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

by Nomer and Elton, two naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

https://github.com/globalbioticinteractions/dmns-para/issues

2024-04-29

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/dmns-para, is 69.5MiB in size and contains 1,647 interaction with 2 unique types of associations (e.g., parasiteOf) between 64 primary taxa (e.g., Phthiraptera) and 464 associated taxa (e.g., Tamias speciosus). 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:

DMNS Parasite collection (Arctos) http://ipt.vertnet.org:8080/ipt/archive.do?r=dmn 2024-04-19T23:39:15.049Z ac79222e8559b9618b5667f85a92fce1f47035610a1504cde6d33bf22b9900a2

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/dmns-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 0.5.8
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. 69.5MiB) under review 
elton pull globalbioticinteractions/dmns-para

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

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

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/dmns-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/dmns-para, is 69.5MiB in size and contains 1,647 interaction with 2 unique types of associations (e.g., parasiteOf) between 64 primary taxa (e.g., Phthiraptera) and 464 associated taxa (e.g., Tamias speciosus).

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
Eumolpianus eumolpi parasiteOf Tamias minimus http://arctos.database.museum/guid/DMNS:Para:572
Eumolpianus eumolpi parasiteOf Tamias quadrivittatus http://arctos.database.museum/guid/DMNS:Para:684
Oxyurida parasiteOf Tamias quadrivittatus http://arctos.database.museum/guid/DMNS:Para:2210
Oxyurida hasHost Tamias quadrivittatus http://arctos.database.museum/guid/DMNS:Para:2210
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
parasiteOf 1011
hasHost 636
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Phthiraptera 303
Eumolpianus eumolpi 270
Nematoda 247
Cestoda 167
Oestridae 84
Rauschtineria eutamii 59
Heteroxynema cucullatum 54
Hoplopleura arboricola 51
Ceratophyllus ciliatus 50
Eumolpianus eutamiadis 44
Siphonaptera 28
Neohaematopinus pacificus 26
Acariformes 22
Aetheca wagneri 21
Ixodidae 20
Acanthocephala 18
Anoplura 16
Acari 15
Oropsylla idahoensis 12
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
Tamias speciosus 162
Tamias minimus 121
Tamias quadrivittatus 100
Bubo virginianus 70
Buteo jamaicensis 51
Tamias minimus operarius 45
Tamias umbrinus 28
Tamias alpinus 26
Tamias rufus 25
Colaptes auratus 22
Tamias dorsalis dorsalis 22
Turdus migratorius 21
Sylvilagus audubonii 20
Accipiter striatus 16
Tamias minimus silvaticus 15
Branta canadensis 13
Peromyscus maniculatus 12
Peromyscus maniculatus rufinus 12
Tamias cinereicollis 12
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Eumolpianus eumolpi parasiteOf Tamias minimus 76
Eumolpianus eumolpi parasiteOf Tamias quadrivittatus 54
Ceratophyllus ciliatus hasHost Tamias speciosus 48
Eumolpianus eutamiadis hasHost Tamias speciosus 41
Eumolpianus eumolpi hasHost Tamias speciosus 37
Phthiraptera parasiteOf Bubo virginianus 28
Phthiraptera parasiteOf Buteo jamaicensis 23
Cestoda parasiteOf Bubo virginianus 22
Eumolpianus eumolpi parasiteOf Tamias minimus operarius 19
Nematoda parasiteOf Buteo jamaicensis 16
Nematoda parasiteOf Accipiter striatus 15
Eumolpianus eumolpi hasHost Tamias alpinus 14
Phthiraptera parasiteOf Branta canadensis 11
Eumolpianus eumolpi parasiteOf Tamias dorsalis dorsalis 11
Rauschtineria eutamii parasiteOf Tamias minimus 10
Nematoda parasiteOf Colaptes auratus 10
Hoplopleura arboricola parasiteOf Tamias quadrivittatus 10
Cestoda parasiteOf Sorex cinereus 10
Rauschtineria eutamii parasiteOf Tamias umbrinus 9

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 Argasidae Argasidae Cervidae Cervidae Argasidae->Cervidae Ceratophyllidae Ceratophyllidae Sciuridae Sciuridae Ceratophyllidae->Sciuridae Ceratophyllidae->Sciuridae Cricetidae Cricetidae Ceratophyllidae->Cricetidae Mustelidae Mustelidae Ceratophyllidae->Mustelidae Ctenophthalmidae Ctenophthalmidae Ctenophthalmidae->Sciuridae Ctenophthalmidae->Sciuridae Heteroxynematidae Heteroxynematidae Heteroxynematidae->Sciuridae Heteroxynematidae->Sciuridae Hippoboscidae Hippoboscidae Hippoboscidae->Cervidae Hippoboscidae->Cervidae Accipitridae Accipitridae Hippoboscidae->Accipitridae Passerellidae Passerellidae Hippoboscidae->Passerellidae Strigidae Strigidae Hippoboscidae->Strigidae Hoplopleuridae Hoplopleuridae Hoplopleuridae->Sciuridae Hoplopleuridae->Sciuridae Hoplopleuridae->Cricetidae Hystrichopsyllidae Hystrichopsyllidae Hystrichopsyllidae->Sciuridae Ixodidae Ixodidae Ixodidae->Sciuridae Ixodidae->Sciuridae Ixodidae->Cricetidae Ixodidae->Cricetidae Geomyidae Geomyidae Ixodidae->Geomyidae Ixodidae->Geomyidae Leporidae Leporidae Ixodidae->Leporidae Ixodidae->Leporidae Canidae Canidae Ixodidae->Canidae Phalacrocoracidae Phalacrocoracidae Ixodidae->Phalacrocoracidae Procyonidae Procyonidae Ixodidae->Procyonidae Soricidae Soricidae Ixodidae->Soricidae Leptopsyllidae Leptopsyllidae Leptopsyllidae->Cricetidae Ochotonidae Ochotonidae Leptopsyllidae->Ochotonidae Macronyssidae Macronyssidae Hirundinidae Hirundinidae Macronyssidae->Hirundinidae Oestridae Oestridae Oestridae->Sciuridae Oestridae->Sciuridae Oestridae->Cricetidae Oestridae->Cricetidae Oestridae->Leporidae Fringillidae Fringillidae Oestridae->Fringillidae Oxyuridae Oxyuridae Oxyuridae->Sciuridae Oxyuridae->Sciuridae Oxyuridae->Strigidae Plagiorhynchidae Plagiorhynchidae Turdidae Turdidae Plagiorhynchidae->Turdidae Polyplacidae Polyplacidae Polyplacidae->Sciuridae Polyplacidae->Sciuridae Polyplacidae->Cricetidae Pulicidae Pulicidae Pulicidae->Canidae Felidae Felidae Pulicidae->Felidae Trichodectidae Trichodectidae Trichodectidae->Geomyidae Trichodectidae->Geomyidae

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
Acanthocephala HAS_ACCEPTED_NAME col Acanthocephala
Acanthocephala SYNONYM_OF col Parodia
Acari NONE col Acari
Acariformes HAS_ACCEPTED_NAME col Acariformes
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 56
col class 2
col family 9
col genus 14
col infraorder 1
col nanorder 1
col order 1
col parvorder 1
col phylum 3
col species 173
col subgenus 3
col suborder 1
col subspecies 28
col superorder 1
discoverlife NA 290
gbif NA 52
gbif class 2
gbif family 9
gbif genus 18
gbif order 1
gbif phylum 3
gbif species 177
gbif subspecies 29
itis NA 77
itis class 2
itis family 9
itis genus 14
itis order 3
itis phylum 3
itis species 150
itis subclass 1
itis suborder 3
itis subspecies 28
itis superorder 1
mdd NA 289
ncbi NA 74
ncbi class 2
ncbi family 9
ncbi genus 14
ncbi infraorder 2
ncbi order 2
ncbi phylum 3
ncbi species 168
ncbi subclass 1
ncbi suborder 2
ncbi subspecies 13
ncbi superorder 1
pbdb NA 137
pbdb class 2
pbdb family 4
pbdb genus 7
pbdb infraorder 1
pbdb order 4
pbdb phylum 2
pbdb species 129
pbdb suborder 1
pbdb subspecies 1
pbdb superorder 1
pbdb unranked clade 2
tpt NA 120
tpt family 2
tpt genus 7
tpt species 160
wfo NA 288
wfo genus 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 HAS_ACCEPTED_NAME 295
col SYNONYM_OF 14
col NONE 58
discoverlife NONE 581
gbif HAS_ACCEPTED_NAME 299
gbif SYNONYM_OF 23
gbif NONE 54
itis HAS_ACCEPTED_NAME 270
itis SYNONYM_OF 15
itis NONE 79
mdd NONE 271
mdd HAS_ACCEPTED_NAME 87
ncbi NONE 304
ncbi SAME_AS 272
ncbi SYNONYM_OF 6
pbdb HAS_ACCEPTED_NAME 197
pbdb SYNONYM_OF 13
pbdb NONE 152
tpt NONE 143
tpt HAS_ACCEPTED_NAME 226
tpt SYNONYM_OF 17
wfo SYNONYM_OF 1
wfo NONE 357
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
2024-04-29T01:21:03Z note found unresolved reference [11125]
2024-04-29T01:21:03Z note found unresolved reference [11174]
2024-04-29T01:21:03Z note found unresolved reference [11433]
2024-04-29T01:21:03Z note found unresolved reference [11498]

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

Most frequently occurring review notes, if any.
reviewComment count
found unresolved reference [11125] 1
found unresolved reference [11174] 1
found unresolved reference [11433] 1
found unresolved reference [11498] 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 (2024-04-29) 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.