• XML - biology links
• XML - biology obsolete links
• XML general resources
• SOAP - biology links
• Examples

• XML for Molecular Biology by Paul.Gordon (a reference list).
• search XML in the BioNetbook
• BSML.
• XML at Bioperl.
• Proteome Template Library
• BioDOM
• XML Cetus links
• Working with XML by Eric Armstrong
• XOL (Ontology Exchange Language)
• Taxonomic Markup Language: applying XML to systematic data
• XML in biology links (in japanese)
• Array XML Working Group (unofficial website of the microarray-format working group)
• xml-mol mailing list
• Paper "Bioinformatics and Extended Markup Language" (OJB)
• XEWA: XML-Enabled Wide Area Search in Bioinformatics.
• XML in Python (in German).
• NETTAB (Network Tools and Applications in Biology): CORBA and XML: Towards a Bioinformatics Integrated Network Environment.
• SubmitData: An XML-based Data Submission Tool (OiB99).
• Entrez output (example)
• MSAML: An XML for Multiple Sequence Alignments
• GEML;
  • Pattern.dtd
  • Profile.dtd
  • feedmag.com
• CellML.
• Known XML work related to biodiversity.
• XML/BioXML Resources for Databases.
• phyloML: phylogenetic trees, by Tom Royce.
• Systems Biology Markup Language (SBML).
• Cellular Models in SBML by H. M Sauro.
• Gepasi and SBML.
• STOCHSIM a stochastic simulator of (bio)chemical reactions.
• Pir/XML.
• XML, bioinformatics and data integration, Fr¨ŒøL¦ŒðLd¨ŒøL¦ŒðLric Achard, Guy Vaysseix and Emmanuel Barillot, Bioinformatics Vol. 17 no. 2 2001.
• XEMBL: EMBL/Genbank/DDBJ Nucleotide Sequences as XML.
• SP-ML, the SWISS-PROT/TrEMBL XML Format.
• AGAVE.
• DAS (XML encoded annotation and sequence messages as result, see specification).
• PROXIML (PROtein eXtensIble Markup Language).
• Petri nets and XML in Bioinformatics.
• BioNOME.
• A Comparison of AGAVE and GAME Genomic Annotation XML (PDF).
• DAML Ontology Library.
• The Clone Annotation DTD
• StarDOM: a software package to transform data provided in the Self Defining Text Archival and Retrieval (STAR) format into XML.
• BioMagResBank/XML: BioMagResBank transformed into XML format. Text Archival and Retrieval (STAR) format into XML.
• ToppredXML: An XML/perl parser for the toppred program.
• RNAML: syntax for exchanging RNA information.
• XML.com: Work being done with XML in the field of Bioinformatics.

• bioxml.org.
• GAME, Genome Annotation Markup Element.
• BIOML (example: blastxml.dtd) (slides at OiB99).
• XFF: An Extensible Feature Format proposed by Thomas Down.

• XML.com
• Perl XML Quickstart.
• XML and databases.
• cours de St¨ŒøL¦ŒðLphane Bortzmeyer
• O'Reilly XML Center

• Blast Web Service, Duke Bioinformatics: Blast service inovek via SOAP messages, with XML result.
• XML vs CORBA, by Alan Robinson, EBI.
• SOAP as the standard transport encapsulation for DAS/2 messages.
• XEMBL SOAP perl client (see Is there a Web Service/SOAP server I can use? on XEMBL page).
• Embreo: the primary implementation uses a Java client using SOAP to communicate with a CGI-based perl server using SOAP::LITE (see why).

Maintainted by Wu Xin, CBI, Peking University, China, 2003