diff --git a/src/patterns/dosdp-dev/abnormalAbsenceOfAnatomicalEntity.yaml b/src/patterns/dosdp-dev/abnormalAbsenceOfAnatomicalEntity.yaml index 1a9eb66c..2bb7e163 100644 --- a/src/patterns/dosdp-dev/abnormalAbsenceOfAnatomicalEntity.yaml +++ b/src/patterns/dosdp-dev/abnormalAbsenceOfAnatomicalEntity.yaml @@ -8,11 +8,13 @@ contributors: - https://orcid.org/0000-0001-5208-3432 - https://orcid.org/0000-0001-7941-2961 - https://orcid.org/0000-0003-4148-4606 + - https://orcid.org/0000-0002-7073-9172 classes: absent: PATO:0000462 abnormal: PATO:0000460 anatomical entity: UBERON:0001062 + 'multicellular organism': UBERON:0000468 relations: inheres_in: RO:0000052 @@ -42,6 +44,7 @@ def: - anatomical_entity equivalentTo: - text: "'has_part' some ('absent' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))" + text: "'has part' some ('lacks all parts of type' and ('inheres in' some 'organism') and ('towards' value %s) and ('has modifier' some 'abnormal'))" + vars: vars: - anatomical_entity diff --git a/src/patterns/dosdp-dev/abnormalAbsenceOfAnatomicalEntityInLocation.yaml b/src/patterns/dosdp-dev/abnormalAbsenceOfAnatomicalEntityInLocation.yaml index 29b8aeee..a76463c8 100644 --- a/src/patterns/dosdp-dev/abnormalAbsenceOfAnatomicalEntityInLocation.yaml +++ b/src/patterns/dosdp-dev/abnormalAbsenceOfAnatomicalEntityInLocation.yaml @@ -4,6 +4,7 @@ description: "Absence of an anatomical entity in a location, such as absent aort contributors: - https://orcid.org/0000-0001-5208-3432 + - https://orcid.org/0000-0002-7073-9172 classes: absent: PATO:0000462 @@ -45,7 +46,8 @@ def: - location equivalentTo: - text: "'has_part' some ('absent' and ('inheres_in' some (%s and ('part_of' some %s))) and ('has_modifier' some 'abnormal'))" + text: "'has part' some ('lacks all parts of type' and ('inheres in' some %s) and ('towards' value %s) and ('has modifier' some 'abnormal'))" vars: - - anatomical_entity - location + - anatomical_entity + diff --git a/src/patterns/dosdp-dev/abnormallyDecreasedNumberOfAnatomicalEntity.yaml b/src/patterns/dosdp-dev/abnormallyDecreasedNumberOfAnatomicalEntity.yaml index c1627fca..52d6e1ea 100644 --- a/src/patterns/dosdp-dev/abnormallyDecreasedNumberOfAnatomicalEntity.yaml +++ b/src/patterns/dosdp-dev/abnormallyDecreasedNumberOfAnatomicalEntity.yaml @@ -38,7 +38,14 @@ def: vars: - anatomical_entity -equivalentTo: - text: "'has_part' some ('decreased amount' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))" - vars: - - anatomical_entity +logical_axioms: + - + axiom_type: EquivalentTo + text: has_part some ('has fewer parts of type' and (inheres_in some 'multicellular organism') and ('towards' value %s) + vars: + - anatomical_entity + - + axiom_type: EquivalentTo + text: has_part some 'has fewer parts of type' and (inheres_in some multicellular organism') and ('towards' some %s) + vars: + - anatomical_entity diff --git a/src/patterns/dosdp-dev/abnormallyDecreasedNumberOfAnatomicalEntityInLocation.yaml b/src/patterns/dosdp-dev/abnormallyDecreasedNumberOfAnatomicalEntityInLocation.yaml index 1aa0cc33..2d15ce0b 100644 --- a/src/patterns/dosdp-dev/abnormallyDecreasedNumberOfAnatomicalEntityInLocation.yaml +++ b/src/patterns/dosdp-dev/abnormallyDecreasedNumberOfAnatomicalEntityInLocation.yaml @@ -6,6 +6,7 @@ contributors: - https://orcid.org/0000-0002-7356-1779 - https://orcid.org/0000-0001-5208-3432 - https://orcid.org/0000-0002-3528-5267 + classes: decreased amount: PATO:0001997 abnormal: PATO:0000460 @@ -45,8 +46,16 @@ def: - anatomical_entity - location -equivalentTo: - text: "'has_part' some ('decreased amount' and ('inheres_in' some (%s and ('part_of' some %s))) and ('has_modifier' some 'abnormal'))" - vars: - - anatomical_entity - - location +logical_axioms: + - + axiom_type: EquivalentTo + text: has_part some ('has fewer parts of type' and ('inheres in' some '%s) and ('towards' value %s) and ('has modifier' some 'abnormal')) + vars: + - location + - anatomical_entity + - + axiom_type: EquivalentTo + text: has_part some 'has fewer parts of type' and ('inheres in' some %s') and ('towards' some %s) and ('has modifier' some 'abnormal')) + vars: + - location + - anatomical_entity