Allyson Lister

Saint: a Web application for model annotation utilising syntactic integration Introduction Quantitative modelling is at the heart of systems biology. Model description languages such as SBML [1] and CellML [2] allow the relationships between biological entities to be captured and the dynamics of these interactions to be described mathematically. Without a biological context to these dynamic models, [...] - Allyson Lister

[...] Chapter 2: SyMBA: a Web-based metadata and data archive for biological experiments [...] - Allyson Lister

[...] a common syntax becomes easier with applications like the collaboratively-developed SyMBA (Chapter 2). The Saint Web application (Chapter ) provides syntactic integration of systems biology data as [...] - Allyson Lister

[...] Overview (Thesis 1.1) « the mind wobbles You must be logged in to post a comment. Chapter 2: SyMBA (Thesis) Background: What are ontologies? (Thesis 1.5) RSS [...] - Allyson Lister

[...] SyMBA makes use of a number of standards, emerging standards, and common formats to save time downstream of data generation by ensuring compatibility with other centres of research and journals complying with the same standards. SyMBA can help research groups follow all of the stewardship methods described above and can limit tedious and repetitive data entry. A brief overview of content, syntax and semantic data standards that are or can be integrated within SyMBA is provided in this section. A more detailed description of these standards is available in Section 1.4. [...] - Allyson Lister

[Previous: Data integration methodologies for systems biology] [Next: Chapter 3: Saint] SyMBA: a Web-based metadata and data archive for biological experiments   Introduction With the development and adoption of high throughput experimentation techniques in the life sciences, vast quantities of heterogeneous data are being produced. Consequently, there is a need to integrate these diverse datasets [...] - Allyson Lister

[...] Background: Data integration methodologies for systems biology (Thesis 1.6) [...] - Allyson Lister

[...] bioinformatics consisted of cross references between databases or links out via URLs (see Section 1.6 for more information). More complex linking became common as ontologies such as the GO [8] made it [...] - Allyson Lister

[...] data successfully, the data needs to be human readable and computationally accessible. Section 1.6 describes data integration methodologies and their use within systems [...] - Allyson Lister

[...] Overview (Thesis 1.1) « the mind wobbles You must be logged in to post a comment. Background: Data integration methodologies for systems biology (Thesis 1.6) Background: Standards as a shared structure for data (Thesis: 1.4) RSS [...] - Allyson Lister

[...] 1.6: Data integration methodologies for systems biology [...] - Allyson Lister

[...] making use of those ontologies, and not just the original, intended, data sources [15]. Section 1.5 provides a detailed description of [...] - Allyson Lister

[...] data standards for guiding the content, syntax and semantics of life-science data (see Section 1.4) provides partial solutions to format and social obstacles. However, there will always be new data [...] - Allyson Lister

Data integration methodologies for systems biology The amount of data available to systems biologists is constantly increasing. However, its integration remains an ongoing challenge due to the heterogeneous nature of biological information, the multitude of data sources and the variability of data formats both in syntax and semantics [1]. Very broadly, integration methodologies resolve this heterogeneity [...] - Allyson Lister

[...] We had a very interesting meeting with Joann Roskoski, Deputy Assistant Director of Biological Sciences at the US National Science Foundation. We already have a number of joint programmes with the NSF, and it was most interesting to see the consonance of our thinking in areas such as sustainability, ‘big data’, open access and the like. In this regard, I read an interesting blog post on the extent to which (non-open-access) scientific journals help or hinder scientific progress, and another that involved blogging a thesis. [...] - Allyson Lister

[...] is a large amount of previous work on data integration (see Section ). As described in Section 1.5, existing technologies such as ontologies, rules and reasoning can bring together heterogeneous [...] - Allyson Lister

[...] types of experiments, but are also due to the variety of ways systems are modelled. Section 1.4 describes the content, syntax and semantics standards relevant for systems biology. Data [...] - Allyson Lister

[...] Systems (Thesis 1.3) « the mind wobbles You must be logged in to post a comment. Background: What are ontologies? (Thesis 1.5) Background: Modelling Biological Systems (Thesis 1.3) RSS [...] - Allyson Lister

[...] 1.5: What are ontologies? [...] - Allyson Lister

[...] Standards as a shared structure for data] [Next: Data integration methodologies for systems [...] - Allyson Lister

[Previous: Standards as a shared structure for data] [Next: Data integration methodologies for systems biology] What are ontologies? 1 Introduction Controlled vocabularies, often just a list of agreed-upon terms, have been used to describe data since the early releases of the first biological databases such as EMBL [1] and Swiss-Prot [2]. As data handling in the life [...] - Allyson Lister