From 5ac53e6670dff04957ca8e97e9c438b81a3ee1a1 Mon Sep 17 00:00:00 2001
From: Erik Segerdell <esegerd3@gmail.com>
Date: Fri, 17 Jan 2025 14:05:18 -0800
Subject: [PATCH 1/3] New pattern for disrupted biological process.

---
 .../abnormallyDisruptedBiologicalProcess.yaml | 37 +++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 src/patterns/dosdp-dev/abnormallyDisruptedBiologicalProcess.yaml

diff --git a/src/patterns/dosdp-dev/abnormallyDisruptedBiologicalProcess.yaml b/src/patterns/dosdp-dev/abnormallyDisruptedBiologicalProcess.yaml
new file mode 100644
index 00000000..d339226a
--- /dev/null
+++ b/src/patterns/dosdp-dev/abnormallyDisruptedBiologicalProcess.yaml
@@ -0,0 +1,37 @@
+pattern_name: abnormallyDisruptedBiologicalProcess
+pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDisruptedBiologicalProcess.yaml
+description: "An interruption of a biological process of its normal course, such as disrupted plasminogen activation."
+
+contributors:
+  - https://orcid.org/0000-0002-9611-1279
+
+classes:
+  disrupted: PATO:0001507
+  abnormal: PATO:0000460
+  biological_process: GO:0008150
+
+relations:
+  inheres_in: RO:0000052
+  has_modifier: RO:0002573
+  has_part: BFO:0000051
+
+annotationProperties:
+  exact_synonym: oio:hasExactSynonym
+
+vars:
+  biological_process: "'biological_process'"
+
+name:
+  text: "disrupted %s"
+  vars:
+   - biological_process
+
+def:
+  text: "Disrupted %s."
+  vars:
+    - biological_process
+
+equivalentTo:
+  text: "'has_part' some ('disrupted' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
+  vars:
+    - biological_process

From dddd33f8def9f73469e2a813fef201f75720132c Mon Sep 17 00:00:00 2001
From: Erik Segerdell <esegerd3@gmail.com>
Date: Fri, 17 Jan 2025 14:09:37 -0800
Subject: [PATCH 2/3] New pattern for mislocalised biological process.

---
 .../mislocalisedBiologicalProcess.yaml        | 37 +++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 src/patterns/dosdp-dev/mislocalisedBiologicalProcess.yaml

diff --git a/src/patterns/dosdp-dev/mislocalisedBiologicalProcess.yaml b/src/patterns/dosdp-dev/mislocalisedBiologicalProcess.yaml
new file mode 100644
index 00000000..da8bfc01
--- /dev/null
+++ b/src/patterns/dosdp-dev/mislocalisedBiologicalProcess.yaml
@@ -0,0 +1,37 @@
+pattern_name: mislocalisedBiologicalProcess
+pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/mislocalisedBiologicalProcess.yaml
+description: "Abnormal anatomic location of a biological process, such as an immune response."
+
+contributors:
+  - https://orcid.org/0000-0002-9611-1279
+
+classes:
+  mislocalised: PATO:0000628
+  abnormal: PATO:0000460
+  biological_process: GO:0008150
+
+relations:
+  inheres_in: RO:0000052
+  has_modifier: RO:0002573
+  has_part: BFO:0000051
+
+annotationProperties:
+  exact_synonym: oio:hasExactSynonym
+
+vars:
+  biological_process: "'biological_process'"
+
+name:
+  text: "mislocalised %s"
+  vars:
+   - biological_process
+
+def:
+  text: "Mislocalised %s."
+  vars:
+    - biological_process
+
+equivalentTo:
+  text: "'has_part' some ('mislocalised' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
+  vars:
+    - biological_process

From d27b407ab01d6c4a1fa715e1fbf19992e0e0d57e Mon Sep 17 00:00:00 2001
From: Erik Segerdell <esegerd3@gmail.com>
Date: Fri, 17 Jan 2025 14:13:10 -0800
Subject: [PATCH 3/3] New pattern for mislocalised molecular function.

---
 .../mislocalisedMolecularFunction.yaml        | 37 +++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 src/patterns/dosdp-dev/mislocalisedMolecularFunction.yaml

diff --git a/src/patterns/dosdp-dev/mislocalisedMolecularFunction.yaml b/src/patterns/dosdp-dev/mislocalisedMolecularFunction.yaml
new file mode 100644
index 00000000..df2579b6
--- /dev/null
+++ b/src/patterns/dosdp-dev/mislocalisedMolecularFunction.yaml
@@ -0,0 +1,37 @@
+pattern_name: mislocalisedMolecularFunction
+pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/mislocalisedMolecularFunction.yaml
+description: "Abnormal cellular location of a molecular function, such as ribosome biogenesis."
+
+contributors:
+  - https://orcid.org/0000-0002-9611-1279
+
+classes:
+  mislocalised: PATO:0000628
+  abnormal: PATO:0000460
+  molecular function: GO:0003674
+
+relations:
+  inheres_in: RO:0000052
+  has_modifier: RO:0002573
+  has_part: BFO:0000051
+
+annotationProperties:
+  exact_synonym: oio:hasExactSynonym
+
+vars:
+  molecular_function: "'molecular function'"
+
+name:
+  text: "mislocalised %s"
+  vars:
+   - molecular_function
+
+def:
+  text: "Mislocalised %s."
+  vars:
+    - molecular_function
+
+equivalentTo:
+  text: "'has_part' some ('mislocalised' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))"
+  vars:
+    - molecular_function