diff options
| -rw-r--r-- | guix.scm | 15 | ||||
| -rw-r--r-- | sql/schema.org | 39 |
2 files changed, 45 insertions, 9 deletions
@@ -31,6 +31,7 @@ (gnu packages databases) (gnu packages statistics) (gnu packages bioconductor) + (gn packages golang) (gnu packages python) (gnu packages python-check) (gnu packages python-crypto) @@ -70,8 +71,8 @@ #:recursive? #t #:select? git-file?)) (propagated-inputs `(("coreutils" ,coreutils) - ("diffutils" ,diffutils) ("gemma-wrapper" ,gemma-wrapper) + ("csvdiff" ,go-github-com-aswinkarthik-csvdiff) ("python" ,python-wrapper) ("python-bcrypt" ,python-bcrypt) ("python-flask" ,python-flask) @@ -84,15 +85,11 @@ ("python-redis" ,python-redis) ("python-requests" ,python-requests) ("python-scipy" ,python-scipy) - ("python-sqlalchemy-stubs" ,python-sqlalchemy-stubs) - ("r" ,r) - ("r-qtl" ,r-qtl) + ("python-sqlalchemy-stubs" + ,python-sqlalchemy-stubs) ("r-optparse" ,r-optparse) - ("r-stringi" ,r-stringi) - ("r-stringr" ,r-stringr) - ("r-testthat" ,r-testthat) - ("r-wgcna" ,r-wgcna) - )) + ("r-qtl" ,r-qtl) + ("r-stringi" ,r-stringi))) (build-system python-build-system) (home-page "https://github.com/genenetwork/genenetwork3") (synopsis "GeneNetwork3 API for data science and machine learning.") diff --git a/sql/schema.org b/sql/schema.org new file mode 100644 index 0000000..2db8a27 --- /dev/null +++ b/sql/schema.org @@ -0,0 +1,39 @@ +#+TITLE: GeneNetwork Database Schema + +This is an attempt to reverse engineer and understand the schema of the +GeneNetwork database. The goal is to prune redundant tables, fields, etc. and +arrive at a simplified schema. This simplified schema will be useful when +migrating the database. + +* Species +** Id + Primary key +** SpeciesId + Looks like a redundant key referred to as a foreign key from many other + tables. This field should be replaced by Id. +** SpeciesName + Common name of the species. This field can be replaced by MenuName. +** Name + Downcased common name used as key for the species in dictionaries +** MenuName + Name in the Species dropdown menu. This is the SpeciesName, but sometimes + with the reference genome identifier mentioned in brackets. +** FullName + Binomial name of the species +** TaxonomyId + Foreign keys? +** OrderId + Foreign keys? + +* Strain +** Id + Primary key +** Name + Name of the strain +** Name2 + A second name. For most rows, this is the same as Name. Why is this + necessary? +** SpeciesId + Foreign key into the Species table +** Symbol +** Alias |