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 :

Farr, David F.; Rossman, Amy Y.; Castlebury, Lisa A. (2021). United States National Fungus Collections Fungus-Host Dataset. Ag Data Commons. https://doi.org/10.15482/USDA.ADC/1524414. https://github.com/globalbioticinteractions/usda-fungus-host/archive/47a3882c0c5365d3e6065e1cf7f3b36945f06fa9.zip 2026-03-28T06:18:26.912Z hash://md5/5836bbb61671a634a8bb614d645a96f9

For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/usda-fungus-host 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.

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

# get versioned copy of the dataset (size approx.  205MiB) under review 
elton pull globalbioticinteractions/usda-fungus-host

# generate review notes
elton review globalbioticinteractions/usda-fungus-host\
 > review.tsv

# export indexed interaction records
elton interactions globalbioticinteractions/usda-fungus-host\
 > interactions.tsv

# export names and align them with the Catalogue of Life using Nomer 
elton names globalbioticinteractions/usda-fungus-host\
 | 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/usda-fungus-host, has fingerprint hash://md5/5836bbb61671a634a8bb614d645a96f9, is 205MiB in size and contains 826,329 interactions with 1 unique type of association (e.g., hasHost) between 98,724 primary taxa (e.g., Oidium sp.) and 64,962 associated taxa (e.g., Zea mays).

An exhaustive list of indexed interaction claims can be found in gzipped csv, tsv, geopackage 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.