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Table 2 Available templates for the geneontology termgenie instance

From: TermGenie – a web-application for pattern-based ontology class generation

Template Input fields Equivalent class statement
regulation: biological process   
regulation X:BP GO:0065007 and ‘regulates’ some ?X
negative_regulation X:BP GO:0065007 and ‘negatively regulates’ some ?X
positive_regulation X:BP GO:0065007 and ‘positively regulates’ some ?X
regulation: molecular function   
regulation X:MF GO:0065007 and ‘regulates’ some ?X
negative_regulation X:MF GO:0065007 and ‘negatively regulates’ some ?X
positive_regulation X:MF GO:0065007 and ‘positively regulates’ some ?X
involved_in P:BP, W:BP ?P and ‘part_of’ some ?W
involved_in_mf_bp P:MF, W:BP ?P and ‘part_of’ some ?W
occurs_in P:BP, C:CC ?P and ‘occurs in’ some ?C
regulation_by R:GO:0050789, P:BP ?R and ‘results_in’ some ?P
part_of_cell_component P:CC, W: CC ?P and ‘part_of’ some ?W
chemical_transport X:chebi GO:0006810 and ‘transports or maintains localization of’ some ?X
chemical_transporter_activity X:chebi GO:0005215 and ‘transports or maintains localization of’ some ?X
chemical_binding X:chebi GO:0005488 and ‘has input’ some ?X
metabolism_catabolism_biosynthesis   
metabolism X:chebi GO:0008152 and ‘has participant’ some ?X
catabolism X:chebi GO:0009056 and ‘has input’ some ?X
biosynthesis X:chebi GO:0009058 and ‘has output’ some ?X
chemical_transmembrane_transport X:chebi GO:0055085 and ‘transports or maintains localization of’ some ?X
chemical_transmembrane_transporter_activity   
transmembrane transporter activity X:chebi GO:0022857 and ‘transports or maintains localization of’ some ?X
secondary active transmembrane transporter activity X:chebi GO:0015291 and ‘transports or maintains localization of’ some ?X
uptake transmembrane transporter activity X:chebi GO:0015563 and ‘transports or maintains localization of’ some ?X
transmembrane-transporting ATPase activity X:chebi GO:0042626 and ‘transports or maintains localization of’ some ?X
chemical_response_to   
response to X:chebi GO:0050896 and ‘has input’ some ?X
cellular response to X:chebi GO:0070887 and ‘has input’ some ?X
chemical_homeostasis   
chemical homeostasis X:chebi GO:0048878 and ‘regulates level of’ some ?X
cellular chemical homeostasis X:chebi GO:0055082 and ‘regulates level of’ some ?X
chemical_import X:chebi GO:0006810 and ‘imports’ some ?X
chemical_export X:chebi GO:0006810 and ‘exports’ some ?X
chemical_import_into S:chebi, T:CC GO:0006810 and ‘has target end location’ some ?T and ‘imports’ some ?S
cc_transport_from_to   
transport F:CC, T:CC GO:0006810 and ‘has target start location’ some ?F and ‘has target end location’ some ?T
vesicle-mediated transport F:CC, T:CC GO:0016192 and ‘has target start location’ some ?F and ‘has target end location’ some ?T
cc_transport   
transport C:CC GO:0006810 and ‘transports or maintains localization of’ some ?C
vesicle-mediated transport C:CC GO:0016192 and ‘transports or maintains localization of’ some ?C
chemical_transport_from_to   
transport X:chebi, [F:CC], [T:CC] GO:0006810 and ‘transports or maintains localization of’ some ?X [and ‘has target start location’ some ?F] [and ‘has target end location’ some ?T]
vesicle-mediated transport X:chebi, [F:CC], [T:CC] GO:0016192 and ‘transports or maintains localization of’ some ?X [and ‘has target start location’ some ?F] [and ‘has target end location’ some ?T]
cc_assembly_disassembly   
assembly C:CC GO:0022607 and ‘results_in_assembly_of’ some ?C
disassembly C:CC GO:0022411 and ‘results_in_disassembly_of’ some ?C
plant_development P:plant anatomical structure development’ and ‘results in development of’ some ?P
plant_formation X:plant anatomical structure formation involved in morphogenesis’ and ‘results in formation of’ some ?X
plant_maturation X:plant developmental maturation’ and ‘results in developmental progression of’ some ?X
plant_morphogenesis X:plant anatomical structure morphogenesis’ and ‘results in morphogenesis of’ some ?X
plant_structural_organization X:plant anatomical structure arrangement’ and ‘results in structural organization of’ some ?X
cell_apoptotic_process C:cell cell-type specific apoptotic process’ and ‘occurs in’ some ?C
cell_differentiation C:cell GO:0030154 and ‘results in acquisition of features of’ some ?C
cell_migration C:cell cell migration’ and ‘alters location of’ some ?C
protein_localization_to   
protein localization C:CC GO:0008104 and ‘has target end location’ some ?C
establishment of protein localization C:CC GO:0045184 and ‘has target end location’ some ?C
protein_complex_by_activity A:MF GO:0043234 and ‘capable_of’ some ?A
single_multi_organism_process   
single-organism P:BP ?P and ‘bearer of’ some PATO:0002487
multi-organism P:BP ?P and ‘bearer of’ some PATO:0002486
biosynthesis_from T:chebi, F:chebi GO:0009058 and ‘has output’ some ?T and ‘has input’ some ?F
biosynthesis_via T:chebi, V:chebi GO:0009058 and ‘has output’ some ?T and ‘has intermediate’ some ?V
catabolism_to S:chebi, R:chebi GO:0009056 and ‘has input’ some ?S and ‘has output’ some ?T
catabolism_via X:chebi, V:chebi GO:0009056 and ‘has input’ some ?X and ‘has intermediate’ some ?V
metazoan_development X:Uberon anatomical structure development’ and ‘results in development of’ some ?X
  1. The first column contains the template names and available templates variations. The second column lists the expected ontology inputs for the equivalent class statement in the third column, with BP = GO:biological_process, MF = GO:molecular_function, CC = GO:cellular_component, chebi = ‘chemical entity’ (CHEBI:24431), plant = ‘plant anatomical entity’ (PO:0025131), cell = ‘native cell’ (CL:0000003), Uberon = ‘anatomical entity’ (UBERON:0001062).