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Add more integrity checks on fields in JSON schema 2 #69
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Continuation of work discussed (at least on GH) from the May sprint at microbiomedata/nmdc-metadata#308 |
Third level of checks handled in microbiomedata/nmdc-metadata#362 |
Removing other assignees. @turbomam let me know if this assignment isn't you. |
RE Is the ID prefix valid? (e.g. KEGG.KO vs KEGG.ORTHOLOG) I see prefix definitions, especially in MAM@MAM-M74 schema % pwd
/Users/MAM/Documents/gitrepos/nmdc-schema/src/schema
MAM@MAM-M74 schema % grep -i kegg *
annotation.yaml: - KEGG.PATHWAY
annotation.yaml: - KEGG.REACTION
annotation.yaml: - KEGG.ORTHOLOGY ## KO number
core.yaml: - KEGG.COMPOUND |
RE Is the local part of the ID syntactically conformant? (e.g. KEGG:K\d+) I don't see patterns for the local parts, at least not in pathway:
aliases:
- biological process
- metabolic pathway
- signaling pathway
is_a: functional annotation term
description: >-
A pathway is a sequence of steps/reactions carried out by an organism or community of organisms
slot_usage:
has_part:
range: reaction
multivalued: true
description: >-
A pathway can be broken down to a series of reaction step
id_prefixes:
- KEGG.PATHWAY
- COG
exact_mappings:
- biolink:Pathway |
very rough example for functional annotation term:
aliases:
- function
- functional annotation
is_a: ontology class
slot_usage:
id:
pattern: "^(KEGG.ORTHOLOG:K\\d+|EC:\\d+\\.ETC)$"
description: >-
Abstract grouping class for any term/descriptor that can be applied to a functional unit of a genome (protein, ncRNA, complex).
abstract: true
todos:
- decide if this should be used for product naming |
Was microbiomedata/nmdc-metadata issue 360 I will be adding local part patterns to the yaml files in this repo. |
@wdduncan and @cmungall : I can't find patterns for COG or RetroRules at the BioRgistry, or sample usages in the MongoDB. example working query:
But neither of these return any matches:
|
example of finding local part of IDs #69
@ssarrafan do you have a sense of who raised this concern? Can I close it? |
It doesn't seem like it's really specific to checks on the contents of a JOSN file by the JSON schema serialization of the schema. |
Is the concern especially about validating KEGG-related CURIes? |
This is from 2021 so I don't remember which meeting this came from. I would say it can probably be closed. |
There are different levels of checks, this issue is to cover the first 2:
2 Is the local part of the ID syntactically conformant? (e.g. KEGG:K\d+)
The first is very easy to do with using the existing id_prefixes annotated in the schema
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