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

by Nomer and Elton, two naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

https://github.com/globalbioticinteractions/ansp-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/ansp-para, is 75.6KiB in size and contains 446 interactions with 1 unique type of association (e.g., interactsWith) between 102 primary taxa (e.g., Myrsidea) and 123 associated taxa (e.g., Sclerurus guatemalensis). 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:

Academy of Natural Sciences Entomology Collection for the Parasite Tracker Project https://github.com/globalbioticinteractions/ansp-para/archive/498ed9d6faa35ffebbdc570e939d9f902189d0ee.zip 2024-04-19T22:44:31.007Z 50662a4034654cad6eef2b8cf8b0de4dbfc97dec9e27a185a71504261f442ed0

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/ansp-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. 75.6KiB) under review 
elton pull globalbioticinteractions/ansp-para

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

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

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/ansp-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/ansp-para, is 75.6KiB in size and contains 446 interactions with 1 unique type of association (e.g., interactsWith) between 102 primary taxa (e.g., Myrsidea) and 123 associated taxa (e.g., Sclerurus guatemalensis).

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
Lipeurus baculus interactsWith Columba livia https://scan-bugs.org:443/portal/collections/individual/index.php?occid=64826523
Lipeurus heterographus interactsWith Gallus gallus https://scan-bugs.org:443/portal/collections/individual/index.php?occid=64826524
Lipeurus squalidus interactsWith Anas carolinensis https://scan-bugs.org:443/portal/collections/individual/index.php?occid=64826525
Lipeurus polytrapezius interactsWith Meleagris https://scan-bugs.org:443/portal/collections/individual/index.php?occid=64826526
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
interactsWith 446
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Myrsidea 111
Philopterus 48
Ricinus 39
Degeeriella 35
Esthiopterum 30
Colpocephalum 23
Physconelloides 19
Columbicola 9
Myrsidea mirabilis 9
Myrsidea thoracica fusca 8
Rallicola 7
Incidifrons 3
Goniodes 3
Philopteridae 3
Myrsidea stenodesmum 3
Lipeurus polytrapezius 2
Degeeriella amblys 2
Trinoton ludirium 2
Trinoton querquedulae 2
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
Sclerurus guatemalensis 27
Ramphocelus passerinii 22
Pionus senilis 17
Phlogothraupis sanguinolenta 16
Gymnostenops montezuma 15
Megarhynchus pitangua mexicanus 14
Manacus candei 14
Saltator magnoides medianus 11
Claravis pretiosa 10
Oenoenas nigrorostris 10
Ramphocelus passerini 10
Xiphorhynchus nanus costaricensis 9
Streptoprocne zonaris 8
Zarhynchus wagleri wagleri 8
Piranga rubra rubra 8
Crypturellus atrocapillus 8
Myiozetetes granadensis 7
Galbula melanogenia 7
Creciscus cineireceps 7
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Esthiopterum interactsWith Sclerurus guatemalensis 27
Degeeriella interactsWith Ramphocelus passerinii 13
Myrsidea interactsWith Phlogothraupis sanguinolenta 13
Colpocephalum interactsWith Pionus senilis 12
Philopterus interactsWith Megarhynchus pitangua mexicanus 11
Physconelloides interactsWith Oenoenas nigrorostris 10
Ricinus interactsWith Ramphocelus passerini 10
Myrsidea interactsWith Saltator magnoides medianus 8
Myrsidea interactsWith Gymnostenops montezuma 8
Myrsidea thoracica fusca interactsWith Ramphocelus passerinii 8
Physconelloides interactsWith Claravis pretiosa 7
Philopterus interactsWith Galbula melanogenia 7
Myrsidea interactsWith Streptoprocne zonaris 7
Myrsidea mirabilis interactsWith Zarhynchus wagleri wagleri 7
Ricinus interactsWith Manacus candei 7
Degeeriella interactsWith Celeus loricatus diversus 6
Philopterus interactsWith Manacus candei 6
Myrsidea interactsWith Thryophilus castaneous costaricensis 6
Myrsidea interactsWith Creciscus cineireceps 6

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 Colpocephalidae Colpocephalidae Cardinalidae Cardinalidae Colpocephalidae->Cardinalidae Icteridae Icteridae Colpocephalidae->Icteridae Passerellidae Passerellidae Colpocephalidae->Passerellidae Pipridae Pipridae Colpocephalidae->Pipridae Psittacidae Psittacidae Colpocephalidae->Psittacidae Thraupidae Thraupidae Colpocephalidae->Thraupidae Menoponidae Menoponidae Menoponidae->Cardinalidae Menoponidae->Icteridae Menoponidae->Passerellidae Menoponidae->Pipridae Menoponidae->Psittacidae Menoponidae->Thraupidae Apodidae Apodidae Menoponidae->Apodidae Caprimulgidae Caprimulgidae Menoponidae->Caprimulgidae Columbidae Columbidae Menoponidae->Columbidae Cotingidae Cotingidae Menoponidae->Cotingidae Hirundinidae Hirundinidae Menoponidae->Hirundinidae Thamnophilidae Thamnophilidae Menoponidae->Thamnophilidae Trochilidae Trochilidae Menoponidae->Trochilidae Tyrannidae Tyrannidae Menoponidae->Tyrannidae Philopteridae Philopteridae Philopteridae->Cardinalidae Philopteridae->Icteridae Philopteridae->Passerellidae Philopteridae->Pipridae Philopteridae->Thraupidae Philopteridae->Apodidae Philopteridae->Columbidae Philopteridae->Cotingidae Philopteridae->Tyrannidae Accipitridae Accipitridae Philopteridae->Accipitridae Alcedinidae Alcedinidae Philopteridae->Alcedinidae Anatidae Anatidae Philopteridae->Anatidae Bucconidae Bucconidae Philopteridae->Bucconidae Corvidae Corvidae Philopteridae->Corvidae Falconidae Falconidae Philopteridae->Falconidae Furnariidae Furnariidae Philopteridae->Furnariidae Laridae Laridae Philopteridae->Laridae Parulidae Parulidae Philopteridae->Parulidae Phasianidae Phasianidae Philopteridae->Phasianidae Picidae Picidae Philopteridae->Picidae Strigidae Strigidae Philopteridae->Strigidae Tinamidae Tinamidae Philopteridae->Tinamidae Trogonidae Trogonidae Philopteridae->Trogonidae Ricinidae Ricinidae Ricinidae->Cardinalidae Ricinidae->Pipridae Ricinidae->Psittacidae Ricinidae->Thraupidae Ricinidae->Caprimulgidae Ricinidae->Hirundinidae Ricinidae->Tyrannidae Trinotonidae Trinotonidae Trinotonidae->Anatidae

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
Cuclotocephalus extraneus HAS_ACCEPTED_NAME col Cuclotocephalus extraneus
Cuclotocephalus secundus HAS_ACCEPTED_NAME col Cuclotocephalus secundus
Degeeriella fusca HAS_ACCEPTED_NAME col Degeeriella fusca
Discocorpus cephalosus HAS_ACCEPTED_NAME col Discocorpus cephalosus
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 95
col family 2
col genus 16
col species 83
col subgenus 1
col subspecies 30
discoverlife NA 225
gbif NA 90
gbif family 2
gbif genus 16
gbif species 86
gbif subspecies 31
itis NA 147
itis family 2
itis genus 3
itis species 45
itis subspecies 28
mdd NA 225
ncbi NA 141
ncbi family 2
ncbi genus 16
ncbi species 60
ncbi subspecies 6
pbdb NA 195
pbdb family 1
pbdb genus 1
pbdb species 28
tpt NA 138
tpt family 2
tpt genus 15
tpt species 70
wfo NA 223
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 116
col SYNONYM_OF 21
col NONE 95
discoverlife NONE 225
gbif HAS_ACCEPTED_NAME 120
gbif SYNONYM_OF 32
gbif NONE 90
itis NONE 147
itis HAS_ACCEPTED_NAME 71
itis SYNONYM_OF 7
mdd NONE 225
ncbi SAME_AS 79
ncbi NONE 141
ncbi SYNONYM_OF 6
pbdb NONE 195
pbdb HAS_ACCEPTED_NAME 30
tpt HAS_ACCEPTED_NAME 80
tpt SYNONYM_OF 15
tpt NONE 138
wfo NONE 223
wfo HAS_ACCEPTED_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
2024-04-28T23:09:54Z note source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder
2024-04-28T23:09:54Z note source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder
2024-04-28T23:09:54Z note source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder
2024-04-28T23:09:54Z 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
source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder 5

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.