[January 10, 2001] In January 2001, LabBook Inc. announced the availability of BSML (XML DTD) version 2.2. "BSML is an extensible language specification and container for bioinformatic data. BSML was developed under a 1997 grant from the National Human Genome Research Institute (NHGRI) as an evolving public domain standard for the bioinformatics community. The objectives of LabBook are to offer BSML and other XML data formats for effective management, communication, and interactive visualization of bioinformatic data." Background: "Genome research projects typically involve a variety of data (sequences, annotations, analysis results, database links, graphical images, etc.) that may be distributed over multiple storage locations and networks. Creation, management, analysis, and communication of these data often require the use of various computer software applications and databases that utilize non-interchangeable data formats. The lack of standards in bioinformatics is a serious obstacle to productivity. Other obstacles include the loss of information content and state by transmission of data in HTML, and a lack of persistence in bioinformatic analyses and searches because the results are simply pictures in viewers."
[April 12, 2000] The proposed Bioinformatic Sequence Markup Language (BSML) is a public domain protocol for Graphic Genomic Displays. The project goals are in some respects similar to those of the Chemical Markup Language. According to the RFC document of December 1997, which specifies a public domain standard for the encoding and display of DNA, RNA and protein sequence information, this markup language is to be based upon SGML and XML: "BSML is written to conform with the XML standard." Goals in the enoding project are to "describe the features of genetic sequences, describe the features of graphic objects used to represent sequence features, determine procedures for assigning graphic objects to sequence features, and determine how to store and transmit encoded sequence and graphic information." BSML is a TopoGEN project, funded by an SBIR [Small Business Innovative Research] from the National Center for Human Genome Research, to develop the public domain protocol. The SBIR with which this project is associated has Joseph Spitzner, Ph. D. (TopoGEN Software Director) as its Principal Investigator.
[July 27, 1999] "VGI Releases Free BSML Basic Browser for Biotech Research." - "Visual Genomics, Inc. (VGI) announced today the release of BSML Basic Browser. This browser is the first in a family of products to bring visual management, analysis, presentation, and communication of the ever increasing amount of bioinformatics data to genomics researchers. Using Bioinformatics Sequence Markup Language (BSML), an open XML standard developed by VGI and sponsored by National Human Genome Research Institute, the BSML Basic Browser's graphical user interface is a gateway to the visualization, analysis, presentation and communication of genomic data. All information underlying the graphical presentation is contained within the BSML document, allowing the user to drill-down through the data to any level of resolution, from the chromosome to the base pair. Dynamic, interactive datamining is made easy by the intuitive 'point and click' visual display. An indispensable bioinformatics tool, the Basic Browser displays BSML documents and even imports gene sequences from local or remote repositories such as GenBank. The Browser is Internet enabled, dynamically loading document references as needed from throughout the world-wide genomics community, including built in access to NCBI's Entrez. Both the BSML Basic Browser and the BSML DTD (documentation) are free when downloaded from the company's WEB site."
XML Data Standard for Genomics: The Bioinformatic Sequence Markup Language (BSML) DTD and the Genomic XML Viewer
XEMBL Public BSML Document Server: access EMBL in BSML Format at the European Bioinformatics Institute
[November 26, 2001] "Fujitsu Endorses the BSML Standard for Biological Information. Fujitsu Will Use BSML as the XML-based Specification for Bioinformatic Data Integration." - "Fujitsu and LabBook, Inc., today announced that Fujitsu has endorsed the BSML standard for communicating genomic information. Fujitsu joins a rapidly growing list of organizations supporting the open BSML standard for genome research. Among the others are the EMBL's European Bioinformatics Institute (EBI), IBM, Bristol-Myers Squibb, John Wiley & Sons, Ohio Supercomputer Center, NetGenics, Celestar Lexico-Sciences, ApoCom Genomics, National Foundation for Cancer Research, and other BIO member companies. BSML (Bioinformatic Sequence Markup Language) is an open and freely available Extensible Markup Language (XML) format that allows life science researchers to integrate, annotate, and visualize complex genetic sequences and rich bioinformatics content. BSML documents are composed of two independent sections, one encoding the biological content and the other encoding visualization information for effective communication of the content... BSML is a standard XML data format that captures the richness of genome research data in documents that retain the biological meanings and relationships of the content. BSML was created as an evolving open public domain standard for the bioinformatics community. LabBook provides BSML for effective management, communication, and interoperability of bioinformatic data, enabling lightweight integration of information from public databases, internal sources, and researchers' annotations. LabBook has created BSML converters for many data sources, including GenBank, EMBL, Ensembl, OHGD, Swiss-Prot, and internal databases, with converters for AGAVE in progress. BSML provides a robust mechanism to exchange data more efficiently across bioinformatics systems. The BSML standard is freely available from www.BSML.org. LabBook, Inc. is an XML-powered life science informatics software and information provider for biotechnology, pharmaceutical, and academic researchers. LabBook's enabling software, including the Genomic XML Browser and XML converters, maximizes the value of bioinformatic data by delivering information as 'live' reusable documents in a highly visual and interactive discovery environment. The combination of the BSML standard for bioinformatics with a biology-smart browser creates the ideal front-end for life science informatics that enables dynamic integration and annotation of diverse databases."
[January 10, 2001] "LabBook Inc. Announces Release of XML Standard for Genomic Research." - "LabBook, Inc. announced the release of its XML data format to provide a common method for communicating genomic research information. This open XML data standard, called BSML (Bioinformatic Sequence Markup Language), will allow life sciences researchers, suppliers, and content and service providers, to interact and exchange information through a universal data language. BSML enables the creation, delivery, integration, and storage of documents containing complex sequence information, features and annotations, plus the ability to describe how to visualize these elements. Researchers will be able to exchange information through an XML/BSML email, the Genogram, which is created and read by LabBook's Genomic XML Viewer and Genomic XML Browser. LabBook will support the standard by providing the language specification (BSML DTD Version 2.2) and Genomic XML Viewer to the life science community. LabBook will also develop 'XML converters' allowing the integration of disparate data in the life science community. Dr. Adel Mikhail, LabBook Vice President for Strategic Development, commented: 'Our clients and partners have come to us because they need an affordable robust XML-based solution for data integration, organization, and visualization that can be used effectively by all their end users, not just the bioinformatics specialists. Our technology is making genomic data more meaningful to biologists.' LabBook's solution is to format data and query results for delivery as a standardized XML representation that is persistent and reusable. A combination of XML data, XML converters, and XML-aware software can facilitate the discovery process by enabling the researcher to integrate and annotate complex data and query results within a highly visual and interactive environment. BSML facilitates integration of 'extragenomic' information (literature, images, documents) with bioinformatics data for improved knowledge management. According to LabBook Chief Science Officer, Dr. Jeffrey Spitzner: 'A major challenge in research today is accessing, organizing, and integrating information that is delivered in diverse, often incompatible formats from various sources distributed locally and over the Internet. For example, results of database queries delivered as database tables or HTML files are hard to manage and difficult to integrate. Yet, scientists must be able to share and work with their data and analytical results in order to apply their expertise and understand the underlying biology. A new era of discovery will be enabled by providing a standard XML data format that captures the richness of the underlying data itself, combined with interactive visual presentations that are meaningful to the life sciences community.' [...] BSML is an extensible language specification and container for bioinformatic data. BSML was created by LabBook developers under a 1997 grant from the National Human Genome Research Institute (NHGRI) as an evolving public domain standard for the bioinformatics community. Improvements to BSML were made in collaboration with leaders in the field. The BSML data specification (DTD) is available for download at LabBook's web site www.labbook.com. LabBook will also provide an information management solution that combines the XML data standard BSML with a true XML browser, the Genomic XML Viewer, that can be freely downloaded from its website. Other XML based life sciences research tools, eLabBook', and XML converters will be available from LabBook, Inc. in February 2001... LabBook, Inc. is an XML-powered life science informatics and information provider for the biotechnology, pharmaceutical, and academic life science researcher. LabBook's enabling software, such as the LabBook Genomic XML Browser' queries, manages, and visualizes heterogeneous genomic data types while retaining their underlying associations, and then LabBook's open XML format and unique browser capabilities deliver genomic data as 'live' reusable documents that integrate underlying bioinformatic content."
References from 1997-2000:
- Visual Genomics, Inc. Home Page
- Bioinformatic Sequence Markup Language (BSML): A Public Domain Protocol for Graphic Genomic Displays - Request for Comments: 971201. [local archive copy]
- Version 2.2 DTDs for BSML; [local archive copy]
- Related Web sites: The BIOpolymer Markup Language (BIOML) and Bioperl Projects: XML.
- A Public Domain Protocol for Graphic Genomic Displays
- DTD Outline - Dec. 1, 1997 - Version 0.1; [local archive copy, December 1997]
- Bioinformatic Sequence Markup Language Document Type Definition DTD - Nov. 15,1998 - Version 2.0 Joseph H. Spitzner, Ph.D. [local archive copy]
- See also: "Gene Expression Markup Language (GEML)."