A Review of Biotic Interactions and Taxon Names Found in globalbioticinteractions/cmnh-izc

by Nomer and Elton, two naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

https://github.com/globalbioticinteractions/cmnh-izc/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/cmnh-izc, is 777KiB in size and contains 2,278 interaction with 1 unique type of association (e.g., hasHost) between 253 primary taxa (e.g., Xenopsylla) and 261 associated taxa (e.g., Apodemus). 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:

Carnegie Invertebrate Zoology Collection https://github.com/globalbioticinteractions/cmnh-izc/archive/668205275612e54e0c0cbc37c14cbf149af712aa.zip 2024-11-16T00:29:25.012Z 654c7c512f98f2a668b89da3a3db452754aa8b235992a6015bd65338e065a4ac

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/cmnh-izc 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.  777KiB) under review 
elton pull globalbioticinteractions/cmnh-izc

# generate review notes
elton review globalbioticinteractions/cmnh-izc\
 > review.tsv

# export indexed interaction records
elton interactions globalbioticinteractions/cmnh-izc\
 > interactions.tsv

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/cmnh-izc\
 | 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/cmnh-izc, is 777KiB in size and contains 2,278 interaction with 1 unique type of association (e.g., hasHost) between 253 primary taxa (e.g., Xenopsylla) and 261 associated taxa (e.g., Apodemus).

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
Medwayella robinsoni hasHost Sundasciurus tenuis dee1b539-cf04-4606-8aa7-7ff80f1fa796
Stivalius hasHost Callosciurus notatus 094f145b-503d-4811-bb72-76ee64cfc112
Stivalius aporus hasHost Rattus 28513060-cd6b-46c1-b4fb-feddd0b58c3b
Xenopsylla cheopis hasHost Soricidae 96fad270-39bf-4ce0-9c7f-7b44fd82126a
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
hasHost 2278
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Xenopsylla 214
Ctenocephalides felis 196
Metastivalius anaxilas 161
Ctenophthalmus 143
Dinopsyllus 139
Leptopsylla 102
Nosopsyllus 70
Frontopsylla 56
Sigmactenus toxopeusi 51
Amphipsylla 43
Neopsylla 43
Acanthopsylla 37
Thaumapsylla breviceps 35
Nosopsyllus simla 31
Callopsylla caspia fragilis 27
Papuapsylla 24
Pulex irritans 21
Callopsylla 21
Metastivalius mordax 20
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
Apodemus 223
Melomys 178
Lophuromys 160
Mastomys 128
Alticola 97
Paramelomys rubex 81
Calomyscus 76
Canis familiaris 67
Aethomys 62
Crocidura 62
Gerbillus 52
Meriones 41
Cricetulus 40
Eonycteris spelaea 37
Akodon 34
Genetta 33
Lemniscomys 30
Mus 29
Lepus 28
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Leptopsylla hasHost Apodemus 81
Ctenophthalmus hasHost Lophuromys 80
Metastivalius anaxilas hasHost Melomys 78
Xenopsylla hasHost Mastomys 64
Dinopsyllus hasHost Lophuromys 50
Ctenocephalides felis hasHost Canis familiaris 49
Xenopsylla hasHost Aethomys 46
Metastivalius anaxilas hasHost Paramelomys rubex 44
Dinopsyllus hasHost Mastomys 42
Frontopsylla hasHost Apodemus 35
Neopsylla hasHost Apodemus 31
Amphipsylla hasHost Alticola 30
Sigmactenus toxopeusi hasHost Melomys 29
Thaumapsylla breviceps hasHost Eonycteris spelaea 26
Xenopsylla hasHost Meriones 24
Ctenocephalides felis hasHost Lepus 23
Ctenocephalides felis hasHost Genetta 22
Nosopsyllus simla hasHost Apodemus 21
Ctenophthalmus hasHost Mus 21

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 Plantae->Animalia
interactions Amaryllidaceae Amaryllidaceae Muridae Muridae Amaryllidaceae->Muridae Ceratophyllidae Ceratophyllidae Ceratophyllidae->Muridae Calomyscidae Calomyscidae Ceratophyllidae->Calomyscidae Cricetidae Cricetidae Ceratophyllidae->Cricetidae Didelphidae Didelphidae Ceratophyllidae->Didelphidae Dipodidae Dipodidae Ceratophyllidae->Dipodidae Fringillidae Fringillidae Ceratophyllidae->Fringillidae Furnariidae Furnariidae Ceratophyllidae->Furnariidae Heteromyidae Heteromyidae Ceratophyllidae->Heteromyidae Hirundinidae Hirundinidae Ceratophyllidae->Hirundinidae Hominidae Hominidae Ceratophyllidae->Hominidae Muscicapidae Muscicapidae Ceratophyllidae->Muscicapidae Nesomyidae Nesomyidae Ceratophyllidae->Nesomyidae Phyllostomidae Phyllostomidae Ceratophyllidae->Phyllostomidae Procyonidae Procyonidae Ceratophyllidae->Procyonidae Sciuridae Sciuridae Ceratophyllidae->Sciuridae Soricidae Soricidae Ceratophyllidae->Soricidae Chimaeropsyllidae Chimaeropsyllidae Chimaeropsyllidae->Muridae Chimaeropsyllidae->Soricidae Macroscelididae Macroscelididae Chimaeropsyllidae->Macroscelididae Coptopsyllidae Coptopsyllidae Coptopsyllidae->Muridae Ctenophthalmidae Ctenophthalmidae Ctenophthalmidae->Muridae Ctenophthalmidae->Calomyscidae Ctenophthalmidae->Cricetidae Ctenophthalmidae->Heteromyidae Ctenophthalmidae->Nesomyidae Ctenophthalmidae->Sciuridae Ctenophthalmidae->Soricidae Bathyergidae Bathyergidae Ctenophthalmidae->Bathyergidae Leporidae Leporidae Ctenophthalmidae->Leporidae Pteropodidae Pteropodidae Ctenophthalmidae->Pteropodidae Hystrichopsyllidae Hystrichopsyllidae Hystrichopsyllidae->Cricetidae Hystrichopsyllidae->Soricidae Ischnopsyllidae Ischnopsyllidae Ischnopsyllidae->Pteropodidae Vespertilionidae Vespertilionidae Ischnopsyllidae->Vespertilionidae Leptopsyllidae Leptopsyllidae Leptopsyllidae->Muridae Leptopsyllidae->Calomyscidae Leptopsyllidae->Cricetidae Leptopsyllidae->Dipodidae Leptopsyllidae->Heteromyidae Leptopsyllidae->Soricidae Bovidae Bovidae Leptopsyllidae->Bovidae Corcoracidae Corcoracidae Leptopsyllidae->Corcoracidae Dasyuridae Dasyuridae Leptopsyllidae->Dasyuridae Erinaceidae Erinaceidae Leptopsyllidae->Erinaceidae Pulicidae Pulicidae Pulicidae->Muridae Pulicidae->Calomyscidae Pulicidae->Cricetidae Pulicidae->Didelphidae Pulicidae->Dipodidae Pulicidae->Hominidae Pulicidae->Muscicapidae Pulicidae->Nesomyidae Pulicidae->Phyllostomidae Pulicidae->Sciuridae Pulicidae->Soricidae Pulicidae->Macroscelididae Pulicidae->Leporidae Pulicidae->Pteropodidae Pulicidae->Bovidae Pulicidae->Dasyuridae Pulicidae->Erinaceidae Anatidae Anatidae Pulicidae->Anatidae Camelidae Camelidae Pulicidae->Camelidae Canidae Canidae Pulicidae->Canidae Cercopithecidae Cercopithecidae Pulicidae->Cercopithecidae Chloropseidae Chloropseidae Pulicidae->Chloropseidae Curculionidae Curculionidae Pulicidae->Curculionidae Felidae Felidae Pulicidae->Felidae Galagidae Galagidae Pulicidae->Galagidae Gliridae Gliridae Pulicidae->Gliridae Herpestidae Herpestidae Pulicidae->Herpestidae Hyaenidae Hyaenidae Pulicidae->Hyaenidae Hystricidae Hystricidae Pulicidae->Hystricidae Locustellidae Locustellidae Pulicidae->Locustellidae Macropodidae Macropodidae Pulicidae->Macropodidae Megalonychidae Megalonychidae Pulicidae->Megalonychidae Meliphagidae Meliphagidae Pulicidae->Meliphagidae Mustelidae Mustelidae Pulicidae->Mustelidae Peramelidae Peramelidae Pulicidae->Peramelidae Petauridae Petauridae Pulicidae->Petauridae Rallidae Rallidae Pulicidae->Rallidae Tachyglossidae Tachyglossidae Pulicidae->Tachyglossidae Tragulidae Tragulidae Pulicidae->Tragulidae Viverridae Viverridae Pulicidae->Viverridae Pygiopsyllidae Pygiopsyllidae Pygiopsyllidae->Muridae Pygiopsyllidae->Cricetidae Pygiopsyllidae->Didelphidae Pygiopsyllidae->Fringillidae Pygiopsyllidae->Sciuridae Pygiopsyllidae->Corcoracidae Pygiopsyllidae->Dasyuridae Pygiopsyllidae->Petauridae Pygiopsyllidae->Rallidae Acanthizidae Acanthizidae Pygiopsyllidae->Acanthizidae Acrobatidae Acrobatidae Pygiopsyllidae->Acrobatidae Meropidae Meropidae Pygiopsyllidae->Meropidae Tupaiidae Tupaiidae Pygiopsyllidae->Tupaiidae Rhopalopsyllidae Rhopalopsyllidae Rhopalopsyllidae->Cricetidae Rhopalopsyllidae->Didelphidae Rhopalopsyllidae->Heteromyidae Rhopalopsyllidae->Vespertilionidae Rhopalopsyllidae->Canidae Caviidae Caviidae Rhopalopsyllidae->Caviidae Ctenomyidae Ctenomyidae Rhopalopsyllidae->Ctenomyidae Cuniculidae Cuniculidae Rhopalopsyllidae->Cuniculidae Dasyproctidae Dasyproctidae Rhopalopsyllidae->Dasyproctidae Molossidae Molossidae Rhopalopsyllidae->Molossidae Psittacidae Psittacidae Rhopalopsyllidae->Psittacidae Stephanocircidae Stephanocircidae Stephanocircidae->Cricetidae Stivaliidae Stivaliidae Stivaliidae->Muridae Stivaliidae->Heteromyidae Stivaliidae->Sciuridae Stivaliidae->Soricidae Stivaliidae->Bovidae Stivaliidae->Dasyuridae Stivaliidae->Canidae Stivaliidae->Meliphagidae Stivaliidae->Peramelidae Stivaliidae->Tachyglossidae Stivaliidae->Tupaiidae Phalangeridae Phalangeridae Stivaliidae->Phalangeridae Podargidae Podargidae Stivaliidae->Podargidae Tungidae Tungidae Tungidae->Hominidae Xiphiopsyllidae Xiphiopsyllidae Xiphiopsyllidae->Muridae

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
Abrothrix olivacea SYNONYM_OF col Abrothrix olivaceus
Acanthopsylla HAS_ACCEPTED_NAME col Acanthopsylla
Acanthopsylla enderleini HAS_ACCEPTED_NAME col Acanthopsylla enderleini
Acanthopsylla eudromiciae HAS_ACCEPTED_NAME col Acanthopsylla eudromiciae
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 25
col class 1
col family 17
col genus 141
col order 3
col species 300
col subgenus 17
col subspecies 23
discoverlife NA 511
gbif NA 28
gbif class 1
gbif family 17
gbif genus 143
gbif order 3
gbif species 298
gbif subspecies 22
itis NA 262
itis class 1
itis family 17
itis genus 89
itis order 3
itis species 138
itis subgenus 1
itis subspecies 2
mdd NA 511
ncbi NA 184
ncbi class 1
ncbi family 17
ncbi genus 123
ncbi order 3
ncbi species 176
ncbi subgenus 1
ncbi subspecies 7
pbdb NA 342
pbdb class 1
pbdb family 17
pbdb genus 72
pbdb order 3
pbdb species 76
tpt NA 63
tpt family 17
tpt genus 81
tpt order 2
tpt species 348
wfo NA 508
wfo genus 3
worms NA 445
worms class 1
worms family 12
worms genus 29
worms order 3
worms species 22
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 SYNONYM_OF 18
col HAS_ACCEPTED_NAME 498
col NONE 25
discoverlife NONE 514
gbif SYNONYM_OF 44
gbif HAS_ACCEPTED_NAME 497
gbif NONE 28
itis SYNONYM_OF 14
itis NONE 265
itis HAS_ACCEPTED_NAME 242
mdd HAS_ACCEPTED_NAME 113
mdd NONE 399
mdd SYNONYM_OF 2
ncbi SYNONYM_OF 15
ncbi SAME_AS 316
ncbi NONE 186
pbdb SYNONYM_OF 15
pbdb NONE 345
pbdb HAS_ACCEPTED_NAME 162
tpt HAS_ACCEPTED_NAME 505
tpt NONE 63
tpt SYNONYM_OF 37
wfo NONE 511
wfo HAS_ACCEPTED_NAME 3
worms NONE 448
worms HAS_ACCEPTED_NAME 64
worms SYNONYM_OF 5
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
2024-11-18T01:28:02Z note date [0000-01-01T00:00:00Z] occurred in the first century AD
2024-11-18T01:28:02Z note date [0000-01-01T00:00:00Z] occurred in the first century AD
2024-11-18T01:28:02Z note date [0000-01-01T00:00:00Z] occurred in the first century AD
2024-11-18T01:28:02Z note date [0000-01-01T00:00:00Z] occurred in the first century AD

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

Most frequently occurring review notes, if any.
reviewComment count
date [0000-01-01T00:00:00Z] occurred in the first century AD 52

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.