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 OMIM diseases, including children of OMIM phenotypic series (OMIMPS), which are represented as grouping classes in Mondo. 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,
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 modifier 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:0018686	acquired Creutzfeldt-Jakob disease	MONDO:0005357	Creutzfeldt Jacob disease
MONDO:0060779	acquired Fanconi syndrome	MONDO:0001083	Fanconi renotubular syndrome
MONDO:0045023	acquired adrenogenital syndrome	MONDO:0015898	adrenogenital syndrome
MONDO:0019624	acquired angioedema	MONDO:0010481	angioedema
MONDO:0015610	acquired aplastic anemia	MONDO:0015909	aplastic anemia

See full table here

Acute

TBD.

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,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label
MONDO:0020686	acute adenoiditis	MONDO:0000261	adenoiditis
MONDO:0001090	acute anterolateral myocardial infarction	MONDO:0006652	anterolateral myocardial infarction
MONDO:0020680	acute bronchiolitis	MONDO:0002465	bronchiolitis (disease)
MONDO:0001081	acute cervicitis	MONDO:0002345	cervicitis (disease)
MONDO:0001930	acute cholangitis	MONDO:0004789	cholangitis

See full table here

Adenocarcinoma

This is auto-generated. Add your description here Examples: adenocarcinoma of cervix uteri, pituitary adenocarcinoma (disease), ureter adenocarcinoma (56 total)

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,
Examples	mondo

Data preview:

defined:class	defined:class:label	v0	v0:label
MONDO:0003853	Bartholin gland adenocarcinoma	UBERON:0000460	major vestibular gland
MONDO:0003410	Wolffian duct adenocarcinoma	UBERON:0003074	mesonephric duct
MONDO:0016275	adenocarcinoma of cervix uteri	UBERON:0000002	uterine cervix
MONDO:0018351	adenocarcinoma of penis	UBERON:0000989	penis
MONDO:0004173	adenocarcinoma of skene gland origin	UBERON:0010145	paraurethral gland

See full table here

Adenoma

This is auto-generated. Add your description here Examples: pituitary gland adenoma, breast adenoma, Bartholin gland adenoma (31 total)

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,
Examples	mondo

Data preview:

defined:class	defined:class:label	v0	v0: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

This is auto-generated. Add your description here Examples: adenosquamous breast carcinoma, Bartholin's gland adenosquamous carcinoma, gastric adenosquamous carcinoma (16 total)

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,
Examples	mondo

Data preview:

defined:class	defined:class:label	v0	v0: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

TBD.

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,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label
MONDO:0000814	B-cell adult acute lymphocytic leukemia	MONDO:0000872	B-cell childhood acute lymphoblastic leukemia
MONDO:0017723	Sandhoff disease, adult form	MONDO:0010006	Sandhoff disease
MONDO:0017617	acquired adult-onset immunodeficiency	MONDO:0017769	acquired immunodeficiency
MONDO:0060778	adult Fanconi syndrome	MONDO:0001083	Fanconi renotubular syndrome
MONDO:0016091	adult Krabbe disease	MONDO:0009499	Krabbe disease

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:0004784	allergic asthma	MONDO:0004979	asthma
MONDO:0006525	allergic contact dermatitis	MONDO:0005480	contact dermatitis
MONDO:0005271	allergic disease	MONDO:0000001	disease or disorder
MONDO:0021202	allergic otitis media	MONDO:0005441	otitis media (disease)
MONDO:0000771	allergic respiratory disease	MONDO:0005087	respiratory system disease

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	mondo

Data preview:

defined:class	defined:class:label	substance	substance:label
MONDO:0000789	Atlantic cod allergy	NCBITaxon:8049	Gadus morhua
MONDO:0000790	Atlantic salmon allergy	NCBITaxon:8030	Salmo salar
MONDO:0000802	Indian prawn allergy	NCBITaxon:29960	Penaeus indicus
MONDO:0000773	Timothy grass allergy	NCBITaxon:15957	Phleum pratense
MONDO:0000779	apple allergy	NCBITaxon:3750	Malus domestica

See full table here

Autoimmune

TBD.

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:0030702	autoimmune atherosclerosis	MONDO:0005311	atherosclerosis
MONDO:0030701	autoimmune cardiomyopathy	MONDO:0004994	cardiomyopathy
MONDO:0007179	autoimmune disease	MONDO:0000001	disease or disorder
MONDO:0000587	autoimmune disease of ear, nose and throat	MONDO:0024623	otorhinolaryngologic disease
MONDO:0020640	autoimmune encephalitis	MONDO:0019956	encephalitis

See full table here

Autoimmune inflammation

TBD.

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

TBD.

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,
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:0020336	autosomal dominant Emery-Dreifuss muscular dystrophy	MONDO:0016830	Emery-Dreifuss muscular dystrophy
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

See full table here

Autosomal recessive

TBD.

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,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label
MONDO:0011551	TH-deficient dopa-responsive dystonia	MONDO:0016812	dopa-responsive dystonia
MONDO:0008719	acrorenal syndrome, autosomal recessive	MONDO:0007059	acrorenal syndrome
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:0008406	autosomal recessive Emery-Dreifuss muscular dystrophy	MONDO:0016830	Emery-Dreifuss muscular dystrophy

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

TBD.

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,
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

TBD.

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,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label
MONDO:0016241	alternating hemiplegia of childhood	MONDO:0016210	alternating hemiplegia
MONDO:0016114	bulbospinal muscular atrophy of childhood	MONDO:0016113	bulbospinal muscular atrophy
MONDO:0000870	childhood acute lymphoblastic leukemia	MONDO:0004967	acute lymphoblastic leukemia (disease)
MONDO:0004996	childhood acute myeloid leukemia	MONDO:0018874	acute myeloid leukemia
MONDO:0044767	childhood adrenal gland pheochromocytoma	MONDO:0004974	adrenal gland pheochromocytoma

See full table here

Chronic

TBD.

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,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label
MONDO:0016169	chronic acquired demyelinating polyneuropathy	MONDO:0015923	acquired peripheral neuropathy
MONDO:0001251	chronic apical periodontitis	MONDO:0004508	periapical periodontitis
MONDO:0005607	chronic bronchitis	MONDO:0003781	bronchitis
MONDO:0004924	chronic canaliculitis	MONDO:0005631	actinomycosis
MONDO:0002030	chronic cervicitis	MONDO:0002345	cervicitis (disease)

See full table here

Congenital

TBD.

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,
Examples	mondo

Data preview:

defined:class	defined:class:label	disease	disease:label
MONDO:0001902	congenital agammaglobulinemia	MONDO:0015977	agammaglobulinemia
MONDO:0000577	congenital anemia	MONDO:0002280	anemia (disease)
MONDO:0017375	congenital enterovirus infection	MONDO:0005747	enterovirus infectious disease
MONDO:0004527	congenital granular cell tumor	MONDO:0006235	granular cell tumor
MONDO:0009332	congenital hematological disorder	MONDO:0005570	hematologic disease

See full table here

Consequence of infectious disease

TBD.

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,
Examples	mondo

Data preview:

defined:class	defined:class:label	cause	cause:label	parent	parent:label
MONDO:0005491	Chagas cardiomyopathy	MONDO:0001444	Chagas disease	MONDO:0004994	cardiomyopathy
MONDO:0000890	Zika virus congenital syndrome	MONDO:0018661	Zika virus infectious disease	MONDO:0000839	congenital abnormality
MONDO:0005448	hepatitis C induced liver cirrhosis	MONDO:0005231	hepatitis C virus infection	MONDO:0005155	cirrhosis of liver
MONDO:0034103	infection-related hemolytic uremic syndrome	MONDO:0005550	infectious disease	MONDO:0001549	hemolytic-uremic syndrome
MONDO:0002812	infectious otitis interna	MONDO:0005550	infectious disease	MONDO:0002008	labyrinthitis

See full table here

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
MONDO:0019744	rare renal tubular disease	UBERON:0009773	renal tubule

See full table here

Disease series by gene

This pattern is for diseases that are caused by a single 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. 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:0007818	Hyper-IgE recurrent infection syndrome 1	MONDO:0018037	hyper-IgE syndrome	http://identifiers.org/hgnc/11364	STAT3	HP:0000006	Autosomal dominant inheritance
MONDO:0100121	SCN4A-related myopathy, autosomal recessive	MONDO:0019952	congenital myopathy	http://identifiers.org/hgnc/10591	SCN4A	HP:0000007	Autosomal recessive inheritance
MONDO:0010338	X-linked distal spinal muscular atrophy type 3	MONDO:0001516	spinal muscular atrophy	http://identifiers.org/hgnc/869	ATP7A	HP:0001417	X-linked inheritance
MONDO:0020721	X-linked sideroblastic anemia 1	MONDO:0015194	sideroblastic anemia	http://identifiers.org/hgnc/397	ALAS2	HP:0001417	X-linked inheritance
MONDO:0007092	amelogenesis imperfecta type 1B	MONDO:0019507	amelogenesis imperfecta	http://identifiers.org/hgnc/3344	ENAM	HP:0000006	Autosomal dominant 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	v0	v0: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, Colorado tick fever

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:0021747	Acanthamoeba infectious disease	MONDO:0005550	infectious disease	NCBITaxon:5754	Acanthamoeba
MONDO:0006635	Acinetobacter infectious disease	MONDO:0005550	infectious disease	NCBITaxon:469	Acinetobacter
MONDO:0006636	Actinobacillus infectious disease	MONDO:0005550	infectious disease	NCBITaxon:713	Actinobacillus
MONDO:0006921	Actinomycetales infectious disease	MONDO:0005550	infectious disease	NCBITaxon:2037	Actinomycetales
MONDO:0005117	Aeromonas hydrophila infectious disease	MONDO:0005550	infectious disease	NCBITaxon:644	Aeromonas hydrophila

See full table here

Genetic

TBD.

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/genetic.yaml
Name	genetic
Classes	MONDO:0021150, MONDO:0000001,
Variables	disease (MONDO:0000001),
Contributors	0000-0002-6601-2165, 0000-0001-5208-3432,
Examples

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	v0	v0: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:0000001	disease or disorder
MONDO:0007573	acute erythroleukemia, familial	MONDO:0017858	acute erythroid leukemia
MONDO:0008734	adrenocortical carcinoma, hereditary	MONDO:0006639	adrenal cortex carcinoma
MONDO:0016072	anomaly of puberty or/and menstrual cycle of genetic origin	MONDO:0015860	anomaly of puberty or/and menstrual cycle
MONDO:0009925	autosomal recessive inherited pseudoxanthoma elasticum	MONDO:0024308	pseudoxanthoma elasticum (inherited or acquired)

See full table here

Inborn metabolic

An acquired 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 (disease)	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 AMP-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	v0	v0:label
MONDO:0009825	5-oxoprolinase deficiency (disease)	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 AMP-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:0000212	hypercalcemia, infantile	MONDO:0001566	hypercalcemia disease
MONDO:0015804	infant botulism	MONDO:0005498	botulism
MONDO:0016089	infantile Krabbe disease	MONDO:0009499	Krabbe disease
MONDO:0043555	infantile diarrhea	MONDO:0001673	diarrheal disease
MONDO:0020071	infantile epilepsy syndrome	MONDO:0015650	epilepsy syndrome

See full table here

Infectious disease by agent

Infectious diseases can be classified by the infectioos 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,
Examples

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	mondo

Data preview:

defined:class	defined:class:label	agent	agent:label	location	location:label
MONDO:0006668	bacterial conjunctivitis	NCBITaxon:2	Bacteria	UBERON:0001811	conjunctiva
MONDO:0006669	bacterial endocarditis (disease)	NCBITaxon:2	Bacteria	UBERON:0002165	endocardium
MONDO:0002842	bacterial gastritis	NCBITaxon:2	Bacteria	UBERON:0000945	stomach
MONDO:0016127	bacterial myositis	NCBITaxon:2	Bacteria	UBERON:0002385	muscle tissue
MONDO:0002843	fungal gastritis	NCBITaxon:4751	Fungi	UBERON:0000945	stomach

See full table here

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:0100232	'psoriatic arthritis, susceptibility to	MONDO:0011849	psoriatic arthritis
MONDO:0007845	Kaposi sarcoma, susceptibility to	MONDO:0005055	Kaposi's sarcoma (disease)
MONDO:0000093	Schistosoma mansoni infection, susceptibility	MONDO:0044345	Schistosoma mansoni infectious disease
MONDO:0013562	aspergillosis, susceptibility to	MONDO:0005657	aspergillosis
MONDO:0020836	autism, susceptiblity to	MONDO:0005260	autism (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:0016342	familial isolated arrhythmogenic right ventricular dysplasia	MONDO:0016587	arrhythmogenic right ventricular cardiomyopathy
MONDO:0020075	genetic non-syndromic obesity	MONDO:0019182	monogenic obesity
MONDO:0017262	inherited non-syndromic ichthyosis	MONDO:0015947	inherited ichthyosis
MONDO:0016520	isolated Klippel-Feil syndrome	MONDO:0001029	Klippel-Feil syndrome
MONDO:0016462	isolated agammaglobulinemia	MONDO:0015977	agammaglobulinemia

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:0003955	juvenile breast papillomatosis	MONDO:0002063	breast papillomatosis
MONDO:0100076	juvenile idiopathic scoliosis	MONDO:0000726	idiopathic scoliosis
MONDO:0009066	juvenile nephropathic cystinosis	MONDO:0100151	nephropathic cystinosis
MONDO:0003741	juvenile type testicular granulosa cell tumor	MONDO:0003395	testicular granulosa cell tumor

See full table here

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	v0	v0: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	v0	v0: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

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	v0	v0: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:0003909	Bartholin gland adenomyoma	MONDO:0005635	adenomyoma	UBERON:0000460	major vestibular gland
MONDO:0004120	Bartholin gland small cell carcinoma	MONDO:0000402	small cell carcinoma	UBERON:0000460	major vestibular gland
MONDO:0005665	Bell's palsy	MONDO:0006496	palsy	UBERON:0001647	facial nerve
MONDO:0024283	Demodex folliculitis	MONDO:0017280	demodicidosis	UBERON:0002073	hair follicle
MONDO:0018675	IgG4-related ophthalmic disease	MONDO:0017287	IgG4-related disease	UBERON:0000970	eye

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:0044965	abdominal and pelvic region disorder	UBERON:0002417	abdominal segment of trunk
MONDO:0020594	abducens nerve disease	UBERON:0001646	abducens nerve
MONDO:0002636	accessory nerve disease	UBERON:0002019	accessory XI nerve
MONDO:0002816	adrenal cortex disease	UBERON:0001235	adrenal cortex
MONDO:0005495	adrenal gland disease	UBERON:0002369	adrenal gland

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	v0	v0: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

TBD.

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 (disease)
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

This is auto-generated. Add your description here 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	v0	v0:label
MONDO:0006081	anal melanoma	UBERON:0001245	anus
MONDO:0005012	cutaneous melanoma (disease)	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

This is auto-generated. Add your description here 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	v0	v0: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

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

Mucoepidermoid carcinoma

This is auto-generated. Add your description here 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,
Examples	mondo

Data preview:

defined:class	defined:class:label	v0	v0: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 a syn for G1 NET

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,
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

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

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

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). Examples: chemically-induced disorder, alcohol amnestic disorder, alcoholic polyneuropathy (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	tetracycline exposure
MONDO:0003245	aflatoxin-related hepatocellular carcinoma	MONDO:0007256	hepatocellular carcinoma	ECTO:0001108	aflatoxin exposure
MONDO:0044663	aquagenic palmoplantar keratoderma	MONDO:0006590	palmoplantar keratosis	ECTO:9000156	water exposure
MONDO:0043523	cadmium poisoning	MONDO:0029000	poisoning	ECTO:0001566	cadmium molecular entity exposure
MONDO:0000706	chemical colitis	MONDO:0005292	colitis (disease)	ECTO:0000231	chemical entity exposure

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:0004110	refractory hairy cell leukemia	MONDO:0018935	hairy cell leukemia
MONDO:0004111	refractory hematologic cancer	MONDO:0002334	hematopoietic and lymphoid system neoplasm
MONDO:0004816	refractory plasma cell neoplasm	MONDO:0004959	plasma cell neoplasm
MONDO:0004404	refractory precursor T-lymphoblastic lymphoma/leukemia	MONDO:0003537	precursor T-lymphoblastic lymphoma/leukemia
MONDO:0004401	testis refractory cancer	MONDO:0003510	malignant testicular germ cell tumor

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	v0	v0: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

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 (disease)	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

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	v0	v0: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/X_disease_disrupts_X
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	v0	v0:label	v1	v1:label
MONDO:0005937	REM sleep behavior disorder	MONDO:0003406	sleep-wake disorder	GO:0042747	circadian sleep/wake cycle, REM sleep
MONDO:0001531	blood coagulation disease	MONDO:0000001	disease or disorder	GO:0007596	blood coagulation
MONDO:0000833	bone remodeling disease	MONDO:0005381	bone disease	GO:0046849	bone remodeling
MONDO:0005557	calcium metabolic disease	MONDO:0005066	metabolic disease	GO:0055074	calcium ion homeostasis
MONDO:0020779	cartilage development disorder	MONDO:0000001	disease or disorder	GO:0051216	cartilage development

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	v0	v0:label	v1	v1:label
MONDO:0008861	3-methylcrotonyl-CoA carboxylase 1 deficiency	MONDO:0018950	3-methylcrotonyl-CoA carboxylase deficiency	http://identifiers.org/hgnc/6936	MCCC1
MONDO:0008862	3-methylcrotonyl-CoA carboxylase 2 deficiency	MONDO:0018950	3-methylcrotonyl-CoA carboxylase deficiency	http://identifiers.org/hgnc/6937	MCCC2
MONDO:0009610	3-methylglutaconic aciduria type 1	MONDO:0017359	3-methylglutaconic aciduria	http://identifiers.org/hgnc/890	AUH
MONDO:0009787	3-methylglutaconic aciduria type 3	MONDO:0017359	3-methylglutaconic aciduria	http://identifiers.org/hgnc/8142	OPA3
MONDO:0012435	3-methylglutaconic aciduria type 5	MONDO:0017359	3-methylglutaconic aciduria	http://identifiers.org/hgnc/30528	DNAJC19

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	mondo

Data preview:

defined:class	defined:class:label	agent	agent:label	disease	disease:label
MONDO:0021747	Acanthamoeba infectious disease	NCBITaxon:5754	Acanthamoeba	MONDO:0005550	infectious disease
MONDO:0006635	Acinetobacter infectious disease	NCBITaxon:469	Acinetobacter	MONDO:0005550	infectious disease
MONDO:0006636	Actinobacillus infectious disease	NCBITaxon:713	Actinobacillus	MONDO:0005550	infectious disease
MONDO:0006921	Actinomycetales infectious disease	NCBITaxon:2037	Actinomycetales	MONDO:0005550	infectious disease
MONDO:0005117	Aeromonas hydrophila infectious disease	NCBITaxon:644	Aeromonas hydrophila	MONDO:0005550	infectious disease

See full table here

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:0001594	Achilles bursitis	MONDO:0002471	bursitis	UBERON:0003701	calcaneal tendon
MONDO:0022901	Crohn disease of the esophagus	MONDO:0005011	Crohn disease	UBERON:0001043	esophagus
MONDO:0000709	Crohn ileitis	MONDO:0005011	Crohn disease	UBERON:0002116	ileum
MONDO:0021207	Crohn jejunitis	MONDO:0005011	Crohn disease	UBERON:0002115	jejunum
MONDO:0004551	Meckel diverticulitis	MONDO:0000001	disease or disorder	UBERON:0003705	Meckel's diverticulum

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:0001594	Achilles bursitis	MONDO:0002471	bursitis	UBERON:0003701	calcaneal tendon
MONDO:0022901	Crohn disease of the esophagus	MONDO:0005011	Crohn disease	UBERON:0001043	esophagus
MONDO:0000709	Crohn ileitis	MONDO:0005011	Crohn disease	UBERON:0002116	ileum
MONDO:0021207	Crohn jejunitis	MONDO:0005011	Crohn disease	UBERON:0002115	jejunum
MONDO:0004551	Meckel diverticulitis	MONDO:0000001	disease or disorder	UBERON:0003705	Meckel's diverticulum

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	v0	v0: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

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

Attribute	Info
IRI	http://purl.obolibrary.org/obo/mondo/patterns/susceptibility_by_gene.yaml
Examples - autism, susceptibility to, X-linked 5, bulimia nervosa, susceptibility to, 2, nephrolithiasis susceptibility caused by SLC26A1'
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:0010340	Asperger syndrome, X-linked, susceptibility to, 1	MONDO:0005259	Asperger syndrome	http://identifiers.org/hgnc/14289	NLGN3
MONDO:0010343	Asperger syndrome, X-linked, susceptibility to, 2	MONDO:0005259	Asperger syndrome	http://identifiers.org/hgnc/14287	NLGN4X
MONDO:0014786	IgA nephropathy, susceptibility to, 3	MONDO:0005342	IgA glomerulonephritis	http://identifiers.org/hgnc/11270	SPRY2
MONDO:0020715	Multiple system atrophy 1, susceptibility to	MONDO:0007803	multiple system atrophy	http://identifiers.org/hgnc/25223	COQ2

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:0015150	complex hereditary spastic paraplegia	MONDO:0019064	hereditary spastic paraplegia
MONDO:0017263	inherited ichthyosis syndromic form	MONDO:0015947	inherited ichthyosis
MONDO:0016463	syndromic agammaglobulinemia	MONDO:0015977	agammaglobulinemia
MONDO:0020148	syndromic aniridia	MONDO:0019172	aniridia
MONDO:0015246	syndromic anorectal malformation	MONDO:0019938	anorectal malformation

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:0018994	Charcot-Marie-Tooth disease type X	MONDO:0015626	Charcot-Marie-Tooth disease
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:0010680	X-linked Emery-Dreifuss muscular dystrophy	MONDO:0016830	Emery-Dreifuss muscular dystrophy

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:0033304	nonsyndromic deafness, Y-linked	MONDO:0019497	nonsyndromic genetic deafness
MONDO:0010761	retinitis pigmentosa Y-linked	MONDO:0019200	retinitis pigmentosa

See full table here