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 Blue Obelisk Community

Poster presented at the VSMF symposium held at the Unilever Centre on 2011-01-17The Internet has brought together a group of chemists who are driven by wanting to do things better, but are frustrated with the Closed systems that chemists currently have to work with. they share a belief in the concepts of Open Data, Open Standards and Open Source. And they express this in software, data, algorithms, specifications, tutorials, demonstrations, articles and anything that helps get the message across. [http://www.blueobelisk.org/

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

Visions of a Semantic Molecular Future

Booklet handout 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

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

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

Chem# - Semantically Enriched Linked Open Chemical Data

The problem: Vast quantities of chemical data (e.g. crystal structures, NMR spectra, experimental reports) are generated every day. The majority of this data is never published, and the data that is published is fragmented,trapped in legacy formats and difficult to discover. The solution: Semantically Enriched Linked Open Chemical Data: browsable, searchable, discoverable and interpretable by humans and machines alike, using standardized extensible data formats (Chemical Markup Language) and technologies (HTTP, RDF).Funded by JISC

CMLLite: a design philosophy for CML.

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.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