A Project of the LMU Bioinformatics Group
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XMLPipeDB

A Reusable, Open Source Tool Chain for Building Relational Databases from XML Sources

XMLPipeDB is an open source suite of Java-based tools for automatically building relational databases from an XML schema (XSD). XMLPipeDB provides functionality for managing, querying, importing, and exporting information to and from XML data with minimum manual processing of the data. While its applicability is fairly general, the original motivation for XMLPipeDB was to create a solution for the management of biological data from different sources that are used to create Gene Databases for GenMAPP (Gene Map Annotator and Pathway Profiler), software for viewing and analyzing DNA microarray and other genomic and proteomic data on biological pathways.

News

March 3, 2011

Helicobacter pylori str. 26695, Salmonella typhimurium ATCC 700720/SGSC1412/LT2, Mycobacterium smegmatis ATCC 700084/mc(2)155, and Updated Mycobacterium tuberculosis ATCC 25618/H37Rv GenMAPP Gene Databases Now Available

The XMLPipeDB project has released standard Helicobacter pylori str. 26695, Salmonella typhimurium ATCC 700720/SGSC1412/LT2, Mycobacterium smegmatis ATCC 700084/mc(2)155, and updated Mycobacterium tuberculosis ATCC 25618/H37Rv Gene Databases. Detailed information on these databases is contained in the included ReadMe files:

October 26, 2010

Mycobacterium tuberculosis ATCC 25618/H37Rv and Updated Vibrio cholerae O1 biovar El Tor str. N16961 GenMAPP Gene Databases Now Available

The XMLPipeDB project has released standard Mycobacterium tuberculosis ATCC 25618/H37Rv and updated Vibrio cholerae O1 biovar El Tor str. N16961 Gene Databases. Detailed information on these databases is contained in the included ReadMe files:

July 8, 2010

XMLPipeDB at Codefest 2010

Dr. Kam Dahlquist and Dr. John David N. Dionisio attended Codefest 2010, held in conjunction with BOSC and ISMB 2010 in Boston, Massachusetts.

May 21–22, 2010

Open Source, Open Science Pedagogy Talk at Beyond Bio 2010 Symposium

Dr. Kam Dahlquist and Dr. John David N. Dioniso presented a talk entitled “An Open Source, Open Science Pedagogy for Computational Biology” at the Beyond BIO2010 Symposium held at the National Academy of Sciences in Washington, D.C.

April 24–28, 2010

XMLPipeDB Posters at Experimental Biology 2010

Kelia McDonald, Bernadette Pak, and Kelly Parks presented posters at Experimental Biology 2010 in Anaheim, California:

April 21, 2010

Kelia McDonald Wins Honorable Mention in the LMU 2010 Undergraduate Library Research Award Competition

XMLPipeDB research group member Kelia McDonald has won Honorable Mention in the LMU 2010 Undergraduate Library Research Award competition for her wiki page, Extending XMLPipeDB to Create a GenMAPP-compatible Database for P. aeruginosa for the Analysis of DNA Microarray Data.

April 15, 2010

Pseudomonas aeruginosa str. PAO1 and Staphylococcus aureus (strain MRSA252) GenMAPP Gene Databases Now Available

The XMLPipeDB project has released standard Pseudomonas aeruginosa str. PAO1 and Staphylococcus aureus (strain MRSA252) Gene Databases. Detailed information on these databases is contained in the included ReadMe files:

September 3, 2009

Recently-Released GenMAPP Gene Databases Now Available Through GenMAPP.org

GenMAPP Gene Databases for Arabidopsis thaliana, Escherichia coli K12, Plasmodium falciparum, and Vibrio cholerae, created using XMLPipeDB, have now been made available at http://www.genmapp.org for automatic download by the GenMAPP program. GenMAPP users can access the new Gene Databases through the GenMAPP Data Acquisition Tool.

June 24, 2009

Vibrio cholerae O1 biovar El Tor str. N16961 GenMAPP Gene Database Now Available

The XMLPipeDB project has released a standard Vibrio cholerae O1 biovar El Tor str. N16961 Gene Database. Detailed information on this database is contained in the included ReadMe.

June 12, 2009

Arabidopsis thaliana GenMAPP Gene Database Now Available

The XMLPipeDB project has released a standard Arabidopsis thaliana Gene Database. Detailed information on this database is contained in the included ReadMe.

June 9, 2009

Plasmodium falciparum (isolate 3D7) GenMAPP Gene Database Now Available

The XMLPipeDB project has released a standard Plasmodium falciparum (isolate 3D7) Gene Database. Detailed information on this database is contained in the included ReadMe.

June 8, 2009

E. coli K12 GenMAPP Gene Database Update: 20090529

The XMLPipeDB project’s Escherichia coli K12 GenMAPP Gene Database has been updated to 20090529. This release is the first major update to the standard E. coli K12 Gene Database. The data are updated according to the Data Source and Version information contained in the included ReadMe. In this release, the following proper ID systems were added: GeneId (NCBI), RefSeq (protein), and W3110. Affymetrix probe set identifiers from the Affy table in the Ec-K12-Std_External_20060731x.gdb Gene Database were directly copied into this database without further annotation or verification of the data. Additional details are provided in the included ReadMe PDF.

June 5, 2009

XMLPipeDB Presence at ISMB, BOSC 2009

Dr. Dahlquist represented the XMLPipeDB group at ISMB and BOSC 2009. She talked about the latest XMLPipeDB developments on Saturday, June 27, from 5:15-5:30pm. Abstract details can be found here (PDF), while the rest of the BOSC schedule can be found here.

April 11, 2009

Schema Documentation Switch to Schema Spy

Our released, XSD-to-DB-generated relational database schemas for UniProt and GO have now been documented via Schema Spy. Visit our Documentation page to see them.

March 12, 2009

XMLPipeDB Presence at RECOMB-BE 2009

Current members of the XMLPipeDB group, including Drs. Dahlquist and Dionisio, will be attending the first RECOMB Satellite Conference on Bioinformatics Education (RECOMB-BE) from March 14-15, 2009, at the University of California, San Diego. We will be presenting three posters and attending various talks and panels, drumming up our ideas regarding undergraduate bioinformatics education. See you there!

June 23, 2008

SIGCSE Bulletin June 2008 Paper

ACM’s SIGCSE Bulletin has published our paper on how open source pedagogy was instrumental to the XMLPipeDB project. The article can be found here, with full citation details listed in the Publications page.

August 21, 2007

BOSC 2007 Slides Now Available Online

Slides from our two BOSC 2007 talks are now available online. They aren't file downloads, but “play back” directly within their respective pages:

Citation details for these presentations are available from the Publications page.

March 2, 2007

Affymetrix IDs Added to E. coli K12 Gene Database

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.

November 14, 2006

LMU Junior Faculty Seminar Presentation

The XMLPipeDB project, and the computer science courses that facilitated it, were presented at an interdisciplinary LMU junior faculty seminar today. Slides from the talk, entitled “Collaborating Early and Often: Bringing Biology and Computer Science Together Through an Open Source Culture” (4.7M PDF), are available from the Publications page.

October 23, 2006

Gladstone Visit

Drs. Dahlquist and Dionisio visited the GenMAPP group at the Gladstone Institute in San Francisco today. They presented the XMLPipeDB project and discussed possible points of collaboration.

September 28, 2006

Minor E. coli K12 Gene Database Update

For consistency with GenMAPP.org naming, the filename for the E. coli K12 Gene Database has been changed, and its Read Me file has also been revised. The data itself remains exactly the same.

September 25, 2006

ISMB/BOSC 2006 Materials Now Available

The XMLPipeDB poster (1.7M PDF) and talk slides (3.6M PDF) presented at ISMB and BOSC 2006, respectively, are now available for download as PDF files. Full citations can be found in the newly-added Publications page.

August 28, 2006

New URL: http://xmlpipedb.cs.lmu.edu

The LMU Computer Science lab infrastructure has undergone some upgrades; as a result, the new URL for the project’s home page is now http://xmlpipedb.cs.lmu.edu.

July 31, 2006

Escherichia coli K12 Gene Database Now Available

Our first GenMAPP Gene Database release for E. coli K12 is now available for download.

July 13, 2006

XMLPipeDB at BOSC and ISMB2006

Dr. Kam D. Dahlquist will give a platform presentation at the BOSC (Bioinformatics Open Source Conference) held in conjunction with the ISMB (Intelligent Systems for Molecular Biology) Conference in Fortaleza, Brazil, August 3-10, 2006. She will also present a poster at the main ISMB meeting.