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metadata/source_triage_log.csv

@@ -135,7 +135,7 @@ decision,judging_use,license_or_access,module_added,phase2_fit,reason,source_id,
 ,supports rigor/transparency by documenting why each source was used or deferred,CC BY; generated variables only; do not reproduce source figures/tables/text,,,High-value modeling rigor source for PK/PD and preclinical-to-clinical translation of GalNAc-siRNAs.,SALIM_GALNAC_SIRNA_WB_PBPK_PD_2025,PBPK_PD_modeling_original_article,Whole-Body Physiologically Based Pharmacokinetic–Pharmacodynamic Modeling for Interspecies Translation and Mechanistic Characterization of Plasma and Tissue Disposition of GalNAc-siRNAs,include_supporting_module_or_context
 ,supports rigor/transparency by documenting why each source was used or deferred,CC BY; not encoded in row-level synthetic tables,,,Deferred from row-level generation to keep source-specific generated rows focused on primary studies and modeling papers.,VAILLANT_HBV_OLIGONUCLEOTIDE_THERAPIES_REVIEW_2022,review_open_access,"Oligonucleotide-Based Therapies for Chronic HBV Infection: A Primer on Biochemistry, Mechanisms and Antiviral Effects",deferred
 ,supports rigor/transparency by documenting why each source was used or deferred,CC BY; not encoded in row-level synthetic tables,,,"Potentially useful later for an optional notebook method, but deferred from the core generator to avoid diluting OligoTox focus.",LACALAMITA_PID_MICROARRAY_HIGH_ORDER_PATTERNS_2025,bioinformatics_methods_original_article,Unveiling complex patterns: An information-theoretic approach to high-order behaviors in microarray data,deferred
-,supports rigor/transparency by documenting why each source was used or deferred,open access CC BY; generated variables only; do not reproduce source figures/tables/text,,,Final supplemental high-priority paper; encoded in the supplemental literature integration phase off-target RISC mechanism table and used to refine seed/off-target hepatotoxicity logic.,AGARWAL_GALNAC_SIRNA_OFFTARGET_2025,mechanistic_original_article_open_access,Mechanistic Insights into Hybridization-Based Off-Target Activity of GalNAc-siRNA Conjugates,include_full_or_direct_module
+,supports rigor/transparency by documenting why each source was used or deferred,open access CC BY; generated variables only; do not reproduce source figures/tables/text,,,Final supplemental high-priority paper; encoded in off-target RISC mechanism table and used to refine seed/off-target hepatotoxicity logic.,AGARWAL_GALNAC_SIRNA_OFFTARGET_2025,mechanistic_original_article_open_access,Mechanistic Insights into Hybridization-Based Off-Target Activity of GalNAc-siRNA Conjugates,include_full_or_direct_module
 ,supports rigor/transparency by documenting why each source was used or deferred,open access CC BY-NC; generated variables only; do not reproduce source figures/tables/text,,,"Used to anchor chemistry/delivery categories, approved landscape context, and data dictionary terminology.",EGLI_MANOHARAN_APPROVED_OLIGO_CHEMISTRY_2023,critical_review_open_access,"Chemistry, Structure and Function of Approved Oligonucleotide Therapeutics",include_context_metadata
 ,supports rigor/transparency by documenting why each source was used or deferred,open access CC BY-NC-ND; generated variables only; do not reproduce source figures/tables/text,,,Adds original PNPLA3 ASO clinical target-engagement evidence beyond the PNPLA3 review already represented.,ARMISEN_AZD2693_PNPLA3_ASO_MASH_2025,phase1_clinical_and_preclinical_original_article_open_access,"AZD2693, a PNPLA3 antisense oligonucleotide, for the treatment of MASH in 148M homozygous participants: Two randomized phase I trials",include_full_or_direct_module
 ,supports rigor/transparency by documenting why each source was used or deferred,freely downloadable PDF; generated variables only; do not reproduce source figures/tables/text,,,Used to encode broad platform distinctions between single-stranded ASOs and double-stranded siRNAs.,CROOKE_RNA_TARGETED_THERAPEUTICS_2018,perspective_article,RNA-Targeted Therapeutics,include_supporting_module_or_context

metadata/sources.csv

@@ -135,7 +135,7 @@ TANG_CUPROPTOSIS_WILSON_DISEASE_2025,Uncovering the Critical Role of Cuproptosis
 SALIM_GALNAC_SIRNA_WB_PBPK_PD_2025,Whole-Body Physiologically Based Pharmacokinetic–Pharmacodynamic Modeling for Interspecies Translation and Mechanistic Characterization of Plasma and Tissue Disposition of GalNAc-siRNAs,2025,PBPK_PD_modeling_original_article,10.3390/pharmaceutics17091154,CC BY; generated variables only; do not reproduce source figures/tables/text,direct_GalNAc_siRNA_PK_PD_species_translation_and_off_target_distribution_module,GalNAc-siRNA|PBPK|PK-PD|ASGPR|RISC|mouse|monkey|human|off-target organs|liver exposure,"adds mechanistic GalNAc-siRNA disposition, cross-species scaling, liver specificity, off-target organ accumulation, and clinical PK-PD translation context",yes_supporting_module,High-value modeling rigor source for PK/PD and preclinical-to-clinical translation of GalNAc-siRNAs.,source_metadata,no,CC BY 4.0,,,,,,,,,,,,,
 VAILLANT_HBV_OLIGONUCLEOTIDE_THERAPIES_REVIEW_2022,"Oligonucleotide-Based Therapies for Chronic HBV Infection: A Primer on Biochemistry, Mechanisms and Antiviral Effects",2022,review_open_access,10.3390/v14092052,CC BY; not encoded in row-level synthetic tables,deferred_review_background_for_HBV_oligonucleotide_mechanisms,ASO|siRNA|NAP|HBV|immunostimulation|GalNAc|LNP|liver uptake|off-target effects,"useful background on oligonucleotide pharmacology and HBV therapeutic classes, but review-only",deferred,Deferred from row-level generation to keep source-specific generated rows focused on primary studies and modeling papers.,source_metadata,no,CC BY 4.0,,,,,,,,,,,,,
 LACALAMITA_PID_MICROARRAY_HIGH_ORDER_PATTERNS_2025,Unveiling complex patterns: An information-theoretic approach to high-order behaviors in microarray data,2025,bioinformatics_methods_original_article,10.1371/journal.pone.0336379,CC BY; not encoded in row-level synthetic tables,deferred_optional_notebook_method_context,microarray|HCC|partial information decomposition|synergy clusters|mutual information|gene expression,general high-order gene-expression methods; not therapeutic oligo toxicity or delivery evidence,deferred,"Potentially useful later for an optional notebook method, but deferred from the core generator to avoid diluting OligoTox focus.",source_metadata,no,CC BY 4.0,,,,,,,,,,,,,
-AGARWAL_GALNAC_SIRNA_OFFTARGET_2025,Mechanistic Insights into Hybridization-Based Off-Target Activity of GalNAc-siRNA Conjugates,2025,mechanistic_original_article_open_access,10.1089/nat.2024.0090,open access CC BY; generated variables only; do not reproduce source figures/tables/text,core_GalNAc_siRNA_RISC_AGO2_TNRC6_seed_offtarget_hepatotoxicity_module,GalNAc-siRNA|AGO2|AGO1|AGO4|TNRC6A|TNRC6B|TNRC6C|RISC|seed_offtarget|hepatotoxicity,direct mechanistic source for RISC-mediated hybridization-based off-target activity and GalNAc-siRNA hepatotoxicity; distinguishes AGO2 on-target requirement from AGO2/TNRC6 off-target toxicity roles,yes_core_module,Final supplemental high-priority paper; encoded in the supplemental literature integration phase off-target RISC mechanism table and used to refine seed/off-target hepatotoxicity logic.,source_metadata,no,CC BY 4.0,,,,,,,,,,,,,
+AGARWAL_GALNAC_SIRNA_OFFTARGET_2025,Mechanistic Insights into Hybridization-Based Off-Target Activity of GalNAc-siRNA Conjugates,2025,mechanistic_original_article_open_access,10.1089/nat.2024.0090,open access CC BY; generated variables only; do not reproduce source figures/tables/text,core_GalNAc_siRNA_RISC_AGO2_TNRC6_seed_offtarget_hepatotoxicity_module,GalNAc-siRNA|AGO2|AGO1|AGO4|TNRC6A|TNRC6B|TNRC6C|RISC|seed_offtarget|hepatotoxicity,direct mechanistic source for RISC-mediated hybridization-based off-target activity and GalNAc-siRNA hepatotoxicity; distinguishes AGO2 on-target requirement from AGO2/TNRC6 off-target toxicity roles,yes_core_module,Final supplemental high-priority paper; encoded in off-target RISC mechanism table and used to refine seed/off-target hepatotoxicity logic.,source_metadata,no,CC BY 4.0,,,,,,,,,,,,,
 EGLI_MANOHARAN_APPROVED_OLIGO_CHEMISTRY_2023,"Chemistry, Structure and Function of Approved Oligonucleotide Therapeutics",2023,critical_review_open_access,10.1093/nar/gkad067,open access CC BY-NC; generated variables only; do not reproduce source figures/tables/text,core_reference_approved_oligonucleotide_chemistry_delivery_landscape_module,ASO|SSO|siRNA|aptamer|phosphorothioate|2prime_F|2prime_OMe|2prime_MOE|PMO|LNP|GalNAc,"core chemistry and delivery reference for approved oligonucleotide therapeutics, chemical modifications, LNPs, and GalNAc hepatocyte targeting",yes_core_reference_module,"Used to anchor chemistry/delivery categories, approved landscape context, and data dictionary terminology.",source_metadata,no,CC BY 4.0,,,,,,,,,,,,,
 ARMISEN_AZD2693_PNPLA3_ASO_MASH_2025,"AZD2693, a PNPLA3 antisense oligonucleotide, for the treatment of MASH in 148M homozygous participants: Two randomized phase I trials",2025,phase1_clinical_and_preclinical_original_article_open_access,10.1016/j.jhep.2024.12.046,open access CC BY-NC-ND; generated variables only; do not reproduce source figures/tables/text,core_PNPLA3_GalNAc_ASO_precision_MASH_target_engagement_module,GalNAc-ASO|PNPLA3|MASH|148M_homozygous|liver_fat|hCRP|IL6|target_engagement|PK|PD,"direct precision hepatology source for liver-targeted ASO target engagement, MASH biomarkers, hepatic fat response, and safety/tolerability context",yes_core_module,Adds original PNPLA3 ASO clinical target-engagement evidence beyond the PNPLA3 review already represented.,source_metadata,no,CC BY 4.0,,,,,,,,,,,,,
 CROOKE_RNA_TARGETED_THERAPEUTICS_2018,RNA-Targeted Therapeutics,2018,perspective_article,10.1016/j.cmet.2018.03.004,freely downloadable PDF; generated variables only; do not reproduce source figures/tables/text,supporting_RNA_targeted_therapeutics_platform_mechanism_module,ASO|siRNA|Watson-Crick_hybridization|Ago2|RNase_H1|chemistry|delivery|structure_matters,"supporting platform source for ASO/siRNA structural, chemical, pharmacokinetic, and mechanism distinctions relevant to safety modeling",yes_supporting_platform_module,Used to encode broad platform distinctions between single-stranded ASOs and double-stranded siRNAs.,source_metadata,no,CC BY 4.0,,,,,,,,,,,,,