LEGO GAF/GPAD September 28, 2016
Review Existing github Tickets and Prioritize
- Not so basic example of transcriptional regulation during neuronal development affecting downstream behavior
- Basic example of a regulates chain
- Basic example from Chris, no transitivity reasoning required
- Example of a simple causally upstream of or within chain
- Example of a chaining annotation extensions (comma-separated)
- Example of annotations to the Molecular Function root node
- Discussion of the behavior of annotation isoform entities in GAF representation
- This is an example of regulates annotations using the Drosophila memory paper from an annotation consistency exercise
- This is an example of creating multiple annotation lines when more than one evidence is cited for a given assertion
- This is a discussion of making use of MF-BP links to create additional BP annotations in the GAF/GPAD files
In some ways it's easiest to get it all right first time round, but as a way of stratifying the work, doing it in this order
1. agreeing on the basic property chain rules that should be encoded in RO. DOS - could you give an update of the most recent changes to RO? 2. deciding on policy for inferred evidence where the inference includes >1 piece of evidence 3. Additional ad-hoc procedural rules, such as whether to filter or include root nodes (#60) 4. Provenance, and ensuring the assigned-by field is correct
Although in some ways 1 is the hardest, from a CS POV it's the cleanest. If we can agree on this and just use inference to produce the core GPAD triple, we're most of the way there (of course, the plumbing required for inference is annoyingly hard, Jim could give an update of some of his thinking here, but that's more of interest to DOS).
DavidH, I added some comments here: I don't think involved in is correct, maybe DOS could comment? https://github.com/geneontology/minerva/issues/59
Good example though!
I also added another example, for a more straightforward case that doesn't require any transitivity reasoning https://github.com/geneontology/minerva/issues/61
This is an example of one that would produce the correct GPAD (I believe) using the existing structural transformation rules that Heiko implemented. But moving forward, for cases like 59, we will need at least some minimal property chain reasoning.