Question re: HP_0000140 Abnormality of the menstrual cycle

[nicolevasilevsky]

HPO term HP_0000140 Abnormality of the menstrual cycle

Question There is a parent term HP_0000858 'Menstrual irregularites'- There is no textual definition, but maybe it should be a child of 'Abnormality of menstrual cycle' or possibly a broad synonym?

Leigh noted that HP_0000858 has a strange logical definition using towards:'has part' some ('irregular rhythm' and (towards some menstruation) and ('has modifier' some abnormal))"

[pnrobinson]

I think this subsection needs to be refactored slightly. There is 1. onset 2. frequency 2a. Abnormal periodicity 3. amount 4. pain

[pnrobinson]

HP:0000858 is used directly to annotate the following diseases

OMIM:110100 BLEPHAROPHIMOSIS, PTOSIS, AND EPICANTHUS INVERSUS       HP:0000858  OMIM:110100 IEA                 P   HPO:iea[2009-02-17]
OMIM:101800 ACRODYSOSTOSIS      HP:0000858  OMIM:101800 TAS                 P   HPO:probinson[2009-02-17]
OMIM:615962 #615962 GLUCOCORTICOID RESISTANCE, GENERALIZED;;GLUCOCORTICOID RECEPTOR DEFICIENCY;;GCCR DEFICIENCY;;GCR DEFICIENCY;;GRL DEFICIENCY;;CORTISOL RESISTANCE FROM GLUCOCORTICOID RECEPTOR DEFECTHP:0000858  OMIM:615962 TAS     HP:0040283          P   HPO:skoehler[2014-10-06]
OMIM:203800 ALSTROM SYNDROME        HP:0000858  OMIM:203800 IEA                 P   HPO:iea[2009-02-17]
OMIM:311360 PREMATURE OVARIAN FAILURE 1     HP:0000858  OMIM:311360 IEA                 P   HPO:iea[2009-02-17]
OMIM:216400 COCKAYNE SYNDROME, TYPE A       HP:0000858  OMIM:216400 TAS                 P   HPO:skoehler[2009-02-17]
OMIM:616831 LUSCAN-LUMISH SYNDROME      HP:0000858  PMID:24852293   PCS                 P   HPO:probinson[2017-06-17]

I think the best thing is to make these annotations more specific.

[pnrobinson]

I think that Menstrual irregularities needs to be renamed to Irregular menses and made a child of Abnormality of the menstrual cycle. def: Abnormally high variation in the amount of time between periods. comment: Most women have between 11 and 13 menstrual periods each year. Bleeding usually lasts around 5 days (range: 2 to 7 days). When menstruation first starts, it can take up to 2 years to establish a regular cycle. After puberty, most women’s menstruation is regular. The length of time between each period is similar. The normal menstrual cycle length is 28 days +/- 7 days with the menstruation lasting between 2 and 7 days. It can take up to 2 years from menarche to develop a mature hypothalamic-pituitary-gonadal (HPG) axis. Within 1 year, 75% of girls have a cycle between 21 and 45 days. By the fifth gynecological year, 90% of girls will have regular cycles with 75% having ovulatory cycles.

PMID:29323693