MicrobeNetNet Dataset Review Corpus and Associated Data Products hash://md5/5981a37a16c25204dc18d9188f185b19 hash://sha256/7448991edd5f79db02519a5b3d4691c50a60c02f45d40f087402a7a492da3a3e

This repository provides workflow for building an integrated review corpus of datasets reviewed by Global Biotic Interactions (GloBI, Poelen et al. 2014). The examples below are applied to the collection of datasets mentioned in various meetings facilitated by MicrobeNetNet (Sikes et al. 2024) and includes about 7M interactions claims extracted from over 60 datasets. These examples show that automated data review is possible at scale across heterogeneous datasets of known origin. filename description data.zip Preston archive containing datasets under review biblio.bib reference list of datasets under review (bibtex) interactions.tsv tab-separated value formatted text file containing interaction claims extracted by Elton, a GloBI commandline tool. interactions.parquet interactions claims captured in parquet file format for optimized data analysis. track-dataset-signatures.sh bash script for listing the digital signatures of datasets under review stage-datasets.sh bash script for staging resources need for data review README.md markdown document describing the workflow producing interactions.tsv and interactions.parquet files Summary of interactions.tsv/parquet record values and schema column_name column_type min max approx_unique null_percentage argumentTypeId VARCHAR https://en.wiktionary.org/wiki/support https://en.wiktionary.org/wiki/support 1 0 sourceOccurrenceId VARCHAR 00000fbd-ee11-4c34-b332-7f7c4fe65e9c https://www.ncbi.nlm.nih.gov/nuccore/LT984406 1805588 46.71 sourceCatalogNumber VARCHAR -CUP 72899.00 wsp75652 1528448 71.83 sourceCollectionCode VARCHAR 292354 VDB 236 95.22 sourceCollectionId VARCHAR 0cd2551b-8166-4c05-a0c9-5c8712ce0eb8 f9d2e3a0-7396-41d7-ab74-e9bab47de676 52 71.8 sourceInstitutionCode VARCHAR AAFC WSP 53 71.79 sourceTaxonId VARCHAR 100001 https://maarjam.ut.ee/vtx/VTX00457 111928 71.98 sourceTaxonName VARCHAR "Peziza" adnata zelleromyces 226938 0 sourceTaxonRank VARCHAR Class var. 26 38.87 sourceTaxonPathIds VARCHAR NULL NULL 0 100 sourceTaxonPath VARCHAR Abrothallus | Abrothallus parmeliarum Zymoseptoria | Zymoseptoria tritici 94908 38.05 sourceTaxonPathNames VARCHAR family phylum | class | order | family | genus 30 38.05 sourceBodyPartId VARCHAR http://purl.obolibrary.org/obo/PO_0025025 http://purl.obolibrary.org/obo/PO_0025025 1 99.2 sourceBodyPartName VARCHAR 1nd year stem – cambium/phloem/bark ± 2 cm fragments of fine Picea roots 346 74.09 sourceLifeStageId VARCHAR NULL NULL 0 100 sourceLifeStageName VARCHAR "Aecidium" I young fruit body 862 98.98 sourceSexId VARCHAR NULL NULL 0 100 sourceSexName VARCHAR +, - male 10 99.99 interactionTypeId VARCHAR http://purl.obolibrary.org/obo/RO_0002220 http://purl.obolibrary.org/obo/RO_0008506 13 0 interactionTypeName VARCHAR adjacentTo symbiontOf 15 0 targetOccurrenceId VARCHAR NULL NULL 0 100 targetCatalogNumber VARCHAR NULL NULL 0 100 targetCollectionCode VARCHAR NULL NULL 0 100 targetCollectionId VARCHAR NULL NULL 0 100 targetInstitutionCode VARCHAR NULL NULL 0 100 targetTaxonId VARCHAR NULL NULL 0 100 targetTaxonName VARCHAR " a bacterial disease. На листьях мака амурского [Leaves of poppy (Papaver anomalum Fedde.)] 253190 0 targetTaxonRank VARCHAR family subspecies 6 97.73 targetTaxonPathIds VARCHAR NULL NULL 0 100 targetTaxonPath VARCHAR Alismatales | Alismataceae | Echinodorus | Echinodorus ranunculoides unspecified family | unspecified genus | unspecified genus unspecified species 676 97.59 targetTaxonPathNames VARCHAR class | order | family | genus order | family | genus | species 9 97.59 targetBodyPartId VARCHAR http://purl.obolibrary.org/obo/PO_0025025 http://purl.obolibrary.org/obo/PO_0025025 1 99.09 targetBodyPartName VARCHAR Ectomycorrhiza wood 23 98.45 targetLifeStageId VARCHAR NULL NULL 0 100 targetLifeStageName VARCHAR NULL NULL 0 100 targetSexId VARCHAR NULL NULL 0 100 targetSexName VARCHAR NULL NULL 0 100 basisOfRecordId VARCHAR NULL NULL 0 100 basisOfRecordName VARCHAR . uredinium-bearing leaves 28 71.5 http://rs.tdwg.org/dwc/terms/eventDate VARCHAR 0000-01-01T00:00:00Z 9164-08-01T00:00:00Z 52511 41.83 decimalLatitude VARCHAR -0.006666667 90 124624 28.03 decimalLongitude VARCHAR -0.002968 99.951591 123002 28.03 localityId VARCHAR An south campus 10 100 localityName VARCHAR Москва, Главный ботанический сад АН СССР. [Moscow, Main Botanical garden, USSR Academy of Sciences.] 488188 8.75 referenceDoi VARCHAR 10.1002/(SICI)1097-4539(199909/10)28:5<335::AID-XRS361>3.0.CO;2-8 10.7717/peerj.8527 2199 73.8 referenceUrl VARCHAR https://doi.org/10.1002/(SICI)1097-4539(199909/10)28:5%3C335::AID-XRS361%3E3.0.CO;2-8 https://www.ncbi.nlm.nih.gov/nuccore/U96145 1652793 44.46 referenceCitation VARCHAR , Chen, C.Q., Zhi, Y., and Gao, J.. 2013. First Report of Fruit Rot on %Schisandra chinensis% Caused by %Penicillium glabrum% and %Penicillium adametzii% in China. Pl. Dis. 97:288 Řezáčová, V., Řezáč, M., Gryndler, M., Hršelová, H., Gryndlerová, H. and Michalová, T., 2021. Plant invasion alters community structure and decreases diversity of arbuscular mycorrhizal fungal communities. 1647520 0 namespace VARCHAR globalbioticinteractions/austraits globalbioticinteractions/usda-fungus-host 17 0 citation VARCHAR AAFC-DAOM DwC-Archive | Darwin Core Archive for Canadian National Mycological Herbarium Öpik, M., Vanatoa, A., Vanatoa, E., Moora, M., Davison, J., Kalwij, J.M., Reier, Ü., Zobel, M. 2010. The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota). New Phytologist 188: 223-241. 70 0 archiveURI VARCHAR hash://md5/1162b1716c486384eddd59d48ae49658 https://mycoportal.org/portal/content/dwca/WSP_DwC-A.zip 54 0 lastSeenAt TIMESTAMP WITH TIME ZONE 2026-02-26 21:45:27.233+01 2026-02-26 22:49:21.019+01 19 0 contentHash VARCHAR urn:uuid:0659a54f-b713-4f86-a917-5be166a14110 urn:uuid:0659a54f-b713-4f86-a917-5be166a14110 1 0 eltonVersion VARCHAR 0.16.6 0.16.6 1 0