A Review of Biotic Interactions and Taxon Names Found in globalbioticinteractions/mycoportal hash://md5/23d7d00bc7f8662173d1efc3f4fb8352
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: AAFC-DAOM DwC-Archive | Darwin Core Archive for Canadian National Mycological Herbarium https://www.mycoportal.org/portal/content/dwca/AAFC-DAOM_DwC-A.zip 2025-04-05T02:30:54.066Z ARIZ DwC-Archive | Darwin Core Archive for University of Arizona, Gilbertson Mycological Herbarium, specimen-based https://mycoportal.org/portal/content/dwca/ARIZ_DwC-A.zip 2025-04-05T02:30:54.066Z BISH DwC-Archive | Darwin Core Archive for Bishop Museum, Herbarium Pacificum https://mycoportal.org/portal/content/dwca/BISH_DwC-A.zip 2025-04-05T02:30:54.066Z BPI DwC-Archive | Darwin Core Archive for USDA United States National Fungus Collections https://www.mycoportal.org/portal/content/dwca/BPI_DwC-A.zip 2025-04-05T02:30:54.066Z BRIT DwC-Archive | Darwin Core Archive for Botanical Research Institute of Texas https://mycoportal.org/portal/content/dwca/BRIT_DwC-A.zip 2025-04-05T02:30:54.066Z BRU DwC-Archive | Darwin Core Archive for Brown University Herbarium https://mycoportal.org/portal/content/dwca/BRU_DwC-A.zip 2025-04-05T02:30:54.066Z CHRB DwC-Archive | Darwin Core Archive for Rutgers University, Chrysler Herbarium - Mycology Collection https://mycoportal.org/portal/content/dwca/CHRB_DwC-A.zip 2025-04-05T02:30:54.066Z CINC DwC-Archive | Darwin Core Archive for University of Cincinnati, Margaret H. Fulford Herbarium - Fungi https://www.mycoportal.org/portal/content/dwca/CINC_DwC-A.zip 2025-04-05T02:30:54.066Z CLEMS DwC-Archive | Darwin Core Archive for Clemson University Herbarium https://www.mycoportal.org/portal/content/dwca/CLEMS_DwC-A.zip 2025-04-05T02:30:54.066Z CSU DwC-Archive | Darwin Core Archive for University of Central Oklahoma Herbarium - Fungi https://www.mycoportal.org/portal/content/dwca/CSU_DwC-A.zip 2025-04-05T02:30:54.066Z CUP DwC-Archive | Darwin Core Archive for Cornell University Plant Pathology Herbarium https://www.mycoportal.org/portal/content/dwca/CUP_DwC-A.zip 2025-04-05T02:30:54.066Z DBG-DBG DwC-Archive | Darwin Core Archive for Denver Botanic Gardens, Sam Mitchel Herbarium of Fungi https://www.mycoportal.org/portal/content/dwca/DBG-DBG_DwC-A.zip 2025-04-05T02:30:54.066Z DEWV DwC-Archive | Darwin Core Archive for Davis & Elkins College Herbarium - Fungi https://www.mycoportal.org/portal/content/dwca/DEWV_DwC-A.zip 2025-04-05T02:30:54.066Z DUKE DwC-Archive | Darwin Core Archive for Duke University Herbarium Fungal Collection https://www.mycoportal.org/portal/content/dwca/DUKE_DwC-A.zip 2025-04-05T02:30:54.066Z FLAS DwC-Archive | Darwin Core Archive for University of Florida Herbarium - Fungi https://www.mycoportal.org/portal/content/dwca/FLAS_DwC-A.zip 2025-04-05T02:30:54.066Z FLD DwC-Archive | Darwin Core Archive for Fort Lewis College Herbarium https://mycoportal.org/portal/content/dwca/FLD_DwC-A.zip 2025-04-05T02:30:54.066Z GAM DwC-Archive | Darwin Core Archive for University of Georgia, Julian H. Miller Mycological Herbarium https://www.mycoportal.org/portal/content/dwca/GAM_DwC-A.zip 2025-04-05T02:30:54.066Z HCOA DwC-Archive | Darwin Core Archive for College of the Atlantic, Acadia National Park Herbarium https://mycoportal.org/portal/content/dwca/HCOA_DwC-A.zip 2025-04-05T02:30:54.066Z ILL DwC-Archive | Darwin Core Archive for University of Illinois Herbarium https://mycoportal.org/portal/content/dwca/ILL_DwC-A.zip 2025-04-05T02:30:54.066Z ISC DwC-Archive | Darwin Core Archive for Iowa State University, Ada Hayden Herbarium https://mycoportal.org/portal/content/dwca/ISC_DwC-A.zip 2025-04-05T02:30:54.066Z LSUM-Fungi DwC-Archive | Darwin Core Archive for Louisiana State University, Bernard Lowy Mycological Herbarium https://www.mycoportal.org/portal/content/dwca/LSUM-Fungi_DwC-A.zip 2025-04-05T02:30:54.066Z MICH DwC-Archive | Darwin Core Archive for University of Michigan Herbarium https://www.mycoportal.org/portal/content/dwca/MICH_DwC-A.zip 2025-04-05T02:30:54.066Z MONTU DwC-Archive | Darwin Core Archive for University of Montana Herbarium https://mycoportal.org/portal/content/dwca/MONTU_DwC-A.zip 2025-04-05T02:30:54.066Z MSC DwC-Archive | Darwin Core Archive for Michigan State University Herbarium https://www.mycoportal.org/portal/content/dwca/MSC_DwC-A.zip 2025-04-05T02:30:54.066Z MU DwC-Archive | Darwin Core Archive for Miami University, Willard Sherman Turrell Herbarium https://mycoportal.org/portal/content/dwca/MU_DwC-A.zip 2025-04-05T02:30:54.066Z NCU-Fungi DwC-Archive | Darwin Core Archive for University of North Carolina at Chapel Hill Herbarium: Fungi https://www.mycoportal.org/portal/content/dwca/NCU-Fungi_DwC-A.zip 2025-04-05T02:30:54.066Z NEB DwC-Archive | Darwin Core Archive for University of Nebraska State Museum, C.E. Bessey Herbarium - Fungi https://www.mycoportal.org/portal/content/dwca/NEB_DwC-A.zip 2025-04-05T02:30:54.066Z PH DwC-Archive | Darwin Core Archive for Academy of Natural Sciences of Drexel University https://www.mycoportal.org/portal/content/dwca/PH_DwC-A.zip 2025-04-05T02:30:54.066Z RMS DwC-Archive | Darwin Core Archive for University of Wyoming, Wilhelm G. Solheim Mycological Herbarium https://mycoportal.org/portal/content/dwca/RMS_DwC-A.zip 2025-04-05T02:30:54.066Z SFSU DwC-Archive | Darwin Core Archive for San Francisco State University, Harry D. Thiers Herbarium https://mycoportal.org/portal/content/dwca/SFSU_DwC-A.zip 2025-04-05T02:30:54.066Z SYRF DwC-Archive | Darwin Core Archive for State University of New York, SUNY College of Environmental Science and Forestry Herbarium https://www.mycoportal.org/portal/content/dwca/SYRF_DwC-A.zip 2025-04-05T02:30:54.066Z TENN-F DwC-Archive | Darwin Core Archive for University of Tennessee Fungal Herbarium https://www.mycoportal.org/portal/content/dwca/TENN-F_DwC-A.zip 2025-04-05T02:30:54.066Z UC DwC-Archive | Darwin Core Archive for University of California Berkeley, University Herbarium https://mycoportal.org/portal/content/dwca/UC_DwC-A.zip 2025-04-05T02:30:54.066Z UCHT-F DwC-Archive | Darwin Core Archive for University of Tennessee, Chattanooga https://mycoportal.org/portal/content/dwca/UCHT-F_DwC-A.zip 2025-04-05T02:30:54.066Z UCSC DwC-Archive | Darwin Core Archive for University of California Santa Cruz Fungal Herbarium https://www.mycoportal.org/portal/content/dwca/UCSC_DwC-A.zip 2025-04-05T02:30:54.066Z UNCA-UNCA DwC-Archive | Darwin Core Archive for University of North Carolina Asheville https://www.mycoportal.org/portal/content/dwca/UNCA-UNCA_DwC-A.zip 2025-04-05T02:30:54.066Z USAM DwC-Archive | Darwin Core Archive for University of South Alabama Herbarium https://mycoportal.org/portal/content/dwca/USAM_DwC-A.zip 2025-04-05T02:30:54.066Z USCH-Fungi DwC-Archive | Darwin Core Archive for University of South Carolina, A. C. Moore Herbarium Fungal Collection https://www.mycoportal.org/portal/content/dwca/USCH-Fungi_DwC-A.zip 2025-04-05T02:30:54.066Z USF DwC-Archive | Darwin Core Archive for University of South Florida Herbarium - Fungi excluding lichens https://www.mycoportal.org/portal/content/dwca/USF_DwC-A.zip 2025-04-05T02:30:54.066Z USU-UTC DwC-Archive | Darwin Core Archive for Intermountain Herbarium (fungi, not lichens), Utah State University https://mycoportal.org/portal/content/dwca/USU-UTC_DwC-A.zip 2025-04-05T02:30:54.066Z UT-M DwC-Archive | Darwin Core Archive for Natural History Museum of Utah Fungarium https://www.mycoportal.org/portal/content/dwca/UT-M_DwC-A.zip 2025-04-05T02:30:54.066Z VPI DwC-Archive | Darwin Core Archive for Virginia Tech University, Massey Herbarium - Fungi https://www.mycoportal.org/portal/content/dwca/VPI_DwC-A.zip 2025-04-05T02:30:54.066Z VT DwC-Archive | Darwin Core Archive for University of Vermont, Pringle Herbarium, Macrofungi https://mycoportal.org/portal/content/dwca/VT_DwC-A.zip 2025-04-05T02:30:54.066Z WIS DwC-Archive | Darwin Core Archive for Wisconsin State Herbarium, Fungi https://www.mycoportal.org/portal/content/dwca/WIS_DwC-A.zip 2025-04-05T02:30:54.066Z WSP DwC-Archive | Darwin Core Archive for Charles Gardner Shaw Mycological Herbarium, Washington State University https://www.mycoportal.org/portal/content/dwca/WSP_DwC-A.zip 2025-04-05T02:30:54.066Z hash://md5/23d7d00bc7f8662173d1efc3f4fb8352 For additional metadata related to this dataset, please visit https://github.com/globalbioticinteractions/mycoportal 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. 403MiB) under review elton pull globalbioticinteractions/mycoportal # generate review notes elton review globalbioticinteractions/mycoportal\ > review.tsv # export indexed interaction records elton interactions globalbioticinteractions/mycoportal\ > interactions.tsv # export names and align them with the Catalogue of Life using Nomer elton names globalbioticinteractions/mycoportal\ | nomer append col\ > name-alignment.tsv or visually, in a process diagram.
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 | 0.007 | 0.028 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.002 |
| Bibliometrics | 0.029 | 0.046 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.004 | 0.005 |
| Open science | 0.002 | 0.003 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.032 | 0.017 |
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".