Table 2.
Available templates for the geneontology termgenie instance
| 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 |
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).