Novel proteins from proteomic analysis of the trunk disease fungus Lasiodiplodia theobromae (Botryosphaeriaceae).

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29450146", "kind": "science-record", "revision": 6, "content_hash": "sha256:693c1b8d58394c50ab55f8f42e1689b76321aac872a3dc9d4afb5d49b0b46412", "created_at": "2026-11-01T15:40:31Z", "updated_at": "2026-11-01T21:21:18Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Novel proteins from proteomic analysis of the trunk disease fungus Lasiodiplodia theobromae (Botryosphaeriaceae).", "doi": "10.1016/j.biopen.2017.03.001", "pmid": "29450146", "authors": ["Carla C Uranga", "Majid Ghassemian", "Rufina Hernández-Martínez"], "journal": "Biochimie open", "year": 2017, "abstract": "Many basic science questions remain regarding protein functions in the pathogen: host interaction, especially in the trunk disease fungi family, the Botryosphaeriaceae, which are a global problem for economically important plants, especially fruiting trees. Proteomics is a highly useful technology for studying protein expression and for discovering novel proteins in unsequenced and poorly annotated organisms. Current fungal proteomics approaches involve 2D SDS-PAGE and extensive, complex, protein extraction methodologies. In this work, a modified Folch extraction was applied to protein extraction to perform both de novo peptide sequencing and peptide fragmentation analysis/protein identification of the plant and human fungal pathogen Lasiodiplodia theobromae. Both bioinformatics approaches yielded novel peptide sequences from proteins produced by L. theobromae in the presence of exogenous triglycerides and glucose. These proteins and the functions they may possess could be targeted for further functional characterization and validation efforts, due to their potential uses in biotechnology and as new paradigms for understanding fungal biochemistry, such as the finding of allergenic enolases, as well as various novel proteases, including zinc metalloproteinases homologous to those found in snake venom. This work contributes to genomic annotation efforts, which, hand in hand with genomic sequencing, will help improve fungal bioinformatics databases for future studies of Botryosphaeriaceae. All data, including raw data, are available via the ProteomeXchange data repository with identifier PXD005283. This is the first study of its kind in Botryosphaeriaceae.", "claims": [{"id": "claim-method", "statement": "The software Cytoscape [42] with the BiNGO plugin [43] was used for GO and enrichment analysis using up-to-date databases, applying a hypergeometric test with a significance level (p-value) < 0.05, as well as a Benjamini and Hochberg false discovery rate (FDR) correction.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29450146", "locator": "sections[5] \"Protein identification\" paragraph 6", "quote": "The software Cytoscape [42] with the BiNGO plugin [43] was used for GO and enrichment analysis using up-to-date databases, applying a hypergeometric test with a significance level (p-value) < 0.05, as well as a Benjamini and Hochberg false discovery rate (FDR) correction."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data, including raw data, are available via the ProteomeXchange data repository with identifier PXD005283.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29450146", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "All data, including raw data, are available via the ProteomeXchange data repository with identifier PXD005283."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used a hypergeometric test with Benjamini–Hochberg false-discovery-rate correction for gene-ontology enrichment analysis, and the source data—including raw data—were deposited in ProteomeXchange under identifier PXD005283.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29450146", "locator": "sections[5] \"Protein identification\" paragraph 6", "quote": "Gene ontology (GO) analysis of enriched proteins was done on all those hits obtained from the Uniprot database [33]. The software Cytoscape [42] with the BiNGO plugin [43] was used for GO and enrichment analysis using up-to-date databases, applying a hypergeometric test with a significance level (p-value) < 0.05, as well as a Benjamini and Hochberg false discovery rate (FDR) correction."}, {"asset": "source:pmid:29450146", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "All data, including raw data, are available via the ProteomeXchange data repository with identifier PXD005283."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used a hypergeometric test with Benjamini–Hochberg false-discovery-rate correction for gene-ontology enrichment analysis, and the source data—including raw data—were deposited in ProteomeXchange under identifier PXD005283.", "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:29450146"], "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:PXD005283"], "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:PXD005283"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29450146", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.biopen.2017.03.001", "sha256": "sha256:f48a6d16699c1c02de76ad7c96b6b3c76b241a440f82f451f3171a6f83ba791d", "bytes": 41024, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.biopen.2017.03.001", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5802045", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD005283", "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=PXD005283", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD005283", "version": null, "note": "All data, including raw data, are available via the ProteomeXchange data repository with identifier PXD005283.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data, including raw data, are available via the ProteomeXchange data repository with identifier PXD005283.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "A novel protein extraction method for proteomics of the trunk disease fungus Lasiodiplodia theobromae (Botryosphaeriaceae)", "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:29450146:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:cd92fd8db37b490cc33c95172e9b83d272cce13bb882a53265a6310f8d14014b", "bytes": 2359, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[1]#tbl1", "version": null, "note": "Proteins identified as “hypothetical” by the MSGF, X! Tandem and OMSSA algorithms, further searched with NCBI BLAST. The top-scoring homologous protein is reported for each search in the last column.", "structure": {"pmcid": "PMC5802045", "section_index": 7, "section_title": "Results and discussion", "row_count": 10, "column_count": 8}, "table": {"label": "Table 1", "caption": "Proteins identified as “hypothetical” by the MSGF, X! Tandem and OMSSA algorithms, further searched with NCBI BLAST. The top-scoring homologous protein is reported for each search in the last column.", "rows": [["Main accession", "Description", "Coverage [%]", "Spectrum counting", "#Validated unique", "Confidence [%]", "Validation", "Homologous protein sequence (BLAST)"], ["407929156", "Hypothetical protein MPH_00684 [Macrophomina phaseolina MS6]", "6.0", "30.1", "2", "100", "Confident", "Neofusicoccum parvum UCRNP2 putative protein mitochondrial targeting protein XM_007580308.1"], ["407928922", "Hypothetical protein MPH_00885 [Macrophomina phaseolina MS6]", "17.1", "228.8", "3", "100", "Confident", "Neofusicoccum parvum UCRNP2 putative phosphotransmitter protein ypd1 protein XM_007584095.1"], ["407927556", "Hypothetical protein MPH_02256 [Macrophomina phaseolina MS6]", "9.1", "124.1", "4", "100", "Confident", "Neofusicoccum parvum UCRNP2 putative nuclear and cytoplasmic polyadenylated rna-binding protein pub1 protein mRNA, XM_007585675.1"], ["407923581", "Hypothetical protein MPH_06104 [Macrophomina phaseolina MS6]", "11.6", "108.6", "2", "100", "Confident", "Sphaerulina musiva SO2202 GTP-binding protein mRNA XM_016910103.1"], ["407922440", "Hypothetical protein MPH_07279 [Macrophomina phaseolina MS6]", "9.9", "242.1", "2", "100", "Confident", "Neofusicoccum parvum UCRNP2 putative fk506-binding protein, XM_007581103.1"], ["407921582", "Hypothetical protein MPH_07998 [Macrophomina phaseolina MS6]", "4.9", "11.8", "2", "100", "Confident", "Neofusicoccum parvum UCRNP2 putative transcription factor (snd1 p100) protein, XM_007582992.1"], ["407921297", "Hypothetical protein MPH_08297 [Macrophomina phaseolina MS6]", "12.3", "74.8", "3", "100", "Confident", "Neofusicoccum parvum UCRNP2 putative g-protein complex beta subunit protein XM_007582859.1"], ["407920925", "Hypothetical protein MPH_08717 [Macrophomina phaseolina MS6]", "23.4", "128.1", "7", "100", "Confident", "Neofusicoccum parvum UCRNP2 putative glycolipid transfer protein het-c2 protein XM_007581974.1"], ["407916430", "Hypothetical protein MPH_13123 [Macrophomina phaseolina MS6]", "21.2", "581.6", "4", "100", "Confident", "Neofusicoccum parvum UCRNP2 putative surface protein 1 protein XM_007588394.1"]], "row_count": 10, "column_count": 8, "numeric_cells": 63, "header_rows": 1, "locator": "section[7]/table-wrap[1]#tbl1"}}, {"id": "asset:table:pmid:29450146:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d42842e756b7ec1f0b1fa31c726e7d63add29dd89a140e47379858fb274bc99f", "bytes": 6728, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[2]#tbl2", "version": null, "note": "Novel de novo peptide sequences from the Novor and PepNovo algorithms and BLASTp search results using an all-Uniprot database of the peptidome from Lasiodiplodia theobromae incubated in 5% grapeseed oil + 5% glucose for 20 days, showing the most probable homolog.", "structure": {"pmcid": "PMC5802045", "section_index": 7, "section_title": "Results and discussion", "row_count": 32, "column_count": 8}, "table": {"label": "Table 2", "caption": "Novel de novo peptide sequences from the Novor and PepNovo algorithms and BLASTp search results using an all-Uniprot database of the peptidome from Lasiodiplodia theobromae incubated in 5% grapeseed oil + 5% glucose for 20 days, showing the most probable homolog.", "rows": [["Query sequence", "Peptide Score", "m/z", "Charge", "E-value", "Uniprot ID", "Organism", "Protein name"], ["ELGFLASLGWNAPPAFPGPELTALDKLSAALSNR", "28.7", "1175.2", "3+", "2", "Q8T9W1", "Dictyostelium discoideum (Slime mold)", "Serine protease/ABC transporter B family protein tagD (EC 3.4.21.-) (Serine protease/ABC transporter tagD)"], ["DDGSMDTCEDDGAGR", "43.1", "808.8", "2+", "8.6", "Q7RTY9", "Homo sapiens (Human)", "Serine protease 41 (EC 3.4.21.-) (Testis serine protease 1) (TESSP-1)"], ["QETSVPGDSQATLDALNEWR", "66.5", "739.7", "3+", "1.6", "Q10749", "Naja mossambica (Mozambique spitting cobra)", "Snake venom metalloproteinase-disintegrin-like mocarhagin (MOC) (Mocarhagin-1) (SVMP) (EC 3.4.24.-) (Zinc metalloproteinase)"], ["LLGTAMHVAGHLCAMMGWYRLTPSLHK", "17.0", "1033.8", "3+", "4.6", "J3RY93", "Crotalus adamanteus", "Snake venom serine proteinase 12 (SVSP) (EC 3.4.21.-)"], ["WLSAKGWAQGVAEGPGDPR", "35.9", "991.5", "2+", "7.7", "P0DL42", "Daboia siamensis (Eastern Russel's viper)", "Snake venom vascular endothelial growth factor toxin VR-1' (svVEGF) (VEGF-F)"], ["DYPPVLEHLLAWEEEQR", "19.0", "708.7", "3+", "7", "B2MVK7", "Rhynchium brunneum (Potter wasp)", "Venom allergen 5 (Antigen 5) (Cysteine-rich venom protein) (CRVP)"], ["VLTVKGSCNLTMLVSFWTFSGNLTNGASTGSHK", "37.4", "1172.3", "3+", "5.7", "C0ITL3", "Pachycondyla chinensis (Asian needle ant)", "Venom allergen 5 (Antigen 5) (Cysteine-rich venom protein) (CRVP) (allergen Pac c 3) (Fragment)"], ["MLPAFLVDVHHSKKVGVPPNYYYQHSK", "15.10", "793.4", "4+", "7.1", "P83370", "Hoplocephalus stephensii (Stephens' banded snake)", "Venom prothrombin activator hopsarin-D (vPA) (EC 3.4.21.6) (Venom coagulation factor Xa-like protease) [Cleaved into: Hopsarin-D light chain; Hopsarin-D heavy chain]"], ["APTPALDGGKLMFVSAK", "38.6", "568.3", "3+", "0.63", "Q5WFT5", "Bacillus clausii (strain KSM-K16)", "Zinc metalloprotease RasP (EC 3.4.24.-) (Regulating alternative sigma factor protease) (Regulating anti-sigma-W factor activity protease)"], ["LASHKPNCFLAPPLGTHDVVPK", "34.5", "800.1", "3+", "6", "B8K1W0", "Daboia russelii (Russel's viper) (Vipera russelii)", "Zinc metalloproteinase-disintegrin-like daborhagin-K (EC 3.4.24.-) (Haemorrhagic metalloproteinase russelysin) (Snake venom metalloproteinase) (SVMP)"], ["VDSDFTVGLAAQWAETDLYK", "49.3", "743.7", "3+", "7", "C5H5D6", "Lachesis muta rhombeata (Bushmaster)", "Zinc metalloproteinase-disintegrin-like lachestatin-2 (EC 3.4.24.-) (Snake venom metalloprotease) (SVMP) (Vascular apoptosis-inducing protein-like) (VAP-like)"], ["YGMKWSLLMLAAGGGR", "54.8", "863.9", "2+", "5.4", "Q5XJ13", "Danio rerio (Zebrafish) (Brachydanio rerio)", "Ankyrin repeat and SAM domain-containing protein 6 (Ankyrin repeat domain-containing protein 14) (SamCystin)"], ["LMAAWGQNPGQAALYVEWNPEVMSAVWK", "37.10", "1054.8", "3+", "1.2", "Q68DC2", "Homo sapiens (Human)", "Ankyrin repeat and SAM domain-containing protein 6 (Ankyrin repeat domain-containing protein 14) (SamCystin)"], ["LGAKWCHHCFAVPMK", "19.9", "929.4", "2+", "0.95", "Q6S8J3", "Homo sapiens (Human)", "POTE ankyrin domain family member E (ANKRD26-like family C member 1A) (Prostate, ovary, testis-expressed protein on chromosome 2) (POTE-2)"], ["ALKGFYLMNPPAPVWWTR", "49.6", "716.4", "3+", "5.6", "B8I4B9", "Clostridium cellulolyticum", "ATP-dependent zinc metalloprotease FtsH (EC 3.4.24.-)"], ["LAAPNPYLWWHDLVPR", "40.5", "974.5", "2+", "6.7", "Q2EEX7", "Helicosporidium sp. subsp. Simulium jonesii", "ATP-dependent zinc metalloprotease FtsH homolog"], ["ELKAKKVGAMDVASSEFYK", "52.7", "701.04", "3+", "1.5", "P30575", "Candida albicans", "Enolase 1 (EC 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (2-phosphoglycerate dehydratase)"], ["TLVAGFFFLAASLTCLLVPSEAPTFSETTR", "45.0", "812.4", "4+", "1.8", "Q9HDT3", "Alternaria alternata", "Enolase (EC 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (2-phosphoglycerate dehydratase) (Allergen Alt a 11) (Allergen Alt a 5) (Allergen Alt a XI)"], ["ELGAHTLGFLESNPKFDPGSYEQLADLYK", "53.2", "1080.5", "3+", "1.7", "Q96X30", "Neosartorya fumigata (Aspergillus fumigatus)", "Enolase (EC 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (2-phosphoglycerate dehydratase) (allergen Asp f 22)"], ["HCLAAVPCMGQSPAAAALLNSSEVQNMAMGFK", "40.4", "1025.5", "2+, 3+, 4+", "1.6", "Q59121", "Arcanobacterium haemolyticum", "Phospholipase D (EC 3.1.4.4) (Choline phosphatase) (PLD-A)"], ["VFRLKDSGNSKPDKAAPPPGPLPR", "29.2", "848.8", "3+", "8.3", "O14939", "Homo sapiens (Human)", "Phospholipase D2 (PLD 2) (hPLD2) (EC 3.1.4.4) (Choline phosphatase 2) (PLD1C) (Phosphatidylcholine-hydrolyzing phospholipase D2)"], ["LHMGTDCAELDCVRSAPK", "33.2", "687.3", "3+", "4.5", "Q9LI83", "Arabidopsis thaliana (Mouse-ear cress)", "Phospholipid-transporting ATPase 10 (AtALA10) (EC 3.6.3.1) (Aminophospholipid flippase 10)"], ["DLADALKAAMGAPKHAVDHVAEPMDVAQLAPGNK", "36.9", "867.7", "4+", "4.2", "P06681", "Homo sapiens (Human)", "Complement C2 (EC 3.4.21.43) (C3/C5 convertase) [Cleaved into: Complement C2b fragment; Complement C2a fragment]"], ["NTLHAPEGTVVHLNAHK", "54.2", "919.5", "2+", "8.7", "P98094", "Eptatretus burgeri (Inshore hagfish)", "Complement C3 [Cleaved into: Complement C3 beta chain; Complement C3 alpha chain; C3a anaphylatoxin; Complement C3 gamma chain] (Fragment)"], ["HNDRCPCMCNCQNDDCRCDTSNVPAK", "16.2", "825.8", "4+", "6.3", "Q00685", "Lethenteron camtschaticum (Japanese lamprey) (Lampetra japonica)", "Complement C3 [Cleaved into: Complement C3 beta chain; Complement C3 alpha chain; C3a anaphylatoxin; Complement C3 gamma chain] (Fragment)"], ["SWFVNVPNCDGALAGMTASFVR", "30.9", "800.4", "3+", "9.7", "P01031", "Homo sapiens (Human)", "Complement C5 (C3 and PZP-like alpha-2-macroglobulin domain-containing protein 4) [Cleaved into: Complement C5 beta chain; Complement C5 alpha chain; C5a anaphylatoxin; Complement C5 alpha chain]"], ["KDLKYLDVYYWRYFWKWRQVDYLVAPAK", "22.6", "928.9", "4+", "4.1", "P15304", "Rattus norvegicus (Rat)", "Hormone-sensitive lipase (HSL) (EC 3.1.1.79)"], ["DPGFLGTLATASGKFGEGDPHAKTSGLNRK", "40.0", "1010.5", "3+", "0.21", "A7L035", "Chironex fleckeri (Box jellyfish)", "Toxin CfTX-1 (Toxin 1)"], ["TLMGYLLAVDGCALGCFFVMPGLGLVAALSK", "28.3", "815.9", "4+", "3.2", "P60262", "Tityus discrepans (Venezuelan scorpion)", "Toxin TdII-3 (Fragment)"], ["SAPDPGTGDEVVMGQMDPR", "37.1", "658.9", "3+", "4.8", "P42211", "Oryza sativa subsp. japonica (Rice)", "Aspartic proteinase (EC 3.4.23.-)"], ["PAYHDLGVVPMADTR", "41.7", "821.4", "2+", "9.2", "Q8VYV9", "Arabidopsis thaliana (Mouse-ear cress)", "Aspartyl protease family protein 1 (EC 3.4.23.-)"]], "row_count": 32, "column_count": 8, "numeric_cells": 172, "header_rows": 1, "locator": "section[7]/table-wrap[2]#tbl2"}}], "gaps": ["asset:data:geo:PXD005283 not downloaded", "asset:data:geo:PXD005283 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Hypergeometric test with Benjamini-Hochberg false discovery rate correction", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The software Cytoscape [42] with the BiNGO plugin [43] was used for GO and enrichment analysis using up-to-date databases, applying a hypergeometric test with a significance level (p-value) < 0.05, as well as a Benjamini and Hochberg false discovery rate (FDR) correction."}}], "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": "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 (Hypergeometric test with Benjamini-Hochberg false discovery rate correction), 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": "R1", "reachable": true, "accessions": ["PXD005283"], "resolved_accessions": ["PXD005283"], "statements": ["All data, including raw data, are available via the ProteomeXchange data repository with identifier PXD005283."], "basis": "The paper names PXD005283 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": [], "assets": ["source:pmid:29450146", "data:geo:PXD005283", "asset:table:pmid:29450146:1", "asset:table:pmid:29450146:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD005283"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:33:40Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 83862, "completion_tokens": 5841, "cached_tokens": 1816}}, "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:29450146", "type": "paper", "label": "pmid:29450146"}, {"id": "source:pmid:29450146", "type": "manuscript", "label": "PMID 29450146 full text"}, {"id": "data:geo:PXD005283", "type": "dataset", "label": "GEO PXD005283"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:29450146", "type": "paper", "label": "pmid:29450146"}, {"id": "source:pmid:29450146", "type": "manuscript", "label": "PMID 29450146 full text"}, {"id": "data:geo:PXD005283", "type": "dataset", "label": "GEO PXD005283"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-29450146", "type": "extraction", "used": ["source:pmid:29450146"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD005283", "type": "accession_resolution", "used": ["data:geo:PXD005283"], "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:29450146", "parent_hash": "sha256:1bce198570b19f405fb23a6b88d5cea1ced399fd73a209ec4df5bdad7213305a", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:PXD005283 licence not read", "asset:data:geo:PXD005283 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["Novel proteins from proteomic analysis of the trunk disease fungus Lasiodi", "important plants, especially fruiting trees. Proteomics is a highly useful technology for studying p", "d poorly annotated organisms. Current fungal proteomics approaches involve 2D SDS-PAGE and extensive", "d to the University of California, San Diego proteomics mass spectrometry department to be processed"], "order_basis": "paper_text_order:0", "id": "assay:1"}]}