LMDB Phenotype/Genotype Store

• lead: bonfacem
• team: fred, alex
• contact: pjotr

Please go through:

https://github.com/BonfaceKilz/gn-dataset-dump

https://github.com/genenetwork/dump-genenetwork-database

Tasks

• Go through the above repository. We'll have a check in on Friday 23 to discuss this.
• Write and package guile-lmdb. Use cl-lmdb as inspiration
• Find out a more efficient way to store utf-8 strings
• Integrate LMDB in GN:
• Rewrite some statistical computations using LMDB+RDF
• Integrate editing LMDB entries using Fred's new auth system

Actionable items (Week 1):

Bonface:

• [A] Setup a directoryallowed for dumping rdf files
• [A] Autogenerate documentation: trees, and labels. How do you test for correctness and completeness in a data store?
• [C] guile bindings for lmdb for important stuff
• [B] Using hashes to track updates on database---proposal

Alex:

• Fetching all the phenotype data from the database using sql and genotype file
• Using LMBD as input for correlations---make proposal for how we can export data in a way we can use

• example implementation for this:

https://github.com/Alexanderlacuna/correlation_rust/pull/3/files#diff-87f0275ed65ae8ffe36df25091c9b975defbc920da7b5ec3c2dadb7d57ad4d67

Fred:

• Fetch metadata in RDF and possibly document things