If you just want to output information from a database, then there are many ways of doing that. I have heard great things about Dancer, which abstracts much of the work for you, allowing you to focus on the presentation of the data. I've never used it, because I don't like this Moose stuff(it just doesn't look right). But you may find differently, so I encourage you to try it.

If you want to use Catalyst, then try the tutorial -- Catalyst::Manual::Tutorial -- which is a very good starting point for both Catalyst and DBIx::Class.

I know next to nothing about biology(except that during DNA replication, the RNA somehow gets the other RNA-thing(tRNA?) to move along it and translate every 3 codas into an amino acid which it strings on to a chain of amino acids...I think), so unfortunately I can't help you with how to organize that data or how to format it to your wishes.

~Thomas~ 

"Excuse me for butting in, but I'm interrupt-driven..."

Moose stuff

Dancer (not talking about Dancer2, which is written in Moo) has nothing in common with Moose.
لսႽ† ᥲᥒ⚪⟊Ⴙᘓᖇ Ꮅᘓᖇ⎱ Ⴙᥲ𝇋ƙᘓᖇ

Unless you do this only as a learning exercise, I think that the main question you should answer for yourself: is it not unnecessary? I am not quite sure, but I think EnsEMBL, UniProt, Entrez between them already have a lot, perhaps even all of the things that that PyCon quote mentions. EBI, EMBL, NCBI, they all have large teams working on both data, website, and interfaces. Make sure you find a useful addition/niche before even starting to work on it.

You also omit to mention what this would be used for. What is the audience? What kind of queries do you want to answer? How fast, how many, how reliably.

In general, I think the size of the source-databases involved (chebi, GO, human and perhaps other genomes) would make a database necessary, unless you envisage a system that makes use their respective API's.

I don't think an ORM (or which ORM) should be your first concern. Such things are pretty much downstream of the above questions.

A last consideration: have you contacted the poster presenters? Most people love it when others show interest in their work, and they are possibly quite willing to share their work. Even if you don't use it it may give you good ideas.

I would agree. The web framework (catalyst or something else) and the ORM (DBIx::Class or something else) are fairly mundane. The really fun part is the semantically related bit. Bringing together diverse data sets and trying to tease apart similar stuff can be either a lot of fun or a pure nightmare ... it all depends on your definition of similar.

-derby

Of possible further interest

Not related to genetics analysis or everything you mention but you might look into UMLS::Similarity and UMLS::Interface. They aren’t drop in, you have to have some MeSH stuff locally (requires registration and involves some very large files) and understand quite a bit of licensing (mostly open but not all), and it’s a technical challenge to set up but it’s extremely interesting and powerful for what it does if you take the trouble.