---
title: Versioned Archive and Review of Biotic Interactions and Taxon Names Found within millerse/Dapstrom-integrated-database-and-portal-for-fish-stomach-records hash://md5/569ae0feab6ee2248e67be6f5ca94786
date: 2026-02-03
author: 
  - by Nomer, Elton and Preston, three naive review bots
  - review@globalbioticinteractions.org
  - https://globalbioticinteractions.org/contribute 
  - https://github.com/millerse/Dapstrom-integrated-database-and-portal-for-fish-stomach-records/issues 
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 and archiving process for such an openly accessible digital interactions dataset of known origin and discuss its outcome. The dataset under review, named millerse/Dapstrom-integrated-database-and-portal-for-fish-stomach-records, has fingerprint hash://md5/569ae0feab6ee2248e67be6f5ca94786, is 32.6MiB in size and contains 225,564 interactions with 1 unique type of association (e.g., eats) between 187 primary taxa (e.g., GADUS MORHUA) and 1,268 associated taxa (e.g., EMPTY). This report includes detailed summaries of interaction data, a taxonomic review from multiple catalogs, and an archived version of the dataset from which the reviews are derived.
bibliography: biblio.bib
keywords:
  - biodiversity informatics
  - ecology
  - species interactions
  - biotic interactions
  - automated manuscripts
  - taxonomic names
  - taxonomic name alignment
  - biology
reference-section-title: References
---

# 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 [@Poelen_2014].

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

> Pinnegar, J.K. (2014). DAPSTOM - An Integrated Database & Portal for Fish Stomach Records. Version 4.7. Centre for Environment, Fisheries & Aquaculture Science, Lowestoft, UK. February 2014, 39pp. https://zenodo.org/records/258222/files/millerse/Dapstrom-integrated-database-and-portal-for-fish-stomach-records-v1.0.zip 2026-01-31T09:39:01.859Z hash://md5/569ae0feab6ee2248e67be6f5ca94786 

For additional metadata related to this dataset, please visit [https://github.com/millerse/Dapstrom-integrated-database-and-portal-for-fish-stomach-records](https://github.com/millerse/Dapstrom-integrated-database-and-portal-for-fish-stomach-records) 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 [@Preston], Elton [@Elton], Nomer [@Nomer], globinizer [@globinizer] combined with third-party tools like grep, mlr, tail and head.

 | tool name | version | 
 | --- | --- | 
 | [preston](https://github.com/bio-guoda/preston) | 0.11.1 |  
 | [elton](https://github.com/globalbioticinteractions/elton) | 0.16.4 | 
 | [nomer](https://github.com/globalbioticinteractions/nomer) | 0.5.17 |  
 | [globinizer](https://github.com/globalbioticinteractions/globinizer) | 0.4.0 |  
 | [mlr](https://miller.readthedocs.io/en/6.8.0/) | 6.0.0 |  
 | [jq](https://jqlang.org/) | 1.6 |  
 | [yq](https://mikefarah.gitbook.io/yq) | 4.25.3 |  
 | [pandoc](https://pandoc.org/) | 3.1.6.1 |  
 | [duckdb](https://duckdb.org/) | 1.3.1 |  
 | [mapserver](https://mapserver.org/) | 7.6.4 |  
: Tools used in this review process

The review process can be described in the form of the script below ^[Note that you have to first get the data (e.g., via elton pull millerse/Dapstrom-integrated-database-and-portal-for-fish-stomach-records) before being able to generate reviews (e.g., elton review millerse/Dapstrom-integrated-database-and-portal-for-fish-stomach-records), extract interaction claims (e.g., elton interactions millerse/Dapstrom-integrated-database-and-portal-for-fish-stomach-records), or list taxonomic names (e.g., elton names millerse/Dapstrom-integrated-database-and-portal-for-fish-stomach-records)].

~~~
# get versioned copy of the dataset (size approx. 32.6MiB) under review 
elton pull millerse/Dapstrom-integrated-database-and-portal-for-fish-stomach-records

# generate review notes
elton review millerse/Dapstrom-integrated-database-and-portal-for-fish-stomach-records\
 > review.tsv

# export indexed interaction records
elton interactions millerse/Dapstrom-integrated-database-and-portal-for-fish-stomach-records\
 > interactions.tsv

# export names and align them with the Catalogue of Life using Nomer 
elton names millerse/Dapstrom-integrated-database-and-portal-for-fish-stomach-records\
 | nomer append col\
 > name-alignment.tsv
~~~

or visually, in a process diagram.

![Review Process Overview](process.svg)

You can find a copy of the full review script at [check-data.sh](check-dataset.sh). See also [GitHub](https://github.com/globalbioticinteractions/globinizer/blob/master/check-dataset.sh) and [Codeberg](https://codeberg.org/globalbioticinteractions/globinizer/src/branch/master/check-dataset.sh). 

# Results

In the following sections, the results of the review are summarized [^1]. Then, links to the detailed review reports are provided.

## Files

The following files are produced in this review:

 filename | description
 --- | ---  
 [biblio.bib](biblio.bib) | list of bibliographic reference of this review 
 [check-dataset.sh](check-dataset.sh) | data review workflow/process as expressed in a bash script
 [data.zip](data.zip) | a versioned archive of the data under review
 [HEAD](HEAD) | the digital signature of the data under review
 [index.docx](index.docx) | review in MS Word format 
 [index.html](index.html) | review in HTML format 
 [index.md](index.md) |  review in Pandoc markdown format
 [index.pdf](index.pdf) | review in PDF format
 [indexed-citations.csv.gz](indexed-citations.csv.gz) | list of distinct reference citations for reviewed species interaction claims in gzipped comma-separated values file format 
 [indexed-citations.html.gz](indexed-citations.html.gz) | list of distinct reference citations for reviewed species interactions claims in gzipped html file format
 [indexed-citations.tsv.gz](indexed-citations.tsv.gz) | list of distinct reference citations for reviewed species interaction claims in gzipped tab-separated values format
 [indexed-interactions-col-family-col-family.svg](indexed-interactions-col-family-col-family.svg) | network diagram showing the taxon family to taxon family interaction claims in the dataset under review as interpreted by the Catalogue of Life via Nomer Corpus of Taxonomic Resources [@NomerCorpus]
 [indexed-interactions-col-kingdom-col-kingdom.svg](indexed-interactions-col-kingdom-col-kingdom.svg) | network diagram showing the taxon kingdom to taxon kingom interaction claims in the dataset under review as interpreted by the Catalogue of Life via Nomer Corpus of Taxonomic Resources [@NomerCorpus]
 [indexed-interactions.csv.gz](indexed-interactions.csv.gz) | species interaction claims indexed from the dataset under review in gzipped comma-separated values format 
 [indexed-interactions.html.gz](indexed-interactions.html.gz) | species interaction claims indexed from the dataset under review in gzipped html format
 [indexed-interactions.tsv.gz](indexed-interactions.tsv.gz) | species interaction claims indexed from the dataset under review in gzipped tab-separated values format
 [indexed-interactions.parquet](indexed-interactions.parquet) | species interaction claims indexed from the dataset under review in Apache Parquet format
 [indexed-interactions.png](indexed-interactions.png) | species interaction claims indexed from the dataset under review plotted on a map
 [indexed-interactions.gpkg](indexed-interactions.dpkg) | species interaction claims indexed from the dataset under review in GeoPackage format
 [indexed-interactions-h3.gpkg](indexed-interactions-h3.dpkg) | geospatially clustered h3 species interaction claims indexed from the dataset under review in GeoPackage format
 [indexed-interactions-sample.csv](indexed-interactions-sample.csv) | list of species interaction claims indexed from the dataset under review in gzipped comma-separated values format
 [indexed-interactions-sample.html](indexed-interactions-sample.html) | first 500 species interaction claims indexed from the dataset under review in html format 
 [indexed-interactions-sample.tsv](indexed-interactions-sample.tsv) | first 500 species interaction claims indexed from the dataset under review in tab-separated values format
 [indexed-names.csv.gz](indexed-names.csv.gz) | taxonomic names indexed from the dataset under review in gzipped comma-separated values format 
 [indexed-names.html.gz](indexed-names.html.gz) | taxonomic names found in the dataset under review in gzipped html format
 [indexed-names.tsv.gz](indexed-names.tsv.gz) | taxonomic names found in the dataset under review in gzipped tab-separated values format
 [indexed-names.parquet](indexed-names.parquet) | taxonomic names found in the dataset under review in Apache Parquet format
 [indexed-names-resolved-col.csv.gz](indexed-names-resolved-col.csv.gz) | taxonomic names found in the dataset under review aligned with the Catalogue of Life as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus] in gzipped comma-separated values format
 [indexed-names-resolved-col.html.gz](indexed-names-resolved-col.html.gz) | taxonomic names found in the dataset under review aligned with the Catalogue of Life as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus] in gzipped html format
 [indexed-names-resolved-col.tsv.gz](indexed-names-resolved-col.tsv.gz) | taxonomic names found in the dataset under review aligned with the Catalogue of Life as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus] in gzipped tab-separated values format
 [indexed-names-resolved-col.parquet](indexed-names-resolved-col.parquet) | taxonomic names found in the dataset under review aligned with the Catalogue of Life as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus] in Apache Parquet format
 [indexed-names-resolved-discoverlife.csv.gz](indexed-names-resolved-discoverlife.csv.gz) | taxonomic names found in the dataset under review aligned with Discover Life bee species checklist as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus] in gzipped comma-separated values format
 [indexed-names-resolved-discoverlife.html.gz](indexed-names-resolved-discoverlife.html.gz) | taxonomic names found in the dataset under review aligned with Discover Life bee species checklist as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus] in gzipped html format
 [indexed-names-resolved-discoverlife.tsv.gz](indexed-names-resolved-discoverlife.tsv.gz) | taxonomic names found in the dataset under review aligned with Discover Life bee species checklist as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus] in gzipped tab-separated values format
 [indexed-names-resolved-discoverlife.parquet](indexed-names-resolved-discoverlife.parquet) | taxonomic names found in the dataset under review aligned with Discover Life bee species checklist as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus] in Apache Parquet format
 [indexed-names-resolved-gbif.csv.gz](indexed-names-resolved-gbif.csv.gz) | taxonomic names found in the dataset under review aligned with GBIF Backbone Taxonomy as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus] in gzipped comma-separated values format
 [indexed-names-resolved-gbif.html.gz](indexed-names-resolved-gbif.html.gz) | taxonomic names found in the dataset under review aligned with GBIF Backbone Taxonomy as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus] in gzipped html format
 [indexed-names-resolved-gbif.tsv.gz](indexed-names-resolved-gbif.tsv.gz) | taxonomic names found in the dataset under review aligned with GBIF Backbone Taxonomy as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus]  in gzipped tab-separated values format
 [indexed-names-resolved-gbif.parquet](indexed-names-resolved-gbif.parquet) | taxonomic names found in the dataset under review aligned with GBIF Backbone Taxonomy as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus]  in Apache Parquet format
 [indexed-names-resolved-itis.csv.gz](indexed-names-resolved-itis.csv.gz) | taxonomic names found in the dataset under review aligned with  Integrated Taxonomic Information System (ITIS) as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus]  in gzipped comma-separated values format
 [indexed-names-resolved-itis.html.gz](indexed-names-resolved-itis.html.gz) | taxonomic names found in the dataset under review aligned with Integrated Taxonomic Information System (ITIS) as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus]  in gzipped html format
 [indexed-names-resolved-itis.tsv.gz](indexed-names-resolved-itis.tsv.gz) | taxonomic names found in the dataset under review aligned with Integrated Taxonomic Information System (ITIS) as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus]  in gzipped tab-separated values format
 [indexed-names-resolved-itis.parquet](indexed-names-resolved-itis.parquet) | taxonomic names found in the dataset under review aligned with Integrated Taxonomic Information System (ITIS) as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus]  in Apache Parquet format
 [indexed-names-resolved-mdd.csv.gz](indexed-names-resolved-mdd.csv.gz) | taxonomic names found in the dataset under review aligned with the Mammal Diversity Database as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus] in gzipped comma-separated values format
 [indexed-names-resolved-mdd.html.gz](indexed-names-resolved-mdd.html.gz) | taxonomic names found in the dataset under review aligned with Mammal Diversity Database as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus] in gzipped html format
 [indexed-names-resolved-mdd.tsv.gz](indexed-names-resolved-mdd.tsv.gz) | taxonomic names found in the dataset under review aligned with Mammal Diversity Database as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus] in gzipped tab-separated values format
 [indexed-names-resolved-mdd.parquet](indexed-names-resolved-mdd.parquet) | taxonomic names found in the dataset under review aligned with Mammal Diversity Database as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus] in Apache Parquet format
 [indexed-names-resolved-ncbi.csv.gz](indexed-names-resolved-ncbi.csv.gz) | taxonomic names found in the dataset under review aligned with the NCBI Taxonomy as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus] in gzipped comma-separated values format
 [indexed-names-resolved-ncbi.html.gz](indexed-names-resolved-ncbi.html.gz) | taxonomic names found in the dataset under review aligned with the NCBI Taxonomy as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus] in gzipped html format
 [indexed-names-resolved-ncbi.tsv.gz](indexed-names-resolved-ncbi.tsv.gz) | taxonomic names found in the dataset under review aligned with the NCBI Taxonomy as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus] in gzipped tab-separated values format
 [indexed-names-resolved-ncbi.parquet](indexed-names-resolved-ncbi.parquet) | taxonomic names found in the dataset under review aligned with the NCBI Taxonomy as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus] in Apache Parquet format
 [indexed-names-resolved-pbdb.csv.gz](indexed-names-resolved-pbdb.csv.gz) | taxonomic names found in the dataset under review aligned with the Paleobiology Database as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus] in gzipped comma-separated values format 
 [indexed-names-resolved-pbdb.html.gz](indexed-names-resolved-pbdb.html.gz) | taxonomic names found in the dataset under review aligned with Paleobiology Database as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus] in gzipped html format
 [indexed-names-resolved-pbdb.tsv.gz](indexed-names-resolved-pbdb.tsv.gz) | taxonomic names found in the dataset under review aligned with Paleobiology Database as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus] in gzipped tab-separated values format
 [indexed-names-resolved-pbdb.parquet](indexed-names-resolved-pbdb.parquet) | taxonomic names found in the dataset under review aligned with Paleobiology Database as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus] in Apache Parquet format
 [indexed-names-resolved-tpt.csv.gz](indexed-names-resolved-tpt.csv.gz) | taxonomic names found in the dataset under review aligned with the Terrestrial Parasite Tracker (TPT) Taxonomic Resource as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus] in gzipped comma-separated values format
 [indexed-names-resolved-tpt.html.gz](indexed-names-resolved-tpt.html.gz) | taxonomic names found in the dataset under review aligned with the Terrestrial Parasite Tracker (TPT) Taxonomic Resource as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus] in gzipped html format
 [indexed-names-resolved-tpt.tsv.gz](indexed-names-resolved-tpt.tsv.gz) | taxonomic names found in the dataset under review aligned with the Terrestrial Parasite Tracker (TPT) Taxonomic Resource as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus] in gzipped tab-separated values format 
 [indexed-names-resolved-tpt.parquet](indexed-names-resolved-tpt.parquet) | taxonomic names found in the dataset under review aligned with the Terrestrial Parasite Tracker (TPT) Taxonomic Resource as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus] in Apache Parquet format 
 [indexed-names-resolved-wfo.csv.gz](indexed-names-resolved-wfo.csv.gz) | taxonomic names found in the dataset under review aligned with the World of Flora Online as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus] in gzipped comma-separated values format
 [indexed-names-resolved-wfo.html.gz](indexed-names-resolved-wfo.html.gz) | taxonomic names found in the dataset under review aligned with the World of Flora Online as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus] in gzipped html format
 [indexed-names-resolved-wfo.tsv.gz](indexed-names-resolved-wfo.tsv.gz) | taxonomic names found in the dataset under review aligned with the World of Flora Online as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus] in gzipped tab-separated values format
 [indexed-names-resolved-wfo.parquet](indexed-names-resolved-wfo.parquet) | taxonomic names found in the dataset under review aligned with the World of Flora Online as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus] in Apache Parquet format
 [indexed-names-resolved-worms.csv.gz](indexed-names-resolved-worms.csv.gz) | taxonomic names found in the dataset under review aligned with the World Register of Marine Species (WoRMS) as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus] in gzipped comma-separated values format
 [indexed-names-resolved-worms.html.gz](indexed-names-resolved-worms.html.gz) | taxonomic names found in the dataset under review aligned with the World Register of Marine Species (WoRMS) as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus] in gzipped html format
 [indexed-names-resolved-worms.tsv.gz](indexed-names-resolved-worms.tsv.gz) | taxonomic names found in the dataset under review aligned with the World Register of Marine Species (WoRMS) as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus] in gzipped tab-separated values format
 [indexed-names-resolved-worms.parquet](indexed-names-resolved-worms.parquet) | taxonomic names found in the dataset under review aligned with the World Register of Marine Species (WoRMS) as accessed through the Nomer Corpus of Taxonomic Resources [@NomerCorpus] in Apache Parquet format
 [indexed-names-sample.csv](indexed-names-sample.csv) | first 500 taxonomic names found in the dataset under review in comma-separated values format
 [indexed-names-sample.html](indexed-names-sample.html) | first 500 taxonomic names found in the dataset under review in html format
 [indexed-names-sample.tsv](indexed-names-sample.tsv) | first 500 taxonomic names found in the dataset under review in tab-separated values format
 [interaction.svg](interaction.svg) | diagram summarizing the data model used to index species interaction claims
 [nanopub-sample.trig](nanopub-sample.trig) | first 500 species interaction claims as expressed in the nanopub format [@Nanopub]
 [nanopub.trig.gz](nanopub.trig.gz) | species interaction claims as expressed in the nanopub format [@Nanopub]
 [process.svg](process.svg) | diagram summarizing the data review processing workflow 
 [prov.nq](prov.nq) | origin of the dataset under review as expressed in rdf/nquads 
 [review.csv.gz](review.csv.gz) | review notes associated with the dataset under review in gzipped comma-separated values format 
 [review.html.gz](review.html.gz) | review notes associated with the dataset under review in gzipped html format
 [review.tsv.gz](review.tsv.gz) | review notes associated with the dataset under review in gzipped tab-separated values format
 [review-sample.csv](review-sample.csv) | first 500 review notes associated with the dataset under review in comma-separated values format
 [review-sample.html](review-sample.html) | first 500 review notes associated with the dataset under review in html format
 [review-sample.tsv](review-sample.tsv) | first 500 review notes associated with the dataset under review in tab-separated values format
 [review.svg](review.svg) | a review badge generated as part of the dataset review process
 [zenodo.json](zenodo.json) | metadata of this review expressed in Zenodo record metadata

## Archived Dataset

Note that [_data.zip_](data.zip) file in this archive contains the complete, unmodified archived dataset under review. 

## Biotic Interactions

![Biotic Interaction Data Model](interaction.svg)

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 millerse/Dapstrom-integrated-database-and-portal-for-fish-stomach-records, has fingerprint hash://md5/569ae0feab6ee2248e67be6f5ca94786, is 32.6MiB in size and contains 225,564 interactions with 1 unique type of association (e.g., eats) between 187 primary taxa (e.g., GADUS MORHUA) and 1,268 associated taxa (e.g., EMPTY).

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

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

 
| sourceTaxonName | interactionTypeName | targetTaxonName | referenceCitation |
| --- | --- | --- | --- |
| SCOMBER SCOMBRUS | eats | ACARTIA CLAUSI | Pinnegar, J.K. (2014). DAPSTOM - An Integrated Database & Portal for Fish Stomach Records. Version 4.7. Centre for Environment, Fisheries & Aquaculture Science, Lowestoft, UK. February 2014, 39pp. Accessed at <https://www.cefas.co.uk/umbraco/CefasPlugins/DapstomSurface/Download?searchType=predator&species=MAC&years=2011&years=2010&years=2006&years=2005&years=2004&years=1991&years=1987&years=1986&years=1979&years=1978&years=1977&years=1976&years=1974&years=1972&years=1965&years=1956&years=1919&years=1917&years=1907&years=1906&years=1902&years=1901&years=1899&areas=VIIIb&areas=Va&areas=VIIj&areas=VIa&areas=VIIIc&areas=XIVb&areas=VIIg&areas=VIIh&areas=VIIa&areas=IIa&areas=XIVa&areas=VIIId&areas=VIIe&areas=VIIf&areas=IVa&areas=IVc&areas=VIIIa&areas=IVb&minlength=0&maxlength=1000&nullLengths=true> on 03 Feb 2026. |
| SCOMBER SCOMBRUS | eats | ACARTIA CLAUSI | Pinnegar, J.K. (2014). DAPSTOM - An Integrated Database & Portal for Fish Stomach Records. Version 4.7. Centre for Environment, Fisheries & Aquaculture Science, Lowestoft, UK. February 2014, 39pp. Accessed at <https://www.cefas.co.uk/umbraco/CefasPlugins/DapstomSurface/Download?searchType=predator&species=MAC&years=2011&years=2010&years=2006&years=2005&years=2004&years=1991&years=1987&years=1986&years=1979&years=1978&years=1977&years=1976&years=1974&years=1972&years=1965&years=1956&years=1919&years=1917&years=1907&years=1906&years=1902&years=1901&years=1899&areas=VIIIb&areas=Va&areas=VIIj&areas=VIa&areas=VIIIc&areas=XIVb&areas=VIIg&areas=VIIh&areas=VIIa&areas=IIa&areas=XIVa&areas=VIIId&areas=VIIe&areas=VIIf&areas=IVa&areas=IVc&areas=VIIIa&areas=IVb&minlength=0&maxlength=1000&nullLengths=true> on 03 Feb 2026. |
| SCOMBER SCOMBRUS | eats | ACARTIA CLAUSI | Pinnegar, J.K. (2014). DAPSTOM - An Integrated Database & Portal for Fish Stomach Records. Version 4.7. Centre for Environment, Fisheries & Aquaculture Science, Lowestoft, UK. February 2014, 39pp. Accessed at <https://www.cefas.co.uk/umbraco/CefasPlugins/DapstomSurface/Download?searchType=predator&species=MAC&years=2011&years=2010&years=2006&years=2005&years=2004&years=1991&years=1987&years=1986&years=1979&years=1978&years=1977&years=1976&years=1974&years=1972&years=1965&years=1956&years=1919&years=1917&years=1907&years=1906&years=1902&years=1901&years=1899&areas=VIIIb&areas=Va&areas=VIIj&areas=VIa&areas=VIIIc&areas=XIVb&areas=VIIg&areas=VIIh&areas=VIIa&areas=IIa&areas=XIVa&areas=VIIId&areas=VIIe&areas=VIIf&areas=IVa&areas=IVc&areas=VIIIa&areas=IVb&minlength=0&maxlength=1000&nullLengths=true> on 03 Feb 2026. |
| SCOMBER SCOMBRUS | eats | ACARTIA CLAUSI | Pinnegar, J.K. (2014). DAPSTOM - An Integrated Database & Portal for Fish Stomach Records. Version 4.7. Centre for Environment, Fisheries & Aquaculture Science, Lowestoft, UK. February 2014, 39pp. Accessed at <https://www.cefas.co.uk/umbraco/CefasPlugins/DapstomSurface/Download?searchType=predator&species=MAC&years=2011&years=2010&years=2006&years=2005&years=2004&years=1991&years=1987&years=1986&years=1979&years=1978&years=1977&years=1976&years=1974&years=1972&years=1965&years=1956&years=1919&years=1917&years=1907&years=1906&years=1902&years=1901&years=1899&areas=VIIIb&areas=Va&areas=VIIj&areas=VIa&areas=VIIIc&areas=XIVb&areas=VIIg&areas=VIIh&areas=VIIa&areas=IIa&areas=XIVa&areas=VIIId&areas=VIIe&areas=VIIf&areas=IVa&areas=IVc&areas=VIIIa&areas=IVb&minlength=0&maxlength=1000&nullLengths=true> on 03 Feb 2026. |
: Sample of Indexed Interaction Claims

| interactionTypeName | count |
| --- | --- |
| eats | 225564 |
: Most Frequently Mentioned Interaction Types (up to 20 most frequent)

| sourceTaxonName | count |
| --- | --- |
| GADUS MORHUA | 67884 |
| MERLANGIUS MERLANGUS | 47017 |
| MELANOGRAMMUS AEGLEFINUS | 19823 |
| PLEURONECTES PLATESSA | 12916 |
| SCOMBER SCOMBRUS | 10489 |
| CLUPEA HARENGUS | 8508 |
| EUTRIGLA GURNARDUS | 8327 |
| LIMANDA LIMANDA | 4837 |
| SPRATTUS SPRATTUS | 4651 |
| LEPIDORHOMBUS WHIFFIAGONIS | 4169 |
| ECHIICHTHYS VIPERA | 2632 |
| SCYLIORHINUS CANICULA | 2617 |
| MERLUCCIUS MERLUCCIUS | 2305 |
| POLLACHIUS VIRENS | 2146 |
| MICROMESISTIUS POUTASSOU | 1583 |
| AMMODYTES SPP | 1389 |
| TRISOPTERUS MINUTUS | 1270 |
| LOPHIUS PISCATORIUS | 1202 |
| PLATICHTHYS FLESUS | 1154 |
: Most Frequently Mentioned Primary Taxa (up to 20 most frequent)

| targetTaxonName | count |
| --- | --- |
| EMPTY | 35805 |
| AMMODYTES SPP | 11880 |
| OSTEICHTHYS - TELEOSTEI | 11751 |
| PSEUDOCALANUS ELONGATUS (FEMALE) | 7076 |
| DIGESTED REMAINS | 6650 |
| POLYCHAETA | 6279 |
| THYSANOESSA INERMIS | 5748 |
| CRUSTACEA | 5627 |
| COPEPODA-CALANOIDA | 4629 |
| COPEPODA (COPEPODITE 1-3) | 4373 |
| EUPHAUSIIDAE | 4230 |
| AMPHIPODA | 3365 |
| CRANGONIDAE | 3337 |
| CALANUS SPP | 3174 |
| OPHIURIDA (ORDER) | 3138 |
| COPEPODA (COPEPODITE 4-5) | 2499 |
| CRANGON CRANGON | 2393 |
| BRACHYURA-CANCRIDEA | 2325 |
| TEMORA SPP (MALE) | 2309 |
: Most Frequently Mentioned Associate Taxa (up to 20 most frequent)

| sourceTaxonName | interactionTypeName | targetTaxonName | count |
| --- | --- | --- | --- |
| MERLANGIUS MERLANGUS | eats | EMPTY | 9732 |
| GADUS MORHUA | eats | EMPTY | 6516 |
| GADUS MORHUA | eats | THYSANOESSA INERMIS | 5483 |
| GADUS MORHUA | eats | OSTEICHTHYS - TELEOSTEI | 5101 |
| MERLANGIUS MERLANGUS | eats | PSEUDOCALANUS ELONGATUS (FEMALE) | 3908 |
| MELANOGRAMMUS AEGLEFINUS | eats | AMMODYTES SPP | 3741 |
| MERLANGIUS MERLANGUS | eats | COPEPODA (COPEPODITE 1-3) | 3196 |
| GADUS MORHUA | eats | PSEUDOCALANUS ELONGATUS (FEMALE) | 3168 |
| MERLANGIUS MERLANGUS | eats | AMMODYTES SPP | 2832 |
| MERLANGIUS MERLANGUS | eats | OSTEICHTHYS - TELEOSTEI | 2696 |
| GADUS MORHUA | eats | AMMODYTES SPP | 2617 |
| PLEURONECTES PLATESSA | eats | EMPTY | 2385 |
| EUTRIGLA GURNARDUS | eats | EMPTY | 2309 |
| MELANOGRAMMUS AEGLEFINUS | eats | OPHIURIDA (ORDER) | 2148 |
| MERLANGIUS MERLANGUS | eats | COPEPODA (COPEPODITE 4-5) | 1899 |
| MERLANGIUS MERLANGUS | eats | TEMORA SPP (FEMALE) | 1795 |
| LEPIDORHOMBUS WHIFFIAGONIS | eats | EMPTY | 1735 |
| MERLANGIUS MERLANGUS | eats | TEMORA SPP (MALE) | 1672 |
| GADUS MORHUA | eats | NEPHROPS NORVEGICUS | 1624 |
: Most Frequent Interactions between Primary and Associate Taxa (up to 20 most frequent)


### 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 on taxonomic kingdom rank as interpreted by the Catalogue of Life [download svg](indexed-interactions-col-kingdom-col-kingdom.svg)](indexed-interactions-col-kingdom-col-kingdom.svg)

![Interactions on the taxonomic family rank as interpreted by the Catalogue of Life. [download svg](indexed-interactions-col-family-col-family.svg)](indexed-interactions-col-family-col-family.svg)

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

## Geospatial Distribution

If geospatial information was extracted from the dataset under review, the map below will show their distribution.

![Hexagonal grid cells indicate that interactions claims are available for selected geospatial area: light yellow means relatively fewer claims, dark green relatively more claims.](indexed-interactions.png)

Associated data can be found in the geopackage files at [indexed-interactions.gpkg](indexed-interactions.gpkg) for point data and [indexed-interactions-h3.gpkg](indexed-interactions-h3.gpkg) for data clustered in geospatial h3 hexagonals.

Learn more about the structure of this download at [GloBI website](https://globalbioticinteractions.org), by opening a [GitHub issue](https://github.com/globalbioticinteractions/globalbioticinteractions/issues/new), or by sending an [email](mailto:info@globalbioticinteractions.org).

Another way to discover the dataset under review is by searching for it on the [GloBI website](https://www.globalbioticinteractions.org/?accordingTo=globi%3Amillerse%2FDapstrom-integrated-database-and-portal-for-fish-stomach-records).


## 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. 

| providedName | relationName | resolvedCatalogName | resolvedName |
| --- | --- | --- | --- |
| Abietinaria abietina | HAS_ACCEPTED_NAME | col | Abietinaria abietina |
| Abludomelita obtusata | HAS_ACCEPTED_NAME | col | Abludomelita obtusata |
| Abra alba | HAS_ACCEPTED_NAME | col | Abra alba |
| Abramis brama | HAS_ACCEPTED_NAME | col | Abramis brama | 
: Sample of Name Alignments

| resolvedCatalogName | resolvedRank | count |
| --- | --- | --- |
| col | NA | 168 |
| col | class | 24 |
| col | family | 119 |
| col | genus | 174 |
| col | gigaclass | 1 |
| col | infraorder | 2 |
| col | kingdom | 1 |
| col | order | 17 |
| col | other | 1 |
| col | parvphylum | 1 |
| col | phylum | 11 |
| col | species | 765 |
| col | subclass | 4 |
| col | subfamily | 2 |
| col | subgenus | 10 |
| col | suborder | 1 |
| col | subspecies | 18 |
| col | superfamily | 1 |
| col | superorder | 1 |
| discoverlife | NA | 1291 |
| gbif | NA | 117 |
| gbif | class | 25 |
| gbif | family | 124 |
| gbif | genus | 201 |
| gbif | kingdom | 1 |
| gbif | order | 16 |
| gbif | phylum | 12 |
| gbif | species | 813 |
| gbif | subspecies | 6 |
| itis | NA | 122 |
| itis | class | 23 |
| itis | division | 1 |
| itis | family | 120 |
| itis | form | 1 |
| itis | genus | 180 |
| itis | infrakingdom | 1 |
| itis | infraorder | 2 |
| itis | infraphylum | 1 |
| itis | kingdom | 1 |
| itis | order | 18 |
| itis | phylum | 9 |
| itis | species | 789 |
| itis | subclass | 7 |
| itis | subfamily | 4 |
| itis | suborder | 4 |
| itis | subphylum | 2 |
| itis | subspecies | 2 |
| itis | superclass | 1 |
| itis | superfamily | 1 |
| itis | superorder | 5 |
| mdd | NA | 1290 |
| ncbi | NA | 256 |
| ncbi | clade | 1 |
| ncbi | class | 24 |
| ncbi | cohort | 1 |
| ncbi | family | 120 |
| ncbi | genus | 174 |
| ncbi | infraorder | 3 |
| ncbi | order | 17 |
| ncbi | phylum | 11 |
| ncbi | series | 1 |
| ncbi | species | 673 |
| ncbi | subclass | 5 |
| ncbi | subfamily | 3 |
| ncbi | subgenus | 2 |
| ncbi | suborder | 3 |
| ncbi | subphylum | 1 |
| ncbi | superclass | 1 |
| ncbi | superorder | 3 |
| pbdb | NA | 845 |
| pbdb | class | 26 |
| pbdb | family | 109 |
| pbdb | genus | 101 |
| pbdb | infraclass | 1 |
| pbdb | infraorder | 2 |
| pbdb | kingdom | 1 |
| pbdb | order | 19 |
| pbdb | phylum | 11 |
| pbdb | species | 157 |
| pbdb | subclass | 5 |
| pbdb | subfamily | 7 |
| pbdb | suborder | 4 |
| pbdb | subspecies | 1 |
| pbdb | superclass | 2 |
| pbdb | superfamily | 1 |
| pbdb | superorder | 3 |
| pbdb | superphylum | 1 |
| pbdb | unranked clade | 7 |
| tpt | NA | 1282 |
| tpt | species | 8 |
| wfo | NA | 1273 |
| wfo | genus | 16 |
| wfo | species | 1 |
| worms | NA | 167 |
| worms | class | 24 |
| worms | family | 113 |
| worms | forma | 1 |
| worms | genus | 164 |
| worms | gigaclass | 1 |
| worms | infraclass | 1 |
| worms | infraorder | 3 |
| worms | infraphylum | 2 |
| worms | kingdom | 1 |
| worms | order | 16 |
| worms | parvphylum | 1 |
| worms | phylum | 10 |
| worms | phylum (division) | 1 |
| worms | species | 769 |
| worms | subclass | 4 |
| worms | subfamily | 1 |
| worms | suborder | 3 |
| worms | subphylum | 2 |
| worms | subspecies | 7 |
| worms | superfamily | 1 |
| worms | superorder | 3 |
: 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 | relationName | count |
| --- | --- | --- |
| col | HAS_ACCEPTED_NAME | 1138 |
| col | SYNONYM_OF | 282 |
| col | NONE | 177 |
| discoverlife | NONE | 1356 |
| gbif | HAS_ACCEPTED_NAME | 1235 |
| gbif | SYNONYM_OF | 331 |
| gbif | NONE | 125 |
| itis | HAS_ACCEPTED_NAME | 1154 |
| itis | SYNONYM_OF | 103 |
| itis | NONE | 129 |
| mdd | NONE | 1350 |
| mdd | HAS_ACCEPTED_NAME | 1 |
| ncbi | SAME_AS | 1039 |
| ncbi | NONE | 267 |
| ncbi | SYNONYM_OF | 67 |
| pbdb | NONE | 872 |
| pbdb | HAS_ACCEPTED_NAME | 463 |
| pbdb | SYNONYM_OF | 74 |
| tpt | NONE | 1343 |
| tpt | SYNONYM_OF | 1 |
| tpt | HAS_ACCEPTED_NAME | 7 |
| wfo | NONE | 1332 |
| wfo | SYNONYM_OF | 10 |
| wfo | HAS_ACCEPTED_NAME | 7 |
| wfo | HAS_UNCHECKED_NAME | 2 |
| worms | HAS_ACCEPTED_NAME | 1049 |
| worms | SYNONYM_OF | 201 |
| worms | NONE | 173 |
: 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). 

| catalog name | alignment results |
| --- | --- |
| col | associated names alignments report in gzipped [html](indexed-names-resolved-col.html.gz), [csv](indexed-names-resolved-col.csv.gz), and [tsv](indexed-names-resolved-col.tsv.gz)) |
| ncbi | associated names alignments report in gzipped [html](indexed-names-resolved-ncbi.html.gz), [csv](indexed-names-resolved-ncbi.csv.gz), and [tsv](indexed-names-resolved-ncbi.tsv.gz)) |
| discoverlife | associated names alignments report in gzipped [html](indexed-names-resolved-discoverlife.html.gz), [csv](indexed-names-resolved-discoverlife.csv.gz), and [tsv](indexed-names-resolved-discoverlife.tsv.gz)) |
| gbif | associated names alignments report in gzipped [html](indexed-names-resolved-gbif.html.gz), [csv](indexed-names-resolved-gbif.csv.gz), and [tsv](indexed-names-resolved-gbif.tsv.gz)) |
| itis | associated names alignments report in gzipped [html](indexed-names-resolved-itis.html.gz), [csv](indexed-names-resolved-itis.csv.gz), and [tsv](indexed-names-resolved-itis.tsv.gz)) |
| wfo | associated names alignments report in gzipped [html](indexed-names-resolved-wfo.html.gz), [csv](indexed-names-resolved-wfo.csv.gz), and [tsv](indexed-names-resolved-wfo.tsv.gz)) |
| mdd | associated names alignments report in gzipped [html](indexed-names-resolved-mdd.html.gz), [csv](indexed-names-resolved-mdd.csv.gz), and [tsv](indexed-names-resolved-mdd.tsv.gz)) |
| tpt | associated names alignments report in gzipped [html](indexed-names-resolved-tpt.html.gz), [csv](indexed-names-resolved-tpt.csv.gz), and [tsv](indexed-names-resolved-tpt.tsv.gz)) |
| pbdb | associated names alignments report in gzipped [html](indexed-names-resolved-pbdb.html.gz), [csv](indexed-names-resolved-pbdb.csv.gz), and [tsv](indexed-names-resolved-pbdb.tsv.gz)) |
| worms | associated names alignments report in gzipped [html](indexed-names-resolved-worms.html.gz), [csv](indexed-names-resolved-worms.csv.gz), and [tsv](indexed-names-resolved-worms.tsv.gz)) | 
: List of Available Name Alignment Reports

## 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.

| reviewDate | reviewCommentType | reviewComment |
| --- | --- | --- |
| 2026-02-03T03:11:40Z | summary | https://zenodo.org/records/258222/files/millerse/Dapstrom-integrated-database-and-portal-for-fish-stomach-records-v1.0.zip |
| 2026-02-03T03:11:40Z | summary | 225564 interaction(s) |
| 2026-02-03T03:11:40Z | summary | 0 note(s) |
| 2026-02-03T03:11:40Z | summary | 225564 info(s) |
: First few lines in the review notes.

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](review-sample.html) in html format or the download full gzipped [csv](review.csv.gz) or [tsv](review.tsv.gz) 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. 

![Picture of a GloBI Review Badge ^[Up-to-date status of the GloBI Review Badge can be retrieved from the [GloBI Review Depot](https://depot.globalbioticinteractions.org/reviews/millerse/Dapstrom-integrated-database-and-portal-for-fish-stomach-records/review.svg)]](review.svg) 

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](https://globalbioticinteractions.org/contribute), 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 ^[Up-to-date status of the GloBI Index Badge can be retrieved from [GloBI's API](https://api.globalbioticinteractions.org/interaction.svg?interactionType=ecologicallyRelatedTo&accordingTo=globi:millerse/Dapstrom-integrated-database-and-portal-for-fish-stomach-records&refutes=true&refutes=false)]](https://api.globalbioticinteractions.org/interaction.svg?interactionType=ecologicallyRelatedTo&accordingTo=globi:millerse/Dapstrom-integrated-database-and-portal-for-fish-stomach-records&refutes=true&refutes=false)

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 (2026-02-03) the version of the GloBI dataset index was available at [https://globalbioticinteractions.org/datasets](https://globalbioticinteractions.org/datasets)] 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-ness[^2] and FAIRness [@Wilkinson_2016; @trekels_maarten_2023_8176978] of the dataset: to perform this review, the data was likely openly available, **F**indable, **A**ccessible, **I**nteroperable and **R**eusable. 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_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.

[^1]: Disclaimer: The results in this review should be considered friendly, yet naive, notes from an unsophisticated robot. Please keep that in mind when considering the review results. 
[^2]: According to http://opendefinition.org/: "Open data is data that can be freely used, re-used and redistributed by anyone - subject only, at most, to the requirement to attribute and sharealike."
