*** THIS DIRECTORY HAS MOVED ***

As of July 2026, RGD ontology annotation files are no longer published in the
'annotated_rgd_objects_by_ontology' directory. They are now published in the
'annotations' directory:

    https://download.rgd.mcw.edu/data_release/annotations/

What changed:

1. LOCATION
   - GAF 2.2 files (the files that used to be in this directory) are now in:
        data_release/annotations/
   - "with terms" files (the files that used to be in the 'with_terms' subdirectory) are now in:
        data_release/annotations/with_terms/

2. FILE NAMES now use the RGD species SHORT NAME instead of the organism genus.
   For example, 'rattus_genes_go' becomes 'rat_genes_go'. This also removes a
   long-standing collision: rat and black rat annotations both used the 'rattus'
   genus prefix; they now use the distinct short names 'rat' and 'blackrat'.

3. FILE EXTENSIONS were added:
   - GAF files now end in '.gaf'
   - "with terms" (tab-delimited text) files now end in '.txt'

4. COMPRESSION: all files are now gzip-compressed and end in '.gz'.


FULL PER-SPECIES RENAMING BREAKDOWN
===================================

The old file-name prefix was the lower-cased organism genus; the new prefix is
the RGD species short name:

    SPECIES                     OLD PREFIX (genus)     NEW PREFIX (short name)
    -------------------------   --------------------   -----------------------
    Human                       homo                   human
    Mouse                       mus                    mouse
    Rat                         rattus                 rat
    Chinchilla                  chinchilla             chinchilla
    Bonobo                      pan                    bonobo
    Dog                         canis                  dog
    Squirrel                    ictidomys              squirrel
    Zebrafish                   danio                  zebrafish
    Pig                         sus                    pig
    Green Monkey (vervet)       chlorocebus            vervet
    Naked Mole-Rat (molerat)    heterocephalus         molerat
    Black Rat                   rattus                 blackrat


EXAMPLES (using rat)
--------------------

    GAF files (annotations/):
        OLD  annotated_rgd_objects_by_ontology/rattus_genes_go
        NEW  annotations/rat_genes_go.gaf.gz

        OLD  annotated_rgd_objects_by_ontology/rattus_qtls_rs
        NEW  annotations/rat_qtls_rs.gaf.gz

    "with terms" files (annotations/with_terms/):
        OLD  annotated_rgd_objects_by_ontology/with_terms/rattus_terms_go
        NEW  annotations/with_terms/rat_terms_go.txt.gz

        OLD  annotated_rgd_objects_by_ontology/with_terms/rattus_terms_rdo
        NEW  annotations/with_terms/rat_terms_rdo.txt.gz


For details on file formats, columns and ontology abbreviations, see the README
files in the new location:

    https://download.rgd.mcw.edu/data_release/annotations/README
    https://download.rgd.mcw.edu/data_release/annotations/with_terms/WITHTERMS_README

Questions: rgd.data@mcw.edu