{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32848694", "kind": "science-record", "revision": 8, "content_hash": "sha256:b796a4c50dbcef96e8aaca07a3500102c9f6731331e64327979fa923e83fb300", "created_at": "2026-11-01T15:41:08Z", "updated_at": "2026-11-01T22:45:14Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Potential Interacting Proteins With the Extracellular Loops of the Neuronal Glycoprotein M6a by TMT/MS.", "doi": "10.3389/fnsyn.2020.00028", "pmid": "32848694", "authors": ["Gabriela I Aparicio", "Karina Formoso", "Antonella León", "Alberto C Frasch", "Camila Scorticati"], "journal": "Frontiers in synaptic neuroscience", "year": 2020, "abstract": "Nowadays, great efforts are made to gain insight into the molecular mechanisms that underlie structural neuronal plasticity. Moreover, the identification of signaling pathways involved in the development of psychiatric disorders aids the screening of possible therapeutic targets. Genetic variations or alterations in GPM6A expression are linked to neurological disorders such as schizophrenia, depression, and Alzheimer's disease. GPM6A encodes the neuronal surface glycoprotein M6a that promotes filopodia/spine, dendrite, and synapse formation by unknown mechanisms. A substantial body of evidence suggests that the extracellular loops of M6a command its function. However, the proteins that associate with them and that modulate neuronal plasticity have not been determined yet. To address this question, we generated a chimera protein that only contains the extracellular loops of M6a and performed a co-immunoprecipitation with rat hippocampus samples followed by TMT/MS. Here, we report 72 proteins, which are good candidates to interact with M6a's extracellular loops and modify its function. Gene ontology (GO) analysis showed that 63% of the potential M6a's interactor proteins belong to the category \"synapse,\" at both sides of the synaptic cleft, \"neuron projections\" (51%) and \"presynapse\" (49%). In this sense, we showed that endogenous M6a interacts with piccolo, synaptic vesicle protein 2B, and synapsin 1 in mature cultured hippocampal neurons. Interestingly, about 28% of the proteins left were related to the \"myelin sheath\" annotation, suggesting that M6a could interact with proteins at the surface of oligodendrocytes. Indeed, we demonstrated the (cis and trans) interaction between M6a and proteolipid protein (PLP) in neuroblastoma N2a cells. Finally, the 72 proteins were subjected to disease-associated genes and variants screening by DisGeNET. Apart from the diseases that have already been associated with M6a, most of the proteins are also involved in \"autistic disorder,\" \"epilepsy,\" and \"seizures\" increasing the spectrum of disorders in which M6a could play a role. Data are available via ProteomeXchange with identifier PXD017347.", "claims": [{"id": "claim-method", "statement": "For differential protein expression analysis between conditions, a t-test was used and applied with Linear Models for Microarray Data (Limma) package (Ritchie et al., 2015).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32848694", "locator": "sections[22] \"Statistical Analysis\" paragraph 2", "quote": "For differential protein expression analysis between conditions, a t-test was used and applied with Linear Models for Microarray Data (Limma) package (Ritchie et al., 2015)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (www.proteomexchange.org) via the PRIDE (Vizcaíno et al., 2016) partner repository with the dataset identifier PXD017347.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32848694", "locator": "sections[30] \"Data Availability Statement\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (www.proteomexchange.org) via the PRIDE (Vizcaíno et al., 2016) partner repository with the dataset identifier PXD017347."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:32848694"], "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:PXD017347"], "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:PXD017347"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32848694", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fnsyn.2020.00028", "sha256": 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(www.proteomexchange.org) via the PRIDE (Vizcaíno et al., 2016) partner repository with the dataset identifier PXD017347.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (www.proteomexchange.org) via the PRIDE (Vizcaíno et al., 2016) partner repository with the dataset identifier PXD017347.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "TMT spectrometry unveils key M6a interactorsTMT spectrometry unveils key M6a interactors", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:32848694:1", "role": "table", "format": "jats-table", "media_type": 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3: 350 μg/each"], ["", "co-IP3 R1", "50 μl", "5 μg/Batch #1905424"], ["", "co-IP3 R2", "50 μl"]], "row_count": 11, "column_count": 6, "numeric_cells": 24, "header_rows": 2, "locator": "section[17]/table-wrap[1]#d38e574"}}, {"id": "asset:table:pmid:32848694:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:15608491cc724bdbce6fb512dc4ba89862758d90b765b764029f3b112fa02203", "bytes": 5396, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[25]/table-wrap[1]#T1", "version": null, "note": "Gene ontology (GO) enrichment analysis of 72 potential M6a’s interactors.", "structure": {"pmcid": "PMC7396582", "section_index": 25, "section_title": "Proteomics Analysis", "row_count": 17, "column_count": 9}, "table": {"label": "Table 1", "caption": "Gene ontology (GO) enrichment analysis of 72 potential M6a’s interactors.", "rows": [["", "ID", "Annotation", "p-value", "FDR B&H", "FDR B&Y", "Bonferroni", "Genes from input (72)", "Protein symbol"], ["Molecular function", "GO:0022853", "active ion transmembrane transporter activity", "1.562E-20", "3.85E-18", "2.602E-17", "7.545E-18", "22 (31%)", "Atp6v1a, Atp6v1b2, Atp6v1c1, Atp6v1e1, Atp6v1g2, Atp6v1h, Atp6v0a1, Anxa5, Slc17a7, Atp1a1, Atp1a2, Atp1a3, Slc4a4, Atp1b1, Atp1b2, Atp2b1, Slc1a2, Atp2b2, Slc1a3, Atp2b4, Slc3a2, Slc12a5"], ["", "GO:0005215", "transporter activity", "1.631E-20", "3.85E-18", "2.602E-17", "7.878E-18", "38 (53%)", "Gja1, Atp6v1a, Dpp6, Atp6v1b2, Atp6v1c1, Atp6v1e1, Cpne6, Stx1a, Atp6v1g2, Atp6v1h, Atp6v0a1, Nrxn3, Sv2b, Sv2a, Anxa5, Scn2a, Syngr3, Syn1, Slc17a7, Grin1, Ttyh3, Snap25, Atp1a1, Atp1a2, Atp1a3, App, Slc4a4, Atp1b1, Atp1b2, Aqp4, Atp2b1, Slc1a2, Atp2b2, Slc1a3, Atp2b4, Slc1a3, Atp2b4, Slc3a2, Vdac1, Slc12a5"], ["", "GO:0019829", "ATPase-coupled cation transmembrane transporter activity", "2.391E-20", "3.85E-18", "2.602E-17", "1.155E-17", "16 (22%)", "Atp6v1a, Atp6v1b2, Atp6v1c1, Atp6v1e1, Atp6v1g2, Atp6v1h, Atp6v0a1, Anxa5, Atp1a1, Atp1a2, Atp1a3, Atp1b1, Atp1b2, Atp2b1, Atp2b2, Atp2b4"], ["", "GO:0042625", "ATPase-coupled ion transmembrane transporter activity", "5.2E-20", "6.279E-18", "4.244E-17", "2.512E-17", "16 (22%)", "Atp6v1a, Atp6v1b2, Atp6v1c1, Atp6v1e1, Atp6v1g2, Atp6v1h, Atp6v0a1, Anxa5, Atp1a1, Atp1a2, Atp1a3, Atp1b1, Atp1b2, Atp2b1, Atp2b2, Atp2b4"], ["", "GO:0022857", "transmembrane transporter activity", "7.159E-19", "6.916E-17", "4.674E-16", "3.458E-16", "35 (49%)", "Gja1, Atp6v1a, Dpp6, Atp6v1b2 Atp6v1c1, Atp6v1e1, Stx1a, Atp6v1g2, Atp6v1h, Atp6v0a1, Nrxn3, Sv2b, Sv2a, Anxa5, Scn2a, Slc17a7, Grin1, Ttyh3, Snap25, Atp1a1, Atp1a2, Atp1a3, App, Slc4a4, Atp1b1, Atp1b2, Aqp4, Atp2b1, Slc1a2, Atp2b2, Slc1a3, Atp2b4, Slc3a2, Vdac1, Slc12a5"], ["Biological Process", "GO:0098916", "anterograde trans-synaptic signaling", "2.463E-20", "2.819E-17", "2.373E-16", "6.274E-17", "31 (43%)", "Dpp6, Nptn, Cpne6, Stx1a, Nrxn3, Stxbp1, Synj1, Cadps, Sv2b, Sv2a, Pclo, Scn2a, Cntnap1, Syn1, Slc17a7, Syn2, Syp, Syt1, Grin1, Snap25, Atp1a2, App, Bsn, Grm1, Plp1, Slc1a2, Atp2b2, Slc1a3, Cnp, Vdac1, Slc12a5"], ["", "GO:0007268", "chemical synaptic transmission", "2.463E-20", "2.819E-17", "2.373E-16", "6.274E-17", "31 (43%)", "Dpp6, Nptn, Cpne6, Stx1a, Nrxn3, Stxbp1, Synj1, Cadps, Sv2b, Sv2a, Pclo, Scn2a, Cntnap1, Syn1, Slc17a7, Syn2, Syp, Syt1, Grin1, Snap25, Atp1a2, App, Bsn, Grm1, Plp1, Slc1a2, Atp2b2, Slc1a3, Cnp, Vdac1, Slc12a5"], ["", "GO:0099537", "trans-synaptic signaling", "3.319E-20", "2.819E-17", "2.373E-16", "8.456E-17", "31 (43%)", "Dpp6, Nptn, Cpne6, Stx1a, Nrxn3, Stxbp1, Synj1, Cadps, Sv2b, Sv2a, Pclo, Scn2a, Cntnap1, Syn1, Slc17a7, Syn2, Syp, Syt1, Grin1, Snap25, Atp1a2, App, Bsn, Grm1, Plp1, Slc1a2, Atp2b2, Slc1a3, Cnp, Vdac1, Slc12a5"], ["", "GO:0099536", "synaptic signaling", "5.078E-20", "3.235E-17", "2.724E-16", "1.294E-16", "31 (43%)", "Dpp6, Nptn, Cpne6, Stx1a, Nrxn3, Stxbp1, Synj1, Cadps, Sv2b, Sv2a, Pclo, Scn2a, Cntnap1, Syn1, Slc17a7, Syn2, Syp, Syt1, Grin1, Snap25, Atp1a2, App, Bsn, Grm1, Plp1, Slc1a2, Atp2b2, Slc1a3, Cnp, Vdac1, Slc12a5"], ["", "GO:0030001", "metal ion transport", "1.414E-18", "7.204E-16", "6.067E-15", "3.602E-15", "31 (43%)", "Gja1, Atp6v1a, Dpp6, Atp6v1b2, Atp6v1c1, Atp6v1e1, Stx1a, Atp6v1g2, Atp6v1h, Atp6v0a1, Thy1, Anxa5, Scn2a, Slc17a7, Grin1, Snap25, Atp1a1, Atp1a2, Atp1a3, Slc4a4, Atp1b1, Atp1b2, Atp2b1, Slc1a2, Atp2b2, Slc1a3, Atp2b4, Epb41, Cntn1, Slc3a2, Vdac1, Slc12a5"], ["Celular Component", "GO:0045202", "synapse", "1.406E-30", "5.552E-28", "3.641E-27", "5.552E-28", "45 (63%)", "Nptn, Dpysl2, Dpysl3, Stx1a, Atp6v1g2, Atp6v0a1, Nrxn3, Stxbp1, Nckap1, Synj1, Scamp5, Cadps, Sv2b, Sv2a, Anxa5, Pclo, Scn2a, Ncan, Syngr3, Cntnap1, Syn1, Slc17a7, Syn2, Syp, Syt1, Bcan, Grin1, Snap25, Atp1a1, Atp1a2, Atp1a3, App, Bsn, Grm1, Epb41l3, Atp2b1, Eno2, Slc1a2, Atp2b2, Slc1a3, Atp2b4, Epb41, Cntn1, Slc3a2, Vdac1"], ["", "GO:0098793", "presynapse", "2.191E-29", "4.328E-27", "2.838E-26", "8.656E-27", "35 (49%)", "Nptn, Dpysl2, Stx1a, Atp6v1g2, Atp6v0a1, Nrxn3, Stxbp1, Synj1, Scamp5, Cadps, Sv2b, Sv2a, Anxa5, Pclo, Scn2a, Syngr3, Cntnap1, Syn1, Slc17a7, Syn2, Syp, Syt1, Grin1, Snap25, Atp1a2, Atp1a3, App, Bsn, Grm1, Atp2b1, Slc1a2, Atp2b2, Atp2b4, Cntn1, Vdac1"], ["", "GO:0043209", "myelin sheath", "1.714E-20", "2.257E-18", "1.48E-17", "6.772E-18", "21 (28%)", "Atp6v1a, Atp6v1b2, Dpysl2, Stxbp1, Thy1, Cntnap1, Syn1, Syn2, Snap25, Atp1a1, Atp1a3, Atp1b1, Ppia, Eno2, Plp1, Omg, Cnp, Mog, Cntn1, Hsp90, Vdac1"], ["", "GO:0030054", "cell junction", "1.073E-19", "1.052E-17", "6.89E-17", "4.208E-17", "35 (63%)", "Vapa, Gja1, Stx1a, Thy1, Nckap1, Scamp5, Cadps, Sv2b, Tnc, Sv2a, Anxa5, Pclo, Scn2a, Syngr3, Cntnap1, Lrp1,"], ["", "", "", "", "", "", "", "", "Syn1, Slc17a7, Syn2, Syp, Syt1, Grin1, Snap25, Atp1a1, Atp1a2, App, Bsn, Epb41l3, Atp1b1, Ppia, Aqp4, Atp2b1, Atp2b2, Epb41, Epb41l2"], ["", "GO:0043005", "neuron projection", "2.962E-19", "2.925E-17", "1.918E-16", "1.17E-16", "37 (51%)", "Nptn, Dpysl2, Dpysl3, Cpne6, Stx1a, Stxbp1, Thy1, Rnpep, Synj1, Sv2b, Sv2a, Anxa5, Pclo, Scn2a, Cntnap1, Lrp1, Syn1, Slc17a7, Syp, Syt1, Bcan, Grin1, Snap25, Atp1a2, Atp1a3, App, Bsn, Grm1, Epb41l3, Atp2b1, Eno2, Slc1a2, Atp2b2, Slc1a3, Atp2b4, Hsp90, Slc12a5"]], "row_count": 17, "column_count": 9, "numeric_cells": 104, "header_rows": 1, "locator": "section[25]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:32848694:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3494d1b42d429ff4af5ebf13857cce2a55f4c53eaa78c4565071829180e0f1c9", "bytes": 2368, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[25]/table-wrap[2]#T2", "version": null, "note": "Disease-associated gene analysis of the 72 potential M6a’s interactors.", "structure": {"pmcid": "PMC7396582", "section_index": 25, "section_title": "Proteomics Analysis", "row_count": 11, "column_count": 9}, "table": {"label": "Table 2", "caption": "Disease-associated gene analysis of the 72 potential M6a’s interactors.", "rows": [["", "ID", "Annotation", "p-value", "FDR B&H", "FDR B&Y", "Bonferroni", "Genes from input (72)", "Protein symbol"], ["Disease", "C0004352", "Autistic Disorder", "1.84E-10", "3.041E-07", "2.43E-06", "3.041E-07", "20 (27%)", "Gja1, Dpysl2, Stx1a, Nrxn3, Stxbp1, Thy1, Scamp5, Tnc, Pclo, Scn2a, Cntnap1, Syn1, Syn2, Snap25, App, Aqp4, Plp1, Slc1a2, Atp2b2, Slc1a3"], ["", "C0014544", "Epilepsy", "1.05E-09", "8.625E-07", "6.89E-06", "1.73E-06", "19 (26%)", "Gja1, Dpysl3, Stx1a, Stxbp1, Sv2a, Scn2a, Syn1, Slc17a7, Syn2, Grin1, Atp1a2, Atp1a3, App, Grm1, Aqp4, Slc1a2, Slc1a3, Vdac1, Slc12a5"], ["", "C0036341", "Schizophrenia", "2.40E-09", "1.32E-06", "1.05E-05", "3.96E-06", "28 (38%)", "Nptn, Dpysl2, Stx1a, Nrxn3, Stxbp1, Sv2a, Pclo, Scn2a, Ncan, Lrp1, Syn1, Slc17a7, Syn2, Syp, Bcan, Grin1, Snap25, App, Grm1, Ppia, Aqp4, Eno2, Plp1, Slc1a2, Slc1a3, Cnp, Mog, Slc12a5"], ["", "C0002395", "Alzheimer’s Disease", "2.10E-05", "6.93E-03", "0.055", "0.035", "26 (34%)", "Gja1, Dpysl2, Dpysl3, Thy1, Synj1, Sv2a, Anxa5, Lrp1, Syn1, Slc17a7, Syn2, Syp, Syt1, Bcan, Grin1, Snap25, App, Ppia, Aqp4, Eno2, Slc1a2, Slc1a3, Cnp, Mog, Hsp90, Vdac1"], ["", "C0086237", "Epilepsy, Cryptogenic", "5.30E-06", "2.19E-03", "0.017", "0.009", "7 (9, 7%)", "Gja1, Scn2a, Grm1, Slc1a2, Slc1a3, Vdac1, Slc12a5"], ["", "C0005586", "Bipolar Disorder", "2.61E-05", "7.18E-03", "0.057", "0.043", "16 (22%)", "Vapa, Dpysl2, Synj1, Pclo, Ncan, Slc17a7, Syn2, Syp, Grin1, Snap25, Atp1a1, Atp1a2, Atp1a3, App, Slc1a2, Slc1a3"], ["", "C0036572", "Seizures", "4.81E-05", "0.010", "0.081", "0.079", "14 (19%)", "Gja1, Stxbp1, Synj1, Sv2a, Scn2a, Slc17a7, Syn2, Grin1, Atp1a2, App, Aqp4, Slc1a2, Slc1a3, Slc12a5"], ["", "C0011570", "Mental Depression", "4.92E-05", "0.010", "0.081", "0.081", "14 (19%)", "Gja1, Dpysl2, Pclo, Syn1, Syp, Grin1, Snap25, Atp1a3, App, Grm1, Aqp4, Slc1a2, Cnp, Hsp90"], ["", "C1269683", "Major Depressive Disorder", "1.27E-04", "2.11E-02", "1.70E-01", "2.19E-01", "13 (19%)", "Gja1, Pclo, Ncan, Lrp1, Slc17a7, Snap25, App, Plp1, Slc1a2, Slc1a3, Cnp, Mog, Hsp90"], ["", "C0011581", "Depressive disorder", "1.28E-04", "0.022", "0.176", "0.211", "14 (19%)", "Gja1, Dpysl2, Pclo, Syn1, Syp, Grin1, Snap25, Atp1a3, App, Grm1, Aqp4, Slc1a2, Cnp, Hsp90"]], "row_count": 11, "column_count": 9, "numeric_cells": 71, "header_rows": 1, "locator": "section[25]/table-wrap[2]#T2"}}], "gaps": ["asset:data:geo:PXD017347 not downloaded", "asset:data:geo:PXD017347 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "For differential protein expression analysis between conditions, a t-test was used and applied with Linear Models for Microarray Data (Limma) package (Ritchie et al., 2015)."}}, {"id": "method-2", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Pearson correlation"}}], "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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": ["PXD017347"], "resolved_accessions": ["PXD017347"], "statements": ["The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (www.proteomexchange.org) via the PRIDE (Vizcaíno et al., 2016) partner repository with the dataset identifier PXD017347."], "basis": "The paper names PXD017347 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:32848694", "data:geo:PXD017347", "asset:table:pmid:32848694:1", "asset:table:pmid:32848694:2", "asset:table:pmid:32848694:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD017347"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:22:08Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 52102, "completion_tokens": 1458, "cached_tokens": 784}}, "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:32848694", "type": "paper", "label": "pmid:32848694"}, {"id": "source:pmid:32848694", "type": "manuscript", "label": "PMID 32848694 full text"}, {"id": "data:geo:PXD017347", "type": "dataset", "label": "GEO PXD017347"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32848694", "type": "paper", "label": "pmid:32848694"}, {"id": "source:pmid:32848694", "type": "manuscript", "label": "PMID 32848694 full text"}, {"id": "data:geo:PXD017347", "type": "dataset", "label": "GEO PXD017347"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32848694", "type": "extraction", "used": ["source:pmid:32848694"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD017347", "type": "accession_resolution", "used": ["data:geo:PXD017347"], "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:32848694", "parent_hash": "sha256:f343ef4b25349d8edc9fe7c3a8fe4f7bf50e8c75687a51454ba2ccddd0c9547d", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:PXD017347 licence not read", "asset:data:geo:PXD017347 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["and performed a co-immunoprecipitation with rat hippocampus samples followed by TMT/MS. Here", "hand, litters from two female Sprague–Dawley rats were used for co-IP experiments. The pups were ho", "and Methods Animals Pregnant Sprague–Dawley rats maintained at the Facultad de Farmacia y Bio", "hippocampal neurons were prepared from fetal rats at embryonic day 19 (CICUAE-UNSAM No. 03/201"], "order_basis": "paper_text_order:1012", "id": "assay:1"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.85, "evidence": ["co-IP experiments. Cell Culture and Plasmid Transfection Sample Preparation and Mass Spectrometry Dat"], "order_basis": "paper_text_order:3508", "id": "assay:2"}, {"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Plasmid Transfection Sample Preparation and Mass Spectrometry Data Acquisition and Analysis Sample Prepara", "ling The nine final samples were sent to the Proteomic Core Facility of the European Molecular Biol"], "order_basis": "paper_text_order:3544", "id": "assay:3"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["was used and applied with Linear Models for Microarray Data (Limma) package (Ritchie et al., 2015)."], "order_basis": "paper_text_order:6630", "id": "assay:4"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["For differential protein expression analysis between conditions, a t-test was used and applied with Linear Models for Microarray Data (Limma) package (Ritchie et al., 2015)."], "order_basis": "consumes_earlier_output", "id": "assay:5"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T03:14:06+00:00","total_papers":5529,"total_assays_tracked":29,"automatable_assay_families":6,"validated":true,"caveat_count":9,"blocking_caveats":5,"caveats":[{"code":"low_evidence_dominates","basis":["4,152 of 5,529 classifications (75.1%) matched no cue evidence and sit at the 0.05 floor.","34 of 230 data_only calls (14.8%) are in that group."],"claim":"Work type and confidence bands","gloss":"Most records were classified from their title and framing alone, with assay-cue coverage at zero.","detail":"Most classifications in this run rest on no matched evidence at all. 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. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}