Table 2 Available templates for the geneontology termgenie instance

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