NEWS

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AnnotationDbi 1.54.0

NEW FEATURES

• There is a new replacement package for the Inparanoid orthology packages, called Orthology.eg.db
• This package uses NCBI orthology data to map NCBI Gene IDs between species using the usual select() interface

MODIFICATIONS

• UniGene data have been removed from OrgDb and ChipDb packages
• Gene type data have been added to OrgDb and ChipDb packages

AnnotationDbi 1.53.0

NEW FEATURES

• organismKEGGFrame() provides a data.frame of species names and KEGG orgs

MODIFICATIONS

• Conversion from KEGG.db (which was deprecated) to KEGGREST - This involved changing how KEGG Ids checked when creating a KEGGFrame object.
• Removal of any use of Inparanoid data/structures since the hom.*.inp.db packages have been removed. The data is extremely outdated and there is no replacement for it. - Removed the InparanoidDb object and all of the methods

AnnotationDbi 1.36.0

BUG FIXES

• fix bug in dbschema method for DBIConnection objects
• keys() no longer fails when global variable 'y' exists

AnnotationDbi 1.34.0

NEW FEATURES

• export ALIAS2EG symbol in NAMESPACE for frog, mosquito, chimp and rhesus OrgDbs
• add how to use EnsDb section to vignette

MODIFICATIONS

• work on code base and exported functions - break up code in geneCentricDbs file - re-name and export functions used by select() in AnnotationForge and GenomicFeatures - re-name and export functions used by annotation package builders in AnnotationForge
• remove library(RSQLite) from dbFileConnect()
• modify unit tests for new PFAM identifiers in Bioconductor 3.3
• use elementNROWS() instead of elementLengths()
• modify mapIds() to preserve data type returned from select()
• reduce time of AnnDbPkg-checker.Rd example

BUG FIXES

• bugfix for select() and mapIds() when there are many:many mappings
• bugfix in test_generateExtraRows unit test.

AnnotationDbi 1.32.0

BUG FIXES

• maps between chip and org packages work with loaded but not attached packages.

AnnotationDbi 1.31.0

NEW FEATURES and API changes

• columns() and keytypes() sort their return values.
• ls() on a Bimap option returns keys in sort()ed order, by default

AnnotationDbi 1.30.0

NEW FEATURES and API changes

• Adds mapIds() which allows users who miss mget() to extract data from AnnnotationDb objects: but without the dangers of using mget() (which fails if you pass in a bad key)
• Adds dbconn() and dbfile() methods to the list of things that AnnotationDb derived objects shoould always be expected to support

BUG FIXES AND CODE MAINTENANCE

• loadDb() now is smarter about whether or not it attaches a supporting package

AnnotationDbi 1.24.0

NEW FEATURES and API changes

• keys method now has new arguments to allow for more sophisticated filtering.
• cols method is now the columns method to make for a more constistent interface.
• cols argument is now the columns argument (for select) to also make the interface consistent across all use cases

BUG FIXES AND CODE MAINTENANCE

• better argument checking for select and related methods
• keys that end with ' will no longer cause grief except to hapless life scientists who will still have to wonder who in their right mind thinks it's a good idea for a gene symbol to be the same except end with a 'prime'.

AnnotationDbi 1.22.0

NEW FEATURES

• There is now a convenience function for extracting data from the GO.db package as a graph object. The function is called: makeGOGraph.
• Adds supportedSeqnameMappings() and findSequenceRenamingMaps() utilities.
• Improved vignette for new users

BUG FIXES AND CODE MAINTENANCE

• Fixes a bug in select for users accessing reactome.db
• Fixes a bug in select for users requesting via a PROBEID
• Fixes a bug in select for users using rat chip packages
• Fixes a bug in mget, for Bimap objects (when ifnotfound=NA) * * * 1.20.x SERIES NEWS * * *

AnnotationDbi 1.20

NEW FEATURES

• There is a new introductory vignette for AnnotationDbi. It explains how to use the new simplified select method interface and also describes how developers can implement their own select interfaces for exposing new annotation resources.
• select support has been added for both the inparanoid and reactome.db packages. These are in addition to existing support for all ChipDb, OrgDb, and TranscriptDb packages. GO.db also has a select interface.
• Code has been added to enhance backwards compatibility between select and bimaps. The aim here is that old code that uses bimaps should still work with packages that have the same kind of data exposed using only a select() interface.

SIGNIFICANT USER-VISIBLE CHANGES

• AnnotationDbi has been split up and simplified. All code needed for building and supporting new packages has been moved to a new package called AnnotationForge. The remaining code is what is needed to support day-to-day interaction with the Annotation interface.

BUG FIXES AND CODE MAINTENANCE

• The code for generating bimaps has been simplified and overhauled.
• The code for making manual pages in annotation packages has been simplified so that there will be far less redundancy
• The select(), cols, keys, and keytypes methods saw several bug fixes and a code overhaul to enhance both speed and reliablity. * * * 1.16.x SERIES NEWS * * *

AnnotationDbi 1.16

NEW FEATURES

• New Object types: Org.Db, ChipDb, GODb. These are loaded when an Annotation package is loaded.
• select method for these new objects to extract data.frames of available annotations. Users can specify keys, along with the keytype, and the columns of data that they want extracted from the annotation package.
• keys now will operate on new objects to expose most ID types as keys
• keytypes will show which kinds of IDs can be used as a key by select
• cols will display the kinds of data that can be extracted by select
• Users who need organism packages for organisms that are annotated at NCBI can now use makeOrgPackageFromNCBI() to generate a basic organism package on the fly

SIGNIFICANT USER-VISIBLE CHANGES

• New objects are always named after the package that loaded them. So if you just loaded the hgu95av2.db package, your ChipDb object will be called hgu95av2.db
• new fields are now required in the metadata table of annotation packages to allow the on-the-fly creation of these new objects. If you are constructing a custom package and want to extend this infrastructure, you may need to add some fields to the metadata table.

BUG FIXES

• makeProbePackage, and other generated Annotation packages have had templates modified so that packages can load and also to enable loading of new objects to allow new features in this release.
• updated GOFrame constructor to allow use of new types of evidence codes.
• generated packages will create databases with the appropiate metadata entries for the new objects. * * * 1.9.x SERIES NEWS * * *

AnnotationDbi 1.9.5

NEW FEATURES

• An organism package has been added for Streptomyces coelicolor
• extensive overhaul of inparanoid packages means that inparanoid packages now match to 100 different organisms
• Extended support for ensembl mappings to yeast and flies.

NOTEWORTHY CHANGES BETWEEN THIS version and 1.3.11

• All chip packages now depend on org packages. This simplifies the schema and also allows for more convenient updating of these packages and smaller downloads for users.
• chip package mappings that contain probes which map to multiple targets are now hidden by default, with the ability to be exposed when required. See the use of the new toggleProbes() method. * * * 1.3.11 SERIES NEWS * * *

AnnotationDbi 1.3.11

NEW FEATURES

• Support has been added for 3 more organisms, this means that the current list of supported organisms as of 1.3.11 is the following: Arabidopsis thaliana Bos taurus Caenorhabditis elegans Canis familiaris Drosophila melanogaster Danio rerio Escherichia coli K12 Strain Escherichia coli Sakai Strain Gallus gallus Homo sapiens Mus musculus Plasmodium falciparum Rattus norvegicus Saccharomyces cerevisiae Sus scrofa
• Added support for GO to canine and pig packages by using BLAST2GO (this data was not available from NCBI for these organisms).
• ZFIN IDs are supported for Zebrafish packages.
• Wormbase IDs are supported for C. elegans packages.
• Uniprot IDs have been added to almost all package types.
• CHRLOCEND mapping has been added which give gene end positions for almost all packages and compliments the CHRLOC mapping which already provides the start positions. * * * 1.3.9 SERIES NEWS * * *

AnnotationDbi 1.3.9

NEW FEATURES

• Support added for Malaria, Zebrafish, two strains of E coli, bovine and canine. * * * 1.1.7 SERIES NEWS * * *

AnnotationDbi 1.1.7

NEW FEATURES

• Annotation packages now have a function to display basic quality control information.
• 5 Inparanoid packages have been added for use in studies involving homology.
• Ensembl gene ID maps have been added to all mammalian packages.
• MGI IDs maps have been added for all Mouse packages.
• Protein to gene mappings have been added to appropriate organism based packages so that it will be possible to get from the IDs in the inparanoid packages to a gene based ID for the 5 main organism types (ie. Human, Mouse, Rat, Fly, Yeast).
• Support has been added for PFAM so that there can now be a PFAM.db package.
• AnnotationDbi is now compliant with the 1.0 schema definition.