← All .science files
pmid:21447175
A 44K microarray dataset of the changing transcriptome in developing Atlantic salmon (Salmo salar L.).
Stuart G Jantzen · Dan S Sanderson · Kris R von Schalburg · Motoshige Yasuike · Francesco Marass · Ben F Koop
BMC research notes · 2011 doi:10.1186/1756-0500-4-88
Paper
complete
Experiment
complete
Data
partial
Analysis
complete
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
paper object · 10 fields
authors array · 6 items
claims array · 3 items
[0] object · 6 fields
[1] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
[2] object · 6 fields
evidence array · 4 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 0 items
data object · 3 fields
assets array · 5 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 51 items
[2] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 34 items
[0] array · 4 items
[1] array · 4 items
[2] array · 1 item
[3] array · 4 items
[4] array · 1 item
[5] array · 4 items
[6] array · 1 item
[7] array · 4 items
[8] array · 1 item
[9] array · 4 items
[10] array · 1 item
[11] array · 4 items
[12] array · 1 item
[13] array · 4 items
[14] array · 1 item
[15] array · 4 items
[16] array · 1 item
[17] array · 4 items
[18] array · 1 item
[19] array · 4 items
[20] array · 1 item
[21] array · 4 items
[22] array · 1 item
[23] array · 4 items
[24] array · 1 item
[25] array · 4 items
[26] array · 1 item
[27] array · 4 items
[28] array · 1 item
[29] array · 4 items
[30] array · 1 item
[31] array · 4 items
[32] array · 1 item
[33] array · 4 items
[3] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 32 items
[0] array · 2 items
[1] array · 2 items
[2] array · 1 item
[3] array · 2 items
[4] array · 1 item
[5] array · 2 items
[6] array · 1 item
[7] array · 2 items
[8] array · 1 item
[9] array · 2 items
[10] array · 1 item
[11] array · 2 items
[12] array · 1 item
[13] array · 2 items
[14] array · 1 item
[15] array · 2 items
[16] array · 1 item
[17] array · 2 items
[18] array · 1 item
[19] array · 2 items
[20] array · 1 item
[21] array · 2 items
[22] array · 1 item
[23] array · 2 items
[24] array · 1 item
[25] array · 2 items
[26] array · 1 item
[27] array · 2 items
[28] array · 1 item
[29] array · 2 items
[30] array · 1 item
[31] array · 2 items
[4] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 34 items
[0] array · 4 items
[1] array · 4 items
[2] array · 1 item
[3] array · 4 items
[4] array · 1 item
[5] array · 4 items
[6] array · 1 item
[7] array · 4 items
[8] array · 1 item
[9] array · 4 items
[10] array · 1 item
[11] array · 4 items
[12] array · 1 item
[13] array · 4 items
[14] array · 1 item
[15] array · 4 items
[16] array · 1 item
[17] array · 4 items
[18] array · 1 item
[19] array · 4 items
[20] array · 1 item
[21] array · 4 items
[22] array · 1 item
[23] array · 4 items
[24] array · 1 item
[25] array · 4 items
[26] array · 1 item
[27] array · 4 items
[28] array · 1 item
[29] array · 4 items
[30] array · 1 item
[31] array · 4 items
[32] array · 1 item
[33] array · 4 items
gaps array · 2 items
analysis object · 4 fields
methods array · 2 items
[0] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[1] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
targets array · 0 items
gaps array · 0 items
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 1 item
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 1 item
resolved_accessions array · 1 item
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 1 item
assets array · 5 items
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 0 items
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 6 items
assays array · 3 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 3 items
[1] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
[2] object · 11 fields
required_operations array · 1 item
source_hashes object · 1 field
evidence array · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:21447175", "kind": "science-record", "revision": 6, "content_hash": "sha256:36f1bbf75f932ea33739b0d47fae7f1db6c0c9469356454991929d11724f6ac0", "created_at": "2026-11-01T15:40:01Z", "updated_at": "2026-11-01T21:19:37Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A 44K microarray dataset of the changing transcriptome in developing Atlantic salmon (Salmo salar L.).", "doi": "10.1186/1756-0500-4-88", "pmid": "21447175", "authors": ["Stuart G Jantzen", "Dan S Sanderson", "Kris R von Schalburg", "Motoshige Yasuike", "Francesco Marass", "Ben F Koop"], "journal": "BMC research notes", "year": 2011, "abstract": "BACKGROUND: Atlantic salmon (Salmo salar L.) is an environmentally and economically important organism and its gene content is reasonably well characterized. From a transcriptional standpoint, it is important to characterize the changes in gene expression over the course of unperturbed early development, from fertilization through to the parr stage.\nFINDINGS: S. salar samples were taken at 17 time points from 2 to 89 days post fertilization. Total RNA was extracted and cRNA was synthesized and hybridized to a newly developed 44K oligo salmonid microarray platform. Quantified results were subjected to preliminary data analysis and submitted to NCBI's Gene Expression Omnibus (GEO). Data can be found under the GEO accession number GSE25938. http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25938\nCONCLUSIONS: Throughout the entire period of development, several thousand genes were found to be differentially regulated. This work represents the trancriptional characterization of a very large geneset that will be extremely valuable in further examination of the transcriptional changes in Atlantic salmon during the first few months of development. The expression profiles can help to annotate salmon genes in addition to being used as references against any number of experimental variables to which developing salmonids might be subjected.", "claims": [{"id": "claim-method", "statement": "Using a t-test assuming unequal variance (Welch) (p ≤ 0.01, fold change ≥ 2.0) without multiple test correction (MTC), each time point was compared to the next time point in the series.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:21447175", "locator": "sections[7] \"Data processing\" paragraph 6", "quote": "Using a t-test assuming unequal variance (Welch) (p ≤ 0.01, fold change ≥ 2.0) without multiple test correction (MTC), each time point was compared to the next time point in the series."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Beyond this preliminary analysis, there is a wealth of information to be gained from these data and we have submitted all normalized and raw data to NCBI's Gene Expression Omnibus (GEO) [19] for others to examine. The data are accessible through GEO Series accession number GSE25938 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25938.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:21447175", "locator": "sections[8] \"Use of dataset\" paragraph 2", "quote": "Beyond this preliminary analysis, there is a wealth of information to be gained from these data and we have submitted all normalized and raw data to NCBI's Gene Expression Omnibus (GEO) [19] for others to examine. The data are accessible through GEO Series accession number GSE25938 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25938."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Throughout development from 2 to 89 dpf, several thousand genes were differentially regulated using a Welch unequal-variance t-test at p ≤ 0.01 and fold change ≥ 2.0, and the normalized and raw source data are available through GEO accession GSE25938.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:21447175", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Throughout the entire period of development, several thousand genes were found to be differentially regulated."}, {"asset": "source:pmid:21447175", "locator": "sections[7] \"Data processing\" paragraph 6", "quote": "Using a t-test assuming unequal variance (Welch) (p ≤ 0.01, fold change ≥ 2.0) without multiple test correction (MTC), each time point was compared to the next time point in the series."}, {"asset": "source:pmid:21447175", "locator": "sections[8] \"Use of dataset\" paragraph 2", "quote": "we have submitted all normalized and raw data to NCBI's Gene Expression Omnibus (GEO) [19] for others to examine"}, {"asset": "source:pmid:21447175", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Data can be found under the GEO accession number GSE25938. http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25938"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Throughout development from 2 to 89 dpf, several thousand genes were differentially regulated using a Welch unequal-variance t-test at p ≤ 0.01 and fold change ≥ 2.0, and the normalized and raw source data are available through GEO accession GSE25938.", "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:21447175"], "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:GSE25938"], "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:GSE25938"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:21447175", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/1756-0500-4-88", "sha256": "sha256:35b0f6816b097cea3594db9bcddd2410322001e0142b432184c65df8e6902c43", "bytes": 31236, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/1756-0500-4-88", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC3073910", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE25938", "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=GSE25938", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE25938", "version": null, "note": "Beyond this preliminary analysis, there is a wealth of information to be gained from these data and we have submitted all normalized and raw data to NCBI's Gene Expression Omnibus (GEO) [19] for others to examine. The data are accessible through GEO Series accession number GSE25938 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25938.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Beyond this preliminary analysis, there is a wealth of information to be gained from these data and we have submitted all normalized and raw data to NCBI's Gene Expression Omnibus (GEO) [19] for others to examine. The data are accessible through GEO Series accession number GSE25938 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25938.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM637444", "GSM637445", "GSM637446", "GSM637447", "GSM637448", "GSM637449", "GSM637450", "GSM637451", "GSM637452", "GSM637453", "GSM637454", "GSM637455", "GSM637456", "GSM637457", "GSM637458", "GSM637459", "GSM637460", "GSM637461", "GSM637462", "GSM637463", "GSM637464", "GSM637465", "GSM637466", "GSM637467", "GSM637468", "GSM637469", "GSM637470", "GSM637471", "GSM637472", "GSM637473", "GSM637474", "GSM637475", "GSM637476", "GSM637477", "GSM637478", "GSM637479", "GSM637480", "GSM637481", "GSM637482", "GSM637483", "GSM637484", "GSM637485", "GSM637486", "GSM637487", "GSM637488", "GSM637489", "GSM637490", "GSM637491", "GSM637492", "GSM637493", "GSM637494"], "sample_count": 51, "group_sizes": null, "group_sizes_basis": null, "platform": "11299", "taxon": "Salmo salar", "title": "Developmental stages after fertilization in Salmo salar", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:21447175:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ea322f34b8e22a399a0336a9ff22f00df1dd3d5207f47133f400b8a99c58d555", "bytes": 1074, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[1]#T1", "version": null, "note": "S. salar developmental stages sampled", "structure": {"pmcid": "PMC3073910", "section_index": 7, "section_title": "Data processing", "row_count": 34, "column_count": 4}, "table": {"label": "Table 1", "caption": "S. salar developmental stages sampled", "rows": [["Days post fertilization (dpf)", "Degree days (12°C * dpf)", "Relative age in τs", "Subperiod"], ["2", "24", "17", "Blastulation"], [""], ["5", "60", "42", "Gastrulation"], [""], ["10", "120", "83", "Somitogenesis"], [""], ["15", "180", "125", "Vascularization of yolksac"], [""], ["20", "240", "167", "Vascularization of yolksac"], [""], ["25", "300", "208", "Formation of caudal rays"], [""], ["30", "360", "250", "Formation of caudal rays"], [""], ["35", "420", "292", "Formation of caudal rays"], [""], ["41", "492", "342", "Free embryo/Alevin"], [""], ["47", "564", "392", "Free embryo/Alevin"], [""], ["53", "636", "442", "Free embryo/Alevin"], [""], ["59", "708", "492", "Alevins have left gravel/Beginning of parr markings"], [""], ["65", "780", "542", "Fry/Appearance of caudal parr marks"], [""], ["71", "852", "592", "Fry/Yolk-sac completely absorbed"], [""], ["77", "924", "642", "Parr"], [""], ["83", "996", "692", "Parr"], [""], ["89", "1068", "742", "Parr"]], "row_count": 34, "column_count": 4, "numeric_cells": 52, "header_rows": 1, "locator": "section[7]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:21447175:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:df84dc575ce76a7af61ddd52970ba3895deac8eec07a617ebd6ac3694180aebc", "bytes": 658, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[2]#T2", "version": null, "note": "Numbers of differentially regulated entities across timeline", "structure": {"pmcid": "PMC3073910", "section_index": 7, "section_title": "Data processing", "row_count": 32, "column_count": 2}, "table": {"label": "Table 2", "caption": "Numbers of differentially regulated entities across timeline", "rows": [["Comparison (dpf)", "Number of differentially regulated entities"], ["2 vs. 5", "3329"], [""], ["5 vs. 10", "2325"], [""], ["10 vs. 15", "804"], [""], ["15 vs. 20", "102"], [""], ["20 vs. 25", "59"], [""], ["25 vs. 30", "62"], [""], ["30 vs. 35", "127"], [""], ["35 vs. 41", "53"], [""], ["41 vs. 47", "47"], [""], ["47 vs. 53", "51"], [""], ["53 vs. 59", "38"], [""], ["59 vs. 65", "54"], [""], ["65 vs. 71", "22"], [""], ["71 vs. 77", "12"], [""], ["77 vs. 83", "68"], [""], ["83 vs. 89", "84"]], "row_count": 32, "column_count": 2, "numeric_cells": 32, "header_rows": 1, "locator": "section[7]/table-wrap[2]#T2"}}, {"id": "asset:table:pmid:21447175:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e0082228e5d64cda3b15f74cab0327316751d3fc8228fa147ca587b5b79e57b1", "bytes": 859, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[3]#T3", "version": null, "note": "Variation among replicate samples across timeline", "structure": {"pmcid": "PMC3073910", "section_index": 7, "section_title": "Data processing", "row_count": 34, "column_count": 4}, "table": {"label": "Table 3", "caption": "Variation among replicate samples across timeline", "rows": [["Condition (dpf)", "Mean", "Median", "Standard deviation"], ["2", "0.574", "0.453", "0.484"], [""], ["5", "0.412", "0.334", "0.359"], [""], ["10", "0.342", "0.279", "0.282"], [""], ["15", "0.511", "0.459", "0.327"], [""], ["20", "0.516", "0.449", "0.344"], [""], ["25", "0.408", "0.354", "0.285"], [""], ["30", "0.495", "0.438", "0.320"], [""], ["35", "0.439", "0.369", "0.339"], [""], ["41", "0.473", "0.421", "0.310"], [""], ["47", "0.440", "0.370", "0.326"], [""], ["53", "0.422", "0.372", "0.290"], [""], ["59", "0.351", "0.288", "0.272"], [""], ["65", "0.427", "0.358", "0.324"], [""], ["71", "0.416", "0.354", "0.311"], [""], ["77", "0.490", "0.427", "0.331"], [""], ["83", "0.437", "0.382", "0.303"], [""], ["89", "0.406", "0.348", "0.291"]], "row_count": 34, "column_count": 4, "numeric_cells": 68, "header_rows": 1, "locator": "section[7]/table-wrap[3]#T3"}}], "gaps": ["asset:data:geo:GSE25938 not downloaded", "asset:data:geo:GSE25938 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "welch_t_test", "label": "Group comparison", "dsl_operations": ["welch_t"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Using a t-test assuming unequal variance (Welch) (p ≤ 0.01, fold change ≥ 2.0) without multiple test correction (MTC), each time point was compared to the next time point in the series."}}, {"id": "method-2", "family": "principal_component_analysis", "specific": "pca", "label": "Principal component analysis", "dsl_operations": ["pca_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["wide_numeric_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "PCA"}}], "targets": [], "gaps": []}, "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["welch_t"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: welch_t_test."}, "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": "R1", "reachable": true, "accessions": ["GSE25938"], "resolved_accessions": ["GSE25938"], "statements": ["Beyond this preliminary analysis, there is a wealth of information to be gained from these data and we have submitted all normalized and raw data to NCBI's Gene Expression Omnibus (GEO) [19] for others to examine. The data are accessible through GEO Series accession number GSE25938 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25938."], "basis": "The paper names GSE25938 in NCBI Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["welch_t"], "assets": ["source:pmid:21447175", "data:geo:GSE25938", "asset:table:pmid:21447175:1", "asset:table:pmid:21447175:2", "asset:table:pmid:21447175:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE25938"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:21:00Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 61938, "completion_tokens": 3788, "cached_tokens": 46980}}, "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:21447175", "type": "paper", "label": "pmid:21447175"}, {"id": "source:pmid:21447175", "type": "manuscript", "label": "PMID 21447175 full text"}, {"id": "data:geo:GSE25938", "type": "dataset", "label": "GEO GSE25938"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:21447175", "type": "paper", "label": "pmid:21447175"}, {"id": "source:pmid:21447175", "type": "manuscript", "label": "PMID 21447175 full text"}, {"id": "data:geo:GSE25938", "type": "dataset", "label": "GEO GSE25938"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-21447175", "type": "extraction", "used": ["source:pmid:21447175"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE25938", "type": "accession_resolution", "used": ["data:geo:GSE25938"], "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:21447175", "parent_hash": "sha256:c0f50f6a3b2972d7464ae0ede9d01c99fda218b208e2db3f6b02dba188ef7198", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:GSE25938 licence not read", "asset:data:geo:GSE25938 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["A 44K microarray dataset of the changing transcriptome in dev", "ized to a newly developed 44K oligo salmonid microarray platform. Quantified results were subjected", "f ontogenetically relevant probes on the 44K microarray, over 900 entities are currently annotated w"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["0 dpf, \"organ development\" and \"induction of apoptosis\" between 10 and 15 dpf, and \"erythrocyte dev"], "order_basis": "paper_text_order:7596", "id": "assay:2"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["welch_t"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Using a t-test assuming unequal variance (Welch) (p ≤ 0.01, fold change ≥ 2.0) without multiple test correction (MTC), each time point was compared to the next time point in the series."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}