Aim 1.1.1 Build a library of phenotype term templates.

[matentzn]

We will collaborate with the phenotype ontology development community, leveraging their expertise in biology and curation to develop a library of phenotype term templates while training them in their design and application. The resulting library will be hosted in an open repository with each template thoroughly documented and accessible via a persistent URL.

Key people

• @rays22
• @dosumis

Action items

• @rays22 to familiarise himself with the goals formulated in the grant
• @rays22 to link all relevant issues and/or pull requests to this issue
• @rays22 to formulate concrete goals to achieve based on last PFR meeting and add to this issue

[rays22]

Issues or pull requests related to phenotype pattern templates

• 1. Abnormal constriction of anatomical entity pattern template pattern Abnormal constriction of anatomical entity pattern template obophenotype/upheno#913
• 2. Dealing with GO obsoletion cell death help wanted pattern urgent Dealing with GO obsoletion cell death obophenotype/upheno#912
• 3. create a pattern for adding anatomy subclass axioms pattern create a pattern for adding anatomy subclass axioms obophenotype/upheno#904
• 4. Investigate cases where the uPheno2 semantic similarity score is lower than the uPheno1 score pattern Investigate cases where the uPheno2 semantic similarity score is lower than the uPheno1 score obophenotype/upheno#900
• 5. Abnormally scaly anatomical entity pattern template pattern Abnormally scaly anatomical entity pattern template obophenotype/upheno#894
• 6. Add abnormally dilated cellular component pattern template pattern Add abnormally dilated cellular component pattern template obophenotype/upheno#891
• 7. Abnormally decreased water composition of anatomical entity pattern template pattern Abnormally decreased water composition of anatomical entity pattern template obophenotype/upheno#877
• 8. Add count density pattern(s) pattern Add count density pattern(s) obophenotype/upheno#827
• 9. Import calcified anatomical entity with calcification pattern template from HP pattern Import calcified anatomical entity with calcification pattern template from HP obophenotype/upheno#813
• 10. Abnormal constriction of anatomical entity pattern template pattern Abnormal constriction of anatomical entity pattern template obophenotype/upheno#913
• 11. Abnormally arched anatomical entity pattern template pattern Abnormally arched anatomical entity pattern template obophenotype/upheno#893
• 12. Add herniated anatomical entity pattern template pattern Add herniated anatomical entity pattern template obophenotype/upheno#889
• 13. Abnormally glistening anatomical entity pattern template pattern Abnormally glistening anatomical entity pattern template obophenotype/upheno#884
• 14. Abnormally greasy anatomical entity pattern template pattern Abnormally greasy anatomical entity pattern template obophenotype/upheno#880
• 15. Update cystInLocation logical definition pattern Update cystInLocation logical definition obophenotype/upheno#878
• 16. Add abnormally decreased wetness of anatomical entity pattern template pattern Add abnormally decreased wetness of anatomical entity pattern template obophenotype/upheno#875
• 17. Add abnormally dry anatomical entity pattern template pattern Add abnormally dry anatomical entity pattern template obophenotype/upheno#873
• 18. Abnormally opaque anatomical entity pattern template pattern Abnormally opaque anatomical entity pattern template obophenotype/upheno#865
• 19. Add abnormally curled anatomical entity pattern template pattern Add abnormally curled anatomical entity pattern template obophenotype/upheno#861
• 20. Add wrinkled anatomical entity pattern template pattern Add wrinkled anatomical entity pattern template obophenotype/upheno#858
• 21. Add folded anatomical entity pattern template pattern Add folded anatomical entity pattern template obophenotype/upheno#857
• 22. Abnormal length of anatomical entity pattern template pattern Abnormal length of anatomical entity pattern template obophenotype/upheno#855
• 23. Deviation of anatomical entity pattern template pattern Deviation of anatomical entity pattern template obophenotype/upheno#853
• 24. Delaminated anatomical entity pattern template pattern Delaminated anatomical entity pattern template obophenotype/upheno#850
• 25. Collapsed anatomical entity pattern template pattern Collapsed anatomical entity pattern template obophenotype/upheno#848
• 26. Non-functional anatomical entity pattern template pattern Non-functional anatomical entity pattern template obophenotype/upheno#844
• 27. Abnormal thickness of anatomical entity pattern template pattern Abnormal thickness of anatomical entity pattern template obophenotype/upheno#842
• 28. Perforate anatomical entity pattern template pattern Perforate anatomical entity pattern template obophenotype/upheno#840
• 29. Deviation towards the lateral side of anatomical entity pattern template pattern Deviation towards the lateral side of anatomical entity pattern template obophenotype/upheno#838
• 30. Abnormally protruding anatomical entity pattern template pattern Abnormally protruding anatomical entity pattern template obophenotype/upheno#836
• 31. Exserted anatomical entity pattern template pattern Exserted anatomical entity pattern template obophenotype/upheno#834
• 32. Deviation towards the medial side of anatomical entity pattern template pattern Deviation towards the medial side of anatomical entity pattern template obophenotype/upheno#832
• 33. Obstructed anatomical entity pattern template pattern Obstructed anatomical entity pattern template obophenotype/upheno#830
• 34. Add new dislocated anatomical entity pattern template pattern Add new dislocated anatomical entity pattern template obophenotype/upheno#828
• 35. Add new abnormal and increased mass density patterns pattern Add new abnormal and increased mass density patterns obophenotype/upheno#825
• 36. Add new abnormally ivory anatomical entity pattern templates pattern Add new abnormally ivory anatomical entity pattern templates obophenotype/upheno#823
• 37. Add new abnormally punctate anatomical entity in location pattern template pattern Add new abnormally punctate anatomical entity in location pattern template obophenotype/upheno#810
• 38. Add new abnormally punctate anatomical entity pattern template pattern Add new abnormally punctate anatomical entity pattern template obophenotype/upheno#808
• 39. Add new edematous anatomical entity pattern template pattern Add new edematous anatomical entity pattern template obophenotype/upheno#805
• 40. Add new premature closure of anatomical entity pattern template pattern Add new premature closure of anatomical entity pattern template obophenotype/upheno#803
• 41. Add new asymmetrical anatomical entity pattern template pattern Add new asymmetrical anatomical entity pattern template obophenotype/upheno#801
• 42. Add new disorganized anatomical entity pattern pattern Add new disorganized anatomical entity pattern obophenotype/upheno#799
• 43. Add new irregular density of anatomical entity pattern final_review Add new irregular density of anatomical entity pattern obophenotype/upheno#797
• 44. Add new hypertrophic anatomical entity pattern final_review Add new hypertrophic anatomical entity pattern obophenotype/upheno#795
• 45. Add new increased volume of anatomical entity pattern final_review Add new increased volume of anatomical entity pattern obophenotype/upheno#793
• 46. Add new hyperplastic anatomical entity related pattern pattern Add new hyperplastic anatomical entity related pattern obophenotype/upheno#789
• 47. Add abnormally dilated anatomical entity pattern pattern Add abnormally dilated anatomical entity pattern obophenotype/upheno#787
• 48. which pattern to use for cysts? pattern which pattern to use for cysts? obophenotype/upheno#611
• 49. HPO classes should use abnormalNumberOfAnatomicalEntity.yaml pattern HPO pattern HPO classes should use abnormalNumberOfAnatomicalEntity.yaml pattern obophenotype/upheno#602
• 50. HP_0012102 Abnormal mitochondrial number should use pattern: abnormalNumberOfCellularComponent.yaml HPO pattern HP_0012102 Abnormal mitochondrial number should use pattern: abnormalNumberOfCellularComponent.yaml obophenotype/upheno#601
• 51. HPO terms should use abnormal size pattern HPO pattern HPO terms should use abnormal size pattern obophenotype/upheno#600
• 52. HP_0410359 Abnormal core 1 O-glycan level should use abnormalLevelOfChemicalEntity pattern HPO pattern HP_0410359 Abnormal core 1 O-glycan level should use abnormalLevelOfChemicalEntity pattern obophenotype/upheno#597
• 53. HPO classes should use shape pattern HPO pattern HPO classes should use shape pattern obophenotype/upheno#596
• 54. HPO terms should use abnormalMorphologyOfAnatomicalEntity.yaml pattern HPO pattern HPO terms should use abnormalMorphologyOfAnatomicalEntity.yaml pattern obophenotype/upheno#595
• 55. HPO terms should use abnormalLevelOfChemicalEntityInLocation.yaml HPO pattern HPO terms should use abnormalLevelOfChemicalEntityInLocation.yaml obophenotype/upheno#594