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LMDB Phenotype/Genotype Store

Please go through:


  • 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):


  • [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


  • 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:


  • Fetch metadata in RDF and possibly document things
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