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Add dislocated anatomical entity pattern template #829

Merged
merged 4 commits into from
Jul 8, 2022
Merged

Add dislocated anatomical entity pattern template #829

merged 4 commits into from
Jul 8, 2022

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rays22
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@rays22 rays22 commented May 26, 2022

If applied, this commit will fix #828

@rays22 rays22 added the pattern label May 26, 2022
@rays22 rays22 requested a review from matentzn May 26, 2022 14:51
@rays22 rays22 self-assigned this May 26, 2022
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sbello commented May 26, 2022 •
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I think the description needs to be expanded to make clear the distinction between dislocated and mislocalized
dislocated = developed in the normal location and something happened to move it out of that position
mislocalized (synonym ectopic) = developed in the wrong location

But lens luxation in HPO http://www.informatics.jax.org/vocab/hp_ontology/HP:0012019 is defined as dislocated but child of ectopia lentis

Also ZFIN has a number of annotations that use dislocated but maybe should use mislocalized?? https://zfin.org/search?q=dislocated&fq=category%3A%22Phenotype%22&category=Phenotype

Need to clarify in PATO the distinction between mislocalised and dislocated

@rays22 rays22 mentioned this pull request Jun 16, 2022
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rays22 commented Jun 16, 2022

Need to clarify in PATO the distinction between mislocalised and dislocated

PATO issue:
pato-ontology/pato#501

rays22
rays22 commented Jun 16, 2022
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src/patterns/dosdp-dev/dislocatedAnatomicalEntity.yaml Outdated
- anatomical_entity

def:
text: "Dislocation or displacement of %s. The effected anatomical entity is assumed to have had developed in its normal location before the dislocation."
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OK

@rays22
Merge branch 'master' into issue828
6a6a15b
@rays22
Fix description and text definition
6b5755f 
to improve the phenotype pattern template based on community feedback.

If applied, this commit will fix #828.
@rays22 rays22 merged commit 798e680 into master Jul 8, 2022
@rays22 rays22 deleted the issue828 branch July 8, 2022 17:22
@rays22 rays22 mentioned this pull request Jul 13, 2022
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Add new dislocated anatomical entity pattern template
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