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

by Nomer and Elton, two naive review bots

[email protected]

https://globalbioticinteractions.org/contribute

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

2024-04-17

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/vectorbase, is 4.75MiB in size and contains 2,043 interaction with 1 unique type of association (e.g., parasiteOf) between 84 primary taxa (e.g., Anopheles darlingi) and 82 associated taxa (e.g., human). 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:

Giraldo-Calderón, G. I., Emrich, S. J., MacCallum, R. M., Maslen, G., Dialynas, E., Topalis, P., … Lawson, D. (2015). VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases. Nucleic acids research, 43(Database issue), D707–D713. doi:10.1093/nar/gku1117. https://github.com/globalbioticinteractions/vectorbase/archive/00d6285cd4e9f4edd18cb2778624ab31b34b23b8.zip 2024-04-13T06:42:10.811Z 97de6d8a4da8cb6b091dcbef550a35d75bc858cf3e647b132ffb6c175b05a287

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/vectorbase 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 0.5.7
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. 4.75MiB) under review 
elton pull globalbioticinteractions/vectorbase

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

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

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/vectorbase\
 | 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/vectorbase, is 4.75MiB in size and contains 2,043 interaction with 1 unique type of association (e.g., parasiteOf) between 84 primary taxa (e.g., Anopheles darlingi) and 82 associated taxa (e.g., human).

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
Anopheles funestus parasiteOf human doi:10.1186/s12936-014-0527-9
Anopheles leesoni parasiteOf human doi:10.1186/s12936-014-0527-9
Anopheles arabiensis parasiteOf human doi:10.1186/s12936-014-0527-9
Anopheles gambiae sensu stricto parasiteOf human doi:10.1186/s12936-014-0527-9
Most Frequently Mentioned Interaction Types (up to 20 most frequent)
interactionTypeName count
parasiteOf 14374
Most Frequently Mentioned Primary Taxa (up to 20 most frequent)
sourceTaxonName count
Anopheles darlingi 5635
Anopheles farauti 1516
Anopheles coustani 1365
Anopheles maculipalpis 694
Anopheles squamosus 670
Anopheles maculipennis sensu lato 568
Anopheles farauti No. 4 544
Anopheles culicifacies BCE subgroup 435
Anopheles rufipes 428
Culex cedecei 347
Anopheles arabiensis 231
Culiseta annulata 205
Anopheles punctulatus 203
Anopheles longirostris 131
Anopheles mascarensis 128
Aedes camptorhynchus 122
Anopheles funestus 106
Culex pipiens 100
Anopheles gambiae sensu stricto 90
Most Frequently Mentioned Associate Taxa (up to 20 most frequent)
targetTaxonName count
human 6204
cow 2337
galliformes 2301
pig 1256
dog 473
vertebrate 454
bovine 293
european rabbit 233
hispid cotton rat 201
rat 82
chicken 71
goat 46
wood pigeon 44
sheep 34
blackbird 33
green anole 27
house sparrow 23
animal 20
white tailed deer 18
Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)
sourceTaxonName interactionTypeName targetTaxonName count
Anopheles darlingi parasiteOf human 3157
Anopheles darlingi parasiteOf galliformes 2301
Anopheles coustani parasiteOf cow 726
Anopheles farauti parasiteOf human 631
Anopheles farauti parasiteOf pig 562
Anopheles maculipalpis parasiteOf cow 482
Anopheles coustani parasiteOf human 454
Anopheles squamosus parasiteOf cow 434
Anopheles maculipennis sensu lato parasiteOf human 281
Anopheles rufipes parasiteOf cow 278
Anopheles farauti No. 4 parasiteOf human 238
Anopheles culicifacies BCE subgroup parasiteOf bovine 220
Anopheles culicifacies BCE subgroup parasiteOf human 215
Anopheles maculipennis sensu lato parasiteOf european rabbit 206
Anopheles farauti No. 4 parasiteOf pig 201
Culex cedecei parasiteOf hispid cotton rat 201
Anopheles farauti parasiteOf vertebrate 195
Culiseta annulata parasiteOf human 187
Anopheles squamosus parasiteOf human 144

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

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
banded armadillo NONE col banded armadillo
Adelaide rosella NONE col Adelaide rosella
Aedes aegypti HAS_ACCEPTED_NAME col Aedes aegypti
Aedes camptorhynchus HAS_ACCEPTED_NAME col Aedes camptorhynchus
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 82
col genus 2
col kingdom 1
col order 3
col species 71
discoverlife NA 159
gbif NA 78
gbif form 1
gbif genus 3
gbif kingdom 1
gbif order 3
gbif species 74
gbif subspecies 1
itis NA 79
itis genus 1
itis kingdom 1
itis order 3
itis species 74
mdd NA 158
ncbi NA 61
ncbi genus 1
ncbi kingdom 1
ncbi order 3
ncbi species 92
ncbi subgenus 1
ncbi subspecies 1
pbdb NA 152
pbdb genus 1
pbdb kingdom 1
pbdb order 3
pbdb species 1
pbdb unranked clade 1
tpt NA 155
tpt order 2
tpt species 1
wfo NA 157
wfo genus 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 NONE 83
col HAS_ACCEPTED_NAME 81
col SYNONYM_OF 58
discoverlife NONE 166
gbif NONE 79
gbif HAS_ACCEPTED_NAME 110
gbif SYNONYM_OF 61
itis NONE 80
itis HAS_ACCEPTED_NAME 84
mdd NONE 164
ncbi NONE 63
ncbi SAME_AS 81
ncbi SYNONYM_OF 4
ncbi COMMON_NAME_OF 19
pbdb NONE 158
pbdb HAS_ACCEPTED_NAME 7
pbdb SYNONYM_OF 7
tpt NONE 161
tpt HAS_ACCEPTED_NAME 3
wfo NONE 163
wfo HAS_UNCHECKED_NAME 1
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
2024-04-17T06:20:29Z note issue handling date range [2019-02/2019-03,2019-05/2019-11]: Invalid format: “2019-03,2019-05/2019-11” is malformed at “,2019-05/2019-11”
2024-04-17T06:20:29Z note issue handling date range [2019-02/2019-03,2019-05/2019-11]: Invalid format: “2019-03,2019-05/2019-11” is malformed at “,2019-05/2019-11”
2024-04-17T06:20:29Z note issue handling date range [2019-02/2019-03,2019-05/2019-11]: Invalid format: “2019-03,2019-05/2019-11” is malformed at “,2019-05/2019-11”
2024-04-17T06:20:29Z note issue handling date range [2019-02/2019-03,2019-05/2019-11]: Invalid format: “2019-03,2019-05/2019-11” is malformed at “,2019-05/2019-11”

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

Most frequently occurring review notes, if any.
reviewComment count
issue handling date range [2019-02/2019-03,2019-05/2019-11]: Invalid format: “2019-03,2019-05/2019-11” is malformed at “,2019-05/2019-11” 90
issue handling date range [2019-01/2019-03,2019-04/2019-06]: Invalid format: “2019-03,2019-04/2019-06” is malformed at “,2019-04/2019-06” 42

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 5 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-ness6 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.