Transcription profiling data set of different states of Mycoplasma gallisepticum.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:27942460", "kind": "science-record", "revision": 6, "content_hash": "sha256:cb833244d7edf2a4e11cef1d793cd1d7c3c47552f10017661eb675647ad75759", "created_at": "2026-11-01T15:40:21Z", "updated_at": "2026-11-01T21:20:44Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Transcription profiling data set of different states of Mycoplasma gallisepticum.", "doi": "10.1016/j.gdata.2016.11.021", "pmid": "27942460", "authors": ["Tatiana A Semashko", "Alexander A Arzamasov", "Gleb Y Fisunov", "Vadim M Govorun"], "journal": "Genomics data", "year": 2017, "abstract": "Mycoplasma gallisepticum belongs to class Mollicutes and causes chronic respiratory disease in birds. It has a reduced genome, lack of cell wall and many metabolic pathways, and also easy to culture and non-pathogenic to humans. Aforementioned made it is a convenient model for studying of systems biology of minimal cell. Studying the transcriptomic level of M. gallisepticum is interesting for both understanding of common principles of transcription regulation of minimal cell and response to definite influence for pathogen bacteria. For rapid investigation of gene expression we developed microarray design including 3366 probes for 678 genes. They included 665 protein coding sequences and 13 antisense RNAs from 816 genes and 17 ncRNAs present in Mycoplasma gallisepticum. The study was performed on Agilent one-color microarray with custom design and random-T7 polymerase primer for cDNA synthesis. Here we present the data for transcription profiling of M. gallisepticum under different types of exposures: genetic knock-out mutants, cell culture exposed to sublethal concentrations of antibiotics and well-characterized heat stress effect. Mutants have transposon insertion to hypothetical membrane protein, lactate dehydrogenase, helicase with unknown function, 1-deoxy-d-xylulose 5-phosphate reductoisomerase or potential sigma factor. For inhibition of important cell systems, treatment with carbonyl cyanide m-chlorophenylhydrazone (CCCP), novobiocin or tetracycline were chosen. Data are available via NCBI Gene Expression Omnibus (GEO) with the accession number GSE85777 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE85777).", "claims": [{"id": "claim-method", "statement": "Spearman correlation coefficient between biological repeats ranges between 0.93 and 1.00.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27942460", "locator": "sections[4] \"Experimental design\" paragraph 6", "quote": "Spearman correlation coefficient between biological repeats ranges between 0.93 and 1.00."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are available via NCBI Gene Expression Omnibus (GEO) with accession number GSE85777 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE85777)", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27942460", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "Data are available via NCBI Gene Expression Omnibus (GEO) with accession number GSE85777 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE85777)"}], "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:27942460"], "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:GSE85777"], "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:GSE85777"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:27942460", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.gdata.2016.11.021", "sha256": "sha256:bdc8cdafa69ebf504d7e0686a691f21d712b4cf46ba0b56af2d882f2cf2541d5", "bytes": 11245, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.gdata.2016.11.021", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5137179", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE85777", "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=GSE85777", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE85777", "version": null, "note": "Data are available via NCBI Gene Expression Omnibus (GEO) with accession number GSE85777 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE85777)", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data are available via NCBI Gene Expression Omnibus (GEO) with accession number GSE85777 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE85777)", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2283924", "GSM2283925", "GSM2283926", "GSM2283927", "GSM2283928", "GSM2283929", "GSM2283930", "GSM2283931", "GSM2283932", "GSM2283933", "GSM2283934", "GSM2283935", "GSM2283936", "GSM2283937", "GSM2283938", "GSM2283939", "GSM2283940", "GSM2283941", "GSM2283942", "GSM2283943"], "sample_count": 20, "group_sizes": null, "group_sizes_basis": null, "platform": "22328", "taxon": "Mycoplasmoides gallisepticum", "title": "Transcription profiling of different state of Mycoplasma gallisepticum", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": 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insertion to 5′ UTR of hypothetical protein GCW_03380", "Cell culture in exponential growth phase"], ["Tn_5UTR_03380_2", "CR1, Transposon insertion to 5′ UTR of hypothetical protein GCW_03380", "Cell culture in exponential growth phase"], ["Tn_RBS_00390_1", "CR19, Transposon insertion to RBS of lactate dehydrogenase GCW_00390", "Cell culture in exponential growth phase"], ["Tn_RBS_00390_2", "CR19, Transposon insertion to RBS of lactate dehydrogenase GCW_00390", "Cell culture in exponential growth phase"], ["Tn_03935_1", "CR30, Transposon insertion to helicase SNF2 GCW_03935", "Cell culture in exponential growth phase"], ["Tn_03935_2", "CR30, Transposon insertion to helicase SNF2 GCW_03935", "Cell culture in exponential growth phase"], ["Tn_00495_1", "CR86, Transposon insertion to 1-deoxy-D-xylulose 5-phosphate reductoisomerase GCW_00495", "Cell culture in exponential growth phase"], ["Tn_00495_2", "CR86, Transposon insertion to 1-deoxy-D-xylulose 5-phosphate reductoisomerase GCW_00495", "Cell culture in exponential growth phase"], ["Tn_00440_1", "5.3, Transposon insertion to potential sigma factor GCW_00440", "Cell culture in exponential growth phase"], ["Tn_00440_2", "5.3, Transposon insertion to potential sigma factor GCW_00440", "Cell culture in exponential growth phase"], ["cccp_1", "WT", "Cell culture in exponential growth phase under treatment with sublethal concentrations of CCCP"], ["cccp_2", "WT", "Cell culture in exponential growth phase under treatment with sublethal concentrations of CCCP"], ["novo_1", "WT", "Cell culture in exponential growth phase under treatment with sublethal concentrations of novobiocin"], ["novo_2", "WT", "Cell culture in exponential growth phase under treatment with sublethal concentrations of novobiocin"], ["tet_1", "WT", "Cell culture in exponential growth phase under treatment with sublethal concentrations of tetracycline"], ["tet_2", "WT", "Cell culture in exponential growth phase under treatment with sublethal concentrations of tetracycline"], ["HS_1", "WT", "Cell culture in exponential growth phase under heat stress at 46 °C during 15 min"], ["HS_2", "WT", "Cell culture in exponential growth phase under heat stress at 46 °C during 15 min"]], "row_count": 21, "column_count": 3, "numeric_cells": 32, "header_rows": 1, "locator": "section[4]/table-wrap[1]#t0005"}}, {"id": "asset:table:pmid:27942460:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:dca76466bfc48f692d1a75386159216b510dac7b999efc19f01a4c850e470c13", "bytes": 7020, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#t0010", "version": null, "note": "RT-qPCR primers.", "structure": {"pmcid": "PMC5137179", "section_index": 13, "section_title": "Validation of microarray data by quantitative RT-PCR", "row_count": 95, "column_count": 4}, "table": {"label": "Table 2", "caption": "RT-qPCR primers.", "rows": [["S6_ID", "gene_name", "for", "rev"], ["GCW_02785", "clpB", "GAAAGATTACAGGCAAAAGGTG", "GCGCTCTTCCTCTTAGTACTGC"], ["GCW_03075", "dnaK", "TTACTCCAGAAGAAGTTTCTGC", "TAACTTCGAAAGTACCATCAGC"], ["GCW_02105", "lon", "TTGTTAAGATCTCACTTGGTGG", "ATCCCTTCAACATAGTTAGCAG"], ["GCW_02710", "groEL", "ACAACAGCTACAATCTTAACTC", "CCCTTGAACTCTAAACCATCAG"], ["GCW_00415", "dnaJ", "TCTTTAGCTTTGAAGGTGTGAG", "GTGAAAGTAGTTCATCGTCTGC"], ["GCW_00845", "dnaJ2", "CATGTAGTGATTGTAATGGCGA", "GGTTATCGCGTAGTTCAAACAC"], ["GCW_01610", "dnaJ4", "CCCGATGTTAATAAAGCTCCTG", "TCAATCTTACGACTCATCTCAG"], ["GCW_01620", "dnaJ5", "AGCTGAGTTTCAGATTGAAGAC", "TAAGCTGATCTAACATCATCAC"], ["GCW_01900", "dnaJ6", "GCGTATGAAGTTCTATCTAACCC", "TTAGCTTGATTTGCACTAGCAC"], ["GCW_04075", "dnaJ7", "AGTTAAGAGACTAATTAATCGACCAG", "CAACATTACCCTTACCAAAGAACTC"], ["GCW_01905", "grpE", "TTAGAGTTTGCTTCACTTGACC", "GTTTGAGGTTGTTCTTGTTCAC"], ["GCW_02005", "hrcA", "AATGATCGGTTAGTTGATACCC", "TTCAATCCCAATATCTTGACCA"], ["GCW_02100", "tig", "GAAAACCCAGAAGTTAGCGTAG", "CTCTAATTCGTAGTTTTTCGCC"], ["GCW_03080", "GCW_03080", "CAGATGCAATTACGGTTGTAGG", "TGATTTACGTATTCCAAACGCT"], ["GCW_02930", "GCW_02930", "GCAAAGTTACTGTAACACCAGG", "CGGCATTAACCATTATTTCACC"], ["GCW_00085", "GCW_00085", "CCAATATAATAGCGAAATGGCTG", "GTTAATTAAAGCCACTTCAGCG"], ["GCW_01140", "dps", "AACTTTCACTGAAATATCAAAGGTG", "TTTCATCTAAGATTGGTTGAACACG"], ["GCW_01335", "16S", "AAGTAACGACTAACTATGTGCC", "TAGGGTATCTAATCCTATTTGCTCC"], ["GCW_00395", "23S", "AGAAATACGTAGTCGATGGAAG", "GAGTTCCTTAGCTATAGTTCACTC"], ["GCW_02860", "eno", "GCGATCTTAGCAGTATCAATGG", "ACCTTCATCACCTTTGTTAGTA"], ["GCW_01780", "gapd", "ACGACTTAACTGATGCTAAGAC", "TGGTTCACGTTGTAAACTACAG"], ["GCW_03290", "tpiA", "TATTCGTACATTTGGCTTTGGC", "CTGATCTTTAAGTACAGCTTTGGTC"], ["GCW_01315", "tuf", "TCAAAATCGTCACTATGCACAC", "TCTGATTACTGGAGTGTTATCACC"], ["GCW_00475", "tsf", "AGTTAGCTGATCAAAAAGCAAC", "TTAACAATAACTCCAATGCGGC"], ["GCW_01635", "osmC", "AGCTAAAGTTGGTAGAGAAGGTC", "ATTCTTTAGCCTTAGCTTCTGG"], ["GCW_03005", "GCW_03005", "ATTCATCAGCAACTAAAGTACC", "TCATCAATTACGATTCTTCCAG"], ["GCW_00065", "glpF", "CAGCTAAAAGAATCATAGTGCC", "GTGGTGTGGTTATTAGTATCCAAG"], ["GCW_00075", "glpO", "GATGAATTGCTACTGAAGAGGTG", "ATTCATGGTGGTTTTGATCCTG"], ["GCW_90066", "glpK", "CTCGTTGAGATCACAAACTAGG", "TCTCAGGGACTAAGATTCGTTG"], ["GCW_01615", "gpsA", "TAATGTAGCTAAGGGAATGGACG", "TGTTCAAAAACAATCCCAGTCC"], ["GCW_02750", "acoA", "GTCTTCTGTGTAAACAACAACC", "CGATTGGATCTGATTTCTTAGCTTC"], ["GCW_02745", "acoB", "CTAAAGCTTTAATTCCACCACCC", "GTATTATACGGTCAAGACGCTG"], ["GCW_02740", "aceF", "TAAACCGATCTTCTTAGAGCGAG", "TACCGTAAGCAAGTTAAGGATG"], ["GCW_00390", "ldh", "CGATTACTGCTTCAATTCCAAC", "CTTCAACAGAGTCAGAATTAACACC"], ["GCW_02760", "ackA", "GAAGCACCATTTCCTAAGTGAC", "AGATCTATGAATTAGCCAAGCTC"], ["GCW_01785", "pgk", "CTAAAAACAGTCCAGAACTAGG", "TAAAGGTATTAACCATTCCCCC"], ["GCW_03700", "fba", "GACCATGGTACTTATGAAGGTG", "AAGTAGGGGGATAAATTCCGTG"], ["GCW_03575", "pgi", "CCAGAAGTAAAGATAACCAAAGCC", "ATTATTCCCAACATACTCCGTG"], ["GCW_02725", "pfkA", "GTGGTGATGGTTCATATCAAGG", "AGATCTACGATCTCTTGGGTTG"], ["GCW_03285", "gpmI", "GAGATCACTATTCAAGACAATGACAG", "ACACCACCATCAAAAAAGAAGG"], ["GCW_02720", "pykF", "CCTTATTATGAAGTACCTTACTGGG", "TCTGTCATTGGGAAATAGTGAG"], ["GCW_00160", "tktA1", "AGAATACAAACAAAGCTCACGG", "CACCTTCCCAAATAAATTACGG"], ["GCW_03235", "tktA2", "AGATTACTGAAACGATCCTTGC", "AAAGTTATCGATCTGATCTCGC"], ["GCW_00795", "rpiB", "ATATTCGTAGCTGATCATACAGG", "CAGTTATCATGTTGAATCGCAAG"], ["GCW_03495", "eutD", "GAAGTTGATGGTGAAGTATGTGG", "AACAGATTCACCTACACCTGAG"], ["GCW_03255", "prsA", "CAGCATTTATTCTTCACTTCACC", "CAGATTTACTAACCAAAGCAGG"], ["GCW_02735", "lpd", "AACTTGATCATTAACTACCCGAC", "CAATCATTAGTTGTGATCGGTG"], ["GCW_03295", "cpsG", "ATCTTTACTGGTCAACATGGAG", "GTAATAAGCAAAGATGATCCCC"], ["GCW_02755", "GCW_02755", "AATACTGTGGTGGAATTGAAGG", "TCAGTGTCAACTAAGTATCCCA"], ["GCW_02490", "GCW_02490", "GAATCTAAGCAATCAGCATACGG", "GAAATCACCTACATAATACGGCTTG"], ["GCW_02495", "GCW_02495", "CGTGAGATAAAATTGAAGGTGC", "TGTATAGGTGAGTGTCATCTGG"], ["GCW_01270", "hatA", "ATGAGAACAGAATGTGAGATGG", "GGTTTGTACCGATTTCTCTTCC"], ["GCW_03695", "rpoE", "GGCTTCATTAATTGATAAGGCT", "CCTTCATTGCTAATTTCAGGAGA"], ["GCW_01075", "spoT", "TTATCATCTTCAGTAACCGCAC", "GTGAAATGACATTCTTCTTGAGG"], ["GCW_02645", "GCW_02645", "TATGACCAAAATAAGGAAGTTGCC", "CTTAGAATCTGGTAACAAGTGGAAG"], ["GCW_02635", "GCW_02635", "CAAGAGGTTAAAAGTGAGATCTGTG", "GCTGTTGTTCTTCTAGTTCGTG"], ["GCW_00440", "GCW_00440", "GTACAACCGATTTGATTCCAAG", "AGTTCTTTTACGATATCACAGATCC"], ["GCW_04025", "hprK", "AGAAGTATATGGTGAAGGGGTTC", "GTTCGTTCGAAATTATAAGGTTGG"], ["GCW_03690", "GCW_03690", "GATTAAGCTGGTTAAACGATCTCC", "GTAACTTCTGAATCCCTTCAACC"], ["GCW_03310", "deoC2", "AAGTTTATGAAGCCAAAACCTC", "CTTATTTTGACTGGCTTGTTGC"], ["GCW_03745", "manA", "TTCTACCCCATTTTGAATACCG", "CTAGTGAGTTAAACTGTTTGGC"], ["GCW_03735", "fruA", "TTCCAAACCACAATCAAACCAG", "TTAATGTGAATGCGACTACACC"], ["GCW_00765", "ptsG1", "TGACGAAAATGGACAAAGAGTG", "ATAGATTGGATTAGTGAAGGGTGG"], ["GCW_03100", "ptsG2", "CCTTTGGTATTCTAAGACTAGTAGC", "GGTTAATCTGTTCAGATAAACTGC"], ["GCW_04065", "gyrA", "ATGATGCTTCAGAACAAGAACC", "CAATCTCAGATTTAGCCCGAAC"], ["GCW_04070", "gyrB", "AATAACATTCACACCAACCAAGG", "TAATCTTAGCAGCTTCTTCTGGA"], ["GCW_02325", "parC", "AAACAACCCTAATCCCAAACC", "CTTAAACTAATGCCAGGACCA"], ["GCW_02330", "parE", "CATGACTTCCACCTTCAGAG", "CATTTATTGCCAAAGACGGGA"], ["GCW_03410", "ruvA", "TGCTTCAATCACGATCTCTG", "GCACTGTTAACGATCAATGG"], ["GCW_03405", "ruvB", "TTGTGGGTGATAACGAATGG", "AGCCAGAATAAAGCATTAGACC"], ["GCW_03920", "ligA", "CTTAGGGATGATCTCAGCAG", "GTTACACCTCTAAGTTTCCCA"], ["GCW_00470", "uvrA", "AAACCCTGCTTCACTTACTG", "TTTCCACTACCAGAAACTCC"], ["GCW_00205", "uvrB", "TGTGTTGTCGGAATTAACCT", "ATCGCTTTAGTCATCTCATCAG"], ["GCW_02010", "uvrC", "TATGAAGTGATCTATCGCAGGT", "AGTGACGATCTTATCTGTTTGG"], ["GCW_92149", "uvrD", "GTGTTGTAAGTTATGGTCCGA", "CAGTGGTTTGACGATCATAGG"], ["GCW_02695", "recA", "TGGTATGAGAATCAACTACCTG", "GTAATCCCGAGGTTACAACTG"], ["GCW_01370", "mutM", "GAACGTCATGTGTTAGTACGA", "GCATAAATATTACCGATCCCAG"], ["GCW_03930", "msrA", "AAAGCCGCTACGATACTGTG", "TTATGCCAACTACAAACCAG"], ["GCW_02085", "nfo", "ATTATGTTGTTCACGCTCCT", "ATCAGCCATTGTTTCAAGAC"], ["GCW_00810", "hup1", "AGGCGGAATTCTAGTTTGTG", "ATTATCGCTGAATGTACTGGAG"], ["GCW_02335", "hup2", "ATTTGTGCGAATCTACTGCA", "AATGGCAGACGAAACTAACC"], ["GCW_03435", "ung", "TGATTAATTCTTCCCAACCCAG", "GTAATCATTGGTCAAGATCCGT"], ["GCW_03245", "umuC", "CCAAGTCTAATGGTTCTATCGT", "ATCGCTTGCAGATATCTCAC"], ["GCW_00770", "putA", "CAAAAGCAGGTTATGAATATCGC", "CTTTGATAATGGAGTGTTTAGGG"], ["GCW_02665", "potD", "CAACTGCTTTATTAAACTCTGACTC", "CATTAACCCCTTCAAGACCAAC"], ["GCW_03110", "spxA", "TCATGTATTGGCTGTACGAGAG", "CCATCAATCTTTTAGGAATCCCTG"], ["GCW_93946", "GCW_93946", "GAATGTCTTCGTGTTAAGTGTC", "AAAGCTAATGGGTTGATTGCTC"], ["GCW_02245", "mraW", "TCGAGTTATCAACTAGATCGAG", "GGAAATATCTTCTTGCAGGATG"], ["GCW_03090", "mscL", "AACGTCATCTTAGTTTCAGCAC", "CTTCAACACTTTGAGGTTCTGG"], ["GCW_03085", "GCW_03085", "ATTATCTGTGTCCTTTCATCCG", "CACTTACTTGAGCTAAGAAAGCAG"], ["GCW_93751", "GCW_93751", "CAATAGTTTCAGGAAGACACGG", "ACAGCATCACCATTATTTCCAG"], ["GCW_02300", "GCW_02300", "TAAGTCTTCAGTTTGCTTCACG", "TACTCTTCTAGTTGCTAGTTGTCC"], ["GCW_92301", "GCW_92301", "TATCAAAGCCTTTCTAGCAACG", "CACTATAAGTAGGTTTAGCTCAGG"], ["GCW_01560", "GCW_01560", "AATCTAATCCAGGGACAGTTTC", "GTGGCTACTAGAACATCATATCTAGG"]], "row_count": 95, "column_count": 4, "numeric_cells": 113, "header_rows": 1, "locator": "section[13]/table-wrap[1]#t0010"}}], "gaps": ["asset:data:geo:GSE85777 not downloaded", "asset:data:geo:GSE85777 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "correlation_analysis", "specific": "spearman", "label": "Correlation analysis", "dsl_operations": ["spearman_rho"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Spearman correlation coefficient between biological repeats ranges between 0.93 and 1.00."}}], "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": ["spearman_rho"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: spearman."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis 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