A Review of Biotic Interactions and Taxon Names Found in globalbioticinteractions/asu-asuhic

by Nomer and Elton, two naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

https://github.com/globalbioticinteractions/asu-asuhic/issues

2024-07-01

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/asu-asuhic, is 20.2MiB in size and contains 24,931 interaction with 4 unique types of associations (e.g., interactsWith) between 578 primary taxa (e.g., Oncerus floralis) and 812 associated taxa (e.g., Allionia incarnata L. (trailing windmills) [USDA]). 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:

Arizona State University Hasbrouck Insect Collection https://github.com/globalbioticinteractions/asu-asuhic/archive/4ed77cb9ca8e526269d4678692e2844c950022f8.zip 2024-06-28T23:03:57.972Z 4209c270399e8d6446cc0457edb818cc5dd9a1c29862201b839710b6fbfc0ab1

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/asu-asuhic 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 0.13.4
nomer 0.5.11
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. 20.2MiB) under review 
elton pull globalbioticinteractions/asu-asuhic

# generate review notes
elton review globalbioticinteractions/asu-asuhic\
 > review.tsv

# export indexed interaction records
elton interactions globalbioticinteractions/asu-asuhic\
 > interactions.tsv

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/asu-asuhic\
 | 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/asu-asuhic, is 20.2MiB in size and contains 24,931 interaction with 4 unique types of associations (e.g., interactsWith) between 578 primary taxa (e.g., Oncerus floralis) and 812 associated taxa (e.g., Allionia incarnata L. (trailing windmills) [USDA]).

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
Hirmoneura flavipes adjacentTo palm shaped leaves https://ecdysis.org/collections/individual/index.php?occid=419701
Neorhynchocephalus sackenii hasHost Ex. Morseiella flaviventris (Bruner) https://ecdysis.org/collections/individual/index.php?occid=419705
Neorhynchocephalus sackenii hasHost Ex. Morseiella flaviventris (Bruner) https://ecdysis.org/collections/individual/index.php?occid=419706
Neorhynchocephalus sackenii hasHost Ex. Morseiella flaviventris (Bruner) https://ecdysis.org/collections/individual/index.php?occid=419707
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
interactsWith 14755
adjacentTo 9901
hasHost 263
eats 12
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Oncerus floralis 1182
Acmaeodera pubiventris lanata 745
Acmaeodera gibbula 689
Paracotalpa ursina 675
Acmaeodera lanata 673
Apidae 646
Acmaeodera diffusa 615
Acmaeodera bowditchi 609
Acmaeodera pulchella 589
Acmaeodera acanthicola 583
Acmaeodera decipiens 560
Acmaeodera cazieri 544
Acmaeodera flavopicta 521
Gyascutus planicosta cribriceps 509
Acmaeodera yuccavora 466
Ripiphorus vierecki 434
Hippomelas sphenicus 422
Acmaeodera parkeri 408
Hippomelas planicosta 404
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
Allionia incarnata L. (trailing windmills) [USDA] 1284
Chaenactis fremontii A. Gary (pincushion flower) [USDA] 1134
Prosopis juliflora (Sw.) DC. (mesquite) [USDA] 878
Sphaeralcea laxa Wooton & Standl. (caliche globemallow) [USDA] 757
Asclepias erosa Torr. (desert milkweed) [USDA] 669
Larrea tridentata (DC.) Coville (creosote bush) [USDA] 622
Poliomintha incana (Torr.) A. Gray (frosted mint) [USDA] 591
Cercidum microphyllum (Torr.) Rose & I.M. Johnst. (yellow paloverde) [USDA] 536
Poliomintha incana (Torr). Gray (frosted mint) [USDA] 464
Tamarix pentandra Pall. (salt cedar) [USDA] 445
Ephedra trifurca Torr. ex S. Watson (longleaf jointfir) [USDA] 429
a 15 watt 12 volt battery black light 402
Baileya multiradiata Harv. & A. Gray ex A. Gray (desert marigold) [USDA] 380
dead Hilaria rigida (Thurb.) Benth 379
Dalea spinosa A. Gray (smoketree) [USDA] 378
grass stems 367
Acacia constricta Benth. (whitethorn acacia) [USDA] 360
propylene glycol pit fall cup trap 346
yellow Compositae sp. 318
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Oncerus floralis interactsWith Chaenactis fremontii A. Gary (pincushion flower) [USDA] 1134
Acmaeodera diffusa adjacentTo Sphaeralcea laxa Wooton & Standl. (caliche globemallow) [USDA] 559
Acmaeodera acanthicola interactsWith Cercidum microphyllum (Torr.) Rose & I.M. Johnst. (yellow paloverde) [USDA] 517
Acmaeodera yuccavora adjacentTo Allionia incarnata L. (trailing windmills) [USDA] 462
Dinacoma caseyi interactsWith a 15 watt 12 volt battery black light 394
Hippomelas planicosta interactsWith Larrea tridentata (DC.) Coville (creosote bush) [USDA] 382
Acmaeodera parkeri adjacentTo Allionia incarnata L. (trailing windmills) [USDA] 381
Acmaeodera pubiventris lanata adjacentTo dead Hilaria rigida (Thurb.) Benth 379
Acmaeodera barri interactsWith Dalea spinosa A. Gray (smoketree) [USDA] 376
Heteropogon johnsoni adjacentTo grass stems 359
Hippomelas sphenicus adjacentTo Prosopis juliflora (Sw.) DC. (mesquite) [USDA] 353
Paracotalpa ursina interactsWith propylene glycol pit fall cup trap 346
Gyascutus planicosta cribriceps interactsWith Tamarix pentandra Pall. (salt cedar) [USDA] 345
Acmaeodera cazieri adjacentTo Allionia incarnata L. (trailing windmills) [USDA] 335
Acmaeodera pubiventris lanata interactsWith Poliomintha incana (Torr). Gray (frosted mint) [USDA] 332
Macrosiagon fernaldum interactsWith Asclepias erosa Torr. (desert milkweed) [USDA] 329
Acmaeodera decipiens adjacentTo yellow Compositae sp. 252
Apidae interactsWith Poliomintha incana (Torr.) A. Gray (frosted mint) [USDA] 239
Paracotalpa ursina interactsWith propylene glycol pit fall trap set 12-December, 2019 239

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 Animalia->Plantae Plantae->Plantae
interactions Apidae Apidae Brassicaceae Brassicaceae Apidae->Brassicaceae Asilidae Asilidae Asilidae->Asilidae Cricetidae Cricetidae Asilidae->Cricetidae Masaridae Masaridae Asilidae->Masaridae Buprestidae Buprestidae Asteraceae Asteraceae Buprestidae->Asteraceae Curculionidae Curculionidae Anacardiaceae Anacardiaceae Curculionidae->Anacardiaceae Cactaceae Cactaceae Curculionidae->Cactaceae Pinaceae Pinaceae Curculionidae->Pinaceae Rutaceae Rutaceae Curculionidae->Rutaceae Halictidae Halictidae Rosaceae Rosaceae Halictidae->Rosaceae Lycaenidae Lycaenidae Fagaceae Fagaceae Lycaenidae->Fagaceae Poaceae Poaceae Poaceae->Asteraceae Sphecidae Sphecidae Sphecidae->Asteraceae

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
Aciurina mexicana HAS_ACCEPTED_NAME col Aciurina mexicana
Aciurina trixa HAS_ACCEPTED_NAME col Aciurina trixa
Archilestris magnificus HAS_ACCEPTED_NAME col Archilestris magnificus
Blepharepium secabile HAS_ACCEPTED_NAME col Blepharepium secabile
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 593
col family 17
col genus 118
col infraspecific name 2
col kingdom 1
col section 1
col species 457
col subfamily 1
col subgenus 2
col subspecies 10
col superfamily 2
col tribe 1
col variety 1
discoverlife NA 1149
discoverlife species 53
gbif NA 537
gbif family 18
gbif genus 127
gbif kingdom 1
gbif species 501
gbif subspecies 21
gbif variety 2
itis NA 609
itis family 17
itis genus 112
itis kingdom 1
itis species 436
itis subfamily 1
itis subspecies 16
itis superfamily 2
itis tribe 1
itis variety 8
mdd NA 1202
ncbi NA 800
ncbi family 16
ncbi genus 118
ncbi species 260
ncbi subgenus 10
ncbi subspecies 3
ncbi superfamily 2
ncbi tribe 1
ncbi varietas 1
pbdb NA 1114
pbdb family 18
pbdb genus 62
pbdb kingdom 1
pbdb species 4
pbdb superfamily 2
pbdb tribe 1
tpt NA 1200
tpt genus 2
wfo NA 1054
wfo family 1
wfo genus 73
wfo phylum 1
wfo species 68
wfo subspecies 6
wfo variety 1
worms NA 1112
worms family 9
worms genus 54
worms kingdom 1
worms species 22
worms subspecies 1
worms superfamily 1
worms 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 HAS_ACCEPTED_NAME 657
col SYNONYM_OF 108
col NONE 682
discoverlife NONE 1339
discoverlife SYNONYM_OF 16
discoverlife HAS_ACCEPTED_NAME 50
gbif HAS_ACCEPTED_NAME 750
gbif SYNONYM_OF 167
gbif NONE 626
itis HAS_ACCEPTED_NAME 630
itis SYNONYM_OF 78
itis NONE 699
mdd NONE 1392
ncbi NONE 896
ncbi SAME_AS 493
ncbi SYNONYM_OF 23
pbdb NONE 1255
pbdb HAS_ACCEPTED_NAME 138
pbdb SYNONYM_OF 3
tpt NONE 1390
tpt HAS_ACCEPTED_NAME 2
wfo NONE 1155
wfo HAS_ACCEPTED_NAME 192
wfo HAS_UNCHECKED_NAME 12
wfo SYNONYM_OF 59
worms NONE 1248
worms HAS_ACCEPTED_NAME 132
worms SYNONYM_OF 22
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
2024-06-30T23:22:00Z note source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder
2024-06-30T23:22:01Z note source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder
2024-06-30T23:22:01Z note found unsupported interaction type with name: [7]
2024-06-30T23:22:02Z 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: [attacks] 54
source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder 27
found unsupported interaction type with name: [Cupressaceae] 3
found unsupported interaction type with name: [Pinaceae] 3

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 (2024-07-01) 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.