Deploying mutation impact text-mining software with the SADI Semantic Web Services framework

Background: Mutation impact extraction is an important task designed to harvest relevant annotations from scientific documents for reuse in multiple contexts. Our previous work on text mining for mutation impacts resulted in (i) the development of a GATE-based pipeline that mines texts for information about impacts of mutations on proteins, (ii) the population of this information into our OWL DL mutation impact ontology, and (iii) establishing an experimental semantic database for storing the results of text mining. Results: This article explores the possibility of using the SADI framework as a medium for publishing our mutation impact software and data. SADI is a set of conventions for creating web services with semantic descriptions that facilitate automatic discovery and orchestration. We describe a case study exploring and demonstrating the utility of the SADI approach in our context. We describe several SADI services we created based on our text mining API and data, and demonstrate how they can be used in a number of biologically meaningful scenarios through a SPARQL interface (SHARE) to SADI services. In all cases we pay special attention to the integration of mutation impact services with external SADI services providing information about related biological entities, such as proteins, pathways, and drugs. Conclusion: We have identified that SADI provides an effective way of exposing our mutation impact data suc

Prototype semantic infrastructure for automated small molecule classification and annotation in lipidomics

<p>Abstract</p> <p>Background</p> <p>The development of high-throughput experimentation has led to astronomical growth in biologically relevant lipids and lipid derivatives identified, screened, and deposited in numerous online databases. Unfortunately, efforts to annotate, classify, and analyze these chemical entities have largely remained in the hands of human curators using manual or semi-automated protocols, leaving many novel entities unclassified. Since chemical function is often closely linked to structure, accurate structure-based classification and annotation of chemical entities is imperative to understanding their functionality.</p> <p>Results</p> <p>As part of an exploratory study, we have investigated the utility of semantic web technologies in automated chemical classification and annotation of lipids. Our prototype framework consists of two components: an ontology and a set of federated web services that operate upon it. The formal lipid ontology we use here extends a part of the LiPrO ontology and draws on the lipid hierarchy in the LIPID MAPS database, as well as literature-derived knowledge. The federated semantic web services that operate upon this ontology are deployed within the Semantic Annotation, Discovery, and Integration (SADI) framework. Structure-based lipid classification is enacted by two core services. Firstly, a structural annotation service detects and enumerates relevant functional groups for a specified chemical structure. A second service reasons over lipid ontology class descriptions using the attributes obtained from the annotation service and identifies the appropriate lipid classification. We extend the utility of these core services by combining them with additional SADI services that retrieve associations between lipids and proteins and identify publications related to specified lipid types. We analyze the performance of SADI-enabled eicosanoid classification relative to the LIPID MAPS classification and reflect on the contribution of our integrative methodology in the context of high-throughput lipidomics.</p> <p>Conclusions</p> <p>Our prototype framework is capable of accurate automated classification of lipids and facile integration of lipid class information with additional data obtained with SADI web services. The potential of programming-free integration of external web services through the SADI framework offers an opportunity for development of powerful novel applications in lipidomics. We conclude that semantic web technologies can provide an accurate and versatile means of classification and annotation of lipids.</p

Superposition as a logical glue

The typical mathematical language systematically exploits notational and logical abuses whose resolution requires not just the knowledge of domain specific notation and conventions, but not trivial skills in the given mathematical discipline. A large part of this background knowledge is expressed in form of equalities and isomorphisms, allowing mathematicians to freely move between different incarnations of the same entity without even mentioning the transformation. Providing ITP-systems with similar capabilities seems to be a major way to improve their intelligence, and to ease the communication between the user and the machine. The present paper discusses our experience of integration of a superposition calculus within the Matita interactive prover, providing in particular a very flexible, "smart" application tactic, and a simple, innovative approach to automation.Comment: In Proceedings TYPES 2009, arXiv:1103.311

Total Haskell is Reasonable Coq

We would like to use the Coq proof assistant to mechanically verify properties of Haskell programs. To that end, we present a tool, named hs-to-coq, that translates total Haskell programs into Coq programs via a shallow embedding. We apply our tool in three case studies -- a lawful Monad instance, "Hutton's razor", and an existing data structure library -- and prove their correctness. These examples show that this approach is viable: both that hs-to-coq applies to existing Haskell code, and that the output it produces is amenable to verification.Comment: 13 pages plus references. Published at CPP'18, In Proceedings of 7th ACM SIGPLAN International Conference on Certified Programs and Proofs (CPP'18). ACM, New York, NY, USA, 201