A Review of Biotic Interactions and Taxon Names Found in globalbioticinteractions/kalro2023

by Nomer and Elton, two naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

https://github.com/globalbioticinteractions/kalro2023/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/kalro2023, is 417KiB in size and contains 1,023 interaction with 8 unique types of associations (e.g., pollinates) between 512 primary taxa (e.g., Apis mellifera) and 331 associated taxa (e.g., Persea americana). 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:

A review of the status of web-based African Plant-Pollinator Interaction data. https://github.com/globalbioticinteractions/kalro2023/archive/b9a45d8f9df251cfb3a2d10519e95c35a3df56d7.zip 2024-11-16T02:08:37.066Z 4745eceb97321c51aee99af75b052191511a8c17b34f2ea0ae000ed15c915a14

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/kalro2023 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.  417KiB) under review 
elton pull globalbioticinteractions/kalro2023

# generate review notes
elton review globalbioticinteractions/kalro2023\
 > review.tsv

# export indexed interaction records
elton interactions globalbioticinteractions/kalro2023\
 > interactions.tsv

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/kalro2023\
 | 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/kalro2023, is 417KiB in size and contains 1,023 interaction with 8 unique types of associations (e.g., pollinates) between 512 primary taxa (e.g., Apis mellifera) and 331 associated taxa (e.g., Persea americana).

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
Leptoconchus incycloseris parasiteOf Fungia (Cycloseris) costulata Gittenberger, A., Gittenberger, E. (2011). Cryptic, adaptive radiation of endoparasitic snails: sibling species of Leptoconchus (Gastropoda: Coralliophilidae) in corals. Org Divers Evol, 11(1), 21–41. doi:10.1007/s13127-011-0039-1
Leptoconchus infungites parasiteOf Fungia (Fungia) fungites Gittenberger, A., Gittenberger, E. (2011). Cryptic, adaptive radiation of endoparasitic snails: sibling species of Leptoconchus (Gastropoda: Coralliophilidae) in corals. Org Divers Evol, 11(1), 21–41. doi:10.1007/s13127-011-0039-1
Leptoconchus ingrandifungi parasiteOf Sandalolitha dentata Gittenberger, A., Gittenberger, E. (2011). Cryptic, adaptive radiation of endoparasitic snails: sibling species of Leptoconchus (Gastropoda: Coralliophilidae) in corals. Org Divers Evol, 11(1), 21–41. doi:10.1007/s13127-011-0039-1
Leptoconchus ingranulosa parasiteOf Fungia (Wellsofungia) granulosa Gittenberger, A., Gittenberger, E. (2011). Cryptic, adaptive radiation of endoparasitic snails: sibling species of Leptoconchus (Gastropoda: Coralliophilidae) in corals. Org Divers Evol, 11(1), 21–41. doi:10.1007/s13127-011-0039-1
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
pollinates 338
acquiresNutrientsFrom 294
visits 197
visitsFlowersOf 184
parasiteOf 11
preysOn 2
parasitoidOf 1
hostOf 1
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Apis mellifera 121
Apis melifera 38
Megachile sp. 2 16
Agrius convolvuli 14
Macrogalea candida 12
Pseudapis sp. 12
Ceratina sp. 3 10
Xylocopa sp. 10
Apis melliferra 9
Apis mellifera Linnaeus 9
Amegilla sp. 1 8
Xylocopa caffra 7
Xylocopa nigrita 7
Xylocopa flavorufa 7
Hypotrigona gribodoi 7
Meliponula ferruginea 6
Lasioglosum sp. 6
Braunsapis sp. 6
Catopsilia florella 6
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
Persea americana 48
Helianthus annuus L. 30
Acacia tortilis 29
Arctotheca calendula(Cape Marigold) 29
Vernonia cinerea 25
Sesamum indicum 22
Citrullus lanatus 21
Agathisanthemum bojeri Klotzsch 20
Mangifera indica 20
Coffee arabica 17
Phaseolus vulgaris 16
Phaseolus coccineus 15
Helianthus annuus L 14
Trifolium alexandrinum 13
Cucumis sativus 13
Phaseolus vulgaris L 12
Agathisanthemum bojeri 11
Zygophyllum sp. 11
Cucumis melo 11
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Asclepias cucullata pollinates Sisyranthus trichostomus 3
Xylocopa caffra acquiresNutrientsFrom Rhynchosia velutina 2
Steganomus sp. acquiresNutrientsFrom Crotalaria emarginata Benth 2
Megachile sp. 2 acquiresNutrientsFrom Indigofera paniculata 2
Xylocopa flavicollis DeGeer acquiresNutrientsFrom Rhynchosia velutina Wight & Arn. 2
Apis mellifera scutellata pollinates Mangifera indica 2
Apis mellifera scutellata pollinates Helianthus annuus 2
Braunsapis spp. visits Lantana camara 2
Belenois aurota Fabricius visitsFlowersOf Helianthus annuus L. 2
Hemipepsis hilaris Smith pollinates Xysmalobium involucratum 2
Leptoconchus incycloseris parasiteOf Fungia (Cycloseris) costulata 1
Leptoconchus infungites parasiteOf Fungia (Fungia) fungites 1
Leptoconchus ingrandifungi parasiteOf Sandalolitha dentata 1
Leptoconchus ingranulosa parasiteOf Fungia (Wellsofungia) granulosa 1
Leptoconchus inlimax parasiteOf Herpolitha limax 1
Leptoconchus inpileus parasiteOf Halomitra pileus 1
Leptoconchus inpleuractis parasiteOf Fungia (Pleuractis) gravis 1
Leptoconchus inpleuractis parasiteOf Fungia (Pleuractis) moluccensis 1
Leptoconchus inpleuractis parasiteOf Fungia (Pleuractis) paumotensis 1

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 Plantae Plantae Animalia->Plantae Animalia->Plantae Animalia->Plantae Animalia->Plantae Animalia->Plantae Plantae->Plantae
interactions Apidae Apidae Arecaceae Arecaceae Apidae->Arecaceae Asteraceae Asteraceae Apidae->Asteraceae Apidae->Asteraceae Apidae->Asteraceae Apidae->Asteraceae Convolvulaceae Convolvulaceae Apidae->Convolvulaceae Fabaceae Fabaceae Apidae->Fabaceae Apidae->Fabaceae Apidae->Fabaceae Apidae->Fabaceae Malvaceae Malvaceae Apidae->Malvaceae Pedaliaceae Pedaliaceae Apidae->Pedaliaceae Rubiaceae Rubiaceae Apidae->Rubiaceae Acanthaceae Acanthaceae Apidae->Acanthaceae Amaryllidaceae Amaryllidaceae Apidae->Amaryllidaceae Anacardiaceae Anacardiaceae Apidae->Anacardiaceae Cucurbitaceae Cucurbitaceae Apidae->Cucurbitaceae Apidae->Cucurbitaceae Lauraceae Lauraceae Apidae->Lauraceae Apidae->Lauraceae Apidae->Lauraceae Rosaceae Rosaceae Apidae->Rosaceae Rutaceae Rutaceae Apidae->Rutaceae Sapindaceae Sapindaceae Apidae->Sapindaceae Solanaceae Solanaceae Apidae->Solanaceae Cupressaceae Cupressaceae Apidae->Cupressaceae Euphorbiaceae Euphorbiaceae Apidae->Euphorbiaceae Annonaceae Annonaceae Apidae->Annonaceae Caricaceae Caricaceae Apidae->Caricaceae Commelinaceae Commelinaceae Apidae->Commelinaceae Polygonaceae Polygonaceae Apidae->Polygonaceae Lamiaceae Lamiaceae Apidae->Lamiaceae Myrtaceae Myrtaceae Apidae->Myrtaceae Verbenaceae Verbenaceae Apidae->Verbenaceae Apocynaceae Apocynaceae Apocynaceae->Apocynaceae Calliphoridae Calliphoridae Calliphoridae->Anacardiaceae Calliphoridae->Anacardiaceae Calliphoridae->Lauraceae Calliphoridae->Lauraceae Carabidae Carabidae Carabidae->Lauraceae Cerambycidae Cerambycidae Cerambycidae->Asteraceae Chrysomelidae Chrysomelidae Chrysomelidae->Anacardiaceae Crabronidae Crabronidae Crabronidae->Fabaceae Dolichopodidae Dolichopodidae Dolichopodidae->Anacardiaceae Erebidae Erebidae Erebidae->Caricaceae Eumenidae Eumenidae Eumenidae->Fabaceae Eumenidae->Pedaliaceae Eumenidae->Lauraceae Fanniidae Fanniidae Fanniidae->Pedaliaceae Formicidae Formicidae Formicidae->Fabaceae Formicidae->Cucurbitaceae Formicidae->Lauraceae Halictidae Halictidae Halictidae->Fabaceae Halictidae->Cucurbitaceae Hesperiidae Hesperiidae Hesperiidae->Cucurbitaceae Ichneumonidae Ichneumonidae Ichneumonidae->Anacardiaceae Limnichidae Limnichidae Limnichidae->Asteraceae Lycaenidae Lycaenidae Lycaenidae->Fabaceae Lycaenidae->Cucurbitaceae Megachilidae Megachilidae Megachilidae->Fabaceae Megachilidae->Fabaceae Megachilidae->Fabaceae Muricidae Muricidae Fungiidae Fungiidae Muricidae->Fungiidae Muscidae Muscidae Muscidae->Anacardiaceae Nectariniidae Nectariniidae Proteaceae Proteaceae Nectariniidae->Proteaceae Nymphalidae Nymphalidae Nymphalidae->Asteraceae Nymphalidae->Malvaceae Nymphalidae->Pedaliaceae Nymphalidae->Cucurbitaceae Papilionidae Papilionidae Papilionidae->Asteraceae Pieridae Pieridae Pieridae->Asteraceae Pieridae->Cucurbitaceae Pieridae->Lauraceae Sarcophagidae Sarcophagidae Sarcophagidae->Asteraceae Sarcophagidae->Lauraceae Scarabaeidae Scarabaeidae Scarabaeidae->Asteraceae Scarabaeidae->Apocynaceae Sphingidae Sphingidae Sphingidae->Pedaliaceae Sphingidae->Caricaceae Capparaceae Capparaceae Sphingidae->Capparaceae Orchidaceae Orchidaceae Sphingidae->Orchidaceae Sphingidae->Orchidaceae Zingiberaceae Zingiberaceae Sphingidae->Zingiberaceae Syrphidae Syrphidae Syrphidae->Anacardiaceae Syrphidae->Cucurbitaceae Syrphidae->Cucurbitaceae Syrphidae->Cucurbitaceae Syrphidae->Lauraceae Syrphidae->Lauraceae Syrphidae->Lauraceae Tettigoniidae Tettigoniidae Tettigoniidae->Pedaliaceae Thripidae Thripidae Thripidae->Malvaceae Zosteropidae Zosteropidae Zosteropidae->Proteaceae

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
Abelmoschus esculentus HAS_ACCEPTED_NAME col Abelmoschus esculentus
Brevispica NONE col Brevispica
Abutilon zanzibaricum SYNONYM_OF col Abutilon mauritianum subsp. zanzibaricum
Acacia brevispica SYNONYM_OF col Senegalia brevispica
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 187
col class 1
col family 14
col genus 91
col order 3
col section 1
col species 343
col subfamily 2
col subspecies 7
col variety 1
discoverlife NA 557
discoverlife species 86
gbif NA 164
gbif class 1
gbif family 15
gbif genus 103
gbif order 3
gbif species 356
gbif subspecies 8
gbif variety 2
itis NA 331
itis class 1
itis family 14
itis genus 68
itis order 3
itis species 221
itis subfamily 3
itis subspecies 1
itis variety 1
mdd NA 643
ncbi NA 236
ncbi class 1
ncbi family 14
ncbi genus 90
ncbi order 3
ncbi species 287
ncbi species group 1
ncbi subfamily 4
ncbi subgenus 15
ncbi subspecies 4
pbdb NA 567
pbdb class 1
pbdb family 15
pbdb genus 47
pbdb order 3
pbdb species 7
pbdb subfamily 3
tpt NA 641
tpt genus 1
tpt species 1
wfo NA 450
wfo genus 16
wfo species 176
wfo subspecies 1
wfo variety 1
worms NA 523
worms class 1
worms family 13
worms genus 34
worms order 3
worms species 68
worms variety 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 593
col NONE 200
col SYNONYM_OF 170
discoverlife NONE 730
discoverlife HAS_ACCEPTED_NAME 94
discoverlife SYNONYM_OF 30
discoverlife HOMONYM_OF 5
gbif HAS_ACCEPTED_NAME 721
gbif NONE 175
gbif SYNONYM_OF 304
itis HAS_ACCEPTED_NAME 427
itis NONE 376
itis SYNONYM_OF 44
mdd NONE 841
ncbi SAME_AS 602
ncbi NONE 258
ncbi SYNONYM_OF 37
pbdb NONE 690
pbdb HAS_ACCEPTED_NAME 149
pbdb SYNONYM_OF 8
tpt NONE 839
tpt HAS_ACCEPTED_NAME 2
wfo HAS_ACCEPTED_NAME 224
wfo NONE 588
wfo SYNONYM_OF 54
wfo HAS_UNCHECKED_NAME 19
worms NONE 650
worms SYNONYM_OF 28
worms HAS_ACCEPTED_NAME 172
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
2024-11-18T02:58:41Z note found unsupported interaction type with name: [Honey production]
2024-11-18T02:58:42Z note found malformed doi [doi.org/10.1093/aob/mcv137]
2024-11-18T02:58:42Z note found malformed doi [doi.org/10.1093/aob/mcv138]
2024-11-18T02:58:42Z note found malformed doi [doi.org/10.1093/aob/mcv139]

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

Most frequently occurring review notes, if any.
reviewComment count
found unsupported interaction type with name: [Honey production] 1
found malformed doi [doi.org/10.1093/aob/mcv137] 1
found malformed doi [doi.org/10.1093/aob/mcv138] 1
found malformed doi [doi.org/10.1093/aob/mcv139] 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 (2024-11-18) 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.