LabBook is now making the specification for its BSML (Bioinformatic Sequence Markup Language) format freely available in an effort to support the standard in the life science community.
BSML is an open XML data format that the company is promoting as an answer to the industry’s data integration woes.
LabBook is also making its Genomic XML Viewer — which combines the BSML standard with a limited XML browser — freely available.
The format works on two levels. It first encodes the bioinformatic data, such as sequences, sets, sequence features, analytical outputs, relationships, or annotations, so that it can be integrated and shared.
The second aspect — and what sets BSML apart from other formats, according to the company — is its display capability, which permits visual representation of the defined objects while keeping the underlying semantic content intact.
Researchers will be able to exchange information through Genogram, an XML/BSML e-mail that is created and read either with the viewer or the company’s Genomic XML Browser, an enhanced version of the viewer.
The company is already selling the browser and software based on BSML. It also plans to develop “XML converters” that will integrate disparate data. The converters will work with GenBank flat files, EMBL formats, SwissProt, and other formats.
Joseph Spitzner, LabBook’s vice president of technology, told BioInform that the company’s strategy for the BSML product line is similar to Adobe’s suite of Acrobat products. “You have a viewer and then you have other software that can create documents, perform analyses on the sequence data, and so on,” he said.
“The viewer will let you go right out onto Entrez, do a search, download a GenBank document and convert it on the fly to a BSML document to visualize it. That’s free.”
Further capabilities, such as a pattern search on the document, would require additional LabBook software.
XML is coming into its own as the language of choice for data migration between programming languages. Proponents claim it can handle the representation and network transmission of rich structured data far better than HTML and other formats.
“HTML doesn’t really give you access to the underlying semantics,” Spitzer said. “Our browser maintains all the active links to the underlying information.”
Spitzner declined to comment on how BSML differs from other bioinformatics XML efforts, such as bioXML.
LabBook created BSML under a 1997 grant from the National Human Genome Research Institute. The language specification (BSML DTD version 2.2) and the Genomic XML Viewer can be freely downloaded from LabBook’s web site (www.labbook.com).
LabBook plans on releasing additional XML-based life sciences research tools and XML converters in February.
— Bernadette Toner