http://www.dspace.cam.ac.uk:80/handle/1810/723 Mon, 20 May 2013 08:21:25 GMT 2013-05-20T08:21:25Z http://www.dspace.cam.ac.uk:80/handle/1810/243749 Title: Open Content Mining Authors: Murray-Rust, Peter Abstract: Abstract— We present evidence that content-mining of scholarly articles is now technically feasible and highly valuable both. However researchers and information technologist are blocked by legal and contractual barries from using it and developing the methodologies. We review the problems and propose changes in legal policy which we have already submitted to the UK's Hargreaves report on intellectual property reform. We put forward the fundamental rights of scholars and embed them in a manifesto: "The right to read is the right to mine", "Users and providers should encourage machine processing, and "Facts don't belong to anyone". Description: Conference for the Fellows of OpenForum Academy - 24th September 2012 Brussels Sun, 23 Sep 2012 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/243749 2012-09-23T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/241669 Title: Predicting the mechanism of phospholipidosis Authors: Lowe, Robert; Mussa, Hamse Y; Nigsch, Florian; Glen, Robert C; Mitchell, John BO Abstract: Abstract The mechanism of phospholipidosis is still not well understood. Numerous different mechanisms have been proposed, varying from direct inhibition of the breakdown of phospholipids to the binding of a drug compound to the phospholipid, preventing breakdown. We have used a probabilistic method, the Parzen-Rosenblatt Window approach, to build a model from the ChEMBL dataset which can predict from a compound's structure both its primary pharmaceutical target and other targets with which it forms off-target, usually weaker, interactions. Using a small dataset of 182 phospholipidosis-inducing and non-inducing compounds, we predict their off-target activity against targets which could relate to phospholipidosis as a side-effect of a drug. We link these targets to specific mechanisms of inducing this lysosomal build-up of phospholipids in cells. Thus, we show that the induction of phospholipidosis is likely to occur by separate mechanisms when triggered by different cationic amphiphilic drugs. We find that both inhibition of phospholipase activity and enhanced cholesterol biosynthesis are likely to be important mechanisms. Furthermore, we provide evidence suggesting four specific protein targets. Sphingomyelin phosphodiesterase, phospholipase A2 and lysosomal phospholipase A1 are shown to be likely targets for the induction of phospholipidosis by inhibition of phospholipase activity, while lanosterol synthase is predicted to be associated with phospholipidosis being induced by enhanced cholesterol biosynthesis. This analysis provides the impetus for further experimental tests of these hypotheses. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Thu, 26 Jan 2012 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/241669 2012-01-26T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/241597 Title: CML: Evolution and Design Authors: Murray-Rust, Peter; Rzepa, Henry S Abstract: Abstract A retrospective view of the design and evolution of Chemical Markup Language (CML) is presented by its original authors. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Thu, 13 Oct 2011 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/241597 2011-10-13T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/241460 Title: On the use of CML in computational materials research Authors: Murray-Rust, Peter; Dove, Martin Thu, 12 Jan 2012 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/241460 2012-01-12T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/241459 Title: Service-oriented science: why good code matters for science and why a fundamental change in thinking is required Authors: Murray-Rust, Peter; Neylon, Cameron Thu, 12 Jan 2012 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/241459 2012-01-12T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/241458 Title: Applied and Implied Semantics in Crystallographic Publishing Authors: Murray-Rust, Peter; McMahon, Brian Thu, 12 Jan 2012 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/241458 2012-01-12T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/241417 Title: Why PNNL are supporting semantic science - Data at EMSL/PNNL Authors: Murray-Rust, Peter; Shelton, William Thu, 12 Jan 2012 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/241417 2012-01-12T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/241416 Title: CMLisation of NWChem and development strategy for FoXification and dictionaries Authors: Murray-Rust, Peter; de Jong, Bert Thu, 12 Jan 2012 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/241416 2012-01-12T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/241415 Title: NMR working group - preliminary discussions Authors: Murray-Rust, Peter; Washton, Nancy Thu, 12 Jan 2012 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/241415 2012-01-12T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/241414 Title: Adventures in Semantic Materials Informatics Authors: Adams, Nico; Murray-Rust, Peter Thu, 12 Jan 2012 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/241414 2012-01-12T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/241373 Title: Semantic Physical Science symposium - introductory address Authors: Murray-Rust, Peter Thu, 12 Jan 2012 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/241373 2012-01-12T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/239929 Title: The semantics of Chemical Markup Language (CML): dictionaries and conventions Authors: Murray-Rust, Peter; Townsend, Joe A; Adams, Sam E; Phadungsukanan, Weerapong; Thomas, Jens Abstract: Abstract The semantic architecture of CML consists of conventions, dictionaries and units. The conventions conform to a top-level specification and each convention can constrain compliant documents through machine-processing (validation). Dictionaries conform to a dictionary specification which also imposes machine validation on the dictionaries. Each dictionary can also be used to validate data in a CML document, and provide human-readable descriptions. An additional set of conventions and dictionaries are used to support scientific units. All conventions, dictionaries and dictionary elements are identifiable and addressable through unique URIs. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Thu, 13 Oct 2011 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/239929 2011-10-13T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/239927 Title: Semantic science and its communication - a personal view Authors: Murray-Rust, Peter Abstract: Abstract The articles in this special issue represent the culmination of about 15 years working with the potential of the web to support chemical and related subjects. The selection of papers arises from a symposium held in January 2011 ('Visions of a Semantic Molecular Future') which gave me an opportunity to invite many people who shared the same vision. I have asked them to contribute their papers and most have been able to do so. They cover a wide range of content, approaches and styles and apart from the selection of the speakers (and hence the authors) I have not exercised any control over the content. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Thu, 13 Oct 2011 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/239927 2011-10-13T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/239926 Title: Open Bibliography for Science, Technology, and Medicine Authors: Jones, Richard; MacGillivray, Mark; Murray-Rust, Peter; Pitman, Jim; Sefton, Peter; O'Steen, Ben; Waites, William Abstract: Abstract The concept of Open Bibliography in science, technology and medicine (STM) is introduced as a combination of Open Source tools, Open specifications and Open bibliographic data. An Openly searchable and navigable network of bibliographic information and associated knowledge representations, a Bibliographic Knowledge Network, across all branches of Science, Technology and Medicine, has been designed and initiated. For this large scale endeavour, the engagement and cooperation of the multiple stakeholders in STM publishing - authors, librarians, publishers and administrators - is sought. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Thu, 13 Oct 2011 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/239926 2011-10-13T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/239925 Title: The Quixote project: Collaborative and Open Quantum Chemistry data management in the Internet age Authors: Adams, Sam; de Castro, Pablo; Echenique, Pablo; Estrada, Jorge; Hanwell, Marcus D; Murray-Rust, Peter; Sherwood, Paul; Thomas, Jens; Townsend, Joe A Abstract: Abstract Computational Quantum Chemistry has developed into a powerful, efficient, reliable and increasingly routine tool for exploring the structure and properties of small to medium sized molecules. Many thousands of calculations are performed every day, some offering results which approach experimental accuracy. However, in contrast to other disciplines, such as crystallography, or bioinformatics, where standard formats and well-known, unified databases exist, this QC data is generally destined to remain locally held in files which are not designed to be machine-readable. Only a very small subset of these results will become accessible to the wider community through publication. In this paper we describe how the Quixote Project is developing the infrastructure required to convert output from a number of different molecular quantum chemistry packages to a common semantically rich, machine-readable format and to build respositories of QC results. Such an infrastructure offers benefits at many levels. The standardised representation of the results will facilitate software interoperability, for example making it easier for analysis tools to take data from different QC packages, and will also help with archival and deposition of results. The repository infrastructure, which is lightweight and built using Open software components, can be implemented at individual researcher, project, organisation or community level, offering the exciting possibility that in future many of these QC results can be made publically available, to be searched and interpreted just as crystallography and bioinformatics results are today. Although we believe that quantum chemists will appreciate the contribution the Quixote infrastructure can make to the organisation and and exchange of their results, we anticipate that greater rewards will come from enabling their results to be consumed by a wider community. As the respositories grow they will become a valuable source of chemical data for use by other disciplines in both research and education. The Quixote project is unconventional in that the infrastructure is being implemented in advance of a full definition of the data model which will eventually underpin it. We believe that a working system which offers real value to researchers based on tools and shared, searchable repositories will encourage early participation from a broader community, including both producers and consumers of data. In the early stages, searching and indexing can be performed on the chemical subject of the calculations, and well defined calculation meta-data. The process of defining more specific quantum chemical definitions, adding them to dictionaries and extracting them consistently from the results of the various software packages can then proceed in an incremental manner, adding additional value at each stage. Not only will these results help to change the data management model in the field of Quantum Chemistry, but the methodology can be applied to other pressing problems related to data in computational and experimental science. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Thu, 13 Oct 2011 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/239925 2011-10-13T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/239924 Title: Ami - The Chemist's Amanuensis Authors: Brooks, Brian J; Thorn, Adam L; Smith, Matthew; Matthews, Peter; Chen, Shaoming; O'Steen, Ben; Adams, Sam E; Townsend, Joe A; Murray-Rust, Peter Abstract: Abstract The Ami project was a six month Rapid Innovation project sponsored by JISC to explore the Virtual Research Environment space. The project brainstormed with chemists and decided to investigate ways to facilitate monitoring and collection of experimental data. A frequently encountered use-case was identified of how the chemist reaches the end of an experiment, but finds an unexpected result. The ability to replay events can significantly help make sense of how things progressed. The project therefore concentrated on collecting a variety of dimensions of ancillary data - data that would not normally be collected due to practicality constraints. There were three main areas of investigation: 1) Development of a monitoring tool using infrared and ultrasonic sensors; 2) Time-lapse motion video capture (for example, videoing 5 seconds in every 60); and 3) Activity-driven video monitoring of the fume cupboard environs. The Ami client application was developed to control these separate logging functions. The application builds up a timeline of the events in the experiment and around the fume cupboard. The videos and data logs can then be reviewed after the experiment in order to help the chemist determine the exact timings and conditions used. The project experimented with ways in which a Microsoft Kinect could be used in a laboratory setting. Investigations suggest that it would not be an ideal device for controlling a mouse, but it shows promise for usages such as manipulating virtual molecules. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Thu, 13 Oct 2011 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/239924 2011-10-13T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/239920 Title: Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on Authors: O'Boyle, Noel M; Guha, Rajarshi; Willighagen, Egon L; Adams, Samuel E; Alvarsson, Jonathan; Bradley, Jean-Claude; Filippov, Igor V; Hanson, Robert M; Hanwell, Marcus D; Hutchison, Geoffrey R; James, Craig A; Jeliazkova, Nina; Lang, Andrew SID; Langner, Karol M; Lonie, David C; Lowe, Daniel M; Pansanel, Jerome; Pavlov, Dmitry; Spjuth, Ola; Steinbeck, Christoph; Tenderholt, Adam L; Theisen, Kevin J; Murray-Rust, Peter Abstract: Abstract Background The Blue Obelisk movement was established in 2005 as a response to the lack of Open Data, Open Standards and Open Source (ODOSOS) in chemistry. It aims to make it easier to carry out chemistry research by promoting interoperability between chemistry software, encouraging cooperation between Open Source developers, and developing community resources and Open Standards. Results This contribution looks back on the work carried out by the Blue Obelisk in the past 5 years and surveys progress and remaining challenges in the areas of Open Data, Open Standards, and Open Source in chemistry. Conclusions We show that the Blue Obelisk has been very successful in bringing together researchers and developers with common interests in ODOSOS, leading to development of many useful resources freely available to the chemistry community. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Thu, 13 Oct 2011 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/239920 2011-10-13T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/239919 Title: OSCAR4: a flexible architecture for chemical text-mining Authors: Jessop, David M; Adams, Sam E; Willighagen, Egon L; Hawizy, Lezan; Murray-Rust, Peter Abstract: Abstract The Open-Source Chemistry Analysis Routines (OSCAR) software, a toolkit for the recognition of named entities and data in chemistry publications, has been developed since 2002. Recent work has resulted in the separation of the core OSCAR functionality and its release as the OSCAR4 library. This library features a modular API (based on reduction of surface coupling) that permits client programmers to easily incorporate it into external applications. OSCAR4 offers a domain-independent architecture upon which chemistry specific text-mining tools can be built, and its development and usage are discussed. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Thu, 13 Oct 2011 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/239919 2011-10-13T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/239918 Title: Mining chemical information from Open patents Authors: Jessop, David M; Adams, Sam E; Murray-Rust, Peter Abstract: Abstract Linked Open Data presents an opportunity to vastly improve the quality of science in all fields by increasing the availability and usability of the data upon which it is based. In the chemical field, there is a huge amount of information available in the published literature, the vast majority of which is not available in machine-understandable formats. PatentEye, a prototype system for the extraction and semantification of chemical reactions from the patent literature has been implemented and is discussed. A total of 4444 reactions were extracted from 667 patent documents that comprised 10 weeks' worth of publications from the European Patent Office (EPO), with a precision of 78% and recall of 64% with regards to determining the identity and amount of reactants employed and an accuracy of 92% with regards to product identification. NMR spectra reported as product characterisation data are additionally captured. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Thu, 13 Oct 2011 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/239918 2011-10-13T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/239917 Title: CMLLite: a design philosophy for CML Authors: Townsend, Joe A.; Murray-Rust, Peter Abstract: Abstract CMLLite is a collection of definitions and processes which provide strong and flexible validation for a document in Chemical Markup Language (CML). It consists of an updated CML schema (schema3), conventions specifying rules in both human and machine-understandable forms and a validator available both online and offline to check conformance. This article explores the rationale behind the changes which have been made to the schema, explains how conventions interact and how they are designed, formulated, implemented and tested, and gives an overview of the validation service. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Thu, 13 Oct 2011 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/239917 2011-10-13T23:00:00Z