axiomatize chromosomal diseases with monochrom ontology

[nicolevasilevsky]

Related to #387

http://obofoundry.org/ontology/monochrom

[nicolevasilevsky]

Per the Monarch huddle on 04/23/20- Nico will look into ‘pushing the button’ on the Monochrom ontology to make this live/usable. He will coordinate with Kent and Dipper group.

Would the next step would be to import it into Mondo? Or would we just bring in the classes we need for the axioms?

[nicolevasilevsky]

• Should we create a design pattern for these axioms too?

[cmungall]

yes, we will need various DPs

[cmungall]

First pass of classes amenable to axiomatization based on crude grep/perl based NER (will have omissions/commissions):

name
X-linked disease
Sotos syndrome 1
chromosome 18p deletion syndrome
chromosome 5q deletion syndrome
chromosome 9p deletion syndrome
recombinant 8 syndrome
split hand-foot malformation 3
mosaic variegated aneuploidy syndrome 1
X-linked myotubular myopathy-abnormal genitalia syndrome
syndromic X-linked intellectual disability Lubs type
X-linked intellectual disability-retinitis pigmentosa syndrome
fragile X syndrome
chromosome Xp21 deletion syndrome
chromosome Xp11.23-p11.22 duplication syndrome
chromosome Xq28 duplication syndrome
Xq27.3q28 duplication syndrome
X-linked acrogigantism due to Xq26 microduplication
Xq25 microduplication syndrome
X-linked diffuse leiomyomatosis-Alport syndrome
X-linked centronuclear myopathy
premature ovarian failure 1
Russell-silver syndrome, X-linked
chromosome 8Q12.1-q21.2 deletion syndrome
2q37 microdeletion syndrome
distal monosomy 10p
tetrasomy 12p
chromosome 18q deletion syndrome
distal monosomy 13q
homozygous 11P15-p14 deletion syndrome
chromosome 1p36 deletion syndrome
paternal uniparental disomy of chromosome 14
8q22.1 microdeletion syndrome
chromosome 22q11.2 microduplication syndrome
15q11q13 microduplication syndrome
chromosome 3q29 microdeletion syndrome
distal 10q deletion syndrome
14q22q23 microdeletion syndrome
7q11.23 microduplication syndrome
Rubinstein-Taybi syndrome due to 16p13.3 microdeletion
chromosome 22q11.2 deletion syndrome, distal
proximal 16p11.2 microdeletion syndrome
chromosome 3q29 microduplication syndrome
chromosome 15q13.3 microdeletion syndrome
chromosome 10q23 deletion syndrome
chromosome 2q32-q33 deletion syndrome
chromosome 2q31.2 deletion syndrome
chromosome 1q21.1 deletion syndrome
chromosome 1q21.1 duplication syndrome
chromosome 2p16.1-p15 deletion syndrome
chromosome 1q41-q42 deletion syndrome
chromosome 6pter-p24 deletion syndrome
chromosome 15q26-qter deletion syndrome
chromosome 6q24-q25 deletion syndrome
chromosome 19q13.11 deletion syndrome
chromosome 5p13 duplication syndrome
chromosome 17p13.3 duplication syndrome
chromosome 17q23.1-q23.2 deletion syndrome
chromosome 15q24 deletion syndrome
distal 16p11.2 microdeletion syndrome
chromosome 14q11-q22 deletion syndrome
chromosome 16p13.3 duplication syndrome
chromosome 4q21 deletion syndrome
chromosome 17q21.31 duplication syndrome
chromosome 6q11-q14 deletion syndrome
chromosome 2p12-p11.2 deletion syndrome
chromosome 16p12.2-p11.2 deletion syndrome
familial clubfoot due to 17q23.1q23.2 microduplication
chromosome 19p13.13 deletion syndrome
chromosome 2q31.1 duplication syndrome
distal 7q11.23 microdeletion syndrome
chromosome 1p32-p31 deletion syndrome
chromosome 17p13.1 deletion syndrome
3p- syndrome
chromosome 13q14 deletion syndrome
mosaic variegated aneuploidy syndrome 2
chromosome 8q21.11 deletion syndrome
tetrasomy 18p
chromosome 15q25 deletion syndrome
chromosome 2P16.3 deletion syndrome
chromosome 17q12 duplication syndrome
chromosome 17q12 deletion syndrome
chromosome 16q22 deletion syndrome
chromosome 16p11.2 duplication syndrome
distal tetrasomy 15q
chromosome 3q13.31 deletion syndrome
chromosome 22q13 duplication syndrome
8q24.3 microdeletion syndrome
chromosome 15q11.2 deletion syndrome
chromosome 5q12 deletion syndrome
motor developmental delay due to 14q32.2 paternally expressed gene defect
14q32 duplication syndrome
ring chromosome 14
16p13.2 microdeletion syndrome
15q14 microdeletion syndrome
chromosome 11p13 deletion syndrome, distal
Sotos syndrome 3
chromosome 19q13.11 deletion syndrome, proximal
48,XXYY syndrome
mosaic trisomy 3
pentasomy X
17q11.2 microduplication syndrome
ring chromosome 1
ring chromosome 10
ring chromosome 12
ring chromosome 17
ring chromosome 18
ring chromosome 19
ring chromosome 20
ring chromosome 21
ring chromosome 22
ring chromosome 4
ring chromosome 6
ring chromosome 7
chromosome 8-derived supernumerary ring/marker
non-distal monosomy 10q
distal monosomy 17q
2q24 microdeletion syndrome
deletion 5q35
distal monosomy 7q36
2p21 microdeletion syndrome
distal monosomy 9p
Xp22.3 microdeletion syndrome
partial chromosome Y deletion
mosaic trisomy 1
non-distal trisomy 10q
mosaic trisomy 12
trisomy 12p
non-distal trisomy 13q
mosaic trisomy 14
distal trisomy 14q
mosaic trisomy 15
distal trisomy 15q
mosaic trisomy 16
mosaic trisomy 17
trisomy 18p
distal trisomy 18q
distal trisomy 19q
6q16 deletion syndrome
trisomy 10p
mosaic trisomy 2
mosaic trisomy 20
trisomy 4p
trisomy 5p
distal trisomy 6p
mosaic trisomy 7
trisomy 8q
45,X/46,XY mixed gonadal dysgenesis
5q14.3 microdeletion syndrome
8q12 microduplication syndrome
2q23.1 microdeletion syndrome
5q35 microduplication syndrome
Beckwith-Wiedemann syndrome due to 11p15 microdeletion
Beckwith-Wiedemann syndrome due to 11p15 translocation/inversion
silver-Russell syndrome due to 7p11.2p13 microduplication
silver-Russell syndrome due to an imprinting defect of 11p15
silver-Russell syndrome due to 11p15 microduplication
silver-Russell syndrome due to maternal uniparental disomy of chromosome 11
trisomy 9p
1q44 microdeletion syndrome
paternal uniparental disomy of chromosome 1
maternal uniparental disomy of chromosome 1
2q31.1 microdeletion syndrome
2q33.1 microdeletion syndrome
ring chromosome 5
6p22 microdeletion syndrome
7q31 microdeletion syndrome
8p11.2 deletion syndrome
8p23.1 microdeletion syndrome
8p23.1 duplication syndrome
19p13.12 microdeletion syndrome
multiple congenital anomalies due to 14q32.2 maternally expressed gene defect
paternal 14q32.2 microdeletion syndrome
distal 7q11.23 microduplication syndrome
14q12 microdeletion syndrome
16p11.2p12.2 microduplication syndrome
14q11.2 microduplication syndrome
16p13.11 microdeletion syndrome
16p13.11 microduplication syndrome
16q24.3 microdeletion syndrome
distal 17p13.3 microdeletion syndrome
trisomy 17p
20p12.3 microdeletion syndrome
paternal 20q13.2q13.3 microdeletion syndrome
20q13.33 microdeletion syndrome
trisomy 20p
21q22.11q22.12 microdeletion syndrome
distal 22q11.2 microduplication syndrome
trisomy 1q
atypical Norrie disease due to monosomy Xp11.3
maternal uniparental disomy of chromosome X
paternal uniparental disomy of chromosome X
ring chromosome Y
49,XXXYY syndrome
Mowat-Wilson syndrome due to monosomy 2q22
blepharophimosis-epicanthus inversus-ptosis due to 3q23 rearrangement syndrome
familial adenomatous polyposis due to 5q22.2 microdeletion
Alagille syndrome due to 20p12 microdeletion
Okihiro syndrome due to 20q13 microdeletion
partial deletion of chromosome 1
partial deletion of chromosome 2
partial deletion of chromosome 3
partial deletion of chromosome 4
partial deletion of chromosome 5
partial deletion of chromosome 6
partial deletion of chromosome 7
partial deletion of chromosome 8
partial deletion of chromosome 9
partial deletion of chromosome 10
partial deletion of chromosome 11
partial deletion of the long arm of chromosome 12
partial deletion of chromosome 16
partial deletion of chromosome 17
partial deletion of chromosome 18
partial deletion of chromosome 19
partial deletion of chromosome 20
partial deletion of the short arm of chromosome 1
partial deletion of the short arm of chromosome 2
partial deletion of the short arm of chromosome 3
partial deletion of the short arm of chromosome 4
partial deletion of the short arm of chromosome 5
partial deletion of the short arm of chromosome 6
partial deletion of the short arm of chromosome 7
partial deletion of the short arm of chromosome 8
partial deletion of the short arm of chromosome 9
partial deletion of the short arm of chromosome 10
partial deletion of the short arm of chromosome 11
partial deletion of the short arm of chromosome 16
partial monosomy of the short arm of chromosome 17
partial deletion of the short arm of chromosome 18
partial deletion of the short arm of chromosome 19
partial monosomy of the short arm of chromosome 20
partial deletion of the long arm of chromosome 1
partial deletion of the long arm of chromosome 2
partial deletion of the long arm of chromosome 3
partial deletion of the long arm of chromosome 4
partial deletion of the long arm of chromosome 5
partial deletion of the long arm of chromosome 6
partial deletion of the long arm of chromosome 7
partial deletion of the long arm of chromosome 8
partial monosomy of the long arm of chromosome 9
partial monosomy of the long arm of chromosome 10
partial deletion of the long arm of chromosome 11
partial deletion of the long arm of chromosome 13
partial deletion of the long arm of chromosome 14
partial deletion of the long arm of chromosome 15
partial deletion of the long arm of chromosome 16
partial deletion of the long arm of chromosome 17
partial deletion of the long arm of chromosome 18
partial deletion of the long arm of chromosome 19
partial deletion of the long arm of chromosome 20
partial deletion of the long arm of chromosome 21
partial deletion of the long arm of chromosome 22
partial duplication of chromosome 1
partial duplication of chromosome 2
partial duplication of chromosome 3
partial duplication of chromosome 4
partial trisomy/tetrasomy of chromosome 5
partial duplication of chromosome 6
partial duplication of chromosome 7
partial duplication of chromosome 8
partial trisomy/tetrasomy of chromosome 9
partial duplication of chromosome 10
partial duplication of chromosome 11
partial trisomy/tetrasomy of the short arm of chromosome 12
partial duplication of chromosome 16
partial duplication of chromosome 17
partial trisomy/tetrasomy of chromosome 18
partial duplication of chromosome 19
partial trisomy of chromosome 20
partial duplication of the short arm of chromosome 2
partial duplication of the short arm of chromosome 3
partial duplication of the short arm of chromosome 4
partial trisomy/tetrasomy of the short arm of chromosome 5
partial duplication of the short arm of chromosome 6
partial duplication of the short arm of chromosome 7
partial duplication of the short arm of chromosome 8
partial trisomy of the short arm of chromosome 9
partial duplication of the short arm of chromosome 10
partial duplication of the short arm of chromosome 11
partial duplication of the short arm of chromosome 16
partial duplication of the short arm of chromosome 17
partial trisomy/tetrasomy of the short arm of chromosome 18
partial duplication of the long arm of chromosome 1
partial duplication of the long arm of chromosome 2
partial duplication of the long arm of chromosome 3
partial duplication of the long arm of chromosome 4
partial trisomy of the long arm of chromosome 5
partial duplication of the long arm of chromosome 6
partial duplication of the long arm of chromosome 7
partial duplication of the long arm of chromosome 8
partial trisomy of the long arm of chromosome 9
partial duplication of the long arm of chromosome 10
partial duplication of the long arm of chromosome 11
partial duplication of the long arm of chromosome 13
partial duplication of the long arm of chromosome 14
partial duplication of the long arm of chromosome 15
partial trisomy of the long arm of chromosome 16
partial duplication of the long arm of chromosome 17
partial trisomy of the long arm of chromosome 18
partial duplication of the long arm of chromosome 19
partial trisomy of the long arm of chromosome 20
partial duplication of the long arm of chromosome 22
X chromosome number anomaly
X chromosome number anomaly with female phenotype
X chromosome number anomaly with male phenotype
polysomy of X chromosome
partial deletion of chromosome X
partial monosomy of the short arm of chromosome X
Y chromosome number anomaly
X and Y chromosomal anomaly
partial deletion of the long arm of chromosome X
partial duplication of chromosome X
partial duplication of the short arm of chromosome X
partial duplication of the long arm of chromosome X
uniparental disomy of chromosome X
partial duplication of the short arm of chromosome 1
trisomy 8p
DYRK1A-related intellectual disability syndrome due to 21q22.13q22.2 microdeletion
10q22.3q23.3 microduplication syndrome
distal monosomy 12p
partial deletion of chromosome 12
facial dysmorphism-developmental delay-behavioral abnormalities syndrome due to 10p11.21p12.31 microdeletion
Xp22.13p22.2 duplication syndrome
12q15q21.1 microdeletion syndrome
microtriplication 11q24.1
distal Xq28 microduplication syndrome
1p21.3 microdeletion syndrome
2q31.1 microduplication syndrome
11p15.4 microduplication syndrome
20p13 microdeletion syndrome
12p12.1 microdeletion syndrome
2q23.1 microduplication syndrome
7p22.1 microduplication syndrome
Xq12-q13.3 duplication syndrome
15q overgrowth syndrome
severe neonatal hypotonia-seizures-encephalopathy syndrome due to 5q31.3 microdeletion
partial deletion of the short arm of chromosome 12
distal 17p13.1 microdeletion syndrome
9p13 microdeletion syndrome
duplication/inversion 15q11
tetrasomy 5p
tetrasomy 9p
trisomy X
trisomy 13
distal trisomy 17q
trisomy 18
16q24.1 microdeletion syndrome
neurodevelopmental disorder-craniofacial dysmorphism-cardiac defect-hip dysplasia syndrome due to 9q21 microdeletion
3q26q27 microdeletion syndrome
20q11.2 microduplication syndrome
distal monosomy 1q
2p13.2 microdeletion syndrome
17q21.31 microdeletion syndrome
2p21 microdeletion syndrome without cystinuria
homozygous 2p21 microdeletion syndrome
3q27.3 microdeletion syndrome
9q31.1q31.3 microdeletion syndrome
14q24.1q24.3 microdeletion syndrome
Angelman syndrome due to imprinting defect in 15q11-q13
13q12.3 microdeletion syndrome
3p25.3 microdeletion syndrome
11q22.2q22.3 microdeletion syndrome
20q11.2 microdeletion syndrome
19p13.3 microduplication syndrome
partial duplication of the short arm of chromosome 19
symptomatic form of fragile X syndrome in female carrier
1p35.2 microdeletion syndrome
22q11.2 deletion syndrome
monosomy 21
6q terminal deletion syndrome
monosomy 9q22.3
47,XYY syndrome
tetrasomy X
12q14 microdeletion syndrome
tetrasomy 21
mosaic trisomy 4
mosaic trisomy 5
mosaic trisomy 8
mosaic trisomy 10
mosaic trisomy 22
distal trisomy 1p36
distal trisomy 2p
distal trisomy 3p
4p16.3 microduplication syndrome
distal trisomy 7p
Beckwith-Wiedemann syndrome due to 11p15 microduplication
8p inverted duplication/deletion syndrome
distal trisomy 2q
3q26 microduplication syndrome
distal trisomy 4q
distal trisomy 5q
distal trisomy 6q
distal trisomy 8q
distal trisomy 9q
distal trisomy 10q
distal trisomy 11q
distal trisomy 13q
distal trisomy 16q
distal trisomy 20q
distal trisomy 22q
non-distal trisomy 9q
monosomy 22
distal monosomy 7p
distal monosomy 19p13.3
non-distal monosomy 7p
distal monosomy 4q
Kleefstra syndrome due to 9q34 microdeletion
distal monosomy 12q
distal monosomy 14q
distal monosomy 20q
non-distal monosomy 12q
non-distal monosomy 20q
monosomy 13q34
ring chromosome 2
ring chromosome 3
ring chromosome 9
ring chromosome 11
ring chromosome 13
ring chromosome 15
ring chromosome 16
maternal uniparental disomy of chromosome 2
maternal uniparental disomy of chromosome 4
maternal uniparental disomy of chromosome 6
silver-Russell syndrome due to maternal uniparental disomy of chromosome 7
maternal uniparental disomy of chromosome 9
maternal uniparental disomy of chromosome 14
maternal uniparental disomy of chromosome 16
maternal uniparental disomy of chromosome 20
maternal uniparental disomy of chromosome 21
maternal uniparental disomy of chromosome 22
paternal uniparental disomy of chromosome 5
paternal uniparental disomy of chromosome 6
paternal uniparental disomy of chromosome 7
Beckwith-Wiedemann syndrome due to paternal uniparental disomy of chromosome 11
paternal uniparental disomy of chromosome 20
paternal uniparental disomy of chromosome 21
X small rings
48,XXXY syndrome
49,XXXXY syndrome
isochromosome Y
maternal uniparental disomy of chromosome 13
46,XY disorder of sex development
syndrome with 46,XY disorder of sex development
chromosome Y structural anomaly
chromosome X structural anomaly
X-linked syndromic intellectual disability
Prader-Willi syndrome due to maternal uniparental disomy of chromosome 15
Prader-Willi syndrome due to paternal 15q11q13 deletion
Angelman syndrome due to maternal 15q11q13 deletion
Angelman syndrome due to paternal uniparental disomy of chromosome 15
isochromosomy Yp
isochromosomy Yq
monosomy X
mosaic monosomy X
paternal uniparental disomy of chromosome 13
48,XYYY syndrome
49,XYYYY syndrome
Turner syndrome due to structural X chromosome anomalies
mosaic trisomy 9
chromosome 17 abnormality
chromosome 11q trisomy
chromosome 12p deletion
chromosome 13q trisomy
chromosome 13q-mosaicism
chromosome 16 trisomy
chromosome 13p duplication
chromosome 16p13.3 deletion syndrome
chromosome 17p deletion
chromosome 18 mosaic monosomy
chromosome 1q deletion
chromosome 20 trisomy
chromosome 22, monosome mosaic
trisomy 22
chromosome 22q deletion
chromosome 3 duplication syndrome
chromosome 4 short arm deletion
chromosome 8 deletion
Kleefstra syndrome 1
partial duplication of chromosome 12
partial duplication of the long arm of chromosome 12
chromosome 1, uniparental disomy 1q12 q21
mosaic trisomy 6
chromosome 8, trisomy
16p12.1p12.3 triplication syndrome
9q33.3q34.11 microdeletion syndrome
4q25 proximal deletion syndrome
mosaic variegated aneuploidy syndrome 3
chromosome 1p35 deletion syndrome

[sabrinatoro]

Except for 2 terms which will be obsoleted in the June release, this project is done. Closing this issue.