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geneontology / signor2gocam

Converting Signor pathways to GO-CAM
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Implement mechanism-specific translation patterns #20

Open dustine32 opened 4 years ago

dustine32 commented 4 years ago

SIGNOR2GO-CAM.pptx

Implement the patterns as described in attached PPTX:

  1. Direct interactions
  2. Indirect or unspecified mechanism; relocalization
  3. Small molecule regulation of protein activity
  4. Small molecule catalysis
  5. Regulation by ubiquitination and degradation
  6. Transcriptional regulation
  7. Post-transcriptional regulation by miRNA
  8. Post-transcriptional regulation by protein

Pattern 1 is the standard pattern currently implemented. Patterns 5-8 involved adding an intermediary BP between entity A function and entity B function, thus requiring two causal relations for the statement.

Edit: Dropping requirements for patterns 7 and 8 due to not having any causal statements in pathways that use the "post transcriptional regulation" mechanism.

dustine32 commented 4 years ago

For quicker access to the slides: image image

dustine32 commented 4 years ago

@vtoure @thomaspd I've implemented most of the patterns from above. Here are some examples for the patterns where they existed in the SIGNOR pathway files along with links to generated models.

Pattern 1: image P49841 (GSK3B)<-protein kinase activity-directly positively regulates->MF->P17676 (CEBPB) SIGNOR-AC

Pattern 2: image P14778 (IL1R1)<-root MF-causally upstream of, positive effect->MF->P51617 (IRAK1) SIGNOR-IL1R

Pattern 3: image Note: @thomaspd This pattern still requires the relations is_small_molecule_activator_of and is_small_molecule_inhibitor_of to be added to RO so no examples yet.

Pattern 4.a: image Q08828 (ADCY1)<-catalytic activity-has_output->CHEBI:17489 (3',5'-cyclic AMP) SIGNOR-Hedgehog 4.b: image P60484 (PTEN)<-catalytic activity-has_input->CHEBI:16618 (1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate) SIGNOR-GBM

Pattern 5: image Q00987 (MDM2)<-enabled_by- GO:0061630 -regulates-> GO:0043161 -regulates-> MF -enabled_by-> P04637 (TP53) SIGNOR-LBC

Pattern 6: image P16220 (CREB1)<-enabled_by- GO:0140110 -positively_regulates-> GO:0009299 -positively_regulates-> MF -enabled_by-> P17676 (CEBPB) SIGNOR-AC

Patterns 7 and 8: "Post-transcriptional regulation by miRNA" and "Post-transcriptional regulation by protein" I couldn't find any causal statements in the pathway files having mechanism = "post transcriptional regulation" nor any where entity A was a miRNA. I believe @thomaspd said a few weeks ago that, due to this, we can just drop pattern 7 but should we drop "Post-transcriptional regulation" altogether?

dustine32 commented 4 years ago

Hooray! Just found https://github.com/oborel/obo-relations/issues/369#issuecomment-648811561 where @pgaudet has added the two RO terms that we need for pattern 3:

# Object Property: obo:RO_0012005 (is small molecule activator)
# Object Property: obo:RO_0012006 (is small molecule inhibitor)

However, I'm not sure how soon these will make it into the released RO available here: http://purl.obolibrary.org/obo/ro.owl

vtoure commented 4 years ago

That's great! We can at least refer to the IDs and the terms - should be ok for now, until the terms gets released.