Phenopacket-tools found a bunch of errors in the EZH1 phenopackets. This PR applies the manual fixes.
@pnrobinson most of these things are probably no-brainer, so I'll merge the PR. So, this is just FYI.
One more check we need to implement is to check presence of duplicate phenotypic features. The phenopackets had a bunch of duplicates (e.g. here), likely a result of parsing the table.
The list of issues:
P3
Problem: Phenotypic features of P3 must not contain both an observed term (Appendicular hypotonia, HP:0012389) and an observed ancestor (Hypotonia, HP:0001252)
Fix: Remove Hypotonia
P4
Problem: Phenotypic features of P4 must not contain both an observed term (Axial hypotonia, HP:0008936) and an observed ancestor (Hypotonia, HP:0001252)
Fix: Remove Hypotonia
Problem: Phenotypic features of P4 must not contain both an observed term (Delayed ability to walk, HP:0031936) and an observed ancestor (Delayed gross motor development, HP:0002194)"
Fix: Remove Delayed gross motor development
P6
Problem: Phenotypic features of P6 must not contain both an observed term (Dysmetria, HP:0001310) and an observed ancestor (Ataxia, HP:0001251)
Fix: Remove Ataxia
P8
Problem: Phenotypic features of P8 must not contain both an observed term (Delayed ability to walk, HP:0031936) and an observed ancestor (Delayed gross motor development, HP:0002194)
Fix: Remove Delayed gross motor development
P9
Problem: Phenotypic features of P9 must not contain both an observed term (Horizontal nystagmus, HP:0000666) and an excluded ancestor (Nystagmus, HP:0000639)
Fix: Remove Nystagmus
P12
Problem: Phenotypic features of P12 must not contain both an observed term (Delayed ability to walk, HP:0031936) and an observed ancestor (Delayed gross motor development, HP:0002194)
Fix: Remove Delayed gross motor development
P18
Problem: Phenotypic features of P18 must not contain both an observed term (Unsteady gait, HP:0002317) and an observed ancestor (Gait disturbance, HP:0001288)
Phenopacket-tools found a bunch of errors in the EZH1 phenopackets. This PR applies the manual fixes.
@pnrobinson most of these things are probably no-brainer, so I'll merge the PR. So, this is just FYI.
One more check we need to implement is to check presence of duplicate phenotypic features. The phenopackets had a bunch of duplicates (e.g. here), likely a result of parsing the table.
The list of issues:
P3
Problem: Phenotypic features of P3 must not contain both an observed term (Appendicular hypotonia, HP:0012389) and an observed ancestor (Hypotonia, HP:0001252) Fix: Remove Hypotonia
P4
Problem: Phenotypic features of P4 must not contain both an observed term (Axial hypotonia, HP:0008936) and an observed ancestor (Hypotonia, HP:0001252)
Fix: Remove Hypotonia
Problem: Phenotypic features of P4 must not contain both an observed term (Delayed ability to walk, HP:0031936) and an observed ancestor (Delayed gross motor development, HP:0002194)"
Fix: Remove Delayed gross motor development
P6
Problem: Phenotypic features of P6 must not contain both an observed term (Dysmetria, HP:0001310) and an observed ancestor (Ataxia, HP:0001251)
Fix: Remove Ataxia
P8
Problem: Phenotypic features of P8 must not contain both an observed term (Delayed ability to walk, HP:0031936) and an observed ancestor (Delayed gross motor development, HP:0002194)
Fix: Remove Delayed gross motor development
P9
Problem: Phenotypic features of P9 must not contain both an observed term (Horizontal nystagmus, HP:0000666) and an excluded ancestor (Nystagmus, HP:0000639)
Fix: Remove Nystagmus
P12
Problem: Phenotypic features of P12 must not contain both an observed term (Delayed ability to walk, HP:0031936) and an observed ancestor (Delayed gross motor development, HP:0002194)
Fix: Remove Delayed gross motor development
P18
Problem: Phenotypic features of P18 must not contain both an observed term (Unsteady gait, HP:0002317) and an observed ancestor (Gait disturbance, HP:0001288)
Fix: Remove Gait disturbance