search

geneontology / pathways2GO

Code for converting between BioPAX pathways and Gene Ontology Causal Activity Models (GO-CAM)
8 stars 0 forks source link

Write manuscript describing the results of this project. #92

Closed goodb closed 2 years ago

goodb commented 4 years ago

Brainstorm document: https://docs.google.com/document/d/1QKVWxWkcbTh-A6VMzidusOS-CIP_SD1yEfAzWR5GiGs/edit

goodb commented 4 years ago

I think we should close the current github project and set up another one specifically on the topic of writing the manuscript.
Here is another document with a fairly technical description of the conversion process. https://docs.google.com/document/d/1x6ZfDuvLlqPC2vUSdf63fOu9j7IWK3jXUJ_JAL1bzsg/edit

I think it or parts of it should be integrated into the main document.

There is a lot of leftover stuff in the main document right now. I think it would be useful to go ahead and start removing things that aren't going to stay. I am assuming this falls to @deustp01 ? But if called upon I would be happy to try.

deustp01 commented 4 years ago

I will work on the main document this week.

goodb commented 4 years ago

I started building the queries for making reports for the manuscript. Table with data emerging here: https://docs.google.com/spreadsheets/d/1OLMyc5gPsBDFNRDlIIN5BmVdQ3DaDwKxtXDt0Wk4uHs/edit?usp=sharing

Let me know if there is something in particular you would like to measure.

deustp01 commented 4 years ago

finished next round of revision of introduction and discussion.

deustp01 commented 4 years ago

Finished another round of revision - I think we now have a coherent introduction - results - discussion draft. (I've moved all previous pieces to the end of the file, in case something essential got cut during revision.) It is definitely missing some pieces, like the meat-and-potatoes summary at the beginning of the discussion of what we have accomplished, but that will be straightforward to assemble.

What we really need now is fresh eyes** to read through the draft. Do we have a coherent description of the project and its rationale? Have we properly handled the PD - AF distinction and how it plays out in this project? Have we left out something crucial? Have we included something unimportant (my sense is that the draft is very long - shorter would be better, but maybe we need all this material)?

** @ukemi @thomaspd @huaiyumi @vanaukenk

ukemi commented 4 years ago

I agree. At this point the manuscript does seem a bit long. And, we still haven't added the concrete examples of the pathways yet. Discussion for tomorrow's call.

ukemi commented 2 years ago

PMID:33964129 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8504636/