Allyson Lister

"Catherine Ashton, who will be the EU’s new foreign minister, has a full-size Dalek — a gift from her husband — in her sitting room." Paul Krugman makes me laugh sometimes :) - Allyson Lister

BMC Bioinformatics, Vol. 10, No. 1. (2009), 377. BACKGROUND:Biological sequences play a major role in molecular and computational biology. They are studied as information-bearing entities that make up DNA, RNA or proteins. The Sequence Ontology, which is part of the OBO Foundry, contains descriptions and definitions of sequences and their properties. Yet the most basic question about sequences remains unanswered: what kind of entity is a biological sequence? An answer to this question benefits formal ontologies that use the notion of biological sequences and analyses in computational biology alike. RESULTS:We provide both an ontological analysis of biological sequences and a formal representation that can be used in knowledge-based applications and other ontologies. We distinguish three distinct kinds of entities that can be referred to as “biological sequence”: chains of molecules, syntactic representations such as those in biological databases, and the abstract information-bearing... - Allyson Lister

In WWW Alt. '04: Proceedings of the 13th international World Wide Web conference on Alternate track papers & posters (2004), pp. 74-83. The new Semantic Web recommendations for RDF, RDFS and OWL have, at their heart, the RDF graph. Jena2, a second-generation RDF toolkit, is similarly centered on the RDF graph. RDFS and OWL reasoning are seen as graph-to-graph transforms, producing graphs of virtual triples. Rich APIs are provided. The Model API includes support for other aspects of the RDF recommendations, such as containers and reification. The Ontology API includes support for RDFS and OWL, including advanced OWL Full support. Jena includes the de facto reference RDF/XML parser, and provides RDF/XML output using the full range of the rich RDF/XML grammar. N3 I/O is supported. RDF graphs can be stored in-memory or in databases. Jena's query language, RDQL, and the Web API are both offered for the next round of standardization. Jeremy Carroll, Ian Dickinson, Chris Dollin, Dave... - Allyson Lister

Bioinformatics (17 November 2009), btp642. Summary: SBML is the leading exchange format for mathematical models in Systems Biology. Semantic annotations connect model elements with external knowledge via unique database identifiers and ontology terms, enabling software to check and process models by their biochemical meaning. Such information is essential for model merging, one of the key steps toward the construction of large kinetic models. The tool semanticSBML helps users to check and edit MIRIAM annotations and SBO terms in SBML models. Using a large collection of biochemical names and database identifiers, it supports modellers in finding the right annotations and in merging existing models. Initially, an element matching is derived from the MIRIAM annotations and conflicting element attributes are categorised and highlighted. Conflicts can be resolved automatically or manually, allowing the user to control the merging process in detail. Availability: SemanticSBML is free... - Allyson Lister

Allyson, that's at least worth a letter to the editor, to me. It's a serious failure of basic scholarship not only on the author's part, but on the part of the reviewers, and the editors. It's not like you're making an obscure point, either. You're talking about stuff a basic literature review would have caught. - Mr. Gunn

Nat Struct Mol Biol, Vol. 14, No. 8. (01 August 2007), pp. 681-681. - Allyson Lister

PLoS Biol, Vol. 7, No. 11. (17 November 2009), e1000242. The authors discuss the value of article-level metrics in determining an article's scientific impact. Cameron Neylon, Shirley Wu - Allyson Lister

Applied Ontology, Vol. 3, No. 4. (1 January 2008), pp. 235-245. The role of proteins and their function in pathways is crucial to understanding complex biological processes and their failures that lead to disease. With over 200 pathway databases in existence, it is not possible for biologists to examine a pathway in all of them. The emergence and adoption of Biological Pathways Exchange (BioPAX), a standardized format for exchanging pathway information, provides a unique opportunity to integrate knowledge from multiple pathway databases. We conducted a case study integrating multiple pathway databases using BioPAX and Oracle's resource description framework (RDF) data repository. This integration enables querying across different species and across multiple pathway resources simultaneously. It also enables comparison of the degree of complementarity across different pathway sources. We find that BioPAX and RDF are powerful mechanisms for data exchange and integration and are... - Allyson Lister

fyi - one of the authors has stated that "the work was done a while back (and originally as a class project)", and I noticed that the website isn't active. However, that doesn't mean it won't be useful as an example of what has gone before. Thanks go to Nikesh Kotecha for the quick response to my query. - Allyson Lister

IET Systems Biology, Vol. 3, No. 5. (2009), pp. 317-328. O Ruebenacker, II Moraru, JC Schaff, ML Blinov - Allyson Lister

Nat Phys, Vol. 5, No. 11. (01 November 2009), pp. 775-775. - Allyson Lister

In Proc. of the 21st Conference on Automated Deduction (CADE-21), Vol. 4603 (July 2007), pp. 67-83. Boris Motik, Rob Shearer, Ian Horrocks - Allyson Lister

(2008) Boris Motik, Rob Shearer, Ian Horrocks - Allyson Lister

A good example of how to use the Jena API with OWL ontologies, and how to persist them. - Allyson Lister

second of three parts describing what DL-safe SWRL rules are and how they can be run within Pellet. Running SWRL rules within Pellet means that you can access them via either the OWLAPI or Jena. - Allyson Lister

second of three parts describing what DL-safe SWRL rules are and how they can be run within Pellet. Running SWRL rules within Pellet means that you can access them via either the OWLAPI or Jena. - Allyson Lister

Hermit 1.1. now supports DL-safe rules. - Allyson Lister

TDB is a component of Jena for RDF storage and query, as well as the full range of Jena APIs. - Allyson Lister

first of three parts describing what DL-safe SWRL rules are and how they can be run within Pellet. Running SWRL rules within Pellet means that you can access them via either the OWLAPI or Jena. - Allyson Lister

Web Semantics: Science, Services and Agents on the World Wide Web In Software Engineering and the Semantic Web, Vol. 5, No. 2. (June 2007), pp. 51-53. In this paper, we present a brief overview of Pellet: a complete OWL-DL reasoner with acceptable to very good performance, extensive middleware, and a number of unique features. Pellet is the first sound and complete OWL-DL reasoner with extensive support for reasoning with individuals (including nominal support and conjunctive query), user-defined datatypes, and debugging support for ontologies. It implements several extensions to OWL-DL including a combination formalism for OWL-DL ontologies, a non-monotonic operator, and preliminary support for OWL/Rule hybrid reasoning. Pellet is written in Java and is open source. E Sirin, B Parsia, B Grau, A Kalyanpur, Y Katz - Allyson Lister

In Proceedings of the International Workshop on OWL: Experiences and Directions (OWLED 2008) (2008) SWRL is an expressive OWL-based rule language that can be used to increase the amount of knowledge encoded in OWL ontologies. While semantically a SWRL rule can be considered as an additional type of OWL axiom, the authoring and management of SWRL rule bases requires specialized tools that are not typically present in standard OWL development environments. In this paper, we describe such a tool—called the SWRLAPI—that provides a rich development environment for working with SWRL rules. The SWRLAPI is built on the widely-used Protégé-OWL ontology toolkit. It provides both a set of highly interactive user interfaces for working with rules and a set of low- level APIs for embedding rules in knowledge-driven applications. This SWRLAPI has been used to develop a number of technologies to support data integration on the Semantic Web, including a SWRL-based query language called SQWRL and a... - Allyson Lister

In Description Logics, Vol. 189 (2006) Vladimir Kolovski, Bijan Parsia, Evren Sirin - Allyson Lister

In Description Logics, Vol. 189 (2006) - Allyson Lister

A comparison of Protege 3 and Protege 4 features - Allyson Lister

Directions on how to convert a standard OWL file (RDF/XML) into a Protege database back-end project. - Allyson Lister

Bioinformatics (Oxford, England), Vol. 25, No. 22. (15 November 2009), pp. 3012-3019. MOTIVATION: The Physiome Project was established in 1997 to develop tools to facilitate international collaboration in the physiological sciences and the sharing of biological models and experimental data. The CellML language was developed to represent and exchange mathematical models of biological processes. CellML models can be very complicated, making it difficult to interpret the underlying physical and biological concepts and relationships captured/described in the mathematical model. RESULTS: To address this issue a set of ontologies was developed to explicitly annotate the biophysical concepts represented in the CellML models. This article presents a framework that combines a visual language, together with CellML ontologies, to support the visualization of the underlying physical and biological concepts described by the mathematical model and also their relationships with the CellML model.... - Allyson Lister