Standardized Data Formats for Quantum Chemistry Based on XML/CML ? - - PowerPoint PPT Presentation

Standardized Data Formats for Quantum Chemistry Based on XML/CML ?

A Literature and Web Resources Research Sarah Gerster 17.01.2007

Overview

• Motivation
• A flavour of XML
• Efforts to develop an XML standard for

computations in quantum chemistry

• Standard?

Motivation

• Facilitate:

– Data exchange – Automated workflows – Metadata – Data storage and retrieval

Workflow used by Andreas Elsener in his Diploma Thesis

What is XML?

• Markup Language

– combines character data and markup

• Extensible

– can create any needed tag

• Structured documents

– querying the XML files is reasonably easy

An XML Example

1 <?xml version="1.0" encoding="ISO-8859-1"?> 2 3 <book> 4 5 <chapter>Introduction to XML 6 <para>What is HTML</para> 7 <para>What is XML</para> 8 </chapter> 9 10 <chapter>XML Syntax 11 <para>Elements must have a closing tag</para> 12 <para>Elements must be properly nested</para> 13 </chapter> 14 15 </book>

XML example given under http://www.w3schools.com/xml/

Some Issues...

• Database to hold the XML files
• XML Schema or Document Type Definition

– outline the structure of an XML file – provide a set of rules – well-formed / valid documents – new standard = new XML Schema

An XML Schema Example

• Structure of an energy entry
• Which energies have to be specified?

Value au, eV, ? Total Value Unit Nuclear Value Unit Electronic Value Unit Energy Unit format? mandatory

• ptional

Strengths of XML

• Platform-independent
• Based on international standards
• Web standard
• File is human as well as machine-readable
• A lot of software around to handle XML
• Based on SGML which exists since 1986

Weaknesses of XML

• Redundant and verbose syntax
• Hierarchical model for representation
• Parsers have to check for improperly

formatted data

• Parsers should be able to recurse

arbitrarily nested data

Chemical Markup Language (CML)

• Implementation of an XML for chemistry
• DTD/Schema covering chemistry in general

– substances – quantities – structure – metadata – properties – ...

• Extensions for specific domains, for

example for computational chemistry

Drawbacks of CML

• Primarily designed for molecular structures

and chemical reactions, not for QC

– Validation: Don't use the extensibility of

CML to define the additional tags

– Efficiency: Not all mandatory fields of

CML are required for QC compuations

• The array format is not consistent with the

standard XML schema => accessibility problems from different platforms

Other projects to create an XML standard for QC

• Quantum Monte Carlo

– ALPS – Zori

• QMWISE
• GAMESS

– structured data output

• QCML

– wrappers

Example from the QCML working group

Standard?

• XML is becoming the de facto standard for

transferring data in QC

• CML is a “patchwork”
• Much experience and knowledge in CML
• No other widespread XML schema for QC
• Put efforts together for a new standard?

Thank you for your attention!

For further information and references, please refer to: http://www.echinops.ch/downloads/