XML for Molecular Biology as compiled by Paul Gordon

For my past and present research work, please see my homepage.
My most current work on XML in Bioinformatics integration is Moby Web Services creation tool called Daggoo.

I've collected here a list of XML resources that may be of use to the bioinformatician. If you have anything to add, or any comments/corrections, please don't hestitate to contact me (gordonp@ucalgary.ca).

• AGAVE - An Architecture for Genomic Annotation, Visualization and Exchange from the AGAVE Community lead by DoubleTwist.
• BIOML - Proteometric's attempt to describe nucleotide and peptide sequences, and they've got a nice browser.
• Bioseq-set - Output format for XML option in readseq
• BSML (data only or full) - LabBook.com's attempt to describe all sorts of molbio information. The latter version contains presentation elements for their browser.
• chadoxml, a yet to be released xml version of the forthcoming Generic Model Organism Database Consotium's database schema.
• clone-annotation - Ole Bents' (formerly of MIPS, now at SD&M) specification of clone annotation elements
• DAS - The one with the strange acronym, the Distributed Sequence Annotation System that is a sort of Napster for annotations. At this point it has several browsers. It has several DTDs, for data source documents(DSN), sequence entry points (SEP), DNA data (DNA), seq and annotation resolving (RES), annotation types (TYPES), features (GFF), and style (STYLE).
• DDBJ-XML - a format for the Database Japan resources, complemented by WSDL and SOAP transaction features at thesame Web site.
• GAME - UC Berkeley derived series of Genome Annotation Markup Elements DTDs
• MaxML - A RIKEN developed format for mouse annotation
• RNAML - born of widespread community collaboration, it is a language to describe the structure and sequence on RNA molecules.
• TIGRXML - the format in which TIGR annotations are distributed, e.g. Arabidopsis.
• XFF - An Extensible Feature Format proposed by Thomas Down.

Protein Specific

• abML - an antibody description language
• InterPro - An integrated documentation resource for protein families, domains and functional sites is available in XML format.
• PSAML - description language for protein secondary structure and relationships
• ProteinDatabase - The PIR database is downloadable in XML format, as are individual entries when that format is selected from their search page.
• PROXIML - The PROtein eXtensIble Markup Language by Douglas C. McArthur, which is still in the works at the moment.
• SP-ML - An XML representation of SwissProt records

Analysis

• BlastOutput - Format of the output of the new web blast package from NCBI
• BlastXML - Description of Basic Local Alignment Search Tool output. Developed for Working Objects' PharmTools SDK.
• BTKML - The XML format used by the BioView Toolkit that runs on Paracel's GeneMatcher.
• phyloML - A nascent language for encoding phylogenetic trees.
• PISE - Catherine Letondal's XML interface to her PISE (molecular biology) application interface generator.
• Seq-entry - The XML format for data returned from Entrez, here's an example of what the query URL must look like.

Physical

• CML - Chemical Markup Language for describing molecules and reactions. Used in lots of stuff, like Jumbo.
• EML - Markup language for the E-CELL project. They are interacting with the SBML people and have XSLT to transform between the two.
• MoDL - Indian Institute of Science developed Molecular Dynamics Language for animated chemical simulations (may be neat for protein interaction and metabolic pathways). It has VRML converters and a Java client.
• Petri Net Markup Language - Ming Chen has proposed encoding metabolic pathways as Petri nets in XML. I don't really know much about the status of this. But, genomicobject.net is using an XML format for display of Petri net information.
• Physiome Markup Languages - Being developed by the University of Auckland and collaborators. Includes markups for cells, gross anatomy, and time/spatially varying fields.
• SBML - The CalTech Systems Biology Workbench Development Group formulated Systems Biology Markup Language
, used to "...[specify] a common, model-based description language for systems biology simulation software".

Expression (old, many supplanted by GEML)

• eXpressML - Folks from the IBM India Research Lab's attempt to provide a common format for gene expression annotation (sits on top of experimental data provided by GEML, etc.)
• GEML - NCGR's gene expression markup language once upon a time vying to be the Array XML Working Group's standard, used in GeneX
• GEML Pattern & Profile - Another one! (unrelated I think) Rosetta Inpharmatics' OMG "Life Science Research" domain task force inspired file format for storing DNA microarray and gene expression data
• GEO-XML - NCBI's soon-to-be-active Gene Expression Omnibus data submission format. Hmm, not sure how this relates to MAGE-ML
• MAGE-ML - The latest consensus for microarray expression data that will be soon submitted to the OMG. The web site hasn't been updated in a while, but you can join the mailing list.

Taxonomy/Ontology

• DAML - An ontology definition language, this site includes some biological ontologies (list by keywords).
• GO - A vocabulary for gene/protein knowledge by the Gene Ontology Group, Berkeley has a cool browser too. It remains to be seen how this relates to OML/CKML and Ontolingua as being investigated by the OMG LSR. Or even SHOE for that matter.
• OIL - The Ontology Inference Layer based on Resource Description Framework (RDF). The trend seems to be to combine this with DAML for rich ontology definition. The new site for applyingthis to GO is here.
• sys (TML) - Ron Gilmour's markup elements for taxonomy, with examples here..
• StarDOM - The Self Defining Text Archival and Retrieval format (used by PDB for example) converted into XML, exemplified by a BioMagResBank/XML conversion application at EMBL.
• SpeciesAnalyst project has an experimental XML stream for querying their species specimen database
• Troeps - An object-based knowledge representation system being developed at INRIA, they have protein information examples.
• XDELTA - an XML formatting of the DEscription Language for TAxonomy.
• XOL - An ontology exchange language by some folks at SRI. XML Schema is going to be much more useful I think.

Miscellaneous

• ArticleSet - PubMed now offers XML formatted versions of medical abstracts.
• The BioMOBY project, which deals with lightweight data interoperation and service discovery in bioinformatics, is developing XML Schema-based objects for interchange.
• BioNOME - The San Diego Supercomputer Center's two simple DTD's (lookup and dataset) for the bio-computational models and observational data they are trying to capture.
• GPML, GENIA Project Markup Language used to annotate the admirable Genia medline abstract corpus (corpus = collection of writings used for linguistic analysis).
• A company called LabBook has an XML based lab book and genomic data suite. Bob Rumpf has updated me, and says that the "DTD available for download free of charge, as well as a Genomic Viewer which takes Genbank files, converts them to XML, and visualizes them as an interactive unit. The Viewer is a freeware version of our commercial package, the Genomic Browser, which has many significant enhancements and adds functionality not found in the Viewer".
• LinkOut - specification format for the NCBI's LinkOut provider services
• NCBI now in fact has a whole slew of DTDs generated from ASN.1 specs for MMDB, Medline, etc.
• XDF - A scientific extensible data format which is being uised as the basis for other XMLs, and has an API in several languages. Key features are a hierarchical data storage, and easy wrapping of tagged, multi-dimensional data.
• XMLMARC, a Standford project encoding MARC bibliographic records as XML. Has an open source API.
• XSIL - Folks at CACR CalTech have made a dubiously (IMHO) useful Extensible Scientific Interchange Language to store hierarchical data. Compare with GXD - 'a "lingua franca" for scientific information'.

Generic

• SVG in stylable or exchange mode - W3C's vector/raster XML compliant file format, the future of Web graphics, and maybe useful in Bluejay eventually. Actually, Malay Basu has beaten me to the punch with his Savvy Plasmid Map Generator. Good work! Adobe has a browser plug-in.
• XHTML - W3C's XML form of HTML 4.01. Not specific to biology, but very useful for text documents.

• Omnigene, a Java ensembl viewer being developed with the people at Whitehead; DASified.
• Bluejay: coming soon, a generic XML graphical browser tailored to plotting data on a linear scale (e.g. DNA)

• Kaiser Yang has a great site showing XML transformations between biological markup languages, something we're doing in Bluejay too.
• XEMBL , an EBI project to make their data available in XML format. At last check this included BSML and AGAVE.
• Proteometrics' Proteome Template Library
• Alan Robinson's XML Workshop for biological data

• Stylus Studio is the industry-leading provider of XML tools and components for advanced data integration.
• A genbank to XML converter by Phillipe Bouige
, using the PISE interface generator. You can use SRS entries or local files.
• BioDOM - Document Object Model software for molbio database information
• XML modules for Perl
• Diff and merge tools for XML from IBM
• A Web interface for DTDGenerator, a program that generates a DTD given an XML document. Handy.
• XEmacs in PSGML mode using SGMLS... validates your documents, dtds, gives you valid tags...

• BioXML

XML reference materials (local)

Please note that it is ill advised to base software on W3C reports until they are recommendations. So far there are five.

• XML 1.0 W3C Recommendation
• XML Stylesheet Language Transformations (XSLT) W3C Recommendation
• XML Path Language (XPath) W3C Recommendation
• Namespaces in XML W3C Recommendation. Read a great line from the press release.
• Associating Stylesheets with XML Documents W3C Recommendation
• RFC on XML Media Types (for MIME encoding)
• RFC on Remembrances of Things Past. Hey, not XML, but still interesting!