dosdp-patterns

Pattern directory

This is a listing of all the patterns hosted as part of this directory

Patterns in dosdp-patterns

Omim disease series by gene

This pattern is meant to be used for (1) OMIM Mendelian diseases (ie unitary genetic diseases, as described in PMID:33417889), including children of OMIM phenotypic series (OMIMPS), which are represented as grouping classes in Mondo, and (2) OMIA Mendelian diseases (https://omia.org/) which are defined by a variation in a gene. Notes about the OMIMPS (see also OMIM_phenotypic_series.yaml): - every instance of the OMIMPS metaclass should be equivalent to (via annotated xref) to something in OMIMPS namespace - the OMIMPS will never have an asserted causative gene as logical axiom (and no single causative gene in text def) - the OMIMPS must never be equivalent to an OMIM:nnnnnn (often redundant with the above rule) - the OMIMPS must have an acronym synonym, e.g. HPE - the OMIMPS must have two or more subclasses (direct or indirect) that are equivalent to OMIMs and conform to this pattern - the subclasses should (not must) have a logical def that uses the PS as a genus - the OMIM subclasses must have acronym synonyms that are the parent syn + number, e.g. HPE1, HPE2 - the primary label for the children should also be parent + {"type"} + number - the first member will usually have the same number local ID as the PS Examples: holoprosencephaly 1, 3M syndrome 1

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/disease_series_by_gene.yaml
Name	OMIM_disease_series_by_gene
Classes	MONDO:0000001, SO:0000704,
Variables	disease (MONDO:0000001), gene (SO:0000704),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432, 0000-0002-4142-7153,
Examples

Omim phenotypic series

This pattern is meant to be used for OMIM phenotypic series (OMIMPS), which are represented as grouping classes in Mondo. Note: - every instance of this metaclass should be equivalent to (via annotated xref) to something in OMIMPS namespace - it will never have an asserted causative gene as logical axiom (and no single causative gene in text def) - it must never be equivalent to an OMIM:nnnnnn (often redundant with the above rule) - it must have an acronym synonym, e.g. HPE - it must have two or more subclasses (direct or indirect) that are equivalent to OMIMs - the subclasses should (not must) have a logical def that uses the PS as a genus (see http://purl.obolibrary.org/obo/mondo/patterns/disease_series_by_gene.yaml) - the OMIM subclasses must have acronym synonyms that are the parent syn + number, e.g. HPE1, HPE2 - the primary label for the children should also be parent + {"type"} + number - the first member will usually have the same number local ID as the PS - the first member in OMIM usually has documentation that is pertinent to the parent PS - the members may(?) generally share high semantic similarity - All OMIMPS disease should have a has characteristic some inherited restricted, see http://purl.obolibrary.org/obo/mondo/sparql/omimps-should-be-inherited-violation.sparql Examples: holoprosencephaly OMIMPS:236100, '3-M syndrome'(http://purl.obolibrary.org/obo/MONDO_0007477) OMIMPS:236100.

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/OMIM_phenotypic_series.yaml
Name	OMIM_phenotypic_series
Classes	MONDO:0000001, MONDO:0021152,
Variables	disease (MONDO:0000001),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples

Acquired

Pattern for extending a etiology-generic disease class to an acquired form. Here acquired means that basis for the disease is acquired during the individuals lifetime. It need not exclude genetic etiology, but it excludes inherited.

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/acquired.yaml
Name	acquired
Classes	MONDO:0021141, MONDO:0000001,
Variables	disease (MONDO:0000001),
Contributors	0000-0002-6601-2165,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label
MONDO:0060779	acquired Fanconi syndrome	MONDO:0001083	Fanconi renotubular syndrome
MONDO:0045023	acquired adrenogenital syndrome	MONDO:0015898	adrenogenital syndrome
MONDO:0019846	acquired central diabetes insipidus	MONDO:0015790	central diabetes insipidus
MONDO:0015130	acquired chronic primary adrenal insufficiency	MONDO:0015129	chronic primary adrenal insufficiency
MONDO:0019193	acquired generalized lipodystrophy	MONDO:0027766	generalized lipodystrophy

See full table here

Acute

This pattern is applied to diseases that are described as having an acute onset, i.e. the sudden appearance of disease manifestations over a short period of time. Examples: acute bronchiolitis, acute liver failure

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/acute.yaml
Name	acute
Classes	PATO:0000389, MONDO:0000001,
Variables	disease (MONDO:0000001),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label
MONDO:0001930	acute cholangitis	MONDO:0004789	cholangitis
MONDO:0020683	acute disease	MONDO:0700096	human disease or disorder
MONDO:0004810	acute ethmoiditis	MONDO:0005756	ethmoid sinusitis
MONDO:0001912	acute frontal sinusitis	MONDO:0001121	frontal sinusitis
MONDO:0001080	acute gonococcal cervicitis	MONDO:0021157	gonococcal cervicitis

See full table here

Adenocarcinoma

Adenocarcinoma is a common cancer characterized by the presence of malignant glandular cells. This is a design pattern for classes representing adenocarcinomas based on their location. This may be the site of origin, but it can also represent a secondary site for metastatized cancer. We use the generic disease has location relation, which generalized over primary and secondary sites. Examples: adenocarcinoma of cervix uteri, pituitary adenocarcinoma (disease)

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/adenocarcinoma.yaml
Name	adenocarcinoma disease has location X
Classes	MONDO:0004970, owl:Thing,
Variables	location (owl:Thing),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples	mondo

Data preview:

defined:class	defined:class:label	location	location:label
MONDO:0003853	Bartholin gland adenocarcinoma	UBERON:0000460	major vestibular gland
MONDO:0003410	Wolffian duct adenocarcinoma	UBERON:0003074	mesonephric duct
MONDO:0018351	adenocarcinoma of penis	UBERON:0000989	penis
MONDO:0004173	adenocarcinoma of skene gland origin	UBERON:0010145	paraurethral gland
MONDO:0002670	ampulla of vater adenocarcinoma	UBERON:0004913	hepatopancreatic ampulla

See full table here

Adenoma

Adenomas are neoplasms arising from epithelium. This is a design pattern for classes representing adenomas based on their location. This may be the site of origin, but it can also represent a secondary site for metastatized cancer. We use the generic disease has location relation, which is generalized over primary and secondary sites. Examples: pituitary gland adenoma, breast adenoma

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/adenoma.yaml
Name	adenoma disease has location X
Classes	MONDO:0004972, owl:Thing,
Variables	location (owl:Thing),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples	mondo

Data preview:

defined:class	defined:class:label	location	location:label
MONDO:0003419	Bartholin gland adenoma	UBERON:0000460	major vestibular gland
MONDO:0021301	adenoma of nipple	UBERON:0002030	nipple
MONDO:0021303	adenoma of small intestine	UBERON:0002108	small intestine
MONDO:0003924	adrenal cortex adenoma	UBERON:0001235	adrenal cortex
MONDO:0006088	appendix adenoma	UBERON:0001154	vermiform appendix

See full table here

Adenosquamous carcinoma

An adenosquamous carcinoma is a carcinoma composed of malignant glandular cells and malignant squamous cells. This is a design pattern for classes representing adenosquamous carcinomas based on their location. This may be the site of origin, but it can also represent a secondary site for metastatized cancer. We use the generic 'disease has location' relation, which generalized over primary and secondary sites. Examples: adenosquamous breast carcinoma, [Bartholin gland adenosquamous carcinoma] (http://purl.obolibrary.org/obo/MONDO_0003555), gastric adenosquamous carcinoma

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/adenosquamous_carcinoma.yaml
Name	adenosquamous carcinoma disease has location X
Classes	MONDO:0006074, UBERON:0010000,
Variables	location (UBERON:0010000),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples	mondo

Data preview:

defined:class	defined:class:label	location	location:label
MONDO:0003555	Bartholin gland adenosquamous carcinoma	UBERON:0000460	major vestibular gland
MONDO:0003549	adenosquamous bile duct carcinoma	UBERON:0002394	bile duct
MONDO:0003548	adenosquamous breast carcinoma	UBERON:0000310	breast
MONDO:0003554	adenosquamous colon carcinoma	UBERON:0001155	colon
MONDO:0004973	adenosquamous lung carcinoma	UBERON:0002048	lung

See full table here

Adult

An instance of a disease that has an onset of signs or symptoms of disease between the age of 16 years or later (adult onset). Examples: adult brain stem neoplasm, adult-onset myasthenia gravis

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/adult.yaml
Name	adult
Classes	HP:0003581, MONDO:0000001,
Variables	disease (MONDO:0000001),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label
MONDO:0017723	Sandhoff disease, adult form	MONDO:0010006	Sandhoff disease
MONDO:0060778	adult Fanconi syndrome	MONDO:0001083	Fanconi renotubular syndrome
MONDO:0016091	adult Krabbe disease	MONDO:0009499	Krabbe disease
MONDO:0100486	adult acne	MONDO:0011438	acne
MONDO:0100130	adult acute respiratory distress syndrome	MONDO:0006502	acute respiratory distress syndrome

See full table here

Allergic form of disease

An etiological pattern that extends an etiology-generic disease to an allergic form (i.e. caused by pathological type I hypersensitivity reaction). The allergy.yaml pattern is to refine an existing disease by trigger. Examples: allergic respiratory disease, atopic eczema, allergic otitis media

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/allergic_form_of_disease.yaml
Name	allergic_form_of_disease
Classes	MONDO:0000001, GO:0016068,
Variables	disease (MONDO:0000001),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label
MONDO:0005271	allergic disease	MONDO:0000001	disease or disorder
MONDO:0021202	allergic otitis media	MONDO:0005441	otitis media
MONDO:0011786	allergic rhinitis	MONDO:0003014	rhinitis

See full table here

Allergy

Allergy classified according to allergic trigger. This pattern is to refine an existing disease by trigger, the allergic_form_of_disease.yaml pattern is for a generic disease. Examples: egg allergy, peach allergy, gluten allergy

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/allergy.yaml
Name	allergy
Classes	MONDO:0005271, owl:Thing,
Variables	substance (owl:Thing),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples

Autoimmune

An instance of a disease that is brought about or caused by autoimmunity. Examples: autoimmune cardiomyopathy, autoimmune pancreatitis

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/autoimmune.yaml
Name	autoimmune
Classes	MONDO:0000001, HP:0002960,
Variables	disease (MONDO:0000001),
Contributors	0000-0002-6601-2165,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label
MONDO:0007179	autoimmune disease	MONDO:0000001	disease or disorder
MONDO:0000587	autoimmune disease of ear, nose and throat	MONDO:0024623	otorhinolaryngologic disease
MONDO:0018242	autoimmune hypoparathyroidism	MONDO:0001220	hypoparathyroidism
MONDO:0022518	autoimmune inner ear disease	MONDO:0002467	inner ear disorder
MONDO:0017979	autoimmune lymphoproliferative syndrome	MONDO:0016537	lymphoproliferative syndrome

See full table here

Autoimmune inflammation

An instance of an autoimmune disease that is described by inflammation in a specific anatomical entity. Example: autoimmune thyroid disease

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/autoimmune_inflammation.yaml
Name	autoimmune_inflammation
Classes	MONDO:0007179, UBERON:0000061,
Variables	location (UBERON:0000061),
Contributors	0000-0002-6601-2165,
Examples	mondo

Data preview:

defined:class	defined:class:label	location	location:label
MONDO:0005623	autoimmune thyroid disease	UBERON:0002046	thyroid gland

See full table here

Autosomal dominant

This pattern is applied to autosomal dominant forms of an inherited disease. Examples: autosomal dominant cerebellar ataxia, autosomal dominant osteopetrosis

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/autosomal_dominant.yaml
Name	autosomal_dominant
Classes	HP:0000006, MONDO:0000001,
Variables	disease (MONDO:0000001),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label
MONDO:0007086	autosomal dominant Alport syndrome	MONDO:0018965	Alport syndrome
MONDO:0007524	autosomal dominant Ehlers-Danlos syndrome, vascular type	MONDO:0017314	Ehlers-Danlos syndrome, vascular type
MONDO:0007478	autosomal dominant Kenny-Caffey syndrome	MONDO:0016516	Kenny-Caffey syndrome
MONDO:0007779	autosomal dominant Opitz G/BBB syndrome	MONDO:0017138	Opitz G/BBB syndrome
MONDO:0008389	autosomal dominant Robinow syndrome	MONDO:0019978	Robinow syndrome

See full table here

Autosomal recessive

This pattern is applied to autosomal recessive forms of an inherited disease. Examples: autosomal recessive brachyolmia, autosomal recessive sideroblastic anemia

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/autosomal_recessive.yaml
Name	autosomal_recessive
Classes	HP:0000007, MONDO:0000001,
Variables	disease (MONDO:0000001),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label
MONDO:0008762	autosomal recessive Alport syndrome	MONDO:0018965	Alport syndrome
MONDO:0002014	autosomal recessive Ehlers-Danlos syndrome, vascular type	MONDO:0017314	Ehlers-Danlos syndrome, vascular type
MONDO:0009486	autosomal recessive Kenny-Caffey syndrome	MONDO:0016516	Kenny-Caffey syndrome
MONDO:0009999	autosomal recessive Robinow syndrome	MONDO:0019978	Robinow syndrome
MONDO:0016647	autosomal recessive Stickler syndrome	MONDO:0019354	Stickler syndrome

See full table here

Basis in disruption of process

A pattern for generic groupings of diseases based around the molecular basis for the disease in terms of a GO molecular function or cellular process. For example: DNA repair or RAS signaling

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/basis_in_disruption_of_process.yaml
Name	basis_in_disruption_of_process
Classes	MONDO:0000001, BFO:0000015,
Variables	process (BFO:0000015),
Contributors	0000-0002-6601-2165,
Examples	mondo

Data preview:

defined:class	defined:class:label	process	process:label
MONDO:0012996	AGAT deficiency	GO:0015068	glycine amidinotransferase activity
MONDO:0021190	DNA repair disease	GO:0006281	DNA repair
MONDO:0018274	GM3 synthase deficiency	GO:0047291	lactosylceramide alpha-2,3-sialyltransferase activity
MONDO:0021060	RASopathy	GO:0007265	Ras protein signal transduction
MONDO:0005271	allergic disease	GO:0016068	type I hypersensitivity

See full table here

Benign

This is a design pattern for classes representing benign neoplasms, extending a generic neoplasm class. For example, a benign adrenal gland pheochromocytoma, defined as being the benign form of the more general adrenal gland pheochromocytoma. TODO: encode alternate way of representing

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/benign.yaml
Name	benign
Classes	MONDO:0005070, PATO:0002096,
Variables	neoplasm (MONDO:0005070),
Contributors	0000-0002-6601-2165,
Examples	mondo

Data preview:

defined:class	defined:class:label	neoplasm	neoplasm:label
MONDO:0036990	benign Leydig cell tumor	MONDO:0006266	Leydig cell tumor
MONDO:0020581	benign PEComa	MONDO:0006359	neoplasm with perivascular epithelioid cell differentiation
MONDO:0006103	benign adrenal gland pheochromocytoma	MONDO:0004974	adrenal gland pheochromocytoma
MONDO:0036781	benign axillary neoplasm	MONDO:0036779	axillary neoplasm
MONDO:0002065	benign breast adenomyoepithelioma	MONDO:0002066	breast adenomyoepithelioma

See full table here

Benign neoplasm

Neoplasms are benign or malignant tissue growths resulting from uncontrolled cell proliferation cell types. This is a design pattern for classes representing benign neoplasms based on their location. See also: benign.yaml TODO: choose one over another

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/benign_neoplasm.yaml
Name	benign_neoplasm
Classes	MONDO:0005165, owl:Thing,
Variables	location (owl:Thing),
Contributors	0000-0002-6601-2165,
Examples	mondo

Data preview:

defined:class	defined:class:label	location	location:label
MONDO:0002193	Bartholin gland benign neoplasm	UBERON:0000460	major vestibular gland
MONDO:0044764	benign choroid plexus neoplasm	UBERON:0001886	choroid plexus
MONDO:0002278	benign colon neoplasm	UBERON:0001155	colon
MONDO:0006105	benign conjunctival neoplasm	UBERON:0001811	conjunctiva
MONDO:0000385	benign digestive system neoplasm	UBERON:0005409	alimentary part of gastrointestinal system

See full table here

Cancer

Cancers are malignant neoplasms arising from a variety of different cell types. This is a design pattern for classes representing cancers based on their location. This may be the site of origin, but it can also represent a secondary site for metastatized cancer. We use the generic 'disease has location' relation, which generalized over primary and secondary sites.

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/cancer.yaml
Name	cancer
Classes	MONDO:0004992, owl:Thing,
Variables	location (owl:Thing),
Contributors	0000-0002-6601-2165,
Examples	mondo

Data preview:

defined:class	defined:class:label	location	location:label
MONDO:0000954	Meckel diverticulum cancer	UBERON:0003705	Meckel's diverticulum
MONDO:0004685	Waldeyer's ring cancer	UBERON:0001735	tonsillar ring
MONDO:0002817	adrenal gland cancer	UBERON:0002369	adrenal gland
MONDO:0003606	adrenal medulla cancer	UBERON:0001236	adrenal medulla
MONDO:0000919	ampulla of vater cancer	UBERON:0004913	hepatopancreatic ampulla

See full table here

Carcinoma

Carcinomas are malignant neoplasms arising from epithelial cells. This is a Design pattern for classes representing carcinomas based on their location. This may be the site of origin, but it can also represent a secondary site for metastatized cancer. We use the generic 'disease has location' relation, which generalized over primary and secondary sites.

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/carcinoma.yaml
Name	carcinoma
Classes	MONDO:0004993, owl:Thing,
Variables	location (owl:Thing),
Contributors	0000-0002-6601-2165,
Examples	mondo

Data preview:

defined:class	defined:class:label	location	location:label
MONDO:0003975	Littre gland carcinoma	UBERON:0010186	male urethral gland
MONDO:0004965	acinar cell carcinoma	CL:0000622	acinar cell
MONDO:0002814	adrenal carcinoma	UBERON:0002369	adrenal gland
MONDO:0006639	adrenal cortex carcinoma	UBERON:0001235	adrenal cortex
MONDO:0004202	adrenal medulla carcinoma	UBERON:0001236	adrenal medulla

See full table here

Carcinoma in situ

This is a Design pattern for classes representing in situ carcinomas based on their location. Examples: breast carcinoma in situ, liver carcinoma in situ

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/carcinoma_in_situ.yaml
Name	carcinoma_in_situ
Classes	MONDO:0004647, owl:Thing,
Variables	location (owl:Thing),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples	mondo

Data preview:

defined:class	defined:class:label	location	location:label
MONDO:0004707	anal canal carcinoma in situ	UBERON:0000159	anal canal
MONDO:0000374	bile duct carcinoma in situ	UBERON:0002394	bile duct
MONDO:0004703	bladder carcinoma in situ	UBERON:0001255	urinary bladder
MONDO:0004658	breast carcinoma in situ	UBERON:0000310	breast
MONDO:0000375	bronchus carcinoma in situ	UBERON:0002185	bronchus

See full table here

Childhood

An instance of a disease that has an onset of signs or symptoms of disease between the age of 1 to 5 years (childhood onset). Examples: childhood astrocytic tumor, childhood malignant melanoma

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/childhood.yaml
Name	childhood
Classes	HP:0011463, MONDO:0000001,
Variables	disease (MONDO:0000001),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label
MONDO:0044767	childhood adrenal gland pheochromocytoma	MONDO:0004974	adrenal gland pheochromocytoma
MONDO:0022642	childhood carcinoid tumor	MONDO:0005369	carcinoid tumor
MONDO:0004535	childhood choriocarcinoma of the ovary	MONDO:0003507	choriocarcinoma of ovary
MONDO:0003788	childhood embryonal testis carcinoma	MONDO:0006446	testicular embryonal carcinoma
MONDO:0004082	childhood immature teratoma of ovary	MONDO:0018369	immature ovarian teratoma

See full table here

Chromosomal region deletion

This pattern is meant to be used for chromosomal disorder which consists of the deletion of chromosomal region in which the chromosomal region is known. Note that to refer to a partial deletion of a chromosome when the region is not know (only the chromosome is known), the partial_chromosome_deletion pattern should be used.

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/chromosomal_region_deletion.yaml
Name	chromosomal_region_deletion
Classes	MONDO:0000761, GO:0098687,
Variables	chromosomal_region (GO:0098687),
Contributors	0000-0002-4142-7153,
Examples	mondo

Data preview:

defined:class	defined:class:label	chromosomal:region	chromosomal:region:label
MONDO:0018632	11q22.2q22.3 microdeletion syndrome	CHR:9606-chr11q22.2-q22.3	11q22.2-q22.3 (Human)
MONDO:0017781	12p12.1 microdeletion syndrome	CHR:9606-chr12p12.1	12p12.1 (Human)
MONDO:0019784	12q14 microdeletion syndrome	CHR:9606-chr12q14	12q14 (Human)
MONDO:0017334	12q15q21.1 microdeletion syndrome	CHR:9606-chr12q15-q21.1	12q15-q21.1 (Human)
MONDO:0018474	13q12.3 microdeletion syndrome	CHR:9606-chr13q12.3	13q12.3 (Human)

See full table here

Chromosomal region duplication

This pattern is meant to be used for chromosomal disorder which consists in the duplication of chromosomal region in which the chromosomal region is known. "Duplication" means an increase of copy number, and includes an extra copy (partial trisomy) and 2 extra copies (partial tetrasomy, also called triplication) of chromosomal region. Note that this pattern does not include the duplication of the entire chromosome (trisomy, tetrasomy, pentasomy).

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/chromosomal_region_duplication.yaml
Name	chromosomal_region_duplication
Classes	MONDO:0000762, GO:0098687,
Variables	chromosomal_region (GO:0098687),
Contributors	0000-0002-4142-7153,
Examples	mondo

Data preview:

defined:class	defined:class:label	chromosomal:region	chromosomal:region:label
MONDO:0017180	10q22.3q23.3 microduplication syndrome	CHR:9606-chr10q22.3-q23.3	10q22.3-q23.3 (Human)
MONDO:0017580	11p15.4 microduplication syndrome	CHR:9606-chr11p15.4	11p15.4 (Human)
MONDO:0016835	14q11.2 microduplication syndrome	CHR:9606-chr14q11.2	14q11.2 (Human)
MONDO:0012081	15q11q13 microduplication syndrome	CHR:9606-chr15q11-q13	15q11-q13 (Human)
MONDO:0016834	16p11.2p12.2 microduplication syndrome	CHR:9606-chr16p11.2-p12.2	16p11.2-p12.2 (Human)

See full table here

Chromosome type

This pattern is meant to be used for chromosomal disorder defined by the chromosome affected.

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/chromosome_type.yaml
Name	chromosome_type
Classes	MONDO:0019040, GO:0005694,
Variables	chromosome (GO:0005694),
Contributors	0000-0002-4142-7153,
Examples	mondo

Data preview:

defined:class	defined:class:label	chromosome	chromosome:label
MONDO:0700008	chromosome 1 disorder	CHR:9606-chr1	chromosome 1 (Human)
MONDO:0700017	chromosome 10 disorder	CHR:9606-chr10	chromosome 10 (Human)
MONDO:0700018	chromosome 11 disorder	CHR:9606-chr11	chromosome 11 (Human)
MONDO:0700019	chromosome 12 disorder	CHR:9606-chr12	chromosome 12 (Human)
MONDO:0700020	chromosome 13 disorder	CHR:9606-chr13	chromosome 13 (Human)

See full table here

Chronic

This pattern is applied to diseases that are described as having an chronic duration, i.e. a disease having a slow progressive course of indefinite duration. Examples: chronic bronchitis, chronic hepatitis B virus infection

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/chronic.yaml
Name	chronic
Classes	PATO:0001863, MONDO:0000001,
Variables	disease (MONDO:0000001),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label
MONDO:0004924	chronic canaliculitis	MONDO:0005631	actinomycosis
MONDO:0004786	chronic cholangitis	MONDO:0004789	cholangitis
MONDO:0015574	chronic cutaneous lupus erythematosus	MONDO:0005282	cutaneous lupus erythematosus
MONDO:0004806	chronic eosinophilic pneumonia	MONDO:0005749	eosinophilic pneumonia
MONDO:0004757	chronic ethmoidal sinusitis	MONDO:0005756	ethmoid sinusitis

See full table here

Congenital

An instance of a disease in which the disease is present at birth, regardless of cause. Examples: congenital agammaglobulinemia, congenital nystagmus

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/congenital.yaml
Name	congenital
Classes	MONDO:0021140, MONDO:0000001,
Variables	disease (MONDO:0000001),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label
MONDO:0001902	congenital agammaglobulinemia	MONDO:0015977	agammaglobulinemia
MONDO:0017375	congenital enterovirus infection	MONDO:0005747	enterovirus infectious disease
MONDO:0018612	congenital hypothyroidism	MONDO:0005420	hypothyroidism
MONDO:0017361	congenital rubella syndrome	MONDO:0004656	rubella
MONDO:0005714	congenital syphilis	MONDO:0005976	syphilis

See full table here

Consequence of infectious disease

This pattern is applied to a disease that is caused by an infectious agent. Examples: hepatitis C induced liver cirrhosis, rubella encephalitis

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/consequence_of_infectious_disease.yaml
Name	consequence_of_infectious_disease
Classes	MONDO:0000001, MONDO:0005550,
Variables	parent (MONDO:0000001), cause (MONDO:0005550),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples	mondo

Data preview:

defined:class	defined:class:label	cause	cause:label	parent	parent:label
MONDO:0020689	AIDS dementia complex	MONDO:0005109	HIV infectious disease	MONDO:0001627	dementia
MONDO:0002812	infectious otitis interna	MONDO:0005550	infectious disease	MONDO:0002008	labyrinthitis
MONDO:0021673	post-bacterial disorder	MONDO:0005113	bacterial infectious disease	MONDO:0000001	disease or disorder
MONDO:0021669	post-infectious disorder	MONDO:0005550	infectious disease	MONDO:0000001	disease or disorder
MONDO:0021670	post-infectious syndrome	MONDO:0005550	infectious disease	MONDO:0002254	syndromic disease

See full table here

Dependence on substance

Dependence on a substance that specifies the environmental stimulus such as alcohol, cocaine, etc. Example: dependence on cocaine.

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/dependence_on_substance.yaml
Name	dependence_on_substance
Classes	MONDO:0004938, CHEBI:24431,
Variables	stimulus (CHEBI:24431),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432, 0000-0002-7463-6306,
Examples

Disease by dysfunctional structure

Diseases classified by a perturbation in an anatomical structure (such as a subcellular component, or an organ)

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/disease_by_dysfunctional_structure.yaml
Name	disease_by_dysfunctional_structure
Classes	MONDO:0000001, UBERON:0000061,
Variables	structure (UBERON:0000061),
Contributors	0000-0002-6601-2165,
Examples	mondo

Data preview:

defined:class	defined:class:label	structure	structure:label
MONDO:0004880	bowel dysfunction	UBERON:0004907	lower digestive tract
MONDO:0001343	impaired renal function disease	UBERON:0002113	kidney

See full table here

Disease has major feature

Diseases which have a phenotype as a major feature of the disease are included in this pattern, e.g. scurvy (MONDO:0009412) which has the major feature of low levels of vitamin C (HP:0100510).

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/disease_has_major_feature.yaml
Name	disease_has_phenotype
Classes	MONDO:0005070, HP:0000118,
Variables	disease (MONDO:0005070), phenotypic abnormality (HP:0000118),
Contributors	0000-0002-7463-6306,
Examples

Disease or disease like

This pattern is for grouping classes to group terms that are disease or disease-like. Sometimes we feel there is insufficient reason to group, and X and X-like are not connected via shared is-a but instead by shares-features-with. Children of this grouping class should be X and X-like disease. Examples: viral disease or post-viral disorder

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/disease-or-disease-like.yaml
Name	disease or disease-like
Classes	MONDO:0000001,
Variables	disease1 (MONDO:0000001), disease2 (MONDO:0000001),
Contributors	0000-0001-5208-3432,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease1	disease1:label	disease2	disease2:label
MONDO:0100318	SARS-CoV-2-related disease	MONDO:0100096	COVID-19	MONDO:0100320	post-COVID-19 disorder
MONDO:0100318	SARS-CoV-2-related disease	MONDO:0100320	post-COVID-19 disorder	MONDO:0100096	COVID-19
MONDO:0700003	obstetric disorder	MONDO:0024575	pregnancy disorder	MONDO:0044013	puerperal disorder
MONDO:0700003	obstetric disorder	MONDO:0044013	puerperal disorder	MONDO:0024575	pregnancy disorder
MONDO:0006964	secondary hyperparathyroidism	MONDO:0001530	secondary hyperparathyroidism of renal origin	MONDO:0001750	non-renal secondary hyperparathyroidism

See full table here

Disease series by gene

This pattern is for diseases that are caused by a single variation or mutation in a single gene, that have gene-based names, such as new disease terms that are requested by ClinGen, like MED12-related intellectual disability syndrome. See more details about disease naming in Mondo here. Examples: MED12-related intellectual disability syndrome, TTN-related myopathy, MYPN-related myopathy

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/disease_series_by_gene.yaml
Name	disease_series_by_gene
Classes	MONDO:0000001, SO:0001217,
Variables	disease (MONDO:0000001), gene (SO:0001217),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples

Disease series by gene and inheritance

This pattern is for diseases that are caused by a single mutation in a single gene, that have gene-based names, and are inherited by a specific mechanism, succh as autosomal dominant and autosomal recessive. Examples: Growth hormone insensitivity syndrome with immune dysregulation, Growth hormone insensitivity with immune dysregulation 1, autosomal recessive and Growth hormone insensitivity with immune dysregulation 2, autosomal dominant

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/disease_series_by_gene.yaml
Name	disease_series_by_gene_and_inheritance
Classes	MONDO:0000001, SO:0000704, HP:0000005,
Variables	disease (MONDO:0000001), gene (SO:0000704), mode_of_inheritance (HP:0000005),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432, 0000-0002-7356-1779,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label	gene	gene:label	mode:of:inheritance	mode:of:inheritance:label
MONDO:0007092	amelogenesis imperfecta type 1B	MONDO:0019507	amelogenesis imperfecta	http://identifiers.org/hgnc/3344	ENAM	HP:0000006	Autosomal dominant inheritance
MONDO:0014865	autosomal recessive severe congenital neutropenia due to CSF3R deficiency	MONDO:0018542	severe congenital neutropenia	http://identifiers.org/hgnc/2439	CSF3R	HP:0000007	Autosomal recessive inheritance
MONDO:0018487	autosomal recessive severe congenital neutropenia due to CXCR2 deficiency	MONDO:0018542	severe congenital neutropenia	http://identifiers.org/hgnc/6027	CXCR2	HP:0000007	Autosomal recessive inheritance
MONDO:0012930	autosomal recessive severe congenital neutropenia due to G6PC3 deficiency	MONDO:0018542	severe congenital neutropenia	http://identifiers.org/hgnc/24861	G6PC3	HP:0000007	Autosomal recessive inheritance
MONDO:0014456	autosomal recessive severe congenital neutropenia due to JAGN1 deficiency	MONDO:0018542	severe congenital neutropenia	http://identifiers.org/hgnc/26926	JAGN1	HP:0000007	Autosomal recessive inheritance

See full table here

Disrupts process

A disease that disrupts a process, like immune system function, or early development. Examples: type III hypersensitivity disease, type IV hypersensitivity disease, neural tube closure defect (55 total)

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/disrupts_process.yaml
Name	disease or disorder disease caused by disruption of X
Classes	MONDO:0000001, owl:Thing,
Variables	process (owl:Thing),
Contributors	0000-0002-6601-2165,
Examples	mondo

Data preview:

defined:class	defined:class:label	process	process:label
MONDO:0012996	AGAT deficiency	GO:0015068	glycine amidinotransferase activity
MONDO:0021190	DNA repair disease	GO:0006281	DNA repair
MONDO:0018274	GM3 synthase deficiency	GO:0047291	lactosylceramide alpha-2,3-sialyltransferase activity
MONDO:0021060	RASopathy	GO:0007265	Ras protein signal transduction
MONDO:0005271	allergic disease	GO:0016068	type I hypersensitivity

See full table here

Environmental stimulus

A disease that is caused by exposure to an environmental stimulus, like the sun or pesticides. Examples: carbon monoxide-induced parkinsonism, cocaine intoxication

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/environmental_stimulus.yaml
Name	environmental_stimulus
Classes	MONDO:0000001, BFO:0000040,
Variables	disease (MONDO:0000001), stimulus (BFO:0000040),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label	stimulus	stimulus:label
MONDO:0003969	amphetamine abuse	MONDO:0002491	substance abuse	CHEBI:2679	amphetamine
MONDO:0004599	barbiturate abuse	MONDO:0002491	substance abuse	CHEBI:29745	barbiturate
MONDO:0043523	cadmium poisoning	MONDO:0029000	poisoning	CHEBI:22977	cadmium atom
MONDO:0004456	cocaine abuse	MONDO:0002491	substance abuse	CHEBI:27958	cocaine
MONDO:0005186	cocaine dependence	MONDO:0005303	drug dependence	CHEBI:27958	cocaine

See full table here

Hemangioma

A hemangioma (a benign vascular lesion characterized by the formation of capillary-sized or cavernous vascular channels) that is located in a specific anatomical site. Examples: skin hemangioma, breast hemangioma, gastric hemangioma (20 total)

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/hemangioma.yaml
Name	hemangioma disease has location X
Classes	MONDO:0006500, UBERON:0001062,
Variables	location (UBERON:0001062),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples	mondo

Data preview:

defined:class	defined:class:label	location	location:label
MONDO:0003126	breast hemangioma	UBERON:0000310	breast
MONDO:0003241	central nervous system hemangioma	UBERON:0001017	central nervous system
MONDO:0003948	cerebral hemangioma	UBERON:0001893	telencephalon
MONDO:0002414	gastric hemangioma	UBERON:0000945	stomach
MONDO:0021542	hemangioma of choroid	UBERON:0001776	optic choroid

See full table here

Hereditary

Pattern for extending a etiology-generic disease class to a hereditary form. Here hereditary means that etiology is largely genetic, and that the disease is passed down or potentially able to be passed down via inheritance (i.e is germline).

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/hereditary.yaml
Name	hereditary
Classes	MONDO:0021152, MONDO:0000001,
Variables	disease (MONDO:0000001),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label
MONDO:0003847	Mendelian disease	MONDO:0700096	human disease or disorder
MONDO:0008734	adrenocortical carcinoma, hereditary	MONDO:0006639	adrenal cortex carcinoma
MONDO:0013099	combined pituitary hormone deficiencies, genetic form	MONDO:0005152	hypopituitarism
MONDO:0006536	congenital generalized lipodystrophy	MONDO:0027766	generalized lipodystrophy
MONDO:0018827	familial chilblain lupus	MONDO:0019557	chilblain lupus

See full table here

Iatrogenic

Some diseases are caused by diagnostic and therapeutic procedures undertaken on a patient, such as a hospital acquired infection like MRSA. Use this pattern to define the iatrogenic form of a disease. Examples: 'iatrogenic botulism', 'iatrogenic Creutzfeldt-Jakob disease'

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/iatrogenic.yaml
Name	iatrogenic
Classes	MONDO:0100426, MONDO:0000001,
Variables	disease (MONDO:0000001),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label
MONDO:0016778	iatrogenic botulism	MONDO:0005498	botulism
MONDO:0043543	iatrogenic disease	MONDO:0700096	human disease or disorder

See full table here

Idiopathic

This pattern is applied to diseases that are described as being idiopathic, i.e. having an uncertain or unknown cause. Examples: idiopathic aplastic anemia, idiopathic avascular necrosis

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/idiopathic.yaml
Name	idiopathic
Classes	MONDO:0700005, MONDO:0000001,
Variables	disease (MONDO:0000001),
Contributors	0000-0002-4142-7153,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label
MONDO:0015713	idiopathic central precocious puberty	MONDO:0019165	central precocious puberty
MONDO:0700007	idiopathic disease	MONDO:0700096	human disease or disorder
MONDO:0011895	idiopathic hypereosinophilic syndrome	MONDO:0015691	hypereosinophilic syndrome
MONDO:0019554	idiopathic localized lipodystrophy	MONDO:0019194	localized lipodystrophy
MONDO:0018170	idiopathic nephrotic syndrome	MONDO:0005377	nephrotic syndrome

See full table here

Inborn metabolic

An inherited metabolic disease that causes disruption of a process.

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/inborn_metabolic.yaml
Name	inborn_metabolic
Classes	MONDO:0019052, BFO:0000015,
Variables	process (BFO:0000015),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples	mondo

Data preview:

defined:class	defined:class:label	process	process:label
MONDO:0009825	5-oxoprolinase deficiency	GO:0017168	5-oxoprolinase (ATP-hydrolyzing) activity
MONDO:0005775	G6PD deficiency	GO:0004345	glucose-6-phosphate dehydrogenase activity
MONDO:0007068	adenylosuccinate lyase deficiency	GO:0070626	(S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido) succinate lyase (fumarate-forming) activity
MONDO:0009665	biotinidase deficiency	GO:0047708	biotinidase activity
MONDO:0015286	congenital disorder of glycosylation	GO:0070085	glycosylation

See full table here

Inborn metabolic disrupts

This pattern is used for inborn errors of metabolism that cause disruption of a specific biological process, such as enzyme activity or ion transport. Examples: '5-oxoprolinase deficiency (disease)', inborn disorder of methionine cycle and sulfur amino acid metabolism, inborn aminoacylase deficiency (51 total)

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/inborn_metabolic_disrupts.yaml
Name	inborn errors of metabolism disease caused by disruption of X
Classes	MONDO:0019052, owl:Thing,
Variables	process (owl:Thing),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples	mondo

Data preview:

defined:class	defined:class:label	process	process:label
MONDO:0009825	5-oxoprolinase deficiency	GO:0017168	5-oxoprolinase (ATP-hydrolyzing) activity
MONDO:0005775	G6PD deficiency	GO:0004345	glucose-6-phosphate dehydrogenase activity
MONDO:0007068	adenylosuccinate lyase deficiency	GO:0070626	(S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido) succinate lyase (fumarate-forming) activity
MONDO:0009665	biotinidase deficiency	GO:0047708	biotinidase activity
MONDO:0015286	congenital disorder of glycosylation	GO:0070085	glycosylation

See full table here

Infantile

An instance of a disease that has an onset of signs or symptoms of disease within the first 12 months of life (infantile onset). Examples: infant botulism, infantile glycine encephalopathy

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/infantile.yaml
Name	infantile
Classes	HP:0003593, MONDO:0000001,
Variables	disease (MONDO:0000001),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label
MONDO:0015804	infant botulism	MONDO:0005498	botulism
MONDO:0016089	infantile Krabbe disease	MONDO:0009499	Krabbe disease
MONDO:0017354	infantile glycine encephalopathy	MONDO:0011612	glycine encephalopathy
MONDO:0019261	infantile neuronal ceroid lipofuscinosis	MONDO:0016295	neuronal ceroid lipofuscinosis
MONDO:0019190	juvenile polyposis of infancy	MONDO:0017380	juvenile polyposis syndrome

See full table here

Infectious disease by agent

Infectious diseases can be classified by the infectious agent, such as bacteria, coronavirus, etc, that causes the disease. Examples: COVID-19, cholera

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/infectious_disease_by_agent.yaml
Name	infectious_disease_by_agent
Classes	MONDO:0000001, NCBITaxon:1, MONDO:0005550,
Variables	agent (NCBITaxon:1),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432, 0000-0002-1780-9872,
Examples	mondo

Data preview:

defined:class	defined:class:label	agent	agent:label
MONDO:0021747	Acanthamoeba infectious disease	NCBITaxon:5754	Acanthamoeba
MONDO:0006635	Acinetobacter infectious disease	NCBITaxon:469	Acinetobacter
MONDO:0006636	Actinobacillus infectious disease	NCBITaxon:713	Actinobacillus
MONDO:0006921	Actinomycetales infectious disease	NCBITaxon:2037	Actinomycetales
MONDO:0005117	Aeromonas hydrophila infectious disease	NCBITaxon:644	Aeromonas hydrophila

See full table here

Infectious inflammation

This combines the infectious disease by agent pattern and the inflammatory disease by site pattern. Examples: bacterial endocarditis (disease), fungal gastritis

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/infectious_inflammation.yaml
Name	infectious_inflammation
Classes	MONDO:0000001, NCBITaxon:1, UBERON:0000061, MONDO:0005550,
Variables	location (UBERON:0000061), agent (NCBITaxon:1),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples

Inflammatory disease by site

Inflammatory diseases can be classified by the location in which the pathological inflammatory process occurs. For inflammatory diseases caused by infection, this may be the site of infection. Examples: 'Achilles bursitis', blepharitis, epiglottitis

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/inflammatory_disease_by_site.yaml
Name	inflammatory_disease_by_site
Classes	MONDO:0000001, UBERON:0000061,
Variables	location (UBERON:0000061),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples	mondo

Data preview:

defined:class	defined:class:label	location	location:label
MONDO:0004551	Meckel diverticulitis	UBERON:0003705	Meckel's diverticulum
MONDO:0019838	adenohypophysitis	UBERON:0002196	adenohypophysis
MONDO:0000261	adenoiditis	UBERON:0001732	pharyngeal tonsil
MONDO:0020710	amnionitis	UBERON:0000305	amnion
MONDO:0006656	aortitis	UBERON:0000947	aorta

See full table here

Inherited susceptibility

This pattern should be used for children of MONDO_0020573'inherited disease susceptibility', including OMIM phenotypic series (OMIMPS) for which the subclasses are susceptibilities. Note, this pattern should not have an asserted causative gene as logical axiom (and no single causative gene in text definition), in those cases, the susceptibility_by_gene pattern should be used instead. The children should have asserted causative genes in the text definitions and in the logical axioms. This pattern is a superclass of the susceptibility_by_gene pattern. Examples: 'microvascular complications of diabetes, susceptibility', 'epilepsy, idiopathic generalized', 'aspergillosis, susceptibility to'.

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/inherited_susceptibility.yaml
Name	inherited_susceptibility
Classes	MONDO:0000001, MONDO:0020573,
Variables	disease (MONDO:0000001),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label
MONDO:0000093	Schistosoma mansoni infection, susceptibility	MONDO:0044345	Schistosoma mansoni infectious disease
MONDO:0013562	aspergillosis, susceptibility to	MONDO:0005657	aspergillosis
MONDO:0000162	autoimmune thyroid disease, susceptibility to	MONDO:0005623	autoimmune thyroid disease
MONDO:0000108	bacteremia, susceptibility	MONDO:0005229	bacterial infectious disease with sepsis
MONDO:0013713	dengue virus, susceptibility to	MONDO:0005502	dengue disease

See full table here

Isolated

Some diseases exist in both isolated and syndromic forms. For example, aniridia (MONDO_0019172 aniridia, MONDO_0020148'syndromic aniridia' and MONDO_0007119 'isolated aniridia'. Use this pattern to define the isolated form of a disease when a term exists for the isolated/syndromic-neutral version. In general, this pattern should be used in parallel with syndromic. E.g. if you make a term 'syndromic disease, you should also have 'isolated disease' [see pattern here(https://github.com/monarch-initiative/mondo/blob/master/src/patterns/dosdp-patterns/syndromic.yaml). Note that the isolated and syndromic forms will be inferred to be disjoint due to the GCI pattern. Examples: 'isolated aniridia', 'isolated dystonia', 'isolated focal palmoplantar keratoderma'

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/isolated.yaml
Name	isolated
Classes	MONDO:0021128, MONDO:0000001,
Variables	disease (MONDO:0000001),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label
MONDO:0020075	genetic non-syndromic obesity	MONDO:0019182	inherited obesity
MONDO:0017262	inherited non-syndromic ichthyosis	MONDO:0015947	inherited ichthyosis
MONDO:0016462	isolated agammaglobulinemia	MONDO:0015977	agammaglobulinemia
MONDO:0016553	isolated congenital hypogonadotropic hypogonadism	MONDO:0015770	congenital hypogonadotropic hypogonadism
MONDO:0017667	isolated diffuse palmoplantar keratoderma	MONDO:0017666	diffuse palmoplantar keratoderma

See full table here

Juvenile

An instance of a disease that has an onset of signs or symptoms of disease between the age of 5 and 15 years (juvenile onset). Examples: juvenile-onset Parkinson disease, 'juvenile idiopathic scoliosis'

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/juvenile.yaml
Name	juvenile
Classes	HP:0003621, MONDO:0000001,
Variables	disease (MONDO:0000001),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label
MONDO:0020655	juvenile ankylosing spondylitis	MONDO:0005306	ankylosing spondylitis
MONDO:0009066	juvenile nephropathic cystinosis	MONDO:0100151	nephropathic cystinosis
MONDO:0019262	juvenile neuronal ceroid lipofuscinosis	MONDO:0016295	neuronal ceroid lipofuscinosis
MONDO:0003741	juvenile type testicular granulosa cell tumor	MONDO:0003395	testicular granulosa cell tumor
MONDO:0000828	juvenile-onset Parkinson disease	MONDO:0005180	Parkinson disease

See full table here

Latent virus reactivation disease

This template is for disease which arises from the reactivation of a virus from a latent phase to a lytic phase. Examples: herpes zoster

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/latent_virus_reactivation_disease.yaml
Name	latent_virus_reactivation_disease
Classes	MONDO:0005108, NCBITaxon:10239,
Variables	virus (NCBITaxon:10239),
Contributors	0000-0002-4142-7153,
Examples

Leiomyoma

A leiomyoma (a well-circumscribed benign smooth muscle neoplasm characterized by the presence of spindle cells with cigar-shaped nuclei, interlacing fascicles, and a whorled pattern) that is located in a specific anatomical entity. Examples: leiomyoma cutis, ureter leiomyoma, urethra leiomyoma (30 total)

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/leiomyoma.yaml
Name	leiomyoma disease has location X
Classes	MONDO:0001572, UBERON:0001062,
Variables	location (UBERON:0001062),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples	mondo

Data preview:

defined:class	defined:class:label	location	location:label
MONDO:0003292	anus leiomyoma	UBERON:0001245	anus
MONDO:0003300	appendix leiomyoma	UBERON:0001154	vermiform appendix
MONDO:0001634	bladder leiomyoma	UBERON:0001255	urinary bladder
MONDO:0002057	breast leiomyoma	UBERON:0000310	breast
MONDO:0003287	central nervous system leiomyoma	UBERON:0001017	central nervous system

See full table here

Leiomyosarcoma

An uncommon, aggressive malignant smooth muscle neoplasm, usually occurring in post-menopausal women that is characterized by a proliferation of neoplastic spindle cells that is located in a specific anatomical location. Examples: leiomyosarcoma of the cervix uteri, cutaneous leiomyosarcoma (disease), breast leiomyosarcoma (29 total)

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/leiomyosarcoma.yaml
Name	leiomyosarcoma disease has location X
Classes	MONDO:0005058, owl:Thing,
Variables	location (owl:Thing),
Contributors	0000-0002-6601-2165,
Examples	mondo

Data preview:

defined:class	defined:class:label	location	location:label
MONDO:0003358	anus leiomyosarcoma	UBERON:0001245	anus
MONDO:0002624	bone leiomyosarcoma	UBERON:0002481	bone tissue
MONDO:0003371	breast leiomyosarcoma	UBERON:0000310	breast
MONDO:0003349	central nervous system leiomyosarcoma	UBERON:0001017	central nervous system
MONDO:0003351	colon leiomyosarcoma	UBERON:0001155	colon

See full table here

Lesioned

This pattern is applied to diseases that are described as having a lesion, where a localized pathological or traumatic structural change, damage, deformity, or discontinuity of tissue, organ, or body part is present. Examples: ulnar nerve lesion, peripheral nerve lesion

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/lesioned.yaml
Name	lesioned
Classes	PATO:0040025, UBERON:0001062,
Variables	anatomical entity (UBERON:0001062),
Contributors	0000-0001-5208-3432,
Examples

Lipoma

A benign, usually painless, well-circumscribed lipomatous tumor composed of adipose tissue that is located in a specific anatomical location. Examples: skin lipoma, colorectal lipoma, tendon sheath lipoma (28 total)

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/lipoma.yaml
Name	lipoma disease has location X
Classes	MONDO:0005106, owl:Thing,
Variables	location (owl:Thing),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples	mondo

Data preview:

defined:class	defined:class:label	location	location:label
MONDO:0000974	axillary lipoma	UBERON:0009472	axilla
MONDO:0000970	breast lipoma	UBERON:0000310	breast
MONDO:0003844	central nervous system lipoma	UBERON:0001017	central nervous system
MONDO:0003843	cerebral hemisphere lipoma	UBERON:0001869	cerebral hemisphere
MONDO:0000971	chest wall lipoma	UBERON:0016435	chest wall

See full table here

Location

A disease that is located in a specific anatomical site. Examples: 'abdominal cystic lymphangioma', 'articular cartilage disease', 'urethral disease'

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/location.yaml
Name	location
Classes	MONDO:0000001, UBERON:0001062, CL:0000000,
Variables	disease (MONDO:0000001), location,
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label	location	location:label
MONDO:0004120	Bartholin gland small cell carcinoma	MONDO:0000402	small cell carcinoma	UBERON:0000460	major vestibular gland
MONDO:0024283	Demodex folliculitis	MONDO:0017280	demodicidosis	UBERON:0002073	hair follicle
MONDO:0006576	Ludwig's angina	MONDO:0005230	cellulitis	UBERON:0003679	mouth floor
MONDO:0001858	Tietze syndrome	MONDO:0002254	syndromic disease	UBERON:0002293	costochondral joint
MONDO:0021726	abdominal cystic lymphangioma	MONDO:0009761	cystic hygroma	UBERON:0000916	abdomen

See full table here

Location top

TBD.

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/location_top.yaml
Name	location_top
Classes	MONDO:0000001, owl:Thing,
Variables	location (owl:Thing),
Contributors	0000-0002-6601-2165,
Examples	mondo

Data preview:

defined:class	defined:class:label	location	location:label
MONDO:0020594	abducens nerve disorder	UBERON:0001646	abducens nerve
MONDO:0002636	accessory nerve disorder	UBERON:0002019	accessory XI nerve
MONDO:0002816	adrenal cortex disorder	UBERON:0001235	adrenal cortex
MONDO:0005495	adrenal gland disorder	UBERON:0002369	adrenal gland
MONDO:0003182	anterior horn disorder	UBERON:0002257	ventral horn of spinal cord

See full table here

Lymphoma

A malignant (clonal) proliferation of B- lymphocytes or T- lymphocytes which involves the lymph nodes, bone marrow and/or extranodal sites. This category includes Non-Hodgkin lymphomas and Hodgkin lymphomas. Examples: marginal zone lymphoma, ureteral lymphoma, colorectal lymphoma (37 total)

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/lymphoma.yaml
Name	lymphoma disease has location X
Classes	MONDO:0005062, owl:Thing,
Variables	location (owl:Thing),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples	mondo

Data preview:

defined:class	defined:class:label	location	location:label
MONDO:0007650	MALT lymphoma	UBERON:0001961	mucosa-associated lymphoid tissue
MONDO:0001888	anus lymphoma	UBERON:0001245	anus
MONDO:0001237	appendix lymphoma	UBERON:0001154	vermiform appendix
MONDO:0001381	bladder lymphoma	UBERON:0001255	urinary bladder
MONDO:0003661	breast lymphoma	UBERON:0000310	breast

See full table here

Malignant

This is a design pattern for classes representing malignant neoplasms, extending a generic neoplasm class. Examples: malignant carotid body paraganglioma, malignant germ cell tumor

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/malignant.yaml
Name	malignant
Classes	MONDO:0005070, PATO:0002097, owl:Thing,
Variables	neoplasm (owl:Thing),
Contributors	0000-0002-6601-2165,
Examples	mondo

Data preview:

defined:class	defined:class:label	neoplasm	neoplasm:label
MONDO:0004992	cancer	MONDO:0005070	neoplasm
MONDO:0003113	extragonadal germ cell cancer	MONDO:0018201	extragonadal germ cell tumor
MONDO:0003252	granular cell cancer	MONDO:0006235	granular cell tumor
MONDO:0000377	malignant Leydig cell tumor	MONDO:0006266	Leydig cell tumor
MONDO:0000378	malignant Sertoli cell tumor	MONDO:0002696	Sertoli cell tumor

See full table here

Melanoma

Melanomas are malignant, usually aggressive tumor composed of atypical, neoplastic melanocytes. This is a design pattern for classes representing melanomas based on their location. This may be the site of origin, but it can also represent a secondary site for metastatized cancer. We use the generic 'disease has location' relation, which generalized over primary and secondary sites. Examples: cutaneous melanoma, malignant breast melanoma, malignant melanoma of the mucosa (22 total)

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/melanoma.yaml
Name	melanoma disease has location X
Classes	MONDO:0005105, owl:Thing,
Variables	location (owl:Thing),
Contributors	0000-0002-6601-2165,
Examples	mondo

Data preview:

defined:class	defined:class:label	location	location:label
MONDO:0006081	anal melanoma	UBERON:0001245	anus
MONDO:0005012	cutaneous melanoma	UBERON:0000014	zone of skin
MONDO:0045070	digestive system melanoma	UBERON:0001007	digestive system
MONDO:0001192	esophageal melanoma	UBERON:0001043	esophagus
MONDO:0000928	eyelid melanoma	UBERON:0001711	eyelid

See full table here

Meningioma

A meningioma is a slow growing tumor attached to the dura mater. This is a design pattern for classes representing meningiomas based on their location. This may be the site of origin, but it can also represent a secondary site for metastatized cancer. We use the generic 'disease has location' relation, which generalized over primary and secondary sites. Examples: skin meningioma, brain meningioma, choroid plexus meningioma (26 total)

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/meningioma.yaml
Name	meningioma disease has location X
Classes	MONDO:0016642, UBERON:0001062,
Variables	location (UBERON:0001062),
Contributors	0000-0002-6601-2165,
Examples	mondo

Data preview:

defined:class	defined:class:label	location	location:label
MONDO:0002997	anterior cranial fossa meningioma	UBERON:0003720	anterior cranial fossa
MONDO:0000642	brain meningioma	UBERON:0000955	brain
MONDO:0002996	cavernous sinus meningioma	UBERON:0003712	cavernous sinus
MONDO:0003860	cerebellopontine angle meningioma	UBERON:0014908	cerebellopontine angle
MONDO:0004422	cerebral falx meningioma	UBERON:0006059	falx cerebri

See full table here

Mild

Pattern for describing the severity of a disease, in this case, a mild form of the disease. Here mild means having a relatively minor degree of severity. This may correspond with specific genetic mutations (or homozygous or heterozygous forms). Examples: mild ichthyosis vulgaris

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/mild.yaml
Name	mild
Classes	HP:0012825, MONDO:0000001,
Variables	disease (MONDO:0000001),
Contributors	0000-0002-6601-2165,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label
MONDO:0100474	mild ichthyosis vulgaris	MONDO:0024304	ichthyosis vulgaris

See full table here

Mitochondrial subtype

A disease that is classified as a mitochondrial subtype, due to a defect in a mitochondrial gene, such as MONDO:0100134 'mitochondrial complex I deficiency, mitochondrial type'.

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/mitochondrial_subtype.yaml
Name	mitochondriaal_subtype
Classes	SO:0000088, MONDO:0000001,
Variables	disease (MONDO:0000001),
Contributors	0000-0002-6601-2165,
Examples

Monosomy

This pattern is meant to be used for chromosomal disorder which consists of the absence of one chromosome from the normal diploid number. Note that the absence of chromosome refers to the entire chromosome, and not to part of a chromosome.

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/monosomy.yaml
Name	monosomy
Classes	MONDO:0020639, GO:0005694,
Variables	chromosome (GO:0005694),
Contributors	0000-0002-4142-7153,
Examples	mondo

Data preview:

defined:class	defined:class:label	chromosome	chromosome:label
MONDO:0019891	monosomy 22	CHR:9606-chr22	chromosome 22 (Human)
MONDO:0020466	monosomy X	CHR:9606-chrX	chromosome X (Human)
MONDO:0700035	monosomy chromosome 8	CHR:9606-chr8	chromosome 8 (Human)

See full table here

Mucoepidermoid carcinoma

Mucoepidermoid carcinomas are carcinomas morphologically characterized the presence of cuboidal mucous cells, goblet-like mucous cells, squamoid cells, cystic changes, and a fibrotic stromal formation. This is a design pattern for classes representing mucoepidermoid carcinomas based on their location. This may be the site of origin, but it can also represent a secondary site for metastatized cancer. We use the generic 'disease has location' relation, which generalized over primary and secondary sites. Examples: cutaneous mucoepidermoid carcinoma, oral cavity mucoepidermoid carcinoma, mucoepidermoid breast carcinoma (18 total)

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/mucoepidermoid_carcinoma.yaml
Name	mucoepidermoid carcinoma disease has location X
Classes	MONDO:0003036, UBERON:0001062,
Variables	location (UBERON:0001062),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples	mondo

Data preview:

defined:class	defined:class:label	location	location:label
MONDO:0000531	bronchus mucoepidermoid carcinoma	UBERON:0002185	bronchus
MONDO:0003091	cutaneous mucoepidermoid carcinoma	UBERON:0000014	zone of skin
MONDO:0003089	extrahepatic bile duct mucoepidermoid carcinoma	UBERON:0003703	extrahepatic bile duct
MONDO:0006213	floor of mouth mucoepidermoid carcinoma	UBERON:0003679	mouth floor
MONDO:0003092	lacrimal gland mucoepidermoid carcinoma	UBERON:0001817	lacrimal gland

See full table here

Neoplasm

Neoplasms are benign or malignant tissue growths resulting from uncontrolled cell proliferation cell types. This is a design pattern for classes representing neoplasms based on their location. This may be the site of origin, but it can also represent a secondary site for malignant neoplasms that have metastasized. We use the generic 'disease has location' relation, which generalized over primary and secondary sites. Note that tumor is typically a synonym for neoplasm, although this can be context dependent. For NETs, NCIT uses the nomenclature 'tumor' to indicate 'well differentiated, low or intermediate grade tumor'. This can also be called carcinoid, see https://www.cancer.org/cancer/gastrointestinal-carcinoid-tumor/about/what-is-gastrointestinal-carcinoid.html We attempt to spell this out in our labels.

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/neoplasm.yaml
Name	neoplasm
Classes	MONDO:0005070, owl:Thing,
Variables	location (owl:Thing),
Contributors	0000-0002-6601-2165,
Examples	mondo

Data preview:

defined:class	defined:class:label	location	location:label
MONDO:0021114	Bartholin gland neoplasm	UBERON:0000460	major vestibular gland
MONDO:0021082	Meckel diverticulum neoplasm	UBERON:0003705	Meckel's diverticulum
MONDO:0001884	abducens nerve neoplasm	UBERON:0001646	abducens nerve
MONDO:0036591	adrenal cortex neoplasm	UBERON:0001235	adrenal cortex
MONDO:0021227	adrenal gland neoplasm	UBERON:0002369	adrenal gland

See full table here

Neoplasm by origin

TBD.

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/neoplasm_by_origin.yaml
Name	neoplasm
Classes	MONDO:0005070, owl:Thing,
Variables	structure (owl:Thing),
Contributors	0000-0002-6601-2165,
Examples	mondo

Data preview:

defined:class	defined:class:label	structure	structure:label
MONDO:0015157	human herpesvirus 8-related tumor	MONDO:0005187	human herpesvirus 8 infection
MONDO:0017341	virus associated tumor	MONDO:0005108	viral infectious disease

See full table here

Neuroendocrine neoplasm

Note that tumor is typically a synonym for neoplasm, although this can be context dependent. For neuroendocrine tumors (NETs), NCIT uses the nomenclature 'tumor' to indicate 'well differentiated, low or intermediate grade tumor'. This can also be called carcinoid, see https://www.cancer.org/cancer/gastrointestinal-carcinoid-tumor/about/what-is-gastrointestinal-carcinoid.html. We attempt to spell this out in our labels. Examples: breast neuroendocrine neoplasm, digestive system neuroendocrine neoplasm, ovarian neuroendocrine neoplasm

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/neuroendocrine_neoplasm.yaml
Name	neoendocrine_neoplasm
Classes	MONDO:0019496, owl:Thing,
Variables	location (owl:Thing),
Contributors	0000-0002-6601-2165,
Examples	mondo

Data preview:

defined:class	defined:class:label	location	location:label
MONDO:0003504	anal canal neuroendocrine neoplasm	UBERON:0000159	anal canal
MONDO:0024501	appendix neuroendocrine neoplasm	UBERON:0001154	vermiform appendix
MONDO:0002485	breast neuroendocrine neoplasm	UBERON:0000310	breast
MONDO:0019963	bronchial endocrine tumor	UBERON:0002185	bronchus
MONDO:0002882	colon neuroendocrine neoplasm	UBERON:0001155	colon

See full table here

Neuroendocrine neoplasm grade1

We follow NCIT in making carcinoid tumor a synonym for neuroendocrine neoplasm G1 (G1 NET). Examples: carcinoid tumor (disease)

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/neuroendocrine_neoplasm_grade1.yaml
Name	neoendocrine_neoplasm_grade1
Classes	MONDO:0019496, MONDO:0024491, owl:Thing,
Variables	location (owl:Thing),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples	mondo

Data preview:

defined:class	defined:class:label	location	location:label
MONDO:0006091	appendix neuroendocrine tumor G1	UBERON:0001154	vermiform appendix
MONDO:0006093	ascending colon neuroendocrine tumor G1	UBERON:0001156	ascending colon
MONDO:0006126	cecum neuroendocrine tumor G1	UBERON:0001153	caecum
MONDO:0006155	colon neuroendocrine tumor G1	UBERON:0001155	colon
MONDO:0006162	colorectal neuroendocrine tumor G1	UBERON:0012652	colorectum

See full table here

Nonhuman disease

This pattern should be used for diseases affecting non-human animal which have a corresponding/an analog disease in human, AND the taxon affected is NOT known. Examples: leukemia, non-human animal, hepatitis, viral, animal

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/nonhuman_disease.yaml
Name	nonhuman_disease
Classes	MONDO:0005583, MONDO:0700096,
Variables	human_disease (MONDO:0700096),
Contributors	0000-0002-4142-7153,
Examples	mondo

Data preview:

defined:class	defined:class:label	human:disease	human:disease:label
MONDO:0700103	nutritional deficiency disease, non-human animal	MONDO:0006873	nutritional deficiency disease

See full table here

Nonhuman disease taxon

This pattern should be used for diseases affecting non-human animal which have a corresponding/an analog disease in human AND the taxon affected is known. Examples: leukemia, feline

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/nonhuman_disease_taxon.yaml
Name	nonhuman_disease_taxon
Classes	MONDO:0005583, MONDO:0700096, NCBITaxon:1,
Variables	human_disease (MONDO:0700096), taxon (NCBITaxon:1),
Contributors	0000-0002-4142-7153,
Examples

Nuclear subtype

A disease that is classified as a nuclear subtype, due to a defect in a nuclear gene, such as MONDO:0009640 'mitochondrial complex I deficiency, nuclear type'.

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/nuclear_subtype.yaml
Name	nuclear_subtype
Classes	SO:0000087, MONDO:0000001,
Variables	disease (MONDO:0000001),
Contributors	0000-0002-6601-2165,
Examples

Partial chromosomal deletion

This pattern is meant to be used for chromosomal disorder which consists of the deletion of part of a chromosome in which only the chromosome which part is deleted is known (the chromosomal region is not known). Note that when the chromosomal region is known, the chromosomal_region_deletion pattern should be used. Also note that this pattern does not include the loss of the entire chromosome (monosomy).

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/partial_chromosomal_deletion.yaml
Name	partial_chromosomal_deletion
Classes	MONDO:0000761, GO:0005694,
Variables	chromosome (GO:0005694),
Contributors	0000-0002-4142-7153,
Examples	mondo

Data preview:

defined:class	defined:class:label	chromosome	chromosome:label
MONDO:0015607	partial chromosome Y deletion	CHR:9606-chrY	chromosome Y (Human)
MONDO:0016866	partial deletion of chromosome 1	CHR:9606-chr1	chromosome 1 (Human)
MONDO:0016875	partial deletion of chromosome 10	CHR:9606-chr10	chromosome 10 (Human)
MONDO:0016876	partial deletion of chromosome 11	CHR:9606-chr11	chromosome 11 (Human)
MONDO:0017277	partial deletion of chromosome 12	CHR:9606-chr12	chromosome 12 (Human)

See full table here

Pentasomy

This pattern is meant to be used for chromosomal disorder which consists of the presence of three additional chromosomes of the same type from the normal diploid number. Note that the presence of additional chromosomes refers to the entire chromosome, and not to part of a chromosome.

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/pentasomy.yaml
Name	pentasomy
Classes	MONDO:0700085, GO:0005694,
Variables	chromosome (GO:0005694),
Contributors	0000-0002-4142-7153,
Examples

Poisoning

A disease that is caused by exposure to an environmental stimulus that causes poisoning. Examples: colchicine poisoning, cocaine intoxication

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/poisoning.yaml
Name	poisoning
Classes	MONDO:0029000, BFO:0000040,
Variables	stimulus (BFO:0000040),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432, 0000-0002-7463-6306,
Examples	mondo

Data preview:

defined:class	defined:class:label	stimulus	stimulus:label
MONDO:0043523	cadmium poisoning	CHEBI:22977	cadmium atom
MONDO:0019544	cocaine intoxication	CHEBI:27958	cocaine
MONDO:0017859	colchicine poisoning	CHEBI:23359	colchicine
MONDO:0017863	digitalis poisoning	CHEBI:4551	digoxin
MONDO:0017861	ethylene glycol poisoning	CHEBI:30742	ethylene glycol

See full table here

Polygenic disorder

This pattern is for diseases that are caused by a variation (or mutation) in a two or more genes. The relation disease has basis in dysfunction should be used for each gene that is affected. For digenic diseases, this would be twice, for polygenic diseases, it would be 3 or more. Examples: Usher syndrome, type 1D/F

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/polygenic_disorder.yaml
Name	polygenic_disorder
Classes	MONDO:0000001, SO:0001217,
Variables	disease (MONDO:0000001), gene (SO:0001217),
Contributors	0000-0002-4142-7153, 0000-0001-5208-3432,
Examples

Post infectious disease

Post-infection disorder follows infection but is distinct from the infection itself and its usual manifestations. Examples: post-COVID-19 disorder

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/post_infectious_disease.yaml
Name	post_infectious_disease
Classes	MONDO:0000001, MONDO:0021669, MONDO:0005550,
Variables	infectiousdisease (MONDO:0005550),
Contributors	0000-0002-4142-7153,
Examples	mondo

Data preview:

defined:class	defined:class:label	infectiousdisease	infectiousdisease:label
MONDO:0021673	post-bacterial disorder	MONDO:0005113	bacterial infectious disease
MONDO:0021669	post-infectious disorder	MONDO:0005550	infectious disease
MONDO:0021674	post-viral disorder	MONDO:0005108	viral infectious disease

See full table here

Postinfectious disease

A design pattern for conditions such as post-herpetic neuralgia or postinfectious encephalitis, where the disease is secondary to the initial infection. TODO: write better guidelines on what constitutes a secondary disease vs primary. * We do not use this pattern for AIDS-HIV for example, instead representing this is using SubClassOf. * We draw a distinction between infectious and postinfectious encepahlitis. * we do not use this pattern for chickenpox, but we do for shingles

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/postinfectious_disease.yaml
Name	postinfectious_disease
Classes	MONDO:0000001, MONDO:0005550, NCBITaxon:1,
Variables	disease (NCBITaxon:1), feature (MONDO:0005550),
Contributors	0000-0002-6601-2165,
Examples

Pregnancy form of disorder

An instance of a disease is associated with a pregnancy. Examples: pregnancy associated osteoporosis, hypertension, pregnancy-induced

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/pregnancy_form_of_disorder.yaml
Name	pregnancy_form_of_disorder
Classes	MONDO:0000001, MONDO:0024575,
Variables	disease (MONDO:0000001),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label
MONDO:0005406	gestational diabetes	MONDO:0005015	diabetes mellitus
MONDO:0100194	pregnancy associated osteoporosis	MONDO:0005298	osteoporosis

See full table here

Primary infectious

Pattern for extending a disease class to a primary infectious form, a characteristic of an infectious disease in which the disease affects an immunologically normal host. Example: MONDO_0000308 'primary systemic mycosis'.

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/primary_infectious.yaml
Name	primary infectious
Classes	MONDO:0045036, MONDO:0000001,
Variables	disease (MONDO:0000001),
Contributors	0000-0002-6601-2165,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label
MONDO:0000314	primary bacterial infectious disease	MONDO:0005113	bacterial infectious disease
MONDO:0000308	primary systemic mycosis	MONDO:0000256	systemic mycosis

See full table here

Rare

TBD.

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/rare.yaml
Name	rare
Classes	MONDO:0021136, MONDO:0000001,
Variables	disease (MONDO:0000001),
Contributors	0000-0002-6601-2165,
Examples

Rare genetic

TBD.

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/rare_genetic.yaml
Name	rare_genetic
Classes	MONDO:0021150, MONDO:0021136, MONDO:0000001,
Variables	disease (MONDO:0000001),
Contributors	0000-0002-6601-2165,
Examples

Realized in response to environmental exposure

This pattern is used for a disease, where the cause of the disease is an exposure to an environmental stimulus (using ECTO exposure terms) or a medical action, such as a therapeutic treatment (using MAxO terms). Note that this pattern does not include infectious disease or classes that would include an organism, virus or viroid. Rather it includes exposures to chemicals (includng drugs), or mixtures. Examples: chemically-induced disorder, alcohol amnestic disorder, alcoholic polyneuropathy, chemotherapy-induced alopecia (26 total)

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/realized_in_response_to_evironmental_exposure.yaml
Name	disease realized in response to environmental exposure
Classes	MONDO:0000001, ExO:0000002,
Variables	disease (MONDO:0000001), exposure (ExO:0000002),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label	exposure	exposure:label
MONDO:0060781	Preeyasombat-Varavithya syndrome	MONDO:0001083	Fanconi renotubular syndrome	ECTO:9000364	exposure to tetracycline
MONDO:0002046	alcohol abuse	MONDO:0002491	substance abuse	ECTO:0001082	exposure to alcohol consumption
MONDO:0021702	alcohol amnestic disorder	MONDO:0001152	amnestic disorder	ECTO:0001082	exposure to alcohol consumption
MONDO:0007079	alcohol dependence	MONDO:0004938	substance dependence	ECTO:0001082	exposure to alcohol consumption
MONDO:0021698	alcohol-related disorders	MONDO:0002494	substance-related disorder	ECTO:0001082	exposure to alcohol consumption

See full table here

Refractory

TBD.

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/refractory.yaml
Name	refractory
Classes	HP:0031375, MONDO:0000001,
Variables	disease (MONDO:0000001),
Contributors	0000-0002-6601-2165,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label
MONDO:0004401	testis refractory cancer	MONDO:0003510	malignant testicular germ cell tumor
MONDO:0005414	treatment-refractory schizophrenia	MONDO:0005090	schizophrenia

See full table here

Rhabdomyosarcoma

This is auto-generated. Add your description here Examples: rhabdomyosarcoma of the cervix uteri, breast rhabdomyosarcoma, testis rhabdomyosarcoma (15 total)

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/rhabdomyosarcoma.yaml
Name	rhabdomyosarcoma disease has location X
Classes	MONDO:0005212, owl:Thing,
Variables	location (owl:Thing),
Contributors	0000-0002-6601-2165,
Examples	mondo

Data preview:

defined:class	defined:class:label	location	location:label
MONDO:0002864	anus rhabdomyosarcoma	UBERON:0001245	anus
MONDO:0002859	breast rhabdomyosarcoma	UBERON:0000310	breast
MONDO:0002850	central nervous system rhabdomyosarcoma	UBERON:0001017	central nervous system
MONDO:0002577	extrahepatic bile duct rhabdomyosarcoma	UBERON:0003703	extrahepatic bile duct
MONDO:0002856	gallbladder rhabdomyosarcoma	UBERON:0002110	gall bladder

See full table here

Ring chromosome anomaly

This pattern is meant to be used for chromosomal disorder which consists of the presence of a ring chromosome. A ring chromosome is a chromosome whose arms have fused together to form a ring, often with the loss of the ends of the chromosome.

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/ring_chromosome_anomaly.yaml
Name	ring_chromosome_anomaly
Classes	MONDO:0700091, GO:0005694,
Variables	chromosome (GO:0005694),
Contributors	0000-0002-4142-7153,
Examples	mondo

Data preview:

defined:class	defined:class:label	chromosome	chromosome:label
MONDO:0019926	X small rings	CHR:9606-chrX	chromosome X (Human)
MONDO:0015443	chromosome 8-derived supernumerary ring/marker	CHR:9606-chr8	chromosome 8 (Human)
MONDO:0015430	ring chromosome 1	CHR:9606-chr1	chromosome 1 (Human)
MONDO:0015431	ring chromosome 10	CHR:9606-chr10	chromosome 10 (Human)
MONDO:0019906	ring chromosome 11	CHR:9606-chr11	chromosome 11 (Human)

See full table here

Sarcoma

Sarcomas are malignant neoplasms arising from soft tissue or bone. This is a design pattern for classes representing sarcomas based on their location. This may be the site of origin, but it can also represent a secondary site for metastatized sarcma. We use the generic 'disease has location' relation, which generalized over primary and secondary sites.

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/sarcoma.yaml
Name	sarcoma
Classes	MONDO:0005089, owl:Thing,
Variables	location (owl:Thing),
Contributors	0000-0002-6601-2165,
Examples	mondo

Data preview:

defined:class	defined:class:label	location	location:label
MONDO:0019480	Langerhans cell sarcoma	CL:0000453	Langerhans cell
MONDO:0016982	angiosarcoma	UBERON:0001981	blood vessel
MONDO:0002865	anus sarcoma	UBERON:0001245	anus
MONDO:0002862	bile duct sarcoma	UBERON:0002394	bile duct
MONDO:0001374	bladder sarcoma	UBERON:0001255	urinary bladder

See full table here

Severe

Pattern for describing the severity of a disease, in this case, a severe form of the disease. Here severe means having a high degree of severity. This may correspond with specific genetic mutations (or homozygous or heterozygous forms). Examples: severe ichthyosis vulgaris

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/severe.yaml
Name	severe
Classes	HP:0012828, MONDO:0000001,
Variables	disease (MONDO:0000001),
Contributors	0000-0002-6601-2165,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label
MONDO:0100475	severe ichthyosis vulgaris	MONDO:0024304	ichthyosis vulgaris

See full table here

Small cell carcinoma

This is auto-generated. Add your description here Examples: cervical small cell carcinoma, pancreatic small cell neuroendocrine carcinoma, ureter small cell carcinoma (16 total)

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/small_cell_carcinoma.yaml
Name	small cell carcinoma disease has location X
Classes	MONDO:0000402, owl:Thing,
Variables	location (owl:Thing),
Contributors	0000-0002-6601-2165,
Examples	mondo

Data preview:

defined:class	defined:class:label	location	location:label
MONDO:0004120	Bartholin gland small cell carcinoma	UBERON:0000460	major vestibular gland
MONDO:0006142	cervical small cell carcinoma	UBERON:0000002	uterine cervix
MONDO:0003978	colon small cell neuroendocrine carcinoma	UBERON:0001155	colon
MONDO:0006197	endometrial small cell carcinoma	UBERON:0001295	endometrium
MONDO:0004116	esophageal small cell neuroendocrine carcinoma	UBERON:0001043	esophagus

See full table here

Specific disease by disrupted process

This is auto-generated. Add your description here Examples: disease of catalytic activity, disease of transporter activity, phagocytic cell dysfunction (49 total)

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/specific_disease_by_disrupted_process.yaml
Name	X disease disrupts X
Classes	owl:Thing, MONDO:0000001,
Variables	disease (MONDO:0000001), process (owl:Thing),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label	process	process:label
MONDO:0001531	blood coagulation disease	MONDO:0000001	disease or disorder	GO:0007596	blood coagulation
MONDO:0005557	calcium metabolic disease	MONDO:0005066	metabolic disease	GO:0055074	calcium ion homeostasis
MONDO:0045024	cancer or benign tumor	MONDO:0700096	human disease or disorder	GO:0008283	cell population proliferation
MONDO:0020779	cartilage development disorder	MONDO:0000001	disease or disorder	GO:0051216	cartilage development
MONDO:0019165	central precocious puberty	MONDO:0000088	precocious puberty	GO:0032274	gonadotropin secretion

See full table here

Specific disease by dysfunctional structure

This is auto-generated. Add your description here Examples: collagenopathy type 2 alpha 1, hemoglobinopathy, blood platelet disease (2195 total)

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/specific_disease_by_dysfunctional_structure.yaml
Name	X disease has basis in dysfunction of X
Classes	owl:Thing, MONDO:0000001,
Variables	disease (MONDO:0000001), structure (owl:Thing),
Contributors	0000-0002-6601-2165,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label	structure	structure:label
MONDO:0002245	blood platelet disease	MONDO:0000001	disease or disorder	CL:0000233	platelet
MONDO:0004880	bowel dysfunction	MONDO:0000001	disease or disorder	UBERON:0004907	lower digestive tract
MONDO:0020144	cerebrovascular dementia	MONDO:0001627	dementia	UBERON:0008998	vasculature of brain
MONDO:0005308	ciliopathy	MONDO:0000001	disease or disorder	GO:0005929	cilium
MONDO:0004603	collagenopathy	MONDO:0000001	disease or disorder	GO:0005581	collagen trimer

See full table here

Specific infectious disease by agent

as for inflammatory_disease_by_site, but refining a specific disease

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/specific_infectious_disease_by_agent.yaml
Name	specific_inflammatory_disease_by_site
Classes	MONDO:0000001, NCBITaxon:1,
Variables	disease (MONDO:0000001), agent (NCBITaxon:1),
Contributors	0000-0002-6601-2165,
Examples

Specific infectious disease by location

TODO

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/specific_infectious_disease_by_location.yaml
Name	specific_infectious_disease_by_location
Classes	MONDO:0000001, UBERON:0000061,
Variables	disease (MONDO:0000001), location (UBERON:0000061),
Contributors	0000-0002-6601-2165,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label	location	location:label
MONDO:0004551	Meckel diverticulitis	MONDO:0000001	disease or disorder	UBERON:0003705	Meckel's diverticulum
MONDO:0019838	adenohypophysitis	MONDO:0000001	disease or disorder	UBERON:0002196	adenohypophysis
MONDO:0000261	adenoiditis	MONDO:0000001	disease or disorder	UBERON:0001732	pharyngeal tonsil
MONDO:0020710	amnionitis	MONDO:0000001	disease or disorder	UBERON:0000305	amnion
MONDO:0006656	aortitis	MONDO:0000001	disease or disorder	UBERON:0000947	aorta

See full table here

Specific inflammatory disease by site

as for inflammatory_disease_by_site, but refining a specific disease

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/specific_inflammatory_disease_by_site.yaml
Name	specific_inflammatory_disease_by_site
Classes	MONDO:0000001, UBERON:0000061,
Variables	disease (MONDO:0000001), location (UBERON:0000061),
Contributors	0000-0002-6601-2165,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label	location	location:label
MONDO:0004551	Meckel diverticulitis	MONDO:0000001	disease or disorder	UBERON:0003705	Meckel's diverticulum
MONDO:0019838	adenohypophysitis	MONDO:0000001	disease or disorder	UBERON:0002196	adenohypophysis
MONDO:0000261	adenoiditis	MONDO:0000001	disease or disorder	UBERON:0001732	pharyngeal tonsil
MONDO:0020710	amnionitis	MONDO:0000001	disease or disorder	UBERON:0000305	amnion
MONDO:0006656	aortitis	MONDO:0000001	disease or disorder	UBERON:0000947	aorta

See full table here

Squamous cell carcinoma

This is auto-generated. Add your description here Examples: cervical squamous cell carcinoma, skin squamous cell carcinoma, ureter squamous cell carcinoma (63 total)

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/squamous_cell_carcinoma.yaml
Name	squamous cell carcinoma disease has location X
Classes	MONDO:0005096, owl:Thing,
Variables	location (owl:Thing),
Contributors	0000-0002-6601-2165,
Examples	mondo

Data preview:

defined:class	defined:class:label	location	location:label
MONDO:0003490	ampulla of vater squamous cell carcinoma	UBERON:0004913	hepatopancreatic ampulla
MONDO:0004132	anal canal squamous cell carcinoma	UBERON:0000159	anal canal
MONDO:0001470	anal margin squamous cell carcinoma	UBERON:0012336	perianal skin
MONDO:0006082	anal squamous cell carcinoma	UBERON:0001245	anus
MONDO:0004053	bartholin gland squamous cell carcinoma	UBERON:0000460	major vestibular gland

See full table here

Substance abuse

A substance abuse that specifies a specific environmental stimulus such as alcohol, cocaine, etc. Examples: alcohol abuse, cocaine abuse

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/substance_abuse.yaml
Name	substance_abuse
Classes	MONDO:0002491, BFO:0000040,
Variables	stimulus (BFO:0000040),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432, 0000-0002-7463-6306,
Examples	mondo

Data preview:

defined:class	defined:class:label	stimulus	stimulus:label
MONDO:0003969	amphetamine abuse	CHEBI:2679	amphetamine
MONDO:0004599	barbiturate abuse	CHEBI:29745	barbiturate
MONDO:0004456	cocaine abuse	CHEBI:27958	cocaine
MONDO:0005912	phencyclidine abuse	CHEBI:8058	phencyclidine

See full table here

Susceptibility by gene

This pattern should be used for terms in which a gene dysfunction causes a predisposition or susceptibility towards developing a specific disease. This pattern is a sub-pattern of inherited_susceptibility.yaml Examples - autism, susceptibility to, X-linked 5, bulimia nervosa, susceptibility to, 2, nephrolithiasis susceptibility caused by SLC26A1'

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/susceptibility_by_gene.yaml
Name	susceptibility_by_gene
Classes	MONDO:0000001, MONDO:0020573, SO:0000704,
Variables	gene (SO:0000704), disease (MONDO:0000001),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label	gene	gene:label
MONDO:0012153	Alzheimer disease 9	MONDO:0015140	early-onset autosomal dominant Alzheimer disease	http://identifiers.org/hgnc/37	ABCA7
MONDO:0011896	Parkinson disease 11, autosomal dominant, susceptibility to	MONDO:0008199	late-onset Parkinson disease	http://identifiers.org/hgnc/11960	GIGYF2
MONDO:0012466	Parkinson disease 13, autosomal dominant, susceptibility to	MONDO:0005180	Parkinson disease	http://identifiers.org/hgnc/14348	HTRA2
MONDO:0013653	Parkinson disease 18, autosomal dominant, susceptibility to	MONDO:0005180	Parkinson disease	http://identifiers.org/hgnc/3296	EIF4G1
MONDO:0013340	Parkinson disease 5, autosomal dominant, susceptibility to	MONDO:0005180	Parkinson disease	http://identifiers.org/hgnc/12513	UCHL1

See full table here

Syndromic

Some diseases exist in both isolated and syndromic forms. For example, aniridia (MONDO_0019172 aniridia, MONDO_0020148'syndromic aniridia' and MONDO_0007119 'isolated aniridia'. Use this pattern to define the syndromic form of a disease when a term exists for the isolated/syndromic-neutral version. In general, this pattern should be used in parallel with isolated. E.g. if you make a term 'syndromic disease, you should also have 'isolated disease' [see pattern here(https://github.com/monarch-initiative/mondo/blob/master/src/patterns/dosdp-patterns/isolated.yaml). Note that the isolated and syndromic forms will be inferred to be disjoint due to the GCI pattern.

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/syndromic.yaml
Name	syndromic
Classes	MONDO:0021127, MONDO:0000001,
Variables	disease (MONDO:0000001),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label
MONDO:0017263	inherited ichthyosis syndromic form	MONDO:0015947	inherited ichthyosis
MONDO:0016463	syndromic agammaglobulinemia	MONDO:0015977	agammaglobulinemia
MONDO:0002254	syndromic disease	MONDO:0700096	human disease or disorder
MONDO:0015905	syndromic dyslipidemia	MONDO:0002525	inherited lipid metabolism disorder
MONDO:0016565	syndromic genetic obesity	MONDO:0019182	inherited obesity

See full table here

Tetrasomy

This pattern is meant to be used for chromosomal disorder which consists of the presence of two additional chromosomes of the same type from the normal diploid number. Note that the presence of additional chromosomes refers to the entire chromosome, and not to part of a chromosome.

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/tetrasomy.yaml
Name	tetrasomy
Classes	MONDO:0030502, GO:0005694,
Variables	chromosome (GO:0005694),
Contributors	0000-0002-4142-7153,
Examples	mondo

Data preview:

defined:class	defined:class:label	chromosome	chromosome:label
MONDO:0019864	tetrasomy 21	CHR:9606-chr21	chromosome 21 (Human)

See full table here

Trisomy

This pattern is meant to be used for chromosomal disorder which consists of the presence of one additional chromosome from the normal diploid number. Note that the presence of additional chromosome refers to the entire chromosome, and not to part of a chromosome.

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/trisomy.yaml
Name	trisomy
Classes	MONDO:0700065, GO:0005694,
Variables	chromosome (GO:0005694),
Contributors	0000-0002-4142-7153,
Examples	mondo

Data preview:

defined:class	defined:class:label	chromosome	chromosome:label
MONDO:0022180	chromosome 16 trisomy	CHR:9606-chr16	chromosome 16 (Human)
MONDO:0022757	chromosome 20 trisomy	CHR:9606-chr20	chromosome 20 (Human)
MONDO:0043452	chromosome 8, trisomy	CHR:9606-chr8	chromosome 8 (Human)
MONDO:0018068	trisomy 13	CHR:9606-chr13	chromosome 13 (Human)
MONDO:0018071	trisomy 18	CHR:9606-chr18	chromosome 18 (Human)

See full table here

Vector borne disease

An infectious disease where a pathogen is carried and transmitted by another organism that acts as disease vector. Examples: MONDO_0020601 'mosquito-borne viral encephalitis', MONDO_0017572 'tick-borne encephalitis'

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/vectorBorneDisease.yaml
Name	vectorBorneDisease
Classes	MONDO:0005550, OBI:0100026,
Variables	infectious_disease (MONDO:0005550), vector (OBI:0100026),
Contributors	0000-0002-6601-2165,
Examples	mondo

Data preview:

defined:class	defined:class:label	infectious:disease	infectious:disease:label	vector	vector:label
MONDO:0020731	arbovirus infection	MONDO:0005108	viral infectious disease	NCBITaxon:6943	Amblyomma americanum
MONDO:0001620	louse-borne relapsing fever	MONDO:0019633	relapsing fever	NCBITaxon:121225	Pediculus humanus
MONDO:0020601	mosquito-borne viral encephalitis	MONDO:0006009	viral encephalitis	NCBITaxon:7157	Culicidae
MONDO:0006941	rat-bite fever	MONDO:0005113	bacterial infectious disease	NCBITaxon:10114	Rattus
MONDO:0001621	tick-borne relapsing fever	MONDO:0019633	relapsing fever	NCBITaxon:6944	Ixodes

See full table here

X linked

TBD.

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/x_linked.yaml
Name	x_linked
Classes	HP:0001417, MONDO:0000001,
Variables	disease (MONDO:0000001),
Contributors	0000-0002-6601-2165,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label
MONDO:0010583	Dyggve-Melchior-Clausen syndrome, X-linked	MONDO:0009130	Dyggve-Melchior-Clausen disease
MONDO:0010520	X-linked Alport syndrome	MONDO:0018965	Alport syndrome
MONDO:0010586	X-linked Ehlers-Danlos syndrome	MONDO:0020066	Ehlers-Danlos syndrome
MONDO:0010222	X-linked Opitz G/BBB syndrome	MONDO:0017138	Opitz G/BBB syndrome
MONDO:0010556	X-linked chondrodysplasia punctata	MONDO:0019701	chondrodysplasia punctata

See full table here

Y linked

TBD.

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/y_linked.yaml
Name	y_linked
Classes	HP:0001450, MONDO:0000001,
Variables	disease (MONDO:0000001),
Contributors	0000-0002-6601-2165,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label
MONDO:0000428	Y-linked disease	MONDO:0000001	disease or disorder
MONDO:0010761	retinitis pigmentosa Y-linked	MONDO:0019200	retinitis pigmentosa

See full table here