Kids first HP terms

[sbello]

Set of terms from the KidsFirst project that have been added to HPO. We would like to determine if these exist in the MP and if not is it appropriate to add the term.

Term list: https://docs.google.com/spreadsheets/d/11EB7Kkbkeubtz3qnxfTqBpmXgyoj3uBYnzY_Jlr7HLw/edit?usp=sharing

[sbello]

New terms to consider adding (red on spreadsheet)

Left ventricular outflow tract obstruction child of "abnormal heart left ventricle outflow tract morphology" (MP:0010429)

facial muscle weakness - child of muscle weakness (MP:0000747) but I do not see any existing annotations mentioning face or facial under this term in MGI ADDED NEW TERM facial muscle weakness MP:0031314

facial hemangioma terms - MP has increased hemangioma incidence (MP:0002947) and specific terms for retinal and oral mucosa. There is also a generic hemangioma term but I think that should be obsoleted. In general for tumors we have abnormal tumor incidence terms rather than just bare tumor terms. We could add an abnormal and/or increased facial hemangioma incidence terms The MP term hemangioma MP:0014086 has been obsoleted. ADDED NEW TERMS: increased facial hemangioma incidence MP:0031292, decreased facial hemangioma incidence MP:0031293

abnormal cerebral vasculature morphology - child of abnormal brain vasculature morphology (MP:0004950) existing terms MP:0013821, MP:0010530, MP:0010023 would fall under this

left heart hypoplasia - child of heart hypoplasia (MP:0002740) there are annotations in MGI that would fall under the new term DISCUSS The MP has a term for ventricular hypoplasia MP:0000279

preauricular skin tag - child of abnormal periauricular region morphology (MP:0030096) no annotations in MGI for this ADDED NEW TERM preauricular skin tag MP:0031305

retractile testis - child of abnormal testis morphology (MP:0001146) 2 mentions of retracted testes in MGI but I don't think this is the same

abnormal facial skeleton morphology - new grouping term for multiple existing MP terms, child of abnormal cranium morphology and abnormal face morphology DISCUSS MP HAS TERM abnormal viscerocranium morphology MP:0005274 only under abnormal cranium morphology MP:0000438

abnormal/increased/decreased nevus incidence - child of MP:0009469 increased skin hamartoma incidence see HP:0003764

tethered cord - child of MP:0000955, need to look at the whole HPO branch from Abnormal conus terminalis morphology down

abdominal situs abnormality - child of MP:0004133, parent of MP:0011250 and MP:0011249 ADDED NEW TERM abdominal situs abnormality MP:0031284 using HPO definition (an abnormality of the abdominal situs, i.e., of the sidedness of the abdomen and its organs)

DONE! increased/decreased enchondroma incidence - child of MP:0010280/MP:0012426 (ADDED NEW TERMS increased enchondroma incidence MP:0031283 and decreased enchondroma incidence MP:0031282)

abnormal intestinal rotation - synonym intestinal malrotation, child of MP:0014023

Plagiocephaly - new child of MP:0000438 we may also want to add an abnormal skull shape parent term to group this and terms like 'domed skull' DISCUSS The MP has terms for abnormal head shape MP:0011495 and flat head MP:0012174

Pectus carinatum - new child of MP:0004134 ADDED NEW MP TERM pectus carinatum MP:0031277 DOUBLE CHECK SYNONYMS

Sacral dimple - need to think about location in MP

increased intermamillary distance - syn Wide intermamillary distance child of abnormal nipple morphology MP:0006078

[sbello]

Terms I have questions about (purple on spreadsheet)

Tetralogy of Fallot - collection of phenotypes

Brain imaging abnormality - I don't think we would want to put in a technique based grouper since a wider range of techniques could be used in model organisms

central nervous system degeneration - I seem to recall the the peripheral/central split was removed from the MP by Cindy at one point although there is still a term for peripheral nervous system degeneration. Should we remove this or add a central term?

[sbello]

Terms with multiple possible MP matches (yellow on spreadsheet)

Microtia - could match small ears (broader?) or outer ear hypoplasia (narrower?)

There are a few tumor terms that we have terms for both both the tumor and the tumor incidence (Hemangioma). This is not the standard MP approach. Usually we have just incidence terms.

Renal dysplasia - the HPO definition specifies "development" but the MP has dysplasia as a synonym for abnormal kidney morphology so should this match the morphology term or the development term in the MP? Based on placement and child terms in HPO this term is way more specific than the MP morphology term. Possibly also way more specific than the MP development term.

Renal agenesis - HPO term groups both bilateral and unilateral agenesis, MP only has the individual child terms no grouping term

[sbello]

Green on spreadsheet are terms that could use a new synonym

Orange - tumor terms. The MP deals with most tumor terms as increased tumor type incidence not just tumor type. This was done as populations have a baseline incidence of tumors and in most cases we are focused on a change in that incidence. It also provides a clear distinction between the tumor phenotype and the tumor as an anatomical entity. Will the mapping from an HPO tumor term to and MP tumor incidence work for KidsFirst?

Examples: Neurofibromas (HP:0001067) vs increased neurofibroma incidence (MP:0010314) Facial hemangioma (HP:0000329) vs increased facial hemangioma incidence (new term)

[sbello]

There are some cases of a mismatch between the upper structure of the MP and HPO. HPO has terms for abnormal X that could cover both morphology and physiology. MP has X phenotype then abnormal X morphology and abnormal X physiology branches. The MP does not have abnormal X that covers both. (gray on spreadsheet)

Examples:

Abnormality of limbs (HP:0040064) vs limbs/digits/tail phenotype (MP:0005371) and abnormal limb morphology (MP:0002109) (no physiology term in this case)

Abnormality of the face (HP:0000271) vs abnormal facial morphology (MP:0003743) (child of craniofacial branch, no physiology branch for the face)

Abnormality of the cardiovascular system (HP:0001626) vs cardiovascular system phenotype/abnormal cardiovascular system morphology/abnormal cardiovascular system physiology

[sbello]

More possible new terms

Single umbilical artery - I would be inclined to add a term for "decreased umbilical artery number" with a more species neutral definition, child of MP:0003230

Abnormality of the orbital region - consider adding abnormal orbital region under abnormal facial morphology DISCUSS THE MP HAS abnormal periorbital region morphology MP:0030038

Pes planus/flat foot/flat feet - possible parent MP:0000572 MP has nothing for foot arch, need to consider how this translates to mammals in general

DONE! Unilateral cryptorchidism - currently the MP has cryptorchidism but no term for unilateral ADDED NEW TERMS unilateral cryptorchism MP:0031286 and bilateral cryptorchism MP:0031287

MP has increased thyroid carcinoma incidence we may want to add an incidence term for papillary thyroid carcinoma (HP:0002895)

Excessive femoral anteversion child of abnormal femur morphology (MP:0000559) need to define this in a more general manner, HPO has this as a sibling to femoral bowing

Venous malformation (HP:0012721) child of abnormal vein morphology MP:0002725

Unilateral cleft palate child of cleft palate MP:0000111

Biliary atresia child of MP:0005083 abnormal biliary tract morphology

Thickened nuchal skin fold child of abnormal nuchal region morphology (MP:0012723)

Tracheobronchomalacia possibly child of abnormal bronchus morphology (MP:0002264) but since it also involves cartilage in the trachea we need to think about the placement ADDED NEW TERMS bronchomalacia MP:0031307 and tracheobronchomalacia MP:0031308. Tracheobronchomalacia is now a child of both bronchomalacia MP:0031307 and tracheomalacia MP:0013753)

Spondylolisthesis child of abnormal vertebral column morphology MP:0004703 ADDED NEW TERM spondylolisthesis MP:0031313

Dandy-Walker malformation - possibly this should be a related term of abnormal cerebellar cyst with the specific loaction in the fourth ventricle, if we add a term it would be a child of abnormal cerebellum morphology MP:0000849, there is one genotype MGI:5292226 with mention of a dandy walker malformation

Bronchopulmonary sequestration and children - child of abnormal lung morphology

[sbello]

Dysplasia issue - HPO generally uses X dysplasia to mean abnormalities arising from developmental issues. The MP has not done this generally dsyplasia is just a synonym of abnormal morphology with reference to a developmental origin. Potentially we could map the dysplasia terms to abnormal X morphology as a broad mapping or possibly it would be better to map to abnormal X development with a close mapping?

[sbello]

more questions

Strabismus exists in both MP and HPO but the definitions are different. I currently have these as "broad" since the MP term covers a broader range of phenotypes (no restricted by "bifoveal fixation"). Should these be exact? The additional restriction in the HPO is really defining the standard alignment of human eyes. Can we ignore this?

Hypothyroidism in HPO maps to decreased activity of thyroid gland in MP (exact synonym hypothyroidism) but the MP has hypothyroidism but defines this as "reduced function of this endocrine gland that normally produces hormones that regulate the metabolic rate of the body" and has separate terms for abnormal thyroid homone levels. HPO has this term defined as "Deficiency of thyroid hormone." and also has terms for thyroid hormone levels but the decreased terms do not relate to hypothyroidism. This makes me question the definition used by HPO.

[sbello]

Pulmonic stenosis (HP:0001642) I think this is an exact match to heart right ventricle outflow tract stenosis (MP:0010449). MP also has pulmonary valve stenosis (MP:0006128) as a child of heart right ventricle outflow tract stenosis. Searching for pulmonic stenosis brings back both but I think the outflow tract is better. The MP terms are located under morphology but the HPO terms are under physiology.

[sbello]

More new terms

Bronchopulmonary sequestration (HP:0010960) - child of lung cysts (MP:0004880)?

Preauricular cyst (HP:0040297) - potential parent MP:0030096 need to clarify definition as the HP uses sinus in the definition and states that may form a cyst so is the term cyst or sinus or are these the same?

Supraumbilical raphe (HP:0410276) - child of MP:0000157 need to consider the definition

Sternal pit (HP:0410277) - child of MP:0000157

Hydrocele testis (HP:0000034) - child of MP:0001146 NOTE: EXISTING MP TERM hydrocele MP:0003623 (synonym: hydrocele testis)

[sbello]

Ureterocele/ureterocele - I suspect these are an exact match but the definitions have details that do not match. Unclear if these are essential.

HP definition - A ureterocele is a congenital saccular dilatation of the distal segment of the ureter.

MP definition - saccular dilation of the terminal portion of the ureter that protrudes into the lumen of the urinary bladder, probably due to a congenital stenosis of the ureteric orifice meatus; most often associated with a duplicated collection system, where two ureters drain their respective kidney instead of one

How essential is: congenital protrudes into the lumen of the urinary bladder

I think we could ignore "probably due to a congenital stenosis of the ureteric orifice meatus; most often associated with a duplicated collection system, where two ureters drain their respective kidney instead of one" This information should be moved into a comment.

[sbello]

Coloboma/coloboma - while the text labels are identical the definitions are not

HP (HP:0000589) - A developmental defect characterized by a cleft of some portion of the eye or ocular adnexa.

MP (MP:0005262) - anomaly in which some of the structures of the eye are absent due to incomplete fusion of the fetal intraocular fissure during gestation

cleft vs absent seems like a big difference to me, but the child terms in MP mostly refer to "some part of the structure is absent" which seems closer to cleft so possibly it is just a language issue?

[sbello]

Review the definition of seizures (MP:0002064) "sudden and often acute manifestation of epileptic attack, sometimes convulsive"

Compare to HP definition - "A seizure is an intermittent abnormality of nervous system physiology characterised by a transient occurrence of signs and/or symptoms due to abnormal excessive or synchronous neuronal activity in the brain"

Is it correct to specify "epileptic attack" in the definition? What exactly does this mean?

[sbello]

Accessory spleen/accessory spleen

HP definition - An accessory spleen is a round, iso-echogenic, homogenic and smooth structure and is seen as a normal variant mostly on the medial contour of the spleen, near the hilus or around the lower pole. This has no pathogenic relevance.

MP definition - the splenic tissue is divided into equal masses; often related to situs inversus

despite identical labels these do not seem the same to me. Which is correct?

Related terms: Polysplenia (HP:0001748) The HP has the parent term Supernumerary spleens (HP:0009799) and the sibling Accessory spleen (HP:0001747). None of the text definitions match what the MP has for accessory spleens.

Definitions:

Polysplenia (HP:0001748) - Polysplenia is a congenital disease manifested by multiple small accessory spleens.

Supernumerary spleens (HP:0009799) - The presence of two or more accessory spleens.

The MP accessory spleen term has polysplenia as a synonym.