Use of "mild" qualifier in HPO

I have conducted an analysis of some of the usages of the "mild" qualifier in HPO. There is a lack of systemization here which can hamper our ability to provide logical definitions. Whilst the items below should be fixed on a case by case basis, there should be a broad policy here of when to pre-coordinate qualified terms.

......is_a HP:0001388 ! Joint laxity .......is_a HP:0002771 ! Joint laxity, mild ***

......is_a HP:0004421 ! Elevated systolic blood pressure .......is_a HP:0004956 ! Systolic hypertension, mild ***

.......is_a HP:0002198 ! Enlarged fourth ventricle ........is_a HP:0007223 ! Enlarged fourth ventricle, mild ***

In these 3 cases, the mild subtype is an orphan.

Recommendation: pre-coordinate either all 3 or NONE of the qualified terms, using the pattern mild, moderate, severe or similar.

Note that this can be easily automated using tools like Obol or Shoge.

......is_a HP:0003390 ! Sensory axonal neuropathy .......is_a HP:0006883 ! Sensory axonal neuropathy, mild *** .......is_a HP:0007345 ! Distal sensory and motor axonal neuropathy

.....is_a HP:0002655 ! Spondyloepiphyseal dysplasia ......is_a HP:0002776 ! Mild spondyloepiphyseal dysplasia *** ......is_a HP:0005893 ! Spondyloepiphyseal dysplasia tarda

is the synonym for tarda not X-linked?

Recommendation: in cases like this we have two subtypes (tarda and non-tarda), and a number of severity bins (say, 3). This gives us 3 x 2 leaf nodes, plus parent classes. These should be pre-composed in a systematic way.

Also: use the same grammatical rules for all terms. Recommend: <condition>, <severity>

......is_a HP:0002109 ! Abnormality of the bronchi .......is_a HP:0002110 ! Bronchiectasis .......is_a HP:0002780 ! Bronchomalacia .......is_a HP:0002786 ! Tracheobronchomalacia .......is_a HP:0004469 ! Chronic bronchitis .......is_a HP:0006533 ! Bronchodysplasia, mild .......is_a HP:0006539 ! Bronchial cartilage hypoplasia .......is_a HP:0010777 ! Bronchomegaly

Here we have a term of the form "<condition>, mild" but no term that is simple <condition>.

These are trivial to find and are obvious areas for improvement.

"Chronic bronchitis" looks like another case (there is no bronchitis in HP), but this one is complicated by the disease/phenotype question.

It looks like DO is actually doing a good job with bronchitis. I suggest eliminating it from HPO:

.......is_a DOID:6132 ! bronchitis *** [DEF: "A bronchial disease that is an inflammation of the bronchial tubes. It is caused by bacteria and viruses. The symptoms include cough with mucus, shortness of breath, a low fever and chest tightness."] ........is_a DOID:6130 ! acute bronchitis [DEF: "A bronchitis that lasts from a few days to 10 days. It is caused by tobacco smoke, air pollution, dust, fumes and viruses that cause colds and the flu. The symptoms include cough, wheezing, low fever, and chest tightness or pain."] ........is_a DOID:9983 ! chronic bronchitis [DEF: "A bronchitis that occurs when the lining of the bronchial tubes is constantly irritated and inflamed, which results in cough with mucus on most days for at least 3 months a year and 2 years in a row. It is caused by smoking and repeatedly breathing in air pollutants, dust or fumes that irritate and damage lung and airway tissues leading to viral or bacterial growth. In severe cases, the lining of airways thicken and lots of thick mucus forms in the airways, making it hard to breathe."]

.....is_a HP:0000405 ! Conductive hearing impairment *** ......is_a HP:0000367 ! Conductive deafness .......is_a HP:0008513 ! Bilateral conductive deafness .......is_a HP:0008525 ! Congenital conductive deafness .......is_a HP:0008607 ! Progressive conductive deafness ......is_a HP:0000410 ! Mixed hearing loss ......is_a HP:0008536 ! Bilateral conductive hearing loss ......is_a HP:0008581 ! Early conductive hearing loss ......is_a HP:0008591 ! Congenital conductive hearing loss ......is_a HP:0008598 ! Mild conductive hearing impairment

Here we have multiple axes each only partially pre-composed:

* Bilateral, but no way to say unilateral

Congenital, but not aquired
Early, but not late
Mild, but no other severity (or is deafness considered = severe?)
Progressive, only available for deafness, no way to indicate non-progressive
Mixed, but no non-sensorineural

Why not just pre-compose the full cross-product?

....is_a HP:0001371 ! Contractures .....is_a HP:0001381 ! Joint contractures late .....is_a HP:0002803 ! Congenital contractures .....is_a HP:0002828 ! Multiple joint contractures .....is_a HP:0003121 ! Limb contractures .....is_a HP:0009473 ! Joint contractures involving the joints of the hand ......is_a HP:0005679 ! Dupuytren contractures ......is_a HP:0005814 ! Severe flexion contractures of hands and feet ......is_a HP:0006137 ! Finger and wrist contractures ......is_a HP:0006173 ! Contractures of the hands, mild ......is_a HP:0100490 ! Camptodactyly (hands)

There is a complete lack of consistent terminology here. Sometimes it's "contractures", sometimes it's "joint contractures". Sometimes it's "joint contractures involving joints of the hand", sometimes "contractures of the hand". And then we have "Severe flexion contractures of hands and feet"! In no other cases do we have the option of indicating the feet, and there is no way to indicate the non-severe version.

The qualifiers are highly inconsistent. We can modify "hand contractures" with mild, but no other qualifiers are available. The generic "contractures" has an exacy synonym which is "contractures, mild", which is bizarre.

........is_a HP:0000926 ! Platyspondyly .........is_a HP:0002940 ! Mild platyspondyly * .........is_a HP:0003321 ! Biconcave flattened vertebrae .........is_a HP:0003421 ! Platyspondyly (childhood) .........is_a HP:0004558 ! cervical platyspondyly .........is_a HP:0004565 ! severe platyspondyly ..........is_a HP:0008452 ! Wafer-thin platyspondyly .........is_a HP:0004588 ! lumbar platyspondyly, mild .........is_a HP:0004592 ! thoracic platyspondyly .........is_a HP:0004595 ! platyspondyly with anterior wedging .........is_a HP:0004598 ! platyspondyly with multiple extra ossification centers .........is_a HP:0004621 ! Large, flattened vertebrae with large pedicles .........is_a HP:0005641 ! Flattened cervical vertebral bodies .........is_a HP:0005644 ! Moderate platyspondyly .........is_a HP:0005752 ! Flattened moderately deformed vertebrae .........is_a HP:0005787 ! Lumbar platyspondyly .........is_a HP:0008418 ! Squared-off platyspondyly

"lumbar platyspondyly, mild" should be placed under "lumbar platyspondyly"

We can say "mild" for the core condition plus the lumbar form, "moderate" for the core form, and no way of saying "severe"

There is a conspicuous lack of definitions here!

No idea how good a source this is: http://www.gpnotebook.co.uk/simplepage.cfm?ID=x20051122114421615030&linkID=68948&cook=no&mentor=1

It suggests

"flattened PATO:0002254 vertebral body FMA:11945 shape with reduced distance PATO:0000375 beween the endplates(??)"

And the precomposition of a term "vertebra plana"

......is_a HP:0010628 ! Facial nerve palsy .......is_a HP:0000353 ! Facial muscle weakness, mild .......is_a HP:0001349 ! Facial diplegia .......is_a HP:0002058 ! Myopathic facies .......is_a HP:0002259 ! Facial muscle weakness, late .......is_a HP:0004661 ! Frontalis muscle weakness .......is_a HP:0005334 ! Facial paresis, usually bilateral .......is_a HP:0007209 ! Facial paralysis due to cranial nerve VII compression .......is_a HP:0200004 ! Facial muscle weakness, moderate

Remove "usually".

The usual mix of partially composed discriminating characteristics: etiology, severity, laterality, time, etc

......is_a HP:0000286 ! Epicanthus .......is_a HP:0000624 ! Epicanthal folds, mild *** .......is_a HP:0007930 ! Prominent epicanthal folds

......is_a HP:0001249 ! Intellectual disability .......is_a HP:0001256 ! Intellectual disability, mild .......is_a HP:0002187 ! Intellectual disability, profound .......is_a HP:0002342 ! Intellectual disability, moderate .......is_a HP:0006887 ! Intellectual disability, progressive .......is_a HP:0006889 ! Intellectual disability, borderline .......is_a HP:0007154 ! Nonprogressive intellectual disability .......is_a HP:0010864 ! Intellectual disability, severe

All qualified terms here are defined using IQ ranges. This one seems mostly fine, except for the lone "nonprogressive"

....is_a HP:0001510 ! Growth delay .....is_a HP:0000823 ! Delayed puberty .....is_a HP:0001508 ! Failure to thrive .....is_a HP:0001515 ! Prenatal growth deficiency .....is_a HP:0001517 ! Growth failure .....is_a HP:0001521 ! Severe growth retardation .....is_a HP:0001530 ! Growth retardation, mild .....is_a HP:0004322 ! Short stature .....is_a HP:0004325 ! Decreased body weight ### .....is_a HP:0008844 ! Mild-severe postnatal growth deficiency .....is_a HP:0008850 ! Postnatal growth retardation, severe .....is_a HP:0008855 ! Moderate growth deficiency .....is_a HP:0008860 ! Mild growth deficiency .....is_a HP:0008865 ! Postnatal growth failure .....is_a HP:0008868 ! Postnatal growth deceleration .....is_a HP:0008897 ! Growth retardation, progressive .....is_a HP:0008901 ! Mild-to-moderate growth deficiency *** .....is_a HP:0008917 ! Postnatal onset of mild growth retardation .....is_a HP:0008918 ! Growth retardation as children

Again a crazy mix of axes. These would be easier to discern if a consistent grammar were to be adopted. E.g. condition, <qualifier1>, ..., <qualifierN>.

"Decreased body weight" is surely placed incorrectly.

"Prenatal growth deficiency" (exact syn "Prenatal growth failure") should surely be a subclass of "Growth failure" rather than a sibling.

What is the relationship between "as children" and "post-natal"? Every "as children" is a subclass of "post-natal", yep?

This needs sorting out!

......is_a HP:0001272 ! Cerebellar atrophy .......is_a HP:0002364 ! Cerebellar atrophy, progressive ........is_a HP:0006879 ! Pontocerebellar atrophy .......is_a HP:0002470 ! Cerebellar ataxia, nonprogressive .......is_a HP:0007072 ! Cerebellar atrophy in most cases .......is_a HP:0007203 ! Cerebellar atrophy, mild *** .......is_a HP:0007263 ! Spinocerebellar atrophy .......is_a HP:0008278 ! Massive cerebellar cortical atrophy with vacuolated or binucleated purkinje cells .......is_a HP:0008303 ! Cerebellar atrophy with degeneration in the olivary nuclei .......is_a HP:0100275 ! Diffuse cerebellar atrophy .......is_a HP:0100321 ! Abnormality of the dentate nucleus ........is_a HP:0002461 ! Dense calcifications in the cerebellar dentate nucleus ........is_a HP:0007047 ! Atrophy of the dentate nucleus

"in most cases" has no place in the HPO. Each term should be applicable to a single case.

"Abnormality of the dentate nucleus" is surely placed wrongly. There are many abnormalities that are not atrophies.

"Cerebellar atrophy" has a bunch of synonyms related to MRI imaging - they should be removed.

Is "Pontocerebellar atrophy" always progressive?

is this the same as "Olivopontocerebellar atrophy"? E.g. http://emedicine.medscape.com/article/1151013-overview

Recommendation: ask Maryann Martone for help with this part of HPO

.....is_a HP:0009830 ! Peripheral neuropathy ......is_a HP:0000763 ! Sensory neuropathy ......is_a HP:0001271 ! Polyneuropathy ......is_a HP:0001301 ! Chronic sensorineural polyneuropathy ......is_a HP:0002934 ! Distal limb muscle atrophy due to peripheral neuropathy ......is_a HP:0002935 ! Distal limb muscle weakness due to peripheral neuropathy ......is_a HP:0003448 ! Decreased sensory nerve conduction velocities (NCV) ......is_a HP:0003489 ! Acute episodes of neuropathic symptoms ......is_a HP:0006865 ! Sensorimotor polyneuropathy affecting arms more than legs ......is_a HP:0006903 ! Congenital peripheral neuropathy ......is_a HP:0006949 ! Episodic peripheral neuropathy ......is_a HP:0007108 ! Demyelinating peripheral neuropathy ......is_a HP:0007133 ! Progressive peripheral neuropathy ......is_a HP:0007141 ! Sensorimotor neuropathy ......is_a HP:0007169 ! Axonal peripheral neuropathy ......is_a HP:0007178 ! Motor polyneuropathy ......is_a HP:0007235 ! Peripheral neuropathy, mild *** ......is_a HP:0007327 ! Mixed demyelinating and axonal polyneuropathy ......is_a HP:0009831 ! Mononeuropathy

Another mixed bag

.....is_a HP:0001324 ! Muscle weakness ......is_a HP:0002460 ! Distal muscle weakness .......is_a HP:0003728 ! Distal limb muscle weakness occurs later ## .......is_a HP:0003810 ! Distal muscle weakness occurs later ## .......is_a HP:0006940 ! Distal muscle weakness and atrophy .......is_a HP:0007340 ! Lower limb muscle weakness .......is_a HP:0008959 ! Distal weakness in arms then legs .......is_a HP:0009008 ! Distal muscle weakness, mild .......is_a HP:0009035 ! Distal muscle weakness in lower limbs, severe .......is_a HP:0009063 ! Muscle weakness, distal, progressive ......is_a HP:0003701 ! Proximal muscle weakness .......is_a HP:0003391 ! Gower sign .......is_a HP:0003694 ! Proximal muscle weakness occurs later .......is_a HP:0007195 ! Proximal neurogenic muscle weakness .......is_a HP:0008994 ! Proximal muscle weakness in lower limbs .......is_a HP:0008997 ! Proximal muscle weakness in upper limbs .......is_a HP:0009033 ! Proximal muscle weakness, mild .......is_a HP:0009073 ! Muscle weakness, progressive, proximal .......is_a HP:0009075 ! Muscle weakness, predominantly proximal

Are the two terms marked "#" not identical?

In addition, all the following marked synonyms are dubious or should at the least be marked as NARROW:

[Term] id: HP:0000252 ! Microcephaly name: Microcephaly synonym: "Decreased head circumference" EXACT [] ****synonym: "Microcephaly, mild" EXACT [] synonym: "Reduced head circumference" EXACT [] synonym: "Small head circumference" EXACT []

[Term] id: HP:0000316 ! Hypertelorism name: Hypertelorism synonym: "Hypertelorism, mild" EXACT [] synonym: "Increased interpupillary distance" EXACT [] synonym: "Marked hypertelorism" EXACT [] ****synonym: "Mild hypertelorism" EXACT [] synonym: "Ocular hypertelorism" EXACT [] synonym: "Wide-set eyes" EXACT []

[Term] id: HP:0000317 ! Facial myokymia name: Facial myokymia ****synonym: "Facial myokymia, mild" EXACT []

[Term] id: HP:0001270 ! Motor delay name: Motor delay synonym: "Delay in motor development" EXACT [] synonym: "Delayed motor development" EXACT [] synonym: "Delayed motor milestones" EXACT [] synonym: "Locomotor delay" EXACT [] ?synonym: "Motor delay" EXACT [] synonym: "Motor developmental delay" EXACT [] synonym: "Motor developmental milestones not achieved" EXACT [] synonym: "Motor retardation" EXACT [] ****synonym: "Motor retardation, mild" EXACT [] synonym: "Retarded motor development" EXACT []

[Term] id: HP:0001371 ! Contractures name: Contractures synonym: "Flexion contracture" EXACT [] synonym: "Flexion contractures" EXACT [] synonym: "Flexion contractures of joints" EXACT [] synonym: "Joint contracture" EXACT [] synonym: "Joint contractures" EXACT [] synonym: "Joint contractures, mild" EXACT [] synonym: "mild joint contractures" EXACT []

[Term] id: HP:0002194 ! Delayed gross motor development name: Delayed gross motor development synonym: "Delayed gross motor skills" EXACT [] synonym: "Delayed motor skills" EXACT [] synonym: "Developmental delay, gross motor" EXACT [] synonym: "Gross motor delay" EXACT [] ***synonym: "Gross motor delay, mild" EXACT [] ???synonym: "Limited gross motor development" EXACT []

[Term] id: HP:0002912 ! Methylmalonic acidemia name: Methylmalonic acidemia synonym: "Methylmalonic aciduria" EXACT [] ****synonym: "Methylmalonic aciduria, mild" EXACT [] synonym: "Methymalonicaciduria" EXACT []

[Term] id: HP:0002987 ! Elbow contractures name: Elbow contractures synonym: "Contractures of elbows" EXACT [] synonym: "Contractures of the elbows" EXACT [] synonym: "Elbow contracture" EXACT [] ***synonym: "Elbow contractures, mild" EXACT [] synonym: "Elbow flexion contracture" EXACT [] synonym: "Elbow flexion contractures" EXACT [] synonym: "Elbow flexion deformity" EXACT []

Reported by: cmungall

Original Ticket: obo/human-phenotype-requests/93

obophenotype / human-phenotype-ontology

Use of "mild" qualifier in HPO #93