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Document the difference between the 4 released OWL files #926
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@dhimmel looking at the 3.11.0 release, the 1st release that contains those files there is some info:
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EFO vs EFO-OTAR node comparisonI compared Nodes added by EFO-OTARHere are the nodes EFO-OTAR adds (in purple outline) and their ancestors:
One question I have is what is the purpose of adding "familial disease", "other", "cyst", since these are all leaf nodes? Are they actually a helpful way for OpenTargets to categorize disease? CC @d0choa. Nodes removed by EFO-OTARHere are the nodes EFO-OTAR removes (in purple outline) and their ancestors: Expand for removed nodes table
CodeCode to produce these figures and tables is not yet available, but is based on nxontology. I hope to make the nxontology importer for EFO available soon. |
Thanks @dhimmel for the analysis. It's really useful. @zoependlington can provide more details. From the Open Targets perspective, the background story behind the slim was that we wanted to align EFO to a more clinical interpretation. EFO has a lot of high-level organisational nodes that attend to anatomical characteristics (many of them can be seen on your analysis). However, they have little or no clinical value (e.g. disease by anatomical system). Instead, the top-nodes of the slim resemble other clinical classifications like Meddra. In the process of reorganising the terms, a few terms have to be removed, relocated or split. You can find the logic behind most of the changes in the respective tickets. For the ones that you raised I found the next:
@paolaroncaglia and @zoependlington can comment on these two. Regarding |
Quoting @zoependlington from #927 (comment) regarding forced relationships in EFO-OTAR:
Great to know about Based on Regarding "the profile is our master EFO with a few extra terms, which will eventually be added to the master EFO file", does that mean the eventual plan is to take all the modifications in Getting back to the original documentation request, it would be nice to have guidance in the README regarding when to use efo-base.owl, efo.owl, efo_otar_profile.owl, versus efo_otar_slim.owl. My current understanding is:
Is this understanding correct? |
EFO Release v3.25.0 contains the following OWL files:
efo-base.owl
60.8 MBefo.owl
175 MBefo_otar_profile.owl
147 MBefo_otar_slim.owl
130 MBI am curious as to how these files differ and haven't been able to find much information.
From an OpenTargets blog post:
From
opentargets/OnToma
:Is there any other documentation I'm missing?
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