The file contains few notes about the changes in this directory. Should you
find something unclear, or buggy, please send an email to rgd.data@mcw.edu.
Thank you!   -- RGD Developers

Beginning 2017, publication of HPRD ids has been discontinued, because these external db ids have been discontinued at NCBI.
No longer these ids will be found in the generated files.
However, the full dump of RGD objects associated with these ids has been made
and the file ftp://ftp.rgd.mcw.edu/pub/legacy_data/HPRD_IDS.txt has been created and made available.

October 2014 - consolidated FTP files for genes, qtls, sslps and strains, as follows:
  RAT
  - Additional columns added to GENES_RAT.txt, QTLS_RAT.txt and SSLPS_RAT.txt files
    to accommodate position data for the 6.0 assembly, and in the case of GENES_RAT.txt,
    the 5.0 assembly, so that all position data for reference assemblies that are currently
    in use (i.e. RGSC Genome Assemblies v3.4, v5.0 and v6.0) are available in a single file for each data type.
  - GENES_RAT_5.0.txt and GENES_RAT_6.0.txt files are retired
  - New columns added to the STRAINS.txt file and new tag fields added to the STRAINS.xml file to supply position
    data for congenic and mutant strains for which such data exist.
  MOUSE
  - Additional columns added to the GENES_MOUSE.txt, QTLS_MOUSE.txt and SSLPS_MOUSE.txt files
    to accommodate position data for all available reference builds (Mouse Genome Assembly Builds 36, 37 and 38).
  - QTLS_MOUSE_B38.txt and GENES_MOUSE_B36.txt files retired
  HUMAN
  - Additional columns added to the GENES_HUMAN.txt, QTLS_HUMAN.txt and SSLPS_HUMAN.txt files
    to accommodate position data for all available reference builds (Human Genome Assembly Builds 36, 37 and 38).
  - GENES_HUMAN_B38.txt file retired

In October 2013, publication of PID ids has been discontinued.
No longer these ids will be found in the generated files.
However, the full dump of RGD objects associated with these ids has been made
and the file ftp://ftp.rgd.mcw.edu/pub/legacy_data/pid_ids.txt.gz has been created and made available.

As of August 5, 2013, four new columns are added to STRAINS.txt file:
AVAILABILITY, RESEARCH_USE, ALLELES, and ALLELE_RGD_IDS. Existing columns
will remain unchanged. STRAINS.xml file is similarly updated.

In May 2013, publication of IPI ids has been discontinued.
No longer these ids will be found in the generated files.
However, the full dump of RGD objects associated with these ids has been made
and the file ipi_ids.txt has been created and made available.

As of July 10, 2011 generation of RGD_ORTHOLOGS file has been discontinued and
the pipeline retired. The file won't be updated any longer. RGD_ORTHOLOGS.txt
file will be generated instead on weekly basis - apart from detailed header,
the contents will be identical like in the old file.

In July 2011, new set of files with annotated object by ontology has been
created and it will be updated on weekly basis. The original set of files,
found in annotated_rgd_objects_by_ontology directory, is in gaf 2.0 format. In
the subdirectory 'with_terms' you can find the new set files in custom format.
For example, in addition to ontology term accession ids, you will find a
column with the ontology term names.

In April 2011, publication of RATMAP_IDs and RHDB_IDs has been discontinued.
No longer these ids will be found in the generated files. However, the full
dump of RGD objects associated with these ids has been made and the files
ratmap_ids.txt and rhdb_ids.txt has been created and made available.

RGD-based ontology files in obo format: clinical measurement, experimental condition, measurement method,
pathway and rat strain, are found in ftp://ftp.rgd.mcw.edu/pub/ontology/ as of March 15, 2011.