Versioned Archive and Review of Biotic Interactions and Taxon Names Found within globalbioticinteractions/pollinators-of-apocynaceae-database hash://md5/ba7bfe57d28af24d7dad244f9882dbc5

by Nomer, Elton and Preston, three naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

https://github.com/globalbioticinteractions/pollinators-of-apocynaceae-database/issues

2025-07-08

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 globalbioticinteractions/pollinators-of-apocynaceae-database, has fingerprint hash://md5/ba7bfe57d28af24d7dad244f9882dbc5, is 1.20MiB in size and contains 5,060 interaction with 3 unique types of associations (e.g., pollinatedBy) between 679 primary taxa (e.g., Asclepias syriaca) and 2,330 associated taxon (e.g., unidentified). This report includes detailed summaries of interaction data, a taxonomic review from multiple catalogs, and an archived version of the dataset from which the reviews are derived.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:

Ollerton J, Liede-Schumann S, Endress ME, Meve U, Rech AR, Shuttleworth A, Keller HA, Fishbein M, Alvarado-Cárdenas LO, Amorim FW, Bernhardt P, Celep F, Chirango Y, Chiriboga-Arroyo F, Civeyrel L, Cocucci A, Cranmer L, da Silva-Batista IC, de Jager L, Deprá MS, Domingos-Melo A, Dvorsky C, Agostini K, Freitas L, Gaglianone MC, Galetto L, Gilbert M, González-Ramírez I, Gorostiague P, Goyder D, Hachuy-Filho L, Heiduk A, Howard A, Ionta G, Islas-Hernández SC, Johnson SD, Joubert L, Kaiser-Bunbury CN, Kephart S, Kidyoo A, Koptur S, Koschnitzke C, Lamborn E, Livshultz T, Machado IC, Marino S, Mema L, Mochizuki K, Morellato LPC, Mrisha CK, Muiruri EW, Nakahama N, Nascimento VT, Nuttman C, Oliveira PE, Peter CI, Punekar S, Rafferty N, Rapini A, Ren ZX, Rodríguez-Flores CI, Rosero L, Sakai S, Sazima M, Steenhuisen SL, Tan CW, Torres C, Trøjelsgaard K, Ushimaru A, Vieira MF, Wiemer AP, Yamashiro T, Nadia T, Queiroz J, Quirino Z. The diversity and evolution of pollination systems in large plant clades: Apocynaceae as a case study. Ann Bot. 2019 Jan 23;123(2):311-325. doi: 10.1093/aob/mcy127. PMID: 30099492; PMCID: PMC6344220. https://github.com/globalbioticinteractions/pollinators-of-apocynaceae-database/archive/c940b96cd5ecd4d26005eb6b65a1ea6b23f898db.zip 2025-07-05T03:48:51.573Z hash://md5/ba7bfe57d28af24d7dad244f9882dbc5

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/pollinators-of-apocynaceae-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. 1.20MiB) under review 
elton pull globalbioticinteractions/pollinators-of-apocynaceae-database

# generate review notes
elton review globalbioticinteractions/pollinators-of-apocynaceae-database\
 > review.tsv

# export indexed interaction records
elton interactions globalbioticinteractions/pollinators-of-apocynaceae-database\
 > interactions.tsv

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/pollinators-of-apocynaceae-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 globalbioticinteractions/pollinators-of-apocynaceae-database, has fingerprint hash://md5/ba7bfe57d28af24d7dad244f9882dbc5, is 1.20MiB in size and contains 5,060 interaction with 3 unique types of associations (e.g., pollinatedBy) between 679 primary taxa (e.g., Asclepias syriaca) and 2,330 associated taxon (e.g., unidentified).

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
Alstonia actinophylla flowersVisitedBy Pteropus scapulatus Mickelburgh et al.1992
Alstonia boonei pollinatedBy Apis mellifera  Albers & Van der Maesen 1994
Alstonia boonei pollinatedBy Hypolimnus missipus  Albers & Van der Maesen 1994
Alstonia boonei pollinatedBy Eumenidae Albers & Van der Maesen 1994
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
pollinatedBy 4794
flowersVisitedBy 248
interactsWith 18
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Asclepias syriaca 222
Asclepias incarnata 182
Asclepias verticillata 161
Asclepias tuberosa 110
Catharanthus roseus 105
Asclepias curassavica 95
Oxypetalum balansae 88
Prestonia coalita 83
Ditassa burchellii 72
Vincetoxicum pycnostelma 68
Allamanda blanchetii 66
Gomphocarpus physocarpus 57
Araujia brachystephana 57
Gonolobus parviflorus 56
Orthosia congesta 56
Calotropis procera 53
Oxypetalum banksii ssp. corymbiferum 51
Hancornia speciosa 49
Periploca laevigata 47
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
unidentified 410
unknown 189
Unidentified 140
Apis mellifera 100
Bees 74
Forcipomyia sp. 50
Zoophily 40
Unidentified 1 27
Unidentified 2 27
Sphingidae 25
Papilio demodocus demodocus 25
Musca domestica 22
Atrichelaphinis tigrina 20
Calliphora sp. 19
Entomophily 18
Megaselia sp. 18
Birds 17
Desmometopa inaurata 17
Polistes sp. 16
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Asclepias syriaca pollinatedBy unknown 34
Catharanthus roseus pollinatedBy Papilio demodocus demodocus 22
Ceropegia gilgiana pollinatedBy unidentified 19
Orbea verrucosa pollinatedBy unidentified 15
Periploca laevigata pollinatedBy unknown 14
Ceropegia ampliata pollinatedBy unidentified 13
Aspidosperma parvifolium pollinatedBy ? 12
Ceropegia aristolochioides ssp. deflersiana pollinatedBy unidentified 12
Chlorocyathus (Kappia) lobulata pollinatedBy unidentified 11
Oxypetalum balansae pollinatedBy Unidentified 11
Ditassa banksii pollinatedBy unidentified 10
Oxypetalum banksii ssp. corymbiferum pollinatedBy unidentified 10
Ceropegia racemosa pollinatedBy Megaselia sp. 10
Hancornia speciosa pollinatedBy Sphingidae 9
Orthosia congesta pollinatedBy Unidentified 9
Aspidosperma quebracho-blanco pollinatedBy unidentified 8
Allamanda blanchetii pollinatedBy Bees 8
Tabernaemontana catharinensis pollinatedBy Zoophily 8
Ceropegia achtenii ssp. adolphii pollinatedBy Forcipomyia sp. 8

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 Plantae Plantae Animalia Animalia Plantae->Animalia Plantae->Animalia Plantae->Animalia
interactions Apocynaceae Apocynaceae Alydidae Alydidae Apocynaceae->Alydidae Anthomyiidae Anthomyiidae Apocynaceae->Anthomyiidae Apocynaceae->Anthomyiidae Apidae Apidae Apocynaceae->Apidae Apocynaceae->Apidae Chrysomelidae Chrysomelidae Apocynaceae->Chrysomelidae Apocynaceae->Chrysomelidae Coreidae Coreidae Apocynaceae->Coreidae Eumenidae Eumenidae Apocynaceae->Eumenidae Apocynaceae->Eumenidae Apocynaceae->Eumenidae Formicidae Formicidae Apocynaceae->Formicidae Apocynaceae->Formicidae Lygaeidae Lygaeidae Apocynaceae->Lygaeidae Apocynaceae->Lygaeidae Muscidae Muscidae Apocynaceae->Muscidae Apocynaceae->Muscidae Nymphalidae Nymphalidae Apocynaceae->Nymphalidae Apocynaceae->Nymphalidae Pieridae Pieridae Apocynaceae->Pieridae Apocynaceae->Pieridae Pteropodidae Pteropodidae Apocynaceae->Pteropodidae Reduviidae Reduviidae Apocynaceae->Reduviidae Sarcophagidae Sarcophagidae Apocynaceae->Sarcophagidae Apocynaceae->Sarcophagidae Trochilidae Trochilidae Apocynaceae->Trochilidae Apocynaceae->Trochilidae Vespidae Vespidae Apocynaceae->Vespidae Apocynaceae->Vespidae Halictidae Halictidae Apocynaceae->Halictidae Apocynaceae->Halictidae Hesperiidae Hesperiidae Apocynaceae->Hesperiidae Apocynaceae->Hesperiidae Megachilidae Megachilidae Apocynaceae->Megachilidae Apocynaceae->Megachilidae Sphecidae Sphecidae Apocynaceae->Sphecidae Apocynaceae->Sphecidae Acroceridae Acroceridae Apocynaceae->Acroceridae Adelidae Adelidae Apocynaceae->Adelidae Andrenidae Andrenidae Apocynaceae->Andrenidae Bibionidae Bibionidae Apocynaceae->Bibionidae Bombyliidae Bombyliidae Apocynaceae->Bombyliidae Calliphoridae Calliphoridae Apocynaceae->Calliphoridae Carnidae Carnidae Apocynaceae->Carnidae Cecidomyiidae Cecidomyiidae Apocynaceae->Cecidomyiidae Cerambycidae Cerambycidae Apocynaceae->Cerambycidae Ceratopogonidae Ceratopogonidae Apocynaceae->Ceratopogonidae Chalcididae Chalcididae Apocynaceae->Chalcididae Chloropidae Chloropidae Apocynaceae->Chloropidae Chrysopidae Chrysopidae Apocynaceae->Chrysopidae Colletidae Colletidae Apocynaceae->Colletidae Conopidae Conopidae Apocynaceae->Conopidae Crabronidae Crabronidae Apocynaceae->Crabronidae Crambidae Crambidae Apocynaceae->Crambidae Culicidae Culicidae Apocynaceae->Culicidae Diopsidae Diopsidae Apocynaceae->Diopsidae Drosophilidae Drosophilidae Apocynaceae->Drosophilidae Empididae Empididae Apocynaceae->Empididae Erebidae Erebidae Apocynaceae->Erebidae Fanniidae Fanniidae Apocynaceae->Fanniidae Geometridae Geometridae Apocynaceae->Geometridae Heleomyzidae Heleomyzidae Apocynaceae->Heleomyzidae Hybotidae Hybotidae Apocynaceae->Hybotidae Ichneumonidae Ichneumonidae Apocynaceae->Ichneumonidae Lampyridae Lampyridae Apocynaceae->Lampyridae Leucospidae Leucospidae Apocynaceae->Leucospidae Limoniidae Limoniidae Apocynaceae->Limoniidae Lycaenidae Lycaenidae Apocynaceae->Lycaenidae Lycidae Lycidae Apocynaceae->Lycidae Milichiidae Milichiidae Apocynaceae->Milichiidae Mydidae Mydidae Apocynaceae->Mydidae Nectariniidae Nectariniidae Apocynaceae->Nectariniidae Nitidulidae Nitidulidae Apocynaceae->Nitidulidae Noctuidae Noctuidae Apocynaceae->Noctuidae Papilionidae Papilionidae Apocynaceae->Papilionidae Platystomatidae Platystomatidae Apocynaceae->Platystomatidae Polleniidae Polleniidae Apocynaceae->Polleniidae Pompilidae Pompilidae Apocynaceae->Pompilidae Pyralidae Pyralidae Apocynaceae->Pyralidae Riodinidae Riodinidae Apocynaceae->Riodinidae Scarabaeidae Scarabaeidae Apocynaceae->Scarabaeidae Scatopsidae Scatopsidae Apocynaceae->Scatopsidae Sepsidae Sepsidae Apocynaceae->Sepsidae Sphingidae Sphingidae Apocynaceae->Sphingidae Staphylinidae Staphylinidae Apocynaceae->Staphylinidae Syrphidae Syrphidae Apocynaceae->Syrphidae Tachinidae Tachinidae Apocynaceae->Tachinidae Tephritidae Tephritidae Apocynaceae->Tephritidae Thripidae Thripidae Apocynaceae->Thripidae Tortricidae Tortricidae Apocynaceae->Tortricidae Ulidiidae Ulidiidae Apocynaceae->Ulidiidae Zygaenidae Zygaenidae Apocynaceae->Zygaenidae

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
Abrostola triplasia HAS_ACCEPTED_NAME col Abrostola triplasia
Abrostola triplasia SYNONYM_OF col Abrostola triplasia
Cantharid beetle NONE col Cantharid beetle
Acanthiophilus helianthi HAS_ACCEPTED_NAME col Acanthiophilus helianthi
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 788
col class 2
col family 37
col genus 292
col order 5
col phylum 1
col species 1508
col subfamily 8
col subgenus 6
col suborder 1
col subspecies 50
col tribe 6
col variety 3
discoverlife NA 2451
discoverlife species 244
gbif NA 555
gbif class 2
gbif family 39
gbif form 1
gbif genus 338
gbif order 5
gbif phylum 1
gbif species 1646
gbif subspecies 108
gbif variety 18
itis NA 1642
itis class 2
itis family 36
itis genus 232
itis order 6
itis phylum 1
itis species 714
itis subfamily 9
itis subgenus 1
itis suborder 3
itis subspecies 43
itis superorder 1
itis tribe 5
mdd NA 2694
ncbi NA 1089
ncbi class 2
ncbi cohort 1
ncbi family 36
ncbi genus 271
ncbi order 5
ncbi phylum 1
ncbi species 1211
ncbi subfamily 14
ncbi subgenus 25
ncbi suborder 2
ncbi subspecies 48
ncbi tribe 4
ncbi varietas 2
pbdb NA 2510
pbdb class 2
pbdb family 38
pbdb genus 111
pbdb infraclass 1
pbdb order 5
pbdb phylum 1
pbdb species 10
pbdb subfamily 11
pbdb suborder 3
pbdb tribe 5
tpt NA 2659
tpt species 35
wfo NA 2087
wfo family 1
wfo genus 41
wfo species 556
wfo subspecies 8
wfo variety 4
worms NA 2506
worms class 1
worms family 28
worms genus 77
worms order 5
worms phylum 1
worms species 71
worms subclass 1
worms subfamily 2
worms suborder 1
worms subspecies 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 1898
col SYNONYM_OF 512
col NONE 860
discoverlife NONE 2734
discoverlife HAS_ACCEPTED_NAME 218
discoverlife SYNONYM_OF 91
discoverlife HOMONYM_OF 17
gbif HAS_ACCEPTED_NAME 2246
gbif NONE 615
gbif SYNONYM_OF 724
itis NONE 1753
itis HAS_ACCEPTED_NAME 1131
itis SYNONYM_OF 131
mdd NONE 2976
mdd HAS_ACCEPTED_NAME 2
ncbi SAME_AS 1753
ncbi NONE 1193
ncbi SYNONYM_OF 121
pbdb NONE 2687
pbdb HAS_ACCEPTED_NAME 286
pbdb SYNONYM_OF 21
tpt NONE 2934
tpt HAS_ACCEPTED_NAME 40
tpt SYNONYM_OF 4
wfo NONE 2348
wfo SYNONYM_OF 108
wfo HAS_ACCEPTED_NAME 560
wfo HAS_UNCHECKED_NAME 19
worms NONE 2706
worms HAS_ACCEPTED_NAME 260
worms SYNONYM_OF 22
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
2025-07-08T06:28:03Z summary https://github.com/globalbioticinteractions/pollinators-of-apocynaceae-database/archive/c940b96cd5ecd4d26005eb6b65a1ea6b23f898db.zip
2025-07-08T06:28:03Z summary 5060 interaction(s)
2025-07-08T06:28:03Z summary 0 note(s)
2025-07-08T06:28:03Z summary 5061 info(s)

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

: Most frequently occurring review notes, if any.

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.