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obophenotype / developmental-stage-ontologies

Source files for various species-specific stage ontologies
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Align HsapDv post-birth stages with HPO age-of-onset vocabulary #10

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
HPO agrees with Bgee that fetus is post-embryo.

However, there are other disagreements:

  * HP:0000004 ! Onset and clinical course
   * HP:0003674 ! Onset [DEF: "The age and speed of the first appearance of the signs or symptoms of an illness."]
    * HP:0011007 ! Age of onset ***  [DEF: "The age group in which disease manifestations appear."]
     * HP:0003577 ! Congenital onset [DEF: "A phenotypic abnormality that is present at birth."]
      * HP:0011460 ! Embryonal onset [DEF: "Onset of disease at up to 8 weeks of gestation."]
      * HP:0011461 ! Fetal onset [DEF: "Onset prior to birth but after 8 weeks of gestation."]
     * HP:0003581 ! Adult onset [DEF: "Onset of disease manifestations in adulthood, defined here as at the age of 20 years or later."]
      * HP:0003584 ! Late onset [DEF: "A type of `adult onset` with onset of symptoms after the age of 60 years."]
      * HP:0003596 ! Middle age onset [DEF: "A type of `adult onset` with onset of symptoms at the age of 40 to 60 years."]
      * HP:0011462 ! Young adult onset [DEF: "Onset of disease at the age of between 15 and 40 years."]
     * HP:0003593 ! Infantile onset [DEF: "Onset of signs or symptoms of disease between 28 days to one year of life."]
     * HP:0003621 ! Juvenile onset [DEF: "Onset of signs or symptoms of disease between the age of 5 and 15 years."]
     * HP:0003623 ! Neonatal onset [DEF: "Onset of signs or symptoms of disease within the first 28 days of life."]
     * HP:0011463 ! Childhood onset [DEF: "Onset of disease at the age of between 1 and 5 years."]

"young adult", "middle age" etc are different in HsapDv. These are 
intrinsically vague and change over time.

One option is to build in the vagueness and agree upon *ranges*.

Another is to have two overlapping systems, and qualify each term. E.g.

 * "young person, sensu system 1"
 * "young person, sensu system 2"

After this is done we have add logical definitions for the HPO terms.

Original issue reported on code.google.com by cmung...@gmail.com on 22 Apr 2013 at 7:54

GoogleCodeExporter commented 9 years ago 
Compare:

  * HsapDv:0000080 ! immature stage [DEF: "Human developmental stage that covers the period from birth until 12 years old."]
   * HsapDv:0000081 ! child stage [DEF: "Immature stage that refers to child who is over 2 and under 13 years old."]
   * HsapDv:0000082 ! newborn human stage ***  [DEF: "Immature stage that refers to a newborn who is under 32 days old."]
   * HsapDv:0000083 ! infant stage [DEF: "Immature stage that refers to an infant who is over 31 days and is under 24 months old."]
  * HsapDv:0000204 ! mature stage [DEF: "Human developmental stage that refers to a sexually mature human."]
   * HsapDv:0000086 ! adolescent stage [DEF: "Mature stage that refers to an adolescent who is over 13 and under 19 years old."]
   * HsapDv:0000087 ! human adult stage ***  [DEF: "Human developmental stage that refers to an adult who is over 19."]
    * HsapDv:0000088 ! human early adulthood stage ***  [DEF: "Adult stage that refers to an adult who is under 45."]
     * HsapDv:0000089 ! young adult stage [DEF: "Early adulthood that refers to an adult who is under 25."]
    * HsapDv:0000091 ! human late adulthood stage ***  [DEF: "Adult stage that refers to an adult who is over 45."]
     * HsapDv:0000092 ! human middle aged stage ***  [DEF: "Late adulthood that refers to an adult who is over 45 and under 65."]
     * HsapDv:0000093 ! human aged stage ***  [DEF: "Late adulthood that refers to an adult who is over 65."]

Original comment by cmung...@gmail.com on 22 Apr 2013 at 7:56