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Review warnings from OBO dashboard ROBOT report #3905

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sbello opened this issue Jan 24, 2024 · 4 comments
Open

Review warnings from OBO dashboard ROBOT report #3905

sbello opened this issue Jan 24, 2024 · 4 comments

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@sbello
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sbello commented Jan 24, 2024

See https://dashboard.obofoundry.org/dashboard/mp/robot_report.html
duplicate synonyms - 7 terms
missing definitions 119 terms

@sbello sbello self-assigned this Jan 24, 2024
sbello added a commit that referenced this issue Jan 24, 2024
fixed one incorrect synonym
@sbello
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sbello commented Jan 24, 2024

MP:0009142 and MP:0014256; MP:0008244and MP:0030944 problem is that the 2 terms share an acronym so the same synonym is an exact match to both - we should look into using the acronym tag but need to consider what this would do to the MP loads at MGI and other resources. Related to this is the use of the acronym ASD in MP and HPO
Autistic behavior (ASD)
Atrial septal defect (ASD)
atrial septal defect (ASD)
ostium primum atrial septal defect (ostium primum ASD)
ostium secundum atrial septal defect (ostium secundum ASD)
common atrium (common atrium ASD)
coronary sinus atrial septal defect (coronary sinus ASD)
sinus venosus atrial septal defect (sinus venosum ASD)

Results in incorrect lexical mapping between atrial septal defect in MP and autistic disorder in HPO

MP:0014312 should have been thick not thin
MP:0010575 report has 'duplicate label synonym' but the label is 'aortic arch dilation' and the synonym is 'aorta arch dilation' these are not duplicates

sbello added a commit that referenced this issue Jan 25, 2024
adding definitions for
MP:0002873
MP:0004050
MP:0004051
MP:0004052
sbello added a commit that referenced this issue Jan 25, 2024
Adding definitions to
MP:0008927
MP:0008931
MP:0009570
MP:0009572
MP:0009573
MP:0009574
MP:0009944
sbello added a commit that referenced this issue Jan 25, 2024
added definitions for
MP:0009948
MP:0009949
MP:0009950
MP:0009951
sbello added a commit that referenced this issue Jan 25, 2024
added definitions to
MP:0009978
MP:0009988
MP:0009989
MP:0009990
MP:0009991
MP:0009992
MP:0009993
MP:0009994
MP:0009995
MP:0009996
MP:0009997
sbello added a commit that referenced this issue Jan 26, 2024
added definitions to
MP:0009998
MP:0009999
MP:0010001
MP:0010004
sbello added a commit that referenced this issue Jan 26, 2024
added definitions to
MP:0010007
MP:0010903
MP:0011149
MP:0011273
MP:0011274
sbello added a commit that referenced this issue Jan 26, 2024
added definitions to
MP:0011324
MP:0011329
MP:0011330
sbello added a commit that referenced this issue Jan 29, 2024
added definitions to
MP:0010465
MP:0013978
MP:0013979
MP:0013980
MP:0013995
MP:0014020
MP:0014217
MP:0014218
MP:0014219
MP:0014330
@sbello
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sbello commented Jan 30, 2024

MP:0011510 - requested PMID:23804932 to try to define

sbello added a commit that referenced this issue Jan 30, 2024
added definitions for
MP:0011674
MP:0011713
MP:0011714
MP:0011715
sbello added a commit that referenced this issue Jan 30, 2024
added definitions for
MP:0011716
MP:0011717
MP:0011718
MP:0012229
sbello added a commit that referenced this issue Jan 30, 2024
added definitions for
MP:0012608
MP:0012609
MP:0012610
MP:0012628
MP:0012629
MP:0012630
MP:0012631
MP:0012632
sbello added a commit that referenced this issue Jan 30, 2024
added or modified definitions to
MP:0012043
MP:0012633
MP:0012634
MP:0012640
MP:0012641
MP:0012642

Also modified labels for
MP:0012640
MP:0012641
MP:0012642
from benz (alpha) to benzo (alpha)
sbello added a commit that referenced this issue Jan 30, 2024
removed extra EQ from MP:0009981
sbello added a commit that referenced this issue Jan 31, 2024
added definitions for
MP:0012646
MP:0012647
MP:0012648
MP:0012649
MP:0012650
MP:0012651
MP:0012652
MP:0012653
MP:0012654
MP:0012655
MP:0012656
MP:0012657
sbello added a commit that referenced this issue Jan 31, 2024
Added definitions for
MP:0012658
MP:0012659
MP:0012660

Modified cross references for
MP:0013994
MP:0013998
MP:0013999
sbello added a commit that referenced this issue Jan 31, 2024
added definitions to
MP:0013925
MP:0013929
MP:0013930
MP:0013931
MP:0013934
MP:0013937

Also fixed some xrefs that were using MGI: instead of orcids
@sbello
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sbello commented Feb 1, 2024

problem terms

  • intraembryonal intestine elongation - only annotations are from DMDD - maybe this was meant to be abnormal intestinal elongation or increased or???
  • no idea what the proximal internal carotid artery is, I find references to this primarily related to proximal obstruction one reference wrote this as proximal (extracranial) ICA but no clue if this is the common way to refer to this
  • symmetric hepatic veins ?

sbello added a commit that referenced this issue Feb 1, 2024
added definitions and synonyms to
MP:0013930
MP:0013944
MP:0013952
MP:0013967
MP:0013968
MP:0013969
MP:0013970
MP:0013971
sbello added a commit that referenced this issue Feb 1, 2024
added definitions for
MP:0013973
MP:0013974
MP:0013975
MP:0013977
MP:0013981
MP:0013988
sbello added a commit that referenced this issue Feb 2, 2024
added definition to
MP:013992
@sbello
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sbello commented Feb 29, 2024

New report https://dashboard.obofoundry.org/dashboard/mp/robot_report.html
17 missing definitions

sbello added a commit that referenced this issue Apr 26, 2024
fixed synonym for MP:0014368
removed extra EQ from MP:0009981
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