Add more species

[eboileau]

Aims/objectives.

Adding more species is likely to be more complicated than expected, and in general we also need to consider the availability of extended annotations, e.g. see #146, #140, #148, ... and how, if at all, we integrate RNA types, cf. #97, #119.

A clear and concise description of todo items.

• Using https://ftp.ensembl.org gives us access to most vertebrates and a few model organisms (yeast, fly, and nematode). If we want to extend to a greater variety of yeasts, other arthropods, plants, bacteria, and/or viruses, we need to reconsider our sources, and how to handle them.

• A "hard coded" check for yeast and worm to wrangle the GTF file name correctly should be better handled, cf.

  scimodom/server/src/scimodom/services/annotation/ensembl.py

  Line 139 in 3c9e100

  # TODO: AD HOC

• We cannot in fact handle yeast, it has no 3'UTR, so we need a more general solution to handle such cases.

• Another general problem is that of chain files. This https://ftp.ensembl.org/pub/release-110/assembly_chain/ is limited to

caenorhabditis_elegans/
danio_rerio/
homo_sapiens/
mus_musculus/
saccharomyces_cerevisiae/

• As for biotypes, we need to check in details how definitions vary between organisms, e.g. using GET info/biotypes/..., and how this differ from this or from our definitions in BIOTYPES (specifications.py). Besides, we have that:

# note that now <rna_type> can be anything...
@api.route("/biotypes/<rna_type>", methods=["GET"])
@cross_origin(supports_credentials=True)
def get_biotypes(rna_type):
    # TODO: do biotypes also depend on RNA type/annotation?
    return {"biotypes": MAPPED_BIOTYPES}