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

by Nomer and Elton, two naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

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

2024-05-06

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/fsca, is 3.71MiB in size and contains 605 interactions with 1 unique type of association (e.g., interactsWith) between 41 primary taxa (e.g., Hylaeus) and 112 associated taxa (e.g., Baccharis). 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:

Florida State Collection of Arthropods https://github.com/globalbioticinteractions/fsca/archive/2cdcf9475b7e0ef2a728a96535608bc0ce2ac5ca.zip 2024-05-04T00:29:15.121Z 6dfea5a2a8a0e6ae8a1eb71c4cedeead2f8553471ba8633cf65d012da8880bb4

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/fsca 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 0.5.9
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. 3.71MiB) under review 
elton pull globalbioticinteractions/fsca

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

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

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/fsca\
 | 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/fsca, is 3.71MiB in size and contains 605 interactions with 1 unique type of association (e.g., interactsWith) between 41 primary taxa (e.g., Hylaeus) and 112 associated taxa (e.g., Baccharis).

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
Hylaeus interactsWith Daucus carota https://ecdysis.org/collections/individual/index.php?occid=1472888
Hylaeus interactsWith Daucus carota https://ecdysis.org/collections/individual/index.php?occid=1472889
Hylaeus interactsWith Aruncus aruncus https://ecdysis.org/collections/individual/index.php?occid=1472891
Hylaeus interactsWith Aruncus aruncus https://ecdysis.org/collections/individual/index.php?occid=1472892
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
interactsWith 605
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Hylaeus 296
Nomiocolletes arnaui 62
Lonchopria semicyaneaus 44
Nomiocolletes 33
Hylaeus ornatus 22
Hylaeus schwarzii 21
Hylaeus formosus 16
Augochlora 11
Bombus californicus 10
Brachyglossula leucothorax 8
Hesperapis 7
Anthidiellum notatum notatum 7
Hylaeus hyalinatus 6
Hylaeus signatus 5
Hylaeus punctatus 5
Lonchopria chalybaea 5
Anthidiellum apicale 5
Bombus rufocinctus 5
Cephalocolletes laticeps 4
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
Baccharis 134
Acacia 34
Aruncus aruncus 32
Solidago 28
Hydrangea arborescens 23
Juncus & wild flower 19
Micromeria brownei 17
Metopium toxiferum 16
Apocynum 13
Melilotus alba 12
Wild lilac 12
Eriogonum 11
Asclepias mexicanus 11
Prosopis 11
Ptilimnium capillaceum 9
Opuntia 9
Clematis 9
Daucus carota 8
Chrysothamnus 8
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Nomiocolletes arnaui interactsWith Baccharis 54
Lonchopria semicyaneaus interactsWith Baccharis 44
Hylaeus interactsWith Acacia 34
Hylaeus interactsWith Aruncus aruncus 32
Nomiocolletes interactsWith Baccharis 29
Hylaeus interactsWith Hydrangea arborescens 23
Hylaeus interactsWith Solidago 21
Hylaeus interactsWith Juncus & wild flower 19
Hylaeus ornatus interactsWith Micromeria brownei 17
Hylaeus formosus interactsWith Metopium toxiferum 16
Hylaeus interactsWith Apocynum 13
Hylaeus interactsWith Wild lilac 12
Hylaeus interactsWith Eriogonum 11
Hylaeus interactsWith Asclepias mexicanus 11
Hylaeus interactsWith Prosopis 11
Hylaeus interactsWith Daucus carota 8
Hylaeus interactsWith Chrysothamnus 8
Hylaeus interactsWith Melilotus alba 8
Brachyglossula leucothorax interactsWith Opuntia 8

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 Chromista Chromista Animalia->Chromista Plantae Plantae Animalia->Plantae
interactions Andrenidae Andrenidae Asteraceae Asteraceae Andrenidae->Asteraceae Brassicaceae Brassicaceae Andrenidae->Brassicaceae Salicaceae Salicaceae Andrenidae->Salicaceae Solanaceae Solanaceae Andrenidae->Solanaceae Viburnaceae Viburnaceae Andrenidae->Viburnaceae Apidae Apidae Apidae->Asteraceae Ephedraceae Ephedraceae Apidae->Ephedraceae Fabaceae Fabaceae Apidae->Fabaceae Fringillidae Fringillidae Apidae->Fringillidae Polygonaceae Polygonaceae Apidae->Polygonaceae Colletidae Colletidae Colletidae->Asteraceae Colletidae->Salicaceae Colletidae->Fabaceae Colletidae->Fringillidae Colletidae->Polygonaceae Amaranthaceae Amaranthaceae Colletidae->Amaranthaceae Anacardiaceae Anacardiaceae Colletidae->Anacardiaceae Apiaceae Apiaceae Colletidae->Apiaceae Apocynaceae Apocynaceae Colletidae->Apocynaceae Araliaceae Araliaceae Colletidae->Araliaceae Arecaceae Arecaceae Colletidae->Arecaceae Cactaceae Cactaceae Colletidae->Cactaceae Euphorbiaceae Euphorbiaceae Colletidae->Euphorbiaceae Hydrangeaceae Hydrangeaceae Colletidae->Hydrangeaceae Hydrophyllaceae Hydrophyllaceae Colletidae->Hydrophyllaceae Hypericaceae Hypericaceae Colletidae->Hypericaceae Lamiaceae Lamiaceae Colletidae->Lamiaceae Malvaceae Malvaceae Colletidae->Malvaceae Plantaginaceae Plantaginaceae Colletidae->Plantaginaceae Pontederiaceae Pontederiaceae Colletidae->Pontederiaceae Ranunculaceae Ranunculaceae Colletidae->Ranunculaceae Resedaceae Resedaceae Colletidae->Resedaceae Rhamnaceae Rhamnaceae Colletidae->Rhamnaceae Rosaceae Rosaceae Colletidae->Rosaceae Sagittariidae Sagittariidae Colletidae->Sagittariidae Sapindaceae Sapindaceae Colletidae->Sapindaceae Halictidae Halictidae Halictidae->Asteraceae Ericaceae Ericaceae Halictidae->Ericaceae Melittidae Melittidae Melittidae->Asteraceae

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
Hylaeus HAS_ACCEPTED_NAME col Hylaeus
Leioproctus HAS_ACCEPTED_NAME col Leioproctus
Lonchopria HAS_ACCEPTED_NAME col Lonchopria
Andrena chlorogaster HAS_ACCEPTED_NAME col Andrena chlorogaster
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 45
col genus 47
col section 1
col species 55
col subspecies 2
col variety 1
discoverlife NA 120
discoverlife species 31
gbif NA 38
gbif genus 50
gbif species 58
gbif subspecies 3
gbif variety 2
itis NA 46
itis genus 44
itis species 56
itis subspecies 2
itis variety 2
mdd NA 150
ncbi NA 59
ncbi genus 46
ncbi species 45
ncbi subgenus 2
ncbi subspecies 1
pbdb NA 129
pbdb genus 19
pbdb species 2
pbdb suborder 1
tpt NA 149
tpt genus 1
wfo NA 77
wfo genus 40
wfo species 33
wfo subspecies 1
wfo 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 102
col NONE 45
col SYNONYM_OF 19
discoverlife NONE 122
discoverlife HAS_ACCEPTED_NAME 29
discoverlife SYNONYM_OF 7
discoverlife HOMONYM_OF 1
gbif HAS_ACCEPTED_NAME 120
gbif NONE 38
gbif SYNONYM_OF 32
itis HAS_ACCEPTED_NAME 97
itis NONE 46
itis SYNONYM_OF 11
mdd NONE 151
ncbi SAME_AS 94
ncbi NONE 60
ncbi SYNONYM_OF 3
pbdb NONE 130
pbdb HAS_ACCEPTED_NAME 22
tpt NONE 150
tpt HAS_ACCEPTED_NAME 1
wfo NONE 77
wfo HAS_ACCEPTED_NAME 66
wfo SYNONYM_OF 11
wfo HAS_UNCHECKED_NAME 4
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
2024-05-06T01:51:16Z note found unsupported interaction type with name: [[Venzuela]
2024-05-06T01:51:16Z note found unsupported interaction type with name: [[Venzuela]
2024-05-06T01:51:16Z note found unsupported interaction type with name: [[Venzuela]
2024-05-06T01:51:16Z note found unsupported interaction type with name: [[Venzuela]

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: [[Florida] 28
found unsupported interaction type with name: [[Venzuela] 10

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 (2024-05-06) 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.