ProML
From BioSchemas
ProML is an XML-schema for describing proteins and protein sets. ProML originally was developed as an XML-DTD by Daniel Hanisch et al. [1]. Regarding flexibility and extensibility, DTD as an implementation standard had some less desirable characteristics. So we decided to reimplement the main properties of ProML as an XML-Schema. The schema has been used and extended in several projects (bachelors' thesis etc.) since.
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Goals and Applications
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. specifical patterns, SCOP classification). New features can be applied to ProML by importing XML from other namespaces. In contrast to the former solution ProML is now based on the BioTypes.
History
- ProML 1.0: deprecated
- ProML 1.1: deprecated; not official released
- ProML 1.2: under development; complete redesign
Developers
ProML was developed and is maintained at the Bioinformatics unit of the Ludwig Maximilians-University, Munich in the PROSEQO II project.
- Gewehr, Jan Erik: Project leader
- Macri, Alessandro Roberto: Technical consultant
- Szugat, Martin: Extended version of the ProML schema and its belonging stylesheets
- Zimek, Arthur: Initial version of the ProML schema
The current maintainer of the ProML project is Gergely Csaba.
Literature
- Hanisch,D., Zimmer,R., Lengauer,T.; "ProML - the Protein Markup Language for specification of protein sequences, structures and families"; In Silico Biology 2, 0029 (2002)
See also
- BioWeka: Contains an XML-Stylesheet to convert ProML 1.0 files into Weka's ARFF format.
