Creation of a tripal_genome extension module and docs repository

[spficklin]

I want to propose to move out the GFF3 and FASTA loaders (and perhaps) others into a tripal_genome extension module. This way, core Tripal really is just core code. We could even fold in the InterPro, KEGG (if possible to do now), GO and Blast modules into the tripal_genome module to make it easier to setup a complete genome website. Whereas right now, it's a bit all over the place. This puts a genomic website on par with any other website (e.g. breeders) which is all through extension modules.

Also in a conversation with Lacey, to unify documentation across all of Tripal, a second proposal is to move the documentation out of the Tripal core repository and move it into a separate module that could be documentation for everything.

[laceysanderson]

I love this idea as I hope it will make it less intimidating for people to contribute to Tripal. This way instead of contributing to CORE they're contributing to a genome-specific extension module which should include less other code. It also provides good examples of best practices in extension modules 🤞

[laceysanderson]

More detail for this proposition from our PMC Meeting:

Overview

• Move content type creation out of Tripal core and into specific modules
• Move all content type specific fields out of Tripal core and into specific modules
• Conversely, leave only generic fields in Tripal core. Specifically,
  • Linking Tables: chado_linker__contact, chado_linker__prop, operation__analysis, sbo__relationship, schema__publication, sio__annotation? (cvterm linker), sio__references (records ref. by pub)
  • Common Columns: data__accession (i.e. uniquename), schema__additional_type, schema__alternate_name
  • Common Foreign Keys: rdfs_type (cvterm), local__contact, obi__organism, sbo__database_cross_reference, sio__vocabulary? (cv of cvterm), taxrank__infraspecific_taxon.
• Move all data-type specific importers into specific modules. Importers which stay: obo/owl, publication.

Proposed Modules

The following modules will be created in the github tripal organization. They will follow the gold standard rating system and be recommended by the Tripal community. They will consolidate existing extension modules, find common ground/needs and reduce the number to extension modules to be maintained. They will be included in the Tripal core documentation.

• tripal_genome
  • Content Types: Gene, mRNA, Genome Assembly, Genome Annotation
  • Importers from Core: GFF3, FASTA Importers
  • tripal_analysis_blast
  • tripal_analysis_interpro
  • tripal_analysis_go
• tripal_germplasm
  • Content Types: Germplasm Accession, Germplasm Variety
  • Importers from Core: NCBI Taxonomy
• tripal_genetics
  • Content Types: Phylogenetic Tree, Physical Map, Genetic Map, Sequence Variant, Genetic Marker, Heritable Phenotypic Marker
  • Importers from Core: Newick Importer
• tripal_genotypes
  • Content Types: Sequence Variant, Genetic Marker
• tripal_phenotypes
  • Content Types: QTL, Heritable Phenotypic Marker
• tripal_breeding
  • Content Types: Breeding Cross, Recombinant Inbred Line
• tripal_expression
  • Content Types: Biological Sample, Assay, Assay Design
  • tripal_analysis_expression

Beyond these core extensions

For the rating system, your module will be categorized into the above categories.

We want to create a wizard for setting up a Tripal site to make it easier. This wizard would pull available extension modules for specific categories using web services. This allows us help web administrators to find extension modules directly in their site. Anyone can add their module to these lists. The lists will be shown to administrators with modules sorted and displaying rating system badges.

Thus the larger modules proposed above still do not need to be the only solution or contain all solutions.

Note: The bulk importer will be moved out of core into a separate module and only upgraded to Tripal 4 if there is enough interest.