A Review of Biotic Interactions and Taxon Names Found in globalbioticinteractions/scan hash://md5/e5ec8ac265ea3826f783d5ec2309e387
Bibliographic record
Abstract
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: ABS-ARTHARCH DwC-Archive | Darwin Core Archive for Archbold Biological Station Arthropod Collection https://scan-bugs.org:443/portal/content/dwca/ABS-ARTHARCH_DwC-A.zip 2025-04-12T10:20:27.018Z BLM-MLFO DwC-Archive | Darwin Core Archive for BLM Mother Lode Field Office: The Bees of Pine Hill Preserve https://scan-bugs.org:443/portal/content/dwca/BLM-MLFO_DwC-A.zip 2025-04-12T10:20:27.018Z BURKLE-LAMANNA DwC-Archive | Darwin Core Archive for Plant–pollinator community assembly across wildfire gradients https://scan-bugs.org:443/portal/content/dwca/BURKLE-LAMANNA_DwC-A.zip 2025-04-12T10:20:27.018Z CC-OBE-COCOA DwC-Archive | Darwin Core Archive for Colorado College Arthropod Collection https://scan-bugs.org:443/portal/content/dwca/CC-OBE-COCOA_DwC-A.zip 2025-04-12T10:20:27.018Z CLEV-CMNHENT DwC-Archive | Darwin Core Archive for Cleveland Museum of Natural History Invertebrate Zoology Collection https://scan-bugs.org:443/portal/content/dwca/CLEV-CMNHENT_DwC-A.zip 2025-04-12T10:20:27.018Z DEBU-ENT DwC-Archive | Darwin Core Archive for University of Guelph Insect Collection (DEBU) https://scan-bugs.org:443/portal/content/dwca/DEBU-ENT_DwC-A.zip 2025-04-12T10:20:27.018Z EGC-EGC_CRC DwC-Archive | Darwin Core Archive for Eric G Chapman Coleoptera Research Collection https://scan-bugs.org:443/portal/content/dwca/EGC-EGC_CRC_DwC-A.zip 2025-04-12T10:20:27.018Z GPSC DwC-Archive | Darwin Core Archive for Gregory P. Setliff Collection - Kutztown University https://scan-bugs.org:443/portal/content/dwca/GPSC_DwC-A.zip 2025-04-12T10:20:27.018Z GUAM-ESUG DwC-Archive | Darwin Core Archive for University of Guam Insect Collection https://scan-bugs.org:443/portal/content/dwca/GUAM-ESUG_DwC-A.zip 2025-04-12T10:20:27.018Z HDOA-HDOAPPC DwC-Archive | Darwin Core Archive for Hawaii Department of Agriculture, Plant Pest Control Branch https://scan-bugs.org:443/portal/content/dwca/HDOA-HDOAPPC_DwC-A.zip 2025-04-12T10:20:27.018Z KY-UKIC DwC-Archive | Darwin Core Archive for University of Kentucky Insect Collection https://scan-bugs.org:443/portal/content/dwca/KY-UKIC_DwC-A.zip 2025-04-12T10:20:27.018Z LEPSOC-LEPSOC DwC-Archive | Darwin Core Archive for The Lepidopterists' Society Season Summary https://scan-bugs.org:443/portal/content/dwca/LEPSOC-LEPSOC_DwC-A.zip 2025-04-12T10:20:27.018Z MC-MCIC DwC-Archive | Darwin Core Archive for Middlebury College Insect Collection https://scan-bugs.org:443/portal/content/dwca/MC-MCIC_DwC-A.zip 2025-04-12T10:20:27.018Z MELU-AFI DwC-Archive | Darwin Core Archive for Australian Freshwater Invertebrates https://scan-bugs.org:443/portal/content/dwca/MELU-AFI_DwC-A.zip 2025-04-12T10:20:27.018Z MISSA-MEM DwC-Archive | Darwin Core Archive for Mississippi Entomological Museum https://scan-bugs.org:443/portal/content/dwca/MISSA-MEM_DwC-A.zip 2025-04-12T10:20:27.018Z MSB-PARA DwC-Archive | Darwin Core Archive for Museum of Southwestern Biology Division of Parasitology - ParasiteTracker https://scan-bugs.org:443/portal/content/dwca/MSB-PARA_DwC-A.zip 2025-04-12T10:20:27.018Z MTU-MTUIC DwC-Archive | Darwin Core Archive for Michigan Technological University Insect Collection https://scan-bugs.org:443/portal/content/dwca/MTU-MTUIC_DwC-A.zip 2025-04-12T10:20:27.018Z MV-MVBC DwC-Archive | Darwin Core Archive for Michael Veit Bee Collection https://scan-bugs.org:443/portal/content/dwca/MV-MVBC_DwC-A.zip 2025-04-12T10:20:27.018Z NAUF-NAUF5F DwC-Archive | Darwin Core Archive for NAU Forest Entomology Collection https://scan-bugs.org:443/portal/content/dwca/NAUF-NAUF5F_DwC-A.zip 2025-04-12T10:20:27.018Z NCSUR-NCSU_ACEYDSC DwC-Archive | Darwin Core Archive for NCSU Research Dataset Collection https://scan-bugs.org:443/portal/content/dwca/NCSUR-NCSU_ACEYDSC_DwC-A.zip 2025-04-12T10:20:27.018Z NYSM-ARTH DwC-Archive | Darwin Core Archive for New York State Museum Arthropod Collection https://scan-bugs.org:443/portal/content/dwca/NYSM-ARTH_DwC-A.zip 2025-04-12T10:20:27.018Z PALA-RES DwC-Archive | Darwin Core Archive for Lasioglossum (Dialictus) new species in Yucatan https://scan-bugs.org:443/portal/content/dwca/PALA-RES_DwC-A.zip 2025-04-12T10:20:27.018Z PSU-LUL DwC-Archive | Darwin Core Archive for López-Uribe Lab Collection https://scan-bugs.org:443/portal/content/dwca/PSU-LUL_DwC-A.zip 2025-04-12T10:20:27.018Z PU-PERC DwC-Archive | Darwin Core Archive for The Purdue Entomological Research Collection https://scan-bugs.org:443/portal/content/dwca/PU-PERC_DwC-A.zip 2025-04-12T10:20:27.018Z RLMC DwC-Archive | Darwin Core Archive for RL Minckley Insect and Plant Collection https://scan-bugs.org:443/portal/content/dwca/RLMC_DwC-A.zip 2025-04-12T10:20:27.018Z RMBL-ENT DwC-Archive | Darwin Core Archive for Rocky Mountain Biological Laboratory Insect Collection https://scan-bugs.org:443/portal/content/dwca/RMBL-ENT_DwC-A.zip 2025-04-12T10:20:27.018Z RUBC-RUAC_ENT DwC-Archive | Darwin Core Archive for Rutgers University Entomological Museum https://scan-bugs.org:443/portal/content/dwca/RUBC-RUAC_ENT_DwC-A.zip 2025-04-12T10:20:27.018Z TAMU-TAMUIC DwC-Archive | Darwin Core Archive for Texas A&M University Insect Collection https://scan-bugs.org:443/portal/content/dwca/TAMU-TAMUIC_DwC-A.zip 2025-04-12T10:20:27.018Z UCM-UCMC DwC-Archive | Darwin Core Archive for University of Colorado Museum of Natural History Entomology Collection https://scan-bugs.org:443/portal/content/dwca/UCM-UCMC_DwC-A.zip 2025-04-12T10:20:27.018Z UD-UDCC DwC-Archive | Darwin Core Archive for University of Delaware Insect Research Collection https://scan-bugs.org:443/portal/content/dwca/UD-UDCC_DwC-A.zip 2025-04-12T10:20:27.018Z UFIFAS-UFFE DwC-Archive | Darwin Core Archive for University of Florida Forestry Entomology Collection https://scan-bugs.org:443/portal/content/dwca/UFIFAS-UFFE_DwC-A.zip 2025-04-12T10:20:27.018Z UI-WFBM DwC-Archive | Darwin Core Archive for William F. Barr Entomological Museum https://scan-bugs.org:443/portal/content/dwca/UI-WFBM_DwC-A.zip 2025-04-12T10:20:27.018Z UKY-HIC-HIC DwC-Archive | Darwin Core Archive for Hymenoptera Institute Collection https://scan-bugs.org:443/portal/content/dwca/UKY-HIC-HIC_DwC-A.zip 2025-04-12T10:20:27.018Z UMD-UMDI DwC-Archive | Darwin Core Archive for University of Minnesota Duluth Insect Collection https://scan-bugs.org:443/portal/content/dwca/UMD-UMDI_DwC-A.zip 2025-04-12T10:20:27.018Z UNI-UNIAW DwC-Archive | Darwin Core Archive for University of Northern Iowa - Wen Research Collection https://scan-bugs.org:443/portal/content/dwca/UNI-UNIAW_DwC-A.zip 2025-04-12T10:20:27.018Z UNL-NSM DwC-Archive | Darwin Core Archive for Harold W. Manter Laboratory of Parasitology Collection (HWML) Parasite Collection https://scan-bugs.org:443/portal/content/dwca/UNL-NSM_DwC-A.zip 2025-04-12T10:20:27.018Z UNM-MSBA DwC-Archive | Darwin Core Archive for Museum of Southwestern Biology, Division of Arthropods https://scan-bugs.org:443/portal/content/dwca/UNM-MSBA_DwC-A.zip 2025-04-12T10:20:27.018Z UNSM-UNSMe DwC-Archive | Darwin Core Archive for University of Nebraska State Museum https://scan-bugs.org:443/portal/content/dwca/UNSM-UNSMe_DwC-A.zip 2025-04-12T10:20:27.018Z UT-UTBFL DwC-Archive | Darwin Core Archive for Pardee et al. 2023: Plant-Pollinator Networks across an Urban Corridor https://scan-bugs.org:443/portal/content/dwca/UT-UTBFL_DwC-A.zip 2025-04-12T10:20:27.018Z UWM-WIRC DwC-Archive | Darwin Core Archive for Wisconsin Insect Research Collection https://scan-bugs.org:443/portal/content/dwca/UWM-WIRC_DwC-A.zip 2025-04-12T10:20:27.018Z WICH-WICHI DwC-Archive | Darwin Core Archive for Wichita State University Collection https://scan-bugs.org:443/portal/content/dwca/WICH-WICHI_DwC-A.zip 2025-04-12T10:20:27.018Z WSU-WSUC DwC-Archive | Darwin Core Archive for Washington State University Collection https://scan-bugs.org:443/portal/content/dwca/WSU-WSUC_DwC-A.zip 2025-04-12T10:20:27.018Z WVW-ENT DwC-Archive | Darwin Core Archive for West Virginia Wesleyan College Katharine B. Gregg Orchid Pollinator Collection https://scan-bugs.org:443/portal/content/dwca/WVW-ENT_DwC-A.zip 2025-04-12T10:20:27.018Z hash://md5/e5ec8ac265ea3826f783d5ec2309e387 For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/scan 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. Tools used in this review process tool name version preston 0.10.1 elton 0.15.9 nomer 0.5.13 globinizer 0.4.0 mlr 6.0.0 jq 1.6 yq 4.25.3 pandoc 3.1.6.1 The review process can be described in the form of the script below 1. # get versioned copy of the dataset (size approx. 351MiB) under review elton pull globalbioticinteractions/scan # generate review notes elton review globalbioticinteractions/scan\ > review.tsv # export indexed interaction records elton interactions globalbioticinteractions/scan\ > interactions.tsv # export names and align them with the Catalogue of Life using Nomer elton names globalbioticinteractions/scan\ | nomer append col\ > name-alignment.tsv or visually, in a process diagram. Review Process Overview You can
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.005 | 0.024 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.002 |
| Bibliometrics | 0.024 | 0.038 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.003 | 0.004 |
| Open science | 0.002 | 0.003 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.042 | 0.021 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".