OMIM labels

[mellybelly]

OMIM URIs are currently mostly leaf nodes (or merged as equiv classes if name is same as parent and there is only one child). However, there will occasionally be terms in DC or DO with the same label that don't meet requirements for the merge. Since we don't want to make equivalencies for these OMIM terms (or Decipher for that matter), these terms should be appended with (OMIM) in the label to distinguish them from their parents.
For example, you could have:

DOID_1932 Angelman's syndrome
--OMIM_105830 Angelman's syndrome
--Orphanet_98794 Angelman syndrome due to maternal 15q11q13 deletion

Here for example, we might like to have OMIM appended like this:
DOID_1932 Angelman's syndrome
--OMIM_105830 Angelman's syndrome (OMIM)
--Orphanet_98794 Angelman syndrome due to maternal 15q11q13 deletion

[pnrobinson]

Dear everybody,
note that Orphanet terms such as Orphanet_98794 Angelman syndrome due to maternal 15q11q13 deletion are not really consistent with the remaining Orphanet "philosophy" of being a clinical disease ontology rather than a molecular one (the latter being much more OMIM's role). I do not think it makes much sense for us to include them because actually to be consistent you would need to have similar terms in a lot of other places. In fact, this is one of the exceptional places where Orphanet has more molecular detail than OMIM. The DO term and the OMIM term are exact synonyms, and the Orphanet term is a subclass thereof.
-Peter

Dr. med. Peter N. Robinson, MSc.
Professor of Medical Genomics
Professor in the Bioinformatics Division of the Department of Mathematics and Computer Science of the Freie Universität Berlin
Institut für Medizinische Genetik und Humangenetik
Charité - Universitätsmedizin Berlin
Augustenburger Platz 1
13353 Berlin
Germany
+4930 450566006
Mobile: 0160 93769872
peter.robinson@charite.de
http://compbio.charite.de
http://www.human-phenotype-ontology.org
Introduction to Bio-Ontologies: http://www.crcpress.com/product/isbn/9781439836651
I have learned from my mistakes, and I am sure I can repeat them exactly
ORCID ID:http://orcid.org/0000-0002-0736-9199
Scopus Author ID 7403719646
Appointment request: http://doodle.com/pnrobinson

---

Von: Melissa Haendel [notifications@github.com]
Gesendet: Freitag, 13. März 2015 02:06
An: monarch-initiative/human-disease-ontology
Betreff: [human-disease-ontology] OMIM labels (#9)

OMIM URIs are currently mostly leaf nodes (or merged as equiv classes if name is same as parent and there is only one child). However, there will occasionally be terms in DC or DO with the same label that don't meet requirements for the merge. Since we don't want to make equivalencies for these OMIM terms (or Decipher for that matter), these terms should be appended with (OMIM) in the label to distinguish them from their parents.
For example, you could have:

DOID_1932 Angelman's syndrome
--OMIM_105830 Angelman's syndrome
--Orphanet_98794 Angelman syndrome due to maternal 15q11q13 deletion

Here for example, we might like to have OMIM appended like this:
DOID_1932 Angelman's syndrome
--OMIM_105830 Angelman's syndrome (OMIM)
--Orphanet_98794 Angelman syndrome due to maternal 15q11q13 deletion

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/9.

[cmungall]

Orphanet puts these under the class 'etiological subtype'. We treat these as metaclasses in our translation, and retain them as subsets (everything is a subclass of disease in mondo).

We could change the merge rule such that OMIMs are merged into their parent if the labels match and its the only non-etiological subtype child.

Just FYI here are all our classes in etiological_subtype subset:

 OMIM:130000 ! Ehlers-Danlos syndrome type 1
 OMIM:130010 ! Ehlers-Danlos syndrome type 2
 OMIM:145980 ! Familial hypocalciuric hypercalcemia type 1
 OMIM:145981 ! Familial hypocalciuric hypercalcemia type 2
 OMIM:215100 ! Rhizomelic chondrodysplasia punctata type 1
 OMIM:222765 ! Rhizomelic chondrodysplasia punctata type 2
 OMIM:261650 ! Phosphoenolpyruvate carboxykinase 2 deficiency
 OMIM:301050 ! X-linked Alport syndrome
 OMIM:600121 ! Rhizomelic chondrodysplasia punctata type 3
 OMIM:603592 ! Xanthinuria type II
 OMIM:608149 ! Paternal uniparental disomy of chromosome 14
 OMIM:614846 ! Distal tetrasomy 15q
 Orphanet:100050 ! Hereditary angioedema type 1
 Orphanet:100051 ! Hereditary angioedema type 2
 Orphanet:100054 ! Hereditary angioedema type 3
 Orphanet:101050 ! Familial hypocalciuric hypercalcemia type 3
 Orphanet:104077 ! Myopathic intestinal pseudoobstruction
 Orphanet:104078 ! Unclassified intestinal pseudoobstruction
 Orphanet:168609 ! Mitochondrial nonsyndromic sensorineural deafness with susceptibility to aminoglycoside exposure
 Orphanet:168629 ! Autosomal thrombocytopenia with normal platelets
 Orphanet:169615 ! Idiopathic central precocious puberty
 Orphanet:169618 ! Secondary central precocious puberty
 Orphanet:1707 ! Distal trisomy 15q
 Orphanet:177901 ! Prader-Willi syndrome due to paternal deletion of 15q11q13 type 1
 Orphanet:177904 ! Prader-Willi syndrome due to paternal deletion of 15q11q13 type 2
 Orphanet:177907 ! Prader-Willi syndrome due to translocation
 Orphanet:177910 ! Prader-Willi syndrome due to imprinting mutation
 Orphanet:1810 ! Autosomal dominant hypohidrotic ectodermal dysplasia
 Orphanet:217023 ! Atypical hemolytic uremic syndrome with thrombomodulin anomaly
 Orphanet:228329 ! CLN1 disease
 Orphanet:228337 ! CLN10 disease
 Orphanet:228340 ! CLN4A disease
 Orphanet:228343 ! CLN4B disease
 Orphanet:228346 ! CLN3 disease
 Orphanet:228349 ! CLN2 disease
 Orphanet:228354 ! CLN8 disease
 Orphanet:228357 ! CLN9 disease
 Orphanet:228360 ! CLN5 disease
 Orphanet:228363 ! CLN6 disease
 Orphanet:228366 ! CLN7 disease
 Orphanet:231117 ! Beckwith-Wiedemann syndrome due to imprinting defect of 11p15
 Orphanet:231120 ! Beckwith-Wiedemann syndrome due to CDKN1C mutation
 Orphanet:231127 ! Beckwith-Wiedemann syndrome due to 11p15 microdeletion
 Orphanet:231130 ! Beckwith-Wiedemann syndrome due to 11p15 translocation/inversion
 Orphanet:231137 ! Silver-Russell syndrome due to 7p11.2p13 microduplication
 Orphanet:231140 ! Silver-Russell syndrome due to imprinting defect of 11p15
 Orphanet:231144 ! Silver-Russell syndrome due to 11p15 microduplication
 Orphanet:231147 ! Silver-Russell syndrome due to maternal uniparental disomy of chromosome 11
 Orphanet:238269 ! Familial renal amyloidosis due to Apolipoprotein AII variant
 Orphanet:238578 ! Familial clubfoot due to 17q23.1q23.2 microduplication
 Orphanet:238613 ! Beckwith-Wiedemann syndrome due to NSD1 mutation
 Orphanet:247798 ! MUTYH-related attenuated familial adenomatous polyposis
 Orphanet:247806 ! APC-related attenuated familial adenomatous polyposis
 Orphanet:247839 ! Oligoarticular juvenile arthritis with anti-nuclear antibodies
 Orphanet:247846 ! Oligoarticular juvenile arthritis without anti-nuclear antibodies
 Orphanet:247854 ! Juvenile rheumatoid factor-negative polyarthritis with anti-nuclear antibodies
 Orphanet:247861 ! Juvenile rheumatoid factor-negative polyarthritis without anti-nuclear antibodies
 Orphanet:248 ! Autosomal recessive hypohidrotic ectodermal dysplasia
 Orphanet:254525 ! Paternal 14q32.2 microdeletion syndrome
 Orphanet:254528 ! Maternal 14q32.2 microdeletion syndrome
 Orphanet:254531 ! Paternal 14q32.2 hypomethylation syndrome
 Orphanet:254534 ! Maternal 14q32.2 hypermethylation syndrome
 Orphanet:261537 ! Mowat-Wilson syndrome due to monosomy 2q22
 Orphanet:261552 ! Mowat-Wilson syndrome due to a point mutation
 Orphanet:261559 ! Blepharophimosis - epicanthus inversus - ptosis due to 3q23 microdeletion
 Orphanet:261572 ! Blepharophimosis - epicanthus inversus - ptosis due to a point mutation
 Orphanet:261579 ! Blepharophimosis - epicanthus inversus - ptosis due to polyA expansion
 Orphanet:261584 ! Familial adenomatous polyposis due to 5q22.2 microdeletion
 Orphanet:261600 ! Alagille syndrome due to 20p12 microdeletion
 Orphanet:261619 ! Alagille syndrome due to a JAG1 point mutation
 Orphanet:261629 ! Alagille syndrome due to a NOTCH2 point mutation
 Orphanet:261638 ! Okihiro syndrome due to 20q13 microdeletion
 Orphanet:261647 ! Okihiro syndrome due to a point mutation
 Orphanet:261652 ! Kleefstra syndrome due to a point mutation
 Orphanet:275766 ! Idiopathic pulmonary arterial hypertension
 Orphanet:275777 ! Heritable pulmonary arterial hypertension
 Orphanet:293144 ! Familial clubfoot due to 5q31 microdeletion
 Orphanet:293150 ! Familial clubfoot due to PITX1 point mutation
 Orphanet:293633 ! PYCR1-related DeBarsy syndrome
 Orphanet:300525 ! Pseudohypoaldosteronism type 2D
 Orphanet:300530 ! Pseudohypoaldosteronism type 2E
 Orphanet:306588 ! Autosomal dominant Opitz G/BBB syndrome
 Orphanet:306597 ! X-linked Opitz G/BBB syndrome
 Orphanet:308386 ! Sulfite oxidase deficiency due to molybdenum cofactor deficiency type A
 Orphanet:308393 ! Sulfite oxidase deficiency due to molybdenum cofactor deficiency type B
 Orphanet:308400 ! Sulfite oxidase deficiency due to molybdenum cofactor deficiency type C
 Orphanet:314629 ! CLN11 disease
 Orphanet:314697 ! Acquired porencephaly
 Orphanet:319205 ! Bilateral massive adrenal hemorrhage
 Orphanet:319612 ! X-linked mendelian susceptibility to mycobacterial diseases due to IKBKG deficiency
 Orphanet:319623 ! X-linked mendelian susceptibility to mycobacterial diseases due to CYBB deficiency
 Orphanet:352709 ! CLN13 disease
 Orphanet:353327 ! Congenital myasthenic syndromes with glycosylation defect
 Orphanet:35664 ! ALDH18A1-related De Barsy syndrome
 Orphanet:357008 ! Atypical hemolytic uremic syndrome with DGKE deficiency
 Orphanet:363700 ! Neurofibromatosis type 1 due to NF1mutation or intragenic deletion
 Orphanet:363965 ! Koolen-De Vries syndrome due to a point mutation
 Orphanet:79271 ! Sanfilippo syndrome type C
 Orphanet:79272 ! Sanfilippo syndrome type D
 Orphanet:79316 ! Phosphoenolpyruvate carboxykinase 1 deficiency
 Orphanet:852 ! X-linked thrombocytopenia with normal platelets
 Orphanet:88918 ! Autosomal dominant Alport syndrome
 Orphanet:88919 ! Autosomal recessive Alport syndrome
 Orphanet:88938 ! Pseudohypoaldosteronism type 2A
 Orphanet:88939 ! Pseudohypoaldosteronism type 2B
 Orphanet:88940 ! Pseudohypoaldosteronism type 2C
 Orphanet:90625 ! X-linked nonsyndromic sensorineural deafness type DFN
 Orphanet:90635 ! Autosomal dominant nonsyndromic sensorineural deafness type DFNA
 Orphanet:90636 ! Autosomal recessive nonsyndromic sensorineural deafness type DFNB
 Orphanet:90641 ! Mitochondrial nonsyndromic sensorineural deafness
 Orphanet:93324 ! Autosomal recessive Kenny-Caffey syndrome
 Orphanet:93325 ! Autosomal dominant Kenny-Caffey syndrome
 Orphanet:93554 ! Type II mixed cryoglobulinemia
 Orphanet:93555 ! Mixed cryoglobulinemia type III
 Orphanet:93560 ! Familial renal amyloidosis due to Apolipoprotein AI variant
 Orphanet:93561 ! Familial renal amyloidosis due to lysozyme variant
 Orphanet:93562 ! Familial renal amyloidosis due to fibrinogen A alpha-chain variant
 Orphanet:93575 ! Atypical hemolytic uremic syndrome with C3 anomaly
 Orphanet:93576 ! Atypical hemolytic uremic syndrome with MCP/CD46 anomaly
 Orphanet:93578 ! Atypical hemolytic uremic syndrome with B factor anomaly
 Orphanet:93579 ! Atypical hemolytic uremic syndrome with H factor anomaly
 Orphanet:93580 ! Atypical hemolytic uremic syndrome with I factor anomaly
 Orphanet:93581 ! Atypical hemolytic uremic syndrome with anti-factor H antibodies
 Orphanet:93612 ! Cystinuria type A
 Orphanet:93613 ! Cystinuria type B
 Orphanet:96076 ! Beckwith-Wiedemann syndrome due to 11p15 microduplication
 Orphanet:96147 ! Kleefstra syndrome due to 9q34 microdeletion
 Orphanet:96182 ! Silver-Russell syndrome due to maternal uniparental disomy of chromosome 7
 Orphanet:96184 ! Maternal uniparental disomy of chromosome 14
 Orphanet:96193 ! Beckwith-Wiedemann syndrome due to paternal uniparental disomy of chromosome 11
 Orphanet:97367 ! Renal tubular dysgenesis due to twin-twin transfusion
 Orphanet:97368 ! Renal tubular dysgenesis drugs-related
 Orphanet:97369 ! Renal tubular dysgenesis of genetic origin
 Orphanet:98754 ! Prader-Willi syndrome due to maternal uniparental disomy of chromosome 15
 Orphanet:98793 ! Prader-Willi syndrome due to paternal 15q11q13 deletion
 Orphanet:98794 ! Angelman syndrome due to maternal 15q11q13 deletion
 Orphanet:98795 ! Angelman syndrome due to paternal uniparental disomy of chromosome 15
 Orphanet:98853 ! Autosomal dominant Emery-Dreifuss muscular dystrophy
 Orphanet:98855 ! Autosomal recessive Emery-Dreifuss muscular dystrophy
 Orphanet:98863 ! X-linked Emery-Dreifuss muscular dystrophy
 Orphanet:98885 ! Bleeding diathesis due to glycoprotein VI deficiency
 Orphanet:98886 ! Bleeding diathesis due to integrin alpha2-beta1 deficiency
 Orphanet:98913 ! Postsynaptic congenital myasthenic syndromes
 Orphanet:98914 ! Presynaptic congenital myasthenic syndromes
 Orphanet:98915 ! Synaptic congenital myasthenic syndromes
 Orphanet:99228 ! Mosaic monosomy X
 Orphanet:99413 ! Turner syndrome due to structural X chromosome anomalies
 Orphanet:99763 ! Familial hyperreninemic hypoaldosteronism type 1
 Orphanet:99764 ! Familial hyperreninemic hypoaldosteronism type 2
 Orphanet:99811 ! Neuronal intestinal pseudoobstruction
 Orphanet:99875 ! Ehlers-Danlos syndrome type 7A
 Orphanet:99876 ! Ehlers-Danlos syndrome type 7B
 Orphanet:99918 ! Streptococcal toxic-shock syndrome
 Orphanet:99919 ! Staphylococcal toxic-shock syndrome

[mellybelly]

I don't understand inclusion/exclusion criteria for subclassing of orphanet 'etiological subtype'. Some diseases are due to chromosomal variations, others to infectious agents, fine, but then there are so many other orphanet diseases that also have chromosomal variations that are not classified as etiological subtypes. Since there are no etiological subclasses other than that parent class, to me it seems we ought to just treat these as if they were subclass of 'disease'?

Also, we should define merge rules for each vocab. For example, maybe it is ok to merge an OMIM term into a DC or DO term (and orphanet?) when they have the same label and no siblings of any kind? Is the same true for an Orphanet term?

[cmungall]

I don't really know what the orphanet criteria are. We turn this into a subset which has no logical meaning (although we could in theory use the subset information to guide the merge procedure, but it seems this may be dangerous).

We should never have to merge an OMIM into a DC due to the way DC is created.

[cmungall]

This issue was moved to monarch-initiative/monarch-disease-ontology-RETIRED#13