mgijax/mammalian-phenotype-ontology

MP-HP terms with more than 1 exact match in the other ontology

Opened this issue · 18 comments

sbello commented

Report generated from MGI MP-HP automated mapping of terms in either ontology with more than 1 predicted exact match in the other ontology.

Matches based on

  • label to label
  • label to exact synonym
  • exact synonym to exact synonym

Need to review the terms and make corrections where needed
VOC_OntologyExactMatch.txt

Google doc
https://docs.google.com/spreadsheets/d/1KidrT6ov_kV2Rn3ihxFxcAhjqvGR3E4PElLn74zLVj4/edit?usp=sharing

sbello commented

Use of dysplasia in MP - HP

  • should dysplasia be an exact or narrow syndrome to abnormal morphology?
  • MP often uses this as an exact synonym but HP sometimes has distinct terms (80+ terms with variable definitions)
  • similar question for dystrophy

definitions of dysplasia include

  • the abnormal growth or development of a tissue or organ.
  • presence of abnormal cells within a tissue or organ
  • HP seems to use both of these and others where the abnormality is very specific

Inclined to make generic dysplasia and dystrophy synonyms narrow

sbello commented

removed hypospermia from oligozoospermia - this is low semen volume not low sperm count
We may need to review annotations and possibly add a term for low semen volume (https://www.institutobernabeu.com/en/blog/what-is-hypospermia-how-can-it-be-detected-how-does-it-affect-my-fertility/)

sbello commented

text definition for arthritis in MP specifies autoimmune so I've changed the label to match this, as other sources define arthritis to be a synonym of joint inflammation and HPO has these as synonyms

anna-anagnostop commented

removed hypospermia from oligozoospermia - this is low semen volume not low sperm count We may need to review annotations and possibly add a term for low semen volume (https://www.institutobernabeu.com/en/blog/what-is-hypospermia-how-can-it-be-detected-how-does-it-affect-my-fertility/)

Currently, there are 6 instances of hypospermia, annotated to oligozoospermia MP:0002687. It looks like, these terms have been used interchangeably in mouse studies when referring to reduced sperm density in the lumen of the epididymal duct; see PMID: 24652767, https://ntp.niehs.nih.gov/atlas/nnl/reproductive-system-male/epididymis/Hypospermia and https://doi.org/10.1177/0192623312454337

@anna-anagnostop
Given that in some instances these have different meanings, I wouldn't include it as an exact synonym but if the annotations are correct we can leave them. Maybe add it back as a related synonym?

@sbello
I added hypospermia back as a related synonym for now see #4028

anna-anagnostop commented

Use of dysplasia in MP - HP

* should dysplasia be an exact or narrow syndrome to abnormal morphology?

* MP often uses this as an exact synonym but HP sometimes has distinct terms (80+ terms with variable definitions)

* similar question for dystrophy

definitions of dysplasia include

* the abnormal growth or development of a tissue or organ.

* presence of abnormal cells within a tissue or organ

* HP seems to use both of these and others where the abnormality is very specific

Inclined to make generic dysplasia and dystrophy synonyms narrow

Agree to make dysplasia and dystrophy narrow synonyms in the MP. Per Taber's Online, dystrophy is " A general term for tissue degeneration such as that caused by diseases of nutrition or metabolism".

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anna-anagnostop commented

arthritis

text definition for arthritis in MP specifies autoimmune so I've changed the label to match this, as other sources define arthritis to be a synonym of joint inflammation and HPO has these as synonyms

Hey Sue, following the term label change from arthritis to autoimmune arthritis, we now have osteoarthritis MP:0003560 sitting under autoimmune arthritis MP:0002993. Most sites I have checked state that osteoarthritis is not an autoimmune disease, unlike rheumatoid arthritis.

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sbello commented

I've changed the parent for osteoarthritis.
We should discuss what to do with susceptibility to induced arthritis terms. Both terms currently have an autoimmune parent but the definitions do not mention 'autoimmune'. I'm inclined to move these out from under autoimmune but we can discuss on Monday.

sbello commented

Working my way through the dysplasia synonyms, there are soooo many of these

sbello commented

fixed all the dysplasia synonyms to be narrow rather than exact

sbello commented

need to discuss synonyms for eyelid muscle spasm (MP:0006244) exact match to Cogan lid twitch (HP:0031786) and Blepharospasm (HP:0000643) due to overlapping synonyms, I think we may need to adjust synonym types on both sides,

need to discuss intestinal polyps (MP:0008011) HP has distinct terms for intestinal polyp (one or more) and Intestinal polyposis (multiple polyps), MP definition uses plural but isn't really clear, should we create a new term that is clearly 1 or more and mae it clear that this term is multiple or make it clear that the term is one or more and make 'intestinal polyposis' a narrow synonym.

impaired olfaction, anosmia - should anosmia be a child of impaired olfaction? HP has Hyposmia as a parent to anosmia

What is the distinction between Orthokeratotic hyperkeratosis and Orthokeratosis? The HP definition for Orthokeratosis is 'Formation of an anuclear keratin layer' and this sits under thickened skin so it should be a thicker layer of skin formed by anuclear cells in the keratin layer. Orthokeratotic hyperkeratosis is defined as ' form of hyperkeratosis characterized by thickening of the cornified layer without retained nuclei.' cornified layer = stratum corneum of epidermis = keratinized squame layer Googling Orthokeratosis I find links to Orthokeratotic hyperkeratosis and descriptions of orthokeratosis as a normal process in skin formation. It is unclear to me if there is an abnormal Orthokeratosis that is not Orthokeratotic hyperkeratosis. Discuss with Anna and then decide

  1. do we need to modify the MP term
  2. do we need to submit an HPO ticket to merge these terms
sbello commented

Does retinal artery = central retinal artery? MP has 'retina artery occlusion' with the synonym 'central retinal artery occlusion' and it uses central retinal artery in the eq but HP has 'Retinal artery occlusion' and this has 'central retinal artery occlusion' as a child. There are also other children like 'Branch retinal artery occlusion' and 'Ophthalmic artery occlusion'. From the definition branch retinal artery sounds like a branch of the central retinal artery.
In Uberon central retinal artery is a sibling of ophthalmic artery and central artery has no child terms.

sbello commented

What should we do about the hypoplasia/small issue? HP tends to use these interchangeably, MP does not. Small in the MP is the parent of hypoplasia when both terms exist. Do we ask HP to make small a broad synonym for hypoplasia across the board?

sbello commented

distinction between atrophy and degeneration
PATO has separate terms for this

  • degenerate 'A structural quality inhering in a bearer whose structure deteriorates or is lost over time due to an active pathological process'
  • atrophied 'A size quality inhering in a bearer by virtue of a part or parts of the bearer's being decreased in size due to reduction in tissue mass through wasting.'
    How real is this distinction in practice? HP has Testicular degeneration as a synonym to Testicular atrophy MP has separate terms for atrophy and degeneration. There are many annotations to each but other than using different words it isn't that clear that the phenotype is really different.
    Need to review annotations and see if we can pin down a real difference.
sbello commented

review annotations to large ureter, seems like these may be mostly 'megaureter' which may really be a more specific type of hydroureter or ureter dilation
references

  • https://link.springer.com/chapter/10.1007/978-3-642-88586-0_3 "hydro-ureter will be used in this chapter for all forms of chronic dilatation, including those for which a urethral obstruction is clearly responsible, while “mega-ureter” is reserved for the clinical group in which no organic obstruction can be found"
  • J:105047 " severe dilatation of both ureters (megaureters)"
  • J:121262 Megaureter and hydronephrosis were found in Dlgh1 –/– mice at E18.5. These disorders are caused by urinary obstruction

We also have dilated ureter (MP:0003586) but it is a sibling to hydroureter and large ureter (MP:0003585), this seems to be wrong. We need to clarify this. I think probably megaureter should be a narrow sibling to dilated ureter. Once this is done we may want to obsolete large ureter and replace this with long ureter.

sbello commented

ureteropelvic junction stenosis vs ureteropelvic junction obstruction

  • MP has 2 separate terms that are siblings, HP has a single term and the tree mixes stenosis and obstruction together
  • is there really a difference? If so should these terms really be siblings not parent-child
  • There are only 2 papers attached to the stenosis term, J:101195 uses stenosis for the mouse but obstruction for the human phenotype, J:101195 uses stenosis in the results but changes to obstruction in the discussion
sbello commented

xerostomia vs reduced salivation
MP has 2 terms for this
xerostomia - dryness of the mouth resulting from reduced salivary secretion

  • decreased salivation - reduction in the flow, secretion, or amount of saliva
  • decreased salivation is the parent of xerostomia

HP has a single term that Xerostomia with reduced salivation as an exact synonym

The bulk of annotations in MGI are attached to decreased salivation

Probably not a big deal since this is the sole child of the MP term

sbello commented

delayed fontanelle closure vs delayed cranial suture closure
currently these are siblings with distinct definitions but the HPO has delayed fontanelle closure as a synonym of delayed cranial suture closure
Looking online it seems like fontanelles are a specific type of cranial suture that remains open at birth
https://www.mayoclinic.org/diseases-conditions/craniosynostosis/multimedia/cranial-sutures-and-fontanels/img-20006785
https://www.mountsinai.org/health-library/special-topic/cranial-sutures
So at least delayed fontanelle closure should be a child of delayed suture closure
We should also review the annotations to these terms
J:56557 - mentions fontanelles in the text but annotated to suture
changed the parents for both fontanelle terms, this is also in keeping with Uberon