Reproducible Physical Science and the Declaratron

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

An Open System for Social Computation

Part of the power of social computation comes from using the collective intelligence of humans to tame the aggregate uncertainty of (otherwise) low veracity data obtained from human and automated sources. We have witnessed a surge in development of social computing systems but, ironically, there have been few attempts to generalise across this activity so that creation of the underlying mechanisms themselves can be made more social. We describe a method for achieving this by standardising patterns of social computation via lightweight formal specifications (we call these social artifacts) that can be connected to existing internet architectures via a single model of computation. Upon this framework we build a mechanism for extracting provenance meta-data across social computations

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

Musical Acts and Musical Agents: theory, implementation and practice

Centre for Intelligent Systems and their ApplicationsMusical Agents are an emerging technology, designed to provide a range of new musical opportunities to human musicians and composers. Current systems in this area lack certain features which are necessary for a high quality musician; in particular, they lack the ability to structure their output in terms of a communicative dialogue, and reason about the responses of their partners. In order to address these issues, this thesis develops Musical Act Theory (MAT). This is a novel theory, which models musical interactions between agents, allowing a dialogue oriented analysis of music, and an exploration of intention and communication in the context of musical performance. The work here can be separated into four main contributions: a specification for a Musical Middleware system, which can be implemented computationally, and allows distributed agents to collaborate on music in real-time; a computational model of musical interaction, which allows musical agents to analyse the playing of others as part of a communicative process, and formalises the workings of the Musical Middleware system; MAMA, a musical agent system which embodies this theory, and which can function in a variety of Musical Middleware applications; a pilot experiment which explores the use of MAMA and the utility of MAT under controlled conditions. It is found that the Musical Middleware architecture is computationally implementable, and allows for a system which can respond to both direct musical communi- cation and extramusical inputs, including the use of a custom-built tangible interface. MAT is found to capture certain aspects of music which are of interest — an intuitive notion of performative actions in music, and an existing model of musical interaction. Finally, the fact that a number of different levels — theory, architecture and implementation — are tied together gives a coherent model which can be applied to many computational musical situations

Mining chemical information from Open patents

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.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.Peer Reviewe

ChemicalTagger: A tool for semantic text-mining in chemistry.

BACKGROUND: The primary method for scientific communication is in the form of published scientific articles and theses which use natural language combined with domain-specific terminology. As such, they contain free owing unstructured text. Given the usefulness of data extraction from unstructured literature, we aim to show how this can be achieved for the discipline of chemistry. The highly formulaic style of writing most chemists adopt make their contributions well suited to high-throughput Natural Language Processing (NLP) approaches. RESULTS: We have developed the ChemicalTagger parser as a medium-depth, phrase-based semantic NLP tool for the language of chemical experiments. Tagging is based on a modular architecture and uses a combination of OSCAR, domain-specific regex and English taggers to identify parts-of-speech. The ANTLR grammar is used to structure this into tree-based phrases. Using a metric that allows for overlapping annotations, we achieved machine-annotator agreements of 88.9% for phrase recognition and 91.9% for phrase-type identification (Action names). CONCLUSIONS: It is possible parse to chemical experimental text using rule-based techniques in conjunction with a formal grammar parser. ChemicalTagger has been deployed for over 10,000 patents and has identified solvents from their linguistic context with >99.5% precision.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

OSCAR4: a flexible architecture for chemical text-mining

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.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.Peer Reviewe

A Collaboration Model for Community-Based Software Development with Social Machines

Crowdsourcing is generally used for tasks with minimal coordination, providing limited support for dynamic reconfiguration. Modern systems, exemplified by social ma chines, are subject to continual flux in both the client and development communities and their needs. To support crowdsourcing of open-ended development, systems must dynamically integrate human creativity with machine support. While workflows can be u sed to handle structured, predictable processes, they are less suitable for social machine development and its attendant uncertainty. We present models and techniques for coordination of human workers in crowdsourced software development environments. We combine the Social Compute Unit—a model of ad-hoc human worker teams—with versatile coordination protocols expressed in the Lightweight Social Calculus. This allows us to combine coordination and quality constraints with dynamic assessments of end-user desires, dynamically discovering and applying development protocols

Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on

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.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.Peer Reviewe