ProML - an XML Schema for Protein and Protein Set Description

ProML originally was developed as an XML-DTD by Daniel Hanisch et al.. We reimplemented and updated the main properties of ProML as an XML-Schema.

The main goal of ProML is not only to allow for the integration of protein data and features into a single data source (e.g. primary, secondary, tertiary structure) but also for the grouping of related proteins, including annotations of the essential characteristics underlying this group (e.g. specific patterns, SCOP classifications). New features can be applied to ProML by importing XML from other namespaces.

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The ProML schema makes use of BioSchemas. In addition to the ProML schema definition file the BioTypes schema definition file is needed:

Documentation

The documentation was generated from the XML Schema using xsddoc.

Tests

A ZIP archive containing XML files for use with SUT (Schema Unit Testing).

Example Documents

d1h5oa_.pml
b.5.1.1.pml

Stylesheets

These are XSLT stylesheets which can be used in conjunction with ProML:

ProML to HTML stylesheet: Displays an ProML document in the HTML format. This stylesheet imports the BioTypes stylesheet.
ProML to ARFF stylesheet: BioWeka's XML-Stylesheets subproject provides a stylesheet to convert ProML files into Weka's ARFF format.

Contributors

Gewehr, Jan Erik: Schema development
Szugat, Martin: Schema development
Macri, Alessandro: Technical advice
Zimek, Arthur: Schema development

Related Work: ProML Resolver

ProML Resolver is a web-service that gives access to a variety of data on proteins and protein sets. Its protocol is based on ProML, but has been decomposed into parts for quick use as a communications protocol. The main contributors to the ProML Resolver are:

Gerick, Fabian: Initial ProML-based webservice development
Csaba, Gergely: Current maintainer, Schema development, ProML-based webservice development

Publications

2002

Papers

Daniel Hanisch, Ralf Zimmer, Thomas Lengauer. ProML - the protein markup language for specification of protein sequences, structures and families. In Silico Biol, vol 2, no. 3, pp. 313-24, 2002.

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ProML - an XML Schema for Protein and Protein Set Description

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