GO-CAM ectopic meeting July 19th 2017: Difference between revisions
(Created page with "= Zoom URL = https://stanford.zoom.us/j/679970729 = Agenda = Discussion of inference on Wnt signaling LEGO model http://noctua.berkeleybop.org/editor/graph/gomodel:5966411...") |
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===Missing/New inferences: === | ===Missing/New inferences: === | ||
==== contributes_to inference: ==== | |||
Added to RO: | Added to RO: | ||
part of'(?x, ?y) ^ enables(?y, ?z) ^ molecular_function(?z) -> 'contributes to'(?x, ?z) | part of'(?x, ?y) ^ enables(?y, ?z) ^ molecular_function(?z) -> 'contributes to'(?x, ?z) | ||
e.g. GP(X) part_of complex(Y) enables MF(Z) -> X contributes_to Z | e.g. GP(X) part_of complex(Y) enables MF(Z) -> X contributes_to Z | ||
====Annotation to compound molecular function => annotation to its parts==== | |||
enables(?x, ?y) ^ 'has part'(?y, ?z) ^ molecular_function(?y) -> enables(?x, ?z) | enables(?x, ?y) ^ 'has part'(?y, ?z) ^ molecular_function(?y) -> enables(?x, ?z) | ||
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e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' | e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' | ||
====Inferences from molecular function regulators==== | |||
https://github.com/geneontology/go-ontology/issues/13492) | |||
e.g.: | e.g.: | ||
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=> | => | ||
X enables ‘protein binding activity' has_input Y * | X enables ‘protein binding activity' has_input Y * | ||
X enables 'protein kinase activator activity’ has_input Y * | X enables 'protein kinase activator activity’ has_input Y * | ||
* Comes from a new rule: | \* Comes from a new rule: | ||
molecular_function(?x) ^ molecular_function(?y) ^ 'directly regulates'(?x, ?y) ^ enables(?z, ?y) -> 'has input'(?x, ?z) | molecular_function(?x) ^ molecular_function(?y) ^ 'directly regulates'(?x, ?y) ^ enables(?z, ?y) -> 'has input'(?x, ?z) | ||
e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z | e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z | ||
=== Wrong inferences that need to be trimmed: === | === Wrong inferences that need to be trimmed: === |
Revision as of 12:03, 19 July 2017
Zoom URL
https://stanford.zoom.us/j/679970729
Agenda
Discussion of inference on Wnt signaling LEGO model
http://noctua.berkeleybop.org/editor/graph/gomodel:5966411600000538
Missing/New inferences:
contributes_to inference:
Added to RO: part of'(?x, ?y) ^ enables(?y, ?z) ^ molecular_function(?z) -> 'contributes to'(?x, ?z) e.g. GP(X) part_of complex(Y) enables MF(Z) -> X contributes_to Z
Annotation to compound molecular function => annotation to its parts
enables(?x, ?y) ^ 'has part'(?y, ?z) ^ molecular_function(?y) -> enables(?x, ?z)
e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'
Inferences from molecular function regulators
https://github.com/geneontology/go-ontology/issues/13492)
e.g.:
X <— enabled by— protein binding —directly_positively_regulates --> protein kinase activity —enabled_by--> Y
=>
X enables ‘protein binding activity' has_input Y * X enables 'protein kinase activator activity’ has_input Y *
\* Comes from a new rule:
molecular_function(?x) ^ molecular_function(?y) ^ 'directly regulates'(?x, ?y) ^ enables(?z, ?y) -> 'has input'(?x, ?z)
e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z
Wrong inferences that need to be trimmed:
regulates o part_of->regulates
https://github.com/geneontology/go-ontology/issues/13926#issuecomment-316054054