| Publication type: | Conference poster |
| Type of review: | Peer review (publication) |
| Title: | Molql : towards a common general purpose molecular query language |
| Authors: | Rose, Alexander S. Sehnal, David Bliven, Spencer Burley, Stephen K. Velankar, Sameer |
| et. al: | No |
| DOI: | 10.1016/j.bpj.2017.11.1910 |
| Published in: | Biophysical Journal |
| Volume(Issue): | 114 |
| Issue: | 3, Supplement 1 |
| Page(s): | 342a |
| Conference details: | 62nd Annual Meeting of the Biophysical Society, San Francisco, USA, 17-21 February 2018 |
| Issue Date: | 2018 |
| Publisher / Ed. Institution: | Cell Press |
| ISSN: | 0006-3495 1542-0086 |
| Language: | English |
| Subjects: | Bioinformatics; Molecular query language |
| Subject (DDC): | 005: Computer programming, programs and data |
| Abstract: | Advances in experimental techniques are providing access to ever more complex and larger macromolecular data sets. Definition and extraction of substructures represents a crucial step required for both analysis and visualization of these data. A common language for defining macromolecular substructures would streamline this step, and enable communication among different computational and visualization tools. However, software tools usually define their own query language or support a language that is not sufficiently general to describe complex spatial and other relationships within macromolecular structures. Herein, we introduce the Molecular Query Language (MolQL), a declarative language for describing substructures within molecular data. The design of the language has three main goals: 1) Make it easy for tool developers to implement the specification; 2) Be expressive enough to describe a wide range of molecular substructures; and 3) Be readily extensible. We describe the initial specification of the language, and provide its reference implementation that can execute MolQL expressions on any Protein Data Bank archival entry (pdb.org) and immediately show the result in a web browser. Moreover, we demonstrate the versatility of the language by translating Jmol, PyMOL, and VMD selection expressions into MolQL. Find out more about MolQL and try it online at http://molql.org/. |
| URI: | https://digitalcollection.zhaw.ch/handle/11475/25613 |
| Fulltext version: | Published version |
| License (according to publishing contract): | Licence according to publishing contract |
| Departement: | Life Sciences and Facility Management |
| Organisational Unit: | Institute of Computational Life Sciences (ICLS) |
| Appears in collections: | Publikationen Life Sciences und Facility Management |
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Rose, A. S., Sehnal, D., Bliven, S., Burley, S. K., & Velankar, S. (2018). Molql : towards a common general purpose molecular query language [Conference poster]. Biophysical Journal, 114(3, Supplement 1), 342a. https://doi.org/10.1016/j.bpj.2017.11.1910
Rose, A.S. et al. (2018) ‘Molql : towards a common general purpose molecular query language’, in Biophysical Journal. Cell Press, p. 342a. Available at: https://doi.org/10.1016/j.bpj.2017.11.1910.
A. S. Rose, D. Sehnal, S. Bliven, S. K. Burley, and S. Velankar, “Molql : towards a common general purpose molecular query language,” in Biophysical Journal, 2018, vol. 114, no. 3, Supplement 1, p. 342a. doi: 10.1016/j.bpj.2017.11.1910.
ROSE, Alexander S., David SEHNAL, Spencer BLIVEN, Stephen K. BURLEY und Sameer VELANKAR, 2018. Molql : towards a common general purpose molecular query language. In: Biophysical Journal. Conference poster. Cell Press. 2018. S. 342a
Rose, Alexander S., David Sehnal, Spencer Bliven, Stephen K. Burley, and Sameer Velankar. 2018. “Molql : Towards a Common General Purpose Molecular Query Language.” Conference poster. In Biophysical Journal, 114:342a. Cell Press. https://doi.org/10.1016/j.bpj.2017.11.1910.
Rose, Alexander S., et al. “Molql : Towards a Common General Purpose Molecular Query Language.” Biophysical Journal, vol. 114, no. 3, Supplement 1, Cell Press, 2018, p. 342a, https://doi.org/10.1016/j.bpj.2017.11.1910.
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