A Review of Biotic Interactions and Taxon Names Found in globalbioticinteractions/inhs-insects

by Nomer and Elton, two naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

https://github.com/globalbioticinteractions/inhs-insects/issues

2024-04-29

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/inhs-insects, is 70.6MiB in size and contains 7,820 interaction with 4 unique types of associations (e.g., adjacentTo) between 1,407 primary taxon (e.g., Mezira granulata (Say, 1832)) and 1,571 associated taxon (e.g., under). 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:

Illinois Natural History Survey Insect Collection https://github.com/globalbioticinteractions/inhs-insects/archive/38692496f590577074c7cecf8ea37f85d0594ae1.zip 2024-04-20T00:26:11.323Z d3e25559e726bcd1e48024f406175898c20b64e9bbf3806f35bbd9c23db961e5

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/inhs-insects 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 0.13.2
nomer 0.5.8
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. 70.6MiB) under review 
elton pull globalbioticinteractions/inhs-insects

# generate review notes
elton review globalbioticinteractions/inhs-insects\
 > review.tsv

# export indexed interaction records
elton interactions globalbioticinteractions/inhs-insects\
 > interactions.tsv

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/inhs-insects\
 | 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/inhs-insects, is 70.6MiB in size and contains 7,820 interaction with 4 unique types of associations (e.g., adjacentTo) between 1,407 primary taxon (e.g., Mezira granulata (Say, 1832)) and 1,571 associated taxon (e.g., under).

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
Sitticus barnesi Cutler, 1965 adjacentTo table in office bd2fc9f8-848f-46fc-9f11-c27ecddb31b6
Hentzia mitrata (Hentz, 1846) interactsWith herbs + shrubs 0c958a87-6372-4572-80af-dcda3013df67
Araneus patagiatus Clerck, 1757 adjacentTo deciduous trees and shrubs a474317b-a3da-4ac3-9905-a94c0dd7bbd2
Araneus patagiatus Clerck, 1757 adjacentTo outside of lab building at night 8744376f-56b9-473d-8030-1b9411263ce6
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
adjacentTo 5193
hasHost 1941
interactsWith 655
eats 31
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Mezira granulata (Say, 1832) 258
Psyllidae Latreille, 1807 138
Pulicidae Billberg, 1820 125
Empoasca 122
Orchopeas howardi (Baker, 1895) 115
Ptinidae Latreille, 1802 98
Siphonaptera 96
Tetraloniella (Tetraloniella) donata (Cresson, 1878) 94
Myrsidea interrupta (Osborn, 1896) 90
Braconidae Nees, 1811 84
Cynipidae 81
Chalcidoidea 72
Phthiraptera Haeckel, 1896 71
Hymenoptera 69
Curculionidae Latreille, 1802 68
Epitrix cucumeris Harris, 1851 63
Cicadellidae 61
Hemiptera Linnaeus, 1758 61
Ichneumonidae 60
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
under 568
flowers 194
ex. log 149
mud 94
flowers of Leguminosae 91
Crow 90
grasses 88
flower 81
tree 78
under oak 74
Cane 73
Alfalfa 69
cottontail 66
pear 65
hips ofRosa blanda 58
wild grape 52
bluff 51
willow 51
screens 50
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Mezira granulata (Say, 1832) adjacentTo under 258
Ptinidae Latreille, 1802 hasHost ex. log 98
Myrsidea interrupta (Osborn, 1896) adjacentTo Crow 89
Tetraloniella (Tetraloniella) donata (Cresson, 1878) adjacentTo flowers of Leguminosae 78
Cynipidae adjacentTo tree 69
Psyllidae Latreille, 1807 adjacentTo pear 63
Chalcidoidea interactsWith hips ofRosa blanda 58
Typocerus confluens Casey, 1913 adjacentTo flowers 57
Trigonotylus tarsalis (Reuter, 1876) adjacentTo grasses 54
Empoasca adjacentTo Alfalfa 53
Psyllidae Latreille, 1807 adjacentTo screens 50
Temnostoma alternans Loew, 1864 adjacentTo flower 49
Corimelaena (Corimelaena) pulicaria (Germar, 1839) adjacentTo flowers 47
Bruchophagus Ashmead, 1888 adjacentTo Corn 45
Stenocranus similis Crawford, 1914 adjacentTo Cane 42
Lasioglossum (Dialictus) illinoense (Robertson, 1892) adjacentTo Monarda sp. 41
Pycnoscelus surinamensis (Linnaeus, 1758) interactsWith rose bench 40
Curculionidae Latreille, 1802 hasHost Cassia 39
Pulicidae Billberg, 1820 hasHost cottontail 39

Interaction Networks

The figures below provide a graph view on the dataset under review. The first shows a summary network on the kingdom level, and the second shows how interactions on the family level. It is important to note that both network graphs were first aligned taxonomically using the Catalogue of Life. Please refer to the original (or verbatim) taxonomic names for a more original view on the interaction data.

interactions Animalia Animalia Animalia->Animalia Animalia->Animalia Animalia->Animalia Plantae Plantae Animalia->Plantae Animalia->Plantae Plantae->Plantae
interactions Agromyzidae Agromyzidae Aquifoliaceae Aquifoliaceae Agromyzidae->Aquifoliaceae Aphididae Aphididae Asteraceae Asteraceae Aphididae->Asteraceae Onagraceae Onagraceae Aphididae->Onagraceae Apidae Apidae Apidae->Asteraceae Cecidomyiidae Cecidomyiidae Moraceae Moraceae Cecidomyiidae->Moraceae Ceraphronidae Ceraphronidae Hydrangeaceae Hydrangeaceae Ceraphronidae->Hydrangeaceae Cicadellidae Cicadellidae Cicadellidae->Asteraceae Cicadellidae->Moraceae Colletidae Colletidae Fabaceae Fabaceae Colletidae->Fabaceae Salicaceae Salicaceae Colletidae->Salicaceae Eulophidae Eulophidae Asparagaceae Asparagaceae Eulophidae->Asparagaceae Halictidae Halictidae Halictidae->Asteraceae Halictidae->Fabaceae Halictidae->Salicaceae Hydrophyllaceae Hydrophyllaceae Halictidae->Hydrophyllaceae Rosaceae Rosaceae Halictidae->Rosaceae Rubiaceae Rubiaceae Halictidae->Rubiaceae Hemerobiidae Hemerobiidae Hemerobiidae->Aphididae Hippoboscidae Hippoboscidae Ardeidae Ardeidae Hippoboscidae->Ardeidae Ichneumonidae Ichneumonidae Ichneumonidae->Asteraceae Ichneumonidae->Salicaceae Betulaceae Betulaceae Ichneumonidae->Betulaceae Euphorbiaceae Euphorbiaceae Ichneumonidae->Euphorbiaceae Megachilidae Megachilidae Megachilidae->Asteraceae Megachilidae->Euphorbiaceae Verbenaceae Verbenaceae Megachilidae->Verbenaceae Pentatomidae Pentatomidae Apiaceae Apiaceae Pentatomidae->Apiaceae Philopteridae Philopteridae Rallidae Rallidae Philopteridae->Rallidae Saxifragaceae Saxifragaceae Celastraceae Celastraceae Saxifragaceae->Celastraceae Tenthredinidae Tenthredinidae Equisetaceae Equisetaceae Tenthredinidae->Equisetaceae Thyreocoridae Thyreocoridae Thyreocoridae->Rubiaceae Torymidae Torymidae Torymidae->Asparagaceae Trichodectidae Trichodectidae Geomyidae Geomyidae Trichodectidae->Geomyidae Mephitidae Mephitidae Trichodectidae->Mephitidae Xenidae Xenidae Eumenidae Eumenidae Xenidae->Eumenidae

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
lined ground squirrel NONE col lined ground squirrel
Burn NONE col Burn
Zonotrichia albicollis white throated sparrow NONE col Zonotrichia albicollis white throated sparrow
Ablabesmyia HAS_ACCEPTED_NAME col Ablabesmyia
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 1361
col class 5
col family 130
col genus 318
col infraorder 1
col kingdom 1
col nanorder 1
col order 20
col parvorder 1
col section 1
col species 652
col subfamily 9
col subgenus 25
col subspecies 23
col subtribe 1
col superfamily 5
col superorder 1
col tribe 3
col variety 2
discoverlife NA 2511
discoverlife species 9
gbif NA 1229
gbif class 5
gbif family 131
gbif genus 341
gbif kingdom 1
gbif order 20
gbif species 775
gbif subspecies 39
gbif variety 3
itis NA 1571
itis class 5
itis family 131
itis genus 260
itis kingdom 1
itis order 23
itis species 487
itis subclass 1
itis subfamily 12
itis suborder 4
itis subspecies 19
itis superfamily 6
itis superorder 1
itis tribe 1
itis variety 1
mdd NA 2519
ncbi NA 1437
ncbi class 5
ncbi family 128
ncbi genus 306
ncbi order 20
ncbi series 1
ncbi species 578
ncbi species group 1
ncbi subclass 1
ncbi subfamily 15
ncbi subgenus 13
ncbi suborder 3
ncbi subspecies 16
ncbi superfamily 4
ncbi superorder 2
ncbi tribe 3
ncbi varietas 1
pbdb NA 2129
pbdb class 5
pbdb family 119
pbdb genus 167
pbdb informal 1
pbdb infraorder 2
pbdb kingdom 1
pbdb order 25
pbdb species 47
pbdb subclass 1
pbdb subfamily 17
pbdb suborder 7
pbdb superfamily 5
pbdb superorder 1
pbdb tribe 4
pbdb unranked clade 1
tpt NA 2348
tpt family 4
tpt genus 19
tpt order 1
tpt species 147
wfo NA 2348
wfo family 2
wfo genus 92
wfo phylum 1
wfo species 75
wfo subspecies 1
wfo variety 2
Name relationship types per catalog. Name relationship type “NONE” means that a name was not recognized by the associated catalog. “SAME_AS” indicates either a “HAS_ACCEPTED_NAME” or “SYNONYM_OF” name relationship type. We recognize that “SYNONYM_OF” encompasses many types of nomenclatural synonymies (ICZN 1999) (e.g., junior synonym, senior synonyms).
resolvedCatalogName relationName count
col NONE 1644
col HAS_ACCEPTED_NAME 1303
col SYNONYM_OF 423
discoverlife NONE 2969
discoverlife HAS_ACCEPTED_NAME 9
gbif NONE 1511
gbif HAS_ACCEPTED_NAME 1618
gbif SYNONYM_OF 496
itis NONE 1858
itis HAS_ACCEPTED_NAME 1080
itis SYNONYM_OF 59
mdd NONE 2911
mdd HAS_ACCEPTED_NAME 53
ncbi NONE 1734
ncbi SAME_AS 1239
ncbi SYNONYM_OF 42
ncbi COMMON_NAME_OF 25
pbdb NONE 2459
pbdb HAS_ACCEPTED_NAME 504
pbdb SYNONYM_OF 40
tpt NONE 2756
tpt HAS_ACCEPTED_NAME 195
tpt SYNONYM_OF 74
wfo NONE 2756
wfo HAS_ACCEPTED_NAME 191
wfo SYNONYM_OF 37
wfo HAS_UNCHECKED_NAME 23
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
2024-04-29T02:30:34Z note found unsupported interaction type with name: [Pond labeled Section D]
2024-04-29T02:30:34Z note found unsupported interaction type with name: [Pond labeled Section E]
2024-04-29T02:30:34Z note source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder
2024-04-29T02:30:34Z note source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder

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: [HostSpecies] 613
found unsupported interaction type with name: [PreviousCrop] 566
found unsupported interaction type with name: [A-C)] 170
found unsupported interaction type with name: [Soil Class] 158

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 (2024-04-29) 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.