From 6a9964a883769256f56608a995e517f0e088a4b0 Mon Sep 17 00:00:00 2001 From: Erik Segerdell Date: Fri, 26 Aug 2022 18:01:04 -0700 Subject: [PATCH] Fix equivalents. --- ...ccurrenceOfBiologicalProcessInLocation.tsv | 2 - ...ccurrenceOfBiologicalProcessInLocation.tsv | 2 - src/patterns/id_map.tsv | 4 -- src/patterns/templates/xpo-replaced.owl | 40 +++++++++++++++++++ src/patterns/templates/xpo-replaced.tsv | 4 ++ 5 files changed, 44 insertions(+), 8 deletions(-) diff --git a/src/patterns/data/manual/abnormallyDecreasedOccurrenceOfBiologicalProcessInLocation.tsv b/src/patterns/data/manual/abnormallyDecreasedOccurrenceOfBiologicalProcessInLocation.tsv index db0a404d..8db0f52d 100644 --- a/src/patterns/data/manual/abnormallyDecreasedOccurrenceOfBiologicalProcessInLocation.tsv +++ b/src/patterns/data/manual/abnormallyDecreasedOccurrenceOfBiologicalProcessInLocation.tsv @@ -42,7 +42,6 @@ http://purl.obolibrary.org/obo/XPO_0136641 decreased apoptosis in zygote GO:0006 http://purl.obolibrary.org/obo/XPO_0136642 decreased apoptosis in animal cap GO:0006915 apoptotic process XAO:0000036 animal cap http://purl.obolibrary.org/obo/XPO_0136643 decreased apoptosis in animal cap inner layer GO:0006915 apoptotic process XAO:0000037 animal cap inner layer http://purl.obolibrary.org/obo/XPO_0136644 decreased apoptosis in animal cap outer layer GO:0006915 apoptotic process XAO:0000038 animal cap outer layer -http://purl.obolibrary.org/obo/XPO_0136645 decreased apoptosis in head region GO:0006915 apoptotic process XAO:0000040 head region http://purl.obolibrary.org/obo/XPO_0136646 decreased apoptosis in epidermis inner layer GO:0006915 apoptotic process XAO:0000041 epidermis inner layer http://purl.obolibrary.org/obo/XPO_0136647 decreased apoptosis in neuroectoderm GO:0006915 apoptotic process XAO:0000042 neuroectoderm http://purl.obolibrary.org/obo/XPO_0136648 decreased apoptosis in neuroectoderm outer layer GO:0006915 apoptotic process XAO:0000043 neuroectoderm outer layer @@ -1541,7 +1540,6 @@ http://purl.obolibrary.org/obo/XPO_0138192 decreased cell population proliferati http://purl.obolibrary.org/obo/XPO_0138193 decreased cell population proliferation in animal cap GO:0008283 cell population proliferation XAO:0000036 animal cap http://purl.obolibrary.org/obo/XPO_0138194 decreased cell population proliferation in animal cap inner layer GO:0008283 cell population proliferation XAO:0000037 animal cap inner layer http://purl.obolibrary.org/obo/XPO_0138195 decreased cell population proliferation in animal cap outer layer GO:0008283 cell population proliferation XAO:0000038 animal cap outer layer -http://purl.obolibrary.org/obo/XPO_0138196 decreased cell population proliferation in head region GO:0008283 cell population proliferation XAO:0000040 head region http://purl.obolibrary.org/obo/XPO_0138197 decreased cell population proliferation in epidermis inner layer GO:0008283 cell population proliferation XAO:0000041 epidermis inner layer http://purl.obolibrary.org/obo/XPO_0138198 decreased cell population proliferation in neuroectoderm GO:0008283 cell population proliferation XAO:0000042 neuroectoderm http://purl.obolibrary.org/obo/XPO_0138199 decreased cell population proliferation in neuroectoderm outer layer GO:0008283 cell population proliferation XAO:0000043 neuroectoderm outer layer diff --git a/src/patterns/data/manual/abnormallyIncreasedOccurrenceOfBiologicalProcessInLocation.tsv b/src/patterns/data/manual/abnormallyIncreasedOccurrenceOfBiologicalProcessInLocation.tsv index cb338d84..322a9b06 100644 --- a/src/patterns/data/manual/abnormallyIncreasedOccurrenceOfBiologicalProcessInLocation.tsv +++ b/src/patterns/data/manual/abnormallyIncreasedOccurrenceOfBiologicalProcessInLocation.tsv @@ -37,7 +37,6 @@ http://purl.obolibrary.org/obo/XPO_0133539 increased apoptosis in zygote GO:0006 http://purl.obolibrary.org/obo/XPO_0133540 increased apoptosis in animal cap GO:0006915 apoptotic process XAO:0000036 animal cap http://purl.obolibrary.org/obo/XPO_0133541 increased apoptosis in animal cap inner layer GO:0006915 apoptotic process XAO:0000037 animal cap inner layer http://purl.obolibrary.org/obo/XPO_0133542 increased apoptosis in animal cap outer layer GO:0006915 apoptotic process XAO:0000038 animal cap outer layer -http://purl.obolibrary.org/obo/XPO_0133543 increased apoptosis in head region GO:0006915 apoptotic process XAO:0000040 head region http://purl.obolibrary.org/obo/XPO_0133544 increased apoptosis in epidermis inner layer GO:0006915 apoptotic process XAO:0000041 epidermis inner layer http://purl.obolibrary.org/obo/XPO_0133545 increased apoptosis in neuroectoderm GO:0006915 apoptotic process XAO:0000042 neuroectoderm http://purl.obolibrary.org/obo/XPO_0133546 increased apoptosis in neuroectoderm outer layer GO:0006915 apoptotic process XAO:0000043 neuroectoderm outer layer @@ -1536,7 +1535,6 @@ http://purl.obolibrary.org/obo/XPO_0135090 increased cell population proliferati http://purl.obolibrary.org/obo/XPO_0135091 increased cell population proliferation in animal cap GO:0008283 cell population proliferation XAO:0000036 animal cap http://purl.obolibrary.org/obo/XPO_0135092 increased cell population proliferation in animal cap inner layer GO:0008283 cell population proliferation XAO:0000037 animal cap inner layer http://purl.obolibrary.org/obo/XPO_0135093 increased cell population proliferation in animal cap outer layer GO:0008283 cell population proliferation XAO:0000038 animal cap outer layer -http://purl.obolibrary.org/obo/XPO_0135094 increased cell population proliferation in head region GO:0008283 cell population proliferation XAO:0000040 head region http://purl.obolibrary.org/obo/XPO_0135095 increased cell population proliferation in epidermis inner layer GO:0008283 cell population proliferation XAO:0000041 epidermis inner layer http://purl.obolibrary.org/obo/XPO_0135096 increased cell population proliferation in neuroectoderm GO:0008283 cell population proliferation XAO:0000042 neuroectoderm http://purl.obolibrary.org/obo/XPO_0135097 increased cell population proliferation in neuroectoderm outer layer GO:0008283 cell population proliferation XAO:0000043 neuroectoderm outer layer diff --git a/src/patterns/id_map.tsv b/src/patterns/id_map.tsv index c66ecc57..ddac3248 100644 --- a/src/patterns/id_map.tsv +++ b/src/patterns/id_map.tsv @@ -13179,7 +13179,6 @@ GO:0006915-XAO:0000035-abnormallyIncreasedOccurrenceOfBiologicalProcessInLocatio GO:0006915-XAO:0000036-abnormallyIncreasedOccurrenceOfBiologicalProcessInLocation.tsv http://purl.obolibrary.org/obo/XPO_0133540 GO:0006915-XAO:0000037-abnormallyIncreasedOccurrenceOfBiologicalProcessInLocation.tsv http://purl.obolibrary.org/obo/XPO_0133541 GO:0006915-XAO:0000038-abnormallyIncreasedOccurrenceOfBiologicalProcessInLocation.tsv http://purl.obolibrary.org/obo/XPO_0133542 -GO:0006915-XAO:0000040-abnormallyIncreasedOccurrenceOfBiologicalProcessInLocation.tsv http://purl.obolibrary.org/obo/XPO_0133543 GO:0006915-XAO:0000041-abnormallyIncreasedOccurrenceOfBiologicalProcessInLocation.tsv http://purl.obolibrary.org/obo/XPO_0133544 GO:0006915-XAO:0000042-abnormallyIncreasedOccurrenceOfBiologicalProcessInLocation.tsv http://purl.obolibrary.org/obo/XPO_0133545 GO:0006915-XAO:0000043-abnormallyIncreasedOccurrenceOfBiologicalProcessInLocation.tsv http://purl.obolibrary.org/obo/XPO_0133546 @@ -14727,7 +14726,6 @@ GO:0008283-XAO:0000035-abnormallyIncreasedOccurrenceOfBiologicalProcessInLocatio GO:0008283-XAO:0000036-abnormallyIncreasedOccurrenceOfBiologicalProcessInLocation.tsv http://purl.obolibrary.org/obo/XPO_0135091 GO:0008283-XAO:0000037-abnormallyIncreasedOccurrenceOfBiologicalProcessInLocation.tsv http://purl.obolibrary.org/obo/XPO_0135092 GO:0008283-XAO:0000038-abnormallyIncreasedOccurrenceOfBiologicalProcessInLocation.tsv http://purl.obolibrary.org/obo/XPO_0135093 -GO:0008283-XAO:0000040-abnormallyIncreasedOccurrenceOfBiologicalProcessInLocation.tsv http://purl.obolibrary.org/obo/XPO_0135094 GO:0008283-XAO:0000041-abnormallyIncreasedOccurrenceOfBiologicalProcessInLocation.tsv http://purl.obolibrary.org/obo/XPO_0135095 GO:0008283-XAO:0000042-abnormallyIncreasedOccurrenceOfBiologicalProcessInLocation.tsv http://purl.obolibrary.org/obo/XPO_0135096 GO:0008283-XAO:0000043-abnormallyIncreasedOccurrenceOfBiologicalProcessInLocation.tsv http://purl.obolibrary.org/obo/XPO_0135097 @@ -16275,7 +16273,6 @@ GO:0006915-XAO:0000035-abnormallyDecreasedOccurrenceOfBiologicalProcessInLocatio GO:0006915-XAO:0000036-abnormallyDecreasedOccurrenceOfBiologicalProcessInLocation.tsv http://purl.obolibrary.org/obo/XPO_0136642 GO:0006915-XAO:0000037-abnormallyDecreasedOccurrenceOfBiologicalProcessInLocation.tsv http://purl.obolibrary.org/obo/XPO_0136643 GO:0006915-XAO:0000038-abnormallyDecreasedOccurrenceOfBiologicalProcessInLocation.tsv http://purl.obolibrary.org/obo/XPO_0136644 -GO:0006915-XAO:0000040-abnormallyDecreasedOccurrenceOfBiologicalProcessInLocation.tsv http://purl.obolibrary.org/obo/XPO_0136645 GO:0006915-XAO:0000041-abnormallyDecreasedOccurrenceOfBiologicalProcessInLocation.tsv http://purl.obolibrary.org/obo/XPO_0136646 GO:0006915-XAO:0000042-abnormallyDecreasedOccurrenceOfBiologicalProcessInLocation.tsv http://purl.obolibrary.org/obo/XPO_0136647 GO:0006915-XAO:0000043-abnormallyDecreasedOccurrenceOfBiologicalProcessInLocation.tsv http://purl.obolibrary.org/obo/XPO_0136648 @@ -17823,7 +17820,6 @@ GO:0008283-XAO:0000035-abnormallyDecreasedOccurrenceOfBiologicalProcessInLocatio GO:0008283-XAO:0000036-abnormallyDecreasedOccurrenceOfBiologicalProcessInLocation.tsv http://purl.obolibrary.org/obo/XPO_0138193 GO:0008283-XAO:0000037-abnormallyDecreasedOccurrenceOfBiologicalProcessInLocation.tsv http://purl.obolibrary.org/obo/XPO_0138194 GO:0008283-XAO:0000038-abnormallyDecreasedOccurrenceOfBiologicalProcessInLocation.tsv http://purl.obolibrary.org/obo/XPO_0138195 -GO:0008283-XAO:0000040-abnormallyDecreasedOccurrenceOfBiologicalProcessInLocation.tsv http://purl.obolibrary.org/obo/XPO_0138196 GO:0008283-XAO:0000041-abnormallyDecreasedOccurrenceOfBiologicalProcessInLocation.tsv http://purl.obolibrary.org/obo/XPO_0138197 GO:0008283-XAO:0000042-abnormallyDecreasedOccurrenceOfBiologicalProcessInLocation.tsv http://purl.obolibrary.org/obo/XPO_0138198 GO:0008283-XAO:0000043-abnormallyDecreasedOccurrenceOfBiologicalProcessInLocation.tsv http://purl.obolibrary.org/obo/XPO_0138199 diff --git a/src/patterns/templates/xpo-replaced.owl b/src/patterns/templates/xpo-replaced.owl index fe4cef52..bd904f5d 100644 --- a/src/patterns/templates/xpo-replaced.owl +++ b/src/patterns/templates/xpo-replaced.owl @@ -5080,6 +5080,16 @@ + + + + + obsolete increased apoptosis in head region + true + + + + @@ -5100,6 +5110,16 @@ + + + + + obsolete increased cell population proliferation in head region + true + + + + @@ -5120,6 +5140,16 @@ + + + + + obsolete decreased apoptosis in head region + true + + + + @@ -5140,6 +5170,16 @@ + + + + + obsolete decreased cell population proliferation in head region + true + + + + diff --git a/src/patterns/templates/xpo-replaced.tsv b/src/patterns/templates/xpo-replaced.tsv index f11dba9a..309fffde 100644 --- a/src/patterns/templates/xpo-replaced.tsv +++ b/src/patterns/templates/xpo-replaced.tsv @@ -517,3 +517,7 @@ http://purl.obolibrary.org/obo/XPO_0133417 obsolete increased cilium motility in http://purl.obolibrary.org/obo/XPO_0133418 obsolete increased cilium motility in ciliated non-epidermal cell true http://purl.obolibrary.org/obo/XPO_0142007 http://purl.obolibrary.org/obo/XPO_0133419 obsolete increased cilium motility in monociliated epidermal cell true http://purl.obolibrary.org/obo/XPO_0142008 http://purl.obolibrary.org/obo/XPO_0133420 obsolete increased cilium motility in multiciliated epidermal cell true http://purl.obolibrary.org/obo/XPO_0142009 +http://purl.obolibrary.org/obo/XPO_0138196 obsolete decreased cell population proliferation in head region true http://purl.obolibrary.org/obo/XPO_0138595 +http://purl.obolibrary.org/obo/XPO_0136645 obsolete decreased apoptosis in head region true http://purl.obolibrary.org/obo/XPO_0137044 +http://purl.obolibrary.org/obo/XPO_0133543 obsolete increased apoptosis in head region true http://purl.obolibrary.org/obo/XPO_0133942 +http://purl.obolibrary.org/obo/XPO_0135094 obsolete increased cell population proliferation in head region true http://purl.obolibrary.org/obo/XPO_0135493