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

by Nomer and Elton, two naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

https://github.com/globalbioticinteractions/unhc/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/unhc, is 3.98MiB in size and contains 3,200 interaction with 5 unique types of associations (e.g., interactsWith) between 212 primary taxa (e.g., Bombus impatiens) and 204 associated taxa (e.g., Trifolium repens). 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:

University of New Hampshire Collection of Insects and other Arthropods UNHC-UNHC https://github.com/globalbioticinteractions/unhc/archive/f72575a72edda8a4e6126de79b4681b25593d434.zip 2024-11-16T12:28:22.379Z f9eea272b0aa928d98d9a6d6085b903775a2746eb46d6b09023695eae5f0083c

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/unhc 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. 3.98MiB) under review 
elton pull globalbioticinteractions/unhc

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

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

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/unhc\
 | 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/unhc, is 3.98MiB in size and contains 3,200 interaction with 5 unique types of associations (e.g., interactsWith) between 212 primary taxa (e.g., Bombus impatiens) and 204 associated taxa (e.g., Trifolium repens).

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
Bombus vagans interactsWith Rubus sp. https://scan-bugs.org:443/portal/collections/individual/index.php?occid=41511725
Bombus impatiens interactsWith Malus sp. https://scan-bugs.org:443/portal/collections/individual/index.php?occid=41511824
Bombus impatiens interactsWith Malus sp. https://scan-bugs.org:443/portal/collections/individual/index.php?occid=41511825
Bombus impatiens interactsWith Malus sp. https://scan-bugs.org:443/portal/collections/individual/index.php?occid=41511826
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
interactsWith 3113
adjacentTo 60
hasHost 22
visits 3
eats 2
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Bombus impatiens 917
Halictus ligatus 246
Bombus vagans 215
Bombus bimaculatus 176
Lasioglossum pilosum 129
Halictus confusus 71
Xylocopa virginica 67
Bombus ternarius 63
Bombus griseocollis 62
Bombus terricola 62
Ceratina calcarata 61
Bombus affinis 50
Andrena wilkella 45
Hylaeus modestus 44
Agapostemon virescens 37
Lasioglossum versatum 35
Lasioglossum cressonii 29
Andrena crataegi 28
Andrena cressonii 27
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
Trifolium repens 295
Monarda fistulosa 283
Aster sp. 163
Trifolium pratense 148
Fagopyrum esculentum 130
Heliopsis helianthoides 108
Solidago speciosa 101
Rudbeckia hirta 93
Daucus carota 72
Solidago canadensis 68
Barbarea vulgaris 59
Taraxacum officinale 56
Rhus glabra 53
Erigeron annuus 53
Solidago altissima 52
Spiraea japonica 51
Ribes sp. 50
Solidago sp. 39
Syringa vulgaris 38
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Bombus impatiens interactsWith Trifolium repens 175
Bombus impatiens interactsWith Monarda fistulosa 116
Bombus impatiens interactsWith Aster sp. 112
Halictus ligatus interactsWith Rudbeckia hirta 80
Bombus impatiens interactsWith Solidago speciosa 67
Bombus impatiens interactsWith Trifolium pratense 52
Lasioglossum pilosum interactsWith Fagopyrum esculentum 46
Bombus impatiens interactsWith Solidago canadensis 42
Xylocopa virginica interactsWith Monarda fistulosa 40
Bombus impatiens interactsWith Solidago altissima 33
Halictus ligatus interactsWith Coreopsis lanceolata 33
Bombus vagans interactsWith Aster sp. 32
Bombus bimaculatus interactsWith Monarda fistulosa 31
Bombus ternarius interactsWith Epigaea repens 29
Hylaeus modestus interactsWith Daucus carota 27
Bombus impatiens interactsWith Ribes sp. 26
Bombus griseocollis interactsWith Monarda fistulosa 25
Lasioglossum pilosum interactsWith Monarda fistulosa 25
Bombus vagans interactsWith Trifolium pratense 24

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 Plantae Plantae Animalia->Plantae Animalia->Plantae
interactions Andrenidae Andrenidae Salicaceae Salicaceae Andrenidae->Salicaceae Andrenidae->Salicaceae Anacardiaceae Anacardiaceae Andrenidae->Anacardiaceae Apocynaceae Apocynaceae Andrenidae->Apocynaceae Asteraceae Asteraceae Andrenidae->Asteraceae Brassicaceae Brassicaceae Andrenidae->Brassicaceae Ericaceae Ericaceae Andrenidae->Ericaceae Fabaceae Fabaceae Andrenidae->Fabaceae Oleaceae Oleaceae Andrenidae->Oleaceae Papaveraceae Papaveraceae Andrenidae->Papaveraceae Ranunculaceae Ranunculaceae Andrenidae->Ranunculaceae Rosaceae Rosaceae Andrenidae->Rosaceae Apidae Apidae Apidae->Salicaceae Apidae->Anacardiaceae Apidae->Apocynaceae Apidae->Asteraceae Apidae->Brassicaceae Apidae->Ericaceae Apidae->Fabaceae Apidae->Oleaceae Apidae->Rosaceae Alismataceae Alismataceae Apidae->Alismataceae Apiaceae Apiaceae Apidae->Apiaceae Araceae Araceae Apidae->Araceae Araliaceae Araliaceae Apidae->Araliaceae Balsaminaceae Balsaminaceae Apidae->Balsaminaceae Caryophyllaceae Caryophyllaceae Apidae->Caryophyllaceae Cucurbitaceae Cucurbitaceae Apidae->Cucurbitaceae Geraniaceae Geraniaceae Apidae->Geraniaceae Grossulariaceae Grossulariaceae Apidae->Grossulariaceae Lamiaceae Lamiaceae Apidae->Lamiaceae Lythraceae Lythraceae Apidae->Lythraceae Orobanchaceae Orobanchaceae Apidae->Orobanchaceae Plantaginaceae Plantaginaceae Apidae->Plantaginaceae Poaceae Poaceae Apidae->Poaceae Polygonaceae Polygonaceae Apidae->Polygonaceae Rubiaceae Rubiaceae Apidae->Rubiaceae Sapindaceae Sapindaceae Apidae->Sapindaceae Violaceae Violaceae Apidae->Violaceae Vitaceae Vitaceae Apidae->Vitaceae Colletidae Colletidae Colletidae->Asteraceae Colletidae->Brassicaceae Colletidae->Fabaceae Colletidae->Rosaceae Colletidae->Apiaceae Colletidae->Lamiaceae Colletidae->Plantaginaceae Colletidae->Polygonaceae Halictidae Halictidae Halictidae->Anacardiaceae Halictidae->Apocynaceae Halictidae->Asteraceae Halictidae->Brassicaceae Halictidae->Ericaceae Halictidae->Fabaceae Halictidae->Oleaceae Halictidae->Papaveraceae Halictidae->Ranunculaceae Halictidae->Rosaceae Halictidae->Apiaceae Halictidae->Caryophyllaceae Halictidae->Lamiaceae Halictidae->Lythraceae Halictidae->Poaceae Halictidae->Polygonaceae Halictidae->Violaceae Orchidaceae Orchidaceae Halictidae->Orchidaceae Halictidae->Orchidaceae Campanulaceae Campanulaceae Halictidae->Campanulaceae Cornaceae Cornaceae Halictidae->Cornaceae Diapensiaceae Diapensiaceae Halictidae->Diapensiaceae Fagaceae Fagaceae Halictidae->Fagaceae Myricaceae Myricaceae Halictidae->Myricaceae Megachilidae Megachilidae Megachilidae->Anacardiaceae Megachilidae->Apocynaceae Megachilidae->Asteraceae Megachilidae->Ericaceae Megachilidae->Fabaceae Megachilidae->Oleaceae Megachilidae->Rosaceae Megachilidae->Apiaceae Megachilidae->Lamiaceae Megachilidae->Lythraceae Megachilidae->Plantaginaceae Megachilidae->Rubiaceae Megachilidae->Violaceae Megachilidae->Orchidaceae Megachilidae->Orchidaceae Liliaceae Liliaceae Megachilidae->Liliaceae Onagraceae Onagraceae Megachilidae->Onagraceae

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
Andrena algida HAS_ACCEPTED_NAME col Andrena algida
Andrena asteris HAS_ACCEPTED_NAME col Andrena asteris
Andrena barbilabris HAS_ACCEPTED_NAME col Andrena barbilabris
Andrena braccata HAS_ACCEPTED_NAME col Andrena braccata
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 57
col genus 45
col kingdom 1
col species 303
col subgenus 1
col subspecies 9
col variety 1
discoverlife NA 231
discoverlife species 177
gbif NA 48
gbif genus 46
gbif kingdom 1
gbif species 309
gbif subspecies 12
gbif variety 2
itis NA 71
itis genus 44
itis kingdom 1
itis species 288
itis subspecies 2
itis variety 2
mdd NA 408
ncbi NA 86
ncbi genus 45
ncbi species 272
ncbi subgenus 2
ncbi subspecies 3
ncbi varietas 2
pbdb NA 372
pbdb genus 30
pbdb kingdom 1
pbdb species 5
tpt NA 402
tpt genus 2
tpt species 4
wfo NA 261
wfo genus 41
wfo species 103
wfo subspecies 6
wfo variety 1
worms NA 337
worms genus 29
worms kingdom 1
worms species 40
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 351
col SYNONYM_OF 105
col NONE 58
discoverlife HAS_ACCEPTED_NAME 171
discoverlife SYNONYM_OF 53
discoverlife NONE 239
discoverlife HOMONYM_OF 15
gbif HAS_ACCEPTED_NAME 417
gbif SYNONYM_OF 130
gbif NONE 49
itis HAS_ACCEPTED_NAME 335
itis SYNONYM_OF 25
itis NONE 72
mdd NONE 416
ncbi SAME_AS 322
ncbi NONE 89
ncbi SYNONYM_OF 11
pbdb NONE 374
pbdb HAS_ACCEPTED_NAME 43
pbdb SYNONYM_OF 3
tpt NONE 410
tpt HAS_ACCEPTED_NAME 5
tpt SYNONYM_OF 6
wfo NONE 264
wfo SYNONYM_OF 37
wfo HAS_ACCEPTED_NAME 144
wfo HAS_UNCHECKED_NAME 29
worms NONE 341
worms HAS_ACCEPTED_NAME 95
worms SYNONYM_OF 17
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
2024-11-18T08:10:39Z note found unsupported interaction type with name: [coll. from]
2024-11-18T08:10:39Z note found unsupported interaction type with name: [coll. from]
2024-11-18T08:10:39Z note found unsupported interaction type with name: [coll. from]
2024-11-18T08:10:39Z note found unsupported interaction type with name: [coll. from]

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

Most frequently occurring review notes, if any.
reviewComment count
found unsupported interaction type with name: [1] 16
found unsupported interaction type with name: [coll. from] 5
found unsupported interaction type with name: [attacks] 4
found unsupported interaction type with name: [CZ-2] 2

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.