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

by Nomer and Elton, two naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

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

2024-06-17

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/mcz, is 3.36GiB in size and contains 8,943 interaction with 8 unique types of associations (e.g., interactsWith) between 1,876 primary taxon (e.g., Gasterosteus aculeatus Linnaeus, 1758) and 2,614 associated taxon (e.g., ground). 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:

Museum of Comparative Zoology, Harvard University - Version 162.430 http://digir.mcz.harvard.edu/ipt/archive.do?r=mczbase 2024-06-15T02:08:36.843Z 04a214d42105ae302af82c6f72fcbe45ab09a147423c3b4f1e6d382750d87abd

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/mcz 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 0.13.4
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. 3.36GiB) under review 
elton pull globalbioticinteractions/mcz

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

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

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/mcz\
 | 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/mcz, is 3.36GiB in size and contains 8,943 interaction with 8 unique types of associations (e.g., interactsWith) between 1,876 primary taxon (e.g., Gasterosteus aculeatus Linnaeus, 1758) and 2,614 associated taxon (e.g., ground).

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
Hemidactylus frenatus Duméril & Bibron, 1836 adjacentTo wall of building http://mczbase.mcz.harvard.edu/guid/MCZ:Herp:R-192777
Draco timorensis Kuhl, 1820 adjacentTo large tree by road http://mczbase.mcz.harvard.edu/guid/MCZ:Herp:R-192808
Cyrtodactylus Gray, 1827 adjacentTo rocks http://mczbase.mcz.harvard.edu/guid/MCZ:Herp:R-192930
Gehyra mutilata adjacentTo walls of building http://mczbase.mcz.harvard.edu/guid/MCZ:Herp:R-192850
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
interactsWith 4794
adjacentTo 2669
hasHost 764
parasiteOf 677
eats 19
hasParasite 9
eatenBy 8
visits 8
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Gasterosteus aculeatus Linnaeus, 1758 756
Perdita sp. Smith, 1853 536
Xylocopa darwini Cockerell, 1926 482
Camallanus Railliet & Henry, 1915 338
Symbion americanus Obst, Funch & Kristensen, 2006 208
Camponotus sp. Mayr, 1861 197
Pheidole sp. Westwood, 1839 184
Cephalochlamys Blanchard, 1908 169
Andrena hirticincta Provancher, 1888 102
Hepialidae Stephens, 1829 94
Bdelloura candida (Girard, 1850) 65
Andrena sp. Fabricius 1775 64
Pontoniinae 60
Formicidae Latreille, 1809 57
Pheidole Westwood, 1839 54
Hylaeus modestus Say, 1837 54
Globicephala melaena (Traill, 1809) 49
Andrena erigeniae Robertson, 1891 47
Pseudopanurgus pauper (Cresson, 1878) 47
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
ground 437
Mites 225
Ceanothus 173
Stylopized 172
Heterotheca 141
ex rotten log 131
Solidago 112
Ophiocordyceps 94
ex dead twig 89
under 88
low vegetation 86
Mentzelia 83
Haplopappus 80
tree 60
gilled mushrooms 56
vegetation 49
Chamaesaracha 46
Globicephala melaena (Traill, 1809) 40
Waltheria 40
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Xylocopa darwini Cockerell, 1926 interactsWith Mites 167
Perdita sp. Smith, 1853 interactsWith Heterotheca 136
Hepialidae Stephens, 1829 interactsWith Ophiocordyceps 94
Andrena hirticincta Provancher, 1888 interactsWith Stylopized 90
Perdita sp. Smith, 1853 interactsWith Mentzelia 83
Perdita sp. Smith, 1853 interactsWith Haplopappus 77
Perdita sp. Smith, 1853 interactsWith Chamaesaracha 46
Camponotus sp. Mayr, 1861 adjacentTo ground 45
Globicephala melaena (Traill, 1809) interactsWith Globicephala melaena (Traill, 1809) 40
Lapethus newtoni Slipinski adjacentTo gilled mushrooms 40
Pseudopanurgus pauper (Cresson, 1878) interactsWith Ceanothus 40
Trigona ceophloei Schwarz hasHost Ex stomach of Ceoploeus lineatus 38
Perdita sp. Smith, 1853 interactsWith Solidago 38
Xylocopa darwini Cockerell, 1926 interactsWith mites 38
Crematogaster laeviuscula Mayr, 1870 adjacentTo cotton wood tree 37
Gasterosteus aculeatus Linnaeus, 1758 interactsWith trout 35
Andrena rehni Viereck, 1907 interactsWith Ceanothus 35
Xylocopa darwini Cockerell, 1926 interactsWith Palo Santo (=Bursera graveolens) nest 35
Camponotus sp. Mayr, 1861 adjacentTo low vegetation 34

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
interactions Andrenidae Andrenidae Salicaceae Salicaceae Andrenidae->Salicaceae Apidae Apidae Asteraceae Asteraceae Apidae->Asteraceae Polygonaceae Polygonaceae Apidae->Polygonaceae Chrysogorgiidae Chrysogorgiidae Cladorhizidae Cladorhizidae Chrysogorgiidae->Cladorhizidae Cladorhizidae->Chrysogorgiidae Delphinidae Delphinidae Delphinidae->Delphinidae Eulophidae Eulophidae Fabaceae Fabaceae Eulophidae->Fabaceae Gonyleptidae Gonyleptidae Araucariaceae Araucariaceae Gonyleptidae->Araucariaceae Neopilionidae Neopilionidae Neopilionidae->Neopilionidae Thomisidae Thomisidae Apiaceae Apiaceae Thomisidae->Apiaceae Tretodictyidae Tretodictyidae Tretodictyidae->Tretodictyidae

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
Pungitius HAS_ACCEPTED_NAME col Pungitius
Salmonids NONE col Salmonids
high plants NONE col high plants
ant attached right hind leg NONE col ant attached right hind leg
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 1625
col class 5
col family 57
col genus 349
col infraspecific name 1
col kingdom 1
col order 5
col phylum 1
col section 1
col species 1415
col subfamily 5
col subgenus 5
col subspecies 51
col variety 7
discoverlife NA 3175
discoverlife species 339
gbif NA 1370
gbif class 5
gbif family 61
gbif genus 387
gbif kingdom 2
gbif order 5
gbif phylum 1
gbif species 1628
gbif subspecies 62
gbif variety 12
itis NA 1829
itis class 5
itis family 56
itis genus 324
itis kingdom 1
itis order 5
itis phylum 1
itis species 1232
itis subfamily 4
itis subspecies 47
itis variety 12
mdd NA 3513
ncbi NA 1936
ncbi class 5
ncbi family 55
ncbi genus 341
ncbi order 5
ncbi phylum 1
ncbi species 1150
ncbi subfamily 4
ncbi subgenus 8
ncbi subspecies 14
ncbi varietas 2
pbdb NA 3155
pbdb class 6
pbdb family 47
pbdb genus 197
pbdb informal 1
pbdb kingdom 1
pbdb order 5
pbdb phylum 1
pbdb species 99
pbdb subfamily 2
pbdb unranked clade 1
tpt NA 3464
tpt genus 3
tpt species 46
wfo NA 3190
wfo family 4
wfo genus 125
wfo phylum 1
wfo species 183
wfo subspecies 5
wfo variety 8
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 1849
col NONE 2450
col SYNONYM_OF 367
discoverlife NONE 4106
discoverlife HAS_ACCEPTED_NAME 318
discoverlife SYNONYM_OF 112
discoverlife HOMONYM_OF 23
gbif HAS_ACCEPTED_NAME 2308
gbif NONE 2187
gbif SYNONYM_OF 554
itis HAS_ACCEPTED_NAME 1683
itis NONE 2655
itis SYNONYM_OF 127
mdd NONE 4408
mdd HAS_ACCEPTED_NAME 14
ncbi NONE 2782
ncbi SAME_AS 1612
ncbi COMMON_NAME_OF 11
ncbi SYNONYM_OF 64
pbdb HAS_ACCEPTED_NAME 410
pbdb NONE 4007
pbdb SYNONYM_OF 36
tpt NONE 4368
tpt HAS_ACCEPTED_NAME 56
tpt SYNONYM_OF 1
wfo NONE 4066
wfo SYNONYM_OF 92
wfo HAS_ACCEPTED_NAME 300
wfo HAS_UNCHECKED_NAME 55
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
2024-06-17T02:27:18Z note found unresolved reference [MCZ:Cryo:14052]
2024-06-17T02:27:18Z note found unresolved reference [MCZ:Cryo:14068]
2024-06-17T02:27:18Z note found unresolved reference [MCZ:Cryo:14075]
2024-06-17T02:27:18Z note found unresolved reference [MCZ:Cryo:14076]

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

Most frequently occurring review notes, if any.
reviewComment count
found unresolved reference [MCZ:Cryo:14052] 1
found unresolved reference [MCZ:Cryo:14068] 1
found unresolved reference [MCZ:Cryo:14075] 1
found unresolved reference [MCZ:Cryo:14076] 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 (2024-06-17) 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.