Semantic physical science by Peter Murray-Rust and Henry S Rzepa. (Journal of Cheminformatics 2012, 4:14 doi:10.1186/1758-2946-4-14)
Abstract:
The articles in this special issue arise from a workshop and symposium held in January 2012 (‘Semantic Physical Science’). We invited people who shared our vision for the potential of the web to support chemical and related subjects. Other than the initial invitations, we have not exercised any control over the content of the contributed articles.
There are pointers to videos and other materials for the following workshop presentations:
- Introduction – Peter Murray-Rust [11]
- Why we (PNNL) are supporting semantic science – Bill Shelton
- Adventures in Semantic Materials Informatics – Nico Adams
- Semantic Crystallographic Publishing – Brian McMahon [12]
- Service-oriented science: why good code matters and why a fundamental change in thinking is required – Cameron Neylon [13]
- On the use of CML in computational materials research – Martin Dove [14]
- FoX, CML and semantic tools for atomistic simulation – Andrew Walker [15]
- Semantic Physical Science: the CML roadmap – Marcus Hanwell [16]
- CMLisattion of NWChem and development strategy for FoXification and dictionaries – Bert de Jong
- NMR working group – Nancy Washton
A remarkable workshop with which I have only one minor difference:
There was remarkable and exciting unanimity that semantics should and could be introduced now and rapidly into the practice of large areas of chemistry. We agreed that we should concentrate on the three main areas of crystallography, computation and NMR spectroscopy. In crystallography, this is primarily a strategy of working very closely with the IUCr, being able to translate crystallographic data automatically into semantic form and exploring the value of semantic publication and repositories. The continued development of Chempound for crystal structures is Open and so can be fed back regularly into mainstream crystallography.
When computers were being introduced to indexing chemistry and other physical sciences in the 1950’s/60’s, the then practitioners were under the impression their data already had semantics. That it did not have to await the next turn of the century in order to have semantics.
Not to take anything away from the remarkable progress that CML and related efforts have made, but they are not the advent of semantics for chemistry.
Clarification of semantics, documentation of semantics, refinement of semantics, all true.
But chemistry (and data) has always had semantics.