search

monarch-initiative / HPO-UMLS-Integration

Repository for HPO UMLS integration QA code and tracking issues
0 stars 0 forks source link

Meta Concepts #26006 Pain in scrotum and #15203 Gait, Unsteady #4

Closed mirandajarnot closed 9 years ago

mirandajarnot commented 9 years ago

The HPO contexts for both of these is Phenotypic Abnormality. The STYs are Sign or Symptom for "pain in scrotum" and Finding for "gait, unsteady". There are other examples like this; do they truly mean Abnormality, or is Sign or Symptom/Finding OK?

CN# 26006 Pain in scrotum CUI C0236078 Concept Status needs Review STY Sign or Symptom R DEF [Release] HPO2015_04_20

CONTEXTS HPO2015_04_20/HPO2015_04_20/PT1/HP:0030155 HPO All Phenotypic abnormality Abnormality of the genitourinary system Abnormality of the genital system Abnormal genital system morphology Abnormal external genitalia Abnormality of male external genitalia Abnormality of the scrotum Abnormal scrotal rugation + Absent scrotum Accessory scrotum Bifid scrotum Ectopic scrotum Neoplasm of the scrotum Penoscrotal transposition Prominent scrotal raphe Scrotal hyperpgimentation Scrotal hypoplasia

Shawl scrotum Small scrotum Vaginal hematocele Vaginal hydrocele Vaginal lymphocele Vaginal pyocele Varicocele HPO2015_04_20/HPO2015_04_20/PT2/HP:0030155 HPO All Phenotypic abnormality Abnormality of the genitourinary system Abnormality of the genital system Abnormal genital system morphology Abnormality of the male genitalia Abnormality of male external genitalia Abnormality of the scrotum Abnormal scrotal rugation + Absent scrotum Accessory scrotum Bifid scrotum Ectopic scrotum Neoplasm of the scrotum Penoscrotal transposition Prominent scrotal raphe Scrotal hyperpgimentation Scrotal hypoplasia Shawl scrotum Small scrotum Vaginal hematocele Vaginal hydrocele Vaginal lymphocele Vaginal pyocele Varicocele NCI2015_02D/NCI2015_02D/PT1/C78607 National Cancer Institute Thesaurus Disease, Disorder or Finding Finding Sign or Symptom Symptom Pain Skin Pain SNOMEDCT_US_2015_03_01/SNOMEDCT_US_2015_03_01/PT2/20502007 SNOMED CT Concept Clinical finding Finding by site Finding of body region Finding of trunk structure Urogenital finding Genital finding Male genitalia finding Pain in male genitalia SNOMEDCT_US_2015_03_01/SNOMEDCT_US_2015_03_01/PT3/20502007 SNOMED CT Concept Clinical finding Finding by site Finding of body region Finding of trunk structure Urogenital finding Genitourinary pain Pain in male genitalia SNOMEDCT_US_2015_03_01/SNOMEDCT_US_2015_03_01/PT4/20502007 SNOMED CT Concept Clinical finding Finding by site Finding of sensation by site Pain finding at anatomical site Pain of truncal structure Pain in pelvis Genitourinary pain Pain in male genitalia SNOMEDCT_US_2015_03_01/SNOMEDCT_US_2015_03_01/PT5/20502007 SNOMED CT Concept Clinical finding Neurological finding Sensory nervous system finding Finding of sensation by site Pain finding at anatomical site Pain of truncal structure Pain in pelvis Genitourinary pain Pain in male genitalia SNOMEDCT_US_2015_03_01/SNOMEDCT_US_2015_03_01/PT6/20502007 SNOMED CT Concept Clinical finding Neurological finding Sensory nervous system finding Pain / sensation finding Pain Pain finding at anatomical site Pain of truncal structure Pain in pelvis Genitourinary pain Pain in male genitalia SNOMEDCT_US_2015_03_01/SNOMEDCT_US_2015_03_01/PT7/20502007 SNOMED CT Concept Clinical finding Finding by site Finding of body region Finding of trunk structure Pain of truncal structure Pain in pelvis Genitourinary pain Pain in male genitalia SNOMEDCT_US_2015_03_01/SNOMEDCT_US_2015_03_01/PT8/20502007 SNOMED CT Concept Clinical finding Finding by site Finding of body region Finding of trunk structure Finding of pelvic region of trunk Pain in pelvis Genitourinary pain Pain in male genitalia CN# 15203 Gait, Unsteady CUI C0231686 Concept Status needs Review STY Finding R ATOMS R [] Gait, Unsteady [MSH2015_2015_01_26/PEN/D020233] M0337784 R Unsteady gait [SNOMEDCT_US_2015_03_01/PT/394616008] M N Unsteady gait [HPO2015_04_20/PT/HP:0002317] R Unsteady gait [OMIM2015_03_18/PTCS/MTHU002478] R Unsteady gait [LNC250/CN/MTHU020852] R Unsteady Gait [MSH2015_2015_01_26/PM/D020233] M0337784 R [] Unsteady gait (finding) [SNOMEDCT_US_2015_03_01/FN/394616008] R [] Unsteady when walking (finding) [SNOMEDCT_US_2015_03_01/FN/22631008] R [] Unsteady when walking [SNOMEDCT_US_2015_03_01/PT/22631008] R [] Disequilibrium when walking [SNOMEDCT_US_2015_03_01/SY/22631008] R [] Instability of gait [SNOMEDCT_US_2015_03_01/SY/394616008] M N Gait instability [HPO2015_04_20/SY/HP:0002317] R Instability gait [MDR18_0/LT/10022455] R [] Unstable when walking [SNOMEDCT_US_2015_03_01/SY/22631008] R [] Unstable gait [OMIM2015_03_18/PTCS/MTHU011036] CONTEXTS HPO2015_04_20/HPO2015_04_20/PT1/HP:0002317 HPO All Phenotypic abnormality Abnormality of the nervous system Abnormality of nervous system physiology Abnormality of movement Gait disturbance Broad-based gait Cerebellar ataxia associated with quadrupedal gait Difficulty walking Falls Gait apraxia Gait ataxia + Gait imbalance Inability to walk + Scissor gait Shuffling gait + Steppage gait Tip-toe gait Toe walking Waddling gait SNOMEDCT_US_2015_03_01/SNOMEDCT_US_2015_03_01/PT1/22631008 SNOMED CT Concept Clinical finding Clinical history and observation findings Functional finding Finding of walking Finding of gait Abnormal gait SNOMEDCT_US_2015_03_01/SNOMEDCT_US_2015_03_01/PT1/394616008 SNOMED CT Concept Clinical finding Clinical history and observation findings Functional finding Finding of walking Finding of gait SNOMEDCT_US_2015_03_01/SNOMEDCT_US_2015_03_01/PT2/22631008 SNOMED CT Concept Clinical finding Clinical history and observation findings Finding of balance Finding of walking balance
pnrobinson commented 9 years ago

The HPO has treated symptoms as a subclass of phenotypic abnormality. This is because there is a clinical abnormality of one sort or another that leads to say pain but if we looked at it under the microscope we would see some sign of inflammation or tissue damage etc. Signs are by definition phenotypic abnormalities because they are things that a doctor observes as abnormal. Do you not agree that a sign/symptom is an abnormality?

mirandajarnot commented 9 years ago

I see your point about symptoms as a subclass of abnormality. Based on your response we have decided that we will leave the HPO atom where it merged into the same concept as strings from other sources including Pain in scrotum [SNOMEDCT /PT/20502007]

And Unsteady Gait will stay in the same concept as: Gait, Unsteady [MSH2015_2015_01_26/PEN/D020233] Unsteady gait [SNOMEDCT_US_2015_03_01/PT/394616008] Along with several other sources.

Thanks, Miranda