Visions of a Semantic Molecular Future

Additional booklet insert distributed at the VSMF Symposium held at the Unilever Centre on 2011-01-17The event looks forward. Scholarship (universities, research, teaching, publishing) has been slow to take up the opportunities of this digital century. This is an opportunity to identify and build the future.EPSRC (Pathways to Impact award). Unilever plc (Unilever Centre for Molecular Science Informatics

Open Chemistry

An invited article on Open Chemistry discussing the importance of Open Access and Open Data and stressing the emerging role of the blogospher

Reproducible Physical Science and the Declaratron

Invited Book ChapterThe Declaratron is a semantic engine for formalising mathematics and science in publication

The social, political and legal aspects of Text and Data Mining (TDM)

The ideas of textual or data mining (TDM) and subsequent analysis go back hundreds if not thousands of years. Originally carried out manually, textual and data analysis has long been a tool which has enabled new insights to be drawn from text corpora. However, for the potential benefits of TDM to be unlocked, a number of non-technological barriers need to be overcome. These include legal uncertainty resulting from complicated copyright, database rights and licensing, the fact that some publishers are not currently embracing the opportunities TDM offers the academic community, and a lack of awareness of TDM among many academics, alongside a skills gap

Semantic science and its communication - a personal view.

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.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

Communication and re-use of chemical information in bioscience.

The current methods of publishing chemical information in bioscience articles are analysed. Using 3 papers as use-cases, it is shown that conventional methods using human procedures, including cut-and-paste are time-consuming and introduce errors. The meaning of chemical terms and the identity of compounds is often ambiguous. valuable experimental data such as spectra and computational results are almost always omitted. We describe an Open XML architecture at proof-of-concept which addresses these concerns. Compounds are identified through explicit connection tables or links to persistent Open resources such as PubChem. It is argued that if publishers adopt these tools and protocols, then the quality and quantity of chemical information available to bioscientists will increase and the authors, publishers and readers will find the process cost-effective.An article submitted to BiomedCentral Bioinformatics, created on request with their Publicon system. The transformed manuscript is archived as PDF. Although it has been through the publishers system this is purely automatic and the contents are those of a pre-refereed preprint. The formatting is provided by the system and tables and figures appear at the end. An accommpanying submission, http://www.dspace.cam.ac.uk/handle/1810/34580, describes the rationale and cultural aspects of publishing , abstracting and aggregating chemical information. BMC is an Open Access publisher and we emphasize that all content is re-usable under Creative Commons Licens

OCK – Open Climate Knowledge

100% open collaborative research for climate change knowledge / using data mining & open science publishing. The climate crisis of the predicted atmosphere temperatures rising to 1.5C + makes it imperative that research related to climate change be put to better use by being open and digitally connected. We are concerned with making all aspects of research open, but as an example, less than 30% of research papers related to climate change are Open Access (Tai and Robinson 2018). This must change now

Engineering Polymer Informatics

The poster describes a strategy of for the development of polymer informatics. In particular, the development of polymer markup language, a polymer ontology and natural language processing tools for polymer literature

Chemistry in Bioinformatics

A preprint of an invited submission to BioMedCentral Bioinformatics. This short manuscript is an overview or the current problems and opportunities in publishing chemical information. Full details of technology are given in the sibling manuscript http://www.dspace.cam.ac.uk/handle/1810/34579 The manuscript is the authors' preprint although it has been automatically transformed into this archived PDF by the submission system. The authors are not responsible for the formattingChemical information is now seen as critical for most areas of life sciences. But unlike Bioinformatics, where data is Openly available and freely re−usable, most chemical information is closed and cannot be re−distributed without permission. This has led to a failure to adopt modern informatics and software techniques and therefore paucity of chemistry in bioinformatics. New technology, however, offers the hope of making chemical data (compounds and properties) Free during the authoring process. We argue that the technology is already available; we require a collective agreement to enhance publication protocols

The Declaratron: Semantic specification for scientific computation using MathML

Abstract. We introduce the Declaratron, a system which takes a declarative approach to specifying mathematically based scientific computation. This uses displayable mathematical notation (Content MathML) and is both executable and semantically well defined. We combine domain specific representations of physical science (e.g. CML, Chemical Markup Language), MathML formulae and computational specifications (DeXML) to create executable documents which include scientific data and mathematical formulae. These documents preserve the provenance of the data used, and build tight semantic links between components of mathematical formulae and domain objects—in effect grounding the mathematical semantics in the scientific domain. The Declaratron takes these specifications and i) carries out entity resolution and decoration to prepare for computation ii) uses a MathML execution engine to run calculations over the revised tree iii) outputs domain objects and the complete document to give both results and an encapsulated history of the computation. A short description of a case study is given to illustrate how the system can be used. Many scientific problems require frequent change of the mathematical functional form and the Declaratron provides this without requiring changes to code. Additionally, it supports reproducible science, machine indexing and semantic search of computations, makes implicit assumptions visible, and separates domain knowledge from computational techniques. We believe that the Declaratron could replace much conventional procedural code in science.