A Semantic eScience Platform for Chemistry

Borkum, Mark; Lagoze, Carl; Frey, Jeremy G.; Coles, Simon J.

doi:10.1109/escience.2010.18

Cited by 11 publications

(12 citation statements)

References 22 publications

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“…This initiated ac onsiderable amounto fc hemical informatics research within Southampton. Particularly relevant for this papera re the research themes on chemical information and the Semantic Web [6][7][8][9][10][11][12][13] and the work on Electronic Laboratory Notebooks. [14,15] The e-Science programme was not the only driver for the Southampton Chemical Information group.…”

Section: Navigationmentioning

confidence: 99%

“…This approach not only gave us metadata in advance,b ut also led directly to the concept of ap lan and forward-looking provenance, which came to fruition in subsequent work on Planning and Enactment (P&E). [40,41] The implementation of the desktop-and tablet-based Smart Te as ystem suffered from being too close to the "bleeding edge" of technology:t he tablet systemsa nd interface then available weren ot ideal, handwriting recognition was poor,a nd the RDF technology was underdeveloped. Specifically,t he latter neededi nventionsl ike ORE (Object Reuse and Exchange), [42,43] RDF manifests, and better RDF databases (triple stores).…”

Section: The Smart Teap Rojectmentioning

confidence: 99%

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The Evolution of Digital Chemistry at Southampton

Bird

Coles

Frey

2015

Molecular Informatics

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In this paper we take a historical view of e‐Science and e‐Research developments within the Chemical Sciences at the University of Southampton, showing the development of several stages of the evolving data ecosystem as Chemistry moves into the digital age of the 21st Century. We cover our research on aspects of the representation of chemical information in the context of the world wide web (WWW) and its semantic enhancement (the Semantic Web) and illustrate this with the example of the representation of quantities and units within the Semantic Web. We explore the changing nature of laboratories as computing power becomes increasing powerful and pervasive and specifically look at the function and role of electronic or digital notebooks. Having focussed on the creation of chemical data and information in context, we finish the paper by following the use and reuse of this data as facilitated by the features provided by digital repositories and their importance in facilitating the exchange of chemical information touching on the issues of open and or intelligent access to the data.

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Section: Navigationmentioning

confidence: 99%

Section: The Smart Teap Rojectmentioning

confidence: 99%

The Evolution of Digital Chemistry at Southampton

Bird

Coles

Frey

2015

Molecular Informatics

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“…Integrated with existing methods in science the fields as modeling, simulation, scientific visualization, dataacquisition, management, high performance and grid computing have created new opportunities for scientific insight [4], [5]. Traditionally scientific knowledge has been achieved either through the establishment of theories, or through observation of nature and experiments in the laboratory.…”

Section: Introductionmentioning

confidence: 99%

Data-oriented research for bioresource utilization: A case study to investigate water uptake in cellulose using Principal Components

Liu

Driemeier

César

2012

2012 IEEE 8th International Conference on E-Science

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Bioresource utilization represents an important interdisciplinary research that integrates academic and industrial expertise across diverse scientific domains, including physics, chemistry, biology, and engineering. The present paper describes a cyber-infrastructure being created at the Brazilian Bioethanol Science and Technology Laboratory (CTBE) to assist scientists working on the field. One key element of the infrastructure is the LignoCel Platform, a tailor-made database for upload, curation, and sharing of lignocellulose data. Particularly, LignoCel allows querying the data and exporting subsets that are analyzed for knowledge extraction. In the present paper, a case-study is described, in which scientists want to investigate the dimensions that relate cellulose structure and water uptake. Data analysis and dimensionality reduction using Principal Component Analysis (PCA) is employed. Different PCA-based measurements are extracted and visualized through automatically-generated HTML pages available for the domain scientists. In this case study, the workflow successfully provided dimensionality reduction from a data matrix originated from a heterogeneous set of materials. PCA scores and loadings are explored for data analysis and visualization. PCA reduced the 11 measured features (obtained from three different experimental techniques, 55 possible combinations of size 2) into a two-dimensional PC1PC2 loadings plot representing 89% of data variance. Examples of the output produced by the system are available at http://data.bioetanol.org. br/ ∼ liu.ling/pca-lignocel/.

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“…Borkum et al (2010) and Theodoridou et al (2010), for example, used OAI-ORE to extract chemicals from chemistry publications. In addition, an extension of the CIDOC-CRM ontology that was able to capture the modelling and query requirements regarding the provenance of digital objects was proposed in Theodoridou et al (2010).…”

Section: Cultural Heritage and The Semantic Webmentioning

confidence: 99%

“…In addition, an extension of the CIDOC-CRM ontology that was able to capture the modelling and query requirements regarding the provenance of digital objects was proposed in Theodoridou et al (2010). (Theodoridou et al, 2010) (Borkum et al, 2010, Theodoridou et al, 2010 Similar to these approaches, this research project plans to extract and represent the semantics of unstructured scientific publications in a form that will facilitate re-use and discovery. It is however unique in that it will focuses on the key concepts associated with art/paint conservation (e.g., painting, paint, artist, genre, pigment, chemical, treatment, characterisation, and deterioration mechanism).…”

Section: Cultural Heritage and The Semantic Webmentioning

confidence: 99%

A Semantic e-Science Platform for 20th Century Paint Conservation

Odat¹

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Throughout the twentieth century, artists in Australia and across the Southeast AsiaPacific region have enthusiastically embraced new materials (synthetic media, new pigments, dyes and additives). But compared to traditional artists' paints, these new materials have affected paint handling and paint stability. These new materials have also resulted in a lack of understanding of the preservation issues associated with the resulting artworks. As a result, today's collectors, curators and conservators are confronted with significant material-based preservation questions associated with 20 th century art/paint preservation -but they lack the sustained and integrated knowledge-base to inform their decision making.In order to understand the causes of paint degradation and the best preservation and treatment approaches, conservators need access to a wide range of distributed and cross-disciplinary datasets.  Use a number of case studies to evaluate OPPRA's ability to capture the detailed workflows and outputs associated with paint conservation experiments (e.g., sampling method, experimental processes and characterisation data); Apply and optimise a combination of semantic tagging and machine learning approaches to extract structured knowledge (compliant with OPPRA) from freetext publications on paint conservation -so it can be shared, integrated, compared and re-used; Evaluate OPPRA's ability to integrate experimental datasets, structured knowledge extracted from free-text publications and external public relevant databases (e.g., on paint chemistry), to answer a set of advanced, exemplar (SPARQL) queries specified by art conservators; Evaluate OWL-DL for inferencing and extracting new facts from the integrated knowledge base (generated from integrating experimental data capture, structured knowledge extracted from past publications and public relevant databases) in order to answer advanced queries specified by art conservators.4

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A Semantic eScience Platform for Chemistry

Cited by 11 publications

References 22 publications

The Evolution of Digital Chemistry at Southampton

The Evolution of Digital Chemistry at Southampton

Data-oriented research for bioresource utilization: A case study to investigate water uptake in cellulose using Principal Components

A Semantic e-Science Platform for 20th Century Paint Conservation

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