A Review of Biotic Interactions and Taxon Names Found in globalbioticinteractions/carvalheiro2023

by Nomer and Elton, two naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

https://github.com/globalbioticinteractions/carvalheiro2023/issues

2024-11-18

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/carvalheiro2023, is 1.65MiB in size and contains 542 interactions with 1 unique type of association (e.g., flowersVisitedBy) between 63 primary taxa (e.g., Scabiosa columbaria) and 171 associated taxa (e.g., Bombus pascuorum). 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:

WorldFAIR pilot data from: VisitationData_Luisa_Carvalheiro. https://github.com/globalbioticinteractions/carvalheiro2023/archive/b71267f81c2e4b3c015a9cc0fafcc884fea1b177.zip 2024-11-16T00:26:53.265Z e2c7fed87c8d5444d914d1bedb42c0a4faa0d3d3b3577a345c8851551a663ca2

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/carvalheiro2023 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 0.13.9
nomer 0.5.13
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. 1.65MiB) under review 
elton pull globalbioticinteractions/carvalheiro2023

# generate review notes
elton review globalbioticinteractions/carvalheiro2023\
 > review.tsv

# export indexed interaction records
elton interactions globalbioticinteractions/carvalheiro2023\
 > interactions.tsv

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/carvalheiro2023\
 | 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/carvalheiro2023, is 1.65MiB in size and contains 542 interactions with 1 unique type of association (e.g., flowersVisitedBy) between 63 primary taxa (e.g., Scabiosa columbaria) and 171 associated taxa (e.g., Bombus pascuorum).

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
Pilosella oficinarum flowersVisitedBy Andrena WorldFAIR pilot data from: VisitationData_Luisa_Carvalheiro. Accessed at https://docs.google.com/spreadsheets/u/1/d/1cJ0qX9ppqHoSyqFykwYJef-DFOzoutthBXjwKRY81T8/export?format=tsv&gid=776329546 on 18 Nov 2024.
Mycelis muralis flowersVisitedBy Baccha WorldFAIR pilot data from: VisitationData_Luisa_Carvalheiro. Accessed at https://docs.google.com/spreadsheets/u/1/d/1cJ0qX9ppqHoSyqFykwYJef-DFOzoutthBXjwKRY81T8/export?format=tsv&gid=776329546 on 18 Nov 2024.
Apiaceae flowersVisitedBy Bombus WorldFAIR pilot data from: VisitationData_Luisa_Carvalheiro. Accessed at https://docs.google.com/spreadsheets/u/1/d/1cJ0qX9ppqHoSyqFykwYJef-DFOzoutthBXjwKRY81T8/export?format=tsv&gid=776329546 on 18 Nov 2024.
Origanum vulgare flowersVisitedBy Bombus WorldFAIR pilot data from: VisitationData_Luisa_Carvalheiro. Accessed at https://docs.google.com/spreadsheets/u/1/d/1cJ0qX9ppqHoSyqFykwYJef-DFOzoutthBXjwKRY81T8/export?format=tsv&gid=776329546 on 18 Nov 2024.
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
flowersVisitedBy 685
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Scabiosa columbaria 44
Solidago virgaurea 39
Rubus fructicosus 36
Helianthemum nummularium 32
Geranium robertianum 32
Senecio 32
Crepis 30
Centranthus ruber 26
Clematis vitalba 24
Hieracium 23
Origanum vulgare 22
Achillea millefolium 22
Pilosella oficinarum 20
Torilis japonica 15
Cotoneaster franchetti 14
Hypericum perforatum 13
Ligustrum vulgare 13
Lactuca serriola 12
Eupatorium cannabinum 11
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
Bombus pascuorum 64
Episyrphus balteatus 25
Lasioglossum morio 22
Formica fusca 21
Meligethes solidus 20
Diptera 17
Syrphus ribesii 17
Heteroptera 16
Lasius alienus 15
Platycheirus albimanus 14
Hymenoptera 13
Halictus tumulorum 13
Anaspis pulicaria 12
Meligethes aeneus 10
Oedemera lurida 10
Paragus haemorrhous 10
Sphaerophoria scripta 10
Coleoptera 9
Thysanoptera 9
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Geranium robertianum flowersVisitedBy Bombus pascuorum 6
Scabiosa columbaria flowersVisitedBy Bombus pascuorum 5
Solidago virgaurea flowersVisitedBy Bombus pascuorum 5
Teucrium scorodonia flowersVisitedBy Bombus pascuorum 5
Clinopodium ascendens flowersVisitedBy Bombus pascuorum 4
Lotus corniculatus flowersVisitedBy Bombus pascuorum 4
Origanum vulgare flowersVisitedBy Bombus pascuorum 4
Rubus fructicosus flowersVisitedBy Bombus pascuorum 4
Achillea millefolium flowersVisitedBy Heteroptera 3
Centranthus ruber flowersVisitedBy Homoptera 3
Solidago virgaurea flowersVisitedBy Sarcophaga 3
Rubus fructicosus flowersVisitedBy Anaspis pulicaria 3
Clematis vitalba flowersVisitedBy Episyrphus balteatus 3
Geranium robertianum flowersVisitedBy Episyrphus balteatus 3
Scabiosa columbaria flowersVisitedBy Episyrphus balteatus 3
Scabiosa columbaria flowersVisitedBy Eristalis tenax 3
Cotoneaster franchetti flowersVisitedBy Formica fusca 3
Clematis vitalba flowersVisitedBy Lasioglossum morio 3
Origanum vulgare flowersVisitedBy Lasioglossum morio 3

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 Plantae Plantae Plantae->Plantae Animalia Animalia Plantae->Animalia
interactions Amaryllidaceae Amaryllidaceae Apidae Apidae Amaryllidaceae->Apidae Halictidae Halictidae Amaryllidaceae->Halictidae Miridae Miridae Amaryllidaceae->Miridae Syrphidae Syrphidae Amaryllidaceae->Syrphidae Apiaceae Apiaceae Apiaceae->Apidae Apiaceae->Halictidae Apiaceae->Miridae Apiaceae->Syrphidae Anthomyiidae Anthomyiidae Apiaceae->Anthomyiidae Crabronidae Crabronidae Apiaceae->Crabronidae Curculionidae Curculionidae Apiaceae->Curculionidae Ephydridae Ephydridae Apiaceae->Ephydridae Formicidae Formicidae Apiaceae->Formicidae Sarcophagidae Sarcophagidae Apiaceae->Sarcophagidae Saxifragaceae Saxifragaceae Apiaceae->Saxifragaceae Tachinidae Tachinidae Apiaceae->Tachinidae Araliaceae Araliaceae Araliaceae->Halictidae Araliaceae->Syrphidae Araliaceae->Formicidae Sciaridae Sciaridae Araliaceae->Sciaridae Vespidae Vespidae Araliaceae->Vespidae Asteraceae Asteraceae Asteraceae->Apidae Asteraceae->Halictidae Asteraceae->Syrphidae Asteraceae->Anthomyiidae Asteraceae->Sarcophagidae Asteraceae->Saxifragaceae Asteraceae->Tachinidae Asteraceae->Sciaridae Andrenidae Andrenidae Asteraceae->Andrenidae Calliphoridae Calliphoridae Asteraceae->Calliphoridae Chloropidae Chloropidae Asteraceae->Chloropidae Colletidae Colletidae Asteraceae->Colletidae Conopidae Conopidae Asteraceae->Conopidae Lycaenidae Lycaenidae Asteraceae->Lycaenidae Muscidae Muscidae Asteraceae->Muscidae Polleniidae Polleniidae Asteraceae->Polleniidae Staphylinidae Staphylinidae Asteraceae->Staphylinidae Brassicaceae Brassicaceae Brassicaceae->Halictidae Brassicaceae->Syrphidae Brassicaceae->Calliphoridae Caprifoliaceae Caprifoliaceae Caprifoliaceae->Apidae Caprifoliaceae->Halictidae Caprifoliaceae->Miridae Caprifoliaceae->Syrphidae Caprifoliaceae->Anthomyiidae Caprifoliaceae->Formicidae Caprifoliaceae->Saxifragaceae Caprifoliaceae->Calliphoridae Caprifoliaceae->Lycaenidae Bombyliidae Bombyliidae Caprifoliaceae->Bombyliidae Erebidae Erebidae Caprifoliaceae->Erebidae Megachilidae Megachilidae Caprifoliaceae->Megachilidae Nymphalidae Nymphalidae Caprifoliaceae->Nymphalidae Pieridae Pieridae Caprifoliaceae->Pieridae Cistaceae Cistaceae Cistaceae->Apidae Cistaceae->Syrphidae Cistaceae->Anthomyiidae Cistaceae->Formicidae Cistaceae->Tachinidae Cistaceae->Pieridae Cornaceae Cornaceae Cornaceae->Formicidae Dioscoreaceae Dioscoreaceae Dioscoreaceae->Formicidae Fabaceae Fabaceae Fabaceae->Apidae Fabaceae->Halictidae Fabaceae->Miridae Fabaceae->Syrphidae Fabaceae->Curculionidae Fabaceae->Formicidae Fabaceae->Chloropidae Fabaceae->Lycaenidae Fabaceae->Muscidae Geraniaceae Geraniaceae Geraniaceae->Apidae Geraniaceae->Syrphidae Geraniaceae->Formicidae Geraniaceae->Saxifragaceae Geraniaceae->Andrenidae Geraniaceae->Calliphoridae Geraniaceae->Bombyliidae Hypericaceae Hypericaceae Hypericaceae->Apidae Hypericaceae->Syrphidae Hypericaceae->Anthomyiidae Hypericaceae->Formicidae Hypericaceae->Saxifragaceae Lamiaceae Lamiaceae Lamiaceae->Apidae Lamiaceae->Halictidae Lamiaceae->Syrphidae Lamiaceae->Formicidae Lamiaceae->Chloropidae Lamiaceae->Nymphalidae Lamiaceae->Pieridae Hesperiidae Hesperiidae Lamiaceae->Hesperiidae Nitidulidae Nitidulidae Lamiaceae->Nitidulidae Pipunculidae Pipunculidae Lamiaceae->Pipunculidae Sepsidae Sepsidae Lamiaceae->Sepsidae Oleaceae Oleaceae Oleaceae->Apidae Oleaceae->Syrphidae Oleaceae->Chloropidae Orobanchaceae Orobanchaceae Orobanchaceae->Apidae Ranunculaceae Ranunculaceae Ranunculaceae->Apidae Ranunculaceae->Halictidae Ranunculaceae->Syrphidae Ranunculaceae->Anthomyiidae Ranunculaceae->Saxifragaceae Ranunculaceae->Tachinidae Ranunculaceae->Colletidae Ranunculaceae->Sepsidae Lauxaniidae Lauxaniidae Ranunculaceae->Lauxaniidae Rosaceae Rosaceae Rosaceae->Apidae Rosaceae->Halictidae Rosaceae->Syrphidae Rosaceae->Curculionidae Rosaceae->Formicidae Rosaceae->Saxifragaceae Rosaceae->Chloropidae Cerambycidae Cerambycidae Rosaceae->Cerambycidae Hybotidae Hybotidae Rosaceae->Hybotidae Phoridae Phoridae Rosaceae->Phoridae Scarabaeidae Scarabaeidae Rosaceae->Scarabaeidae Rubiaceae Rubiaceae Rubiaceae->Syrphidae Rubiaceae->Ephydridae Rubiaceae->Formicidae Rubiaceae->Vespidae Rubiaceae->Chloropidae Scrophulariaceae Scrophulariaceae Scrophulariaceae->Apidae Scrophulariaceae->Halictidae Solanaceae Solanaceae Solanaceae->Apidae Solanaceae->Syrphidae Solanaceae->Curculionidae Solanaceae->Saxifragaceae Viburnaceae Viburnaceae Viburnaceae->Formicidae

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, pbdb, and worms). 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
Achillea millefolium SYNONYM_OF col Achillea aspleniifolia
Achillea millefolium HAS_ACCEPTED_NAME col Achillea millefolium
Aglais urticae HAS_ACCEPTED_NAME col Aglais urticae
Agrypnus murinus NONE col Agrypnus murinus
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 48
col family 9
col genus 22
col order 5
col species 137
col subfamily 1
col subspecies 6
discoverlife NA 203
discoverlife species 21
gbif NA 19
gbif family 9
gbif genus 30
gbif order 5
gbif species 164
gbif subspecies 7
itis NA 91
itis family 9
itis genus 19
itis order 5
itis species 96
itis subfamily 1
itis suborder 2
itis subspecies 1
mdd NA 224
ncbi NA 23
ncbi family 9
ncbi genus 22
ncbi order 5
ncbi species 159
ncbi subfamily 1
ncbi subgenus 6
ncbi suborder 2
ncbi subspecies 2
pbdb NA 187
pbdb family 9
pbdb genus 17
pbdb infraorder 1
pbdb order 5
pbdb species 3
pbdb subfamily 1
pbdb suborder 2
tpt NA 223
tpt species 1
wfo NA 163
wfo family 2
wfo genus 6
wfo species 51
wfo subspecies 3
worms NA 169
worms family 9
worms genus 13
worms order 5
worms species 25
worms subfamily 1
worms suborder 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 SYNONYM_OF 47
col HAS_ACCEPTED_NAME 165
col NONE 58
discoverlife NONE 213
discoverlife HAS_ACCEPTED_NAME 21
discoverlife HOMONYM_OF 2
discoverlife SYNONYM_OF 5
gbif HAS_ACCEPTED_NAME 230
gbif SYNONYM_OF 85
gbif NONE 29
itis HAS_ACCEPTED_NAME 128
itis NONE 101
itis SYNONYM_OF 7
mdd NONE 234
ncbi SAME_AS 189
ncbi SYNONYM_OF 17
ncbi NONE 33
pbdb NONE 197
pbdb HAS_ACCEPTED_NAME 39
tpt NONE 233
tpt SYNONYM_OF 1
wfo HAS_ACCEPTED_NAME 52
wfo NONE 173
wfo SYNONYM_OF 16
wfo HAS_UNCHECKED_NAME 18
worms HAS_ACCEPTED_NAME 62
worms NONE 179
worms SYNONYM_OF 3
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)
worms 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
2024-11-18T01:18:57Z summary https://github.com/globalbioticinteractions/carvalheiro2023/archive/b71267f81c2e4b3c015a9cc0fafcc884fea1b177.zip
2024-11-18T01:18:57Z summary 685 interaction(s)
2024-11-18T01:18:57Z summary 0 note(s)
2024-11-18T01:18:57Z summary 685 info(s)

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

: Most frequently occurring review notes, if any.

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 (2024-11-18) 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.