Extensions2GO-CAM: Difference between revisions
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#REDIRECT [[Noctua_MOD_Imports]] | |||
[[Category:GO-CAM]] | [[Category:GO-CAM]] | ||
'''Note that the current set of rules is now documented here: [http://wiki.geneontology.org/index.php/Noctua_MOD_Imports Noctua MOD Imports]''' | |||
=Simple conversions= | =Simple conversions= | ||
These are relations that are essentially identical in extensions and GO-CAM | These are relations that are essentially identical in extensions and GO-CAM, and can be combined together into a "standard" GO-CAM activity. | ||
*If the aspect is F (column A) | *If the aspect is F (column A) | ||
**No more than one occurs_in(CC) | **No more than one occurs_in(CC) | ||
**No more than one occurs_in(CL) | **No more than one occurs_in(CL) | ||
**No more than one occurs_in(UBERON or EMAPA) | **No more than one occurs_in(UBERON or EMAPA or WBbt) | ||
**No more than one has_input/has_direct_input(geneID or ChEBI) | **No more than one has_input/has_direct_input(geneID or ChEBI) | ||
*** EXCEPTION: if term is "molecular function regulator activity" or descendant, can also add -directly-regulates->[MF of GP-B] | |||
**No more than one happens_during(BP) | **No more than one happens_during(BP) | ||
**No more than one part_of(BP) | **No more than one part_of(BP) | ||
**No more than one activated_by(ChEBI) | **No more than one activated_by(ChEBI) | ||
**No more than one inhibited_by(ChEBI) | **No more than one inhibited_by(ChEBI) | ||
*If the aspect is C | *If the aspect is C | ||
**No more than one | **No more than one part_of(CC) | ||
**No more than one | **No more than one part_of(CL) | ||
**No more than one | **No more than one part_of(UBERON or EMAPA) | ||
*If the aspect is P | *If the aspect is P | ||
**No more than one occurs_in(CC) | **No more than one occurs_in(CC) | ||
**No more than one occurs_in(CL) | **No more than one occurs_in(CL) | ||
**No more than one occurs_in(UBERON or EMAPA) | **No more than one occurs_in(UBERON or EMAPA or WBbt) | ||
**No more than one has_input/has_direct_input(geneID or ChEBI) | **No more than one has_input/has_direct_input(geneID or ChEBI) | ||
**No more than one part_of(BP) | **No more than one part_of(BP) | ||
=has_regulation_target= | =has_regulation_target= | ||
NOTE CAN ONLY BE USED ON AN MF ANNOTATION; CARDINALITY MUST BE 0 OR 1 | |||
*GP-A [regulation of molecular function Z] has_regulation_target GP-B | *GP-A [regulation of molecular function Z] has_regulation_target GP-B | ||
**can be expressed as [GP-A]<-enabled_by-[ | ** term is GO:0065009 and descendants | ||
**The variations on this are all children of the term “regulation of molecular function” (GO:0065009). Variations are “positive regulation of MF Z”, which would be expressed with the positively_regulates relation instead; “negative regulation of MF Z”. **Note that MF Z should appear in the logical definition of the term “regulation of MF Z”, so | **can be expressed as [GP-A]<-enabled_by-[root MF]-regulates->[molecular function Z]-enabled_by->[GP-B] | ||
*GP-A [regulation of | **The variations on this are all children of the term “regulation of molecular function” (GO:0065009). Variations are “positive regulation of MF Z”, which would be expressed with the positively_regulates relation instead; “negative regulation of MF Z”. **Note that MF Z should appear in the logical definition of the term “regulation of MF Z”, or in a triple with the regulates relation, so we can get the GO ID from that. | ||
**can be | *GP-A [regulation of gene expression OR regulation of protein biosynthetic process Z] has_regulation_target GP-B | ||
** | **These can be modeled as GP-A<-enabled_by-[root MF]-part_of->[regulation of Z]-has_input->GP-B,-regulates->[root MF]-enabled_by->GP-B | ||
*Regulation of | **Will be positively or negatively regulates instead, if in the original term. | ||
**These can be modeled as GP-A<-enabled_by-[ | *GP-A [Regulation of receptor internalization (GO:0002092) OR regulation of protein catabolic process Z] has_regulation_target GP-B | ||
* | ** These are GO:0002092 and descendants, or GO:0042176 and descendants | ||
**These can be modeled | **These can be modeled as GP-A<-enabled_by-[root MF]-part_of->[regulation of Z]-has_input->GP-B,-regulates->[root MF]-enabled_by->GP-B | ||
**If term is positive regulation, relation will be negatively-regulates; if negative reg, relation will be positively-regulates | |||
* GP-A [regulation of protein metabolic process Z, not including cases above, or regulation of protein localization] has_regulation_target GP-B | |||
* These are GO:0019538 and the descendants that are not also descendants of terms listed above, or GO:0032880 and descendants | |||
**These can be modeled as GP-A<-enabled_by-[root MF]-part_of->[regulation of Z]-has_input->GP-B | |||
* | |||
* | =extensions that need to be handled= | ||
==MGI== | |||
** | P has_participant(EMAPA) | ||
P results_in_development_of(EMAPA) | |||
P regulates_o_occurs_in(EMAPA) | |||
P has_regulation_target(geneID) | |||
P regulates_o_occurs_in(CL) | |||
P regulates_o_occurs_in(CL),regulates_o_occurs_in(EMAPA) | |||
P has_participant(CL) | |||
P occurs_in(EMAPA),results_in_acquisition_of_features_of(CL) | |||
P has_output_o_axis_of(EMAPA) | |||
P has_participant(CL),occurs_in(EMAPA) | |||
P has_participant(CL),has_participant(EMAPA) | |||
P regulates_o_acts_on_population_of(CL) | |||
F has_participant(geneID) | |||
P regulates_o_acts_on_population_of(CL),regulates_o_occurs_in(EMAPA) | |||
C part_of(CL),part_of(EMAPA),part_of(EMAPA) | |||
P regulates_o_results_in_acquisition_of_features_of(CL) | |||
P has_participant(CL),results_in_development_of(EMAPA) | |||
P results_in_acquisition_of_features_of(CL) | |||
P regulates_o_has_participant(EMAPA) | |||
P regulates_o_has_agent(CL) | |||
P occurs_in(EMAPA),regulates_o_results_in_acquisition_of_features_of(CL) | |||
P results_in_formation_of(EMAPA) | |||
P occurs_in(EMAPA),results_in_movement_of(CL) | |||
P occurs_in(EMAPA),regulates_o_occurs_in(CL) | |||
P occurs_in(CL),occurs_in(EMAPA),occurs_in(EMAPA) | |||
P acts_on_population_of(CL) | |||
P acts_on_population_of(CL),occurs_in(EMAPA) | |||
P occurs_in(EMAPA),results_in_development_of(CL) | |||
C part_of(CL),part_of(EMAPA),part_of(EMAPA),part_of(EMAPA) | |||
P occurs_in(EMAPA),regulates_o_acts_on_population_of(CL) | |||
P regulates_o_has_participant(CL) | |||
P has_participant(geneID) | |||
P regulates_o_has_participant(geneID) | |||
P occurs_in(CL),regulates_o_occurs_in(CL) | |||
P occurs_in(EMAPA),results_in_acquisition_of_features_of(CL),results_in_acquisition_of_features_of(CL) | |||
P regulates_o_has_participant(CL),regulates_o_occurs_in(EMAPA) | |||
P has_participant(CL),occurs_in(EMAPA),occurs_in(EMAPA) | |||
P has_participant(CL),has_participant(EMAPA),has_participant(EMAPA) | |||
P has_regulation_target(geneID),regulates_o_occurs_in(CL) | |||
P regulates_o_has_participant(CL),regulates_o_has_participant(EMAPA) | |||
P has_participant(CL),results_in_development_of(EMAPA),results_in_development_of(EMAPA) | |||
P results_in_movement_of(CL) | |||
P transports_or_maintains_localization_of(geneID) | |||
P results_in_development_of(CL) | |||
C part_of(CL),part_of(EMAPA),part_of(EMAPA),part_of(EMAPA),part_of(EMAPA) | |||
P has_regulation_target(geneID),regulates_o_occurs_in(EMAPA) | |||
P regulates_o_occurs_in(EMAPA),regulates_o_results_in_acquisition_of_features_of(CL) | |||
P regulates_o_acts_on_population_of(CL),regulates_o_occurs_in(EMAPA),regulates_o_occurs_in(EMAPA) | |||
P regulates_o_occurs_in(CL),regulates_o_occurs_in(EMAPA),regulates_o_occurs_in(EMAPA) | |||
P regulates_o_results_in_movement_of(CL) | |||
P results_in_morphogenesis_of(EMAPA) | |||
P occurs_in(EMAPA),regulates_o_occurs_in(EMAPA) | |||
P has_regulation_target(geneID),regulates_o_occurs_in(CL),regulates_o_occurs_in(EMAPA) | |||
P has_regulation_target(geneID),occurs_in(CL) | |||
P regulates_o_occurs_in(EMAPA),regulates_o_results_in_movement_of(CL) | |||
P occurs_in(EMAPA),results_in_commitment_to(CL) | |||
P occurs_in(EMAPA),occurs_in(EMAPA) | |||
P occurs_in(EMAPA),results_in_movement_of(CL),results_in_movement_of(CL) | |||
P occurs_in(EMAPA),results_in_maturation_of(CL) | |||
P has_regulation_target(geneID),occurs_in(EMAPA) | |||
P occurs_in(CL),transports_or_maintains_localization_of(geneID) | |||
C part_of(EMAPA),part_of(EMAPA) | |||
P occurs_in(EMAPA),regulates_o_results_in_acquisition_of_features_of(CL),regulates_o_results_in_acquisition_of_features_of(CL) | |||
P occurs_in(CL),occurs_in(EMAPA),occurs_in(EMAPA),occurs_in(EMAPA) | |||
P occurs_in(EMAPA),regulates_o_acts_on_population_of(CL),regulates_o_acts_on_population_of(CL) | |||
P regulates_o_has_participant(geneID),regulates_o_occurs_in(CL) | |||
P has_participant(EMAPA),results_in_commitment_to(CL) | |||
P occurs_in(CL),occurs_in(EMAPA),transports_or_maintains_localization_of(geneID) | |||
P regulates_o_results_in_development_of(EMAPA) | |||
P acts_on_population_of(CL),occurs_in(EMAPA),occurs_in(EMAPA) | |||
P occurs_in(EMAPA),occurs_in(EMAPA),occurs_in(EMAPA) | |||
P regulates_o_has_participant(geneID),regulates_o_occurs_in(EMAPA) | |||
C part_of(CL),part_of(EMAPA),part_of(EMAPA),part_of(EMAPA),part_of(EMAPA),part_of(EMAPA) | |||
P has_regulation_target(geneID),occurs_in(CL),regulates_o_occurs_in(CL) | |||
C adjacent_to(CL) | |||
P regulates_o_has_output(geneID) | |||
P has_input(PR),has_output(PR) | |||
P has_input(geneID),negatively_regulates(GO:P),positively_regulates(GO:F) | |||
P has_regulation_target(geneID),occurs_in(CL),occurs_in(EMAPA) | |||
P has_participant(geneID),occurs_in(CL) | |||
P regulates_o_results_in_formation_of(EMAPA) | |||
P occurs_in(EMAPA),results_in_morphogenesis_of(CL) | |||
P results_in_commitment_to(CL) | |||
P regulates_o_has_agent(CL),regulates_o_occurs_in(EMAPA) | |||
C part_of(GO:C) | |||
P results_in_morphogenesis_of(CL) | |||
P results_in_maturation_of(CL) | |||
P part_of(EMAPA) | |||
F occurs_in(CL),occurs_in(EMAPA),occurs_in(EMAPA) | |||
P occurs_in(CL),occurs_in(EMAPA),occurs_in(EMAPA),transports_or_maintains_localization_of(geneID),transports_or_maintains_localization_of(geneID) | |||
P occurs_in(EMAPA),regulates_o_occurs_in(CL),regulates_o_occurs_in(CL) | |||
P has_participant(geneID),occurs_in(CL),occurs_in(EMAPA) | |||
C part_of(CL),part_of(CL) | |||
P has_participant(geneID),occurs_in(EMAPA) | |||
P occurs_in(EMAPA),results_in_maturation_of(CL),results_in_maturation_of(CL) | |||
P regulates_o_has_input(geneID) | |||
C part_of(CL),part_of(EMAPA),part_of(EMAPA),part_of(EMAPA),part_of(EMAPA),part_of(EMAPA),part_of(EMAPA) | |||
P has_participant(CL),occurs_in(EMAPA),occurs_in(EMAPA),occurs_in(EMAPA),occurs_in(EMAPA) | |||
P acts_on_population_of(CL),regulates_o_occurs_in(EMAPA) | |||
P has_agent(CL) | |||
P occurs_in(CL),occurs_in(EMAPA),occurs_in(EMAPA),occurs_in(EMAPA),occurs_in(EMAPA) | |||
P has_direct_input(PR) | |||
P occurs_in(EMAPA),transports_or_maintains_localization_of(geneID) | |||
==PomBase== | |||
*C exists_during(GO:P) | |||
*P happens_during(GO:P) | |||
*C coincident_with(SO) | |||
*F occurs_at(SO) | |||
==UCL== | |||
P regulates_expression_of(geneID) | |||
P happens_during(GO:P),results_in_movement_of(geneID) | |||
==IntAct== | |||
F occurs_in() | |||
==SGD== | |||
P regulates_transcription_of(geneID) |
Latest revision as of 10:23, 31 October 2019
Redirect to:
Note that the current set of rules is now documented here: Noctua MOD Imports
Simple conversions
These are relations that are essentially identical in extensions and GO-CAM, and can be combined together into a "standard" GO-CAM activity.
- If the aspect is F (column A)
- No more than one occurs_in(CC)
- No more than one occurs_in(CL)
- No more than one occurs_in(UBERON or EMAPA or WBbt)
- No more than one has_input/has_direct_input(geneID or ChEBI)
- EXCEPTION: if term is "molecular function regulator activity" or descendant, can also add -directly-regulates->[MF of GP-B]
- No more than one happens_during(BP)
- No more than one part_of(BP)
- No more than one activated_by(ChEBI)
- No more than one inhibited_by(ChEBI)
- If the aspect is C
- No more than one part_of(CC)
- No more than one part_of(CL)
- No more than one part_of(UBERON or EMAPA)
- If the aspect is P
- No more than one occurs_in(CC)
- No more than one occurs_in(CL)
- No more than one occurs_in(UBERON or EMAPA or WBbt)
- No more than one has_input/has_direct_input(geneID or ChEBI)
- No more than one part_of(BP)
has_regulation_target
NOTE CAN ONLY BE USED ON AN MF ANNOTATION; CARDINALITY MUST BE 0 OR 1
- GP-A [regulation of molecular function Z] has_regulation_target GP-B
- term is GO:0065009 and descendants
- can be expressed as [GP-A]<-enabled_by-[root MF]-regulates->[molecular function Z]-enabled_by->[GP-B]
- The variations on this are all children of the term “regulation of molecular function” (GO:0065009). Variations are “positive regulation of MF Z”, which would be expressed with the positively_regulates relation instead; “negative regulation of MF Z”. **Note that MF Z should appear in the logical definition of the term “regulation of MF Z”, or in a triple with the regulates relation, so we can get the GO ID from that.
- GP-A [regulation of gene expression OR regulation of protein biosynthetic process Z] has_regulation_target GP-B
- These can be modeled as GP-A<-enabled_by-[root MF]-part_of->[regulation of Z]-has_input->GP-B,-regulates->[root MF]-enabled_by->GP-B
- Will be positively or negatively regulates instead, if in the original term.
- GP-A [Regulation of receptor internalization (GO:0002092) OR regulation of protein catabolic process Z] has_regulation_target GP-B
- These are GO:0002092 and descendants, or GO:0042176 and descendants
- These can be modeled as GP-A<-enabled_by-[root MF]-part_of->[regulation of Z]-has_input->GP-B,-regulates->[root MF]-enabled_by->GP-B
- If term is positive regulation, relation will be negatively-regulates; if negative reg, relation will be positively-regulates
- GP-A [regulation of protein metabolic process Z, not including cases above, or regulation of protein localization] has_regulation_target GP-B
- These are GO:0019538 and the descendants that are not also descendants of terms listed above, or GO:0032880 and descendants
- These can be modeled as GP-A<-enabled_by-[root MF]-part_of->[regulation of Z]-has_input->GP-B
extensions that need to be handled
MGI
P has_participant(EMAPA) P results_in_development_of(EMAPA) P regulates_o_occurs_in(EMAPA) P has_regulation_target(geneID) P regulates_o_occurs_in(CL) P regulates_o_occurs_in(CL),regulates_o_occurs_in(EMAPA) P has_participant(CL) P occurs_in(EMAPA),results_in_acquisition_of_features_of(CL) P has_output_o_axis_of(EMAPA) P has_participant(CL),occurs_in(EMAPA) P has_participant(CL),has_participant(EMAPA) P regulates_o_acts_on_population_of(CL) F has_participant(geneID) P regulates_o_acts_on_population_of(CL),regulates_o_occurs_in(EMAPA) C part_of(CL),part_of(EMAPA),part_of(EMAPA) P regulates_o_results_in_acquisition_of_features_of(CL) P has_participant(CL),results_in_development_of(EMAPA) P results_in_acquisition_of_features_of(CL) P regulates_o_has_participant(EMAPA) P regulates_o_has_agent(CL) P occurs_in(EMAPA),regulates_o_results_in_acquisition_of_features_of(CL) P results_in_formation_of(EMAPA) P occurs_in(EMAPA),results_in_movement_of(CL) P occurs_in(EMAPA),regulates_o_occurs_in(CL) P occurs_in(CL),occurs_in(EMAPA),occurs_in(EMAPA) P acts_on_population_of(CL) P acts_on_population_of(CL),occurs_in(EMAPA) P occurs_in(EMAPA),results_in_development_of(CL) C part_of(CL),part_of(EMAPA),part_of(EMAPA),part_of(EMAPA) P occurs_in(EMAPA),regulates_o_acts_on_population_of(CL) P regulates_o_has_participant(CL) P has_participant(geneID) P regulates_o_has_participant(geneID) P occurs_in(CL),regulates_o_occurs_in(CL) P occurs_in(EMAPA),results_in_acquisition_of_features_of(CL),results_in_acquisition_of_features_of(CL) P regulates_o_has_participant(CL),regulates_o_occurs_in(EMAPA) P has_participant(CL),occurs_in(EMAPA),occurs_in(EMAPA) P has_participant(CL),has_participant(EMAPA),has_participant(EMAPA) P has_regulation_target(geneID),regulates_o_occurs_in(CL) P regulates_o_has_participant(CL),regulates_o_has_participant(EMAPA) P has_participant(CL),results_in_development_of(EMAPA),results_in_development_of(EMAPA) P results_in_movement_of(CL) P transports_or_maintains_localization_of(geneID) P results_in_development_of(CL) C part_of(CL),part_of(EMAPA),part_of(EMAPA),part_of(EMAPA),part_of(EMAPA) P has_regulation_target(geneID),regulates_o_occurs_in(EMAPA) P regulates_o_occurs_in(EMAPA),regulates_o_results_in_acquisition_of_features_of(CL) P regulates_o_acts_on_population_of(CL),regulates_o_occurs_in(EMAPA),regulates_o_occurs_in(EMAPA) P regulates_o_occurs_in(CL),regulates_o_occurs_in(EMAPA),regulates_o_occurs_in(EMAPA) P regulates_o_results_in_movement_of(CL) P results_in_morphogenesis_of(EMAPA) P occurs_in(EMAPA),regulates_o_occurs_in(EMAPA) P has_regulation_target(geneID),regulates_o_occurs_in(CL),regulates_o_occurs_in(EMAPA) P has_regulation_target(geneID),occurs_in(CL) P regulates_o_occurs_in(EMAPA),regulates_o_results_in_movement_of(CL) P occurs_in(EMAPA),results_in_commitment_to(CL) P occurs_in(EMAPA),occurs_in(EMAPA) P occurs_in(EMAPA),results_in_movement_of(CL),results_in_movement_of(CL) P occurs_in(EMAPA),results_in_maturation_of(CL) P has_regulation_target(geneID),occurs_in(EMAPA) P occurs_in(CL),transports_or_maintains_localization_of(geneID) C part_of(EMAPA),part_of(EMAPA) P occurs_in(EMAPA),regulates_o_results_in_acquisition_of_features_of(CL),regulates_o_results_in_acquisition_of_features_of(CL) P occurs_in(CL),occurs_in(EMAPA),occurs_in(EMAPA),occurs_in(EMAPA) P occurs_in(EMAPA),regulates_o_acts_on_population_of(CL),regulates_o_acts_on_population_of(CL) P regulates_o_has_participant(geneID),regulates_o_occurs_in(CL) P has_participant(EMAPA),results_in_commitment_to(CL) P occurs_in(CL),occurs_in(EMAPA),transports_or_maintains_localization_of(geneID) P regulates_o_results_in_development_of(EMAPA) P acts_on_population_of(CL),occurs_in(EMAPA),occurs_in(EMAPA) P occurs_in(EMAPA),occurs_in(EMAPA),occurs_in(EMAPA) P regulates_o_has_participant(geneID),regulates_o_occurs_in(EMAPA) C part_of(CL),part_of(EMAPA),part_of(EMAPA),part_of(EMAPA),part_of(EMAPA),part_of(EMAPA) P has_regulation_target(geneID),occurs_in(CL),regulates_o_occurs_in(CL) C adjacent_to(CL) P regulates_o_has_output(geneID) P has_input(PR),has_output(PR) P has_input(geneID),negatively_regulates(GO:P),positively_regulates(GO:F) P has_regulation_target(geneID),occurs_in(CL),occurs_in(EMAPA) P has_participant(geneID),occurs_in(CL) P regulates_o_results_in_formation_of(EMAPA) P occurs_in(EMAPA),results_in_morphogenesis_of(CL) P results_in_commitment_to(CL) P regulates_o_has_agent(CL),regulates_o_occurs_in(EMAPA) C part_of(GO:C) P results_in_morphogenesis_of(CL) P results_in_maturation_of(CL) P part_of(EMAPA) F occurs_in(CL),occurs_in(EMAPA),occurs_in(EMAPA) P occurs_in(CL),occurs_in(EMAPA),occurs_in(EMAPA),transports_or_maintains_localization_of(geneID),transports_or_maintains_localization_of(geneID) P occurs_in(EMAPA),regulates_o_occurs_in(CL),regulates_o_occurs_in(CL) P has_participant(geneID),occurs_in(CL),occurs_in(EMAPA) C part_of(CL),part_of(CL) P has_participant(geneID),occurs_in(EMAPA) P occurs_in(EMAPA),results_in_maturation_of(CL),results_in_maturation_of(CL) P regulates_o_has_input(geneID) C part_of(CL),part_of(EMAPA),part_of(EMAPA),part_of(EMAPA),part_of(EMAPA),part_of(EMAPA),part_of(EMAPA) P has_participant(CL),occurs_in(EMAPA),occurs_in(EMAPA),occurs_in(EMAPA),occurs_in(EMAPA) P acts_on_population_of(CL),regulates_o_occurs_in(EMAPA) P has_agent(CL) P occurs_in(CL),occurs_in(EMAPA),occurs_in(EMAPA),occurs_in(EMAPA),occurs_in(EMAPA) P has_direct_input(PR) P occurs_in(EMAPA),transports_or_maintains_localization_of(geneID)
PomBase
- C exists_during(GO:P)
- P happens_during(GO:P)
- C coincident_with(SO)
- F occurs_at(SO)
UCL
P regulates_expression_of(geneID) P happens_during(GO:P),results_in_movement_of(geneID)
IntAct
F occurs_in()
SGD
P regulates_transcription_of(geneID)