HumanDiseaseOntology
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DiseaseOntology
clean up OMIM IDs from MGI/RGD splits
Not all of the OMIM IDs for series that were split using the ROBOT tool were removed from the parent term. These splits should be reviewed and:
- OMIM IDs removed from parent DOID term
- OMIM PS IDs added where these were missed I'll pull the list of terms to review from the split spreadsheet and link it here
Spreadsheet https://docs.google.com/spreadsheets/d/1hN9KoB3UgfTXS9N4U-w-JTHQv1jlFyKH-wol1W1MmZA/edit?usp=sharing
@lschriml I'm noticing some OMIM IDs that appear to have been removed from the DO file (comparing the version of DO on MGI to the doid-edit.owl file) See for example OMIM:300557, OMIM:556500, OMIM:602404, OMIM:606852, OMIM:613164. These all are entries without a known locus. Were these removed intentionally?
Hello Sue, this was cleanup, removing they OMIM IDs that belong to subtypes that were assigned to the parent term.
These appear to have disappeared from the file completely. There is no child term of Parkinson that these are attached to.
yes that is true, we need to add in the child terms. It is in my to do before the next release. Please go ahead and add them if you like.
On Mon, Mar 25, 2019 at 4:25 PM Sue Bello [email protected] wrote:
These appear to have disappeared from the file completely. There is no child term of Parkinson that these are attached to.
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-- Lynn M. Schriml, Ph.D. Associate Professor
Institute for Genome Sciences University of Maryland School of Medicine Department of Epidemiology and Public Health 670 W. Baltimore St., HSFIII, Room 3061 Baltimore, MD 21201 P: 410-706-6776 | F: 410-706-6756 [email protected]
New spreadsheet of OMIM IDs that are xref's for more than one DO term https://docs.google.com/spreadsheets/d/1fXY2QsspLGa1DCsKWvxjNkQwuMds_lR7alKLoWrKE5M/edit?usp=sharing From a new MGI QC report
Thank you Sue !!
Sent from my iPhone
On Apr 22, 2019, at 1:53 PM, Sue Bello [email protected] wrote:
New spreadsheet of OMIM IDs that are xref's for more than one DO term https://docs.google.com/spreadsheets/d/1fXY2QsspLGa1DCsKWvxjNkQwuMds_lR7alKLoWrKE5M/edit?usp=sharing From a new MGI QC report
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The OMIM phenoseries OMIM:PS151660 is currently an xref to lipoatrophic diabetes mellitus and not to familial partial lipodystrophy but the series is 'Lipodystrophy, familial partial' and 'LIPOATROPHIC DIABETES' is a synonym for OMIM:151660 only. This could be an instance where OMIM did not redistribute the synonyms after modifying the record so the synonym may be more general than the term it is attached to. I'm adding the PS ID to familial partial lipodystrophy the placement of it on the second DO term and if the two terms should be combined needs further review.
@lschriml OMIM:137400 We discussed this with the OMIM team the last time we met and the record has now been updated to indicate that this term in OMIM is specifically for fissured and geographic tongue not for cases of one or the other in isolation. Is it okay with you if I remove the ID from both, DOID:11514 and DOID:1455? This would remove the OMIM ID completely from DO until we created a new disease.
@lschriml I've come across a couple of instances where OMIM IDs have been xrefs for diseases that are 'included entities' in an OMIM record. According to OMIM the included entities are not the same disease and are not meant to be associated with the ID that is for the primary entity. They are included entities in OMIM as OMIM does not yet feel there is sufficient data to support creating an independent record. I have been removing the OMIM ID from the included entity and making a note in the new spreadsheet. Please let me know if you would prefer I leave these in.
@lschriml The DO term 'muscular dystrophy-dystroglycanopathy' (DOID:0050588) has multiple OMIM xrefs that are also entered as independent terms but the independent terms are descendants of 'limb-girdle muscular dystrophy' (DOID:11724) and have no relation to 'muscular dystrophy-dystroglycanopathy'. We may want to review the organization of these terms.
Thank you Sue, please remove the 'included entity' OMIMs.
Cheers, Lynn
On Tue, Apr 23, 2019 at 11:23 AM Sue Bello [email protected] wrote:
@lschriml https://github.com/lschriml I've come across a couple of instances where OMIM IDs have been xrefs for diseases that are 'included entities' in an OMIM record. According to OMIM the included entities are not the same disease and are not meant to be associated with the ID that is for the primary entity. They are included entities in OMIM as OMIM does not yet feel there is sufficient data to support creating an independent record. I have been removing the OMIM ID from the included entity and making a note in the new spreadsheet. Please let me know if you would prefer I leave these in.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/DiseaseOntology/HumanDiseaseOntology/issues/679#issuecomment-485850957, or mute the thread https://github.com/notifications/unsubscribe-auth/ABBB4DJIQIOKRAVWS6UORILPR4SYNANCNFSM4HAII72Q .
-- Lynn M. Schriml, Ph.D. Associate Professor
Institute for Genome Sciences University of Maryland School of Medicine Department of Epidemiology and Public Health 670 W. Baltimore St., HSFIII, Room 3061 Baltimore, MD 21201 P: 410-706-6776 | F: 410-706-6756 [email protected]