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

By Nomer and Elton, two naive review bots.

2023-09-28

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 describe a review process of such an openly accessible digital interaction datasets of known origin, and discuss their outcome. The dataset under review (aka globalbioticinteractions/fsca) contains 570 interactions with 1 (e.g., interactsWith) unique types of associations between 34 primary taxa (e.g., Hylaeus) and 93 associated taxa (e.g., Baccharis). The report includes detailed summaries of interactions data as well as a taxonomic review from multiple perspectives.

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 2023-09-22T23:27:55.758Z 6dfea5a2a8a0e6ae8a1eb71c4cedeead2f8553471ba8633cf65d012da8880bb4

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 0.12.7
nomer 0.5.5
mlr 6.0.0
pandoc 3.1.6.1

The review process can be described in the form of a script:

# get versioned copy of the dataset 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 1. 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 (aka globalbioticinteractions/fsca) contains 570 interactions with 1 (e.g., interactsWith) unique types of associations between 34 primary taxa (e.g., Hylaeus) and 93 associated taxa (e.g., Baccharis).

An exhaustive list of indexed interaction claims can be found at indexed-interactions (csv/tsv/html). The list was used to create the following data summaries.

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 570
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
Brachyglossula leucothorax 8
Hesperapis 7
Hylaeus hyalinatus 6
Hylaeus signatus 5
Hylaeus punctatus 5
Lonchopria chalybaea 5
Cephalocolletes laticeps 4
Augochlora pura mosieri 4
Leioproctus nitidiventris 2
Hesperapis rhodocerata 2
Andrena concinnula 2
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
Baccharis 130
Acacia 34
Aruncus aruncus 32
Solidago 25
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. Note that both network graphs were first aligned taxonomically via 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 Colletidae Colletidae Colletidae->Asteraceae Colletidae->Salicaceae 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 Fabaceae Fabaceae Colletidae->Fabaceae Fringillidae Fringillidae Colletidae->Fringillidae Hydrangeaceae Hydrangeaceae Colletidae->Hydrangeaceae Hydrophyllaceae Hydrophyllaceae Colletidae->Hydrophyllaceae Hypericaceae Hypericaceae Colletidae->Hypericaceae Lamiaceae Lamiaceae Colletidae->Lamiaceae Malvaceae Malvaceae Colletidae->Malvaceae Plantaginaceae Plantaginaceae Colletidae->Plantaginaceae Polygonaceae Polygonaceae Colletidae->Polygonaceae 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 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 globi mdd tpt). These alignments may serve as a way to review name usage or aid in selecting of a suitable taxonomic name resource to use.

Sample of Name Alignments
providedName relationName resolvedCatalogName resolvedName
Acacia HAS_ACCEPTED_NAME col Acacia
Acacia SAME_AS ncbi Acacia
Acacia NONE discoverlife Acacia
Acacia HAS_ACCEPTED_NAME gbif Acacia
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
tpt NA 126
tpt genus 1
ncbi NA 45
ncbi genus 44
ncbi species 37
ncbi subgenus 2
ncbi subspecies 1
mdd NA 127
itis species 46
itis genus 40
itis NA 38
itis variety 2
itis subspecies 1
globi NA 66
globi genus 63
globi species 59
globi subspecies 4
globi variety 2
globi subgenus 2
globi suborder 1
gbif species 48
gbif genus 46
gbif NA 30
gbif variety 2
gbif subspecies 2
discoverlife NA 102
discoverlife species 25
col species 45
col genus 44
col NA 36
col section 1
col subspecies 1
col 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 87
col NONE 36
col SYNONYM_OF 15
discoverlife NONE 102
discoverlife HAS_ACCEPTED_NAME 23
discoverlife SYNONYM_OF 5
gbif HAS_ACCEPTED_NAME 104
gbif NONE 30
gbif SYNONYM_OF 26
globi SAME_AS 1050
globi NONE 32
itis HAS_ACCEPTED_NAME 82
itis NONE 38
itis SYNONYM_OF 8
mdd NONE 127
ncbi SAME_AS 83
ncbi NONE 45
ncbi SYNONYM_OF 3
tpt NONE 126
tpt HAS_ACCEPTED_NAME 1
List of Available Name Alignment Reports
catalog name alignment results
col associated names alignments (csv/tsv/html)
ncbi associated names alignments (csv/tsv/html)
discoverlife associated names alignments (csv/tsv/html)
gbif associated names alignments (csv/tsv/html)
itis associated names alignments (csv/tsv/html)
globi associated names alignments (csv/tsv/html)
mdd associated names alignments (csv/tsv/html)
tpt associated names alignments (csv/tsv/html)

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
2023-09-28T02:26:06Z summary https://github.com/globalbioticinteractions/fsca/archive/2cdcf9475b7e0ef2a728a96535608bc0ce2ac5ca.zip
2023-09-28T02:26:06Z summary 570 interaction(s)
2023-09-28T02:26:06Z summary 0 note(s)
2023-09-28T02:26:06Z summary 572 info(s)

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

: Most frequently occurring review notes, if any.

For more exhaustive list of review notes, please have a look at the Review Notes (csv/tsv/html).

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.

Sample 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 4 for badge examples.

Discussion

This review is intended to provide a perspective on the dataset to aid understanding of species interaction claims discovered. However, this review should not be considered as fitness of use or other kind of quality assessment. Instead, the review may be used as in indication of the open-ness5 and FAIRness (Wilkinson et al. 2016; Trekels et al. 2023) of the dataset: in order to perform this review, the data was likely openly available, Findable, Accessible, Interoperable and Reusable. Currently, this Open-FAIR assessment is qualitative, and with measurement units specified, a more quantitative approach can be implemented.

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.

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.