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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 |
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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 |
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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 |
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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 |