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Our OMIM prefix and our OMIMPS URI prefix are no longer canonical. We would like to update them, but this is tricky, if / when we do this, it should be with care. Some prerequisite updates to our tooling might be necessary. We'd also have to update these prefixes in multiple places: omim, mondo-ingest, and mondo repos at the very least, and we'd want to do careful QC before merging.
Sub-task matrix
Do these changes:
1. URI prefix updates
2. Possible prefix updates
In these repos:
I. omim
II. mondo-ingest
III. mondo?
Sub-task details
1. URI prefix updates
Prerequisites:
Not sure if we need to fix any tooling that bugs out when : is in the URI prefix
If we choose to use https://omim.org/MIM:PS for the OMIMPS URI prefix, curies will likely first need an update to account for conflict with it being a substring of https://omim.org/MIM:, which would be the new URI prefix for OMIM
Bioregistry (https://bioregistry.io/registry/omim.ps) shows that our current OMIMPS URI prefix, https://omim.org/phenotypicSeries/PS, is legacy. We want to change the URI prefix to one of the canonical ones: https://omim.org/MIM:PSor https://bioregistry.io/omim.ps:. If we do this, then we may also want to update the URI prefix for OMIM.
2. Possible prefix updates
New canonical prefix: Some folks (the OMIM team itself, I think), want the canonical prefix to be mim.
New prefix synonyms: Then, the following would/could become prefix synonyms: MIM, omim and OMIM.
@twhetzel@matentzn I've taken our related discussions on slack and in #109 (comment) and created this issue for later. IDK how high priority this is, but I think it will be time consuming if / when we ever work on it.
Overview
Our OMIM prefix and our OMIMPS URI prefix are no longer canonical. We would like to update them, but this is tricky, if / when we do this, it should be with care. Some prerequisite updates to our tooling might be necessary. We'd also have to update these prefixes in multiple places:
omim
,mondo-ingest
, andmondo
repos at the very least, and we'd want to do careful QC before merging.Sub-task matrix
Do these changes:
In these repos:
omim
mondo-ingest
mondo
?Sub-task details
1. URI prefix updates
Prerequisites:
:
is in the URI prefixhttps://omim.org/MIM:PS
for the OMIMPS URI prefix,curies
will likely first need an update to account for conflict with it being a substring ofhttps://omim.org/MIM:
, which would be the new URI prefix for OMIMBioregistry (https://bioregistry.io/registry/omim.ps) shows that our current OMIMPS URI prefix,
https://omim.org/phenotypicSeries/PS
, is legacy. We want to change the URI prefix to one of the canonical ones:https://omim.org/MIM:PS
orhttps://bioregistry.io/omim.ps:
. If we do this, then we may also want to update the URI prefix for OMIM.2. Possible prefix updates
mim
.MIM
,omim
andOMIM
.Additional details
Background information:
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