GNAT / News: Recent posts

New human dictionaries can now be found in the data folder, to replace earlier versions. Please make sure to delete all old files from the "dictionaries/9606/" folder: dictionaries data are split into multiple files, bearing the same naming scheme between GNAT versions, and therefore problems with existing files may arise should you keep them in the same folder.

We have just posted a new binary release. The Java JARs and BASH scripts in this release are meant to seemlessly replace the corresponding files in the full release 1.22. Check the "Files" menu to download this binary release 1.3.

We are working on an updated release of the gene annotation database and dictionaries.

• Dictionaries will reflect the latest gene names from NCBI Entrez Gene
• Annotation database will reflect latest data from NCBI Entrez Gene and UniProt KB.
• There will be minor changes to the database schema.
• The release will contain methods to update GNAT's annotation database yourself
• Methods to update dictionaries or create new ones can already be found in the library; also seee examples in the scripts/makeDictionaries/ folder

GNAT now comes with a pipeline that annotates genes as inline XML; can read Medline/Pubmed article sets (incl. Medline FTP files such as "medline12n0001.xml.gz"). Main class: JustAnnotateInline.

Uploaded a new version of the backend SQL database (1.2). Added GO codes/terms and GeneRIFs.