A Review of Biotic Interactions and Taxon Names Found in globalbioticinteractions/uwsp-para

by Nomer and Elton, two naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

https://github.com/globalbioticinteractions/uwsp-para/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/uwsp-para, is 823KiB in size and contains 6,423 interaction with 2 unique types of associations (e.g., interactsWith) between 350 primary taxa (e.g., Acari) and 300 associated taxa (e.g., Great Horned Owl). 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 Wisconsin Stevens Point, Stephen J. Taft Parasitological Collection https://github.com/globalbioticinteractions/uwsp-para/archive/f9d0d52cd671731c7f002325e84187979bca4a5b.zip 2024-04-13T06:41:50.776Z 77269a76cc9cd288d5d4dfc2cc97be0bc27d180f9c67a6700dd4b864ef50cca3

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/uwsp-para 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.  823KiB) under review 
elton pull globalbioticinteractions/uwsp-para

# generate review notes
elton review globalbioticinteractions/uwsp-para\
 > review.tsv

# export indexed interaction records
elton interactions globalbioticinteractions/uwsp-para\
 > interactions.tsv

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/uwsp-para\
 | 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/uwsp-para, is 823KiB in size and contains 6,423 interaction with 2 unique types of associations (e.g., interactsWith) between 350 primary taxa (e.g., Acari) and 300 associated taxa (e.g., Great Horned Owl).

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
Acari interactsWith blackbird https://scan-bugs.org:443/portal/collections/individual/index.php?occid=41979394
Acari interactsWith blackbird https://scan-bugs.org:443/portal/collections/individual/index.php?occid=41979395
Acari interactsWith blackbird https://scan-bugs.org:443/portal/collections/individual/index.php?occid=41979621
Acari interactsWith blackbird https://scan-bugs.org:443/portal/collections/individual/index.php?occid=41981993
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
interactsWith 5420
hasHost 1004
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Acari 1630
Phthiraptera 1199
Mite 532
Siphonaptera 238
Strigiphilus ceblebrachys 221
Strigiphilus 209
Oeciacus vicarius 181
Philopteridae 171
Menoponidae 142
Piagetiella peralis 130
Kurodaia magna 127
Quadraceps falcigerus 97
Q. falcigerus 93
Carduiceps zonarius 90
Dermanyssus 78
Amyrsida megalosoma 70
Digeeriella 69
Ceratophyllus 54
Otodectes cynotis 54
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
Great Horned Owl 479
snowy owl 224
great horned owl 217
lesser yellowlegs 188
muskrat 180
Osprey 180
Saw Whet Owl 168
Red Tail Hawk 154
A. Coot 133
starling 124
Brown Pelican 118
pectoral sandpiper 116
prairie chicken 113
swan 108
tree swallow 103
Cowbird 100
Great horned owl 97
Barn Swallow 95
Barn swallow 91
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Acari interactsWith Great Horned Owl 231
Strigiphilus ceblebrachys interactsWith snowy owl 221
Acari interactsWith muskrat 180
Kurodaia magna interactsWith Great Horned Owl 106
Mite hasHost Brown Pelican 100
Acari hasHost Great Horned Owl 100
Acari interactsWith Osprey 100
Acari interactsWith Cowbird 97
Acari interactsWith great horned owl 95
Oeciacus vicarius interactsWith Barn Swallow 94
Q. falcigerus interactsWith lesser yellowlegs 93
Strigiphilus hasHost Great horned owl 93
Oeciacus vicarius interactsWith Barn swallow 86
Carduiceps zonarius interactsWith pectoral sandpiper 85
Phthiraptera interactsWith Red Tail Hawk 84
Acari interactsWith saw whet owl 83
Strigiphilus interactsWith great horned owl 79
Mite hasHost Female Cooper’s Hawk 79
Quadraceps falcigerus interactsWith lesser yellowlegs 77

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
interactions Dermanyssidae Dermanyssidae Turdidae Turdidae Dermanyssidae->Turdidae Leptopsyllidae Leptopsyllidae Cricetidae Cricetidae Leptopsyllidae->Cricetidae Leptopsyllidae->Cricetidae Polyplacidae Polyplacidae Polyplacidae->Cricetidae Pulicidae Pulicidae Leporidae Leporidae Pulicidae->Leporidae Trichodectidae Trichodectidae Canidae Canidae Trichodectidae->Canidae

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
Kurodaia fulvofasciata HAS_ACCEPTED_NAME col Kurodaia fulvofasciata
Otodectes cynotis NONE col Otodectes cynotis
Rhynonirmus parsonsae HAS_ACCEPTED_NAME col Rhynonirmus parsonsae
Oeciacus SYNONYM_OF col Cimex
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 494
col class 1
col family 20
col genus 32
col nanorder 1
col order 4
col parvorder 1
col phylum 1
col species 46
col subgenus 4
col suborder 1
col subspecies 1
discoverlife NA 598
gbif NA 487
gbif class 1
gbif family 21
gbif genus 39
gbif order 4
gbif phylum 1
gbif species 50
itis NA 532
itis class 1
itis family 20
itis genus 16
itis order 5
itis phylum 1
itis species 19
itis subclass 2
itis suborder 3
mdd NA 598
ncbi NA 479
ncbi class 1
ncbi family 20
ncbi genus 28
ncbi order 5
ncbi phylum 1
ncbi species 60
ncbi subclass 2
ncbi subgenus 1
ncbi suborder 2
pbdb NA 564
pbdb class 3
pbdb family 8
pbdb genus 8
pbdb order 4
pbdb phylum 1
pbdb species 7
pbdb suborder 3
pbdb unranked clade 1
tpt NA 516
tpt family 6
tpt genus 13
tpt species 63
wfo NA 596
wfo genus 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 120
col NONE 543
col SYNONYM_OF 11
discoverlife NONE 663
gbif HAS_ACCEPTED_NAME 121
gbif SYNONYM_OF 21
gbif NONE 546
itis NONE 582
itis SYNONYM_OF 22
itis HAS_ACCEPTED_NAME 66
mdd NONE 657
mdd HAS_ACCEPTED_NAME 6
ncbi SAME_AS 110
ncbi NONE 527
ncbi SYNONYM_OF 2
ncbi COMMON_NAME_OF 26
pbdb NONE 615
pbdb HAS_ACCEPTED_NAME 54
pbdb SYNONYM_OF 14
tpt HAS_ACCEPTED_NAME 82
tpt SYNONYM_OF 24
tpt NONE 574
wfo NONE 661
wfo SYNONYM_OF 1
wfo HAS_ACCEPTED_NAME 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
2024-04-17T06:19:47Z note source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder
2024-04-17T06:19:48Z note source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder
2024-04-17T06:19:48Z note source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder
2024-04-17T06:19:48Z 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: [{associates with] 244
source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder 231
found unsupported interaction type with name: [Broad-Winged Hawk] 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.