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Design Patterns

Pattern Description
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.
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
adenocarcinoma disease has location X 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)
adenoma disease has location X
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
adenosquamous carcinoma disease has location X 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
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
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
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
autoimmune An instance of a disease that is brought about or caused by autoimmunity.
Examples: autoimmune cardiomyopathy, autoimmune pancreatitis
autoimmune_inflammation An instance of an autoimmune disease that is described by inflammation in a specific anatomical entity.
Example: autoimmune thyroid disease
autosomal_dominant This pattern is applied to autosomal dominant forms of an inherited disease.
Examples: autosomal dominant cerebellar ataxia, autosomal dominant osteopetrosis
autosomal_recessive This pattern is applied to autosomal recessive forms of an inherited disease.
Examples: autosomal recessive brachyolmia, autosomal recessive sideroblastic anemia
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
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
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
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.
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.
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
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
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
congenital An instance of a disease in which the disease is present at birth, regardless of cause.
Examples: congenital agammaglobulinemia, congenital nystagmus
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
dependence_on_substance Dependence on a substance that specifies the environmental stimulus such as alcohol, cocaine, etc. Example: dependence on cocaine.
disease or disorder disease caused by disruption of X 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)
disease 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). 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 (26 total)
disease_by_dysfunctional_structure
Diseases classified by a perturbation in an anatomical structure (such as a subcellular component, or an organ)
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. Examples: MED12-related intellectual disability syndrome, TTN-related myopathy, MYPN-related myopathy
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
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
hemangioma disease has location X 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)
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).
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
inborn errors of metabolism disease caused by disruption of X 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)
inborn_metabolic An acquired metabolic disease that causes disruption of a process.
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
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
infectious_inflammation
This combines the infectious disease by agent pattern and the inflammatory disease by site pattern.
Examples: bacterial endocarditis (disease), fungal gastritis
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
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'.
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'
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'
leiomyoma disease has location X 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)
leiomyosarcoma disease has location X 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)
lipoma disease has location X 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)
location A disease that is located in a specific anatomical site.
Examples: 'abdominal cystic lymphangioma', 'articular cartilage disease', 'urethral disease'
location_top TBD.
lymphoma disease has location X 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)
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
melanoma disease has location X 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)
meningioma disease has location X 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)
mitochondriaal_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'.
mucoepidermoid carcinoma disease has location X 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)
neoendocrine_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
neoendocrine_neoplasm_grade1 We follow NCIT in making carcinoid tumor a synonym for neuroendocrine neoplasm G1 (G1 NET).
Examples: carcinoid tumor (disease)
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.
neoplasm TBD.
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'.
OMIM_disease_series_by_gene
This pattern is meant to be used for 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. 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
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 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 omimps-should-be-inherited-violation.sparql
Examples: holoprosencephaly OMIMPS:236100, '3-M syndrome'(http://purl.obolibrary.org/obo/MONDO_0007477) OMIMPS:236100.
poisoning A disease that is caused by exposure to an environmental stimulus that causes poisoning. Examples: colchicine poisoning, cocaine intoxication
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
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'.
rare TBD.
rare_genetic TBD.
refractory TBD.
rhabdomyosarcoma disease has location X This is auto-generated. Add your description here
Examples: rhabdomyosarcoma of the cervix uteri, breast rhabdomyosarcoma, testis rhabdomyosarcoma (15 total)
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.
small cell carcinoma disease has location X This is auto-generated. Add your description here
Examples: cervical small cell carcinoma, pancreatic small cell neuroendocrine carcinoma, ureter small cell carcinoma (16 total)
specific_infectious_disease_by_location
TODO
specific_inflammatory_disease_by_site
as for inflammatory_disease_by_site, but refining a specific disease
specific_inflammatory_disease_by_site
as for inflammatory_disease_by_site, but refining a specific disease
squamous cell carcinoma disease has location X This is auto-generated. Add your description here
Examples: cervical squamous cell carcinoma, skin squamous cell carcinoma, ureter squamous cell carcinoma (63 total)
substance_abuse A substance abuse that specifies a specific environmental stimulus such as alcohol, cocaine, etc. Examples: alcohol abuse, cocaine abuse
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
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.
vectorBorneDisease 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'
X disease disrupts X This is auto-generated. Add your description here
Examples: disease of catalytic activity, disease of transporter activity, phagocytic cell dysfunction (49 total)
X disease has basis in dysfunction of X This is auto-generated. Add your description here
Examples: collagenopathy type 2 alpha 1, hemoglobinopathy, blood platelet disease (2195 total)
x_linked TBD.
y_linked TBD.