Genotyping data of French wild boar populations using porcine genome-wide genotyping array.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35562745", "kind": "science-record", "revision": 2, "content_hash": "sha256:727c30bd7924ec1354e75ef8a29ebc005d223db0f3d1bd76a021e4937f078708", "created_at": "2026-11-01T18:14:27Z", "updated_at": "2026-11-01T18:58:56Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Genotyping data of French wild boar populations using porcine genome-wide genotyping array.", "doi": "10.1186/s13104-022-06052-w", "pmid": "35562745", "authors": ["Nathalie Iannuccelli", "Nicolas Mary", "Nathalie Bonnet", "Geoffrey Petit", "Carine Valle", "Alain Ducos", "Juliette Riquet"], "journal": "BMC research notes", "year": 2022, "abstract": "OBJECTIVE: The admixture of domestic pig into wild boar populations is controlled until now, by cytogenetic analysis. Even if a first-generation hybrid animal is discernable because of its 37-chromosome karyotype, the cytogenetic method is not applicable in the case of advanced intercrosses. The aim of this study is therefore to evaluate the use of SNP (Single Nucleotide Polymorphism) markers as an alternative technology to characterize recent or past hybridization between the two sub-species. The final goal would be to develop a molecular diagnostic tool.\nDATA DESCRIPTION: The Geneseek Genomic Profiler High-Density porcine beadchip (GGP70KHD, Illumina, USA), comprising 68,516 porcine SNPs, was used on a set of 362 wild boars with diverse chromosomal statuses collected from different areas and breeding environments in France. We generated approximately 62,192-64,046 genotypes per wild boar. The present dataset might be useful for the community (i) for developing molecular tools to evaluate the admixture of domestic pig into wild boar populations, and (ii) for genetic diversity studies including wild boar species or phylogeny analyses of Suidae populations. Raw data files and a processed matrix data file were deposited in the ArrayExpress at European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI) data portal under accession number E-MTAB-10591.", "claims": [{"id": "claim-data-access", "statement": "The data presented in this Data Note can be freely and openly accessed on the EMBL-EBI ArrayExpress portal under accession number E-MTAB-10591, https://identifiers.org/arrayexpress:E-MTAB-10591 [10].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35562745", "locator": "sections[13] \"Availability of data and materials\" paragraph 2", "quote": "The data presented in this Data Note can be freely and openly accessed on the EMBL-EBI ArrayExpress portal under accession number E-MTAB-10591, https://identifiers.org/arrayexpress:E-MTAB-10591 [10]."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:35562745"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:E-MTAB-10591"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:E-MTAB-10591"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35562745", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s13104-022-06052-w", "sha256": "sha256:e1158c31beb19fe899e27a81fc3222d9471bb3368f6f7faca06c0256f63cb99d", "bytes": 12738, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s13104-022-06052-w", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9102940", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:E-MTAB-10591", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=E-MTAB-10591", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "E-MTAB-10591", "version": null, "note": "The data presented in this Data Note can be freely and openly accessed on the EMBL-EBI ArrayExpress portal under accession number E-MTAB-10591, https://identifiers.org/arrayexpress:E-MTAB-10591 [10].", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data presented in this Data Note can be freely and openly accessed on the EMBL-EBI ArrayExpress portal under accession number E-MTAB-10591, https://identifiers.org/arrayexpress:E-MTAB-10591 [10].", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-11-01T18:06:51Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:E-MTAB-10591 not downloaded", "asset:data:geo:E-MTAB-10591 licence not read"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "operations"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (not named), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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