Tripal: Show publication on feature pages

[almasaeed2010]

Feature Request/Discussion

• This feature [does] attempt to solve an existing problem with Tripal
• I [am] open to developing or collaborating on an extension module if this is not a good fit for Tripal Core
  
• This feature is [Not Urgent]

Description

It would be nice to see which publication a particular feature (gene, mRNA) is associated with if the parent analysis is associated with a publication. Since the analysisfeature table is populated with the relationship, it should be simple to add to the schema__publication field to display all associated pubs with features.

Your Specific Use Case

Example from our site:

• visit this feature page
• Publication field is not showing up although the analysis this feature is associated has a publication associated with it

[bradfordcondon]

I think you need to distinguish between pubs associated via feature_analysis => analysis_pub and pubs associated via feature_pub. To me this suggests a custom "analysis-linked pub" field.

[almasaeed2010]

If we are taking this route (new field), I think this warrants a PMC vote since it's a new feature. @tripal/project-managent-commitee-pmc

[laceysanderson]

I vote in favour of adding a new field to show publications associated with an analysis on a related feature page. I think this would be extremely helpful to users and is generic enough to be useful for multiple groups 👍

[bradfordcondon]

I'm also ok with it.

While we're talking, do we have an ontology term?

[almasaeed2010]

I've developed a field to do this for features specifically. I think we can take this field and expand on it to include other types of records as well.

• Code https://github.com/statonlab/tripal_feature_pub
• Demo https://hardwoodgenomics.org/bio_data/158359?tripal_pane=gp_schema__publication49321

The term used here is sio:000087 (publication) but if needed we can migrate to a different term.

Let me know what you think!

Thanks.

[bradfordcondon]

Awesome!

Looking at the code everything seems 👍
The only thing im wondering about is the term. Is it confusing to have schema:publication and sio:publication in use? I wonder if it would be better to use a local term, to the tune of "indirectly associated publication"

[spficklin]

@almasaeed2010 were you going to submit a PR for this field? It's been several months since this was discussed?

[bradfordcondon]

@almasaeed2010 are you still interested in this field?

[laceysanderson]

@almasaeed2010 I'm going to close the issue as there has been no movement on this issue for awhile and you do have a working solution. We would still greatly welcome a contribution back so feel free to open a PR to that effect when you find time!