public data. For protected data the author can pass a key to researchers to enable
them to access his/her protected data. An alternative would be to label the publication private so that only the original authors can access the data.
Data also comes with tags set by the authors that help define the search. For
example an author might add a tag, “used_32bit_gpu” if he/she thought it worthwhile to distinguish calculations on a 32-bit only graphical processing unit from
those on a normal CPU. Once data has been put into a semantic web form elaborate
searches can be performed and the retrieved summary data could also be added as
new data if so desired. Examples of SPAROL queries are shown below after the
SPARQL query language is described.
2 Portal Technologies
The semantic web and our portal use a number of “new” technologies that are
briefly described here. Most of these are new to chemists at this point and the
following therefore provides somewhat of a primer on the semantic web so that the
next section describing the actual operation of publishing and querying using the
facilities of Chemical Semantics, Inc. can be better understood. There are many
good reference books on the semantic web but they generally are written for
computer scientists not chemists.
This tutorial will focus on describing quantum chemistry data as applied to the
semantic web.
2.1 CSX—A Chemical Semantics Markup Language
The semantic web uses RDF and triple stores to hold data in a graphical database.
The data of Quantum Chemistry needs to be put into this form using an ontology
for Quantum Chemistry. As a practical matter it makes sense to have a way of
structuring computed quantum data prior to converting it into RDF semantic web
data. A fundamental issue here is that the data should always be put into a structured form from its inception so that computers can be taught this structure. We
have introduced a markup language that we call a Common Standard for eXchange
of quantum data (CSX).
2.1.1 Overview
Chemical Semantics, Inc. uses an Extensible Markup Language (XML) format file
to capture information about quantum chemistry calculations. Specifically, a
Common Standard for eXchange (CSX) file is used to transfer structured data and
A Portal for Quantum Chemistry Data …
7
them to access his/her protected data. An alternative would be to label the publication private so that only the original authors can access the data.
Data also comes with tags set by the authors that help define the search. For
example an author might add a tag, “used_32bit_gpu” if he/she thought it worthwhile to distinguish calculations on a 32-bit only graphical processing unit from
those on a normal CPU. Once data has been put into a semantic web form elaborate
searches can be performed and the retrieved summary data could also be added as
new data if so desired. Examples of SPAROL queries are shown below after the
SPARQL query language is described.
2 Portal Technologies
The semantic web and our portal use a number of “new” technologies that are
briefly described here. Most of these are new to chemists at this point and the
following therefore provides somewhat of a primer on the semantic web so that the
next section describing the actual operation of publishing and querying using the
facilities of Chemical Semantics, Inc. can be better understood. There are many
good reference books on the semantic web but they generally are written for
computer scientists not chemists.
This tutorial will focus on describing quantum chemistry data as applied to the
semantic web.
2.1 CSX—A Chemical Semantics Markup Language
The semantic web uses RDF and triple stores to hold data in a graphical database.
The data of Quantum Chemistry needs to be put into this form using an ontology
for Quantum Chemistry. As a practical matter it makes sense to have a way of
structuring computed quantum data prior to converting it into RDF semantic web
data. A fundamental issue here is that the data should always be put into a structured form from its inception so that computers can be taught this structure. We
have introduced a markup language that we call a Common Standard for eXchange
of quantum data (CSX).
2.1.1 Overview
Chemical Semantics, Inc. uses an Extensible Markup Language (XML) format file
to capture information about quantum chemistry calculations. Specifically, a
Common Standard for eXchange (CSX) file is used to transfer structured data and
A Portal for Quantum Chemistry Data …
7