A Review of Biotic Interactions and Taxon Names Found in globalbioticinteractions/usnm-ixodes

by Nomer and Elton, two naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

https://github.com/globalbioticinteractions/usnm-ixodes/issues

2024-05-18

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/usnm-ixodes, is 8.03MiB in size and contains 10,199 interaction with 1 unique type of association (e.g., hasHost) between 394 primary taxa (e.g., IXODES SP.) and 2,334 associated taxon (e.g., DRAG). 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:

US National Museum of Natural History Ixodes Records https://github.com/globalbioticinteractions/usnm-ixodes/archive/2c2454bece9307bedc01a5dee5a09e459b879641.zip 2024-05-11T06:52:58.768Z be07d893994692bb9a464c2a290efcc1db75ed2ebd8327a9df90f53210c568b3

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/usnm-ixodes 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 0.5.9
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. 8.03MiB) under review 
elton pull globalbioticinteractions/usnm-ixodes

# generate review notes
elton review globalbioticinteractions/usnm-ixodes\
 > review.tsv

# export indexed interaction records
elton interactions globalbioticinteractions/usnm-ixodes\
 > interactions.tsv

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/usnm-ixodes\
 | 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/usnm-ixodes, is 8.03MiB in size and contains 10,199 interaction with 1 unique type of association (e.g., hasHost) between 394 primary taxa (e.g., IXODES SP.) and 2,334 associated taxon (e.g., DRAG).

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
IXODES (ENDOPALPIGER) hasHost PARAMYTHIA MONTIUM Copy_of_Ixodes_June29_complete.tsv
IXODES (ENDOPALPIGER) SP. hasHost CRATEROSCELIS ROBUSTA Copy_of_Ixodes_June29_complete.tsv
IXODES (ENDOPALPIGER) SP. hasHost PENEOTHELLO SIGILLATUS Copy_of_Ixodes_June29_complete.tsv
IXODES (IXODES) NEAR LORICATUS hasHost DIDELPHIS MARSUPIALIS Copy_of_Ixodes_June29_complete.tsv
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
hasHost 15845
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
IXODES SP. 3333
IXODES PACIFICUS 952
IXODES SCAPULARIS 943
IXODES RICINUS 810
IXODES ANGUSTUS 779
IXODES GRANULATUS 776
IXODES SCULPTUS 665
IXODES OVATUS 561
IXODES ARBORICOLA 408
IXODES COOKEI 330
IXODES ACUTITARSUS 319
IXODES URIAE 251
IXODES SPINIPALPIS 248
IXODES LORICATUS 211
IXODES KINGI 202
IXODES LUCIAE 197
IXODES DENTATUS 192
IXODES SORICIS 160
IXODES TEXANUS 155
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
DRAG 611
HOMO SAPIENS 490
LUSCINIA LUSCINIA 428
SPERMOPHILUS RICHARDSONI 403
PASSER DOMESTICUS 272
PEROMYSCUS MANICULATUS 263
DOG 252
STENOMYS NIOBE 245
ODOCOILEUS VIRGINIANUS 212
CATTLE 196
SYLVILAGUS SP. 183
GOPHER 181
MICROTUS CANICAUDUS 172
PROCYON LOTOR 151
DIDELPHIS MARSUPIALIS 137
PUMA CONCOLOR FLORIDANUS 130
RATTUS MUELLERI 122
SPERMOPHILUS BEECHEYI 120
SQUIRREL GROUND 116
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
IXODES PACIFICUS hasHost DRAG 539
IXODES RICINUS hasHost LUSCINIA LUSCINIA 412
IXODES ARBORICOLA hasHost PASSER DOMESTICUS 272
IXODES SCULPTUS hasHost SPERMOPHILUS RICHARDSONI 248
IXODES SP. hasHost STENOMYS NIOBE 230
IXODES SCAPULARIS hasHost ODOCOILEUS VIRGINIANUS 185
IXODES SP. hasHost GOPHER 156
IXODES ANGUSTUS hasHost MICROTUS CANICAUDUS 150
IXODES ACUTITARSUS hasHost HOMO SAPIENS 144
IXODES DENTATUS hasHost SYLVILAGUS SP. 120
IXODES GRANULATUS hasHost RATTUS MUELLERI 114
IXODES ANGUSTUS hasHost PEROMYSCUS MANICULATUS 112
IXODES SP. hasHost SPERMOPHILUS RICHARDSONI 106
IXODES SP. hasHost MELOMYS PLATYOPS 104
IXODES ARBORICOLA hasHost PASSER DOMESTICUS NILOTICUS 103
IXODES SCAPULARIS hasHost HOMO SAPIENS 88
IXODES TEXANUS hasHost PROCYON LOTOR 83
IXODES SCULPTUS hasHost SPERMOPHILUS BEECHEYI 82
IXODES SCAPULARIS hasHost PUMA CONCOLOR FLORIDANUS 78

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
interactions Ixodidae Ixodidae Canidae Canidae Ixodidae->Canidae Cheirogaleidae Cheirogaleidae Ixodidae->Cheirogaleidae Cricetidae Cricetidae Ixodidae->Cricetidae Felidae Felidae Ixodidae->Felidae Leporidae Leporidae Ixodidae->Leporidae Muridae Muridae Ixodidae->Muridae Mustelidae Mustelidae Ixodidae->Mustelidae Phalangeridae Phalangeridae Ixodidae->Phalangeridae Phrynosomatidae Phrynosomatidae Ixodidae->Phrynosomatidae Scincidae Scincidae Ixodidae->Scincidae Soricidae Soricidae Ixodidae->Soricidae

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
Abrocoma bennetti NONE col Abrocoma bennetti
Abrothrix longipilis HAS_ACCEPTED_NAME col Abrothrix longipilis
Acanthiza ewingii HAS_ACCEPTED_NAME col Acanthiza ewingii
Acanthiza pusilla HAS_ACCEPTED_NAME col Acanthiza pusilla
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 1161
col class 1
col family 3
col genus 178
col kingdom 1
col species 1119
col subfamily 1
col subgenus 25
col subspecies 156
discoverlife NA 2621
gbif NA 1055
gbif class 1
gbif family 3
gbif form 1
gbif genus 198
gbif kingdom 1
gbif species 1202
gbif subspecies 162
itis NA 1172
itis class 1
itis family 3
itis genus 175
itis kingdom 1
itis order 1
itis species 1108
itis subfamily 1
itis subgenus 2
itis subspecies 157
mdd NA 2620
ncbi NA 1369
ncbi class 1
ncbi family 3
ncbi genus 171
ncbi kingdom 1
ncbi species 996
ncbi subfamily 1
ncbi subgenus 2
ncbi subspecies 79
pbdb NA 1888
pbdb class 1
pbdb family 3
pbdb genus 165
pbdb kingdom 1
pbdb order 1
pbdb species 555
pbdb subfamily 1
pbdb suborder 1
pbdb subspecies 5
pbdb unranked clade 1
tpt NA 1522
tpt family 3
tpt genus 157
tpt species 938
wfo NA 2616
wfo genus 3
wfo phylum 1
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 1222
col HAS_ACCEPTED_NAME 1721
col SYNONYM_OF 718
discoverlife NONE 3110
gbif NONE 1110
gbif HAS_ACCEPTED_NAME 1756
gbif SYNONYM_OF 834
itis NONE 1233
itis HAS_ACCEPTED_NAME 1648
itis SYNONYM_OF 244
mdd NONE 2348
mdd HAS_ACCEPTED_NAME 757
ncbi NONE 1492
ncbi SAME_AS 1412
ncbi SYNONYM_OF 209
ncbi COMMON_NAME_OF 1
pbdb NONE 2147
pbdb HAS_ACCEPTED_NAME 889
pbdb SYNONYM_OF 80
tpt NONE 1649
tpt HAS_ACCEPTED_NAME 1478
wfo NONE 3100
wfo SYNONYM_OF 1
wfo HAS_ACCEPTED_NAME 3
wfo HAS_UNCHECKED_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
2024-05-18T02:38:18Z note target taxon name missing
2024-05-18T02:38:18Z note target taxon name missing
2024-05-18T02:38:18Z note target taxon name missing
2024-05-18T02:38:18Z note target taxon name missing

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

Most frequently occurring review notes, if any.
reviewComment count
target taxon name missing 846
date [2043-01-01T00:00:00Z] is in the future 2
failed to parse value [196722–] from column [Host1::FMTDTE2] into column [http://rs.tdwg.org/dwc/terms/eventDate] with datatype: {“base”:“date”,“format”:“YYYYMMdd”,“id”:“string”} 1
failed to parse value [19690631] from column [Host1::FMTDTE2] into column [http://rs.tdwg.org/dwc/terms/eventDate] with datatype: {“base”:“date”,“format”:“YYYYMMdd”,“id”:“string”} 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 ^[At time of writing (2024-05-18) 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.