DMSO Solubility Assessment for Fragment-Based Screening.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34203441", "kind": "science-record", "revision": 8, "content_hash": "sha256:cbfa56baae10efe649b81c72b0642f281db7bbf55d84f72afe1b8f45bab9abe7", "created_at": "2026-11-01T15:41:41Z", "updated_at": "2026-11-01T22:46:58Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "DMSO Solubility Assessment for Fragment-Based Screening.", "doi": "10.3390/molecules26133950", "pmid": "34203441", "authors": ["Shamkhal Baybekov", "Gilles Marcou", "Pascal Ramos", "Olivier Saurel", "Jean-Luc Galzi", "Alexandre Varnek"], "journal": "Molecules (Basel, Switzerland)", "year": 2021, "abstract": "In this paper, we report comprehensive experimental and chemoinformatics analyses of the solubility of small organic molecules (\"fragments\") in dimethyl sulfoxide (DMSO) in the context of their ability to be tested in screening experiments. Here, DMSO solubility of 939 fragments has been measured experimentally using an NMR technique. A Support Vector Classification model was built on the obtained data using the ISIDA fragment descriptors. The analysis revealed 34 outliers: experimental issues were retrospectively identified for 28 of them. The updated model performs well in 5-fold cross-validation (balanced accuracy = 0.78). The datasets are available on the Zenodo platform (DOI:10.5281/zenodo.4767511) and the model is available on the website of the Laboratory of Chemoinformatics.", "claims": [{"id": "claim-data-access", "statement": "The data presented in this study are available on the Zenodo platform (DOI:10.5281/zenodo.4767511) and in Supplementary Materials.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34203441", "locator": "sections[23] \"notes\" paragraph 1", "quote": "The data presented in this study are available on the Zenodo platform (DOI:10.5281/zenodo.4767511) and in Supplementary Materials."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:34203441"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": {"cross_validation_folds": "sification evaluated by 5-fold cross-validation"}, "inputs": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34203441", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/molecules26133950", "sha256": "sha256:0b4de80429e6c05c5054766eed2aca43ede7720e904cbb9752421848eac4a0d2", "bytes": 22195, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/molecules26133950", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8271413", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}], "gaps": []}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "machine_learning", "specific": "support_vector_machine", "label": "Machine learning", "dsl_operations": ["train_classifier", "cross_validate", "roc_auc"], "missing_operations": [], "expressible": true, "parameters": {"cross_validation_folds": "sification evaluated by 5-fold cross-validation"}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 1.0, "band": "reordered", "quote": "“Classification models were built using the Support Vector Machine (SVM) machine learning (ML) algorithm.” “Optimization was performed to maximize 5-fold cross-validation (5-CV) balanced accuracy (BA).”"}}], "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": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["train_classifier", "cross_validate", "roc_auc"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: support_vector_machine."}, "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": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": ["The data presented in this study are available on the Zenodo platform (DOI:10.5281/zenodo.4767511) and in Supplementary Materials."], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": ["train_classifier", "cross_validate", "roc_auc"], "assets": ["source:pmid:34203441"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T19:39:30Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 17012, "completion_tokens": 1443, "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:34203441", "type": "paper", "label": "pmid:34203441"}, {"id": "source:pmid:34203441", "type": "manuscript", "label": "PMID 34203441 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34203441", "type": "paper", "label": "pmid:34203441"}, {"id": "source:pmid:34203441", "type": "manuscript", "label": "PMID 34203441 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34203441", "type": "extraction", "used": ["source:pmid:34203441"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "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:34203441", "parent_hash": "sha256:a56f028698b32ff9f7d7ed1ae9451faf440697133bbe411f70388adfce4d1b3d", "fork_of": null, "generation": 7}, "gaps": ["execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "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": 0.77, "evidence": ["ERETIC2 [16] (Electronic Reference to access in vivo Concentrations) software based on the PULCON"], "order_basis": "paper_text_order:2183", "id": "assay:1"}, {"role": "analysis", "definition_id": "machine_learning", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["train_classifier", "cross_validate", "roc_auc"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["“Classification models were built using the Support Vector Machine (SVM) machine learning (ML) algorithm.” “Optimization was performed to maximize 5-fold cross-validation (5-CV) balanced accuracy (BA).”"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}