Bulk-add deep research files

pyproject.toml

@@ -74,6 +74,7 @@ skip = [
   "project/*",
   "src/dismech/datamodel/dismech_pydantic.py",
   "src/dismech/datamodel/dismech.py",
+  "research/*",
 ]
 
 # Reminder: words have to be lowercased for the ignore-words-list

research/2-Methylbutyryl-CoA_Dehydrogenase_Deficiency-deep-research-falcon.md.citations.md

@@ -0,0 +1,97 @@
+# Citations for Research Query
+
+**Query:** # Disease Pathophysiology Research Template
+
+## Target Disease
+- **Disease Name:** 2-Methylbutyryl-CoA Dehydrogenase Deficiency
+- **MONDO ID:**  (if available)
+- **Category:** Genetic
+
+## Research Objectives
+
+Please provide a comprehensive research report on the pathophysiology of **2-Methylbutyryl-CoA Dehydrogenase Deficiency**.
+Focus on the molecular and cellular mechanisms underlying disease progression.
+
+### Required Information
+
+#### 1. Core Pathophysiology
+- What are the primary pathophysiological mechanisms?
+- What molecular pathways are dysregulated?
+- What cellular processes are affected?
+
+#### 2. Key Molecular Players
+- **Genes/Proteins**: Which genes are causally involved or implicated?
+- **Chemical Entities**: What metabolites, drugs, or small molecules are relevant?
+- **Cell Types**: Which cell types are primarily affected?
+- **Anatomical Locations**: Which tissues/organs are involved?
+
+#### 3. Biological Processes (for GO annotation)
+- What biological processes (GO terms) are disrupted?
+- Consider: signaling pathways, metabolic processes, cellular responses, transport, etc.
+
+#### 4. Cellular Components
+- Where in the cell do key processes occur?
+- Consider: organelles, membrane compartments, extracellular space, etc.
+
+#### 5. Disease Progression
+- What is the sequence of events from initial trigger to clinical manifestation?
+- Are there distinct stages or phases?
+
+#### 6. Phenotypic Manifestations
+- What are the key clinical phenotypes?
+- How do they relate to the underlying mechanisms?
+
+### Citation Requirements
+
+- Cite primary literature (PMID preferred) for all mechanistic claims
+- Prioritize recent reviews and landmark papers
+- Include direct quotes where possible to support key statements
+
+### Output Format
+
+Structure your response as a narrative that could be used to populate a disease knowledge base entry with:
+- Pathophysiology description
+- Gene/protein annotations with ontology terms (HGNC, GO)
+- Phenotype associations (HP terms)
+- Cell type involvement (CL terms)
+- Anatomical locations (UBERON terms)
+- Chemical entities (CHEBI terms)
+- Evidence items with PMIDs
+
+**Provider:** falcon
+**Generated:** 2026-02-23T23:38:51.539350
+
+1. porta2019clinicalbiochemicaland pages 1-2
+2. calcar2013prevalenceandmutation pages 1-3
+3. jaffar2010characterizationofnew pages 5-7
+4. jaffar2010characterizationofnew pages 1-2
+5. korman2006inbornerrorsof pages 8-9
+6. wanders2015branchedchainamino pages 10-12
+7. jaffar2010characterizationofnew pages 11-14
+8. lin2019biochemicalclinicaland pages 1-2
+9. calcar2013prevalenceandmutation pages 3-4
+10. calcar2013prevalenceandmutation pages 4-6
+11. matern2003prospectivediagnosisof pages 5-7
+12. jaffar2010characterizationofnew pages 2-4
+13. porta2019clinicalbiochemicaland pages 3-5
+14. matern2003prospectivediagnosisof pages 2-4
+15. nasri2026identificationofa pages 1-2
+16. porta2019clinicalbiochemicaland pages 2-3
+17. porta2019clinicalbiochemicaland pages 6-7
+18. https://doi.org/10.3389/fgene.2024.1387423
+19. https://doi.org/10.1002/jimd.12642
+20. https://doi.org/10.1016/j.ymgme.2013.03.021
+21. https://doi.org/10.1515/jpem-2018-0311
+22. https://doi.org/10.1373/clinchem.2004.043265
+23. https://doi.org/10.1542/peds.112.1.74
+24. https://doi.org/10.1002/jimd.12642,
+25. https://doi.org/10.3389/fgene.2024.1387423,
+26. https://doi.org/10.1515/jpem-2018-0311,
+27. https://doi.org/10.1016/j.ymgme.2013.03.021,
+28. https://doi.org/10.3389/fgene.2019.00802,
+29. https://doi.org/10.1016/j.ymgme.2010.04.014,
+30. https://doi.org/10.1373/clinchem.2004.043265,
+31. https://doi.org/10.1016/j.ymgme.2006.07.010,
+32. https://doi.org/10.1007/978-1-4939-1923-9\_11,
+33. https://doi.org/10.1542/peds.112.1.74,
+34. https://doi.org/10.1186/s13023-025-04163-8,

research/22q11.2_Deletion_Syndrome-deep-research-cyberian-codex.md

@@ -0,0 +1,46 @@
+---
+provider: cyberian-codex
+model: codex-local-synthesis
+cached: true
+start_time: '2026-02-17T08:45:14Z'
+end_time: '2026-02-17T08:45:14Z'
+duration_seconds: 0.0
+template_file: codex_supplement_local
+template_variables:
+  disease_name: 22q11.2 Deletion Syndrome
+  category: Genetic
+citation_count: 10
+source_providers:
+- cyberian-codex
+- perplexity
+
+## Question
+
+        Codex secondary synthesis for disorder curation.
+
+        ## Output
+
+        ### Disorder
+        - Name: 22q11.2 Deletion Syndrome
+        - Category: Genetic
+        - Existing deep-research providers: cyberian-codex, perplexity
+        - Existing evidence reference count in YAML: 26
+
+        ### Key Pathophysiology Nodes
+        - TBX1 haploinsufficiency and pharyngeal arch development
+- Cardiac neural crest migration defect
+- Thymic hypoplasia and T-cell immunodeficiency
+- Parathyroid hypoplasia and hypocalcemia
+- Deep research literature mapping
+
+        ### Citation Inventory (for evidence mapping)
+        - DOI:10.1002/pd.6566
+- DOI:10.1016/s0022-5347(05)64215-2
+- DOI:10.1073/pnas.0905696106
+- DOI:10.3389/fendo.2023.1209577
+- DOI:10.3389/fpsyg.2014.00566
+- PMID:18769474
+- PMID:20664180
+- PMID:22318985
+- PMID:25452572
+- PMID:9708481

research/22q11.2_Deletion_Syndrome-deep-research-cyberian-codex.md.citations.md

@@ -0,0 +1,16 @@
+# Citations for Research Query
+
+**Query:** Codex secondary synthesis for 22q11.2 Deletion Syndrome
+**Provider:** cyberian-codex
+**Generated:** 2026-02-17T08:45:14Z
+
+1. DOI:10.1002/pd.6566
+2. DOI:10.1016/s0022-5347(05)64215-2
+3. DOI:10.1073/pnas.0905696106
+4. DOI:10.3389/fendo.2023.1209577
+5. DOI:10.3389/fpsyg.2014.00566
+6. PMID:18769474
+7. PMID:20664180
+8. PMID:22318985
+9. PMID:25452572
+10. PMID:9708481