Introduction

Data Review and Archive

Data review and archiving can be a time-consuming process, especially when done manually. This review report aims to help facilitate both activities. It automates the archiving of datasets, including Darwin Core archives, and is a citable backup of a version of the dataset. Additionally, an automatic review of species interaction claims made in the dataset is generated and registered with Global Biotic Interactions (J. H. Poelen, Simons, and Mungall 2014).

This review includes summary statistics about, and observations about, the dataset under review:

Botany Division, Yale Peabody Museum - Version 396.3342 http://ipt.peabody.yale.edu/archive.do?r=ypm-bot 2025-06-21T17:13:38.231Z Entomology Division, Yale Peabody Museum - Version 395.3248 http://ipt.peabody.yale.edu/archive.do?r=ypm-ent 2025-06-21T17:13:38.231Z Invertebrate Paleontology Division, Yale Peabody Museum - Version 395.3280 http://ipt.peabody.yale.edu/archive.do?r=ypm-ip 2025-06-21T17:13:38.231Z Invertebrate Zoology Division, Yale Peabody Museum - Version 395.3347 http://ipt.peabody.yale.edu/archive.do?r=ypm-iz 2025-06-21T17:13:38.231Z Paleobotany Division, Yale Peabody Museum - Version 395.3324 http://ipt.peabody.yale.edu/archive.do?r=ypm-pb 2025-06-21T17:13:38.231Z Vertebrate Paleontology Division, Yale Peabody Museum - Version 395.3345 http://ipt.peabody.yale.edu/archive.do?r=ypm-vp 2025-06-21T17:13:38.231Z Vertebrate Zoology Division - Herpetology, Yale Peabody Museum - Version 395.3309 http://ipt.peabody.yale.edu/archive.do?r=ypm-vz-her 2025-06-21T17:13:38.231Z Vertebrate Zoology Division - Ichthyology, Yale Peabody Museum - Version 395.3263 http://ipt.peabody.yale.edu/archive.do?r=ypm-vz-ich 2025-06-21T17:13:38.231Z Vertebrate Zoology Division - Mammalogy, Yale Peabody Museum - Version 397.3320 http://ipt.peabody.yale.edu/archive.do?r=ypm-vz-mam 2025-06-21T17:13:38.231Z Vertebrate Zoology Division - Ornithology, Yale Peabody Museum - Version 395.3294 http://ipt.peabody.yale.edu/archive.do?r=ypm-vz-orn 2025-06-21T17:13:38.231Z hash://md5/65ffb1fbba6a21d01e17a3ac8931c6e2

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/yale-peabody 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 (Elliott et al. 2025), Elton (Kuhn, Poelen, and Leinweber 2025), Nomer (Salim and Poelen 2025), globinizer (J. Poelen, Seltmann, and Mietchen 2024) combined with third-party tools like grep, mlr, tail and head.

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: Tools used in this review process

The review process can be described in the form of the script below ¹.

# get versioned copy of the dataset (size approx.  467MiB) under review 
elton pull globalbioticinteractions/yale-peabody

# generate review notes
elton review globalbioticinteractions/yale-peabody\
 > review.tsv

# export indexed interaction records
elton interactions globalbioticinteractions/yale-peabody\
 > interactions.tsv

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/yale-peabody\
 | nomer append col\
 > name-alignment.tsv

or visually, in a process diagram.

You can find a copy of the full review script at check-data.sh. See also GitHub and Codeberg.

Results

In the following sections, the results of the review are summarized ². Then, links to the detailed review reports are provided.

Files

The following files are produced in this review:

Archived Dataset

Note that data.zip file in this archive contains the complete, unmodified archived dataset under review.

Biotic Interactions

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/yale-peabody, has fingerprint hash://md5/65ffb1fbba6a21d01e17a3ac8931c6e2, is 467MiB in size and contains 117,150 interaction with 10 unique types of associations (e.g., interactsWith) between 6,665 primary taxon (e.g., undet. Foraminiferida) and 77,307 associated taxon (e.g., rocks).

An exhaustive list of indexed interaction claims can be found in gzipped csv, tsv and parquet archives. To facilitate discovery, a preview of claims available in the gzipped html page at indexed-interactions.html.gz are shown below.

The exhaustive list was used to create the following data summaries below.

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.

You can download the indexed dataset under review at indexed-interactions.csv.gz. A tab-separated file can be found at indexed-interactions.tsv.gz

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.

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.

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

: Most frequently occurring review notes, if any.

For additional information on review notes, please have a look at the first 500 Review Notes in html format or the download full gzipped 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.

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.

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 and archive provides a means of creating citable versions of datasets that change frequently. This may be useful for dataset managers, including natural history collection data managers, as a backup archive of a shared Darwin Core archive. It also serves as a means of creating a trackable citation for the dataset in an automated way, while also including some information about the contents of the dataset.

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. Also, thanks to https://github.com/zygoballus for helping improve the layout of the review tables.

Author contributions

Nomer was responsible for name alignments. Elton carried out dataset extraction, and generated the review notes. Preston tracked, versioned, and packaged, the dataset under review.

References