Allyson Lister

[...] 20, 2012 at 10:27 | #4 Chapter 5: Rule-based mediation (Thesis) « the mind wobbles You must be logged in to post a comment. Chapter 5: Rule-based mediation (Thesis) [...] - Allyson Lister

[...] Section 1 describes the importance of linking biology to models, and why the syntax of those links is vital to their usefulness. Section 2 describes the technology used to implement Saint, while Section 3 focuses on how Saint retrieves model annotation and how it can be used to pick and choose the annotation to keep. Section 4 provides practical examples of annotating models using Saint. Finally, Section 5 describes the future plans for Saint, the collaborations that have been developed, and how Saint can be used with rule-based mediation (see Chapter 5). [...] - Allyson Lister

[...] This section provides a review of those data integration structures and methodologies relevant to systems biology and to the work described in this thesis. Section 1 describes the three main obstacles facing researchers attempting to integrate systems biology data. Section 2 describes the difference between structuring the integration methodology syntactically and semantically. The methods of integration described in this section can be classified along two axes: firstly, the mapping type (Section 3) determines how the integration interface is connected to the underlying data sources; and secondly, the integration interface (Section 4) determines how the data is retrieved and structured for the end application or user. The implications for the work presented in this thesis and the design decisions made with regard to integration structure and methodology are described in Chapter 5. [...] - Allyson Lister

[...] of appropriate additions. More information on such tools is available in Chapters 3 and 5. Ultimately, there is a need for computational approaches that automate the integration of multiple [...] - Allyson Lister

[...] identification of appropriate additions. More information on such tools is available in Chapters 3 and 5. Ultimately, there is a need for computational approaches that automate the integration of [...] - Allyson Lister

[...] Chapter 5: Rule-based mediation (Thesis) [...] - Allyson Lister

[...] Chapter 5: Rule-based mediation for the semantic integration of systems biology data [...] - Allyson Lister

[...] However, while large amounts of data can be gathered and queried in this manner, the syntactic integration process is limited to resolving formatting differences without attempting to address semantic heterogeneity. While existing syntactic tools for model annotation are suitable for many tasks, semantic data integration methods can resolve differences in the meaning of the data and theoretically provide a more useful level of integration. A number of semantic integration approaches have been applied to many different research areas [6, Section 9], and are beginning to be used in the life sciences (see also Sections 1.6 and 1.5). [...] - Allyson Lister

[...] majority of systems biology model annotation tools such as those described in Section 1.3 rely on syntactic data integration methods. Taverna workflows can act as query translation services [...] - Allyson Lister

[...] There is a need for computational approaches that automate the integration of multiple sources to enable the model annotation process. Ideally, the retrieval and integration of biological knowledge for model annotation should be performed quickly, precisely, and with a minimum of manual effort. If information is added manually, it is very difficult for the modeller to annotate exhaustively. Current systems biology model annotation tools rely mainly on syntactic data integration methods such as query translation. A review of data integration methodologies in the life sciences is available in Section 1.6, and the Saint syntactic integration system for model annotation is described in detail in Chapter 3. [...] - Allyson Lister

[...] A review of data integration methodologies in the life sciences is available in Section 1.6, and the Saint syntactic integration system for model annotation is described in detail in [...] - Allyson Lister

[...] Chapter 4: MFO] [Next: Chapter 6: General [...] - Allyson Lister

[Previous: Chapter 4: MFO] [Next: Chapter 6: General Discussion] Rule-based mediation for the semantic integration of systems biology data Introduction The creation of accurate quantitative SBML models is a time-intensive manual process. Modellers need to know and understand both the systems they are modelling and the intricacies of the SBML format. However, the amount of [...] - Allyson Lister

[...] Chapter 4: Model Format OWL integrates multiple SBML specification documents [...] - Allyson Lister

[...] accessibility. This problem is resolved for SBML models through the use of MFO (Chapter 4), an ontology which holds SBML data as well as rules and restrictions on the SBML structure. MFO [...] - Allyson Lister

[...] WordPress Posts « the mind wobbles You must be logged in to post a comment. Chapter 4: MFO (Thesis) Chapter 2: SyMBA (Thesis) RSS [...] - Allyson Lister

[...] SBO is a hierarchy of terms developed by the systems biology modelling community to assist compliance with MIRIAM, ensure unambiguous understanding of the meaning of the annotated entities and foster mapping between annotated elements from multiple formats making use of the ontology [10]. By adding SBO terms, modellers take an essential step towards such compliance [3]. Each term in SBO is related to its direct parent with an is a subsumption relationship such as catalyst is a modifier. For a full description of SBO itself and its relationship to other systems biology standards, see Section 1.4. [...] - Allyson Lister

[Previous: Chapter 3: Saint] [Next: Chapter 5: Rule-based mediation] Model Format OWL integrates multiple SBML specification documents   Introduction The creation of quantitative SBML models that simulate the system under study is a time-consuming manual process. Currently, the rules and constraints of model creation, curation, and annotation are distributed over at least three separate specification [...] - Allyson Lister

[...] Chapter 3: Saint: a Web application for model annotation utilising syntactic integration [...] - Allyson Lister

[...] like the collaboratively-developed SyMBA (Chapter 2). The Saint Web application (Chapter 3) provides syntactic integration of systems biology data as well as a simple interface for viewing, [...] - Allyson Lister

[...] on a Tomcat (Note: http://tomcat.apache.org/) server. For more information on GWT, see Chapter 2. GWT was chosen for a number of [...] - Allyson Lister

[...] an integrated view of data sources and suggested ontological terms. As described in Section 1.6, query translation uses a mediator to distribute a single query across known data sources. When the [...] - 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