Versioned Archive and Review of Biotic Interactions
and Taxon Names Found within globalbioticinteractions/ecdysis
hash://md5/1eb9f1b706eef2ac25114f3e382a157b
by Nomer, Elton and Preston, three naive review
bots
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
globalbioticinteractions/ecdysis, has fingerprint
hash://md5/1eb9f1b706eef2ac25114f3e382a157b, is 498MiB in size and
contains 659,189 interaction with 10 unique types of associations (e.g.,
interactsWith) between 83,704 primary taxon (e.g., Augochlora pura) and
34,716 associated taxon (e.g., Prunus). 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catalogs, and an archived version of the dataset from which the reviews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.
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:
AHAB | Adam Haberski Research Collection
https://ecdysis.org/content/dwca/AHAB_DwC-A.zip 2025-06-21T00:26:38.116Z
ANSP-ENT | Academy of Natural Sciences Entomology Collection
https://ecdysis.org/content/dwca/ANSP-ENT_DwC-A.zip
2025-06-21T00:26:38.116Z ANSP-ORTH | Academy of Natural Sciences
Entomology Collection – OrthopNet
https://ecdysis.org/content/dwca/ANSP-ORTH_DwC-A.zip
2025-06-21T00:26:38.116Z ASU-ASUCOB | Arizona State University Charles
W. O’Brien Collection
https://ecdysis.org/content/dwca/ASU-ASUCOB_DwC-A.zip
2025-06-21T00:26:38.116Z ASU-ASUHIC | Arizona State University Hasbrouck
Insect Collection https://ecdysis.org/content/dwca/ASU-ASUHIC_DwC-A.zip
2025-06-21T00:26:38.116Z ASU-ROLS | Rick Overson and Laura Steger
Invertebrate Observations
https://ecdysis.org/content/dwca/ASU-ROLS_DwC-A.zip
2025-06-21T00:26:38.116Z AZDA-AZDA-ENT | Arizona Department of
Agriculture Entomology Collection
https://ecdysis.org/content/dwca/AZDA-AZDA-ENT_DwC-A.zip
2025-06-21T00:26:38.116Z BP-BLM | Butterfly Pavilion’s Colorado
Invertebrate Surveys https://ecdysis.org/content/dwca/BP-BLM_DwC-A.zip
2025-06-21T00:26:38.116Z BROW-BCIC | Broward College Insect Collection
https://ecdysis.org/content/dwca/BROW-BCIC_DwC-A.zip
2025-06-21T00:26:38.116Z BYU-BYUC | Brigham Young University Arthropod
Museum https://ecdysis.org/content/dwca/BYU-BYUC_DwC-A.zip
2025-06-21T00:26:38.116Z CAES-CAES | Connecticut Agricultural Experiment
Station Arthropod Collection
https://ecdysis.org/content/dwca/CAES-CAES_DwC-A.zip
2025-06-21T00:26:38.116Z CMNH-IZ | Carnegie Museum Invertebrate Zoology
Collection https://ecdysis.org/content/dwca/CMNH-IZ_DwC-A.zip
2025-06-21T00:26:38.116Z CPSLO-PSEC | California Polytechnic State
University, San Luis Obispo Plant Sciences Entomology Collection
https://ecdysis.org/content/dwca/CPSLO-PSEC_DwC-A.zip
2025-06-21T00:26:38.116Z CSEB-CSEB | California State University East
Bay Insect Collection
https://ecdysis.org/content/dwca/CSEB-CSEB_DwC-A.zip
2025-06-21T00:26:38.116Z CSU-CSUC | C.P. Gillette Museum of Arthropod
Diversity https://ecdysis.org/content/dwca/CSU-CSUC_DwC-A.zip
2025-06-21T00:26:38.116Z CU-CUAC | Clemson University Arthropod
Collection https://ecdysis.org/content/dwca/CU-CUAC_DwC-A.zip
2025-06-21T00:26:38.116Z DBG-DBGA | Denver Botanic Gardens Collection of
Arthropods https://ecdysis.org/content/dwca/DBG-DBGA_DwC-A.zip
2025-06-21T00:26:38.116Z DCH-DCEC | The Davidson College Entomology
Collection https://ecdysis.org/content/dwca/DCH-DCEC_DwC-A.zip
2025-06-21T00:26:38.116Z DDPC-DDPC | Davide Dal Pos Research Collection
https://ecdysis.org/content/dwca/DDPC-DDPC_DwC-A.zip
2025-06-21T00:26:38.116Z DMNS-Arac | Denver Museum of Nature &
Science - Arachnology
https://ecdysis.org/content/dwca/DMNS-Arac_DwC-A.zip
2025-06-21T00:26:38.116Z DMNS-Ento | Denver Museum of Nature &
Science - Entomology
https://ecdysis.org/content/dwca/DMNS-Ento_DwC-A.zip
2025-06-21T00:26:38.116Z DUGWAY-DUG-ENT | Dugway Proving Ground Natural
History Collection
https://ecdysis.org/content/dwca/DUGWAY-DUG-ENT_DwC-A.zip
2025-06-21T00:26:38.116Z ERWC-ERWC | Ethan Richard Wright Collection
https://ecdysis.org/content/dwca/ERWC-ERWC_DwC-A.zip
2025-06-21T00:26:38.116Z EWIC-EWIC | Evan Waite Invertebrate Collection
https://ecdysis.org/content/dwca/EWIC-EWIC_DwC-A.zip
2025-06-21T00:26:38.116Z FSCA | Florida State Collection of Arthropods
https://ecdysis.org/content/dwca/FSCA_DwC-A.zip 2025-06-21T00:26:38.116Z
GMNH-UGCA | University of Georgia Collection of Arthropods
https://ecdysis.org/content/dwca/GMNH-UGCA_DwC-A.zip
2025-06-21T00:26:38.116Z HNU-HNUSEL | Hannam University Systematic
Entomology Laboratory
https://ecdysis.org/content/dwca/HNU-HNUSEL_DwC-A.zip
2025-06-21T00:26:38.116Z IAW-IAW-US | Ian Watkinson Lepidoptera
Collection https://ecdysis.org/content/dwca/IAW-IAW-US_DwC-A.zip
2025-06-21T00:26:38.116Z IIBZ | Insectos asociados a las sabanas de
montañas altas de República Dominicana
https://ecdysis.org/content/dwca/IIBZ_DwC-A.zip 2025-06-21T00:26:38.116Z
IKBC-IKBC | Ilgoo Kang Braconid Collection
https://ecdysis.org/content/dwca/IKBC-IKBC_DwC-A.zip
2025-06-21T00:26:38.116Z KY-UKIC | University of Kentucky Insect
Collection https://ecdysis.org/content/dwca/KY-UKIC_DwC-A.zip
2025-06-21T00:26:38.116Z LCDI-LERC | Luther Entomological Research
Collection https://ecdysis.org/content/dwca/LCDI-LERC_DwC-A.zip
2025-06-21T00:26:38.116Z MAJC-INDD | Insect Diversity and Diagnostics
Lab https://ecdysis.org/content/dwca/MAJC-INDD_DwC-A.zip
2025-06-21T00:26:38.116Z MAJC-MAJC | M. Andrew Johnston Research
Collection https://ecdysis.org/content/dwca/MAJC-MAJC_DwC-A.zip
2025-06-21T00:26:38.116Z MEPN-INV | Escuela Politécnica Nacional, Quito,
Ecuador https://ecdysis.org/content/dwca/MEPN-INV_DwC-A.zip
2025-06-21T00:26:38.116Z MHNU-E-MHNU | Museo de Historia Natural
Unillanos-Entomology
https://ecdysis.org/content/dwca/MHNU-E-MHNU_DwC-A.zip
2025-06-21T00:26:38.116Z MISSA-MEM | Mississippi Entomological Museum
https://ecdysis.org/content/dwca/MISSA-MEM_DwC-A.zip
2025-06-21T00:26:38.116Z MSU-MSUC | The Albert J. Cook Arthropod
Research Collection https://ecdysis.org/content/dwca/MSU-MSUC_DwC-A.zip
2025-06-21T00:26:38.116Z MUCR-MI-CIPROC | Museo de Insectos, Centro de
Investigaciones en Protección de Cultivos (CIPROC), Escuela de
Agronomía, Universidad de Costa Rica
https://ecdysis.org/content/dwca/MUCR-MI-CIPROC_DwC-A.zip
2025-06-21T00:26:38.116Z MWLR-NZAC | New Zealand Arthropod Collection -
Symbiota https://ecdysis.org/content/dwca/MWLR-NZAC_DwC-A.zip
2025-06-21T00:26:38.116Z NARO | Uganda National Insect Collection
https://ecdysis.org/content/dwca/NARO_DwC-A.zip 2025-06-21T00:26:38.116Z
NAU-NAAC | Northern Arizona University - Arthropod Collection
https://ecdysis.org/content/dwca/NAU-NAAC_DwC-A.zip
2025-06-21T00:26:38.116Z NAU-NAUFEC | Forest Entomology Collection -
Northern Arizona University
https://ecdysis.org/content/dwca/NAU-NAUFEC_DwC-A.zip
2025-06-21T00:26:38.116Z NAU-WACA | Northern Arizona University - Walnut
Canyon National Monument Collection
https://ecdysis.org/content/dwca/NAU-WACA_DwC-A.zip
2025-06-21T00:26:38.116Z NMDG-NMDG | Nathaniel Green Research Collection
https://ecdysis.org/content/dwca/NMDG-NMDG_DwC-A.zip
2025-06-21T00:26:38.116Z NMSU-NMSU | New Mexico State Collection of
Arthropods https://ecdysis.org/content/dwca/NMSU-NMSU_DwC-A.zip
2025-06-21T00:26:38.116Z NPRC-NPRC | Northern Plains Research Collection
https://ecdysis.org/content/dwca/NPRC-NPRC_DwC-A.zip
2025-06-21T00:26:38.116Z NTSC-EFIC | University of North Texas Elm Fork
Insect Collection https://ecdysis.org/content/dwca/NTSC-EFIC_DwC-A.zip
2025-06-21T00:26:38.116Z OSAL-spiders | Ohio State University Spider
Collection https://ecdysis.org/content/dwca/OSAL-spiders_DwC-A.zip
2025-06-21T00:26:38.116Z PSUC-ENTO | Frost Entomological Museum
https://ecdysis.org/content/dwca/PSUC-ENTO_DwC-A.zip
2025-06-21T00:26:38.116Z RUAC_ENT | Rutgers University Entomological
Museum https://ecdysis.org/content/dwca/RUAC_ENT_DwC-A.zip
2025-06-21T00:26:38.116Z SBMNH-SBMNHENT | Santa Barbara Museum of
Natural History Entomology Collection
https://ecdysis.org/content/dwca/SBMNH-SBMNHENT_DwC-A.zip
2025-06-21T00:26:38.116Z SCAN-ARTSYS | Collection of Externally
Processed Specimens (Arthropod Systematics Research)
https://ecdysis.org/content/dwca/SCAN-ARTSYS_DwC-A.zip
2025-06-21T00:26:38.116Z SCFS-ENTO | Sagehen Creek Field Station
(UC-Berkeley) – Insects
https://ecdysis.org/content/dwca/SCFS-ENTO_DwC-A.zip
2025-06-21T00:26:38.116Z SDNHM-SDMC | San Diego Natural History Museum
Entomology Department
https://ecdysis.org/content/dwca/SDNHM-SDMC_DwC-A.zip
2025-06-21T00:26:38.116Z SDSU-TAC | San Diego State University -
Terrestrial Arthropods Collection
https://ecdysis.org/content/dwca/SDSU-TAC_DwC-A.zip
2025-06-21T00:26:38.116Z SLRC-SLRC | Sangmi Lee Research Collection
https://ecdysis.org/content/dwca/SLRC-SLRC_DwC-A.zip
2025-06-21T00:26:38.116Z SOVT-FBL | State of Vermont Forest Biology Lab
https://ecdysis.org/content/dwca/SOVT-FBL_DwC-A.zip
2025-06-21T00:26:38.116Z SSAC-SSAC | Salvatore S. Anzaldo Collection
https://ecdysis.org/content/dwca/SSAC-SSAC_DwC-A.zip
2025-06-21T00:26:38.116Z TJHC-THJC | Tyler J. Hedlund Collection
https://ecdysis.org/content/dwca/TJHC-THJC_DwC-A.zip
2025-06-21T00:26:38.116Z TTU-TTU-Z | Museum of Texas Tech University
Invertebrate Zoology Collection
https://ecdysis.org/content/dwca/TTU-TTU-Z_DwC-A.zip
2025-06-21T00:26:38.116Z UA-RLMC | University of Arizona Insect
Collection RL Minckley Insect Collection
https://ecdysis.org/content/dwca/UA-RLMC_DwC-A.zip
2025-06-21T00:26:38.116Z UA-RLMPC | RL Minckley Plant Collection
https://ecdysis.org/content/dwca/UA-RLMPC_DwC-A.zip
2025-06-21T00:26:38.116Z UASD-IIBZ-ENT | Colección Entomológica del
Instituto de Investigaciones Botánicas y Zoológicas/ Insect Collection
IIBZ https://ecdysis.org/content/dwca/UASD-IIBZ-ENT_DwC-A.zip
2025-06-21T00:26:38.116Z UA-UAIC | University of Arizona Insect
Collection https://ecdysis.org/content/dwca/UA-UAIC_DwC-A.zip
2025-06-21T00:26:38.116Z UCD-BMEC | R. M. Bohart Museum of Entomology
https://ecdysis.org/content/dwca/UCD-BMEC_DwC-A.zip
2025-06-21T00:26:38.116Z UCONN-INV | UConn Biodiversity Research
Collection https://ecdysis.org/content/dwca/UCONN-INV_DwC-A.zip
2025-06-21T00:26:38.116Z UCRG-UCRG | Colección Entomológica de la
Carrera de Agronomía de la UCR Sede Guanacaste
https://ecdysis.org/content/dwca/UCRG-UCRG_DwC-A.zip
2025-06-21T00:26:38.116Z UCSB-IZC | University of California Santa
Barbara Invertebrate Zoology Collection
https://ecdysis.org/content/dwca/UCSB-IZC_DwC-A.zip
2025-06-21T00:26:38.116Z UCSC-RMIC | Kenneth S. Norris Center for
Natural History, University of California Santa Cruz, Insect Collection
https://ecdysis.org/content/dwca/UCSC-RMIC_DwC-A.zip
2025-06-21T00:26:38.116Z UF-SPDR | Spider Parasite Digital Research
Collection https://ecdysis.org/content/dwca/UF-SPDR_DwC-A.zip
2025-06-21T00:26:38.116Z UHIM-UHIM | University of Hawaii Insect Museum
https://ecdysis.org/content/dwca/UHIM-UHIM_DwC-A.zip
2025-06-21T00:26:38.116Z UI-WFBM | William F. Barr Entomological Museum
https://ecdysis.org/content/dwca/UI-WFBM_DwC-A.zip
2025-06-21T00:26:38.116Z UMNH-ENT | Entomology Collection at the Natural
History Museum of Utah
https://ecdysis.org/content/dwca/UMNH-ENT_DwC-A.zip
2025-06-21T00:26:38.116Z UM-WRME | J. B. Wallis / R. E. Roughley Museum
of Entomology https://ecdysis.org/content/dwca/UM-WRME_DwC-A.zip
2025-06-21T00:26:38.116Z UNACHI-MUPADI | Colección Entomológica del
Museo de Peces de Agua Dulce e Invertebrados de la Universidad Autónoma
de Chiriquí https://ecdysis.org/content/dwca/UNACHI-MUPADI_DwC-A.zip
2025-06-21T00:26:38.116Z USNM-USNMENT | United States National Museum,
Entomology Collections
https://ecdysis.org/content/dwca/USNM-USNMENT_DwC-A.zip
2025-06-21T00:26:38.116Z UTAH-PIPR | Price Institute of Parasite
Research, School of Biological Sciences, University of Utah
https://ecdysis.org/content/dwca/UTAH-PIPR_DwC-A.zip
2025-06-21T00:26:38.116Z UTC-UTCI | University of Tennessee at
Chattanooga Insect Collection
https://ecdysis.org/content/dwca/UTC-UTCI_DwC-A.zip
2025-06-21T00:26:38.116Z UVM-VTZT | University of Vermont Zadock
Thompson Zoological Collection-Invertebrates
https://ecdysis.org/content/dwca/UVM-VTZT_DwC-A.zip
2025-06-21T00:26:38.116Z UWSP-PARA | University of Wisconsin-Stevens
Point https://ecdysis.org/content/dwca/UWSP-PARA_DwC-A.zip
2025-06-21T00:26:38.116Z VPI-VTEC | Virginia Polytechnic Institute and
State University Insect Collection
https://ecdysis.org/content/dwca/VPI-VTEC_DwC-A.zip
2025-06-21T00:26:38.116Z WILK-ENT | Wilkes University Entomological
Collection https://ecdysis.org/content/dwca/WILK-ENT_DwC-A.zip
2025-06-21T00:26:38.116Z WSU-WSUC | Washington State University
Collection https://ecdysis.org/content/dwca/WSU-WSUC_DwC-A.zip
2025-06-21T00:26:38.116Z hash://md5/1eb9f1b706eef2ac25114f3e382a157b
For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/ecdysis
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. 498MiB) under review
elton pull globalbioticinteractions/ecdysis
# generate review notes
elton review globalbioticinteractions/ecdysis\
> review.tsv
# export indexed interaction records
elton interactions globalbioticinteractions/ecdysis\
> interactions.tsv
# export names and align them with the Catalogue of Life using Nomer
elton names globalbioticinteractions/ecdysis\
| nomer append col\
> name-alignment.tsv
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 (J. H. (ed. ). Poelen 2024)
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 (J. H. (ed. ). Poelen
2024)
taxonomic names found in the dataset under review aligned with the
Catalogue of Life as accessed through the Nomer Corpus of Taxonomic
Resources (J. H. (ed. ).
Poelen 2024) in gzipped comma-separated values format
taxonomic names found in the dataset under review aligned with the
Catalogue of Life as accessed through the Nomer Corpus of Taxonomic
Resources (J. H. (ed. ).
Poelen 2024) in gzipped html format
taxonomic names found in the dataset under review aligned with the
Catalogue of Life as accessed through the Nomer Corpus of Taxonomic
Resources (J. H. (ed. ).
Poelen 2024) in gzipped tab-separated values format
taxonomic names found in the dataset under review aligned with the
Catalogue of Life as accessed through the Nomer Corpus of Taxonomic
Resources (J. H. (ed. ).
Poelen 2024) in Apache Parquet format
taxonomic names found in the dataset under review aligned with
Discover Life bee species checklist as accessed through the Nomer Corpus
of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped
comma-separated values format
taxonomic names found in the dataset under review aligned with
Discover Life bee species checklist as accessed through the Nomer Corpus
of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped
html format
taxonomic names found in the dataset under review aligned with
Discover Life bee species checklist as accessed through the Nomer Corpus
of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped
tab-separated values format
taxonomic names found in the dataset under review aligned with
Discover Life bee species checklist as accessed through the Nomer Corpus
of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in Apache
Parquet format
taxonomic names found in the dataset under review aligned with GBIF
Backbone Taxonomy as accessed through the Nomer Corpus of Taxonomic
Resources (J. H. (ed. ).
Poelen 2024) in gzipped comma-separated values format
taxonomic names found in the dataset under review aligned with GBIF
Backbone Taxonomy as accessed through the Nomer Corpus of Taxonomic
Resources (J. H. (ed. ).
Poelen 2024) in gzipped html format
taxonomic names found in the dataset under review aligned with GBIF
Backbone Taxonomy as accessed through the Nomer Corpus of Taxonomic
Resources (J. H. (ed. ).
Poelen 2024) in gzipped tab-separated values format
taxonomic names found in the dataset under review aligned with GBIF
Backbone Taxonomy as accessed through the Nomer Corpus of Taxonomic
Resources (J. H. (ed. ).
Poelen 2024) in Apache Parquet format
taxonomic names found in the dataset under review aligned with
Integrated Taxonomic Information System (ITIS) as accessed through the
Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped
comma-separated values format
taxonomic names found in the dataset under review aligned with
Integrated Taxonomic Information System (ITIS) as accessed through the
Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped
html format
taxonomic names found in the dataset under review aligned with
Integrated Taxonomic Information System (ITIS) as accessed through the
Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in gzipped
tab-separated values format
taxonomic names found in the dataset under review aligned with
Integrated Taxonomic Information System (ITIS) as accessed through the
Nomer Corpus of Taxonomic Resources (J. H. (ed. ). Poelen 2024) in Apache
Parquet format
taxonomic names found in the dataset under review aligned with the
Mammal Diversity Database as accessed through the Nomer Corpus of
Taxonomic Resources (J.
H. (ed. ). Poelen 2024) in gzipped comma-separated values
format
taxonomic names found in the dataset under review aligned with
Mammal Diversity Database as accessed through the Nomer Corpus of
Taxonomic Resources (J.
H. (ed. ). Poelen 2024) in gzipped html format
taxonomic names found in the dataset under review aligned with
Mammal Diversity Database as accessed through the Nomer Corpus of
Taxonomic Resources (J.
H. (ed. ). Poelen 2024) in gzipped tab-separated values
format
taxonomic names found in the dataset under review aligned with
Mammal Diversity Database as accessed through the Nomer Corpus of
Taxonomic Resources (J.
H. (ed. ). Poelen 2024) in Apache Parquet format
taxonomic names found in the dataset under review aligned with the
NCBI Taxonomy as accessed through the Nomer Corpus of Taxonomic
Resources (J. H. (ed. ).
Poelen 2024) in gzipped comma-separated values format
taxonomic names found in the dataset under review aligned with the
NCBI Taxonomy as accessed through the Nomer Corpus of Taxonomic
Resources (J. H. (ed. ).
Poelen 2024) in gzipped html format
taxonomic names found in the dataset under review aligned with the
NCBI Taxonomy as accessed through the Nomer Corpus of Taxonomic
Resources (J. H. (ed. ).
Poelen 2024) in gzipped tab-separated values format
taxonomic names found in the dataset under review aligned with the
NCBI Taxonomy as accessed through the Nomer Corpus of Taxonomic
Resources (J. H. (ed. ).
Poelen 2024) in Apache Parquet format
taxonomic names found in the dataset under review aligned with the
Paleobiology Database as accessed through the Nomer Corpus of Taxonomic
Resources (J. H. (ed. ).
Poelen 2024) in gzipped comma-separated values format
taxonomic names found in the dataset under review aligned with
Paleobiology Database as accessed through the Nomer Corpus of Taxonomic
Resources (J. H. (ed. ).
Poelen 2024) in gzipped html format
taxonomic names found in the dataset under review aligned with
Paleobiology Database as accessed through the Nomer Corpus of Taxonomic
Resources (J. H. (ed. ).
Poelen 2024) in gzipped tab-separated values format
taxonomic names found in the dataset under review aligned with
Paleobiology Database as accessed through the Nomer Corpus of Taxonomic
Resources (J. H. (ed. ).
Poelen 2024) in Apache Parquet format
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 (J. H. (ed. ). Poelen 2024) in gzipped
comma-separated values format
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 (J. H. (ed. ). Poelen 2024) in gzipped
html format
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 (J. H. (ed. ). Poelen 2024) in gzipped
tab-separated values format
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 (J. H. (ed. ). Poelen 2024) in Apache
Parquet format
taxonomic names found in the dataset under review aligned with the
World of Flora Online as accessed through the Nomer Corpus of Taxonomic
Resources (J. H. (ed. ).
Poelen 2024) in gzipped comma-separated values format
taxonomic names found in the dataset under review aligned with the
World of Flora Online as accessed through the Nomer Corpus of Taxonomic
Resources (J. H. (ed. ).
Poelen 2024) in gzipped html format
taxonomic names found in the dataset under review aligned with the
World of Flora Online as accessed through the Nomer Corpus of Taxonomic
Resources (J. H. (ed. ).
Poelen 2024) in gzipped tab-separated values format
taxonomic names found in the dataset under review aligned with the
World of Flora Online as accessed through the Nomer Corpus of Taxonomic
Resources (J. H. (ed. ).
Poelen 2024) in Apache Parquet format
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 (J. H. (ed. ). Poelen 2024) in gzipped
comma-separated values format
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 (J. H. (ed. ). Poelen 2024) in gzipped
html format
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 (J. H. (ed. ). Poelen 2024) in gzipped
tab-separated values format
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 (J. H. (ed. ). Poelen 2024) in Apache
Parquet format
metadata of this review expressed in Zenodo record metadata
Archived Dataset
Note that data.zip file in this
archive contains the complete, unmodified archived dataset under
review.
Biotic Interactions
Biotic Interaction Data
Model
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/ecdysis, has
fingerprint hash://md5/1eb9f1b706eef2ac25114f3e382a157b, is 498MiB in
size and contains 659,189 interaction with 10 unique types of
associations (e.g., interactsWith) between 83,704 primary taxon (e.g.,
Augochlora pura) and 34,716 associated taxon (e.g., Prunus).
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.
Most Frequently Mentioned Interaction Types (up to 20 most
frequent)
interactionTypeName
count
interactsWith
517504
hasHost
91976
adjacentTo
47508
visits
1493
eats
464
killedBy
143
hostOf
48
visitsFlowersOf
43
hasParasite
9
parasiteOf
1
Most Frequently Mentioned Primary Taxa (up to 20 most
frequent)
sourceTaxonName
count
Augochlora pura
12834
Ceratophyllus
8310
Lasioglossum
7887
Ceratina calcarata
7248
Apis mellifera
6885
Eucera hamata
6579
Heterodoxus spiniger
5604
Aetheca wagneri
5177
Taenia pisiformis
5040
Andrena
5014
Bombus impatiens
4277
Meringis parkeri
4255
Arthropoda
4241
Lasioglossum pilosum
3191
Bombus vagans
3039
Melissodes bimaculatus
2853
Alaria marcianae
2701
Phthiraptera
2652
Agapostemon virescens
2644
Most Frequently Mentioned Associate Taxa (up to 20 most
frequent)
targetTaxonName
count
Prunus
31529
none
28861
Malus
23709
host
16661
Canis latrans (Canidae)
11333
Peromyscus maniculatus
9054
CLSW
8749
N/A
4654
ex. snags
3086
Dipodomys ordii
3035
Larrea tridentata
2593
male
2548
Neotoma lepida
2411
Oak
2261
Agastache Blue Fortune
2233
Eriogonum fasciculatum
2074
Sycamore
1930
Daucus carota
1861
Salix
1816
Most Frequent Interactions between Primary and Associate Taxa
(up to 20 most frequent)
sourceTaxonName
interactionTypeName
targetTaxonName
count
Ceratophyllus
interactsWith
CLSW
8301
Augochlora pura
interactsWith
Malus
7160
Eucera hamata
interactsWith
Prunus
6279
Augochlora pura
interactsWith
Prunus
4327
Ceratina calcarata
interactsWith
Malus
3463
Aetheca wagneri
hasHost
Peromyscus maniculatus
3455
Ceratina calcarata
interactsWith
Prunus
3335
Heterodoxus spiniger
interactsWith
Canis latrans (Canidae)
2825
Lasioglossum pilosum
interactsWith
Prunus
2642
Taenia pisiformis
interactsWith
host
2345
Heterodoxus spiniger
interactsWith
male
2276
Agapostemon virescens
interactsWith
Prunus
2174
Melissodes bimaculatus
interactsWith
Prunus
2100
Meringis parkeri
hasHost
Dipodomys ordii
1745
Bombus vagans
interactsWith
Malus
1714
Taenia pisiformis
interactsWith
Canis latrans (Canidae)
1672
Apis mellifera
interactsWith
Prunus
1612
Anomiopsyllus amphibolus
interactsWith
Neotoma lepida
1565
Alaria marcianae
interactsWith
Canis latrans (Canidae)
1476
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
svgInteractions on the taxonomic family rank
as interpreted by the Catalogue of Life. download
svg
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
Distichlis spicata
HAS_ACCEPTED_NAME
col
Distichlis spicata
Viii
NONE
col
Viii
Arrenodes minutus
HAS_ACCEPTED_NAME
col
Arrenodes minutus
Asaphococcus agninus
HAS_ACCEPTED_NAME
col
Asaphococcus agninus
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
82147
col
class
13
col
family
499
col
genus
3653
col
gigaclass
1
col
infraspecific name
6
col
kingdom
3
col
nanorder
2
col
order
48
col
other
1
col
parvorder
1
col
phylum
7
col
section
1
col
species
20017
col
subclass
2
col
subfamily
99
col
subgenus
155
col
suborder
6
col
subspecies
1131
col
subterclass
1
col
subtribe
5
col
superfamily
16
col
superorder
2
col
tribe
42
col
variety
109
discoverlife
NA
105886
discoverlife
species
1637
gbif
NA
79027
gbif
class
15
gbif
family
566
gbif
form
7
gbif
genus
4087
gbif
kingdom
4
gbif
order
47
gbif
phylum
7
gbif
species
22431
gbif
subspecies
1492
gbif
variety
225
itis
NA
88138
itis
class
13
itis
division
2
itis
family
494
itis
genus
2770
itis
infraorder
3
itis
kingdom
3
itis
order
53
itis
phylum
6
itis
section
1
itis
species
14641
itis
subclass
4
itis
subfamily
120
itis
subgenus
4
itis
subkingdom
2
itis
suborder
26
itis
subphylum
1
itis
subspecies
1091
itis
subtribe
1
itis
superclass
1
itis
superfamily
15
itis
superorder
4
itis
tribe
30
itis
variety
124
mdd
NA
107522
ncbi
NA
87914
ncbi
clade
5
ncbi
class
12
ncbi
cohort
1
ncbi
family
503
ncbi
genus
3439
ncbi
infraorder
5
ncbi
kingdom
2
ncbi
order
50
ncbi
phylum
6
ncbi
section
4
ncbi
series
1
ncbi
species
14882
ncbi
species group
1
ncbi
subclass
4
ncbi
subfamily
144
ncbi
subgenus
64
ncbi
suborder
15
ncbi
subphylum
1
ncbi
subspecies
442
ncbi
subtribe
2
ncbi
superclass
1
ncbi
superfamily
17
ncbi
superorder
4
ncbi
tribe
33
ncbi
varietas
23
pbdb
NA
103871
pbdb
class
16
pbdb
family
426
pbdb
genus
1390
pbdb
informal
1
pbdb
infraclass
1
pbdb
infraorder
7
pbdb
kingdom
3
pbdb
order
58
pbdb
phylum
6
pbdb
species
1545
pbdb
subclass
4
pbdb
subfamily
130
pbdb
subgenus
1
pbdb
suborder
24
pbdb
subspecies
6
pbdb
subtribe
4
pbdb
superclass
1
pbdb
superfamily
18
pbdb
superorder
2
pbdb
superphylum
1
pbdb
tribe
34
pbdb
unranked clade
14
tpt
NA
102553
tpt
family
30
tpt
genus
405
tpt
order
9
tpt
species
4525
tpt
specificepithet
1
tpt
subspecificepithet
3
wfo
NA
102093
wfo
family
43
wfo
genus
1098
wfo
order
1
wfo
phylum
1
wfo
section
1
wfo
species
4164
wfo
subfamily
1
wfo
subsection
1
wfo
subspecies
109
wfo
subtribe
1
wfo
tribe
1
wfo
variety
81
worms
NA
102729
worms
class
12
worms
family
350
worms
genus
1464
worms
gigaclass
1
worms
infraorder
3
worms
kingdom
3
worms
order
43
worms
phylum
5
worms
phylum (division)
2
worms
species
2816
worms
subclass
5
worms
subfamily
10
worms
subgenus
2
worms
suborder
16
worms
subphylum
1
worms
subspecies
57
worms
subterclass
1
worms
subtribe
1
worms
superfamily
5
worms
superorder
2
worms
tribe
2
worms
variety
21
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
HAS_ACCEPTED_NAME
38678
col
NONE
91265
col
SYNONYM_OF
10323
discoverlife
NONE
129235
discoverlife
HAS_ACCEPTED_NAME
3470
discoverlife
SYNONYM_OF
1040
discoverlife
HOMONYM_OF
148
gbif
HAS_ACCEPTED_NAME
46168
gbif
NONE
87325
gbif
SYNONYM_OF
15047
itis
HAS_ACCEPTED_NAME
31817
itis
NONE
98425
itis
SYNONYM_OF
3194
mdd
NONE
131300
mdd
HAS_ACCEPTED_NAME
1258
mdd
SYNONYM_OF
62
ncbi
NONE
98081
ncbi
SAME_AS
33299
ncbi
SYNONYM_OF
2124
ncbi
COMMON_NAME_OF
82
pbdb
NONE
123162
pbdb
SYNONYM_OF
787
pbdb
HAS_ACCEPTED_NAME
9201
tpt
NONE
125561
tpt
SYNONYM_OF
1682
tpt
HAS_ACCEPTED_NAME
6986
wfo
HAS_ACCEPTED_NAME
10445
wfo
NONE
120776
wfo
HAS_UNCHECKED_NAME
997
wfo
SYNONYM_OF
2529
worms
HAS_ACCEPTED_NAME
10904
worms
NONE
121542
worms
SYNONYM_OF
1442
List of Available Name Alignment Reports
catalog name
alignment results
col
associated names alignments report in gzipped html, csv, and tsv)
ncbi
associated names alignments report in gzipped html, csv, and tsv)
discoverlife
associated names alignments report in gzipped html, csv, and tsv)
gbif
associated names alignments report in gzipped html, csv, and tsv)
itis
associated names alignments report in gzipped html, csv, and tsv)
wfo
associated names alignments report in gzipped html, csv, and tsv)
mdd
associated names alignments report in gzipped html, csv, and tsv)
tpt
associated names alignments report in gzipped html, csv, and tsv)
pbdb
associated names alignments report in gzipped html, csv, and tsv)
worms
associated names alignments report in gzipped html, csv, and 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
2025-06-27T15:37:34Z
note
[] Caused by: org.eol.globi.data.StudyImporterException: failed to
read archive
[https://ecdysis.org/collections/misc/collprofiles.php?collid=151] at
org.eol.globi.data.DatasetImporterForDwCA.importStudy(DatasetImporterForDwCA.java:356)
at
org.eol.globi.util.DatasetImportUtil.importDataset(DatasetImportUtil.java:71)
at
org.eol.globi.util.DatasetImportUtil.importDataset(DatasetImportUtil.java:42)
at
org.eol.globi.util.DatasetImportUtil.importDatasets(DatasetImportUtil.java:141)
at
org.eol.globi.util.DatasetImportUtil.indexDatasetWithResolvedDependencies(DatasetImportUtil.java:97)
at
org.eol.globi.util.DatasetImportUtil.resolveAndImportDatasets(DatasetImportUtil.java:88)
at
org.eol.globi.data.DatasetImporterForRSS.importStudy(DatasetImporterForRSS.java:45)
at
org.eol.globi.util.DatasetImportUtil.importDataset(DatasetImportUtil.java:71)
at
org.globalbioticinteractions.elton.cmd.CmdReview.review(CmdReview.java:248)
at
org.globalbioticinteractions.elton.cmd.CmdReview.reviewLocal(CmdReview.java:201)
at
org.globalbioticinteractions.elton.cmd.CmdReview.doRun(CmdReview.java:159)
at
org.globalbioticinteractions.elton.cmd.CmdDefaultParams.run(CmdDefaultParams.java:223)
at
org.globalbioticinteractions.elton.cmd.CmdTabularWriterParams.run(CmdTabularWriterParams.java:12)
at picocli.CommandLine.executeUserObject(CommandLine.java:1939) at
picocli.CommandLine.access1300(CommandLine.java:145)atpicocli.CommandLineRunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)
at picocli.CommandLineRunLast.handle(CommandLine.java:2352)atpicocli.CommandLineRunLast.handle(CommandLine.java:2314)
at picocli.CommandLineAbstractParseResultHandler.execute(CommandLine.java:2179)atpicocli.CommandLineRunLast.execute(CommandLine.java:2316)
at picocli.CommandLine.execute(CommandLine.java:2078) at
org.globalbioticinteractions.elton.Elton.run(Elton.java:103) at
org.globalbioticinteractions.elton.Elton.main(Elton.java:94) Caused by:
java.io.IOException: failed to read
[file:/tmp/dwca4790424870104248827tmp.zip] at
org.globalbioticinteractions.dataset.DwCAUtil.archiveFor(DwCAUtil.java:29)
at
org.eol.globi.data.DatasetImporterForDwCA.importStudy(DatasetImporterForDwCA.java:329)
… 22 more Caused by: org.gbif.dwc.UnsupportedArchiveException: Parts of
DwC-A are missing at org.gbif.dwc.Archive.validate(Archive.java:157) at
org.gbif.dwc.DwcFiles.fromCompressed(DwcFiles.java:75) at
org.globalbioticinteractions.dataset.DwCAUtil.archiveFor(DwCAUtil.java:24)
… 23 more
2025-06-27T15:37:35Z
note
[] Caused by: org.eol.globi.data.StudyImporterException: failed to
read archive
[https://ecdysis.org/collections/misc/collprofiles.php?collid=153] at
org.eol.globi.data.DatasetImporterForDwCA.importStudy(DatasetImporterForDwCA.java:356)
at
org.eol.globi.util.DatasetImportUtil.importDataset(DatasetImportUtil.java:71)
at
org.eol.globi.util.DatasetImportUtil.importDataset(DatasetImportUtil.java:42)
at
org.eol.globi.util.DatasetImportUtil.importDatasets(DatasetImportUtil.java:141)
at
org.eol.globi.util.DatasetImportUtil.indexDatasetWithResolvedDependencies(DatasetImportUtil.java:97)
at
org.eol.globi.util.DatasetImportUtil.resolveAndImportDatasets(DatasetImportUtil.java:88)
at
org.eol.globi.data.DatasetImporterForRSS.importStudy(DatasetImporterForRSS.java:45)
at
org.eol.globi.util.DatasetImportUtil.importDataset(DatasetImportUtil.java:71)
at
org.globalbioticinteractions.elton.cmd.CmdReview.review(CmdReview.java:248)
at
org.globalbioticinteractions.elton.cmd.CmdReview.reviewLocal(CmdReview.java:201)
at
org.globalbioticinteractions.elton.cmd.CmdReview.doRun(CmdReview.java:159)
at
org.globalbioticinteractions.elton.cmd.CmdDefaultParams.run(CmdDefaultParams.java:223)
at
org.globalbioticinteractions.elton.cmd.CmdTabularWriterParams.run(CmdTabularWriterParams.java:12)
at picocli.CommandLine.executeUserObject(CommandLine.java:1939) at
picocli.CommandLine.access1300(CommandLine.java:145)atpicocli.CommandLineRunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)
at picocli.CommandLineRunLast.handle(CommandLine.java:2352)atpicocli.CommandLineRunLast.handle(CommandLine.java:2314)
at picocli.CommandLineAbstractParseResultHandler.execute(CommandLine.java:2179)atpicocli.CommandLineRunLast.execute(CommandLine.java:2316)
at picocli.CommandLine.execute(CommandLine.java:2078) at
org.globalbioticinteractions.elton.Elton.run(Elton.java:103) at
org.globalbioticinteractions.elton.Elton.main(Elton.java:94) Caused by:
java.io.IOException: failed to read
[file:/tmp/dwca2091397650674758656tmp.zip] at
org.globalbioticinteractions.dataset.DwCAUtil.archiveFor(DwCAUtil.java:29)
at
org.eol.globi.data.DatasetImporterForDwCA.importStudy(DatasetImporterForDwCA.java:329)
… 22 more Caused by: org.gbif.dwc.UnsupportedArchiveException: Parts of
DwC-A are missing at org.gbif.dwc.Archive.validate(Archive.java:157) at
org.gbif.dwc.DwcFiles.fromCompressed(DwcFiles.java:75) at
org.globalbioticinteractions.dataset.DwCAUtil.archiveFor(DwCAUtil.java:24)
… 23 more
2025-06-27T15:37:53Z
note
[] Caused by: org.eol.globi.data.StudyImporterException: failed to
read archive
[https://ecdysis.org/collections/misc/collprofiles.php?collid=172] at
org.eol.globi.data.DatasetImporterForDwCA.importStudy(DatasetImporterForDwCA.java:356)
at
org.eol.globi.util.DatasetImportUtil.importDataset(DatasetImportUtil.java:71)
at
org.eol.globi.util.DatasetImportUtil.importDataset(DatasetImportUtil.java:42)
at
org.eol.globi.util.DatasetImportUtil.importDatasets(DatasetImportUtil.java:141)
at
org.eol.globi.util.DatasetImportUtil.indexDatasetWithResolvedDependencies(DatasetImportUtil.java:97)
at
org.eol.globi.util.DatasetImportUtil.resolveAndImportDatasets(DatasetImportUtil.java:88)
at
org.eol.globi.data.DatasetImporterForRSS.importStudy(DatasetImporterForRSS.java:45)
at
org.eol.globi.util.DatasetImportUtil.importDataset(DatasetImportUtil.java:71)
at
org.globalbioticinteractions.elton.cmd.CmdReview.review(CmdReview.java:248)
at
org.globalbioticinteractions.elton.cmd.CmdReview.reviewLocal(CmdReview.java:201)
at
org.globalbioticinteractions.elton.cmd.CmdReview.doRun(CmdReview.java:159)
at
org.globalbioticinteractions.elton.cmd.CmdDefaultParams.run(CmdDefaultParams.java:223)
at
org.globalbioticinteractions.elton.cmd.CmdTabularWriterParams.run(CmdTabularWriterParams.java:12)
at picocli.CommandLine.executeUserObject(CommandLine.java:1939) at
picocli.CommandLine.access1300(CommandLine.java:145)atpicocli.CommandLineRunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)
at picocli.CommandLineRunLast.handle(CommandLine.java:2352)atpicocli.CommandLineRunLast.handle(CommandLine.java:2314)
at picocli.CommandLineAbstractParseResultHandler.execute(CommandLine.java:2179)atpicocli.CommandLineRunLast.execute(CommandLine.java:2316)
at picocli.CommandLine.execute(CommandLine.java:2078) at
org.globalbioticinteractions.elton.Elton.run(Elton.java:103) at
org.globalbioticinteractions.elton.Elton.main(Elton.java:94) Caused by:
java.io.IOException: failed to read
[file:/tmp/dwca5112787931735347811tmp.zip] at
org.globalbioticinteractions.dataset.DwCAUtil.archiveFor(DwCAUtil.java:29)
at
org.eol.globi.data.DatasetImporterForDwCA.importStudy(DatasetImporterForDwCA.java:329)
… 22 more Caused by: org.gbif.dwc.UnsupportedArchiveException: Parts of
DwC-A are missing at org.gbif.dwc.Archive.validate(Archive.java:157) at
org.gbif.dwc.DwcFiles.fromCompressed(DwcFiles.java:75) at
org.globalbioticinteractions.dataset.DwCAUtil.archiveFor(DwCAUtil.java:24)
… 23 more
2025-06-27T15:37:53Z
note
[] Caused by: org.eol.globi.data.StudyImporterException: failed to
read archive
[https://ecdysis.org/collections/misc/collprofiles.php?collid=178] at
org.eol.globi.data.DatasetImporterForDwCA.importStudy(DatasetImporterForDwCA.java:356)
at
org.eol.globi.util.DatasetImportUtil.importDataset(DatasetImportUtil.java:71)
at
org.eol.globi.util.DatasetImportUtil.importDataset(DatasetImportUtil.java:42)
at
org.eol.globi.util.DatasetImportUtil.importDatasets(DatasetImportUtil.java:141)
at
org.eol.globi.util.DatasetImportUtil.indexDatasetWithResolvedDependencies(DatasetImportUtil.java:97)
at
org.eol.globi.util.DatasetImportUtil.resolveAndImportDatasets(DatasetImportUtil.java:88)
at
org.eol.globi.data.DatasetImporterForRSS.importStudy(DatasetImporterForRSS.java:45)
at
org.eol.globi.util.DatasetImportUtil.importDataset(DatasetImportUtil.java:71)
at
org.globalbioticinteractions.elton.cmd.CmdReview.review(CmdReview.java:248)
at
org.globalbioticinteractions.elton.cmd.CmdReview.reviewLocal(CmdReview.java:201)
at
org.globalbioticinteractions.elton.cmd.CmdReview.doRun(CmdReview.java:159)
at
org.globalbioticinteractions.elton.cmd.CmdDefaultParams.run(CmdDefaultParams.java:223)
at
org.globalbioticinteractions.elton.cmd.CmdTabularWriterParams.run(CmdTabularWriterParams.java:12)
at picocli.CommandLine.executeUserObject(CommandLine.java:1939) at
picocli.CommandLine.access1300(CommandLine.java:145)atpicocli.CommandLineRunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)
at picocli.CommandLineRunLast.handle(CommandLine.java:2352)atpicocli.CommandLineRunLast.handle(CommandLine.java:2314)
at picocli.CommandLineAbstractParseResultHandler.execute(CommandLine.java:2179)atpicocli.CommandLineRunLast.execute(CommandLine.java:2316)
at picocli.CommandLine.execute(CommandLine.java:2078) at
org.globalbioticinteractions.elton.Elton.run(Elton.java:103) at
org.globalbioticinteractions.elton.Elton.main(Elton.java:94) Caused by:
java.io.IOException: failed to read
[file:/tmp/dwca1040859268717128705tmp.zip] at
org.globalbioticinteractions.dataset.DwCAUtil.archiveFor(DwCAUtil.java:29)
at
org.eol.globi.data.DatasetImporterForDwCA.importStudy(DatasetImporterForDwCA.java:329)
… 22 more Caused by: org.gbif.dwc.UnsupportedArchiveException: Parts of
DwC-A are missing at org.gbif.dwc.Archive.validate(Archive.java:157) at
org.gbif.dwc.DwcFiles.fromCompressed(DwcFiles.java:75) at
org.globalbioticinteractions.dataset.DwCAUtil.archiveFor(DwCAUtil.java:24)
… 23 more
In addition, you can find the most frequently occurring notes in the
table below.
Most frequently occurring review notes, if any.
reviewComment
count
[] Caused by: org.eol.globi.data.StudyImporterException: failed to
read archive
[https://ecdysis.org/collections/misc/collprofiles.php?collid=151] at
org.eol.globi.data.DatasetImporterForDwCA.importStudy(DatasetImporterForDwCA.java:356)
at
org.eol.globi.util.DatasetImportUtil.importDataset(DatasetImportUtil.java:71)
at
org.eol.globi.util.DatasetImportUtil.importDataset(DatasetImportUtil.java:42)
at
org.eol.globi.util.DatasetImportUtil.importDatasets(DatasetImportUtil.java:141)
at
org.eol.globi.util.DatasetImportUtil.indexDatasetWithResolvedDependencies(DatasetImportUtil.java:97)
at
org.eol.globi.util.DatasetImportUtil.resolveAndImportDatasets(DatasetImportUtil.java:88)
at
org.eol.globi.data.DatasetImporterForRSS.importStudy(DatasetImporterForRSS.java:45)
at
org.eol.globi.util.DatasetImportUtil.importDataset(DatasetImportUtil.java:71)
at
org.globalbioticinteractions.elton.cmd.CmdReview.review(CmdReview.java:248)
at
org.globalbioticinteractions.elton.cmd.CmdReview.reviewLocal(CmdReview.java:201)
at
org.globalbioticinteractions.elton.cmd.CmdReview.doRun(CmdReview.java:159)
at
org.globalbioticinteractions.elton.cmd.CmdDefaultParams.run(CmdDefaultParams.java:223)
at
org.globalbioticinteractions.elton.cmd.CmdTabularWriterParams.run(CmdTabularWriterParams.java:12)
at picocli.CommandLine.executeUserObject(CommandLine.java:1939) at
picocli.CommandLine.access1300(CommandLine.java:145)atpicocli.CommandLineRunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)
at picocli.CommandLineRunLast.handle(CommandLine.java:2352)atpicocli.CommandLineRunLast.handle(CommandLine.java:2314)
at picocli.CommandLineAbstractParseResultHandler.execute(CommandLine.java:2179)atpicocli.CommandLineRunLast.execute(CommandLine.java:2316)
at picocli.CommandLine.execute(CommandLine.java:2078) at
org.globalbioticinteractions.elton.Elton.run(Elton.java:103) at
org.globalbioticinteractions.elton.Elton.main(Elton.java:94) Caused by:
java.io.IOException: failed to read
[file:/tmp/dwca4790424870104248827tmp.zip] at
org.globalbioticinteractions.dataset.DwCAUtil.archiveFor(DwCAUtil.java:29)
at
org.eol.globi.data.DatasetImporterForDwCA.importStudy(DatasetImporterForDwCA.java:329)
… 22 more Caused by: org.gbif.dwc.UnsupportedArchiveException: Parts of
DwC-A are missing at org.gbif.dwc.Archive.validate(Archive.java:157) at
org.gbif.dwc.DwcFiles.fromCompressed(DwcFiles.java:75) at
org.globalbioticinteractions.dataset.DwCAUtil.archiveFor(DwCAUtil.java:24)
… 23 more
1
[] Caused by: org.eol.globi.data.StudyImporterException: failed to
read archive
[https://ecdysis.org/collections/misc/collprofiles.php?collid=153] at
org.eol.globi.data.DatasetImporterForDwCA.importStudy(DatasetImporterForDwCA.java:356)
at
org.eol.globi.util.DatasetImportUtil.importDataset(DatasetImportUtil.java:71)
at
org.eol.globi.util.DatasetImportUtil.importDataset(DatasetImportUtil.java:42)
at
org.eol.globi.util.DatasetImportUtil.importDatasets(DatasetImportUtil.java:141)
at
org.eol.globi.util.DatasetImportUtil.indexDatasetWithResolvedDependencies(DatasetImportUtil.java:97)
at
org.eol.globi.util.DatasetImportUtil.resolveAndImportDatasets(DatasetImportUtil.java:88)
at
org.eol.globi.data.DatasetImporterForRSS.importStudy(DatasetImporterForRSS.java:45)
at
org.eol.globi.util.DatasetImportUtil.importDataset(DatasetImportUtil.java:71)
at
org.globalbioticinteractions.elton.cmd.CmdReview.review(CmdReview.java:248)
at
org.globalbioticinteractions.elton.cmd.CmdReview.reviewLocal(CmdReview.java:201)
at
org.globalbioticinteractions.elton.cmd.CmdReview.doRun(CmdReview.java:159)
at
org.globalbioticinteractions.elton.cmd.CmdDefaultParams.run(CmdDefaultParams.java:223)
at
org.globalbioticinteractions.elton.cmd.CmdTabularWriterParams.run(CmdTabularWriterParams.java:12)
at picocli.CommandLine.executeUserObject(CommandLine.java:1939) at
picocli.CommandLine.access1300(CommandLine.java:145)atpicocli.CommandLineRunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)
at picocli.CommandLineRunLast.handle(CommandLine.java:2352)atpicocli.CommandLineRunLast.handle(CommandLine.java:2314)
at picocli.CommandLineAbstractParseResultHandler.execute(CommandLine.java:2179)atpicocli.CommandLineRunLast.execute(CommandLine.java:2316)
at picocli.CommandLine.execute(CommandLine.java:2078) at
org.globalbioticinteractions.elton.Elton.run(Elton.java:103) at
org.globalbioticinteractions.elton.Elton.main(Elton.java:94) Caused by:
java.io.IOException: failed to read
[file:/tmp/dwca2091397650674758656tmp.zip] at
org.globalbioticinteractions.dataset.DwCAUtil.archiveFor(DwCAUtil.java:29)
at
org.eol.globi.data.DatasetImporterForDwCA.importStudy(DatasetImporterForDwCA.java:329)
… 22 more Caused by: org.gbif.dwc.UnsupportedArchiveException: Parts of
DwC-A are missing at org.gbif.dwc.Archive.validate(Archive.java:157) at
org.gbif.dwc.DwcFiles.fromCompressed(DwcFiles.java:75) at
org.globalbioticinteractions.dataset.DwCAUtil.archiveFor(DwCAUtil.java:24)
… 23 more
1
[] Caused by: org.eol.globi.data.StudyImporterException: failed to
read archive
[https://ecdysis.org/collections/misc/collprofiles.php?collid=172] at
org.eol.globi.data.DatasetImporterForDwCA.importStudy(DatasetImporterForDwCA.java:356)
at
org.eol.globi.util.DatasetImportUtil.importDataset(DatasetImportUtil.java:71)
at
org.eol.globi.util.DatasetImportUtil.importDataset(DatasetImportUtil.java:42)
at
org.eol.globi.util.DatasetImportUtil.importDatasets(DatasetImportUtil.java:141)
at
org.eol.globi.util.DatasetImportUtil.indexDatasetWithResolvedDependencies(DatasetImportUtil.java:97)
at
org.eol.globi.util.DatasetImportUtil.resolveAndImportDatasets(DatasetImportUtil.java:88)
at
org.eol.globi.data.DatasetImporterForRSS.importStudy(DatasetImporterForRSS.java:45)
at
org.eol.globi.util.DatasetImportUtil.importDataset(DatasetImportUtil.java:71)
at
org.globalbioticinteractions.elton.cmd.CmdReview.review(CmdReview.java:248)
at
org.globalbioticinteractions.elton.cmd.CmdReview.reviewLocal(CmdReview.java:201)
at
org.globalbioticinteractions.elton.cmd.CmdReview.doRun(CmdReview.java:159)
at
org.globalbioticinteractions.elton.cmd.CmdDefaultParams.run(CmdDefaultParams.java:223)
at
org.globalbioticinteractions.elton.cmd.CmdTabularWriterParams.run(CmdTabularWriterParams.java:12)
at picocli.CommandLine.executeUserObject(CommandLine.java:1939) at
picocli.CommandLine.access1300(CommandLine.java:145)atpicocli.CommandLineRunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)
at picocli.CommandLineRunLast.handle(CommandLine.java:2352)atpicocli.CommandLineRunLast.handle(CommandLine.java:2314)
at picocli.CommandLineAbstractParseResultHandler.execute(CommandLine.java:2179)atpicocli.CommandLineRunLast.execute(CommandLine.java:2316)
at picocli.CommandLine.execute(CommandLine.java:2078) at
org.globalbioticinteractions.elton.Elton.run(Elton.java:103) at
org.globalbioticinteractions.elton.Elton.main(Elton.java:94) Caused by:
java.io.IOException: failed to read
[file:/tmp/dwca5112787931735347811tmp.zip] at
org.globalbioticinteractions.dataset.DwCAUtil.archiveFor(DwCAUtil.java:29)
at
org.eol.globi.data.DatasetImporterForDwCA.importStudy(DatasetImporterForDwCA.java:329)
… 22 more Caused by: org.gbif.dwc.UnsupportedArchiveException: Parts of
DwC-A are missing at org.gbif.dwc.Archive.validate(Archive.java:157) at
org.gbif.dwc.DwcFiles.fromCompressed(DwcFiles.java:75) at
org.globalbioticinteractions.dataset.DwCAUtil.archiveFor(DwCAUtil.java:24)
… 23 more
1
[] Caused by: org.eol.globi.data.StudyImporterException: failed to
read archive
[https://ecdysis.org/collections/misc/collprofiles.php?collid=178] at
org.eol.globi.data.DatasetImporterForDwCA.importStudy(DatasetImporterForDwCA.java:356)
at
org.eol.globi.util.DatasetImportUtil.importDataset(DatasetImportUtil.java:71)
at
org.eol.globi.util.DatasetImportUtil.importDataset(DatasetImportUtil.java:42)
at
org.eol.globi.util.DatasetImportUtil.importDatasets(DatasetImportUtil.java:141)
at
org.eol.globi.util.DatasetImportUtil.indexDatasetWithResolvedDependencies(DatasetImportUtil.java:97)
at
org.eol.globi.util.DatasetImportUtil.resolveAndImportDatasets(DatasetImportUtil.java:88)
at
org.eol.globi.data.DatasetImporterForRSS.importStudy(DatasetImporterForRSS.java:45)
at
org.eol.globi.util.DatasetImportUtil.importDataset(DatasetImportUtil.java:71)
at
org.globalbioticinteractions.elton.cmd.CmdReview.review(CmdReview.java:248)
at
org.globalbioticinteractions.elton.cmd.CmdReview.reviewLocal(CmdReview.java:201)
at
org.globalbioticinteractions.elton.cmd.CmdReview.doRun(CmdReview.java:159)
at
org.globalbioticinteractions.elton.cmd.CmdDefaultParams.run(CmdDefaultParams.java:223)
at
org.globalbioticinteractions.elton.cmd.CmdTabularWriterParams.run(CmdTabularWriterParams.java:12)
at picocli.CommandLine.executeUserObject(CommandLine.java:1939) at
picocli.CommandLine.access1300(CommandLine.java:145)atpicocli.CommandLineRunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)
at picocli.CommandLineRunLast.handle(CommandLine.java:2352)atpicocli.CommandLineRunLast.handle(CommandLine.java:2314)
at picocli.CommandLineAbstractParseResultHandler.execute(CommandLine.java:2179)atpicocli.CommandLineRunLast.execute(CommandLine.java:2316)
at picocli.CommandLine.execute(CommandLine.java:2078) at
org.globalbioticinteractions.elton.Elton.run(Elton.java:103) at
org.globalbioticinteractions.elton.Elton.main(Elton.java:94) Caused by:
java.io.IOException: failed to read
[file:/tmp/dwca1040859268717128705tmp.zip] at
org.globalbioticinteractions.dataset.DwCAUtil.archiveFor(DwCAUtil.java:29)
at
org.eol.globi.data.DatasetImporterForDwCA.importStudy(DatasetImporterForDwCA.java:329)
… 22 more Caused by: org.gbif.dwc.UnsupportedArchiveException: Parts of
DwC-A are missing at org.gbif.dwc.Archive.validate(Archive.java:157) at
org.gbif.dwc.DwcFiles.fromCompressed(DwcFiles.java:75) at
org.globalbioticinteractions.dataset.DwCAUtil.archiveFor(DwCAUtil.java:24)
… 23 more
1
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.
Kuhn, Tobias, and Michel Dumontier. 2014. “Trusty URIs:
Verifiable, Immutable, and Permanent Digital Artifacts for Linked
Data.” In The Semantic Web: Trends and Challenges,
edited by Valentina Presutti, Claudia d’Amato, Fabien Gandon, Mathieu
d’Aquin, Steffen Staab, and Anna Tordai, 395–410. Cham: Springer
International Publishing.
Poelen, Jorrit H. (ed.). 2024. “Nomer Corpus of Taxonomic
Resources Hash://Sha256/
B60c0d25a16ae77b24305782017b1a270b79b5d1746f832650 F2027ba536e276
Hash://Md5/17f1363a277ee0e4ecaf1b91c665e47e.” Zenodo. https://doi.org/10.5281/zenodo.12695629.
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.
