Versioned Archive and Review of Biotic Interactions and Taxon Names Found within Extended-Bee-Network/bee-interaction-database hash://md5/426a5c3cc3007991759a6b413043cc8f

by Nomer, Elton and Preston, three naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

https://github.com/Extended-Bee-Network/bee-interaction-database/issues

2025-07-09

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 and archiving process for such an openly accessible digital interactions dataset of known origin and discuss its outcome. The dataset under review, named Extended-Bee-Network/bee-interaction-database, has fingerprint hash://md5/426a5c3cc3007991759a6b413043cc8f, is 2.58MiB in size and contains 3,231 interaction with 19 unique types of associations (e.g., visitsFlowersOf) between 499 primary taxa (e.g., Andrena Imitatrix) and 860 associated taxa (e.g., Limnanthes). This report includes detailed summaries of interaction data, a taxonomic review from multiple catalogs, and an archived version of the dataset from which the reviews are derived.

Introduction

Data Review and Archive

Data review and archiving can be a time-consuming process, especially when done manually. This review report aims to help facilitate both activities. It automates the archiving of datasets, including Darwin Core archives, and is a citable backup of a version of the dataset. Additionally, an automatic review of species interaction claims made in the dataset is generated and registered with Global Biotic Interactions (J. H. Poelen, Simons, and Mungall 2014).

This review includes summary statistics about, and observations about, the dataset under review:

Seltmann, K., Van Wagner, J., Behm, R., Brown, Z., Tan, E., & Liu, K. (2020). BID: A project to share biotic interaction and ecological trait data about bees (Hymenoptera: Anthophila). UC Santa Barbara: Cheadle Center for Biodiversity and Ecological Restoration. Retrieved from https://escholarship.org/uc/item/1g21k7bf https://github.com/Extended-Bee-Network/bee-interaction-database/archive/2b6280426c667024918e73622bf4b6c24a906bf1.zip 2025-07-04T22:42:24.629Z hash://md5/426a5c3cc3007991759a6b413043cc8f

For additional metadata related to this dataset, please visit https://github.com/Extended-Bee-Network/bee-interaction-database 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 (Elliott et al. 2025), Elton (Kuhn, Poelen, and Leinweber 2025), Nomer (Salim and Poelen 2025), globinizer (J. Poelen, Seltmann, and Mietchen 2024) combined with third-party tools like grep, mlr, tail and head.

Tools used in this review process
tool name version
preston 0.10.1
elton 0.15.13
nomer 0.5.17
globinizer 0.4.0
mlr 6.0.0
jq 1.6
yq 4.25.3
pandoc 3.1.6.1
duckdb 1.3.1

The review process can be described in the form of the script below 1.

# get versioned copy of the dataset (size approx. 2.58MiB) under review 
elton pull Extended-Bee-Network/bee-interaction-database

# generate review notes
elton review Extended-Bee-Network/bee-interaction-database\
 > review.tsv

# export indexed interaction records
elton interactions Extended-Bee-Network/bee-interaction-database\
 > interactions.tsv

# export names and align them with the Catalogue of Life using Nomer 
elton names Extended-Bee-Network/bee-interaction-database\
 | 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 copy of the full review script at check-data.sh. See also GitHub and Codeberg.

Results

In the following sections, the results of the review are summarized 2. Then, links to the detailed review reports are provided.

Files

The following files are produced in this review:

filename description
biblio.bib list of bibliographic reference of this review
check-dataset.sh data review workflow/process as expressed in a bash script
data.zip a versioned archive of the data under review
HEAD the digital signature of the data under review
index.docx review in MS Word format
index.html review in HTML format
index.md review in Pandoc markdown format
index.pdf review in PDF format
indexed-citations.csv.gz list of distinct reference citations for reviewed species interaction claims in gzipped comma-separated values file format
indexed-citations.html.gz list of distinct reference citations for reviewed species interactions claims in gzipped html file format
indexed-citations.tsv.gz list of distinct reference citations for reviewed species interaction claims in gzipped tab-separated values format
indexed-interactions-col-family-col-family.svg network diagram showing the taxon family to taxon family interaction claims in the dataset under review as interpreted by the Catalogue of Life via Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024)
indexed-interactions-col-kingdom-col-kingdom.svg network diagram showing the taxon kingdom to taxon kingom interaction claims in the dataset under review as interpreted by the Catalogue of Life via Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024)
indexed-interactions.csv.gz species interaction claims indexed from the dataset under review in gzipped comma-separated values format
indexed-interactions.html.gz species interaction claims indexed from the dataset under review in gzipped html format
indexed-interactions.tsv.gz species interaction claims indexed from the dataset under review in gzipped tab-separated values format
indexed-interactions.parquet species interaction claims indexed from the dataset under review in Apache Parquet format
indexed-interactions-sample.csv list of species interaction claims indexed from the dataset under review in gzipped comma-separated values format
indexed-interactions-sample.html first 500 species interaction claims indexed from the dataset under review in html format
indexed-interactions-sample.tsv first 500 species interaction claims indexed from the dataset under review in tab-separated values format
indexed-names.csv.gz taxonomic names indexed from the dataset under review in gzipped comma-separated values format
indexed-names.html.gz taxonomic names found in the dataset under review in gzipped html format
indexed-names.tsv.gz taxonomic names found in the dataset under review in gzipped tab-separated values format
indexed-names.parquet taxonomic names found in the dataset under review in Apache Parquet format
indexed-names-resolved-col.csv.gz taxonomic names found in the dataset under review aligned with the Catalogue of Life as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped comma-separated values format
indexed-names-resolved-col.html.gz taxonomic names found in the dataset under review aligned with the Catalogue of Life as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped html format
indexed-names-resolved-col.tsv.gz taxonomic names found in the dataset under review aligned with the Catalogue of Life as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped tab-separated values format
indexed-names-resolved-col.parquet taxonomic names found in the dataset under review aligned with the Catalogue of Life as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in Apache Parquet format
indexed-names-resolved-discoverlife.csv.gz taxonomic names found in the dataset under review aligned with Discover Life bee species checklist as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped comma-separated values format
indexed-names-resolved-discoverlife.html.gz taxonomic names found in the dataset under review aligned with Discover Life bee species checklist as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped html format
indexed-names-resolved-discoverlife.tsv.gz taxonomic names found in the dataset under review aligned with Discover Life bee species checklist as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped tab-separated values format
indexed-names-resolved-discoverlife.parquet taxonomic names found in the dataset under review aligned with Discover Life bee species checklist as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in Apache Parquet format
indexed-names-resolved-gbif.csv.gz taxonomic names found in the dataset under review aligned with GBIF Backbone Taxonomy as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped comma-separated values format
indexed-names-resolved-gbif.html.gz taxonomic names found in the dataset under review aligned with GBIF Backbone Taxonomy as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped html format
indexed-names-resolved-gbif.tsv.gz taxonomic names found in the dataset under review aligned with GBIF Backbone Taxonomy as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped tab-separated values format
indexed-names-resolved-gbif.parquet taxonomic names found in the dataset under review aligned with GBIF Backbone Taxonomy as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in Apache Parquet format
indexed-names-resolved-itis.csv.gz taxonomic names found in the dataset under review aligned with Integrated Taxonomic Information System (ITIS) as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped comma-separated values format
indexed-names-resolved-itis.html.gz taxonomic names found in the dataset under review aligned with Integrated Taxonomic Information System (ITIS) as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped html format
indexed-names-resolved-itis.tsv.gz taxonomic names found in the dataset under review aligned with Integrated Taxonomic Information System (ITIS) as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped tab-separated values format
indexed-names-resolved-itis.parquet taxonomic names found in the dataset under review aligned with Integrated Taxonomic Information System (ITIS) as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in Apache Parquet format
indexed-names-resolved-mdd.csv.gz taxonomic names found in the dataset under review aligned with the Mammal Diversity Database as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped comma-separated values format
indexed-names-resolved-mdd.html.gz taxonomic names found in the dataset under review aligned with Mammal Diversity Database as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped html format
indexed-names-resolved-mdd.tsv.gz taxonomic names found in the dataset under review aligned with Mammal Diversity Database as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped tab-separated values format
indexed-names-resolved-mdd.parquet taxonomic names found in the dataset under review aligned with Mammal Diversity Database as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in Apache Parquet format
indexed-names-resolved-ncbi.csv.gz taxonomic names found in the dataset under review aligned with the NCBI Taxonomy as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped comma-separated values format
indexed-names-resolved-ncbi.html.gz taxonomic names found in the dataset under review aligned with the NCBI Taxonomy as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped html format
indexed-names-resolved-ncbi.tsv.gz taxonomic names found in the dataset under review aligned with the NCBI Taxonomy as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped tab-separated values format
indexed-names-resolved-ncbi.parquet taxonomic names found in the dataset under review aligned with the NCBI Taxonomy as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in Apache Parquet format
indexed-names-resolved-pbdb.csv.gz taxonomic names found in the dataset under review aligned with the Paleobiology Database as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped comma-separated values format
indexed-names-resolved-pbdb.html.gz taxonomic names found in the dataset under review aligned with Paleobiology Database as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped html format
indexed-names-resolved-pbdb.tsv.gz taxonomic names found in the dataset under review aligned with Paleobiology Database as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped tab-separated values format
indexed-names-resolved-pbdb.parquet taxonomic names found in the dataset under review aligned with Paleobiology Database as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in Apache Parquet format
indexed-names-resolved-tpt.csv.gz taxonomic names found in the dataset under review aligned with the Terrestrial Parasite Tracker (TPT) Taxonomic Resource as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped comma-separated values format
indexed-names-resolved-tpt.html.gz taxonomic names found in the dataset under review aligned with the Terrestrial Parasite Tracker (TPT) Taxonomic Resource as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped html format
indexed-names-resolved-tpt.tsv.gz taxonomic names found in the dataset under review aligned with the Terrestrial Parasite Tracker (TPT) Taxonomic Resource as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped tab-separated values format
indexed-names-resolved-tpt.parquet taxonomic names found in the dataset under review aligned with the Terrestrial Parasite Tracker (TPT) Taxonomic Resource as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in Apache Parquet format
indexed-names-resolved-wfo.csv.gz taxonomic names found in the dataset under review aligned with the World of Flora Online as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped comma-separated values format
indexed-names-resolved-wfo.html.gz taxonomic names found in the dataset under review aligned with the World of Flora Online as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped html format
indexed-names-resolved-wfo.tsv.gz taxonomic names found in the dataset under review aligned with the World of Flora Online as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped tab-separated values format
indexed-names-resolved-wfo.parquet taxonomic names found in the dataset under review aligned with the World of Flora Online as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in Apache Parquet format
indexed-names-resolved-worms.csv.gz taxonomic names found in the dataset under review aligned with the World Register of Marine Species (WoRMS) as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped comma-separated values format
indexed-names-resolved-worms.html.gz taxonomic names found in the dataset under review aligned with the World Register of Marine Species (WoRMS) as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped html format
indexed-names-resolved-worms.tsv.gz taxonomic names found in the dataset under review aligned with the World Register of Marine Species (WoRMS) as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped tab-separated values format
indexed-names-resolved-worms.parquet taxonomic names found in the dataset under review aligned with the World Register of Marine Species (WoRMS) as accessed through the Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in Apache Parquet format
indexed-names-sample.csv first 500 taxonomic names found in the dataset under review in comma-separated values format
indexed-names-sample.html first 500 taxonomic names found in the dataset under review in html format
indexed-names-sample.tsv first 500 taxonomic names found in the dataset under review in tab-separated values format
interaction.svg diagram summarizing the data model used to index species interaction claims
nanopub-sample.trig first 500 species interaction claims as expressed in the nanopub format (Kuhn and Dumontier 2014)
nanopub.trig.gz species interaction claims as expressed in the nanopub format (Kuhn and Dumontier 2014)
process.svg diagram summarizing the data review processing workflow
prov.nq origin of the dataset under review as expressed in rdf/nquads
review.csv.gz review notes associated with the dataset under review in gzipped comma-separated values format
review.html.gz review notes associated with the dataset under review in gzipped html format
review.tsv.gz review notes associated with the dataset under review in gzipped tab-separated values format
review-sample.csv first 500 review notes associated with the dataset under review in comma-separated values format
review-sample.html first 500 review notes associated with the dataset under review in html format
review-sample.tsv first 500 review notes associated with the dataset under review in tab-separated values format
review.svg a review badge generated as part of the dataset review process
zenodo.json metadata of this review expressed in Zenodo record metadata

Archived Dataset

Note that data.zip file in this archive contains the complete, unmodified archived dataset under review.

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 Extended-Bee-Network/bee-interaction-database, has fingerprint hash://md5/426a5c3cc3007991759a6b413043cc8f, is 2.58MiB in size and contains 3,231 interaction with 19 unique types of associations (e.g., visitsFlowersOf) between 499 primary taxa (e.g., Andrena Imitatrix) and 860 associated taxa (e.g., Limnanthes).

An exhaustive list of indexed interaction claims can be found in gzipped csv, tsv and parquet archives. To facilitate discovery, a preview of claims available in the gzipped html page at indexed-interactions.html.gz are shown below.

The exhaustive list was used to create the following data summaries below.

Sample of Indexed Interaction Claims
sourceTaxonName interactionTypeName targetTaxonName referenceCitation
Melissodes pullatella visitsFlowersOf Grindelia integrifolia x Grindelia nana Severns, P. M. & Moldenke, A. R. (2010) Management tradeoffs between focal species and biodiversity: Endemic plant) conservation and solitary bee extinction. Biodivers. Conserv. 19, 3605-3609.
Melissodes pullatella visitsFlowersOf Grindelia integrifolia x Grindelia nana Severns, P. M. & Moldenke, A. R. (2010) Management tradeoffs between focal species and biodiversity: Endemic plant) conservation and solitary bee extinction. Biodivers. Conserv. 19, 3605-3609.
Melissodes pullatella visitsFlowersOf Grindelia integrifolia x Grindelia nana Severns, P. M. & Moldenke, A. R. (2010) Management tradeoffs between focal species and biodiversity: Endemic plant) conservation and solitary bee extinction. Biodivers. Conserv. 19, 3605-3609.
Melissodes pullatella visitsFlowersOf Grindelia integrifolia x Grindelia nana Severns, P. M. & Moldenke, A. R. (2010) Management tradeoffs between focal species and biodiversity: Endemic plant) conservation and solitary bee extinction. Biodivers. Conserv. 19, 3605-3609.
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
visitsFlowersOf 2396
visits 432
pollinates 86
kleptoparasiteOf 82
coOccursWith 73
eats 43
interactsWith 36
hasParasitoid 22
hasHost 19
parasiteOf 14
hasPathogen 9
hasParasite 6
ectoparasiteOf 3
adjacentTo 3
commensalistOf 2
vectorOf 2
preyedUponBy 1
laysEggsOn 1
preysOn 1
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Andrena Imitatrix 208
Andrena cressonii 151
Habropoda depressa 144
Andrena thaspii 124
Apis mellifera 123
Andrena (Hesperandrena) limnanthis 68
Bombus 59
Perdita nuda 58
Panurginus atriceps 54
Andrena milwaukeensis 44
Panurginus occidentalis 43
Andrena mandibularis 41
Andrena alleghaniensis 38
Andrena rubi 36
Andrena topazana 36
Andrena fenningeri 34
Andrena atlantica 34
Andrena birtwelli 34
Andrena (Hesperandrena) 33
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
Limnanthes 138
Cucurbita pepo L. 88
Lasthenia 80
Persea americana 79
Salix 68
Homo sapiens 56
Augochlorella 39
Prunus 33
Ribes 32
Platystemon californicus 30
Salix lasiolepis 30
Ceanothus 29
Arctostaphylos 26
Phacelia 26
Sphecodes 26
Blennosperma 24
Crataegus 24
Rubus 23
Downingia 22
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Andrena (Hesperandrena) limnanthis visitsFlowersOf Limnanthes 67
Panurginus occidentalis visitsFlowersOf Limnanthes 36
Andrena (Hesperandrena) visitsFlowersOf Lasthenia 33
Sphecodes pimpinellae kleptoparasiteOf Augochlorella 32
Andrena subrubicunda visitsFlowersOf Salix lasiolepis 28
Perdita nuda coOccursWith Sphecodes 26
Andrena (Diandrena) submoesta visitsFlowersOf Lasthenia 22
Peponapis Pruinosa visitsFlowersOf Cucurbita pepo L. 16
Perdita nuda coOccursWith Mucor 14
Micralictoides ruficaudus visits Escholtzia californica 11
Micralictoides chaenactidis visits Chaenactis glabriuscula 10
Andrena (Diandrena) blennospermatis visitsFlowersOf Blennosperma 10
Andrena stipator visitsFlowersOf Cryptantha 10
Andrena biareola visitsFlowersOf Platystemon californicus 10
Andrena buccata visitsFlowersOf Platystemon 10
Panurginus atriceps visitsFlowersOf Downingia 9
Panurginus atriceps visitsFlowersOf Downingia bicornuta 9
Panurginus atriceps visitsFlowersOf Downingia concolor 9
Panurginus atriceps visitsFlowersOf Downingia cuspidata 9

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 Animalia->Animalia Animalia->Animalia Animalia->Animalia Animalia->Animalia Animalia->Animalia Animalia->Animalia Animalia->Animalia Animalia->Animalia Fungi Fungi Animalia->Fungi Animalia->Fungi Plantae Plantae Animalia->Plantae Animalia->Plantae Animalia->Plantae Animalia->Plantae Animalia->Plantae Orthornavirae Orthornavirae Animalia->Orthornavirae Plantae->Plantae
interactions Adelidae Adelidae Asteraceae Asteraceae Adelidae->Asteraceae Campanulaceae Campanulaceae Adelidae->Campanulaceae Limnanthaceae Limnanthaceae Adelidae->Limnanthaceae Asteraceae->Asteraceae Asteraceae->Campanulaceae Asteraceae->Limnanthaceae Onagraceae Onagraceae Asteraceae->Onagraceae Boraginaceae Boraginaceae Asteraceae->Boraginaceae Fabaceae Fabaceae Asteraceae->Fabaceae Geraniaceae Geraniaceae Asteraceae->Geraniaceae Hydrangeaceae Hydrangeaceae Asteraceae->Hydrangeaceae Lamiaceae Lamiaceae Asteraceae->Lamiaceae Plantaginaceae Plantaginaceae Asteraceae->Plantaginaceae Rosaceae Rosaceae Asteraceae->Rosaceae Phrymaceae Phrymaceae Asteraceae->Phrymaceae Andrenidae Andrenidae Andrenidae->Asteraceae Andrenidae->Asteraceae Andrenidae->Asteraceae Andrenidae->Campanulaceae Andrenidae->Limnanthaceae Andrenidae->Andrenidae Andrenidae->Andrenidae Anthomyiidae Anthomyiidae Andrenidae->Anthomyiidae Berberidaceae Berberidaceae Andrenidae->Berberidaceae Andrenidae->Berberidaceae Cupressaceae Cupressaceae Andrenidae->Cupressaceae Halictidae Halictidae Andrenidae->Halictidae Meloidae Meloidae Andrenidae->Meloidae Mucoraceae Mucoraceae Andrenidae->Mucoraceae Phoridae Phoridae Andrenidae->Phoridae Andrenidae->Phoridae Conopidae Conopidae Andrenidae->Conopidae Andrenidae->Conopidae Stylopidae Stylopidae Andrenidae->Stylopidae Cucurbitaceae Cucurbitaceae Andrenidae->Cucurbitaceae Andrenidae->Onagraceae Andrenidae->Onagraceae Apidae Apidae Andrenidae->Apidae Orchidaceae Orchidaceae Andrenidae->Orchidaceae Acanthaceae Acanthaceae Andrenidae->Acanthaceae Anacardiaceae Anacardiaceae Andrenidae->Anacardiaceae Apiaceae Apiaceae Andrenidae->Apiaceae Apocynaceae Apocynaceae Andrenidae->Apocynaceae Aquifoliaceae Aquifoliaceae Andrenidae->Aquifoliaceae Asparagaceae Asparagaceae Andrenidae->Asparagaceae Andrenidae->Boraginaceae Brassicaceae Brassicaceae Andrenidae->Brassicaceae Buxaceae Buxaceae Andrenidae->Buxaceae Caprifoliaceae Caprifoliaceae Andrenidae->Caprifoliaceae Caryophyllaceae Caryophyllaceae Andrenidae->Caryophyllaceae Cleomaceae Cleomaceae Andrenidae->Cleomaceae Colchicaceae Colchicaceae Andrenidae->Colchicaceae Commelinaceae Commelinaceae Andrenidae->Commelinaceae Cornaceae Cornaceae Andrenidae->Cornaceae Cyprididae Cyprididae Andrenidae->Cyprididae Ebenaceae Ebenaceae Andrenidae->Ebenaceae Ericaceae Ericaceae Andrenidae->Ericaceae Euphorbiaceae Euphorbiaceae Andrenidae->Euphorbiaceae Andrenidae->Fabaceae Fagaceae Fagaceae Andrenidae->Fagaceae Gentianaceae Gentianaceae Andrenidae->Gentianaceae Andrenidae->Geraniaceae Grossulariaceae Grossulariaceae Andrenidae->Grossulariaceae Andrenidae->Hydrangeaceae Hydrophyllaceae Hydrophyllaceae Andrenidae->Hydrophyllaceae Andrenidae->Lamiaceae Lauraceae Lauraceae Andrenidae->Lauraceae Liliaceae Liliaceae Andrenidae->Liliaceae Linaceae Linaceae Andrenidae->Linaceae Loasaceae Loasaceae Andrenidae->Loasaceae Magnoliaceae Magnoliaceae Andrenidae->Magnoliaceae Malvaceae Malvaceae Andrenidae->Malvaceae Melanthiaceae Melanthiaceae Andrenidae->Melanthiaceae Metacapnodiaceae Metacapnodiaceae Andrenidae->Metacapnodiaceae Montiaceae Montiaceae Andrenidae->Montiaceae Namaceae Namaceae Andrenidae->Namaceae Nesomyidae Nesomyidae Andrenidae->Nesomyidae Nyssaceae Nyssaceae Andrenidae->Nyssaceae Oleaceae Oleaceae Andrenidae->Oleaceae Paeoniaceae Paeoniaceae Andrenidae->Paeoniaceae Papaveraceae Papaveraceae Andrenidae->Papaveraceae Parkinsoniidae Parkinsoniidae Andrenidae->Parkinsoniidae Andrenidae->Plantaginaceae Poaceae Poaceae Andrenidae->Poaceae Polemoniaceae Polemoniaceae Andrenidae->Polemoniaceae Polygonaceae Polygonaceae Andrenidae->Polygonaceae Primulaceae Primulaceae Andrenidae->Primulaceae Ranunculaceae Ranunculaceae Andrenidae->Ranunculaceae Rhamnaceae Rhamnaceae Andrenidae->Rhamnaceae Andrenidae->Rosaceae Andrenidae->Rosaceae Rubiaceae Rubiaceae Andrenidae->Rubiaceae Rutaceae Rutaceae Andrenidae->Rutaceae Salicaceae Salicaceae Andrenidae->Salicaceae Sapindaceae Sapindaceae Andrenidae->Sapindaceae Saturniidae Saturniidae Andrenidae->Saturniidae Saxifragaceae Saxifragaceae Andrenidae->Saxifragaceae Scrophulariaceae Scrophulariaceae Andrenidae->Scrophulariaceae Smilacaceae Smilacaceae Andrenidae->Smilacaceae Tamaricaceae Tamaricaceae Andrenidae->Tamaricaceae Viburnaceae Viburnaceae Andrenidae->Viburnaceae Violaceae Violaceae Andrenidae->Violaceae Pinaceae Pinaceae Andrenidae->Pinaceae Anthomyiidae->Apidae Anthomyiidae->Apidae Halictidae->Asteraceae Halictidae->Asteraceae Halictidae->Asteraceae Halictidae->Limnanthaceae Halictidae->Andrenidae Halictidae->Andrenidae Halictidae->Halictidae Halictidae->Halictidae Halictidae->Halictidae Halictidae->Halictidae Halictidae->Halictidae Halictidae->Onagraceae Halictidae->Apidae Halictidae->Apidae Halictidae->Anacardiaceae Halictidae->Apiaceae Halictidae->Boraginaceae Halictidae->Brassicaceae Halictidae->Fabaceae Halictidae->Fabaceae Halictidae->Hydrophyllaceae Halictidae->Hydrophyllaceae Halictidae->Lamiaceae Halictidae->Nesomyidae Halictidae->Papaveraceae Halictidae->Polemoniaceae Halictidae->Polemoniaceae Halictidae->Rosaceae Amaryllidaceae Amaryllidaceae Halictidae->Amaryllidaceae Halictidae->Amaryllidaceae Myrtaceae Myrtaceae Halictidae->Myrtaceae Tomopteridae Tomopteridae Halictidae->Tomopteridae Halictidae->Tomopteridae Meloidae->Asteraceae Meloidae->Campanulaceae Meloidae->Halictidae Conopidae->Asteraceae Conopidae->Limnanthaceae Stylopidae->Halictidae Apidae->Asteraceae Apidae->Asteraceae Apidae->Campanulaceae Apidae->Limnanthaceae Apidae->Phoridae Apidae->Conopidae Apidae->Cucurbitaceae Apidae->Cucurbitaceae Apidae->Onagraceae Apidae->Onagraceae Apidae->Apidae Apidae->Apidae Apidae->Anacardiaceae Apidae->Anacardiaceae Apidae->Apiaceae Apidae->Apocynaceae Apidae->Boraginaceae Apidae->Boraginaceae Apidae->Brassicaceae Apidae->Brassicaceae Apidae->Caprifoliaceae Apidae->Cleomaceae Apidae->Ericaceae Apidae->Ericaceae Apidae->Fabaceae Apidae->Fabaceae Apidae->Fabaceae Apidae->Fagaceae Apidae->Fagaceae Apidae->Geraniaceae Apidae->Geraniaceae Apidae->Grossulariaceae Apidae->Hydrangeaceae Apidae->Hydrophyllaceae Apidae->Hydrophyllaceae Apidae->Lamiaceae Apidae->Lamiaceae Apidae->Lauraceae Apidae->Lauraceae Apidae->Loasaceae Apidae->Loasaceae Apidae->Magnoliaceae Apidae->Malvaceae Apidae->Malvaceae Apidae->Oleaceae Apidae->Papaveraceae Apidae->Parkinsoniidae Apidae->Plantaginaceae Apidae->Plantaginaceae Apidae->Polemoniaceae Apidae->Polygonaceae Apidae->Ranunculaceae Apidae->Rhamnaceae Apidae->Rhamnaceae Apidae->Rosaceae Apidae->Rosaceae Apidae->Rutaceae Apidae->Salicaceae Apidae->Sapindaceae Apidae->Sapindaceae Apidae->Scrophulariaceae Apidae->Pinaceae Apidae->Amaryllidaceae Apidae->Amaryllidaceae Apidae->Myrtaceae Apidae->Myrtaceae Apidae->Myrtaceae Oxalidaceae Oxalidaceae Apidae->Oxalidaceae Apidae->Oxalidaceae Pittosporaceae Pittosporaceae Apidae->Pittosporaceae Apidae->Pittosporaceae Apidae->Pittosporaceae Pyralidae Pyralidae Apidae->Pyralidae Bovidae Bovidae Apidae->Bovidae Canidae Canidae Apidae->Canidae Hominidae Hominidae Apidae->Hominidae Apidae->Hominidae Varroidae Varroidae Apidae->Varroidae Aphrophoridae Aphrophoridae Apidae->Aphrophoridae Cactaceae Cactaceae Apidae->Cactaceae Apidae->Cactaceae Convolvulaceae Convolvulaceae Apidae->Convolvulaceae Apidae->Convolvulaceae Crambidae Crambidae Apidae->Crambidae Aizoaceae Aizoaceae Apidae->Aizoaceae Alstroemeriaceae Alstroemeriaceae Apidae->Alstroemeriaceae Araliaceae Araliaceae Apidae->Araliaceae Combretaceae Combretaceae Apidae->Combretaceae Hypericaceae Hypericaceae Apidae->Hypericaceae Juglandaceae Juglandaceae Apidae->Juglandaceae Apidae->Juglandaceae Solanaceae Solanaceae Apidae->Solanaceae Apidae->Solanaceae Verbenaceae Verbenaceae Apidae->Verbenaceae Apidae->Verbenaceae Not assigned Not assigned Apidae->Not assigned Theaceae Theaceae Apidae->Theaceae Vitaceae Vitaceae Apidae->Vitaceae Dicistroviridae Dicistroviridae Varroidae->Dicistroviridae Bombyliidae Bombyliidae Bombyliidae->Asteraceae Bombyliidae->Apidae Calliphoridae Calliphoridae Calliphoridae->Asteraceae Calliphoridae->Campanulaceae Calliphoridae->Limnanthaceae Calliphoridae->Lauraceae Calliphoridae->Hominidae Colletidae Colletidae Colletidae->Asteraceae Colletidae->Campanulaceae Colletidae->Andrenidae Colletidae->Anacardiaceae Colletidae->Apiaceae Colletidae->Brassicaceae Colletidae->Fabaceae Colletidae->Lauraceae Colletidae->Rosaceae Drosophilidae Drosophilidae Drosophilidae->Hominidae Drosophilidae->Hominidae Empididae Empididae Empididae->Asteraceae Eumenidae Eumenidae Eumenidae->Lauraceae Formicidae Formicidae Formicidae->Halictidae Megachilidae Megachilidae Megachilidae->Asteraceae Megachilidae->Limnanthaceae Megachilidae->Halictidae Megachilidae->Apidae Megachilidae->Apidae Megachilidae->Anacardiaceae Megachilidae->Apiaceae Megachilidae->Fabaceae Megachilidae->Lamiaceae Megachilidae->Rosaceae Megachilidae->Hominidae Megachilidae->Aizoaceae Megachilidae->Megachilidae Megachilidae->Megachilidae Melittidae Melittidae Melittidae->Onagraceae Noctuidae Noctuidae Noctuidae->Asteraceae Noctuidae->Limnanthaceae Polleniidae Polleniidae Polleniidae->Lauraceae Pompilidae Pompilidae Pompilidae->Lauraceae Scoliidae Scoliidae Scoliidae->Lauraceae Sepsidae Sepsidae Sepsidae->Asteraceae Sepsidae->Limnanthaceae Stratiomyidae Stratiomyidae Stratiomyidae->Lauraceae Syrphidae Syrphidae Syrphidae->Limnanthaceae Syrphidae->Lauraceae Tachinidae Tachinidae Tachinidae->Lauraceae Tiphiidae Tiphiidae Tiphiidae->Lauraceae Vespidae Vespidae Vespidae->Lauraceae

You can download the indexed dataset under review at indexed-interactions.csv.gz. A tab-separated file can be found at indexed-interactions.tsv.gz

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, pbdb, and worms). 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
Acacia HAS_ACCEPTED_NAME col Acacia
Acacia verticillata HAS_ACCEPTED_NAME col Acacia verticillata
Acacia verticillata SYNONYM_OF col Acacia verticillata
Aesculus hippocastanum HAS_ACCEPTED_NAME col Aesculus hippocastanum
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 198
col family 12
col genus 272
col section 1
col species 779
col subfamily 1
col subgenus 2
col subspecies 44
col variety 10
discoverlife NA 981
discoverlife species 316
gbif NA 145
gbif family 15
gbif genus 289
gbif species 794
gbif subspecies 65
gbif variety 23
itis NA 253
itis family 15
itis genus 256
itis species 731
itis subspecies 26
itis variety 16
mdd NA 1297
ncbi NA 402
ncbi family 13
ncbi genus 261
ncbi section 1
ncbi species 603
ncbi subgenus 17
ncbi subspecies 7
ncbi varietas 3
pbdb NA 1131
pbdb family 14
pbdb genus 121
pbdb kingdom 1
pbdb species 30
pbdb tribe 1
tpt NA 1293
tpt genus 2
tpt species 2
wfo NA 612
wfo family 11
wfo genus 209
wfo section 2
wfo species 445
wfo subsection 1
wfo subspecies 20
wfo variety 10
worms NA 1061
worms family 8
worms genus 134
worms species 93
worms subspecies 2
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 1051
col SYNONYM_OF 478
col NONE 204
discoverlife NONE 1121
discoverlife SYNONYM_OF 152
discoverlife HAS_ACCEPTED_NAME 258
discoverlife HOMONYM_OF 12
gbif HAS_ACCEPTED_NAME 1379
gbif SYNONYM_OF 686
gbif NONE 145
itis HAS_ACCEPTED_NAME 1028
itis SYNONYM_OF 211
itis NONE 255
mdd NONE 1463
mdd HAS_ACCEPTED_NAME 2
ncbi SAME_AS 994
ncbi SYNONYM_OF 102
ncbi NONE 418
pbdb HAS_ACCEPTED_NAME 218
pbdb NONE 1237
pbdb SYNONYM_OF 13
tpt NONE 1461
tpt HAS_ACCEPTED_NAME 4
wfo HAS_ACCEPTED_NAME 641
wfo SYNONYM_OF 213
wfo NONE 684
wfo HAS_UNCHECKED_NAME 132
worms NONE 1177
worms HAS_ACCEPTED_NAME 291
worms SYNONYM_OF 50
List of Available Name Alignment Reports
catalog name alignment results
col associated names alignments report in gzipped html, csv, and tsv)
ncbi associated names alignments report in gzipped html, csv, and tsv)
discoverlife associated names alignments report in gzipped html, csv, and tsv)
gbif associated names alignments report in gzipped html, csv, and tsv)
itis associated names alignments report in gzipped html, csv, and tsv)
wfo associated names alignments report in gzipped html, csv, and tsv)
mdd associated names alignments report in gzipped html, csv, and tsv)
tpt associated names alignments report in gzipped html, csv, and tsv)
pbdb associated names alignments report in gzipped html, csv, and tsv)
worms associated names alignments report in gzipped html, csv, and 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
2025-07-09T17:35:58Z note target taxon name missing
2025-07-09T17:35:58Z note target taxon name missing
2025-07-09T17:35:58Z summary https://github.com/Extended-Bee-Network/bee-interaction-database/archive/2b6280426c667024918e73622bf4b6c24a906bf1.zip
2025-07-09T17:35:58Z summary 3231 interaction(s)

In addition, 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 2

For additional information on review notes, please have a look at the first 500 Review Notes in html format or the download full gzipped 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 and archive provides a means of creating citable versions of datasets that change frequently. This may be useful for dataset managers, including natural history collection data managers, as a backup archive of a shared Darwin Core archive. It also serves as a means of creating a trackable citation for the dataset in an automated way, while also including some information about the contents of the dataset.

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. Also, thanks to https://github.com/zygoballus for helping improve the layout of the review tables.

Author contributions

Nomer was responsible for name alignments. Elton carried out dataset extraction, and generated the review notes. Preston tracked, versioned, and packaged, the dataset under review.

References

Elliott, Michael, Jorrit Poelen, Icaro Alzuru, Emilio Berti, and partha04patel. 2025. “Bio-Guoda/Preston: 0.10.5.” Zenodo. https://doi.org/10.5281/zenodo.14662206.
ICZN. 1999. “International Code of Zoological Nomenclature.” The International Trust for Zoological Nomenclature, London, UK. https://www.iczn.org/the-code/the-code-online/.
Kuhn, Tobias, and Michel Dumontier. 2014. “Trusty URIs: Verifiable, Immutable, and Permanent Digital Artifacts for Linked Data.” In The Semantic Web: Trends and Challenges, edited by Valentina Presutti, Claudia d’Amato, Fabien Gandon, Mathieu d’Aquin, Steffen Staab, and Anna Tordai, 395–410. Cham: Springer International Publishing.
Kuhn, Tobias, Jorrit Poelen, and Katrin Leinweber. 2025. “Globalbioticinteractions/Elton: 0.15.1.” Zenodo. https://doi.org/10.5281/zenodo.14927734.
Poelen, Jorrit H. (ed.). 2024. “Nomer Corpus of Taxonomic Resources Hash://Sha256/ B60c0d25a16ae77b24305782017b1a270b79b5d1746f832650 F2027ba536e276 Hash://Md5/17f1363a277ee0e4ecaf1b91c665e47e.” Zenodo. https://doi.org/10.5281/zenodo.12695629.
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.
Poelen, Jorrit, Katja Seltmann, and Daniel Mietchen. 2024. “Globalbioticinteractions/Globinizer: 0.4.0.” Zenodo. https://doi.org/10.5281/zenodo.10647565.
Salim, José Augusto, and Jorrit Poelen. 2025. “Globalbioticinteractions/Nomer: 0.5.15.” Zenodo. https://doi.org/10.5281/zenodo.14893840.
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.