A Review of Biotic Interactions and Taxon Names Found in globalbioticinteractions/wis-ih-wirc

by Nomer and Elton, two naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

https://github.com/globalbioticinteractions/wis-ih-wirc/issues

2024-04-22

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/wis-ih-wirc, is 4.48MiB in size and contains 2,484 interaction with 5 unique types of associations (e.g., adjacentTo) between 201 primary taxa (e.g., Cediopsylla simplex) and 481 associated taxa (e.g., Mearns Cottontail). 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:

WIRC / University of Wisconsin Madison WIS-IH / Wisconsin Insect Research Collection https://github.com/globalbioticinteractions/wis-ih-wirc/archive/b486a8c34b00ac686637d6dc11ecf86087e2f58c.zip 2024-04-20T19:35:08.163Z b35029a5a63ca99c6673d286a5175dec05dc764a5fb4a6dc3a3022cd5d28046b

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/wis-ih-wirc 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. 4.48MiB) under review 
elton pull globalbioticinteractions/wis-ih-wirc

# generate review notes
elton review globalbioticinteractions/wis-ih-wirc\
 > review.tsv

# export indexed interaction records
elton interactions globalbioticinteractions/wis-ih-wirc\
 > interactions.tsv

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/wis-ih-wirc\
 | 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/wis-ih-wirc, is 4.48MiB in size and contains 2,484 interaction with 5 unique types of associations (e.g., adjacentTo) between 201 primary taxa (e.g., Cediopsylla simplex) and 481 associated taxa (e.g., Mearns Cottontail).

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
Acmaeodera pulchella hasHost Flowers of Achillea millefolium https://scan-bugs.org:443/portal/collections/individual/index.php?occid=57411456
Acmaeodera pulchella hasHost Flowers of Achillea millefolium https://scan-bugs.org:443/portal/collections/individual/index.php?occid=57411457
Acmaeodera pulchella hasHost Flowers of Achillea millefolium https://scan-bugs.org:443/portal/collections/individual/index.php?occid=57411458
Acmaeodera pulchella hasHost Flowers of Achillea millefolium https://scan-bugs.org:443/portal/collections/individual/index.php?occid=57411459
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
adjacentTo 2730
hasHost 328
interactsWith 326
eats 106
ectoparasiteOf 1
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Cediopsylla simplex 1850
Odontopsyllus multispinosus 244
Ceratopogonidae 215
Brachys aerosus 89
Reduviidae 78
Phymata americana 46
Muscidae 44
Sinea diadema 31
Phaenops fulvoguttata 27
Agrilus ruficollis 26
Pachyschelus laevigatus 26
Chrysobothris harrisi 26
Tabanidae 26
Culicidae 26
Agrilus anxius 25
Brachys ovatus 22
Pulicidae 22
Acmaeodera pulchella 19
Agrilus masculinus 18
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
Mearns Cottontail 1579
Mearns Cottontail Male 222
cacao 221
Mearns Cottontail Female 205
Mearns Cottontail female 47
Pinus strobus 43
flight intercept trap in mesic oak forest 30
sandy trail 29
dead Meloe campanicollis 29
Foliage of oak 22
Recently felled Betula papyrifera 22
: Mearns Cottontail 21
pupa 21
Foliage of Rubis 18
Mearns Cottontail nest 17
1-3 Inch diameter black maple branches 16
ex UV & merc. vap. lights 16
Quercus 15
foliage 12
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Cediopsylla simplex adjacentTo Mearns Cottontail 1472
Cediopsylla simplex adjacentTo Mearns Cottontail Female 168
Ceratopogonidae adjacentTo cacao 156
Cediopsylla simplex adjacentTo Mearns Cottontail Male 152
Odontopsyllus multispinosus adjacentTo Mearns Cottontail 104
Odontopsyllus multispinosus adjacentTo Mearns Cottontail Male 70
Odontopsyllus multispinosus adjacentTo Mearns Cottontail Female 37
Odontopsyllus multispinosus adjacentTo Mearns Cottontail female 33
Reduviidae adjacentTo cacao 30
Ceratopogonidae adjacentTo sandy trail 29
Ceratopogonidae adjacentTo dead Meloe campanicollis 29
Chrysobothris harrisi interactsWith Pinus strobus 24
Brachys aerosus interactsWith flight intercept trap in mesic oak forest 21
Agrilus ruficollis hasHost Foliage of Rubis 18
Cediopsylla simplex interactsWith Mearns Cottontail nest 17
Agrilus masculinus interactsWith 1-3 Inch diameter black maple branches 16
Reduviidae hasHost ex UV & merc. vap. lights 16
Brachys aerosus hasHost Foliage of oak 15
Culicidae adjacentTo cacao 15

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 Plantae Plantae Animalia->Plantae Animalia->Plantae Animalia->Plantae Animalia->Plantae
interactions Buprestidae Buprestidae Cannabaceae Cannabaceae Buprestidae->Cannabaceae Buprestidae->Cannabaceae Ebenaceae Ebenaceae Buprestidae->Ebenaceae Ericaceae Ericaceae Buprestidae->Ericaceae Fabaceae Fabaceae Buprestidae->Fabaceae Buprestidae->Fabaceae Fagaceae Fagaceae Buprestidae->Fagaceae Buprestidae->Fagaceae Oleaceae Oleaceae Buprestidae->Oleaceae Pinaceae Pinaceae Buprestidae->Pinaceae Buprestidae->Pinaceae Buprestidae->Pinaceae Sphingidae Sphingidae Buprestidae->Sphingidae Sapindaceae Sapindaceae Buprestidae->Sapindaceae Tingidae Tingidae Buprestidae->Tingidae Ceratophyllidae Ceratophyllidae Cricetidae Cricetidae Ceratophyllidae->Cricetidae Leporidae Leporidae Ceratophyllidae->Leporidae Mustelidae Mustelidae Ceratophyllidae->Mustelidae Ceratopogonidae Ceratopogonidae Ceratopogonidae->Sapindaceae Culicidae Culicidae Culicidae->Fabaceae Culicidae->Sapindaceae Ulmaceae Ulmaceae Culicidae->Ulmaceae Muscidae Muscidae Muscidae->Pinaceae Oestridae Oestridae Oestridae->Cricetidae Cardinalidae Cardinalidae Oestridae->Cardinalidae Pulicidae Pulicidae Muridae Muridae Pulicidae->Muridae Reduviidae Reduviidae Apiaceae Apiaceae Reduviidae->Apiaceae Asteraceae Asteraceae Reduviidae->Asteraceae Combretaceae Combretaceae Reduviidae->Combretaceae

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
Mydaea HAS_ACCEPTED_NAME col Mydaea
Tabanini HAS_ACCEPTED_NAME col Tabanini
inch diameter Hickory branches NONE col inch diameter Hickory branches
Monopsyllus vison HAS_ACCEPTED_NAME col Monopsyllus vison
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 352
col family 11
col genus 49
col kingdom 2
col species 185
col subgenus 2
col subspecies 1
col tribe 1
col variety 1
discoverlife NA 601
gbif NA 341
gbif family 11
gbif genus 58
gbif kingdom 2
gbif species 191
gbif subspecies 1
gbif variety 3
itis NA 372
itis family 11
itis genus 44
itis kingdom 2
itis species 169
itis tribe 1
itis variety 2
mdd NA 600
ncbi NA 400
ncbi family 11
ncbi genus 45
ncbi kingdom 1
ncbi species 143
ncbi subgenus 5
ncbi tribe 1
pbdb NA 539
pbdb family 9
pbdb genus 35
pbdb kingdom 2
pbdb species 14
pbdb tribe 1
pbdb unranked clade 1
tpt NA 563
tpt family 2
tpt genus 4
tpt species 31
wfo NA 549
wfo genus 23
wfo phylum 1
wfo species 27
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 255
col NONE 422
col SYNONYM_OF 53
discoverlife NONE 682
gbif HAS_ACCEPTED_NAME 307
gbif NONE 411
gbif SYNONYM_OF 75
itis HAS_ACCEPTED_NAME 235
itis NONE 442
itis SYNONYM_OF 7
mdd NONE 675
mdd HAS_ACCEPTED_NAME 5
ncbi SAME_AS 208
ncbi NONE 472
ncbi SYNONYM_OF 5
ncbi COMMON_NAME_OF 5
pbdb NONE 612
pbdb HAS_ACCEPTED_NAME 67
pbdb SYNONYM_OF 7
tpt NONE 643
tpt HAS_ACCEPTED_NAME 35
tpt SYNONYM_OF 12
wfo NONE 622
wfo HAS_ACCEPTED_NAME 55
wfo SYNONYM_OF 9
wfo HAS_UNCHECKED_NAME 2
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
2024-04-22T08:49:17Z note found unsupported interaction type with name: [Taken from flowers of]
2024-04-22T08:49:17Z note found unsupported interaction type with name: [Taken from flowers of]
2024-04-22T08:49:17Z note found unsupported interaction type with name: [Taken from flowers of]
2024-04-22T08:49:17Z note found unsupported interaction type with name: [Coll.]

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: [coll.] 229
found unsupported interaction type with name: [coll. from] 115
found unsupported interaction type with name: [5] 68
found unsupported interaction type with name: [Elev.] 49

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.