiidae->Betulaceae Raphidiidae->Rosaceae Raphidiidae->Polygonaceae Raphidiidae->Ericaceae Raphidiidae->Rhamnaceae Raphidiidae->Pinaceae Raphidiidae->Pinaceae Namaceae Namaceae Raphidiidae->Namaceae Simuliidae Simuliidae Simuliidae->Salicaceae Tephritidae Tephritidae Tephritidae->Myrtaceae Tephritidae->Fagaceae Tephritidae->Apiaceae Tephritidae->Asteraceae Tephritidae->Poaceae Tephritidae->Rosaceae Tephritidae->Polygonaceae Tephritidae->Apocynaceae Tephritidae->Grossulariaceae Tephritidae->Malvaceae Tephritidae->Pinaceae Tephritidae->Brassicaceae Tephritidae->Amaranthaceae Tephritidae->Salicaceae Tephritidae->Juglandaceae Tephritidae->Pittosporaceae Aizoaceae Aizoaceae Tephritidae->Aizoaceae Eremiaphilidae Eremiaphilidae Tephritidae->Eremiaphilidae Parkinsoniidae Parkinsoniidae Tephritidae->Parkinsoniidae Rubiaceae Rubiaceae Tephritidae->Rubiaceae Timematidae Timematidae Timematidae->Fagaceae Timematidae->Rosaceae Timematidae->Rhamnaceae Torymidae Torymidae Torymidae->Anacardiaceae Triaenonychidae Triaenonychidae Podocarpaceae Podocarpaceae Triaenonychidae->Podocarpaceae

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
Angelica SYNONYM_OF col Bunaea
Angelica HAS_ACCEPTED_NAME col Angelica
Slopes NONE col Slopes
January NONE col January
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 1537
col class 4
col family 96
col genus 449
col infraspecific name 2
col kingdom 1
col order 12
col parvorder 1
col phylum 1
col section 1
col species 1694
col subfamily 2
col subgenus 21
col subspecies 43
col tribe 1
col variety 18
discoverlife NA 3808
discoverlife species 36
gbif NA 1417
gbif class 4
gbif family 102
gbif genus 478
gbif kingdom 1
gbif order 12
gbif phylum 1
gbif species 1782
gbif subspecies 58
gbif variety 23
itis NA 1907
itis class 4
itis family 100
itis genus 381
itis kingdom 1
itis order 15
itis phylum 1
itis species 1380
itis subclass 1
itis subfamily 2
itis subgenus 1
itis suborder 1
itis subspecies 32
itis variety 19
mdd NA 3843
ncbi NA 2315
ncbi clade 2
ncbi class 4
ncbi family 98
ncbi genus 424
ncbi order 15
ncbi phylum 1
ncbi species 961
ncbi subclass 1
ncbi subfamily 4
ncbi subgenus 11
ncbi suborder 1
ncbi subspecies 12
ncbi tribe 1
ncbi varietas 6
pbdb NA 3413
pbdb class 6
pbdb family 85
pbdb genus 212
pbdb infraorder 1
pbdb kingdom 1
pbdb order 15
pbdb phylum 1
pbdb species 105
pbdb subclass 1
pbdb subfamily 2
pbdb superfamily 1
pbdb tribe 2
pbdb unranked clade 3
tpt NA 3685
tpt family 2
tpt genus 23
tpt species 133
wfo NA 3261
wfo family 7
wfo genus 206
wfo phylum 1
wfo species 355
wfo subspecies 12
wfo variety 13
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 SYNONYM_OF 676
col HAS_ACCEPTED_NAME 2350
col NONE 1590
discoverlife NONE 4089
discoverlife HAS_ACCEPTED_NAME 34
discoverlife SYNONYM_OF 7
gbif HAS_ACCEPTED_NAME 2648
gbif SYNONYM_OF 1118
gbif NONE 1467
itis HAS_ACCEPTED_NAME 1996
itis NONE 1970
itis SYNONYM_OF 195
mdd NONE 4097
mdd HAS_ACCEPTED_NAME 18
ncbi SAME_AS 1630
ncbi NONE 2402
ncbi SYNONYM_OF 94
ncbi COMMON_NAME_OF 31
pbdb NONE 3577
pbdb HAS_ACCEPTED_NAME 527
pbdb SYNONYM_OF 32
tpt NONE 3953
tpt HAS_ACCEPTED_NAME 163
tpt SYNONYM_OF 50
wfo HAS_ACCEPTED_NAME 633
wfo NONE 3355
wfo HAS_UNCHECKED_NAME 78
wfo SYNONYM_OF 190
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
2024-04-29T00:45:50Z summary https://github.com/globalbioticinteractions/cas-ent/archive/47d385b73a63aa379cd5e6d3615005ba78b0ffc1.zip
2024-04-29T00:45:50Z summary 17333 interaction(s)
2024-04-29T00:45:50Z summary 0 note(s)
2024-04-29T00:45:50Z summary 4 info(s)

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

: Most frequently occurring review notes, if any.

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.