MP-HPO phenotype alignment: check if axiom matches agree with text definitions

rays22 commented 11 months ago

From the 2023-08-03 pattern review call: We should do a pull of mapped terms where both ontologies have eqs, the eqs are the same, but the match type is not exact

MP-HPO phenotype alignment: check if axiom matches agree with text definitions in SSSOM: Mouse-Human Ontology Mapping Initiative (MHMI) table mh_mapping_initiative/mappings/mp_hp_mgi_all.sssom.tsv

[x] robot export EQs from HPO

robot export --input ~/human-phenotype-ontology/src/ontology/hp-edit.owl \
    --header "ID|Equivalent Class [ID]|LABEL|definition|Equivalent Class" \
    --sort "ID" \
    --include "classes" \
    --export ~/tmp/hp-mp/hp-full-EQs-2023-09-14.tsv

[x] robot export EQs from MP

robot export --input ~/mammalian-phenotype-ontology/src/ontology/mp-edit.owl \
    --header "ID|Equivalent Class [ID]|LABEL|definition|Equivalent Class" \
    --sort "ID" \
    --include "classes" \
    --export ~/tmp/hp-mp/mp-full-EQs-2023-09-14.tsv

[x] find HPO:MP exactMatch EQs
[x] find non-exactMatches in mh_mapping_initiative/mappings/mp_hp_mgi_all.sssom.tsv
[x] compare tables from the previous two steps

rays22 commented 9 months ago

[x] find HPO:MP exactMatch EQs

A table of 25 24 of the 698 matching HP-MP classes that are not mapped as `skos:exactMatch`:

HP ID	LABEL	definition	Equivalent Class	predicate	Matching MP Class	LABEL	definition
HP:0011102	Ileal atresia	An abnormal closure, or atresia of the tubular structure of the ileum.	has part' some (atretic and ('characteristic of' some ileum) and ('has modifier' some abnormal))	skos:broadMatch	MP:0011879	ileum atresia	congenital blockage or absence of the lumen of the ileum
HP:0032210	Decreased circulating free T3	A reduced concentration of free 3,3',5-triiodo-L-thyronine in the blood circulation.	has part' some ('decreased amount' and ('characteristic of' some (3,3',5-triiodo-L-thyronine and (part_of some blood))) and ('has modifier' some abnormal))	skos:broadMatch	MP:0005479	decreased circulating triiodothyronine level	reduced amount of a thyroid hormone present in the blood that regulates growth and development, controls some metabolic processes and body temperature, and negatively regulates secretion of thyrotropin by the pituitary gland
HP:0003572	Low plasma citrulline	A decreased concentration of citrulline in the blood.	has part' some ('decreased amount' and ('characteristic of' some (citrulline and (part_of some blood))) and ('has modifier' some abnormal))	skos:closeMatch	MP:0020837	decreased circulating citrulline level	reduction in the amount per unit of blood of citrulline
HP:0000316	Hypertelorism	Interpupillary distance more than 2 SD above the mean (alternatively, the appearance of an increased interpupillary distance or widely spaced eyes).	has part' some ('increased length' and ('characteristic of' some 'anatomical line between pupils') and ('has modifier' some abnormal))	skos:closeMatch	MP:0001300	ocular hypertelorism	increased interpupillary distance, i.e. increased distance between the center of the pupils of the two eyes
HP:0012368	Flat face	Absence of concavity or convexity of the face when viewed in profile.	has part' some (flat and ('characteristic of' some face) and ('has modifier' some abnormal))	skos:closeMatch	MP:0012175	flat face	the appearance of a flattened surface outline or contour of a normally rounded face of an organism
HP:0011800	Midface retrusion	Posterior positions and/or vertical shortening of the infraorbital and perialar regions, or increased concavity of the face and/or reduced nasolabial angle.	has part' some (hypoplastic and ('characteristic of' some midface) and ('has modifier' some abnormal))	skos:closeMatch	MP:0012085	midface hypoplasia	decrease in the number of normal cells in normal arrangement in the midface, typically resulting in decreased size and leading to a concave-looking face
HP:0010808	Protruding tongue	Tongue extending beyond the alveolar ridges or teeth at rest.	has part' some (protruding and ('characteristic of' some tongue) and ('has modifier' some abnormal))	skos:closeMatch	MP:0009908	protruding tongue	the tongue extends out beyond the oral cavity past the lips; may be due to paralysis, oral cavity size, tongue hypoplasia or dysfunction of the hypoglossal nerve
HP:0000050	Hypoplastic male external genitalia	Underdevelopment of part or all of the male external reproductive organs (which include the penis, the scrotum and the urethra).	has part' some (hypoplastic and ('characteristic of' some 'external male genitalia') and ('has modifier' some abnormal))	skos:closeMatch	MP:0009203	external male genitalia hypoplasia	decrease in the number of normal cells in normal arrangement in the externa; male genitalia, typically resulting in decreased size
HP:0002900	Hypokalemia	An abnormally decreased potassium concentration in the blood.	has part' some ('decreased amount' and ('characteristic of' some ('potassium atom' and (part_of some blood))) and ('has modifier' some abnormal))	skos:closeMatch	MP:0005628	decreased circulating potassium level	less than the normal concentration in the blood of this alkaline metallic element, the most abundant intracellular ion; anomalies in the extracellular (circulating) concentration have important implications for the function of excitable tissues, such as nerve and muscle
HP:0003075	Hypoproteinemia	A decreased concentration of protein in the blood.	has part' some ('decreased amount' and ('characteristic of' some ('protein polypeptide chain' and (part_of some blood))) and ('has modifier' some abnormal))	skos:closeMatch	MP:0005567	decreased circulating total protein level	total circulating protein level below the normal range
HP:0002984	Hypoplasia of the radius	Underdevelopment of the radius.	has part' some (hypoplastic and ('characteristic of' some 'radius bone') and ('has modifier' some abnormal))	skos:closeMatch	MP:0004356	radius hypoplasia	decrease in the number of normal cells in normal arrangement in the radius, typically resulting in decreased size
HP:0001508	Failure to thrive	Failure to thrive (FTT) refers to a child whose physical growth is substantially below the norm.	has part' some ('decreased rate' and ('characteristic of' some growth) and ('has modifier' some abnormal))	skos:closeMatch	MP:0001732	postnatal growth retardation	slow or limited development after birth
HP:0000113	Polycystic kidney dysplasia	The presence of multiple cysts in both kidneys.	has part' some (polycystic and ('characteristic of' some kidney) and ('has modifier' some abnormal))	skos:narrowMatch	MP:0008528	polycystic kidney	presence of multiple fluid-filled cysts in one or both kidneys
HP:0000322	Short philtrum	Distance between nasal base and midline upper lip vermilion border more than 2 SD below the mean. Alternatively, an apparently decreased distance between nasal base and midline upper lip vermilion border.	has part' some ('decreased length' and ('characteristic of' some philtrum) and ('has modifier' some abnormal))	skos:narrowMatch	MP:0030193	short philtrum	decreased length of the vertical groove found on the median line of the upper lip
HP:0000218	High palate	Height of the palate more than 2 SD above the mean (objective) or palatal height at the level of the first permanent molar more than twice the height of the teeth (subjective).	has part' some ('increased height' and ('characteristic of' some 'secondary palate') and ('has modifier' some abnormal))	skos:narrowMatch	MP:0003757	high palate	greater distance upward to the roof of the oral cavity than usual
HP:0000034	Hydrocele testis	Accumulation of clear fluid in the between the layers of membrane (tunica vaginalis) surrounding the testis.	has part' some ('increased accumulation' and ('characteristic of' some testis) and (towards some 'bodily fluid') and ('has modifier' some abnormal))	skos:narrowMatch	MP:0003623	hydrocele	accumulation of fluid around testes
HP:0000821	Hypothyroidism	Deficiency of thyroid hormone.	has part' some ('decreased functionality' and ('characteristic of' some 'thyroid gland') and ('has modifier' some abnormal))	skos:narrowMatch	MP:0003503	decreased activity of thyroid gland	reduced function of this endocrine gland that normally produces hormones that regulate the metabolic rate of the body
HP:0002032	Esophageal atresia	A developmental defect resulting in complete obliteration of the lumen of the esophagus such that the esophagus ends in a blind pouch rather than connecting to the stomach.	has part' some (atretic and ('characteristic of' some esophagus) and ('has modifier' some abnormal))	skos:narrowMatch	MP:0003276	esophageal atresia	congenital blockage or absence of the lumen of the esophagus
HP:0001274	Agenesis of corpus callosum	Absence of the corpus callosum as a result of the failure of the corpus callosum to develop, which can be the result of a failure in any one of the multiple steps of callosal development including cellular proliferation and migration, axonal growth or glial patterning at the midline.	has part' some (absent and ('characteristic of' some 'corpus callosum') and ('has modifier' some abnormal))	skos:narrowMatch	MP:0002196	absent corpus callosum	absence of the commissural plate interconnecting the cortical hemispheres of the brain
HP:0003074	Hyperglycemia	An increased concentration of glucose in the blood.	has part' some ('increased amount' and ('characteristic of' some blood) and (towards some glucose) and ('has modifier' some abnormal) and ('has modifier' some pathological))	skos:narrowMatch	MP:0001559	hyperglycemia	abnormally high concentration of glucose in the blood; generally refers to a pathological state
HP:0005815	Supernumerary ribs	The presence of more than 12 rib pairs.	has part' some ('increased amount' and ('characteristic of' some rib) and ('has modifier' some abnormal))	skos:narrowMatch	MP:0000480	increased rib number	greater than normal numbers of the pairs of bony structures that are elements of the body wall
HP:0000369	Low-set ears	Upper insertion of the ear to the scalp below an imaginary horizontal line drawn between the inner canthi of the eye and extending posteriorly to the ear.	has part' some ('decreased position' and ('characteristic of' some 'external ear') and ('has modifier' some abnormal))	skos:narrowMatch	MP:0000024	lowered ear position	outer ears are situated below the normal location often giving the perception of protruding from the head
HP:0000219	Thin upper lip vermilion	Height of the vermilion of the upper lip in the midline more than 2 SD below the mean. Alternatively, an apparently reduced height of the vermilion of the upper lip in the frontal view (subjective).	has part' some ('decreased thickness' and ('characteristic of' some 'upper lip') and ('has modifier' some abnormal))	skos:relatedMatch	MP:0030168	thin upper lip	upper lips having a reduced amount of soft tissue
HP:0004322	Short stature	A height below that which is expected according to age and gender norms. Although there is no universally accepted definition of short stature, many refer to "short stature" as height more than 2 standard deviations below the mean for age and gender (or below the 3rd percentile for age and gender dependent norms).	has part' some ('decreased height' and ('characteristic of' some 'multicellular organism') and ('has modifier' some abnormal))	skos:relatedMatch	MP:0001255	decreased body height	decreased shoulder to floor distance compared to controls

rays22 commented 9 months ago

The comparison table is also included in the gsheet here.

sbello commented 9 months ago

The match types in the table don't match the match types in the MGI mapping file for some term pairs HP:0000506-MP:0030166 in the mapping file these are exact in the Google sheet it shows as related HP:0000098-MP:0001254 not in MGI mapping file, in Google sheet as related HP:0007886-MP:0030171 not in MGI mapping file, in Google sheet as related

rays22 commented 9 months ago

The match types in the table don't match the match types in the MGI mapping file for some term pairs HP:0000506-MP:0030166 in the mapping file these are exact in the Google sheet it shows as related HP:0000098-MP:0001254 not in MGI mapping file, in Google sheet as related HP:0007886-MP:0030171 not in MGI mapping file, in Google sheet as related

Thank you @sbello for checking the table. I have removed the three incorrect lines from both the gsheet and the table above.

sbello commented 9 months ago

@rays22 we didn't check the entire spreadsheet just those 3 lines, once we saw they were all incorrect we stopped. We were hoping you could figure out why there were matches in the report that were not in the mapping file.

rays22 commented 9 months ago

@rays22 we didn't check the entire spreadsheet just those 3 lines, once we saw they were all incorrect we stopped. We were hoping you could figure out why there were matches in the report that were not in the mapping file.

There are some formatting issues with mh_mapping_initiative/mappings/mp_hp_mgi_all.sssom.tsv that that resulted in improper sorting of my results. I have fixed the tables now. I have spot checked a few lines in the updated table and they look fine to me. Please, give it another go.

obophenotype / upheno