CHANGES IN VERSION 1.41.1
------------------------

MODIFICATIONS

    o (v. 1.41.1) Convert OrganismDbi.Rnw to OrganismDbi.Rmd


CHANGES IN VERSION 1.32.0
------------------------

BUG FIXES

    o (v. 1.31.2) Remove deprecated org.Pf.plasmo.db info
    o (v. 1.31.1) Load OrganismDb objects even if not on search
      path. See https://support.bioconductor.org/p/134141/

CHANGES IN VERSION 1.18.0
------------------------

BUG FIXES

    o avoid duplicate factor levels during compression of metadata for 
      cdsBy and friends; previously introduced incorrectly empty metadata


CHANGES IN VERSION 1.16.0
------------------------

NEW FEATURES

    o add check for missing OrgDb package in .taxIdToOrgDb()

    o add 'orgdb' argument to makeOrganismDbFromBiomart()

MODIFICATIONS

    o modify error message in .taxIdToOrgDb()


CHANGES IN VERSION 1.14.0
------------------------

MODIFICATIONS

    o replace www.biomart.org with www.ensembl.org

    o import 'mcols', 'mcols<-' from S4Vectors

    o follow name change for GenomicFeatures:::.set_group_names()

    o add biomaRt, rtracklayer to 'Suggests'; used in unit tests/man pages

    o elementLengths was renamed -> elementNROWS in S4Vectors

    o replace require() with requireNamespace()

    o adjustments in response to the 'vals' -> 'filter' renaming 
      in GenomicFeatures

    o update unit tests to reflect new PFAM data

    o load RSQLite in unit tests; no longer free from 
      AnnotationDbi::dbFileConnect

    o use newly exported functions from AnnotationDbi related to select() 
      and building annotation packages


CHANGES IN VERSION 1.10.0
------------------------

NEW FEATURES

    o OrganismDb objects now have methods for most reasonable TxDb methods.  
    If you can do it with a TxDb, it should also work for an OrganismDb.

    o Supports dbconn() and dbfile()

    o Exports getTxDbIfAvailable() for those who may want convenient access to 
    the underlying TxDb object.
 
BUG FIXES

    o use.names arguments now work with exonsBy and related methods.


CHANGES IN VERSION 1.4.0
------------------------

NEW FEATURES

    o genes method now works on these objects
 
BUG FIXES

    o safer argument handling for 'by' arguments on accessors that use it.


CHANGES IN VERSION 1.4.0
------------------------

NEW FEATURES

    o keys method now has new arguments to allow for more
    sophisticated filtering.

BUG FIXES

    o cols arguments and methods will now be columns arguments and methods

    o stricter argument checking for select and friends


CHANGES IN VERSION 1.2.0
------------------------

NEW FEATURES

    o There are now range based accessors (transcripts, exons, cds)
    that can be used to get data out of OrganismDb objects. 

    o There are now list oriented range based accesors (transcriptsBy,
    exonsBy, cdsBy) that can be used to get data out of OrganismDb
    objects

    o All these new ranged based operations allow users to extract
    additional metadata via mcols slot in the resulting object.  The
    extra data is specified via the columns argument to these methods.

SIGNIFICANT USER-VISIBLE CHANGES

    o New range based accessors allow you to get data back organized
    by range.  Please see associated manual pages and vignette for
    more details.


BUG FIXES

    o Show method for these objects is improved.

    o Documentation, tests and vignette updates for new methods.



CHANGES IN VERSION 1.0.0
------------------------

NEW FEATURES

    o OrganismDbi is for the creation and support of a new class of
    super-annotation packages

    o 'Stock' OrganismDbi packages are available for human mouse and
    rat with the 2.11 release of Bioconductor.

    o OrganismDbi has functionality for generating these packages.

    o OrganismDbi has methods that allow these packages to function.

    o OrganismDbi works by combining resources from Annotation
    packages that implement the four methods needed for a "select"
    style interface.  The essense of this is detailed in the
    AnnotationDbi package, along with base classes etc.
