ECO terms in PV - Githubissues

DeniseSl22 commented 3 years ago

@egonw provided information on the Evidence and Conclusion Ontology (ECO) some time ago. I thought about how to add a feature allowing users to add ECO terms without us having to change the GPML directly, so I though about letting users add this ontology as a comment. I've started working on this (in my free time) in this branch. So the outline of the idea would be (in chronological order):

[x] Add button on comments panel for adding ECO terms.
[ ] On click of button, open another panel (like the add literature references).
[ ] This panel fetches the ECO-terms (layout as expendable tree structure, there are 2947 terms in this ontology, so a search function would also be a good idea later on).
[ ] Upon selecting one of these terms, and clicking a button "add this term", the term is added as (URL?ID only?) to a comment.

From there on, the comment should be added to the GPML automatically, and people can add more info to the term (such as: http://purl.obolibrary.org/obo/ECO_0000218 (Manual assertion): DataNode Identifier ).

I'm not sure if the structure above should be added in the Core, or as a plugin.... At a later stage, we could role out adding ECO terms on the other panels (literature, identifier) for DataNodes and Interactions (but this would require changes in the GPML I believe). @egonw @mkutmon : let me know what you think of the idea above, then I'll work on that when I have some spare time ;).

egonw commented 3 years ago

For example, in comment as [eco:ECO_0000218]. @DeniseSl22, please add some example GPML code.

mkutmon commented 3 years ago

I'll read through this but be aware that this is a task that the scientific programmer will take up once he/she starts in November latest. But these kind of suggested workflows are very nice to get started!

DeniseSl22 commented 3 years ago

Oh great that the scientific programmer (SP) will also help with this :) But I wanted to get back into Java programming, so thought this would be a nice small project to start with; and the the SP can give me some pointers later on, on how to improve it, or just take over from me.

mkutmon commented 3 years ago

before you start with the programming, let's have a short meeting next week (after Wednesday).

DeniseSl22 commented 3 years ago

As an example, I would start with WP4971; I've added several textual explanations as comments in this PW. We could use this example to see how ECO could be implemented in the future.

PathVisio / pathvisio

ECO terms in PV #165