GO-CAM ectopic meeting July 19th 2017

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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:

1. 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

2. 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'

3. Inferences from Implementing the design pattern for 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


Strategies for trimming down superfluous inference