A Review of Biotic Interactions and Taxon Names Found in globalbioticinteractions/ummz-ummzi

by Nomer and Elton, two naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

https://github.com/globalbioticinteractions/ummz-ummzi/issues

2024-07-04

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/ummz-ummzi, is 20.8MiB in size and contains 54,339 interaction with 3 unique types of associations (e.g., interactsWith) between 1,830 primary taxon (e.g., Proctophyllodes) and 4,247 associated taxon (e.g., Mammalia / Chiroptera / Vespertilionidae / Myotis / velifer). 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:

University of Michigan Museum of Zoology, Division of Insects https://github.com/globalbioticinteractions/ummz-ummzi/archive/0f20ed99288f6668fb894b69b98c01658c08debe.zip 2024-06-29T05:45:08.244Z 3994ee5d7e1d1b0b11a4ea8841a996e9c5d1fed4e1fbdbe3c81e0302ee737e6b

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/ummz-ummzi 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 0.5.12
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. 20.8MiB) under review 
elton pull globalbioticinteractions/ummz-ummzi

# generate review notes
elton review globalbioticinteractions/ummz-ummzi\
 > review.tsv

# export indexed interaction records
elton interactions globalbioticinteractions/ummz-ummzi\
 > interactions.tsv

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/ummz-ummzi\
 | 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/ummz-ummzi, is 20.8MiB in size and contains 54,339 interaction with 3 unique types of associations (e.g., interactsWith) between 1,830 primary taxon (e.g., Proctophyllodes) and 4,247 associated taxon (e.g., Mammalia / Chiroptera / Vespertilionidae / Myotis / velifer).

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
Proctophyllodes interactsWith Aves / Passeriformes / Furnariidae / Leptasthenura / andicola University of Michigan Museum of Zoology, Division of Insects. Accessed at https://ipt.lsa.umich.edu/archive.do?r=ummz_insects on 04 Jul 2024.
Lilioceris lilii adjacentTo Asiatic lily University of Michigan Museum of Zoology, Division of Insects. Accessed at https://ipt.lsa.umich.edu/archive.do?r=ummz_insects on 04 Jul 2024.
Lilioceris lilii adjacentTo Asiatic lily University of Michigan Museum of Zoology, Division of Insects. Accessed at https://ipt.lsa.umich.edu/archive.do?r=ummz_insects on 04 Jul 2024.
Halyomorpha halys (Stal) hasHost car University of Michigan Museum of Zoology, Division of Insects. Accessed at https://ipt.lsa.umich.edu/archive.do?r=ummz_insects on 04 Jul 2024.
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
interactsWith 53662
hasHost 407
adjacentTo 270
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Proctophyllodes 3207
Chiroptoglyphus americanus 1641
Macronyssus crosbyi 1553
Proterothrix 1170
Proctophyllodes polyxenus 926
Macronyssus unidens 882
Pterodectes 625
Freyana anatina 597
Trouessartia trouessarti 552
Freyana largifolia 502
Alloptellus coniventris 499
Amerodectes 498
Prolistrophorus bidentatus 478
Proctophyllodes spini 471
Eustathia cultrifera 457
Freyana nyrocae 441
Trouessartia lonchurae 411
Pterolichus obtusus 393
Plicatalloptes fregatae 386
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
Mammalia / Chiroptera / Vespertilionidae / Myotis / velifer 3923
Aves / Passeriformes / Acrocephalidae / Acrocephalus / arundinaceus 800
Aves / Passeriformes / Icteridae / Quiscalus / quiscula 437
Aves / Suliformes / Fregatidae / Fregata / ariel / ariel 437
Aves / Passeriformes / Turdidae / Turdus / migratorius 363
Aves / Galliformes / Phasianidae / Gallus / gallus / domesticus 360
Aves / Passeriformes / Fringillidae / Spinus / tristis 335
Aves / Passeriformes / Cardinalidae / Pheucticus / ludovicianus 309
Aves / Passeriformes / Parulidae / Seiurus / aurocapilla 297
Salix 270
Aves / Apodiformes / Apodidae / Chaetura / pelagica 267
Aves / Apodiformes / Apodidae / Apus / apus / apus 267
Aves / Passeriformes / Fringillidae / Haemorhous / mexicanus 263
Aves / Passeriformes / Bombycillidae / Bombycilla / cedrorum 250
Mammalia / Rodentia / Cricetidae / Akodon / aerosus 244
Aves / Strigiformes / Strigidae / Bubo / virginianus 223
Apodiformes / Apodidae / Collocalia / C. esculenta 220
Mammalia / Didelphimorphia / Didelphidae / Metachirus / nudicaudatus 215
Charadrius / vociferus 207
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Macronyssus crosbyi interactsWith Mammalia / Chiroptera / Vespertilionidae / Myotis / velifer 1544
Chiroptoglyphus americanus interactsWith Mammalia / Chiroptera / Vespertilionidae / Myotis / velifer 1530
Macronyssus unidens interactsWith Mammalia / Chiroptera / Vespertilionidae / Myotis / velifer 849
Trouessartia trouessarti interactsWith Aves / Passeriformes / Acrocephalidae / Acrocephalus / arundinaceus 441
Trouessartia trouessartii interactsWith Aves / Passeriformes / Acrocephalidae / Acrocephalus / arundinaceus 348
Pterolichus obtusus interactsWith Aves / Galliformes / Phasianidae / Gallus / gallus / domesticus 347
Proctophyllodes interactsWith Aves / Passeriformes / Turdidae / Turdus / migratorius 336
Proctophyllodes spini interactsWith Aves / Passeriformes / Fringillidae / Spinus / tristis 308
Prolistrophorus bidentatus interactsWith Mammalia / Rodentia / Cricetidae / Akodon / aerosus 244
Alloptellus coniventris interactsWith Aves / Suliformes / Fregatidae / Fregata / ariel / ariel 243
Proctophyllodes ampelidis interactsWith Aves / Passeriformes / Bombycillidae / Bombycilla / cedrorum 239
Eustathia cultrifera interactsWith Aves / Apodiformes / Apodidae / Apus / apus / apus 228
Echineustathia tricapitosetosa interactsWith Aves / Apodiformes / Apodidae / Chaetura / pelagica 208
Proctophyllodes interactsWith Aves / Passeriformes / Fringillidae / Haemorhous / mexicanus 204
Prolistrophorus bidentatus interactsWith Mammalia / Rodentia / Cricetidae / Akodon / torques 170
Metachiroecius brasiliensis interactsWith Mammalia / Didelphimorphia / Didelphidae / Metachirus / nudicaudatus 170
Proctophyllodes polyxenus interactsWith Aves / Passeriformes / Passerellidae / Junco / hyemalis 163
Plicatalloptes fregatae interactsWith Aves / Suliformes / Fregatidae / Fregata / ariel / ariel 160
Kramerella interactsWith Aves / Strigiformes / Strigidae / Bubo / virginianus 153

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 Fungi Fungi Animalia->Fungi
interactions Andrenidae Andrenidae Anacardiaceae Anacardiaceae Andrenidae->Anacardiaceae Apocynaceae Apocynaceae Andrenidae->Apocynaceae Asparagaceae Asparagaceae Andrenidae->Asparagaceae Asteraceae Asteraceae Andrenidae->Asteraceae Brassicaceae Brassicaceae Andrenidae->Brassicaceae Caprifoliaceae Caprifoliaceae Andrenidae->Caprifoliaceae Cornaceae Cornaceae Andrenidae->Cornaceae Ericaceae Ericaceae Andrenidae->Ericaceae Fabaceae Fabaceae Andrenidae->Fabaceae Gentianaceae Gentianaceae Andrenidae->Gentianaceae Geraniaceae Geraniaceae Andrenidae->Geraniaceae Grossulariaceae Grossulariaceae Andrenidae->Grossulariaceae Hydrangeaceae Hydrangeaceae Andrenidae->Hydrangeaceae Hydrophyllaceae Hydrophyllaceae Andrenidae->Hydrophyllaceae Melanthiaceae Melanthiaceae Andrenidae->Melanthiaceae Metacapnodiaceae Metacapnodiaceae Andrenidae->Metacapnodiaceae Montiaceae Montiaceae Andrenidae->Montiaceae Namaceae Namaceae Andrenidae->Namaceae Polemoniaceae Polemoniaceae Andrenidae->Polemoniaceae Polygonaceae Polygonaceae Andrenidae->Polygonaceae Ranunculaceae Ranunculaceae Andrenidae->Ranunculaceae Rhamnaceae Rhamnaceae Andrenidae->Rhamnaceae Rosaceae Rosaceae Andrenidae->Rosaceae Salicaceae Salicaceae Andrenidae->Salicaceae Apidae Apidae Apidae->Apocynaceae Apidae->Asteraceae Apidae->Brassicaceae Apidae->Ericaceae Apidae->Fabaceae Apidae->Gentianaceae Apidae->Grossulariaceae Apidae->Hydrangeaceae Apidae->Hydrophyllaceae Apidae->Metacapnodiaceae Apidae->Rosaceae Apidae->Salicaceae Boraginaceae Boraginaceae Apidae->Boraginaceae Bromeliaceae Bromeliaceae Apidae->Bromeliaceae Bunocotylidae Bunocotylidae Apidae->Bunocotylidae Cleomaceae Cleomaceae Apidae->Cleomaceae Cucurbitaceae Cucurbitaceae Apidae->Cucurbitaceae Lamiaceae Lamiaceae Apidae->Lamiaceae Malvaceae Malvaceae Apidae->Malvaceae Pinaceae Pinaceae Apidae->Pinaceae Sapindaceae Sapindaceae Apidae->Sapindaceae Braconidae Braconidae Braconidae->Salicaceae Colletidae Colletidae Colletidae->Hydrangeaceae Colletidae->Rosaceae Colletidae->Salicaceae Apiaceae Apiaceae Colletidae->Apiaceae Aquifoliaceae Aquifoliaceae Colletidae->Aquifoliaceae Psilostomidae Psilostomidae Colletidae->Psilostomidae Saxifragaceae Saxifragaceae Colletidae->Saxifragaceae Halictidae Halictidae Halictidae->Apocynaceae Halictidae->Asparagaceae Halictidae->Asteraceae Halictidae->Metacapnodiaceae Halictidae->Rhamnaceae Halictidae->Rosaceae Halictidae->Rosaceae Halictidae->Salicaceae Halictidae->Lamiaceae Hypericaceae Hypericaceae Halictidae->Hypericaceae Violaceae Violaceae Halictidae->Violaceae Leeuwenhoekiidae Leeuwenhoekiidae Crotaphytidae Crotaphytidae Leeuwenhoekiidae->Crotaphytidae Macronyssidae Macronyssidae Cricetidae Cricetidae Macronyssidae->Cricetidae Viperidae Viperidae Macronyssidae->Viperidae Megachilidae Megachilidae Megachilidae->Anacardiaceae Megachilidae->Apocynaceae Megachilidae->Asteraceae Megachilidae->Fabaceae Megachilidae->Rosaceae Megachilidae->Lamiaceae Megachilidae->Violaceae

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
Acanthonyssus dentipes HAS_ACCEPTED_NAME col Acanthonyssus dentipes
Acanthonyssus HAS_ACCEPTED_NAME col Acanthonyssus
Acanthonyssus proechimys HAS_ACCEPTED_NAME col Acanthonyssus proechimys
Accipiter cooperi SYNONYM_OF col Accipiter cooperii
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 1329
col class 6
col family 24
col genus 160
col kingdom 1
col order 29
col parvorder 1
col phylum 1
col species 1205
col subgenus 11
col subspecies 26
col variety 5
discoverlife NA 2493
discoverlife species 283
gbif NA 962
gbif class 6
gbif family 25
gbif genus 256
gbif kingdom 1
gbif order 29
gbif phylum 1
gbif species 1476
gbif subspecies 39
gbif variety 11
itis NA 1469
itis class 7
itis division 1
itis family 22
itis genus 143
itis kingdom 1
itis order 30
itis species 1083
itis subgenus 1
itis subspecies 15
itis variety 5
mdd NA 2775
ncbi NA 1476
ncbi clade 1
ncbi class 6
ncbi family 22
ncbi genus 185
ncbi kingdom 1
ncbi order 29
ncbi phylum 1
ncbi species 1045
ncbi subgenus 3
ncbi subspecies 8
ncbi varietas 2
pbdb NA 2421
pbdb class 6
pbdb family 13
pbdb genus 56
pbdb kingdom 1
pbdb order 30
pbdb species 246
pbdb subclass 1
pbdb superorder 1
pbdb unranked clade 6
tpt NA 1223
tpt family 10
tpt genus 24
tpt order 24
tpt species 1494
wfo NA 2509
wfo family 1
wfo genus 77
wfo order 2
wfo species 180
wfo subspecies 14
wfo variety 4
worms NA 2405
worms class 4
worms family 15
worms genus 71
worms kingdom 1
worms order 26
worms phylum (division) 1
worms species 251
worms subclass 1
worms subspecies 3
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 4614
col SYNONYM_OF 225
col NONE 1398
discoverlife NONE 5799
discoverlife HAS_ACCEPTED_NAME 279
discoverlife SYNONYM_OF 87
discoverlife HOMONYM_OF 21
gbif HAS_ACCEPTED_NAME 5277
gbif SYNONYM_OF 422
gbif NONE 1025
itis HAS_ACCEPTED_NAME 4454
itis SYNONYM_OF 107
itis NONE 1543
mdd NONE 5929
mdd HAS_ACCEPTED_NAME 145
mdd SYNONYM_OF 6
ncbi NONE 1561
ncbi SYNONYM_OF 64
ncbi SAME_AS 4470
pbdb NONE 2510
pbdb SYNONYM_OF 9924
pbdb HAS_ACCEPTED_NAME 3560
tpt NONE 4127
tpt SYNONYM_OF 409
tpt HAS_ACCEPTED_NAME 1866
wfo NONE 5794
wfo HAS_ACCEPTED_NAME 253
wfo HAS_UNCHECKED_NAME 83
wfo SYNONYM_OF 83
worms NONE 2510
worms SYNONYM_OF 59
worms HAS_ACCEPTED_NAME 3567
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
2024-07-04T17:33:48Z note found unsupported interaction type with name: [Nest HV Cell 05 em Host]
2024-07-04T17:33:48Z note found unsupported interaction type with name: [Nest KS Cell 04 em. Host]
2024-07-04T17:33:48Z note found unsupported interaction type with name: [Nest SW Cell 03 em. Host]
2024-07-04T17:33:48Z note target taxon name missing

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

Most frequently occurring review notes, if any.
reviewComment count
target taxon name missing 818
found unsupported interaction type with name: [Locality verbatim from label] 750
found unsupported interaction type with name: [Proctophyllodidae] 570
found unsupported interaction type with name: [Trombiculidae] 520

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 (2024-07-04) 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.