Merge branch 'main' into add_tarp

Author: dragon-ai-agent

cache/enums/phenotypeterm_939f99dde0f5.csv

@@ -319,3 +319,6 @@ HP:0011024
 HP:0000085
 HP:0000565
 HP:0000448
+HP:0100726
+HP:0020102
+HP:0005401

cache/enums/treatmentactionterm_02908ba82bf0.csv

@@ -38,3 +38,5 @@ MAXO:0000451
 MAXO:0000616
 MAXO:0000930
 MAXO:0001351
+MAXO:0000609
+MAXO:0000594

cache/hp/terms.csv

@@ -1,41 +1,43 @@
 curie,label,retrieved_at
-MAXO:0000011,physical therapy,2025-12-15T10:56:23.744510
-MAXO:0000079,genetic counseling,2025-12-15T10:56:23.744520
-MAXO:0000004,surgical procedure,2025-12-15T10:56:23.744523
-MAXO:0000088,dietary intervention,2025-12-15T10:56:23.744526
-MAXO:0001001,gene therapy,2025-12-15T10:56:23.744528
-MAXO:0000058,pharmacotherapy,2025-12-15T10:56:23.744860
-MAXO:0010039,organ transplantation,2025-12-15T10:56:23.744867
-MAXO:0000950,supportive care,2025-12-15T10:56:23.744870
-MAXO:0000573,antiretroviral therapy,2025-12-15T10:56:23.744873
-MAXO:0000017,preventative therapy,2025-12-15T10:56:23.744875
-MAXO:0000283,hormone modifying therapy,2025-12-15T10:56:23.744877
-MAXO:0000106,nutritional supplementation,2025-12-15T10:56:23.744880
-MAXO:0000077,behavioral counseling,2025-12-15T10:56:23.744882
-MAXO:0000312,respiratory tract agent therapy,2025-12-15T10:56:23.744885
-MAXO:0000015,biologic therapy,2025-12-15T10:56:23.744887
-MAXO:0001017,vaccination,2025-12-15T10:56:23.744890
-MAXO:0000458,hydrotherapy,2025-12-15T10:56:23.744892
-MAXO:0000503,artificial respiration,2025-12-15T10:56:23.744894
-MAXO:0000756,blood transfusion,2025-12-15T10:56:23.744897
-MAXO:0000168,antiviral agent therapy,2025-12-15T10:56:23.744899
-MAXO:0000267,gastrointestinal agent therapy,2025-12-15T10:56:23.744901
-MAXO:0001014,medical action avoidance,2025-12-15T10:56:23.744904
-MAXO:0000186,beta adrenergic agent therapy,2025-12-15T10:56:23.744906
-MAXO:0000181,cardiovascular agent therapy,2025-12-15T10:56:23.744908
-MAXO:0000652,ACE inhibitor therapy,2025-12-15T10:56:23.744911
-MAXO:0000434,calcium channel blocking agent therapy,2025-12-15T10:56:23.744913
-MAXO:0000014,radiation therapy,2025-12-15T10:56:23.744916
-MAXO:0000647,chemotherapy,2025-12-15T10:56:23.744918
-MAXO:0000601,renal dialysis,2025-12-15T10:56:23.744920
-MAXO:0000259,insulin treatment,2025-12-15T10:56:23.744922
-MAXO:0010203,echocardiography,2025-12-15T10:56:23.744925
-MAXO:0035118,cardiac catheterization,2025-12-15T10:56:23.744927
-MAXO:0000473,medical device implantation,2025-12-15T10:56:23.744930
-MAXO:0000010,cognitive and behavioral intervention,2025-12-15T10:56:23.744932
-MAXO:0000518,extubation procedure,2025-12-15T10:56:23.744935
-MAXO:0000194,opioid analgesic agent therapy,2025-12-15T10:56:23.744937
-MAXO:0000451,implantation,2025-12-15T10:56:23.744939
-MAXO:0000616,oxygen saturation measurement,2025-12-15T10:56:23.744942
-MAXO:0000930,speech therapy,2025-12-15T10:56:23.744944
-MAXO:0001351,occupational therapy,2025-12-15T10:56:23.744946
+MAXO:0000011,physical therapy,2026-01-05T11:11:57.897277
+MAXO:0000079,genetic counseling,2026-01-05T11:11:57.897285
+MAXO:0000004,surgical procedure,2026-01-05T11:11:57.897288
+MAXO:0000088,dietary intervention,2026-01-05T11:11:57.897290
+MAXO:0001001,gene therapy,2026-01-05T11:11:57.897292
+MAXO:0000058,pharmacotherapy,2026-01-05T11:11:57.897294
+MAXO:0010039,organ transplantation,2026-01-05T11:11:57.897296
+MAXO:0000950,supportive care,2026-01-05T11:11:57.897298
+MAXO:0000573,antiretroviral therapy,2026-01-05T11:11:57.897300
+MAXO:0000017,preventative therapy,2026-01-05T11:11:57.897302
+MAXO:0000283,hormone modifying therapy,2026-01-05T11:11:57.897304
+MAXO:0000106,nutritional supplementation,2026-01-05T11:11:57.897306
+MAXO:0000077,behavioral counseling,2026-01-05T11:11:57.897308
+MAXO:0000312,respiratory tract agent therapy,2026-01-05T11:11:57.897310
+MAXO:0000015,biologic therapy,2026-01-05T11:11:57.897312
+MAXO:0001017,vaccination,2026-01-05T11:11:57.897314
+MAXO:0000458,hydrotherapy,2026-01-05T11:11:57.897316
+MAXO:0000503,artificial respiration,2026-01-05T11:11:57.897318
+MAXO:0000756,blood transfusion,2026-01-05T11:11:57.897320
+MAXO:0000168,antiviral agent therapy,2026-01-05T11:11:57.897322
+MAXO:0000267,gastrointestinal agent therapy,2026-01-05T11:11:57.897324
+MAXO:0001014,medical action avoidance,2026-01-05T11:11:57.897326
+MAXO:0000186,beta adrenergic agent therapy,2026-01-05T11:11:57.897330
+MAXO:0000181,cardiovascular agent therapy,2026-01-05T11:11:57.897332
+MAXO:0000652,ACE inhibitor therapy,2026-01-05T11:11:57.897334
+MAXO:0000434,calcium channel blocking agent therapy,2026-01-05T11:11:57.897336
+MAXO:0000014,radiation therapy,2026-01-05T11:11:57.897338
+MAXO:0000647,chemotherapy,2026-01-05T11:11:57.897340
+MAXO:0000601,renal dialysis,2026-01-05T11:11:57.897342
+MAXO:0000259,insulin treatment,2026-01-05T11:11:57.897344
+MAXO:0010203,echocardiography,2026-01-05T11:11:57.897345
+MAXO:0035118,cardiac catheterization,2026-01-05T11:11:57.897347
+MAXO:0000473,medical device implantation,2026-01-05T11:11:57.897349
+MAXO:0000010,cognitive and behavioral intervention,2026-01-05T11:11:57.897351
+MAXO:0000518,extubation procedure,2026-01-05T11:11:57.897353
+MAXO:0000194,opioid analgesic agent therapy,2026-01-05T11:11:57.897355
+MAXO:0000451,implantation,2026-01-05T11:11:57.897357
+MAXO:0000616,oxygen saturation measurement,2026-01-05T11:11:57.897359
+MAXO:0000930,speech therapy,2026-01-05T11:11:57.897361
+MAXO:0001351,occupational therapy,2026-01-05T11:11:57.897363
+MAXO:0000609,serology testing,2026-01-05T11:11:57.897365
+MAXO:0000594,clinical quantitative reverse transcription PCR testing,2026-01-05T11:11:57.897367

cache/maxo/terms.csv

@@ -249,6 +249,19 @@ pathophysiology:
     term:
       id: GO:0042110
       label: T cell activation
+  genes:
+  - preferred_term: CD4
+    term:
+      id: HGNC:1678
+      label: CD4
+  - preferred_term: CCR5
+    term:
+      id: HGNC:1606
+      label: CCR5
+  - preferred_term: CXCR4
+    term:
+      id: HGNC:2561
+      label: CXCR4
   locations:
   - preferred_term: lymph node
     term:
@@ -382,13 +395,57 @@ pathophysiology:
     term:
       id: CL:0000235
       label: macrophage
+  genes:
+  - preferred_term: SAMHD1
+    term:
+      id: HGNC:15925
+      label: SAMHD1
   locations:
   - preferred_term: brain
     term:
       id: UBERON:0000955
       label: brain
+  evidence:
+  - reference: PMID:37317962
+    supports: SUPPORT
+    snippet: These data demonstrate that MG harbor replication-competent HIV and serve as a persistent reservoir in the brain.
+    explanation: This study directly demonstrates that brain microglia harbor replication-competent HIV and serve as a persistent CNS reservoir.
+  - reference: PMID:25604237
+    supports: SUPPORT
+    snippet: Recent work suggests that the stage for HIV neuropathogenesis may be set with initial viral entry into the CNS, followed by initiation of pathogenetic processes including neuroinflammation and neurotoxicity, and establishment of local, compartmentalized HIV replication that may reflect a tissue reservoir for HIV.
+    explanation: This review describes early CNS invasion by HIV and the establishment of compartmentalized CNS reservoirs with associated neuroinflammation.
+- name: Host Restriction Factor Defense
+  description: Multiple host restriction factors inhibit HIV replication through distinct molecular mechanisms, but are counteracted by viral accessory proteins (Vif, Vpu, Nef).
+  genes:
+  - preferred_term: APOBEC3G
+    term:
+      id: HGNC:17357
+      label: APOBEC3G
+  - preferred_term: TRIM5
+    term:
+      id: HGNC:16276
+      label: TRIM5
+  - preferred_term: BST2
+    term:
+      id: HGNC:1119
+      label: BST2
+  - preferred_term: SERINC5
+    term:
+      id: HGNC:18825
+      label: SERINC5
+  biological_processes:
+  - preferred_term: defense response to virus
+    term:
+      id: GO:0051607
+      label: defense response to virus
 - name: AIDS-related Cancers
   description: Weakened immune surveillance increases risk of certain cancers.
+  biological_processes:
+  - preferred_term: immune response to tumor cell
+    term:
+      id: GO:0002418
+      label: immune response to tumor cell
+    modifier: DECREASED
   examples:
   - Kaposi Sarcoma
   evidence:
@@ -421,10 +478,10 @@ phenotypes:
   frequency: FREQUENT
   diagnostic: true
   phenotype_term:
-    preferred_term: Recurrent infections
+    preferred_term: Pneumocystis jirovecii pneumonia
     term:
-      id: HP:0002719
-      label: Recurrent infections
+      id: HP:0020102
+      label: Pneumocystis jirovecii pneumonia
   evidence:
   - reference: PMID:1979021
     supports: SUPPORT
@@ -462,10 +519,10 @@ phenotypes:
   name: Candidiasis
   frequency: FREQUENT
   phenotype_term:
-    preferred_term: Recurrent infections
+    preferred_term: Recurrent candida infections
     term:
-      id: HP:0002719
-      label: Recurrent infections
+      id: HP:0005401
+      label: Recurrent candida infections
   evidence:
   - reference: PMID:6496525
     supports: SUPPORT
@@ -503,6 +560,11 @@ phenotypes:
   name: Kaposi Sarcoma
   frequency: FREQUENT
   diagnostic: true
+  phenotype_term:
+    preferred_term: Kaposi's sarcoma
+    term:
+      id: HP:0100726
+      label: Kaposi's sarcoma
   evidence:
   - reference: PMID:2661499
     supports: SUPPORT
@@ -661,6 +723,11 @@ biochemical:
 diagnosis:
 - name: HIV Antibody Test
   presence: Positive
+  diagnosis_term:
+    preferred_term: serology testing
+    term:
+      id: MAXO:0000609
+      label: serology testing
   evidence:
   - reference: PMID:2672903
     supports: PARTIAL
@@ -693,6 +760,11 @@ diagnosis:
       these tests for diagnosing AIDS.
 - name: HIV Viral Load Test
   presence: Positive
+  diagnosis_term:
+    preferred_term: clinical quantitative reverse transcription PCR testing
+    term:
+      id: MAXO:0000594
+      label: clinical quantitative reverse transcription PCR testing
   evidence:
   - reference: PMID:29641941
     supports: SUPPORT