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Add four more test cases
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caufieldjh committed Nov 16, 2023
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40 changes: 40 additions & 0 deletions src/ontogpt/evaluation/maxo/test_cases/maxo_case_20301675.yaml
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---
input_text: >-
"McKusick-Kaufman Syndrome
Clinical characteristics: McKusick-Kaufman syndrome (MKS) is characterized by
the combination of postaxial polydactyly (PAP), congenital heart disease
(CHD), and hydrometrocolpos (HMC) in females and genital malformations in
males (most commonly hypospadias, cryptorchidism, and chordee). HMC in infants
usually presents as a large cystic abdominal mass arising out of the pelvis,
caused by dilatation of the vagina and uterus as a result of the accumulation
of cervical secretions from maternal estrogen stimulation. HMC can be caused
by failure of the distal third of the vagina to develop (vaginal agenesis),
a transverse vaginal membrane, or an imperforate hymen. PAP is the presence of
additional digits on the ulnar side of the hand and the fibular side of the
foot. A variety of congenital heart defects have been reported including
atrioventricular canal, atrial septal defect, ventricular septal defect,
or a complex congenital heart malformation. Diagnosis/testing: The clinical
diagnosis of MKS can be established in a proband based on clinical diagnostic
criteria of HMC and PAP in the absence of clinical or molecular genetic
findings suggestive of an alternative diagnosis. The molecular diagnosis can
be established in proband with suggestive findings and biallelic pathogenic
variants in MKKS identified by molecular genetic testing. However, care must
be taken to ensure that the proband does not have Bardet-Biedl syndrome, an
allelic condition with considerable clinical overlap and age-dependent
features including retinal dystrophy, obesity, and intellectual disability.
Management: Treatment of manifestations: Surgical repair of the obstruction
causing HMC and drainage of the accumulated fluid. Treatment for polydactyly
and congenital heart defects and any other anomalies is standard."
named_entities:
- id: MONDO:0009367
label: McKusick-Kaufman syndrome
- id: MAXO:0000004
label: surgical repair
- id: HP:0030010
label: hydrometrocolpos
extracted_object:
action_to_symptom:
- subject: MAXO:0000004
predicate: TREATS
object:
- HP:0030010
41 changes: 41 additions & 0 deletions src/ontogpt/evaluation/maxo/test_cases/maxo_case_26110198.yaml
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---
input_text: >-
"Prolidase Deficiency
Treatment of manifestations: Skin ulcers may require treatment by a wound
care specialist; topical proline (often 5%) or topical 5% proline-5% glycine
ointment applied with dressing changes has been successful in some affected
individuals. Standard treatment for developmental delay / intellectual
disability, seizures, infections, reactive airways disease / pulmonary
hypertension, SLE-like features, hemophagocytic lymphohistiocytosis, mast
cell activation, osteopenia, dental anomalies, and refractive errors. Anemia
and thrombocytopenia rarely require treatment, but packed red blood cell or
platelet transfusions may be considered in those with severe anemia or
thrombocytopenia, respectively."
named_entities:
- id: MONDO:0008221
label: Prolidase Deficiency
- id: MAXO:0000061
label: antibacterial agent therapy
- id: HP:0200042
label: Skin ulcer
- id: MAXO:0000756
label: blood transfusion
- id: HP:0001903
label: anemia
- id: MAXO:0010020
label: amino acid supplementation
extracted_object:
action_to_symptom:
- subject: MAXO:0000061
predicate: TREATS
object:
- HP:0200042
- subject: MAXO:0000756
predicate: TREATS
object:
- HP:0001903
action_to_disease:
- subject: MAXO:0010020
predicate: TREATS
object:
- MONDO:0008221
26 changes: 26 additions & 0 deletions src/ontogpt/evaluation/maxo/test_cases/maxo_case_27077170.yaml
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---
input_text: >-
"Adams-Oliver Syndrome – RETIRED CHAPTER, FOR HISTORICAL
REFERENCE ONLY
Adams-Oliver syndrome (AOS) is characterized by aplasia cutis
congenita (ACC) of the scalp and terminal transverse limb
defects (TTLD).
Management. Treatment of manifestations: ACC. Care by a
pediatric dermatologist and/or plastic surgeon depending on
severity. Goals of non-operative therapy are to prevent infection
and promote healing. Large and/or deep lesions with calvarial
involvement require acute care and may eventually also require
reconstruction by a neurosurgeon."
named_entities:
- id: MONDO:0013895
label: Adams-oliver Syndrome 3
- id: MAXO:0000946
label: neurosurgical procedure
- id: HP:0001057
label: aplasia cutis congenita
extracted_object:
action_to_symptom:
- subject: MAXO:0000946
predicate: TREATS
object:
- HP:0001057
72 changes: 72 additions & 0 deletions src/ontogpt/evaluation/maxo/test_cases/maxo_case_28406602.yaml
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---
input_text: >-
"Myhre Syndrome
The diagnosis of Myhre syndrome is established in a proband
with characteristic clinical findings and a heterozygous
pathogenic (or likely pathogenic) variant in SMAD4 detected
by molecular genetic testing. Management. Treatment of
manifestations: Feeding therapy with a low threshold for a
clinical and/or radiographic swallowing study; referral to
nutrition for poor weight gain or obesity; medical therapy
for systemic and/or pulmonary hypertension; long-term
tracheostomy may be required for those with complete or
recurrent tracheal stenosis; aggressive medical management
for constipation; physical therapy to keep joints mobile;
hearing aids may be helpful for those with hearing loss;
some keloids can be treated with intralesional steroids
with minimal invasiveness for lesion removal; and standard
treatment for orofacial clefting / velopharyngeal
insufficiency, congenital heart defects / pericardial disease,
restrictive lung disease, gastrointestinal stenosis,
developmental delay / intellectual disability, refractive
errors / strabismus / cataracts, persistent middle ear
effusions, immunodeficiency, diabetes mellitus, and
pubertal/menstrual irregularities.
Orofacial clefting /Velopharyngeal insufficiency
Standard treatment, ideally by craniofacial team
Multidisciplinary teams may incl surgical team (craniofacial
surgeon), clinical geneticist, otolaryngologist, pediatrician,
radiologist, psychologist, multiple dental specialists,
audiologist, speech therapist, & social worker.
Restrictive lung disease Symptomatic & standard treatment
per pulmonologist Oxygen supplementation as necessary"
named_entities:
- id: MONDO:0007688
label: Myhre Syndrome
- id: MAXO:0000011
label: physical therapy
- id: HP:0001376
label: Limitation of joint mobility
- id: HP:0001387
label: Joint stiffness
- id: MAXO:0000066
label: Oxygen supplementation
- id: HP:0002093
label: restrictive lung disease
- id: MAXO:0000504
label: tracheostomy
- id: HP:0004894
label: tracheal stenosis
- id: MAXO:0000930
label: speech therapist
- id: HP:0001608
label: Abnormality of the voice
extracted_object:
action_to_symptom:
- subject: MAXO:0000011
predicate: TREATS
object:
- HP:0001376
- HP:0001387
- subject: MAXO:0000066
predicate: TREATS
object:
- HP:0002093
- subject: MAXO:0000504
predicate: TREATS
object:
- HP:0004894
- subject: MAXO:0000930
predicate: TREATS
object:
- HP:0001608

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