Signaling Pathway Annotation Guidelines

[hattrill]

We have made our own guidelines for annotating signaling pathways in FlyBase for the Pathway Pages. FB_Pathway_Curation_Manual.pdf (google doc here)

We would like to role this out to the rest of the GOC and reach some understanding about how to go forward with: a. Annotating signaling pathways using extensions b. Annotating signaling pathways using Noctua c. Linking the tagets of pathways e.g. transcriptional target genes, etc to the pathway. d. How to capture the activity of miRNAs

We are planning to hold a workshop: Ruth has started a doc for this and miRNAs

This ticket is to keep check of the work progress of the project for FB.

[hattrill]

Meeting with Pascale, Ruth & Giulia on Monday to dicuss issues with linking signaling pathways with transcription targets.

The main aim, from our perspective, is to make a very standardized way to capture this data so that it is querriable with a simple pattern. See working notes and proposals doc here

This is the doc to be updated to hold current model

[hattrill]

Discussion with SIB and Paul T on how to capture these in noctua: GO-CAM Modeling Guidelines: Signaling receptor activity

GO-CAM Modeling Guidelines: DNA binding transcription factor activity

[hattrill]

To demonstrate importance of consistency:

• [ ] scRNAseq user story

To demonstrate why we need to say where the protein is as a whole, not just where the MF happens

• [ ] bad case study (membrane proteins)

[hattrill]

New working doc for regulation of transcription & other effector targets by signaling pathways. To be discussed with GOC on Monday May.