[Pipet Devel] Re: Bioperl: Re: BioML/XML (fwd)

Gary Van Domselaar gvd at redpoll.pharmacy.ualberta.ca
Wed Aug 11 18:50:37 EDT 1999

Here is a message recently forwarded to me from my newfound buddy Paul 
Gordon, who works for the nrc in Halifax, and is the chief programmer (he 
designed and implemented the interface for MAGPIE:

http://www.cbr.nrc.ca/newdocs/services/index.html > MAGPIE

This message is from the BioPerl project.

> The XML thread in this group has not been very active recently, but I think
> that this community is still interested in the subject, so I am posting this
> message here.
> We have recently completed the development of an open and freely-available
> source of BIOML (BIOpolymer Markup Language) content, for use by the
> bioinformatics community interested in proteins and proteomes. We are
> calling it the Proteome Template Library and it is available at
>, or at
> (mime-type=text/xml)
> It consists of approximately 4900 files. Each file represents all of the
> protein sequence information, database references and additional information
> about a particular species' proteome found in the Protein Identification
> Resource (PIR) and NRL3D databases, represented in BIOML. For example, the
> BIOML file for Homo sapiens contains all of the protein sequences and
> database references for human sequences (~ 15 MB). Any organism with more
> than twenty protein sequences in a file has the sequences arranged into a
> set of categories, describing either its function, tissue specificity or
> subcellular location (if known).
> The library is organised around the NCBI organism taxonomy, so individual
> organisms can be found by following the directory structure through to the
> appropriate classification. For example, to find "Canis familiaris.bml"
> (dog), you look in "Eukaryota", then "Metazoa", then "Chordate", and finally
> "Mammalia". If you were not trained in biology, you can search the site
> using either a GET or POST request by CGI. For example, to find all proteome
> entries matching dog and/or wolf, a request would be made to
> The search finds
> complete word matches and partial matches and it is case-insensitive. For
> example, using just "strep" as the query word will find all of the
> Streptococcus and Streptomyces species (as well as several other things).
> The reply to the query is in BIOML.
> The complete library is approximately 152 MB. We currently have not packaged
> the entire library for download: we will make this available once we are
> sure that the library is completely accurate and free of XML bugs. This
> release should be considered to be a beta-release: all reports of bugs or
> parsing difficulties should be made to bioml at proteometrics.com. These
> comments and reports will be posted on a bulletin board, that will be made
> available from the main BIOML site ( We take
> compatibility and parsing difficulties very seriously.
> The BIOML files in the library can be displayed as is, using Internet
> Explorer (v. 5). Explorer doesn't deal with large files (> 1 megabyte)  very
> well, so not all of the files can be viewed in this way. The browser
> available at the website can deal with the large files, but it can only be
> used on Windows 95, 98 or NT platforms that have IE 4.01 or later installed
> on them.
> The standard version of the BIOML DTD has been moved to
> because our corporate server was receiving too much BIOML traffic. This new
> server is mainly reserved for BIOML. Revised documentation and  information
> can be obtained at The new and considerably
> improved version of the BIOML browser and BIOML Visual Editor for Windows
> 95, 98 and NT can be obtained from this site, as well as an open source
> version of all of the code used to create the browser.
> Ron Beavis
> Proteometrics
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Gary Van Domselaar		gvd at redpoll.pharmacy.ualberta.ca
Faculty of Pharmacy 		Phone: (780) 492-4493
University of Alberta		FAX:   (780) 492-5305
Edmonton, Alberta, Canada

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