************************************************** * * * 1.9.x SERIES NEWS * * * ************************************************** CHANGES IN AnnotationDbi VERSION 1.9.5 NEW FEATURES o An organism package has been added for Streptomyces coelicolor o extensive overhaul of inparanoid packages means that inparanoid packages now match to 100 different organisms o Extended support for ensembl mappings to yeast and flies. NOTEWORTHY CHANGES BETWEEN THIS version and 1.3.11 o 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. o 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 * * * ************************************************** CHANGES IN AnnotationDbi VERSION 1.3.11 NEW FEATURES o 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 o Added support for GO to canine and pig packages by using BLAST2GO (this data was not available from NCBI for these organisms). o ZFIN IDs are supported for Zebrafish packages. o Wormbase IDs are supported for C. elegans packages. o Uniprot IDs have been added to almost all package types. o 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 * * * ************************************************** CHANGES IN AnnotationDbi VERSION 1.3.9 NEW FEATURES o Support added for Malaria, Zebrafish, two strains of E coli, bovine and canine. ************************************************** * * * 1.1.7 SERIES NEWS * * * ************************************************** CHANGES IN AnnotationDbi VERSION 1.1.7 NEW FEATURES o Annotation packages now have a function to display basic quality control information. o 5 Inparanoid packages have been added for use in studies involving homology. o Ensembl gene ID maps have been added to all mammalian packages. o MGI IDs maps have been added for all Mouse packages. o 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). o Support has been added for PFAM so that there can now be a PFAM.db package. o AnnotationDbi is now compliant with the 1.0 schema definition.