SSPsyGene Knowledge Base — data export bundle
=============================================

This bundle contains the processed data tables used by https://psypheno.gi.ucsc.edu/.
Gene identifiers have been resolved to gene symbols (HGNC for human, MGI for mouse)
where mappings exist; rows otherwise carry the raw identifier they were loaded with.

Layout
------
  manifest.tsv                Index: one row per data table, with row counts,
                              columns, and pointers to the per-table files.
  tables/{table}.tsv          Full per-table data dump, tab-separated.
  metadata/{table}.yaml       Per-table metadata: description, columns +
                              field labels, source, links, gene mappings,
                              and citation.
  preprocessing/{table}.yaml  Per-table preprocessing provenance: which
                              gene-symbol rescues fired, what was dropped,
                              row counts before/after each step. Only
                              present for tables whose dataset ships a
                              preprocessing.yaml.
  ensembl_to_symbol.tsv       Ensembl ID ↔ gene symbol mapping used by
                              the website.
  README.txt                  This file.

Loading in R
------------
  manifest <- read.delim("manifest.tsv", stringsAsFactors = FALSE)
  tbl      <- read.delim("tables/perturb_fish_astro.tsv", stringsAsFactors = FALSE)
  head(tbl)

Loading in Python (pandas)
--------------------------
  import pandas as pd
  manifest = pd.read_csv("manifest.tsv", sep="\t")
  tbl      = pd.read_csv("tables/perturb_fish_astro.tsv", sep="\t")

Citing a dataset
----------------
Each metadata/{table}.yaml file includes the underlying publication block
(first/last author, year, journal, DOI, PMID, SSPsyGene grants). Please cite
the original publication when using a dataset.