A Review of Biotic Interactions and Taxon Names Found in globalbioticinteractions/mpm

by Nomer and Elton, two naive review bots

[email protected]





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/mpm, is 19.5MiB in size and contains 665 interactions with 3 unique types of associations (e.g., interactsWith) between 230 primary taxa (e.g., Anisota senatoria) and 306 associated taxa (e.g., At flowers.). The report includes detailed summaries of interactions data as well as a taxonomic review from multiple catalogs.


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:

MPM Lepidoptera of North America Network (LepNet) - Version 1.3 https://ipt.mpm.edu/archive.do?r=lepnet 2024-04-13T02:45:09.015Z 5a9f08e21c44bf4450b3bc9715ea0cd55f5951be9d923765f2063460d0ecc5ef MPM Terrestrial Parasite Tracker (TPT) - Version 1.11 https://ipt.mpm.edu/archive.do?r=tpt 2024-04-13T02:45:09.015Z 5a9f08e21c44bf4450b3bc9715ea0cd55f5951be9d923765f2063460d0ecc5ef

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/mpm and inspect associated metadata files including, but not limited to, README.md, eml.xml, and/or globi.json.


The review is performed through programmatic scripts that leverage tools like Preston, Elton, Nomer combined with third-party tools like grep, mlr, tail and head.

Tools used in this review process
tool name version
elton 0.13.2
nomer 0.5.7
mlr 6.0.0

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

# get versioned copy of the dataset (size approx. 19.5MiB) under review 
elton pull globalbioticinteractions/mpm

# generate review notes
elton review globalbioticinteractions/mpm\
 > review.tsv

# export indexed interaction records
elton interactions globalbioticinteractions/mpm\
 > interactions.tsv

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/mpm\
 | 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.


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/mpm, is 19.5MiB in size and contains 665 interactions with 3 unique types of associations (e.g., interactsWith) between 230 primary taxa (e.g., Anisota senatoria) and 306 associated taxa (e.g., At flowers.).

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
Wyeomyia smithii interactsWith From Pitcher Plant cup. dd99e7ac-88e8-403e-9440-97e291eb42df
Wyeomyia smithii interactsWith In Pitcher Plant leaves. 06dfe2c8-ce4b-4ede-93cf-299fa891c291
Wyeomyia smithii interactsWith In Pitcher Plant leaves. 1c9995da-b9f2-420e-a465-31130cc1c927
Culicidae interactsWith Found on Silphium terebinthinaceum. c21d269d-ef2b-4711-b412-b0c52228b566
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
interactsWith 639
adjacentTo 18
eats 8
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Anisota senatoria 28
Amphion floridensis 21
Atalopedes campestris 19
Yponomeuta padella 17
Achlyodes pallida 15
Prochoerodes lineola 15
Papilio polyxenes asterius 14
Hemaris diffinis 12
Papilio brevicauda brevicauda 9
Hyles gallii 9
Hyles lineata 9
Papilio glaucus 8
Amorpha juglandis 8
Papilio cresphontes 8
Nastra julia 8
Lymantria dispar 8
Papilio brevicauda bretonensis 7
Lintneria eremitus 7
Actias luna 7
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
At flowers. 48
On oak. 29
Reared on Ligusticum scoticum. 18
Locality label reads at porch light or flowers. 18
On flowers. 12
On Euonymus tree. 10
On tree. 9
On scrub oak. 9
Flowers. 8
Found on silver linden trees. 8
Woodbine 8
Epilobium. 8
Bred from red pepper. 7
On tree trunk. 7
At lilacs. 6
On garden flowers. 6
Ex pupa on wild cherry twigs. 6
Visiting Cnidoscolus multilobus. 6
On juniper. 6
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Anisota senatoria interactsWith On oak. 23
Prochoerodes lineola interactsWith Locality label reads at porch light or flowers. 13
Yponomeuta padella interactsWith On Euonymus tree. 10
Papilio brevicauda brevicauda interactsWith Reared on Ligusticum scoticum. 9
Atalopedes campestris interactsWith At flowers. 8
Nastra julia interactsWith At flowers. 8
Lymantria dispar interactsWith Found on silver linden trees. 8
Amphion floridensis interactsWith Woodbine 8
Amphion floridensis interactsWith Epilobium. 8
Idaea bonifata interactsWith Bred from red pepper. 7
Gluphisia severa interactsWith On tree trunk. 7
Nastra lherminier interactsWith At flowers. 7
Papilio brevicauda bretonensis interactsWith Reared on Ligusticum scoticum. 6
Archips cerasivorana interactsWith Ex pupa on wild cherry twigs. 6
Thyridopteryx ephemeraeformis interactsWith On juniper. 6
Papilio polyxenes asterius interactsWith On carrot. 5
Hyles gallii interactsWith Bred from fireweed. 5
Achlyodes pallida interactsWith On citrus. 5
Yponomeuta padella interactsWith On Euonymus sp. 5

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.


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
th instar fed prickly ash NONE col th instar fed prickly ash
Abaeis nicippe HAS_ACCEPTED_NAME col Abaeis nicippe
Bromeliad NONE col Bromeliad
Achlyodes busirus heros HAS_ACCEPTED_NAME col Achlyodes busirus heros
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 251
col family 1
col genus 28
col kingdom 1
col species 206
col subspecies 3
col variety 1
discoverlife NA 491
gbif NA 221
gbif family 1
gbif genus 29
gbif kingdom 1
gbif species 220
gbif subspecies 19
gbif variety 1
itis NA 256
itis family 1
itis genus 27
itis kingdom 1
itis species 187
itis subspecies 16
itis tribe 1
itis variety 1
mdd NA 490
ncbi NA 233
ncbi family 1
ncbi genus 27
ncbi species 220
ncbi subspecies 9
ncbi varietas 1
pbdb NA 474
pbdb family 1
pbdb genus 12
pbdb kingdom 1
pbdb species 2
tpt NA 490
wfo NA 447
wfo genus 21
wfo phylum 1
wfo species 21
Name relationship types per catalog. Name relationship type “NONE” means that a name was not recognized by the associated catalog. “SAME_AS” indicates either a “HAS_ACCEPTED_NAME” or “SYNONYM_OF” name relationship type. We recognize that “SYNONYM_OF” encompasses many types of nomenclatural synonymies (ICZN 1999) (e.g., junior synonym, senior synonyms).
resolvedCatalogName relationName count
col NONE 282
discoverlife NONE 536
gbif NONE 252
gbif SYNONYM_OF 52
itis NONE 287
mdd NONE 535
ncbi NONE 269
ncbi SAME_AS 255
pbdb NONE 509
tpt NONE 535
wfo NONE 482
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
2024-04-17T01:24:20Z summary https://github.com/globalbioticinteractions/mpm/archive/9f44e99c49ec5aba3f8592cfced07c38d3223dcd.zip
2024-04-17T01:24:20Z summary 665 interaction(s)
2024-04-17T01:24:20Z summary 0 note(s)
2024-04-17T01:24:20Z summary 10 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 5 for badge examples.


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.


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.


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.