{"data":{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29900348", "kind": "science-record", "revision": 3, "content_hash": "sha256:4c2f804c05b6a477a4024288543de1ac4511ed1317399fd7425f2c24e9ad93ba", "created_at": "2026-11-01T15:40:34Z", "updated_at": "2026-11-01T18:49:35Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Transcriptome of Xenopus andrei, an octoploid frog, during embryonic development.", "doi": "10.1016/j.dib.2018.05.017", "pmid": "29900348", "authors": ["Mark E Pownall", "Ronald R Cutler", "Margaret S Saha"], "journal": "Data in brief", "year": 2018, "abstract": "Although polyploidy occurs throughout the fish and amphibian lineages, the Xenopus genus exhibits a high incidence of polyploidy, with 25 out of the 26 known species being polyploid. However, transcriptomic information is currently available for only one of these species, the tetraploid Xenopus laevis. Xenopus andrei, an octoploid species within the Xenopus genus, offers an opportunity for assessing a novel polyploid transcriptome during vertebrate development. RNA-Seq data was generated at nine different developmental stages ranging from unfertilized eggs through swimming tadpole stages and raw FASTQ files were deposited in the NCBI SRA database (accession number SRP134281). Additionally, RNA-seq data from all nine stages were pooled to create a de novo assembly of the transcriptome using Trinity and has been deposited in the NCBI GEO database (accession number GSE111639). To our knowledge, this represents the first published assembly of an octoploid vertebrate transcriptome. In total, 849 Mb were assembled, which led to the identification of 1,650,048 transcripts in the assembly with a contig N50 of 630 bases. This RNA-Seq and transcriptome data will be valuable for comparing polyploid transcriptomes across Xenopus species, as well as understanding evolutionary implications of whole-genome duplication and polyploidy in vertebrates.", "claims": [{"id": "claim-data-access", "statement": "The data presented here can be accessed at SRA: SRP134281 for raw FASTQ files of all sequencing, and GEO: GSE111639 for assembly of the transcriptome.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29900348", "locator": "sections[3] \"Data\" paragraph 2", "quote": "The data presented here can be accessed at SRA: SRP134281 for raw FASTQ files of all sequencing, and GEO: GSE111639 for assembly of the transcriptome."}], "state": "complete"}, {"id": "claim-target-result", "statement": "RNA-Seq data from nine developmental stages were assembled de novo with Trinity to produce the first published assembly of an octoploid vertebrate transcriptome, totaling 849 Mb and 1,650,048 transcripts with a contig N50 of 630 bases; raw FASTQ files are available through NCBI SRA under accession SRP134281, and the transcriptome assembly is available through NCBI GEO under accession GSE111639.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29900348", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "RNA-Seq data was generated at nine different developmental stages ranging from unfertilized eggs through swimming tadpole stages and raw FASTQ files were deposited in the NCBI SRA database (accession number SRP134281)."}, {"asset": "source:pmid:29900348", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Additionally, RNA-seq data from all nine stages were pooled to create a de novo assembly of the transcriptome using Trinity and has been deposited in the NCBI GEO database (accession number GSE111639)."}, {"asset": "source:pmid:29900348", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "To our knowledge, this represents the first published assembly of an octoploid vertebrate transcriptome."}, {"asset": "source:pmid:29900348", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "In total, 849 Mb were assembled, which led to the identification of 1,650,048 transcripts in the assembly with a contig N50 of 630 bases."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "RNA-Seq data from nine developmental stages were assembled de novo with Trinity to produce the first published assembly of an octoploid vertebrate transcriptome, totaling 849 Mb and 1,650,048 transcripts with a contig N50 of 630 bases; raw FASTQ files are available through NCBI SRA under accession SRP134281, and the transcriptome assembly is available through NCBI GEO under accession GSE111639.", "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:29900348"], "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. 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Library preparation and sequencing was performed by OMRF. Analysis was carried out in-house."], ["Data source location", "Adult X. andrei were purchased from Xenopus Express Inc. (Brooksville, FL, USA)."], ["Data accessibility", "Raw FASTQ files were deposited on NCBI SRA database with accession number SRP134281. Transcriptome fasta file was deposited on NCBI GEO database with accession number GSE111639. All data can be accessed at the following link https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE111639."]], "row_count": 9, "column_count": 2, "numeric_cells": 2, "header_rows": 0, "locator": "section[1]/table-wrap[1]#t0010"}}, {"id": "asset:table:pmid:29900348:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:aab41cdf50f2b9a21873b7405cd275d811733b410384da0f996007d13c97cfb8", "bytes": 493, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#t0005", "version": null, "note": "Statistics of X. andrei transcriptome assembly.", "structure": {"pmcid": "PMC5997840", "section_index": 3, "section_title": "Data", "row_count": 8, "column_count": 2}, "table": {"label": "Table 1", "caption": "Statistics of X. andrei transcriptome assembly.", "rows": [["Number of reads used in assembly", "341,149,792"], ["Number assembled bases", "849,005,380"], ["Number of assembled genes", "1,023,069"], ["Number of assembled transcripts", "1,650,048"], ["Assembly GC percent", "41.15"], ["Contig N50", "631"], ["Contig Ex90N50", "1215"], ["Average contig length", "514.53"]], "row_count": 8, "column_count": 2, "numeric_cells": 10, "header_rows": 0, "locator": "section[3]/table-wrap[1]#t0005"}}], "gaps": ["asset:data:geo:GSE111639 not downloaded", "asset:data:geo:GSE111639 licence not read", "asset:data:geo:SRP134281 not downloaded", "asset:data:geo:SRP134281 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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At the evidence floor the work type comes from title framing and a fixed prior, not from anything in the paper, so the published work-type split should be read as a rough triage signal rather than a measured distribution. The impact is bounded but not removed: since 2026-10-23 the engine excludes floor-confidence records from the shortlist entirely and publishes them separately as held out, so the recommendation is unaffected even though the census is.","status":"unverified","severity":"high"},{"code":"runtime_is_modelled","basis":["Runtime is summed from published per-assay hour figures. Timing awaits the first executed replication.","4,407 of 5,529 records (79.7%) model to 0.00 hours because no assay was matched, which the ranking then reads as \"cheapest\".","0 of 10 shortlisted records carry a 0.00-hour estimate."],"claim":"Estimated replication runtime","gloss":"The hour figures are estimates built from assay mentions; timing awaits the first executed replication.","detail":"The hour figures are a cost model derived from the bench steps implied by each matched assay family. The first executed replication will supply measured timing. Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. 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