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.
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:
- Helicobacter pylori str. 26695
- Salmonella typhimurium ATCC 700720/SGSC1412/LT2
- Mycobacterium smegmatis ATCC 700084/mc(2)155
- Mycobacterium tuberculosis ATCC 25618/H37Rv
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:
- Extending XMLPipeDB to Create GenMAPP-compatible Gene Databases for the Analysis of DNA Microarray Data from Human Pathogens
- Extending XMLPipeDB with GO Slim to Update the GenMAPP-compatible Gene Database for Budding Yeast, Saccharomyces cerevisiae, for the Analysis of DNA Microarray Data
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
June 12, 2009
Arabidopsis thaliana GenMAPP Gene Database Now Available
June 9, 2009
Plasmodium falciparum (isolate 3D7) GenMAPP Gene Database Now Available
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
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:
- An Open Source Framework for Teaching Bioinformatics
- XMLPipeDB: A Reusable, Open Source Tool Chain for Building Relational Databases from XML Sources
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
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.