XMLPipeDB / News: Recent posts

GenMAPP Builder 2.0 Beta 13 has been released. This release seeks to address an issue with due to leading/trailing spaces, which resulted in the elimination of a number of RefSeq IDs as well as the inclusion of leading/trailing spaces in system and relationship tables.

GenMAPP Builder 2.0 Beta 12 has been released. This release seeks to propagate ".n" version pruning to all segments that output IDs.

GenMAPP Builder 2.0 Beta 11 has been released. This release addresses a bug in beta 10 where IDs with leading spaces that need to have ".n" suffixes pruned were not processed properly and would cause an export to stop.

GenMAPP Builder 2.0 Beta 10 has been released. This version of GenMAPP Builder implements the following changes:
- Removal of ".n" version suffix from RefSeq IDs
- Replacement of template database with updated Systems table
- Unification of UniProt columns (through the new template database)
- Removal of extraneous .mdb file from the release

GenMAPP Builder 2.0 Beta 9 has been released. This release removes ".n" version numbers from TAIR IDs so that they get treated (and stored) identically when exported to a GenMAPP Gene Database file.

GenMAPP Builder 2.0 Beta 8 has been released. This release continues on-going adoptions to the latest GOA format, modifying regular expression group number used to extract UniProt IDs from the GOA content. The tally engine now also includes additional contexts within which a <dbxref> tag may appear in the GO OBO XML file.

GenMAPP Builder 2.0 Beta 7 has been released. This release modifies the regular expressions used to match UniProt and GO IDs in the GO associations file, to correspond to the latest terms, keys, and format for GOA.

GenMAPP Builder 2.0 Beta 6 is now available. This is a supporting-file-only update: all SQL schemas affected by changes in the most recent versions of UniProt's XSD and GO's DTD have now been synchronized to the new database code. Otherwise, it is identical to GenMAPP Builder 2.0 Beta 5.

GenMAPP Builder 2.0 Beta 5 is now available. This version updates UniProtDB and GODB to match the latest UniProt XSD and Gene Ontology OBO-XML DTD versions. The Gene Ontology OBO XML DTD was itself out of date (at least in terms of what is publicly available), and needed manual edits to match the latest downloadable GO term OBO XML file.

GenMAPP Builder 2.0 Beta 4 is now available. The release adds protein name and comment to the search space from which TAIR IDs are collected.

The first beta release of an Arabidopsis thaliana GenMAPP Gene Database is now available for download. Documentation is currently minimal, but the database file itself can be tried out.

GenMAPP Builder 2.0 Beta 3 is now available. The release fixes an issue with generating the temporary TAIR ID table and clusters some debug statements within an "if isDebugEnabled()" block.

GenMAPP Builder 2.0 Beta 2 is now available. The release improves upon the way that Arabidopsis Thaliana's TAIR IDs are collected from the XML source. More fields are taken into account, and parsing of IDs is improved for fields which may contain more information that just the ID itself.

This release builds on the previous alphas and not only fully supports Arabidopsis Thaliana export, but has the long anticipated Import speed improvement. This solution can take any size file and burns through about 3.9 entries per second (or 206 per minute) handling the 225MB A. thaliana file in about 3 hours. The code for the improved import is a generic solution in the new xmlpipedb utils release 2.1 (see that release) and is used as a library of this release.

GenMAPP.org has added Affymetrix probe set identifiers for all Affymetrix Escherichia coli microarrays (E_coli_2 Array, E. coli Genome Sense Array, E. coli Genome Antisense Array) to the 20060731 release of the E. coli K12 Gene Database. These
Affymetrix probe set identifiers were related to both UniProt and Blattner identifiers.

This version of the database is now available as Ec-K12-Std_External_20060731x.

This alpha fixes issues with the A. thaliana export caused by the uniqueness of the data. Some validation is still needed.

GenMAPP Builder 2.0 promises automated imports and exports, expanded species support including A. thaliana. Enhanced logging, testing and reporting features. And more.

GenMAPP Builder 2.0 promises automated imports and exports, expanded species support including A. thaliana. Enhanced logging, testing and reporting features. And more. This alpha has some of this capability already and is ready for you to extract and use!

The E. coli K12 has undergone a very minor revision, now reflecting a name change that is consistent with GenMAPP.org naming conventions, as well as including additional notes in its Read Me file.

Because of the nature of the changes, the original release has been replaced by this version. The gene database content itself remains the same.

Our first GenMAPP Gene Database release for is now available for download:

http://sourceforge.net/project/showfiles.php?group_id=158533&package_id=199426&release_id=436841

Today, we've release GenMAPP Builder version 1.0! With this software, you can create your own GenMAPP databases with the species of your choice (though we've only rigorously tested with e-coli). Download the zip, read the readme - Fire it up and have fun with those DNA micro-arrays!

XSD2DB has been released. After downloading, open the zip file and read the readme.txt for installation and usage instructions.