A Review of Biotic Interactions and Taxon Names Found in globalbioticinteractions/min-umsp

by Nomer and Elton, two naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

https://github.com/globalbioticinteractions/min-umsp/issues

2024-11-18

Abstract

Life on Earth is sustained by complex interactions between organisms and their environment. These biotic interactions can be captured in datasets and published digitally. We present a review process of such an openly accessible digital interactions dataset of known origin, and discuss its outcome. The dataset under review, named globalbioticinteractions/min-umsp, is 1.65MiB in size and contains 7,593 interaction with 3 unique types of associations (e.g., interactsWith) between 230 primary taxa (e.g., Orchopeas leucopus) and 420 associated taxa (e.g., Peromyscus maniculatus). The report includes detailed summaries of interactions data as well as a taxonomic review from multiple catalogs.

Introduction

Data Review

Data review can be a time consuming process, especially when done manually. This review report aims to help facilitate data review of species interaction claims made in datasets registered with Global Biotic Interactions (Poelen, Simons, and Mungall 2014). The review includes summary statistics of, and observations about, the dataset under review:

UMSP / University of Minnesota / University of Minnesota Insect Collection https://github.com/globalbioticinteractions/min-umsp/archive/3f1b9d32f947dcb80b9aaab50523e097f0e8776e.zip 2024-11-16T09:52:14.084Z e4d255bdef6b41b0bde73ab4b0b3e774f42a0e1ad53fa1d6657596d3e0c6aa03

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

Methods

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

Tools used in this review process
tool name version
elton 0.13.9
nomer 0.5.13
mlr 6.0.0
pandoc 3.1.6.1

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

# get versioned copy of the dataset (size approx. 1.65MiB) under review 
elton pull globalbioticinteractions/min-umsp

# generate review notes
elton review globalbioticinteractions/min-umsp\
 > review.tsv

# export indexed interaction records
elton interactions globalbioticinteractions/min-umsp\
 > interactions.tsv

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/min-umsp\
 | nomer append col\
 > name-alignment.tsv

or visually, in a process diagram.

review origin dataset origin elton Elton (a naive review bot) elton->origin pull (1) interactions indexed interactions elton->interactions generates (2) alignment name alignments nomer Nomer (a naive review bot) nomer->interactions extract names (3) nomer->alignment generates (5) catalog name catalog nomer->catalog uses (4)

You can find a recent copy of the full review script at check-data.sh.

Results

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

Biotic Interactions

model primaryTaxon Primary Taxon associatedTaxon Associated Taxon primaryOrganism Primary Organism primaryOrganism->primaryTaxon classifiedAs associatedOrganism Associated Organism primaryOrganism->associatedOrganism interactsWith associatedOrganism->associatedTaxon classifiedAs

In this review, biotic interactions (or biotic associations) are modeled as a primary (aka subject, source) organism interacting with an associate (aka object, target) organism. The dataset under review classified the primary/associate organisms with specific taxa. The primary and associate organisms The kind of interaction is documented as an interaction type.

The dataset under review, named globalbioticinteractions/min-umsp, is 1.65MiB in size and contains 7,593 interaction with 3 unique types of associations (e.g., interactsWith) between 230 primary taxa (e.g., Orchopeas leucopus) and 420 associated taxa (e.g., Peromyscus maniculatus).

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
Anthrenus lepidus interactsWith Adenostoma UMSP / University of Minnesota / University of Minnesota Insect Collection. Accessed at https://github.com/globalbioticinteractions/min-umsp/archive/3f1b9d32f947dcb80b9aaab50523e097f0e8776e.zip on 18 Nov 2024.
Anthrenus lepidus interactsWith Adenostoma UMSP / University of Minnesota / University of Minnesota Insect Collection. Accessed at https://github.com/globalbioticinteractions/min-umsp/archive/3f1b9d32f947dcb80b9aaab50523e097f0e8776e.zip on 18 Nov 2024.
Dermestes caninus interactsWith Apocynum cannabinum var. pubescens UMSP / University of Minnesota / University of Minnesota Insect Collection. Accessed at https://github.com/globalbioticinteractions/min-umsp/archive/3f1b9d32f947dcb80b9aaab50523e097f0e8776e.zip on 18 Nov 2024.
Dermestes caninus adjacentTo dead mouse UMSP / University of Minnesota / University of Minnesota Insect Collection. Accessed at https://github.com/globalbioticinteractions/min-umsp/archive/3f1b9d32f947dcb80b9aaab50523e097f0e8776e.zip on 18 Nov 2024.
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
interactsWith 7534
hasHost 76
adjacentTo 71
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Orchopeas leucopus 1063
Ctenophthalmus pseudagyrtes 494
Megabothris quirini 465
Orchopeas caedens 343
Monopsyllus vison 275
Cediopsylla simplex 273
Aetheca wagneri 229
Oropsylla bruneri 223
Foxella ignota ignota 218
Orchopeas howardi 214
Epitedia wenmanni 204
Buprestidae 188
Ceratophyllus styx riparius 187
Myodopsylla insignis 143
Ctenocephalides felis 126
Trogoderma versicolor 117
Euchoplopsyllus glacialis affinis 112
Xenopsylla cheopis 112
Peromyscopsylla hesperomys 104
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
Peromyscus maniculatus 1151
Clethrionomys gapperi 868
Tamiasciurus hudsonicus 564
Peromyscus leucopus 286
Sylvilagus floridanus 149
Blarina brevicauda 149
Geomys bursarius 146
Microtus pennsylvanicus 136
Myotis lucifugus 135
Bank Swallow 129
Peromyscus maniculatus gracilis 110
Rattus norvegicus 107
Phalacrocorax auritus 97
Quercus rubra 92
Sciurus carolinensis 80
Vulpes fulva 76
Citellus tridecemlineatus 76
Larix occidentalis 69
Pinus banksiana 67
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Orchopeas leucopus interactsWith Peromyscus maniculatus 742
Megabothris quirini interactsWith Clethrionomys gapperi 390
Ctenophthalmus pseudagyrtes interactsWith Clethrionomys gapperi 246
Orchopeas caedens interactsWith Tamiasciurus hudsonicus 241
Monopsyllus vison interactsWith Tamiasciurus hudsonicus 221
Aetheca wagneri interactsWith Peromyscus maniculatus 152
Foxella ignota ignota interactsWith Geomys bursarius 146
Orchopeas leucopus interactsWith Peromyscus leucopus 138
Myodopsylla insignis interactsWith Myotis lucifugus 135
Ceratophyllus styx riparius interactsWith Bank Swallow 124
Cediopsylla simplex interactsWith Sylvilagus floridanus 107
Peromyscopsylla hesperomys interactsWith Peromyscus maniculatus 103
Xenopsylla cheopis interactsWith Rattus norvegicus 101
Ceratophyllus niger interactsWith Phalacrocorax auritus 97
Buprestidae interactsWith Quercus rubra 79
Orchopeas howardi interactsWith Sciurus carolinensis 74
Orchopeas leucopus interactsWith Microtus pennsylvanicus 71
Ctenocephalides felis interactsWith Cat 66
Phaenops drummondi interactsWith Larix occidentalis 65

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 Plantae Plantae Animalia->Plantae
interactions Buprestidae Buprestidae Betulaceae Betulaceae Buprestidae->Betulaceae Fagaceae Fagaceae Buprestidae->Fagaceae Juglandaceae Juglandaceae Buprestidae->Juglandaceae Pinaceae Pinaceae Buprestidae->Pinaceae Ceratophyllidae Ceratophyllidae Canidae Canidae Ceratophyllidae->Canidae Cricetidae Cricetidae Ceratophyllidae->Cricetidae Dipodidae Dipodidae Ceratophyllidae->Dipodidae Geomyidae Geomyidae Ceratophyllidae->Geomyidae Hersiliidae Hersiliidae Ceratophyllidae->Hersiliidae Heteromyidae Heteromyidae Ceratophyllidae->Heteromyidae Hirundinidae Hirundinidae Ceratophyllidae->Hirundinidae Mephitidae Mephitidae Ceratophyllidae->Mephitidae Muridae Muridae Ceratophyllidae->Muridae Mustelidae Mustelidae Ceratophyllidae->Mustelidae Ochotonidae Ochotonidae Ceratophyllidae->Ochotonidae Passeridae Passeridae Ceratophyllidae->Passeridae Phalacrocoracidae Phalacrocoracidae Ceratophyllidae->Phalacrocoracidae Phasianidae Phasianidae Ceratophyllidae->Phasianidae Sciuridae Sciuridae Ceratophyllidae->Sciuridae Soricidae Soricidae Ceratophyllidae->Soricidae Strigidae Strigidae Ceratophyllidae->Strigidae Troglodytidae Troglodytidae Ceratophyllidae->Troglodytidae Turdidae Turdidae Ceratophyllidae->Turdidae Ctenophthalmidae Ctenophthalmidae Ctenophthalmidae->Canidae Ctenophthalmidae->Cricetidae Ctenophthalmidae->Dipodidae Ctenophthalmidae->Heteromyidae Ctenophthalmidae->Muridae Ctenophthalmidae->Mustelidae Ctenophthalmidae->Sciuridae Ctenophthalmidae->Soricidae Ctenophthalmidae->Strigidae Aplodontiidae Aplodontiidae Ctenophthalmidae->Aplodontiidae Procyonidae Procyonidae Ctenophthalmidae->Procyonidae Talpidae Talpidae Ctenophthalmidae->Talpidae Hystrichopsyllidae Hystrichopsyllidae Hystrichopsyllidae->Cricetidae Hystrichopsyllidae->Sciuridae Hystrichopsyllidae->Aplodontiidae Ischnopsyllidae Ischnopsyllidae Vespertilionidae Vespertilionidae Ischnopsyllidae->Vespertilionidae Leptopsyllidae Leptopsyllidae Leptopsyllidae->Cricetidae Leptopsyllidae->Muridae Leptopsyllidae->Ochotonidae Leptopsyllidae->Soricidae Leptopsyllidae->Aplodontiidae Leporidae Leporidae Leptopsyllidae->Leporidae Pulicidae Pulicidae Pulicidae->Canidae Pulicidae->Cricetidae Pulicidae->Dipodidae Pulicidae->Heteromyidae Pulicidae->Mephitidae Pulicidae->Muridae Pulicidae->Phasianidae Pulicidae->Sciuridae Pulicidae->Procyonidae Pulicidae->Leporidae Didelphidae Didelphidae Pulicidae->Didelphidae Rhopalopsyllidae Rhopalopsyllidae Rhopalopsyllidae->Cricetidae Rhopalopsyllidae->Didelphidae Trichodectidae Trichodectidae Procaviidae Procaviidae Trichodectidae->Procaviidae Vermipsyllidae Vermipsyllidae Vermipsyllidae->Canidae Vermipsyllidae->Mephitidae Vermipsyllidae->Mustelidae Vermipsyllidae->Procyonidae Felidae Felidae Vermipsyllidae->Felidae

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, 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
Ft circled NONE col Ft circled
Ft NONE col Ft
Pm NONE col Pm
Acmaeodera pulchella HAS_ACCEPTED_NAME col Acmaeodera pulchella
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 279
col class 1
col family 1
col genus 39
col species 267
col subgenus 6
col subspecies 16
discoverlife NA 603
gbif NA 222
gbif class 1
gbif family 1
gbif genus 47
gbif species 293
gbif subspecies 39
gbif variety 1
itis NA 382
itis class 1
itis family 1
itis genus 29
itis species 181
itis subspecies 8
mdd NA 602
ncbi NA 339
ncbi class 1
ncbi family 1
ncbi genus 36
ncbi species 213
ncbi subgenus 1
ncbi subspecies 13
pbdb NA 463
pbdb class 1
pbdb family 1
pbdb genus 23
pbdb species 113
pbdb subspecies 1
tpt NA 378
tpt genus 15
tpt species 209
wfo NA 589
wfo genus 3
wfo species 10
worms NA 541
worms class 1
worms family 1
worms genus 12
worms species 47
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 316
col HAS_ACCEPTED_NAME 300
col SYNONYM_OF 57
discoverlife NONE 650
gbif NONE 258
gbif HAS_ACCEPTED_NAME 347
gbif SYNONYM_OF 74
itis NONE 419
itis HAS_ACCEPTED_NAME 198
itis SYNONYM_OF 34
mdd NONE 556
mdd HAS_ACCEPTED_NAME 83
mdd SYNONYM_OF 9
ncbi NONE 379
ncbi SAME_AS 238
ncbi SYNONYM_OF 32
ncbi COMMON_NAME_OF 2
pbdb NONE 500
pbdb HAS_ACCEPTED_NAME 120
pbdb SYNONYM_OF 30
tpt NONE 418
tpt HAS_ACCEPTED_NAME 271
tpt SYNONYM_OF 44
wfo NONE 635
wfo HAS_ACCEPTED_NAME 11
wfo SYNONYM_OF 3
worms NONE 581
worms HAS_ACCEPTED_NAME 61
worms SYNONYM_OF 7
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)
worms 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
2024-11-18T03:30:44Z note invalid date string [06-06-1928]
2024-11-18T03:30:44Z note invalid date string [06-06-1928]
2024-11-18T03:30:44Z note invalid date string [06-06-1928]
2024-11-18T03:30:44Z note invalid date string [06-06-1928]

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

Most frequently occurring review notes, if any.
reviewComment count
date [0007-01-01T00:00:00Z] occurred in the first century AD 602
invalid date string [05-05-1961] 470
date [0008-01-01T00:00:00Z] occurred in the first century AD 436
invalid date string [11-08-1963] 196

For addition information on review notes, please have a look at the first 500 Review Notes or the download full csv or tsv archives.

GloBI Review Badge

As part of the review, a review badge is generated. This review badge can be included in webpages to indicate the review status of the dataset under review.

review review 💬 💬

Note that if the badge is green, no review notes were generated. If the badge is yellow, the review bots may need some help with interpreting the species interaction data.

GloBI Index Badge

If the dataset under review has been registered with GloBI, and has been succesfully indexed by GloBI, the GloBI Index Status Badge will turn green. This means that the dataset under review was indexed by GloBI and is available through GloBI services and derived data products.

Picture of a GloBI Index Badge

If you’d like to keep track of reviews or index status of the dataset under review, please visit [GloBI’s dataset index ^[At time of writing (2024-11-18) the version of the GloBI dataset index was available at https://globalbioticinteractions.org/datasets for badge examples.

Discussion

This review aims to provide a perspective on the dataset to aid in understanding of species interaction claims discovered. However, it is important to note that this review does not assess the quality of the dataset. Instead, it serves as an indication of the open-ness5 and FAIRness (Wilkinson et al. 2016; Trekels et al. 2023) of the dataset: to perform this review, the data was likely openly available, Findable, Accessible, Interoperable and Reusable. The current Open-FAIR assessment is qualitative, and a more quantitative approach can be implemented with specified measurement units.

This report also showcases the reuse of machine-actionable (meta)data, something highly recommended by the FAIR Data Principles (Wilkinson et al. 2016). Making (meta)data machine-actionable enables more precise procesing by computers, enabling even naive review bots like Nomer and Elton to interpret the data effectively. This capability is crucial for not just automating the generation of reports, but also for facilitating seamless data exchanges, promoting interoperability.

Acknowledgements

We thank the many humans that created us and those who created and maintained the data, software and other intellectual resources that were used for producing this review. In addition, we are grateful for the natural resources providing the basis for these human and bot activities.

Author contributions

Nomer was responsible for name alignments. Elton carried out dataset extraction, and generated the review notes.

References

ICZN. 1999. “International Code of Zoological Nomenclature.” The International Trust for Zoological Nomenclature, London, UK. https://www.iczn.org/the-code/the-code-online/.
Poelen, Jorrit H., James D. Simons, and Chris J. Mungall. 2014. “Global Biotic Interactions: An Open Infrastructure to Share and Analyze Species-Interaction Datasets.” Ecological Informatics 24 (November): 148–59. https://doi.org/10.1016/j.ecoinf.2014.08.005.
Trekels, Maarten, Debora Pignatari Drucker, José Augusto Salim, Jeff Ollerton, Jorrit Poelen, Filipi Miranda Soares, Max Rünzel, Muo Kasina, Quentin Groom, and Mariano Devoto. 2023. “WorldFAIR Project (D10.1) Agriculture-related pollinator data standards use cases report.” Zenodo. https://doi.org/10.5281/zenodo.8176978.
Wilkinson, Mark D., Michel Dumontier, IJsbrand Jan Aalbersberg, Gabrielle Appleton, Myles Axton, Arie Baak, Niklas Blomberg, et al. 2016. “The FAIR Guiding Principles for Scientific Data Management and Stewardship.” Scientific Data 3 (1). https://doi.org/10.1038/sdata.2016.18.