Molecular investigation of bacterial communities: Data from two frequently used surfaces in the São Paulo Institute of Tropical Medicine.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:27331120", "kind": "science-record", "revision": 6, "content_hash": "sha256:03a56a6d71b3bf124a574ce83349de98968a34287c811586da6678acc066d405", "created_at": "2026-11-01T15:40:18Z", "updated_at": "2026-11-01T21:20:34Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Molecular investigation of bacterial communities: Data from two frequently used surfaces in the São Paulo Institute of Tropical Medicine.", "doi": "10.1016/j.dib.2016.05.064", "pmid": "27331120", "authors": ["Tairacan Augusto Pereira da Fonseca", "Rodrigo Pessôa", "Sabri Saeed Sanabani"], "journal": "Data in brief", "year": 2016, "abstract": "This article contains data on the bacterial population of two frequently used surfaces in the São Paulo Institute of Tropical Medicine (ITM) using the Illumina sequencing for massive parallel investigation of the bacterial 16S ribosomal RNA gene. Surface samples were obtained from restroom surfaces and the fingerprint door clock system. Mothur package and Shannon-ace-table.pl software programs (Chunlab Inc.: Seoul, Korea) were used to compute the diversity indices of bacterial community. The sequencing data from both surfaces have been uploaded to Zenodo: http://dx.doi.org/10.5281/zenodo.47709.", "claims": [{"id": "claim-method", "statement": "The Chao1 estimation and the Shannon diversity index at a 3% distance were used calculate the richness and diversity of samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27331120", "locator": "sections[4] \"Experimental design, materials, and methods\" paragraph 4", "quote": "The Chao1 estimation and the Shannon diversity index at a 3% distance were used calculate the richness and diversity of samples."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All sequence data described here are available in the online Zenodo repository: http://dx.doi.org/10.5281/zenodo.47709.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27331120", "locator": "sections[3] \"Data\" paragraph 2", "quote": "All sequence data described here are available in the online Zenodo repository: http://dx.doi.org/10.5281/zenodo.47709."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:27331120"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:27331120", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2016.05.064", "sha256": "sha256:ce523a2bbc6d1fc9b2f1eac9a83fcb7e9eb08a1a47382ea7982f53d1efe26547", "bytes": 7717, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2016.05.064", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4908281", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:27331120:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:632ae3efffc337cc49491b78dee818535ed4d716cfef2754dec79d004e6d5a06", "bytes": 1003, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#t0010", "version": null, "note": null, "structure": {"pmcid": "PMC4908281", "section_index": 1, "section_title": "Specifications Table", "row_count": 9, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Subject area", "Biology"], ["More specific subject area", "Microbiome"], ["Type of data", "Text files: sequences"], ["How data was acquired", "Culture-independent Illumina massively parallel sequencing approach of the 16S rRNA genes using the Illumina sequencing-by-synthesis method (MiSeq platform)."], ["Data format", "Sequencing"], ["Experimental factors", "Bacterial genomic DNA was extracted and used as a template to amplify the V4 region of the 16S rRNA gene. The amplicons were molecularly barcoded, pooled, and sequenced by a paired-end protocol (Illumina)."], ["Experimental features", "Illumina massively parallel sequencing of the 16S rRNA gene libraries and subsequent analysis."], ["Data source location", "São Paulo, Brazil"], ["Data accessibility", "Data is within this article and have been uploaded to Zenodo (http://dx.doi.org/10.5281/zenodo.47709)."]], "row_count": 9, "column_count": 2, "numeric_cells": 4, "header_rows": 0, "locator": "section[1]/table-wrap[1]#t0010"}}, {"id": "asset:table:pmid:27331120:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:95c73d5b20a0d170b79b142803c30f965a7d67040684a065692c0514b4ad0104", "bytes": 708, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#t0005", "version": null, "note": "Identities of the six most abundant OTUs in the bacterial communities.", "structure": {"pmcid": "PMC4908281", "section_index": 4, "section_title": "Experimental design, materials, and methods", "row_count": 8, "column_count": 3}, "table": {"label": "Table 1", "caption": "Identities of the six most abundant OTUs in the bacterial communities.", "rows": [["Abundance order", "Taxa (% of abundance)"], ["IMT-FDLS", "IMT-restrooms"], ["1", "Propionibacterium acnes (7.9%)", "Moraxella osloensis (5.6%)"], ["2", "Streptococcus dentisani (3.5%)", "Methylobacterium phyllostachyos (5.4%)"], ["3", "Staphylococcus epidermidis (3%)", "EU440723_s (4.2%)"], ["4", "Staphylococcus capitis (2.4%)", "Sphingomonas ginsenosidimutans (3.8%)"], ["5", "Streptococcus_uc m(1.9%)", "Roseomonas mucosa (3.7%)"], ["6", "Streptococcaceae_uc_s (1.9%)", "Sphingomonadaceae_uc_s (3.4%)"]], "row_count": 8, "column_count": 3, "numeric_cells": 18, "header_rows": 2, "locator": "section[4]/table-wrap[1]#t0005"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Chao1 estimation and Shannon diversity index", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The Chao1 estimation and the Shannon diversity index at a 3% distance were used calculate the richness and diversity of samples."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Chao1 estimation and Shannon diversity index), 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. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": ["All sequence data described here are available in the online Zenodo repository: http://dx.doi.org/10.5281/zenodo.47709."], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:27331120", "asset:table:pmid:27331120:1", "asset:table:pmid:27331120:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:28:41Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 19487, "completion_tokens": 2081, "cached_tokens": 1832}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:27331120", "type": "paper", "label": "pmid:27331120"}, {"id": "source:pmid:27331120", "type": "manuscript", "label": "PMID 27331120 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:27331120", "type": "paper", "label": "pmid:27331120"}, {"id": "source:pmid:27331120", "type": "manuscript", "label": "PMID 27331120 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-27331120", "type": "extraction", "used": ["source:pmid:27331120"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:27331120", "parent_hash": "sha256:f394e827ba2ef866e8b2f062414822c0d2535e3dbc85e8446d26c0a782b605ca", "fork_of": null, "generation": 5}, "gaps": ["execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "assays": [{"role": "data_generation", "definition_id": "amplicon_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["to the amplification of the V4 region of the 16S rRNA gene using the previously published primers"], "order_basis": "paper_text_order:1427", "id": "assay:1"}]}