Knowledge Rich Natural Language Queries over Structured Biological Databases

Increasingly, keyword, natural language and NoSQL queries are being used for information retrieval from traditional as well as non-traditional databases such as web, document, image, GIS, legal, and health databases. While their popularity are undeniable for obvious reasons, their engineering is far from simple. In most part, semantics and intent preserving mapping of a well understood natural language query expressed over a structured database schema to a structured query language is still a difficult task, and research to tame the complexity is intense. In this paper, we propose a multi-level knowledge-based middleware to facilitate such mappings that separate the conceptual level from the physical level. We augment these multi-level abstractions with a concept reasoner and a query strategy engine to dynamically link arbitrary natural language querying to well defined structured queries. We demonstrate the feasibility of our approach by presenting a Datalog based prototype system, called BioSmart, that can compute responses to arbitrary natural language queries over arbitrary databases once a syntactic classification of the natural language query is made

Data access and integration in the ISPIDER proteomics grid

Grid computing has great potential for supporting the integration of complex, fast changing biological data repositories to enable distributed data analysis. One scenario where Grid computing has such potential is provided by proteomics resources which are rapidly being developed with the emergence of affordable, reliable methods to study the proteome. The protein identifications arising from these methods derive from multiple repositories which need to be integrated to enable uniform access to them. A number of technologies exist which enable these resources to be accessed in a Grid environment, but the independent development of these resources means that significant data integration challenges, such as heterogeneity and schema evolution, have to be met. This paper presents an architecture which supports the combined use of Grid data access (OGSA-DAI), Grid distributed querying (OGSA-DQP) and data integration (AutoMed) software tools to support distributed data analysis. We discuss the application of this architecture for the integration of several autonomous proteomics data resources

Customisable Handling of Java References in Prolog Programs

Integration techniques for combining programs written in distinct language paradigms facilitate the implementation of specialised modules in the best language for their task. In the case of Java-Prolog integration, a known problem is the proper representation of references to Java objects on the Prolog side. To solve it adequately, multiple dimensions should be considered, including reference representation, opacity of the representation, identity preservation, reference life span, and scope of the inter-language conversion policies. This paper presents an approach that addresses all these dimensions, generalising and building on existing representation patterns of foreign references in Prolog, and taking inspiration from similar inter-language representation techniques found in other domains. Our approach maximises portability by making few assumptions about the Prolog engine interacting with Java (e.g., embedded or executed as an external process). We validate our work by extending JPC, an open-source integration library, with features supporting our approach. Our JPC library is currently compatible with three different open source Prolog engines (SWI, YAP} and XSB) by means of drivers. To appear in Theory and Practice of Logic Programming (TPLP).Comment: 10 pages, 2 figure

Heterogeneous biomedical database integration using a hybrid strategy: a p53 cancer research database.

Complex problems in life science research give rise to multidisciplinary collaboration, and hence, to the need for heterogeneous database integration. The tumor suppressor p53 is mutated in close to 50% of human cancers, and a small drug-like molecule with the ability to restore native function to cancerous p53 mutants is a long-held medical goal of cancer treatment. The Cancer Research DataBase (CRDB) was designed in support of a project to find such small molecules. As a cancer informatics project, the CRDB involved small molecule data, computational docking results, functional assays, and protein structure data. As an example of the hybrid strategy for data integration, it combined the mediation and data warehousing approaches. This paper uses the CRDB to illustrate the hybrid strategy as a viable approach to heterogeneous data integration in biomedicine, and provides a design method for those considering similar systems. More efficient data sharing implies increased productivity, and, hopefully, improved chances of success in cancer research. (Code and database schemas are freely downloadable, http://www.igb.uci.edu/research/research.html.)

An introduction to Graph Data Management

A graph database is a database where the data structures for the schema and/or instances are modeled as a (labeled)(directed) graph or generalizations of it, and where querying is expressed by graph-oriented operations and type constructors. In this article we present the basic notions of graph databases, give an historical overview of its main development, and study the main current systems that implement them

A Database Interface for Complex Objects

We describe a formal design for a logical query language using psi-terms as data structures to interact effectively and efficiently with a relational database. The structure of psi-terms provides an adequate representation for so-called complex objects. They generalize conventional terms used in logic programming: they are typed attributed structures, ordered thanks to a subtype ordering. Unification of psi-terms is an effective means for integrating multiple inheritance and partial information into a deduction process. We define a compact database representation for psi-terms, representing part of the subtyping relation in the database as well. We describe a retrieval algorithm based on an abstract interpretation of the psi-term unification process and prove its formal correctness. This algorithm is efficient in that it incrementally retrieves only additional facts that are actually needed by a query, and never retrieves the same fact twice

Cross-concordances: terminology mapping and its effectiveness for information retrieval

The German Federal Ministry for Education and Research funded a major terminology mapping initiative, which found its conclusion in 2007. The task of this terminology mapping initiative was to organize, create and manage 'cross-concordances' between controlled vocabularies (thesauri, classification systems, subject heading lists) centred around the social sciences but quickly extending to other subject areas. 64 crosswalks with more than 500,000 relations were established. In the final phase of the project, a major evaluation effort to test and measure the effectiveness of the vocabulary mappings in an information system environment was conducted. The paper reports on the cross-concordance work and evaluation results.Comment: 19 pages, 4 figures, 11 tables, IFLA conference 200

Profiling Web Archive Coverage for Top-Level Domain and Content Language

The Memento aggregator currently polls every known public web archive when serving a request for an archived web page, even though some web archives focus on only specific domains and ignore the others. Similar to query routing in distributed search, we investigate the impact on aggregated Memento TimeMaps (lists of when and where a web page was archived) by only sending queries to archives likely to hold the archived page. We profile twelve public web archives using data from a variety of sources (the web, archives' access logs, and full-text queries to archives) and discover that only sending queries to the top three web archives (i.e., a 75% reduction in the number of queries) for any request produces the full TimeMaps on 84% of the cases.Comment: Appeared in TPDL 201