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updated files because of GO changes
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@pfey03
pfey03 authored Aug 24, 2023
1 parent 0d1c479 commit 415fb95
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Showing 5 changed files with 34 additions and 7 deletions.
10 changes: 5 additions & 5 deletions src/patterns/data/default/abnormalAbsenceOfBiologicalProcessInLocation.tsv
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Expand Up @@ -13,9 +13,9 @@ DDPHENO:0000721 abolished prestalk gene expression GO:0010467 gene expression DD
DDPHENO:0000722 abolished prespore gene expression GO:0010467 gene expression DDANAT:0000405 prespore cell
DDPHENO:0001076 abolished prestalk A cell differentiation GO:0030154 cell differentiation DDANAT:0000408 pstA cell
DDPHENO:0001164 abolished prestalk B cell differentiation GO:0030154 cell differentiation DDANAT:0000417 pstB cell
DDPHENO:0001356 abolished basal disc formation GO:0048856 anatomical structure development DDANAT:0000089 basal disc
DDPHENO:0001359 abolished outer basal disc formation GO:0048856 anatomical structure development DDANAT:0000099 outer basal disc
DDPHENO:0001360 abolished inner basal disc formation GO:0048856 anatomical structure development DDANAT:0000098 inner basal disc
DDPHENO:0001367 abolished lower cup formation GO:0048856 anatomical structure development DDANAT:0000105 lower cup
DDPHENO:0001368 abolished upper cup formation GO:0048856 anatomical structure development DDANAT:0000107 upper cup
DDPHENO:0001356 abolished basal disc formation GO:0032502 developmental process DDANAT:0000089 basal disc
DDPHENO:0001359 abolished outer basal disc formation GO:0032502 developmental process DDANAT:0000099 outer basal disc
DDPHENO:0001360 abolished inner basal disc formation GO:0032502 developmental process DDANAT:0000098 inner basal disc
DDPHENO:0001367 abolished lower cup formation GO:0032502 developmental process DDANAT:0000105 lower cup
DDPHENO:0001368 abolished upper cup formation GO:0032502 developmental process DDANAT:0000107 upper cup
DDPHENO:0001528 abolished prestalk U cell differentiation GO:0030154 cell differentiation DDANAT:0001001 pstU cell
3 changes: 3 additions & 0 deletions src/patterns/data/default/abnormalAbsenceOfChemicalEntity.tsv
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defined_class defined_class_label chemical chemical_label Pattern
DDPHENO:0000312 abolished MPBD level CHEBI:61089 4-methyl-5-pentylbenzene-1,3-diol
DDPHENO:0001244 abolished protein level CHEBI:36080 protein
16 changes: 15 additions & 1 deletion src/patterns/data/default/abnormalAbsenceOfMolecularFunction.tsv
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defined_class defined_class_label molecular_function molecular_function_label
defined_class defined_class_label molecular_function molecular_function_label
DDPHENO:0000150 abolished chemorepellant activity GO:0045499 chemorepellant activity
DDPHENO:0000295 abolished protein binding GO:0005515 protein binding
DDPHENO:0000322 abolished cellulose binding GO:0030248 cellulose binding
Expand All @@ -7,12 +7,26 @@ DDPHENO:0000328 abolished small molecule binding GO:0036094 small molecule bindi
DDPHENO:0000330 abolished cAMP binding GO:0030552 cAMP binding
DDPHENO:0000334 abolished folic acid binding GO:0005542 folic acid binding
DDPHENO:0000347 abolished protein kinase activity GO:0004672 protein kinase activity
DDPHENO:0000724 abolished protein tyrosine kinase activity GO:0004713 protein tyrosine kinase activity
DDPHENO:0000730 abolished histone H3K4 methyltransferase activity GO:0042800 histone H3K4 methyltransferase activity
DDPHENO:0000732 abolished histone H3K79 methyltransferase activity GO:0031151 histone H3K79 methyltransferase activity
DDPHENO:0000734 abolished histone H3K9 methyltransferase activity GO:0046974 histone H3K9 methyltransferase activity
DDPHENO:0000736 abolished myosin heavy chain kinase activity GO:0016905 myosin heavy chain kinase activity
DDPHENO:0000746 abolished prenylcysteine carboxyl methyltransferase activity GO:0004671 protein C-terminal S-isoprenylcysteine carboxyl O-methyltransferase activity
DDPHENO:0000751 abolished phosphatase activity GO:0016791 phosphatase activity
DDPHENO:0000755 abolished protein tyrosine phosphatase activity GO:0004725 protein tyrosine phosphatase activity
DDPHENO:0000784 abolished DNA (cytosine-5-)-methyltransferase activity GO:0003886 DNA (cytosine-5-)-methyltransferase activity
DDPHENO:0000788 abolished adenylate cyclase regulator activity GO:0010854 adenylate cyclase regulator activity
DDPHENO:0000791 abolished adenylate cyclase activator activity GO:0010856 adenylate cyclase activator activity
DDPHENO:0000795 abolished protein kinase regulator activity GO:0019887 protein kinase regulator activity
DDPHENO:0000802 abolished GTPase activator activity GO:0005096 GTPase activator activity
DDPHENO:0001289 abolished catalytic activity GO:0003824 catalytic activity
DDPHENO:0001290 abolished 3',5'-cyclic-AMP phosphodiesterase activity GO:0004115 3',5'-cyclic-AMP phosphodiesterase activity
DDPHENO:0001291 abolished 3',5'-cyclic-GMP phosphodiesterase activity GO:0047555 3',5'-cyclic-GMP phosphodiesterase activity
DDPHENO:0001293 abolished adenylate cyclase activity GO:0004016 adenylate cyclase activity
DDPHENO:0001295 abolished guanylyl cyclase activity GO:0004383 guanylyl cyclase activity
DDPHENO:0001299 abolished guanyl-nucleotide exchange factor activity GO:0005085 guanyl-nucleotide exchange factor activity
DDPHENO:0001322 abolished peptidyl-proline 4-dioxygenase activity GO:0031545 peptidyl-proline 4-dioxygenase activity
DDPHENO:0001332 abolished catalase activity GO:0004096 catalase activity
DDPHENO:0001386 abolished cytochrome C oxidase activity GO:0004129 cytochrome-c oxidase activity
DDPHENO:0001409 abolished phosphatidylinositol binding GO:0035091 phosphatidylinositol binding
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3 changes: 2 additions & 1 deletion src/patterns/data/default/abnormalAbsenceOfProteinLocalizationInCellularComponent.tsv
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defined_class defined_class_label location location_label
defined_class defined_class_label cellular_component cellular_component_label
DDPHENO:0000105 abolished protein localization to nucleolus GO:0005730 nucleolus
DDPHENO:0000453 abolished protein localization to nucleus GO:0005634 nucleus
DDPHENO:0000517 abolished protein localization to contractile vacuole GO:0000331 contractile vacuole
Expand All @@ -23,6 +23,7 @@ DDPHENO:0000669 abolished protein localization to cytoplasmic vesicle GO:0031410
DDPHENO:0000673 abolished protein localization to cell periphery GO:0071944 cell periphery
DDPHENO:0000675 abolished protein localization to apical plasma membrane GO:0016324 apical plasma membrane
DDPHENO:0000677 abolished protein localization to endolysosome GO:0036019 endolysosome
DDPHENO:0000797 abolished protein localization to mitotic actomyosin contractile ring GO:0110085 mitotic actomyosin contractile ring
DDPHENO:0001392 abolished protein localization to cytoplasm GO:0005737 cytoplasm
DDPHENO:0001394 abolished protein localization to plasma membrane GO:0005886 plasma membrane
DDPHENO:0001399 abolished protein localization to microtubules GO:0005874 microtubule
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9 changes: 9 additions & 0 deletions src/patterns/data/default/abnormalArrestedDevelopmentDuringStage.tsv
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defined_class defined_class_label stage stage_label Pattern
DDPHENO:0000026 development arrests at mound stage DDDEV:0000002 mound stage abnormalArrestedDevelopmentDuringStage
DDPHENO:0000155 development arrests at tipped mound stage DDDEV:0000004 tipped mound stage abnormalArrestedDevelopmentDuringStage
DDPHENO:0000159 development arrests at loose mound stage DDDEV:0000003 loose mound stage abnormalArrestedDevelopmentDuringStage
DDPHENO:0000168 development arrests at slug stage DDDEV:0000006 slug stage abnormalArrestedDevelopmentDuringStage
DDPHENO:0000685 development arrests at standing slug stage DDDEV:0000005 standing slug stage abnormalArrestedDevelopmentDuringStage
DDPHENO:0000686 development arrests at early culminant stage DDDEV:0000007 early culminant stage abnormalArrestedDevelopmentDuringStage
DDPHENO:0000687 development arrests at mid culminant stage DDDEV:0000008 mid culminant stage abnormalArrestedDevelopmentDuringStage
DDPHENO:0000688 development arrests at late culminant stage DDDEV:0000009 late culminant stage abnormalArrestedDevelopmentDuringStage

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