Add a bunch of test cases from @enockniyonkuru

src/ontogpt/evaluation/maxo/test_cases/maxo_case_12958596.yaml

@@ -0,0 +1,25 @@
+---
+input_text: >-
+  Activation-induced cytidine deaminase (AID) is a 'master molecule' in immunoglobulin (Ig) 
+  class-switch recombination (CSR) and somatic hypermutation (SHM) generation, AID deficiencies are 
+  associated with hyper-IgM phenotypes in humans and mice. We show here that recessive mutations of 
+  the gene encoding uracil-DNA glycosylase (UNG) are associated with profound impairment in CSR at a 
+  DNA precleavage step and with a partial disturbance of the SHM pattern in three patients with hyper-IgM 
+  syndrome. Together with the finding that nuclear UNG expression was induced in activated B cells, 
+  these data support a model of CSR and SHM in which AID deaminates cytosine into uracil in targeted DNA 
+  (immunoglobulin switch or variable regions), followed by uracil removal by UNG.
+
+named_entities:
+  - id: MONDO:0011971
+    label: Immunodeficiency With Hyper-igm, Type 5
+  - id: MAXO:0001480
+    label: immunoglobulin infusion therapy
+  - id: HP:0004315
+    label: Decreased circulating IgG level
+
+extracted_object:
+  action_to_disease:
+    - subject: MAXO:0001480
+      predicate: TREATS
+      object:
+        - MONDO:0011971

src/ontogpt/evaluation/maxo/test_cases/maxo_case_20301519.yaml

@@ -0,0 +1,50 @@
+---
+input_text: >-
+
+  APC-associated polyposis conditions include (classic or attenuated) familial adenomatous polyposis (FAP) and gastric adenocarcinoma 
+  and proximal polyposis of the stomach (GAPPS).
+
+  Resection of all colonic polyps larger than 5 mm found on colonic surveillance. There is an absolute indication for colectomy when 
+  CRC is diagnosed or suspected, or when there are significant symptoms (e.g., bleeding, obstruction). Relative indications for colectomy 
+  include presence of multiple adenomas larger than 10 mm that cannot be reasonably removed endoscopically, a significant increase in adenoma 
+  number between surveillance exams, presence of adenomas with high-grade dysplasia, or inability to adequately survey the colon (e.g., due to 
+  innumerable diminutive adenomas or limited access to or compliance with colonoscopy). Endoscopic or surgical removal of duodenal adenomas is 
+  considered if polyps exhibit villous change or severe dysplasia, exceed 1 cm in diameter, or exhibit advanced stage using Spigelman scoring system. 
+  Gastrectomy is considered if advanced gastric neoplasia is found on upper endoscopy. Osteomas may be removed for cosmetic reasons. 
+  Desmoid tumors may be surgically excised or treated with nonsteroidal anti-inflammatory drugs (NSAIDs), anti-estrogens, 
+  cytotoxic chemotherapy, and/or radiation if at advanced stage. Standard treatment when needed for adrenal masses and thyroid carcinoma. 
+  Several studies have shown that NSAIDs and erlotinib have caused regression of adenomas and decreased the polyp burden in individuals with FAP, 
+  though there are currently no FDA-approved chemopreventive agents for FAP, given an unclear effect on subsequent cancer risk.
+
+named_entities:
+  - id: MONDO:0021056
+    label: denomatous Polyposis Coli
+  - id: MAXO:0000014
+    label: radiation therapy
+  - id: HP:0100245
+    label: Desmoid tumors
+  - id: MAXO:0000646
+    label: cancer chemotherapy
+  - id: MAXO:0000635
+    label: anti-estrogen agent therapy
+  - id: MAXO:0000221
+    label: nonsteroidal anti-inflammatory agent therapy
+
+extracted_object:
+  action_to_symptom:
+    - subject: MAXO:0000014
+      predicate: TREATS
+      object:
+        - HP:0100245
+    - subject: MAXO:0000646
+      predicate: TREATS
+      object:
+        - HP:0100245
+    - subject: MAXO:0000635
+      predicate: TREATS
+      object:
+        - HP:0100245
+    - subject: MAXO:0000221
+      predicate: TREATS
+      object:
+        - HP:0100245

src/ontogpt/evaluation/maxo/test_cases/maxo_case_20301527.yaml

@@ -0,0 +1,36 @@
+---
+input_text: >-
+  "
+  Adult Refsum disease (ARD is associated with elevated plasma phytanic acid levels, late childhood-onset (or later) retinitis pigmentosa, 
+  and variable combinations of anosmia, polyneuropathy, deafness, ataxia, and ichthyosis.
+
+  Plasmapheresis or lipid apheresis to decrease phytanic acid levels is used only for acute arrhythmias or extreme weakness. 
+  Dietary restriction of phytanic acid intake helps resolve ichthyosis, sensory neuropathy, and ataxia. A high-calorie diet 
+  and avoidance of fasting prevent mobilization of phytanic acid stored in adipose tissue into the plasma. Hypercaloric parenteral 
+  infusions are required during periods of severe illness or postoperatively. Supportive treatment includes hydrating creams for
+  ichthyosis and drugs for cardiac arrhythmias and cardiomyopathy
+  "
+
+named_entities:
+  - id: MAXO:0010119
+    label: dietary phytanic acid intake avoidance
+  - id: HP:0010571
+    label: Elevated circulating phytanic acid concentration
+  - id: HP:0008064
+    label: Ichthyosis
+  - id: MONDO:0009958
+    label: Refsum Disease
+
+extracted_object:
+  action_to_disease:
+    - subject: MAXO:0010119
+      predicate: TREATS
+      object:
+        - MONDO:0009958
+
+  action_to_symptom:
+    - subject: MAXO:0010119
+      predicate: TREATS
+      object:
+        - HP:0008064
+        - HP:0010571

src/ontogpt/evaluation/maxo/test_cases/maxo_case_20301572.yaml

@@ -0,0 +1,31 @@
+---
+input_text: >-
+
+  "
+  Bloom syndrome (BSyn) is characterized by severe pre- and postnatal growth deficiency, immune abnormalities, sensitivity to sunlight, 
+  insulin resistance, and a high risk for many cancers that occur at an early age. 
+
+  Agents/circumstances to avoid: Sun exposure to the face and other exposed skin, particularly in infancy and early childhood,
+  should be avoided. Exposure to ionizing radiation should be minimized. Dose reductions and shortened courses of chemotherapy 
+  when needed to avoid significant side effects and toxicity (including secondary malignancies). Alkylating agents and radiation 
+  therapy are considered high risk and are avoided when possible in those with BSyn.
+  "
+
+named_entities:
+  - id: MONDO:0008876
+    label: Bloom Syndrome
+  - id: MAXO:0000054
+    label: radiation exposure avoidance
+  - id: MAXO:0000055
+    label: sunlight avoidance
+
+extracted_object:
+  action_to_disease:
+    - subject: MAXO:0000054
+      predicate: PREVENTS
+      object:
+        - MONDO:0008876
+    - subject: MAXO:0000055
+      predicate: PREVENTS
+      object:
+        - MONDO:0008876

src/ontogpt/evaluation/maxo/test_cases/maxo_case_20301765.yaml

@@ -0,0 +1,25 @@
+---
+input_text: >-
+  Von Willebrand disease (VWD), a congenital bleeding disorder caused by deficient or defective plasma von Willebrand factor (VWF), 
+  may only become apparent on hemostatic challenge, and bleeding history may become more apparent with increasing age.  
+  Affected individuals benefit from care in a comprehensive bleeding disorders program. 
+  The two main treatments are desmopressin (1-deamino-8-D-arginine vasopressin [DDAVP]) 
+  and clotting factor concentrates (recombinant and plasma-derived) containing both VWF 
+  and FVIII (VWF/FVIII concentrate). Indirect hemostatic treatments that can reduce symptoms 
+  include fibrinolytic inhibitors; hormones for menorrhagia are also beneficial. 
+  Individuals with VWD should receive prompt treatment for severe bleeding episodes. 
+  Pregnant women with VWD are at increased risk for bleeding complications at or following childbirth.
+named_entities:
+  - id: MAXO:0000446
+    label: desmopressin agent therapy
+  - id: HP:0012147
+    label: Reduced quantity of Von Willebrand factor
+  - id: MONDO:0008668
+    label: Von Willebrand Disease, Type 1
+
+extracted_object:
+  action_to_disease:
+    - subject: MAXO:0000446
+      predicate: TREATS
+      object:
+        - MONDO:0008668

src/ontogpt/evaluation/maxo/test_cases/maxo_case_2063868.yaml

@@ -0,0 +1,25 @@
+---
+input_text: >-
+  delta-Aminolevulinate dehydratase deficient porphyria, a recently recognized inborn error of heme biosynthesis, 
+  results from the markedly deficient activity of the heme biosynthetic enzyme, delta-aminolevulinate dehydratase (ALA-D). 
+  The four homozygotes described to date with this disorder have remarkably distinct phenotypes, ranging from a severely 
+  affected infant with failure to thrive to an essentially asymptomatic 68-year-old male. To investigate the molecular nature 
+  of the lesions causing the severe infantile-onset form, total RNA was isolated from cultured lymphoblasts of the affected homozygote, 
+  RNA was reverse-transcribed to cDNA, and the 990-bp ALA-D-coding region was amplified by the PCR. Heterozygosity for an RsaI RFLP within 
+  the ALA-dehydratase-coding region permitted identification of the paternal and maternal mutant alleles prior to sequencing. 
+
+  The maternal mutation (designated G133R), a G-to-A transition of nucleotide 397, predicted a glycine-to-arginine substitution at residue 
+  133 at the carboxyl end of the highly conserved zinc-binding site in the enzyme subunit.
+
+named_entities:
+  - id: MAXO:0001175
+    label: liver transplantation
+  - id: MONDO:0013000
+    label: Porphyria, Acute Hepatic	
+
+extracted_object:
+  action_to_disease:
+    - subject: MAXO:0001175
+      predicate: TREATS
+      object:
+        - MONDO:0013000

src/ontogpt/evaluation/maxo/test_cases/maxo_case_29478819.yaml

@@ -0,0 +1,34 @@
+---
+input_text: >-
+To overcome these challenges, a novel Blind Start design was utilized in a study of vestronidase alfa
+ in mucopolysaccharidosis VII (Sly syndrome), an ultra-rare lysosomal disease, that demonstrates the strengths of 
+ this approach in a challenging drug-development setting. Twelve subjects were randomized to 1 of 4 blinded groups, 
+ each crossing over to active treatment in a blinded fashion at different timepoints with efficacy analysis comparing 
+ the last assessment before cross over to after 24 weeks of treatment. Study assessments included Percentage change from baseline 
+ in urinary GAG (uGAG); a Multi-Domain Responder Index (MDRI) using prespecified minimal important differences (6-Minute Walk Test, 
+ Forced Vital Capacity, shoulder flexion, visual acuity, and Bruininks-Oseretsky Test of Motor Proficiency); fatigue as assessed by 
+ the Pediatric Quality of Life Inventory™ Multidimensional Fatigue Scale; and safety.
+
+We report a novel approach used in development of vestronidase alfa (recombinant human β-glucuronidase or rhGUS),
+ an enzyme replacement therapy (ERT) for MPS VII, that included a unique Phase 3 Blind Start study design with a 
+ variable placebo run-in period masking the start of vestronidase alfa, and allowing all subjects to be assessed for efficacy. 
+ Another unique feature was the use of a Multi-Domain Responder Index (MDRI) that allowed translation of multiple clinical measures 
+ into a combination responder endpoint assessed using minimally important difference (MID) thresholds without penalizing for 
+ non-assessable endpoints in a heterogeneous patient population. 
+
+named_entities:
+  - id: MONDO:0009662
+    label: Mucopolysaccharidosis Type Vii
+  - id: MAXO:0000933
+    label: enzyme replacement or supplementation therapy
+  - id: HP:0003541
+    label: Urinary glycosaminoglycan excretion
+
+ extracted_object:
+  action_to_symptom:
+    - subject: MAXO:0000933
+      predicate: TREATS
+      object:
+        - HP:0003541
+
+

src/ontogpt/evaluation/maxo/test_cases/maxo_case_30488337.yaml

@@ -0,0 +1,29 @@
+---
+input_text: >-
+  "
+  Canaloplasty in the Treatment of Open-Angle Glaucoma: A Review of Patient Selection and Outcomes
+  Canaloplasty is a relatively new non-penetrating surgery for the reduction of intraocular pressure 
+  in patients affected by glaucoma. The technique uses a microcatheter to perform a 360 º cannulation of 
+  Schlemm's canal and leaves in place a tension suture providing an inward distension. It aims to restore 
+  the physiological outflow pathways of the aqueous humour and is independent of external wound healing
+
+  Several studies have shown that canaloplasty is effective in reducing intraocular pressure and has a low rate 
+  of complications, especially compared with trabeculectomy, the gold standard for glaucoma surgery. Currently, 
+  canaloplasty is indicated in patients with open-angle glaucoma, having a mild to moderate disease, and the combination
+  with cataract phacoemulsification may provide further intraocular pressure reduction.
+  "
+
+named_entities:
+  - id: MAXO:0000959
+    label: canaloplasty
+  - id: HP:0012108
+    label: Open angle glaucoma
+  - id: MONDO:0007665
+    label: Glaucoma, Primary Open Angle
+
+extracted_object:
+  action_to_disease:
+    - subject: MAXO:0000959
+      predicate: TREATS
+      object:
+        - MONDO:0007665

src/ontogpt/evaluation/maxo/test_cases/maxo_case_36977302.yaml

@@ -0,0 +1,25 @@
+---
+input_text: >-
+  Corneal dystrophies are a group of non-inflammatory inherited disorders of the cornea. This review considers treatment options for epithelial-stromal 
+  and stromal corneal dystrophies namely Reis-Bücklers, Thiel-Behnke, lattice, Avellino, granular, macular and Schnyder corneal dystrophies. 
+  Where there is visual reduction, treatment options may include either phototherapeutic keratectomy (PTK) or corneal transplantation. 
+  Due to the anterior location of the deposits in Reis-Bücklers and Thiel-Behnke dystrophies, PTK is considered the treatment of choice. 
+  For lattice, Avellino, granular and macular corneal dystrophies, PTK provides temporary visual improvement; however, with recurrences, 
+  repeat PTK or a corneal transplant would be needed. For Schnyder dystrophy, should treatment be required, PTK may be the preferred option 
+  due to the potential for recurrence of the disease in corneal transplantation. This review discusses the literature and evidence base for 
+  the treatment of corneal dystrophies in terms of visual outcomes and recurrence rate.
+
+named_entities:
+  - id: MONDO:0012043
+    label: Corneal Dystrophy, Reis-bucklers Type
+  - id: MAXO:0010034
+    label: corneal transplantation
+  - id: HP:0001131
+    label: Corneal dystrophy
+
+extracted_object:
+  action_to_symptom:
+    - subject: MAXO:0010034
+      predicate: TREATS
+      object:
+        - HP:0001131

src/ontogpt/evaluation/maxo/test_cases/maxo_case_9543069.yaml

@@ -0,0 +1,27 @@
+---
+input_text: >-
+  A 12-year-old girl with Sly disease (mucopolysaccharidosis VII; beta-glucuronidase deficiency), who is homozygous for the A619V mutation, 
+  had a successful allogeneic BMT, donored by an HLA-identical unrelated female to replace the deficient enzyme. Within 5 months after BMT, 
+  the enzyme activity of the recipient's lymphocytes increased to normal range. No signs of acute or chronic GVHD were observed. 
+  For the successive 31 months post-BMT, beta-glucuronidase activity in her lymphocytes was maintained at almost normal levels and excretion 
+  of glycosaminoglycans in the urine was greatly diminished. Ultrastructural findings demonstrated no abnormal vacuoles and inclusion bodies 
+  in the cytoplasm of her rectal mucosal cells. Coincident with the restoration of the enzyme activity, clinical improvement was dramatic.
+  Especially notable were improvements in motor function. The patient was able to walk alone for a long time without aid, 
+  and she even became able to ride a bicycle and take a bath. In addition, recurrent infections of the upper respiratory tract and 
+  the middle ears decreased in frequency and severity, and dyspnea on exertion, severe snoring and vertigo have substantially improved. 
+  Thus, allogeneic BMT in this patient produced a better quality of life and provided a more promising outlook.
+
+named_entities:
+  - id: MONDO:0009662
+    label: Mucopolysaccharidosis Type Vii
+  - id: MAXO:0001479
+    label: allogeneic hematopoietic stem cell transplantation	
+  - id: HP:0003541
+    label: Urinary glycosaminoglycan excretion
+
+extracted_object:
+  action_to_symptom:
+    - subject: MAXO:0001479
+      predicate: TREATS
+      object:
+        - HP:0003541