TCRD v6.0.0
===================
This README describes TCRDv6 which has many changes and additions from
versions 5.*.*. Datasets were added and modified as described below,
mostly to support MetaPath-ML.

Mouse and Rat Proteins
======================
Mouse and Rat proteins from UniProt have been added to the new table
nhprotein.

Disease Ontology
================
Added new table do_xref for xrefs to other Ontologies/Terminologies.

Rat Disease Ontology
====================
Added new tables rdo and rdo_xref and populated with Rat Disease
Ontology data. RDO.obo file has DOID:xxxxxxx ids and RGO ids as
alt_ids. TCRD uses doids in rdo and stores RGO ids as xrefs.

Mammalian Phenotype Ontology
============================
Added new table mpo and populated with the Mammalian Phenotype Ontology
data.

Uberon
======
Added new tables uberon and uberon_xref and populated with the Uberon
ontology data. Added the new uberon_id column to the expression table
and populated all rows for which an Uberon ID could by found.

IMPC Phenotypes
===============
The phenotype table has been refactored to associate IMPC phenotypes to
mouse nhproteins. Mouse phenotypes from IMPC (those with statistical
results, but only those with p-value < 0.05) have been added to the
phenotype table (with foreign key nhprotein_id to nhprotein).

RGD Phenotypes
==============
Added new tables rat_term and rat_qtl and populated with rat phenotypes.

GWAS Catalog
============
GWas catalog data has been expanded and is now in the new table gwas,
not in the phenotype table.

GTex
====
GTex expression data has been expanded to include sex-specific values
and is now in the new table gtex, not in the expression table.

OMIM
====
Added new tables omim and omin_ps for MIM phenotypes and phenotype
series IDs and titles, respectively. Confidence confirmed (C) did not
mean what I thought it did in previous versions. TCRDv6 has all OMIM
phenotypes that are not provisional and not contiguous gene duplication
or deletion syndromes in which genes are involved

Gene Ontology Annotations
=========================
Added column assigned_by to the goa table.

STRINGDB
========
Protein-protein interactions from STRING have been added to the ppi
table (where ppitype = 'STRINGDB'). Added scores from STRINGDB to the
new column score in the ppi table.

Homologene
==========
Homology data from Homologene has been added to the new homologene
table. TCRDv6 now has homology data from Homologene and our in-house
generated homolog data in the ortholog table.

CCLE
====
Expression data from the Cancer Cell Line Encyclopedia has been added to
the expression table.

LINCS
=====
Added the new table lincs and populated with cell pertebation expression
data from LINCS.