Closed drseb closed 6 years ago
we've been piggybacking off the EBI ORDO effort, looks like these aren't present:
Maybe ORDO lags behind?
@siiraa @SimonJupp I forgot what we discussed, should we take over the XML2OWL part? Would be good to stay in sync here.
Orphanet maintain the Ordo OWL file that was last updated in July (according to OLS). Maybe Marc @Orphanet can comment on how often this is being generated from the Orphanet db?
The Ordo imported into EFO will most likely be further behind as we don't have a clean way to import and update Ordo in EFO just yet, although we have been manually importing new Ordo terms into EFO as we've needed them.
On 6 Dec 2017, at 18:03, Simon Jupp wrote:
Orphanet maintain the Ordo OWL file that was last updated in July (according to OLS). Maybe Marc @Orphanet can comment on how often this is being generated from the Orphanet db?
OK, thanks for the clarification. I'll want to hear back
The Ordo imported into EFO will most likely be further behind as we don't have a clean way to import and update Ordo in EFO just yet, although we have been manually importing new Ordo terms into EFO as we've needed them.
OK. Just to clarify for others reading this thread, mondo is not using the Ordo with EFO (although EFO is itself integrated), we treat Ordo as it's own first class entity and we pull from http://www.orphadata.org/data/ORDO/ordo_orphanet.owl.zip of which the latest is ordo_orphanet_2.4.owl from July as you say.
This issue was moved to monarch-initiative/mondo#150
Hi,
I can't seem to find several Orphanet diseases in MONDO (obo version).
The complete list is:
To show an example I took "Orphanet:156177" which is "Retinal ciliopathy due to mutation in Usher gene". When looking at the disease hierachy in Orphanet, I find that all of the following are not found:
Only Usher syndrome ORPHA:886 is found. I especially wonder why "Ciliopathy ORPHA:363250" is not in MONDO, as I found a seemingly good match, i.e.:
Can you clarify why these Orphanet entries are excluded and especially why MONDO:0005308 does not have an xref to ORPHA:363250?
Thanks for any clarifications.