A Review of Biotic Interactions and Taxon Names Found in globalbioticinteractions/cu-cuac

by Nomer and Elton, two naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

https://github.com/globalbioticinteractions/cu-cuac/issues

2024-04-17

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/cu-cuac, is 8.17MiB in size and contains 565 interactions with 3 unique types of associations (e.g., hasHost) between 553 primary taxa (e.g., Arianops) and 73 associated taxa (e.g., ex. Mushrooms). 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:

Clemson University Arthropod Collection https://github.com/globalbioticinteractions/cu-cuac/archive/6cdcbbaa4f7cec8e1eac705be3a999bc5259e00f.zip 2024-04-12T23:33:04.898Z 2431adc8ba4d672d7a8ef1a9e5a8a4acea745a42f3f58ac48104437ae62a816f

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/cu-cuac 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 0.5.7
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. 8.17MiB) under review 
elton pull globalbioticinteractions/cu-cuac

# generate review notes
elton review globalbioticinteractions/cu-cuac\
 > review.tsv

# export indexed interaction records
elton interactions globalbioticinteractions/cu-cuac\
 > interactions.tsv

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/cu-cuac\
 | 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/cu-cuac, is 8.17MiB in size and contains 565 interactions with 3 unique types of associations (e.g., hasHost) between 553 primary taxa (e.g., Arianops) and 73 associated taxa (e.g., ex. Mushrooms).

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
Trichophaga tapetzella interactsWith owl pellets https://scan-bugs.org:443/portal/collections/individual/index.php?occid=25945744
Thyridopteryx ephemeraeformis hasHost larvae https://scan-bugs.org:443/portal/collections/individual/index.php?occid=25945747
Phyllonorycter blancardella interactsWith apple foilage https://scan-bugs.org:443/portal/collections/individual/index.php?occid=25945749
Cosmopterix attenuatella hasHost reared ex Lespedeza https://scan-bugs.org:443/portal/collections/individual/index.php?occid=25945761
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
hasHost 276
adjacentTo 273
interactsWith 16
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Arianops 3
Paranthrene simulans 2
CU | CUAC | d198856b-3b84-4738-aa59-97ad8bc5c234 | CUAC000122368 | c25eec7b-5dd7-478a-9ffe-5a6dbe928bf9 2
CU | CUAC | d198856b-3b84-4738-aa59-97ad8bc5c234 | CUAC000122369 | 96511200-6583-4b6e-a6d3-83c549e76e40 2
CU | CUAC | d198856b-3b84-4738-aa59-97ad8bc5c234 | CUAC000122370 | 6bfd0638-dc01-4b42-a3f2-02891077c18b 2
CU | CUAC | d198856b-3b84-4738-aa59-97ad8bc5c234 | CUAC000122371 | ecadbb68-42f3-4051-a970-a077ad93ce3b 2
CU | CUAC | d198856b-3b84-4738-aa59-97ad8bc5c234 | CUAC000122372 | 70da6ace-03ce-4e1c-afe7-6f0eff656014 2
CU | CUAC | d198856b-3b84-4738-aa59-97ad8bc5c234 | CUAC000122373 | 76f91ef0-d4df-45b6-b42b-9dff7f41e44a 2
Stenomorphus californicus 2
Pentacora ligata 2
Aradidae 2
Trichophaga tapetzella 1
Thyridopteryx ephemeraeformis 1
Phyllonorycter blancardella 1
Cosmopterix attenuatella 1
Episimus tyrius 1
Endothenia hebesana 1
Epiblema strenuana 1
Tortrix viridana 1
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
ex. Mushrooms 84
dying pinus 61
ex. rotten log 59
flowers 55
ex. Polypore 32
ex. Dead turtle 29
ex. Maclura fruit 25
Under Hemlock 17
dead squirrel 14
freshly cut pine stump 12
ex. Asimina fruit 11
dead pine at night 11
bark dead tree 10
exposed rock face 9
mud bank 9
palmetto leaf at night 6
nymph 6
vegetation 6
Ex. Crepe myrtle 5
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Arianops adjacentTo underside of embedded rock. 2
Pentacora ligata adjacentTo bare rock beside rapids 2
Aradidae adjacentTo dead wood at night 2
Trichophaga tapetzella interactsWith owl pellets 1
Thyridopteryx ephemeraeformis hasHost larvae 1
Phyllonorycter blancardella interactsWith apple foilage 1
Cosmopterix attenuatella hasHost reared ex Lespedeza 1
Paranthrene simulans hasHost Japanese Maple 1
Paranthrene simulans hasHost emerged 5. May. 1999 1
Episimus tyrius hasHost 7 Aug. 1989 1
Endothenia hebesana adjacentTo Snap-Dragon 1
Epiblema strenuana interactsWith ragweed 1
Tortrix viridana hasHost ex. Oak 1
Lerema accius hasHost pupa inside rolled up leaf of Johnson grass 1
Atalopedes campestris hasHost apple tree 1
Megathymus yuccae hasHost pupae 1
Erynnis juvenalis adjacentTo wing 1
Papilio troilus adjacentTo spice bush 1
CU | CUAC | d198856b-3b84-4738-aa59-97ad8bc5c234 | CUAC000055434 | 4d7feb7a-8ea6-4085-9f3a-c071d9737f6f adjacentTo dying pinus 1

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

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
Cosmopterix attenuatella HAS_ACCEPTED_NAME col Cosmopterix attenuatella
Atalopedes campestris HAS_ACCEPTED_NAME col Atalopedes campestris
Erynnis juvenalis HAS_ACCEPTED_NAME col Erynnis juvenalis
Osorius HAS_ACCEPTED_NAME col Osorius
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 586
col class 1
col family 2
col genus 10
col kingdom 1
col order 1
col species 19
discoverlife NA 621
gbif NA 583
gbif class 1
gbif family 2
gbif genus 11
gbif kingdom 1
gbif order 1
gbif species 21
gbif subspecies 1
itis NA 591
itis family 2
itis genus 10
itis kingdom 1
itis order 2
itis species 13
itis subclass 1
mdd NA 620
ncbi NA 586
ncbi family 2
ncbi genus 10
ncbi order 2
ncbi species 20
ncbi subclass 1
pbdb NA 606
pbdb class 1
pbdb family 2
pbdb genus 6
pbdb kingdom 1
pbdb order 2
pbdb species 2
tpt NA 618
tpt species 2
wfo NA 613
wfo genus 4
wfo phylum 1
wfo species 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 35
col SYNONYM_OF 5
col NONE 587
discoverlife NONE 626
gbif HAS_ACCEPTED_NAME 46
gbif SYNONYM_OF 9
gbif NONE 584
itis HAS_ACCEPTED_NAME 29
itis NONE 592
itis SYNONYM_OF 3
mdd NONE 622
ncbi NONE 590
ncbi SAME_AS 34
ncbi COMMON_NAME_OF 2
pbdb NONE 607
pbdb HAS_ACCEPTED_NAME 14
pbdb SYNONYM_OF 7
tpt NONE 620
tpt HAS_ACCEPTED_NAME 2
wfo NONE 615
wfo HAS_ACCEPTED_NAME 7
wfo SYNONYM_OF 1
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
2024-04-16T22:35:47Z note found unsupported interaction type with name: [Division]
2024-04-16T22:35:47Z note found unsupported interaction type with name: [Comp]
2024-04-16T22:35:48Z note found unsupported interaction type with name: [Stand]
2024-04-16T22:35:48Z note found unsupported interaction type with name: [Inkto Collection]

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

Most frequently occurring review notes, if any.
reviewComment count
source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder 530
found unsupported interaction type with name: [Inkto Collection] 2
found unsupported interaction type with name: [Division] 1
found unsupported interaction type with name: [Comp] 1

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.

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-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.

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.