From 601ba5d1ccf14ed56dc631c730fee17c355ca0a0 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Tue, 30 Aug 2022 10:53:45 -0700 Subject: [PATCH] remove deprecated items --- biolink-model.yaml | 1954 ++------------------------------------------ 1 file changed, 71 insertions(+), 1883 deletions(-) diff --git a/biolink-model.yaml b/biolink-model.yaml index fc634b35b4..34f332ef9f 100644 --- a/biolink-model.yaml +++ b/biolink-model.yaml @@ -1073,13 +1073,6 @@ slots: - SNOMED:has_dose_form_intended_site - SNOMED:has_route_of_administration - has population context: - deprecated: true - description: >- - a biological population (general, study, cohort, etc.) with a specific - set of characteristics to constrain an association. - is_a: association slot - range: population of individual organisms population context qualifier: description: >- @@ -1088,12 +1081,6 @@ slots: is_a: association slot range: population of individual organisms - has temporal context: - deprecated: true - description: >- - a constraint of time placed upon the truth value of an association. - is_a: association slot - range: time type temporal context qualifier: description: >- @@ -1775,9 +1762,6 @@ slots: - https://doi.org/10.1101/108977 - https://github.com/biolink/biolink-model/issues/657 - has real world evidence of association with: - deprecated: true - associated with likelihood of: is_a: associated with description: >- @@ -2117,31 +2101,6 @@ slots: indirectly physically interacts with: is_a: physically interacts with - chemically interacts with: - deprecated: true - is_a: physically interacts with - domain: chemical entity - range: chemical entity - in_subset: - - translator_minimal - symmetric: true - - molecularly interacts with: - deprecated: true - is_a: physically interacts with - aliases: [ 'targets' ] - domain: molecular entity - range: molecular entity - in_subset: - - translator_minimal - symmetric: true - annotations: - canonical_predicate: true - related_mappings: - - DGIdb:antibody - exact_mappings: - - RO:0002436 - genetically interacts with: is_a: interacts with description: >- @@ -2262,1462 +2221,81 @@ slots: range: disease or phenotypic feature annotations: canonical_predicate: true - close_mappings: - - NCIT:C15220 # diagnosis - - SIO:001331 # diagnosis - exact_mappings: - - DrugCentral:5271 - - SEMMEDDB:diagnoses - - is diagnosed by: - is_a: related to at instance level - inverse: diagnoses - range: chemical or drug or treatment - domain: disease or phenotypic feature - - increases amount or activity of: - is_a: related to at instance level - mixin: true - description: >- - A grouping mixin to help with searching for all the predicates that increase the amount - or activity of the object. - - decreases amount or activity of: - is_a: related to at instance level - mixin: true - description: >- - A grouping mixin to help with searching for all the predicates that decrease the amount - or activity of the object. - - ## role mixins for use in tagging corresponding role predicates - - chemical role mixin: - description: >- - A role played by the chemical entity or part thereof within a chemical context. - mixin: true - exact_mappings: - - CHEBI:51086 - - biological role mixin: - description: >- - A role played by the chemical entity or part thereof within a biological context. - mixin: true - narrow_mappings: - - CHEBI:24432 - - affects abundance of: - deprecated: true - description: >- - holds between two chemical or gene/gene product entities where the action or effect of one changes the amount of the - other within a system of interest - is_a: affects - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - annotations: - canonical_predicate: true - exact_mappings: - - CTD:affects_abundance_of - - abundance affected by: - deprecated: true - is_a: affected by - inverse: affects abundance of - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - - increases abundance of: - deprecated: true - description: >- - holds between two chemical or gene/gene product entities where the action or effect of one increases the - amount of the other within a system of interest - is_a: affects abundance of - in_subset: - - translator_minimal - mixins: - - increases amount or activity of - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - annotations: - canonical_predicate: true - opposite_of: decreases abundance of - related_mappings: - - UBERGRAPH:is_increase_of - - abundance increased by: - deprecated: true - is_a: abundance affected by - inverse: increases abundance of - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - - decreases abundance of: - deprecated: true - description: >- - holds between two chemical or gene/gene product where the action or effect of one - decreases the amount of the other within a system of interest - is_a: affects abundance of - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - mixins: - - decreases amount or activity of - annotations: - canonical_predicate: true - opposite_of: increases abundance of - - related_mappings: - - UBERGRAPH:is_decrease_of - - abundance decreased by: - deprecated: true - is_a: abundance affected by - inverse: decreases abundance of - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - - increases activity of: - deprecated: true - description: >- - holds between two chemical or gene/gene product where the action or effect of one - increases the activity of the other within a system of interest - is_a: affects activity of - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - mixins: - - increases amount or activity of - related_mappings: - - GAMMA:ec50 - - GAMMA:ac50 - narrow_mappings: - - GAMMA:activator - - GAMMA:partial_agonist - - GAMMA:agonist - - GAMMA:opener - - GAMMA:positive_allosteric_modulator - - GAMMA:positive_modulator - - GAMMA:inducer - - GAMMA:potentiator - - GAMMA:stimulator - - CHEMBL.MECHANISM:agonist - - CHEMBL.MECHANISM:opener - - CHEMBL.MECHANISM:partial_agonist - - CHEMBL.MECHANISM:positive_allosteric_modulator - - CHEMBL.MECHANISM:positive_modulator - - DGIdb:agonist - - DGIdb:partial_agonist - - DGIdb:inducer - - DGIdb:positive_allosteric_modulator - - DGIdb:stimulator - annotations: - opposite_of: decreases activity of - - affects activity of: - deprecated: true - description: >- - holds between two chemical or gene/gene product where the action or effect of one changes the activity of the - other within a system of interest - is_a: affects - annotations: - canonical_predicate: true - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - narrow_mappings: - - GAMMA:allosteric_modulator - - GAMMA:modulator - - GAMMA:regulator - - DGIdb:modulator - - DGIdb:allosteric_modulator - - activity affected by: - deprecated: true - description: >- - holds between two chemical or gene/gene product where the action or effect of one is changed by the - activity of the other within a system of interest - is_a: affected by - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - inverse: affects activity of - - activity increased by: - deprecated: true - is_a: activity affected by - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - inverse: increases activity of - - decreases activity of: - deprecated: true - description: >- - holds between two chemical or gene/gene product where the action or effect of one decreases the - activity of the other within a system of interest - is_a: affects activity of - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - annotations: - canonical_predicate: true - opposite_of: increases activity of - mixins: - - decreases amount or activity of - related_mappings: - - GAMMA:ic50 - - GAMMA:ki - - DGIdb:vaccine - narrow_mappings: - - GAMMA:allosteric_antagonist - - GAMMA:partial_antagonist - - GAMMA:antagonist - - GAMMA:weak_inhibitor - - GAMMA:inhibitor - - GAMMA:channel_blocker - - GAMMA:gating_inhibitor - - GAMMA:blocker - - GAMMA:inverse_agonist - - GAMMA:inactivator - - GAMMA:downregulator - - GAMMA:negative_modulator - - GAMMA:negative_allosteric_modulator - - GAMMA:inhibitory_allosteric_modulator - - GAMMA:aggregation_inhibitor - - GAMMA:conversion_inhibitor - - GAMMA:suppressor - - CHEMBL.MECHANISM:antagonist - - CHEMBL.MECHANISM:allosteric_antagonist - - CHEMBL.MECHANISM:inverse_agonist - - DGIdb:antagonist - - DGIdb:blocker - - DGIdb:channel_blocker - - DGIdb:gating_inhibitor - - DGIdb:inhibitor - - DGIdb:negative_modulator - - DGIdb:inhibitory_allosteric_modulator - - DGIdb:inverse_agonist - - activity decreased by: - deprecated: true - is_a: activity affected by - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - inverse: decreases activity of - - - affects expression of: - deprecated: true - description: >- - holds between a named thing (most often a chemical or gene/gene product, but can also be used to link an - environmental affect on expression) and a nucleic acid entity where the action or effect of one changes the - level of expression of the other within a system of interest - is_a: affects - in_subset: - - translator_minimal - domain: named thing - range: nucleic acid entity - - expression affected by: - deprecated: true - is_a: affected by - in_subset: - - translator_minimal - domain: nucleic acid entity - range: named thing - inverse: affects expression of - - increases expression of: - deprecated: true - description: >- - holds between a chemical or gene/gene product entity and a nucleic acid entity - where the action or effect of one increases the level of expression of the - other within a system of interest - is_a: affects expression of - in_subset: - - translator_minimal - domain: named thing - range: nucleic acid entity - mixins: - - increases amount or activity of - close_mappings: - # Agent of the action or effect, not the relationship itself - - CHEMBL.MECHANISM:releasing_agent - exact_mappings: - - RO:0003003 - - expression increased by: - deprecated: true - is_a: expression affected by - in_subset: - - translator_minimal - domain: nucleic acid entity - range: named thing - inverse: increases expression of - - decreases expression of: - deprecated: true - description: >- - holds between a chemical or gene/gene product entity and a nucleic acid entity where the action or effect of one decreases the level of expression of the - other within a system of interest - is_a: affects expression of - in_subset: - - translator_minimal - domain: named thing - range: nucleic acid entity - mixins: - - decreases amount or activity of - related_mappings: - - DGIdb:antisense - - DGIdb:antisense_oligonucleotide - exact_mappings: - - RO:0003002 - narrow_mappings: - - CHEMBL.MECHANISM:antisense_inhibitor - - expression decreased by: - deprecated: true - is_a: expression affected by - in_subset: - - translator_minimal - domain: nucleic acid entity - range: named thing - inverse: decreases expression of - - affects folding of: - deprecated: true - description: >- - holds between a chemical or gene/gene product entity and a nucleic acid entity where the action or effect of one changes the rate - or quality of folding of the other - is_a: affects - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: nucleic acid entity - annotations: - canonical_predicate: true - exact_mappings: - - CTD:affects_folding_of - - - folding affected by: - deprecated: true - is_a: affected by - inverse: affects folding of - domain: nucleic acid entity - range: chemical entity or gene or gene product - - increases folding of: - deprecated: true - description: >- - holds between a chemical or gene/gene product entity and a nucleic acid entity where the action or effect of one - increases the rate or quality of folding of the other - is_a: affects folding of - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: nucleic acid entity - mixins: - - increases amount or activity of - annotations: - canonical_predicate: true - opposite_of: decreases folding of - exact_mappings: - - CTD:increases_folding_of - - folding increased by: - deprecated: true - is_a: folding affected by - inverse: increases folding of - domain: nucleic acid entity - range: chemical entity or gene or gene product - - decreases folding of: - deprecated: true - description: >- - holds between a chemical or gene or gene product entity and a - nucleic acid entity where the action or effect of one - decreases the rate or quality of folding of the other - is_a: affects folding of - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: nucleic acid entity - mixins: - - decreases amount or activity of - annotations: - canonical_predicate: true - opposite_of: increases folding of - exact_mappings: - - CTD:decreases_folding_of - - folding decreased by: - deprecated: true - is_a: folding affected by - inverse: decreases folding of - domain: nucleic acid entity - range: chemical entity or gene or gene product - - affects localization of: - deprecated: true - description: >- - holds between two chemical or gene/gene product entities where the action or effect of one changes the - localization of the other within a system of interest - is_a: affects - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - annotations: - canonical_predicate: true - related_mappings: - - GAMMA:storage - exact_mappings: - - GOREL:0002003 - - localization affected by: - deprecated: true - is_a: affected by - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - inverse: affects localization of - - increases localization of: - deprecated: true - description: >- - holds between two chemical or gene/gene product entities where the action or effect of one increases the proper - localization of the other within a system of interest - is_a: affects localization of - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - mixins: - - increases amount or activity of - annotations: - canonical_predicate: true - opposite_of: decreases localization of - exact_mappings: - - CTD:increases_localization_of - - localization increased by: - deprecated: true - is_a: localization affected by - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - inverse: increases localization of - - decreases localization of: - deprecated: true - description: >- - holds between two chemical or gene/gene product entities where the action or effect of one decreases the proper localization of the other within a system of interest - is_a: affects localization of - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - mixins: - - decreases amount or activity of - annotations: - canonical_predicate: true - opposite_of: increases localization of - exact_mappings: - - CTD:decreases_localization_of - - - localization decreased by: - deprecated: true - is_a: localization affected by - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - inverse: decreases localization of - - affects metabolic processing of: - deprecated: true - description: >- - holds between two chemical or gene/gene product entities where the action or effect of one impacts the - metabolic processing of the other within a system of interest - is_a: affects - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - in_subset: - - translator_minimal - annotations: - canonical_predicate: true - related_mappings: - - GAMMA:catalytic_activity - - metabolic processing affected by: - deprecated: true - is_a: affected by - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - inverse: affects metabolic processing of - - increases metabolic processing of: - deprecated: true - description: >- - holds between two chemical or gene/gene product entities where the action or effect of one increases the rate of - metabolic processing of the other within a system of interest - is_a: affects metabolic processing of - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - mixins: - - increases amount or activity of - annotations: - canonical_predicate: true - opposite_of: decreases metabolic processing of - exact_mappings: - - CTD:increases_metabolic_processing_of - narrow_mappings: - - NCIT:enzyme_metabolizes_chemical_or_drug - - metabolic processing increased by: - deprecated: true - is_a: metabolic processing affected by - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - inverse: increases metabolic processing of - - decreases metabolic processing of: - deprecated: true - description: >- - holds between two chemical or gene/gene product entities where the action or effect of one decreases the rate of - metabolic processing of the other within a system of interest - is_a: affects metabolic processing of - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - mixins: - - decreases amount or activity of - annotations: - canonical_predicate: true - opposite_of: increases metabolic processing of - exact_mappings: - - CTD:decreases_metabolic_processing_of - - metabolic processing decreased by: - deprecated: true - is_a: metabolic processing affected by - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - inverse: decreases metabolic processing of - - affects molecular modification of: - deprecated: true - description: >- - holds between two chemical or gene/gene product entities where the action or effect of one leads changes in the molecular - modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of - phosphoryl group, or via redox reaction that adds or subtracts electrons) - is_a: affects - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - annotations: - canonical_predicate: true - exact_mappings: - - CTD:affects_molecular_modification_of - narrow_mappings: - - CTD:affects_acetylation - - CTD:affects_acylation - - CTD:affects_alkylation - - CTD:affects_amination - - CTD:affects_carbamoylation - - CTD:affects_ethylation - - CTD:affects_glutathionylation - - CTD:affects_glycation - - CTD:affects_glycosylation - - CTD:affects_glucuronidation - - CTD:affects_N-linked_glycosylation - - CTD:affects_O-linked_glycosylation - - CTD:affects_hydroxylation - - CTD:affects_lipidation - - CTD:affects_farnesylation - - CTD:affects_geranoylation - - CTD:affects_myristoylation - - CTD:affects_palmitoylation - - CTD:affects_prenylation - - CTD:affects_methylation - - CTD:affects_nitrosation - - CTD:affects_nucleotidylation - - CTD:affects_phosphorylation - - CTD:affects_ribosylation - - CTD:affects_ADP-ribosylation - - CTD:affects_sulfation - - CTD:affects_sumoylation - - CTD:affects_ubiquitination - - CTD:affects_oxidation - - CTD:affects_reduction - - CTD:affects_carboxylation - - molecular modification affected by: - deprecated: true - is_a: affected by - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - inverse: affects molecular modification of - - increases molecular modification of: - deprecated: true - description: >- - holds between two chemical or gene/gene product entities where the action or effect of one leads to - increased molecular modification(s) of the other (e.g. via post-translational modifications of - proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons) - is_a: affects molecular modification of - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - mixins: - - increases amount or activity of - annotations: - canonical_predicate: true - opposite_of: decreases molecular modification of - exact_mappings: - - CTD:increases_molecular_modification_of - narrow_mappings: - - CTD:increases_acetylation - - CTD:increases_acylation - - CTD:increases_alkylation - - CTD:increases_amination - - CTD:increases_carbamoylation - - CTD:increases_ethylation - - CTD:increases_glutathionylation - - CTD:increases_glycation - - CTD:increases_glycosylation - - CTD:increases_glucuronidation - - CTD:increases_N-linked_glycosylation - - CTD:increases_O-linked_glycosylation - - CTD:increases_hydroxylation - - CTD:increases_lipidation - - CTD:increases_farnesylation - - CTD:increases_geranoylation - - CTD:increases_myristoylation - - CTD:increases_palmitoylation - - CTD:increases_prenylation - - CTD:increases_methylation - - CTD:increases_nitrosation - - CTD:increases_nucleotidylation - - CTD:increases_phosphorylation - - CTD:increases_ribosylation - - CTD:increases_ADP-ribosylation - - CTD:increases_sulfation - - CTD:increases_sumoylation - - CTD:increases_ubiquitination - - CTD:increases_oxidation - - CTD:increases_reduction - - CTD:increases_carboxylation - - GAMMA:acetylation - - GAMMA:oxidizer - - molecular modification increased by: - deprecated: true - is_a: molecular modification affected by - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - inverse: increases molecular modification of - - decreases molecular modification of: - deprecated: true - description: >- - holds between two chemical entities where the action or effect of one leads to - decreased molecular modification(s) of the other (e.g. via post-translational modifications of - proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons) - is_a: affects molecular modification of - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - mixins: - - decreases amount or activity of - annotations: - canonical_predicate: true - opposite_of: increases molecular modification of - exact_mappings: - - CTD:decreases_molecular_modification_of - narrow_mappings: - - CTD:decreases_acetylation - - CTD:decreases_acylation - - CTD:decreases_alkylation - - CTD:decreases_amination - - CTD:decreases_carbamoylation - - CTD:decreases_ethylation - - CTD:decreases_glutathionylation - - CTD:decreases_glycation - - CTD:decreases_glycosylation - - CTD:decreases_glucuronidation - - CTD:decreases_N-linked_glycosylation - - CTD:decreases_O-linked_glycosylation - - CTD:decreases_hydroxylation - - CTD:decreases_lipidation - - CTD:decreases_farnesylation - - CTD:decreases_geranoylation - - CTD:decreases_myristoylation - - CTD:decreases_palmitoylation - - CTD:decreases_prenylation - - CTD:decreases_methylation - - CTD:decreases_nitrosation - - CTD:decreases_nucleotidylation - - CTD:decreases_phosphorylation - - CTD:decreases_ribosylation - - CTD:decreases_ADP-ribosylation - - CTD:decreases_sulfation - - CTD:decreases_sumoylation - - CTD:decreases_ubiquitination - - CTD:decreases_oxidation - - CTD:decreases_reduction - - CTD:decreases_carboxylation - - GAMMA:deoxidizer - - molecular modification decreased by: - deprecated: true - is_a: molecular modification affected by - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - inverse: decreases molecular modification of - - affects synthesis of: - deprecated: true - description: >- - holds between two chemical entities where the action or effect - of one impacts the rate of chemical synthesis of the other - is_a: affects - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - in_subset: - - translator_minimal - annotations: - canonical_predicate: true - exact_mappings: - - CTD:affects_synthesis_of - - synthesis affected by: - deprecated: true - is_a: affected by - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - inverse: affects synthesis of - in_subset: - - translator_minimal - - increases synthesis of: - deprecated: true - description: >- - holds between two chemical entities where the action or effect - of one increases the rate of chemical synthesis of the other - is_a: affects synthesis of - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - mixins: - - increases amount or activity of - annotations: - canonical_predicate: true - opposite_of: decreases synthesis of - exact_mappings: - - CTD:increases_synthesis_of - - synthesis increased by: - deprecated: true - is_a: synthesis affected by - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - inverse: increases synthesis of - - decreases synthesis of: - deprecated: true - description: >- - holds between two chemical entities where the action or effect - of one decreases the rate of chemical synthesis of the other - is_a: affects synthesis of - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - mixins: - - decreases amount or activity of - in_subset: - - translator_minimal - annotations: - canonical_predicate: true - opposite_of: increases synthesis of - exact_mappings: - - GAMMA:inhibition_of_synthesis - - synthesis decreased by: - deprecated: true - is_a: synthesis affected by - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - inverse: decreases synthesis of - - affects degradation of: - deprecated: true - description: >- - holds between two chemical entities where the action or effect of one - impacts the rate of degradation of the other within a system of interest, - where chemical degradation is defined act or process of simplifying or breaking - down a molecule into smaller parts, either naturally or artificially - (Oxford English Dictionary, UK, 1995) - is_a: affects - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - in_subset: - - translator_minimal - annotations: - canonical_predicate: true - exact_mappings: - - CTD:affects_degradation_of - narrow_mappings: - - CTD:affects_cleavage - - CTD:affects_hydrolysis - - degradation affected by: - deprecated: true - is_a: affected by - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - inverse: affects degradation of - - increases degradation of: - deprecated: true - description: >- - holds between two chemical entities where the action or effect of one - increases the rate of degradation of the other within a system of interest - is_a: affects degradation of - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - mixins: - - decreases amount or activity of - annotations: - canonical_predicate: true - opposite_of: decreases degredation of - related_mappings: - # An enzyme or reagent acts upon a substrate but that substrate may - # not necessarily be "degraded", i.e. broken into smaller parts - - GAMMA:substrate - # RTX put this under "biolink:physically_interacts_with" but rather we also put next to the GAMMA mapping - # That said, neither mapping feels like a comfortable fit here - - CHEMBL.MECHANISM:substrate - close_mappings: - # terms refer less to the action or effect than the agent of that action or effect - - CHEMBL.MECHANISM:degrader - narrow_mappings: - - CTD:increases_cleavage - - CTD:increases_hydrolysis - - GOREL:0002004 - - degradation increased by: - deprecated: true - is_a: degradation affected by - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - inverse: increases degradation of - - decreases degradation of: - deprecated: true - description: >- - holds between two chemical entities where the action or effect of one - decreases the rate of degradation of the other within a system of interest - is_a: affects degradation of - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - mixins: - - increases amount or activity of - annotations: - canonical_predicate: true - opposite_of: increases degredation of - exact_mappings: - - CTD:decreases_degradation_of - narrow_mappings: - - CTD:decreases_cleavage - - CTD:decreases_hydrolysis - - degradation decreased by: - deprecated: true - is_a: degradation affected by - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - inverse: decreases degradation of - - affects mutation rate of: - deprecated: true - description: >- - holds between a chemical entity and a nucleic acid entity where the action or effect of the - chemical entity impacts the rate of mutation of the nucleic acid entity within a system of interest - is_a: affects - domain: chemical entity or gene or gene product - range: nucleic acid entity - broad_mappings: - # Term 'mutagenesis' generally speaks generally of the process of - # 'production of genetic mutations': this term says it is affected - # but not specifically how - in_subset: - - translator_minimal - annotations: - canonical_predicate: true - exact_mappings: - - CTD:affects_mutation_rate_of - - mutation rate affected by: - deprecated: true - is_a: affected by - in_subset: - - translator_minimal - domain: nucleic acid entity - range: chemical entity or gene or gene product - inverse: affects mutation rate of - - increases mutation rate of: - deprecated: true - description: >- - holds between a chemical entity and a nucleic acid entity where the action or effect of the - chemical entity increases the rate of mutation of the nucleic acid entity within a system of interest - is_a: affects mutation rate of - in_subset: - - translator_minimal - domain: chemical entity - range: nucleic acid entity - mixins: - - increases amount or activity of - annotations: - canonical_predicate: true - opposite_of: decreases mutation rate of - exact_mappings: - - CTD:increases_mutation_rate_of - broad_mappings: - # See 'affects mutation rate of' above - - CTD:increases_mutagenesis - - mutation rate increased by: - deprecated: true - is_a: mutation rate affected by - in_subset: - - translator_minimal - domain: nucleic acid entity - range: chemical entity - inverse: increases mutation rate of - - decreases mutation rate of: - deprecated: true - description: >- - holds between a chemical entity and a nucleic acid entity where the action or effect of the - chemical entity decreases the rate of mutation of the nucleic acid entity within a system of interest - is_a: affects mutation rate of - in_subset: - - translator_minimal - domain: chemical entity - range: nucleic acid entity - mixins: - - decreases amount or activity of - annotations: - canonical_predicate: true - opposite_of: increases mutation rate of - exact_mappings: - - CTD:decreases_mutation_rate_of - broad_mappings: - # See 'affects mutation rate of' above - - CTD:decreases_mutagenesis - - mutation rate decreased by: - deprecated: true - is_a: mutation rate affected by - in_subset: - - translator_minimal - domain: nucleic acid entity - range: chemical entity - inverse: decreases mutation rate of - - affects response to: - is_a: affects - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - inverse: response affected by - annotations: - canonical_predicate: true - exact_mappings: - - CTD:affects_response_to - - response affected by: - description: >- - holds between two chemical entities where the susceptibility of a biological entity or system - (e.g. an organism, cell, cellular component, macromolecular machine mixin, - biological or pathological process) of one is affected by the action of the other. - is_a: affected by - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - annotations: - canonical_predicate: true - - increases response to: - description: >- - holds between two chemical entities where the action or effect of one - increases the susceptibility of a biological entity or system (e.g. an - organism, cell, cellular component, macromolecular machine mixin, biological - or pathological process) to the other - is_a: affects response to - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - mixins: - - increases amount or activity of - annotations: - canonical_predicate: true - opposite_of: decreases response to - exact_mappings: - - CTD:increases_response_to - - response increased by: - is_a: response affected by - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - inverse: increases response to - - decreases response to: - description: >- - holds between two chemical entities where the action or effect of one - decreases the susceptibility of a biological entity or system (e.g. an - organism, cell, cellular component, macromolecular machine mixin, biological - or pathological process) to the other - is_a: affects response to - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - mixins: - - decreases amount or activity of - annotations: - canonical_predicate: true - opposite_of: increases response to - exact_mappings: - - CTD:decreases_response_to - narrow_mappings: - - CTD:decreases_response_to_substance - - GAMMA:desensitize_the_target - - response decreased by: - is_a: response affected by - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - inverse: decreases response to - - affects splicing of: - deprecated: true - description: >- - holds between a chemical entity and an mRNA where the action or effect - of the chemical entity impacts the splicing of the mRNA - is_a: affects - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: transcript - annotations: - canonical_predicate: true - exact_mappings: - - CTD:affects_RNA_splicing - broad_mappings: - - CTD:affects_splicing_of - - splicing affected by: - deprecated: true - is_a: affected by - in_subset: - - translator_minimal - domain: transcript - range: chemical entity or gene or gene product - inverse: affects splicing of - - increases splicing of: - deprecated: true - description: >- - holds between a chemical entity and an mRNA where the action or effect - of the chemical entity increases the proper splicing of the mRNA - is_a: affects splicing of - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: transcript - mixins: - - increases amount or activity of - annotations: - canonical_predicate: true - opposite_of: decreases splicing of - exact_mappings: - - CTD:increases_RNA_splicing - broad_mappings: - - CTD:increases_splicing_of - - splicing increased by: - deprecated: true - is_a: splicing affected by - in_subset: - - translator_minimal - domain: transcript - range: chemical entity or gene or gene product - inverse: increases splicing of - - decreases splicing of: - deprecated: true - description: >- - holds between a chemical entity and an mRNA where the action or - effect of the chemical entity decreases the proper splicing of the mRNA - is_a: affects splicing of - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: transcript - mixins: - - decreases amount or activity of - annotations: - canonical_predicate: true - opposite_of: increases splicing of - exact_mappings: - - CTD:decreases_RNA_splicing - broad_mappings: - - CTD:decreases_splicing_of - - splicing decreased by: - deprecated: true - is_a: splicing affected by - in_subset: - - translator_minimal - domain: transcript - range: chemical entity or gene or gene product - inverse: decreases splicing of - - affects stability of: - deprecated: true - description: >- - holds between two entities where the action or effect of one impacts - the stability of the other within a system of interest - is_a: affects - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - annotations: - canonical_predicate: true - close_mappings: - - GAMMA:stabilization - - stability affected by: - deprecated: true - is_a: affected by - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - inverse: affects stability of - - increases stability of: - deprecated: true - description: >- - holds between two chemical or gene/gene product entities where the action or effect of one - increases the stability of the other within a system of interest - is_a: affects stability of - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - mixins: - - increases amount or activity of - annotations: - canonical_predicate: true - opposite_of: decreases stability of - close_mappings: - # agent of the action or effect, not the relationship - - CHEMBL.MECHANISM:stabiliser - - stability increased by: - deprecated: true - is_a: stability affected by - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - inverse: increases stability of - - decreases stability of: - deprecated: true - description: >- - holds between two chemical or gene/gene product entities where the action or effect of one decreases - the stability of the other within a system of interest - is_a: affects stability of - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - mixins: - - decreases amount or activity of - in_subset: - - translator_minimal - annotations: - canonical_predicate: true - opposite_of: increases stability of - exact_mappings: - - CTD:decreases_stability_of - - stability decreased by: - deprecated: true - is_a: stability affected by - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - inverse: decreases stability of - - affects transport of: - deprecated: true - description: >- - holds between two chemical or gene/gene product entities where the action or effect of one impacts - the rate of transport of the other across some boundary in a system of interest - is_a: affects - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - annotations: - canonical_predicate: true - exact_mappings: - - CTD:affects_transport_of - narrow_mappings: - - RO:0002313 - - RO:0002340 - - RO:0002345 - - transport affected by: - deprecated: true - is_a: affected by - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - inverse: affects transport of - - increases transport of: - deprecated: true - description: >- - holds between two chemical or gene/gene product entities where the action or effect of one - increases the rate of transport of the other across some boundary in a system of interest - is_a: affects transport of - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - mixins: - - increases amount or activity of - annotations: - canonical_predicate: true - opposite_of: decreases transport of - close_mappings: - - GAMMA:carrier - - GAMMA:transporter - - transport increased by: - deprecated: true - is_a: transport affected by - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - inverse: increases transport of - - decreases transport of: - deprecated: true - description: >- - holds between two chemical or gene/gene product entities where the action or effect of one - decreases the rate of transport of the other across some boundary in a system of interest - is_a: affects transport of - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - mixins: - - decreases amount or activity of - annotations: - canonical_predicate: true - opposite_of: increases transport of - exact_mappings: - - CTD:decreases_transport_of - - transport decreased by: - deprecated: true - is_a: transport affected by - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - inverse: decreases transport of - - affects secretion of: - deprecated: true - description: >- - holds between two chemical or gene/gene product entities where the action or effect of one impacts the - rate of secretion of the other out of a cell, gland, or organ - is_a: affects - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - annotations: - canonical_predicate: true - exact_mappings: - - CTD:affects_secretion_of - broad_mappings: - # 'export' more general than 'secretion' - - CTD:affects_export - - secretion affected by: - deprecated: true - is_a: affected by - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - inverse: affects secretion of - - increases secretion of: - deprecated: true - description: >- - holds between two chemical or gene/gene product entities where the action or effect of one increases the - rate of secretion of the other out of a cell, gland, or organ - is_a: affects secretion of - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - mixins: - - increases amount or activity of - annotations: - canonical_predicate: true - opposite_of: decreases secretion of + close_mappings: + - NCIT:C15220 # diagnosis + - SIO:001331 # diagnosis exact_mappings: - - CTD:increases_secretion_of - broad_mappings: - # 'export' more general than 'secretion' - - CTD:increases_export + - DrugCentral:5271 + - SEMMEDDB:diagnoses - secretion increased by: - deprecated: true - is_a: secretion affected by - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - inverse: increases secretion of + is diagnosed by: + is_a: related to at instance level + inverse: diagnoses + range: chemical or drug or treatment + domain: disease or phenotypic feature - decreases secretion of: - deprecated: true + increases amount or activity of: + is_a: related to at instance level + mixin: true description: >- - holds between two chemical or gene/gene product entities where the action or effect of one decreases the - rate of secretion of the other out of a cell, gland, or organ - is_a: affects secretion of - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - mixins: - - decreases amount or activity of - annotations: - canonical_predicate: true - opposite_of: increases secretion of - exact_mappings: - - CTD:decreases_secretion_of - broad_mappings: - # 'export' more general than 'secretion' - - CTD:decreases_export + A grouping mixin to help with searching for all the predicates that increase the amount + or activity of the object. - secretion decreased by: - deprecated: true - is_a: secretion affected by - in_subset: - - translator_minimal - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - inverse: decreases secretion of + decreases amount or activity of: + is_a: related to at instance level + mixin: true + description: >- + A grouping mixin to help with searching for all the predicates that decrease the amount + or activity of the object. + + ## role mixins for use in tagging corresponding role predicates + + chemical role mixin: + description: >- + A role played by the chemical entity or part thereof within a chemical context. + mixin: true + exact_mappings: + - CHEBI:51086 - affects uptake of: - deprecated: true + biological role mixin: description: >- - holds between two chemical or gene/gene product entities where the action or effect of one impacts the rate of - uptake of the other into of a cell, gland, or organ + A role played by the chemical entity or part thereof within a biological context. + mixin: true + narrow_mappings: + - CHEBI:24432 + + affects response to: is_a: affects in_subset: - translator_minimal domain: chemical entity or gene or gene product range: chemical entity or gene or gene product + inverse: response affected by annotations: canonical_predicate: true exact_mappings: - - CTD:affects_uptake_of - broad_mappings: - # 'import' more general than 'uptake' - - CTD:affects_import + - CTD:affects_response_to - uptake affected by: - deprecated: true + response affected by: + description: >- + holds between two chemical entities where the susceptibility of a biological entity or system + (e.g. an organism, cell, cellular component, macromolecular machine mixin, + biological or pathological process) of one is affected by the action of the other. is_a: affected by in_subset: - translator_minimal domain: chemical entity or gene or gene product range: chemical entity or gene or gene product - inverse: affects uptake of + annotations: + canonical_predicate: true - increases uptake of: - deprecated: true + increases response to: description: >- - holds between two chemical or gene/gene product entities where the action or effect of one increases the rate of - uptake of the other into of a cell, gland, or organ - is_a: affects uptake of + holds between two chemical entities where the action or effect of one + increases the susceptibility of a biological entity or system (e.g. an + organism, cell, cellular component, macromolecular machine mixin, biological + or pathological process) to the other + is_a: affects response to in_subset: - translator_minimal domain: chemical entity or gene or gene product @@ -3726,28 +2304,25 @@ slots: - increases amount or activity of annotations: canonical_predicate: true - opposite_of: decreases uptake of + opposite_of: decreases response to exact_mappings: - - CTD:increases_uptake_of - broad_mappings: - # 'import' more general than 'uptake' - - CTD:increases_import + - CTD:increases_response_to - uptake increased by: - deprecated: true - is_a: uptake affected by + response increased by: + is_a: response affected by in_subset: - translator_minimal domain: chemical entity or gene or gene product range: chemical entity or gene or gene product - inverse: increases uptake of + inverse: increases response to - decreases uptake of: - deprecated: true + decreases response to: description: >- - holds between two chemical or gene/gene product entities where the action or effect - of one decreases the rate of uptake of the other into of a cell, gland, or organ - is_a: affects uptake of + holds between two chemical entities where the action or effect of one + decreases the susceptibility of a biological entity or system (e.g. an + organism, cell, cellular component, macromolecular machine mixin, biological + or pathological process) to the other + is_a: affects response to in_subset: - translator_minimal domain: chemical entity or gene or gene product @@ -3756,21 +2331,20 @@ slots: - decreases amount or activity of annotations: canonical_predicate: true - opposite_of: increases uptake of + opposite_of: increases response to exact_mappings: - - CTD:decreases_uptake_of - broad_mappings: - # 'import' more general than 'uptake' - - CTD:decreases_import + - CTD:decreases_response_to + narrow_mappings: + - CTD:decreases_response_to_substance + - GAMMA:desensitize_the_target - uptake decreased by: - deprecated: true - is_a: uptake affected by + response decreased by: + is_a: response affected by in_subset: - translator_minimal domain: chemical entity or gene or gene product range: chemical entity or gene or gene product - inverse: decreases uptake of + inverse: decreases response to regulates: is_a: affects @@ -3803,203 +2377,6 @@ slots: mixin: true inverse: regulates - positively regulates: - deprecated: true - comments: - - This is a grouping for positive process-process and entity-entity regulation. - is_a: regulates - mixin: true - annotations: - opposite_of: negatively regulates - close_mappings: - # This RTX contributed term is tagged as a inverse of this Biolink predicate - - RO:0002336 - exact_mappings: - - RO:0002213 - narrow_mappings: - - CHEMBL.MECHANISM:activator - - DGIdb:activator - - RO:0004032 - - RO:0004034 - - RO:0002629 - - positively regulated by: - deprecated: true - is_a: regulated by - mixin: true - inverse: positively regulates - - negatively regulates: - deprecated: true - comments: - - This is a grouping for negative process-process and entity-entity regulation. - is_a: regulates - mixin: true - annotations: - canonical_predicate: true - close_mappings: - # This RTX contributed term is tagged as a inverse of this Biolink predicate - - RO:0002335 - exact_mappings: - # Strict interpretation here is that entity A causally affects levels of B - - RO:0004035 - - RO:0002212 - broad_mappings: - # This term is slightly broader in that it includes that A acts within B as well - - RO:0004033 - narrow_mappings: - - CHEMBL.MECHANISM:blocker - - CHEMBL.MECHANISM:inhibitor - - CHEMBL.MECHANISM:negative_allosteric_modulator - - CHEMBL.MECHANISM:negative_modulator - - RO:0002630 - - negatively regulated by: - deprecated: true - is_a: regulated by - mixin: true - inverse: negatively regulates - - process regulates process: - deprecated: true - is_a: affects - mixins: - - regulates - domain: occurrent - range: occurrent - annotations: - canonical_predicate: true - exact_mappings: - - RO:0002211 - - process regulated by process: - deprecated: true - is_a: affected by - domain: occurrent - range: occurrent - inverse: process regulates process - - process positively regulates process: - deprecated: true - is_a: process regulates process - mixins: - - positively regulates - annotations: - canonical_predicate: true - opposite_of: process negatively regulates process - exact_mappings: - - RO:0002213 - - process positively regulated by process: - deprecated: true - is_a: process regulated by process - inverse: process positively regulates process - - process negatively regulates process: - deprecated: true - is_a: process regulates process - mixins: - - negatively regulates - annotations: - canonical_predicate: true - opposite_of: process positively regulates process - exact_mappings: - - RO:0002212 - - process negatively regulated by process: - deprecated: true - is_a: process regulated by process - inverse: process negatively regulates process - - entity regulates entity: - deprecated: true - aliases: [ 'activity directly regulates activity of' ] - is_a: affects - mixins: - - regulates - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - inverse: entity regulated by entity - annotations: - canonical_predicate: true - local_names: - translator: regulates - ro: activity directly regulates activity of - in_subset: - - translator_minimal - exact_mappings: - - RO:0002448 - narrow_mappings: - # Wikidata mapping copied over from 'regulates' above; - # considered a slightly narrower term since it applies to - # protein and RNA as subject regulator whereas molecular_entity - # may also be another class of chemical_substance? - - WIKIDATA_PROPERTY:P128 - - entity regulated by entity: - deprecated: true - is_a: affected by - domain: chemical entity or gene or gene product - range: chemical entity or gene or gene product - inverse: entity regulates entity - - entity positively regulates entity: - deprecated: true - aliases: [ 'activity directly positively regulates activity of', 'anatomy upregulates gene', 'disease upregulates gene' ] - is_a: entity regulates entity - mixins: - - positively regulates - annotations: - canonical_predicate: true - opposite_of: entity negatively regulates entity - local_names: - translator: positively regulates - ro: activity directly positively regulates activity of - in_subset: - - translator_minimal - exact_mappings: - - RO:0002450 - broad_mappings: - # causally positive effect of A over B but not specific to nature of B - - RO:0004034 - narrow_mappings: - # Defined more narrowly as increasing, facilitating the - # action or function of a "substance interaction", where "substance" is deemed a subclass of possible entity - - SEMMEDDB:STIMULATES - - SEMMEDDB:stimulates - - SEMMEDDB:augments - - entity positively regulated by entity: - deprecated: true - is_a: entity regulated by entity - inverse: entity positively regulates entity - - entity negatively regulates entity: - deprecated: true - aliases: [ 'activity directly negatively regulates activity of', 'anatomy downregulates gene', 'disease downregulates gene' ] - is_a: entity regulates entity - mixins: - - negatively regulates - annotations: - canonical_predicate: true - opposite_of: entity positively regulates entity - local_names: - translator: negatively regulates - ro: activity directly negatively regulates activity of - in_subset: - - translator_minimal - exact_mappings: - - RO:0002449 - narrow_mappings: - # SemMedDb definition focuses on (chemical?) "substance interactions" which is a bit narrower? - - SEMMEDDB:INHIBITS - - SEMMEDDB:inhibits - - entity negatively regulated by entity: - deprecated: true - is_a: entity regulated by entity - inverse: entity negatively regulates entity - disrupts: is_a: affects aliases: [ 'disease causes disruption of' ] @@ -5886,57 +4263,6 @@ slots: - RO:0002087 - RO:0002285 - directly interacts with: - deprecated: true - is_a: interacts with - description: Holds between chemical entities that physically and directly interact - with each other - domain: chemical entity - range: chemical entity or gene or gene product - symmetric: true - annotations: - canonical_predicate: true - related_mappings: - - GAMMA:kd - - GAMMA:kb - - GAMMA:potency - exact_mappings: - - GAMMA:interacts_with - broad_mappings: - # Definition of this term is more generic than direct physical molecular interactions: - # A is connected to B iff there exists a fiat, material or temporal path between A and B. - - SIO:000203 - narrow_mappings: - - PHAROS:drug_targets - - DRUGBANK:chelator - - GAMMA:antibody_binding - - GAMMA:pharmacological_chaperone - - GAMMA:releasing_agent - - GAMMA:pharmacological_chaperone - - GAMMA:releasing_agent - - GAMMA:binder - - GAMMA:binding - - GAMMA:ligand - - GAMMA:cofactor - - GAMMA:multitarget - - GAMMA:chaperone - - GAMMA:component - - GAMMA:adduct - - GAMMA:antibody - - CTD:affects_binding - - DGIdb:binder - - DGIdb:cofactor - - affects expression in: - deprecated: true - is_a: affects - annotations: - canonical_predicate: true - description: Holds between a variant and an anatomical entity where the expression of the variant - is located in. - exact_mappings: - - GTEx:affects_expression_in - has variant part: is_a: has part description: holds between a nucleic acid entity and a nucleic acid entity that is a sub-component of it @@ -6191,42 +4517,6 @@ slots: is_a: related to at instance level inverse: has completed - decreases molecular interaction: - deprecated: true - is_a: molecularly interacts with - description: indicates that the source decreases the molecular interaction between - the target and some other chemical entity - annotations: - canonical_predicate: true - opposite_of: increases molecular interaction - exact_mappings: - - CTD:decreases_molecular_interaction_with - mixins: - - decreases amount or activity of - - molecular interaction decreased by: - deprecated: true - is_a: molecularly interacts with - inverse: decreases molecular interaction - - increases molecular interaction: - deprecated: true - is_a: molecularly interacts with - description: indicates that the source increases the molecular interaction between - the target and some other chemical entity - annotations: - canonical_predicate: true - opposite_of: decreases molecular interaction - exact_mappings: - - CTD:increases_molecular_interaction_with - mixins: - - increases amount or activity of - - molecular interaction increased by: - deprecated: true - is_a: molecularly interacts with - inverse: increases molecular interaction - in linkage disequilibrium with: is_a: related to at instance level description: holds between two sequence variants, the presence of which are correlated @@ -6434,9 +4724,6 @@ slots: exact_mappings: - os:LogicalInterpretation - relation: - deprecated: true - negated: is_a: association slot range: boolean @@ -6485,9 +4772,6 @@ slots: close_mappings: - pav:providedBy - source: - deprecated: true - provided by: is_a: node property description: >- @@ -6539,14 +4823,6 @@ slots: range: information resource multivalued: true - association type: - is_a: association slot - range: category type - deprecated: >- - This slot is deprecated in favor of 'category' slot. - deprecated_element_has_exact_replacement: category - description: >- - connects an association to the category of association (e.g. gene to phenotype) chi squared statistic: is_a: association slot @@ -7139,12 +5415,6 @@ classes: description: >- An OWL property used as an edge label - gene ontology class: - deprecated: true - - unclassified ontology class: - deprecated: true - taxonomic rank: description: >- A descriptor for the rank within a taxonomic classification. @@ -8293,36 +6563,6 @@ classes: # substance role - CHEBI:64047 - nutrient: - deprecated: true - is_a: chemical entity - related_mappings: - # substance role - - CHEBI:33284 - - macronutrient: - deprecated: true - is_a: nutrient - related_mappings: - # substance role - - CHEBI:33937 - - micronutrient: - deprecated: true - is_a: nutrient - related_mappings: - # substance role - - CHEBI:27027 - - vitamin: - deprecated: true - is_a: micronutrient - related_mappings: - # substance role - - CHEBI:33229 - # Vitamin - - STY:T127 - food: is_a: chemical mixture description: >- @@ -8359,23 +6599,6 @@ classes: mappings: - PATO:0000001 - inheritance: - deprecated: true - is_a: organism attribute - description: >- - The name of this attribute and its inheritance from organism attribute, indeed, - its designation as an attribute is problematic. First, the isolated word 'inheritance' - is too ambiguous (especially when embedded inside an ontology with inheritance!). - 'Genetic inheritance' would be more precise. Second, in terms of the scientific usage here, - genetic inheritance would not be a direct property at the topmost organism level, but rather - (as hinted in the definition) is more a commentary on the nature of phenotype (including - genetic disease as a characteristic set of associated phenotypes) against the (hidden) - context of (meiotic/somatic/mitochondrial) DNA segregation and expression. Third, placing - the term in the attribute, rather than named thing category concept hierarchy, is perhaps - less flexible in terms of its usage as a first class concept for semantic queries. - Thus, we deprecate this term, moving it to the 'new' category of 'genetic inheritance', - as a child of 'biological entity' (to emphasize its biological conceptual nature). - genetic inheritance: aliases: [ 'inheritance' ] is_a: biological entity @@ -9492,7 +7715,6 @@ classes: exact_mappings: - ECTO:0000509 - # TODO: deprecate? drug to gene interaction exposure: description: >- drug to gene interaction exposure is a drug exposure is where the @@ -10145,22 +8367,6 @@ classes: object context qualifier: range: ontology class - chemical to gene association: - deprecated: true - description: >- - An interaction between a chemical entity and a gene or gene product. - is_a: association - defining_slots: - - subject - - object - mixins: - - chemical to entity association mixin - slot_usage: - object: - range: gene or gene product - description: >- - the gene or gene product that is affected by the chemical. - chemical gene interaction association: description: >- describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical @@ -10355,9 +8561,6 @@ classes: - subject - object - exposure event to entity association mixin: - deprecated: true - entity to outcome association mixin: description: >- An association between some entity and an outcome @@ -11309,21 +9512,6 @@ classes: object: range: transcript - gene regulatory relationship: - deprecated: true - is_a: association - description: >- - A regulatory relationship between two genes - slot_usage: - predicate: - description: >- - the direction is always from regulator to regulated - subject: - range: gene or gene product - role: regulatory gene - object: - range: gene or gene product - role: regulated gene chemical entity or gene or gene product regulates gene association: is_a: association