A Review of Biotic Interactions and Taxon Names Found in globalbioticinteractions/usnmentflea

by Nomer and Elton, two naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

https://github.com/globalbioticinteractions/usnmentflea/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/usnmentflea, is 6.29MiB in size and contains 2,786 interaction with 1 unique type of association (e.g., parasiteOf) between 25 primary taxa (e.g., Echidnophaga gallinacea) and 134 associated taxa (e.g., Rattus norvegicus_Berkenhout 1769). 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:

Data were obtained from specimens belonging to the United States National Museum of Natural History (USNM), Smithsonian Institution, Washington DC and digitized by the Walter Reed Biosystematics Unit (WRBU). https://github.com/globalbioticinteractions/usnmentflea/archive/ce5cb1ed2bbc13ee10062b6f75a158fd465ce9bb.zip 2024-04-13T06:40:27.230Z 0e0edfcc10e00d61725f0c4761322649dd780c0fb5ca0af5f5d2a4efb43fadec

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/usnmentflea 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. 6.29MiB) under review 
elton pull globalbioticinteractions/usnmentflea

# generate review notes
elton review globalbioticinteractions/usnmentflea\
 > review.tsv

# export indexed interaction records
elton interactions globalbioticinteractions/usnmentflea\
 > interactions.tsv

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/usnmentflea\
 | 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/usnmentflea, is 6.29MiB in size and contains 2,786 interaction with 1 unique type of association (e.g., parasiteOf) between 25 primary taxa (e.g., Echidnophaga gallinacea) and 134 associated taxa (e.g., Rattus norvegicus_Berkenhout 1769).

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
Echidnophaga gallinacea parasiteOf Thallomys paedulcus_Sundevall 1846 USNM_Flea_and_Associated_Host_Records.tsv
Ctenocephalides felis strongylus parasiteOf Arvicanthis niloticus_É. Geoffroy 1803 USNM_Flea_and_Associated_Host_Records.tsv
Ctenocephalides felis strongylus parasiteOf Arvicanthis niloticus_É. Geoffroy 1803 USNM_Flea_and_Associated_Host_Records.tsv
Ctenocephalides felis strongylus parasiteOf Arvicanthis niloticus_É. Geoffroy 1803 USNM_Flea_and_Associated_Host_Records.tsv
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
parasiteOf 2786
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Echidnophaga gallinacea 896
Xenopsylla cheopis 534
Ctenocephalides felis 377
Ctenocephalides felis strongylus 169
Ctenocephalides canis 168
Oropsylla montana 134
Polygenis gwyni 122
Oropsylla hirsuta 96
Oropsylla tuberculata 83
Megabothris abantis 51
Oropsylla tuberculata cynomuris 46
Oropsylla tuberculata tuberculata 31
Anomiopsyllus nudatus 26
Oropsylla bruneri 16
Thrassis bacchi bacchi 8
Thrassis bacchi gladiolis 7
Thrassis bacchi 6
Oropsylla rupestris 4
Ctenocephalides felis felis 4
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
Rattus norvegicus_Berkenhout 1769 419
Canis lupus familiaris_Linnaeus 1758 241
Arvicanthis niloticus_É. Geoffroy 1803 195
Genetta genetta_Linnaeus 1758 190
Cynomys ludovicianus Ord 1815 133
Sigmodon hispidus_Say and Ord 1825 113
Lepus capensis_Linnaeus 1758 112
Spermophilus beecheyi_Richardson 1829 111
Suricata suricatta_Schreber 1776 111
Spermophilus columbianus_Ord 1815 109
Canis mesomelas_Schreber 1775 94
Atelerix albiventris_Wagner 1841 93
Felis catus_Linnaeus 1758 68
Vulpes chama_A. Smith 1833 53
Homo sapiens_Linnaeus 1758 40
Cerdocyon thous_Linnaeus 1766 36
Felis nigripes_Burchell 1824 35
Genetta thierryi_Matschie 1902 34
Canis latrans_Say 1823 33
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Xenopsylla cheopis parasiteOf Rattus norvegicus_Berkenhout 1769 259
Xenopsylla cheopis parasiteOf Arvicanthis niloticus_É. Geoffroy 1803 182
Echidnophaga gallinacea parasiteOf Genetta genetta_Linnaeus 1758 175
Ctenocephalides felis parasiteOf Canis lupus familiaris_Linnaeus 1758 132
Echidnophaga gallinacea parasiteOf Rattus norvegicus_Berkenhout 1769 131
Polygenis gwyni parasiteOf Sigmodon hispidus_Say and Ord 1825 111
Echidnophaga gallinacea parasiteOf Suricata suricatta_Schreber 1776 110
Ctenocephalides canis parasiteOf Canis lupus familiaris_Linnaeus 1758 98
Echidnophaga gallinacea parasiteOf Canis mesomelas_Schreber 1775 94
Oropsylla montana parasiteOf Spermophilus beecheyi_Richardson 1829 94
Echidnophaga gallinacea parasiteOf Lepus capensis_Linnaeus 1758 88
Oropsylla hirsuta parasiteOf Cynomys ludovicianus Ord 1815 86
Ctenocephalides felis strongylus parasiteOf Atelerix albiventris_Wagner 1841 85
Oropsylla tuberculata parasiteOf Spermophilus columbianus_Ord 1815 74
Ctenocephalides felis parasiteOf Felis catus_Linnaeus 1758 56
Echidnophaga gallinacea parasiteOf Vulpes chama_A. Smith 1833 53
Oropsylla tuberculata cynomuris parasiteOf Cynomys ludovicianus Ord 1815 41
Ctenocephalides felis parasiteOf Cerdocyon thous_Linnaeus 1766 36
Echidnophaga gallinacea parasiteOf Felis nigripes_Burchell 1824 35

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 Pulicidae Pulicidae Accipitridae Accipitridae Pulicidae->Accipitridae Anatidae Anatidae Pulicidae->Anatidae Strigidae Strigidae Pulicidae->Strigidae Timaliidae Timaliidae Pulicidae->Timaliidae Troglodytidae Troglodytidae Pulicidae->Troglodytidae Viverridae Viverridae Pulicidae->Viverridae Rhopalopsyllidae Rhopalopsyllidae Cardinalidae Cardinalidae Rhopalopsyllidae->Cardinalidae

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
Accipiter striatus HAS_ACCEPTED_NAME col Accipiter striatus
Acomys cineraceus HAS_ACCEPTED_NAME col Acomys cineraceus
Allactaga tetradactyla HAS_ACCEPTED_NAME col Allactaga tetradactyla
Alouatta macconnelli HAS_ACCEPTED_NAME col Alouatta macconnelli
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 5
col family 3
col genus 2
col order 1
col species 144
col subspecies 5
discoverlife NA 159
gbif family 3
gbif genus 2
gbif order 1
gbif species 144
gbif subspecies 10
itis NA 21
itis family 3
itis genus 1
itis order 1
itis species 132
itis subspecies 2
mdd NA 159
ncbi NA 9
ncbi family 3
ncbi genus 1
ncbi order 1
ncbi species 141
ncbi subspecies 4
pbdb NA 62
pbdb family 3
pbdb order 1
pbdb species 93
tpt NA 25
tpt family 1
tpt genus 1
tpt species 132
wfo NA 159
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 147
col SYNONYM_OF 9
col NONE 5
discoverlife NONE 159
gbif HAS_ACCEPTED_NAME 154
gbif SYNONYM_OF 9
itis HAS_ACCEPTED_NAME 132
itis NONE 21
itis SYNONYM_OF 10
mdd NONE 49
mdd HAS_ACCEPTED_NAME 110
ncbi SAME_AS 140
ncbi SYNONYM_OF 10
ncbi NONE 9
pbdb HAS_ACCEPTED_NAME 90
pbdb NONE 62
pbdb SYNONYM_OF 7
tpt HAS_ACCEPTED_NAME 138
tpt NONE 25
tpt SYNONYM_OF 2
wfo NONE 159
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
2024-04-17T06:10:49Z note found [136] column definitions, but only [119] values: assuming undefined values are empty.
2024-04-17T06:10:49Z note found [136] column definitions, but only [18] values: assuming undefined values are empty.
2024-04-17T06:10:49Z note source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder
2024-04-17T06:10:49Z 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
found [136] column definitions, but only [119] values: assuming undefined values are empty. 3
found [136] column definitions, but only [18] values: assuming undefined values are empty. 3
source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder 3
target taxon name missing 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 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.