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dosdp pattern for cancer predisposition
sabrinatoro
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sabrinatoro
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@MeeSiing
Please see my comment in the text, though you might need to go back to the commit to see what these comments refer to. In addition, the name of the file should be cancer_predisposition.yaml (the ".yaml" is important)
I am submitting changes. You can see them in the next commit so you can see what I changed.
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| pattern_iri: http://purl.obolibrary.org/obo/mondo/patterns/cancer_predisposition.yaml | ||
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| description: 'This pattern should be used for terms in which hereditary cancer predisposition due to variation(s) in a gene confers the predisposition to a cancer. |
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The closing apostrophe is missing.
| - https://orcid.org/0000-0002-7638-4659 | ||
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| classes: | ||
| cancer or benign tumor: MONDO:0700096 |
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this is the wrong ID for cancer or benign tumor
| - gene | ||
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| annotations: | ||
| - annotationProperty: exact_synonym |
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This synonym is not usually used. I don't think there is a commonly used synonym.
Also, this synonym would not be correct all the time since some of these susceptibilities are not to tumors.
| text: Hereditary cancer predisposition due to variation (s) in %s, which confers the predisposition to a %s. | ||
| vars: | ||
| - gene | ||
| - cancer |
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"cancer" is not defined as a variable. you named the variable "disease" in line 24
| text: '''hereditary neoplastic syndrome'' and (''has material basis in germline mutation in'' some %s)' | ||
| vars: | ||
| - gene | ||
| - cancer No newline at end of file |
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It makes no sense to have cancer as var here unless you mention it in the definition
| vars: | ||
| - gene | ||
| - cancer | ||
| #note that the cancer variable is not always known, or might be variable (ie their could be more than one term) |
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This is not great.. In this case you need more than one pattern, one were the target predisposition is known, and one where its not. (and if there are cases where there is more than one, I dont remember if dosdp can do that, probably)
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| text: '%s-related cancer predisposition' | ||
| vars: | ||
| - gene |
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either always cancer variable or never
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| equivalentTo: | ||
| text: '''hereditary neoplastic syndrome'' and (''has material basis in germline mutation in'' some %s)' |
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Missing: and (''predisposes_towards'' some %s)
4 participants
created a dosdp pattern for cancer predisposition