g2d_sabrina notes

	A	B	C	D	E	F
1						definition
2	causes or contributes to condition			Question: Is a gene an "entity"? If not, we would need a similar term where entity = gene - note: this fits the data from the Alliance	RO_0003302	A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition.
3		causes condition alternative: is causal mutation/variation in		- condition = disease - variant in gene is causal to disease - could be Mendelian or not (ie germline and somatic)	RO_0003303	A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition.
4			is causal germline mutation in	(from Peter's notes): Variants in gene cause disease in Mendelian fashion	RO_0004013	Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring
5			is causal somatic mutation in	(from Peter's notes): Cancer related variants, simplest case of somatic mutation	RO_0004014	Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring
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8		contributes to condition		- condition = disease - variant in gene does not "on its own" cause the disease	RO_0003304	A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition.
9			is causal germline mutation partially giving rise to	- for digenic, olygogenic	RO_0004016	Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition
10			contributes/is correlated to condition (=cancer) note: we might not need a new RO term, we might be ok with using the parent term.	Cancer related variants - But cancer is rarely caused by one somatic mutation and so the relation of the gene to disease is not simple. Suggestion: Somatic_mutation_somehow_related_to_tumorigenesis (come up with label to express this)		(new!) or use the parent term
11			confers susceptibility to condition	- variant in gene confers or influence susceptibility to a condition - could be mendelian or not - note: 'is causal susceptibiltity factor for': the definition is probably too strong for what we want to communicate (def: relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition)	(new!)	(new!) Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition.
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