Oktie Hassanzadeh

Linked open drug data for pharmaceutical research and development

There is an abundance of information about drugs available on the Web. Data sources range from medicinal chemistry results, over the impact of drugs on gene expression, to the outcomes of drugs in clinical trials. These data are typically not connected together, which reduces the ease with which insights can be gained. Linking Open Drug Data (LODD) is a task force within the World Wide Web Consortiums (W3C) Health Care and Life Sciences Interest Group (HCLS IG). LODD has surveyed publicly available data about drugs, created Linked Data representations of the data sets, and identified interesting scientific and business questions that can be answered once the data sets are connected. The task force provides recommendations for the best practices of exposing data in a Linked Data representation. In this paper, we present past and ongoing work of LODD and discuss the growing importance of Linked Data as a foundation for pharmaceutical R&D data sharing.

Framework for evaluating clustering algorithms in duplicate detection

The presence of duplicate records is a major data quality concern in large databases. To detect duplicates, entity resolution also known as duplication detection or record linkage is used as a part of the data cleaning process to identify records that potentially refer to the same real-world entity. We present the Stringer system that provides an evaluation framework for understanding what barriers remain towards the goal of truly scalable and general purpose duplication detection algorithms. In this paper, we use Stringer to evaluate the quality of the clusters (groups of potential duplicates) obtained from several unconstrained clustering algorithms used in concert with approximate join techniques. Our work is motivated by the recent significant advancements that have made approximate join algorithms highly scalable. Our extensive evaluation reveals that some clustering algorithms that have never been considered for duplicate detection, perform extremely well in terms of both accuracy and scalability.

Benchmarking declarative approximate selection predicates

Declarative data quality has been an active research topic. The fundamental principle behind a declarative approach to data quality is the use of declarative statements to realize data quality primitives on top of any relational data source. A primary advantage of such an approach is the ease of use and integration with existing applications. Over the last few years several similarity predicates have been proposed for common quality primitives (approximate selections, joins, etc) and have been fully expressed using declarative SQL statements. In this paper we propose new similarity predicates along with their declarative realization, based on notions of probabilistic information retrieval. In particular we show how language models and hidden Markov models can be utilized as similarity predicates for data quality and present their full declarative instantiation. We also show how other scoring methods from information retrieval, can be utilized in a similar setting. We then present full declarative specifications of previously proposed similarity predicates in the literature, grouping them into classes according to their primary characteristics. Finally, we present a thorough performance and accuracy study comparing a large number of similarity predicates for data cleaning operations. We quantify both their runtime performance as well as their accuracy for several types of common quality problems encountered in operational databases.

Creating probabilistic databases from duplicated data

A major source of uncertainty in databases is the presence of duplicate items, i.e., records that refer to the same real-world entity. However, accurate deduplication is a difficult task and imperfect data cleaning may result in loss of valuable information. A reasonable alternative approach is to keep duplicates when the correct cleaning strategy is not certain, and utilize an efficient probabilistic query-answering technique to return query results along with probabilities of each answer being correct. In this paper, we present a flexible modular framework for scalably creating a probabilistic database out of a dirty relation of duplicated data and overview the challenges raised in utilizing this framework for large relations of string data. We study the problem of associating probabilities with duplicates that are detected using state-of-the-art scalable approximate join methods. We argue that standard thresholding techniques are not sufficiently robust for this task, and propose new clustering algorithms suitable for inferring duplicates and their associated probabilities. We show that the inferred probabilities accurately reflect the error in duplicate records.

A framework for semantic link discovery over relational data

Discovering links between different data items in a single data source or across different data sources is a challenging problem faced by many information systems today. In particular, the recent Linking Open Data (LOD) community project has highlighted the paramount importance of establishing semantic links among web data sources. Currently, LOD sources provide billions of RDF triples, but only millions of links between data sources. Many of these data sources are published using tools that operate over relational data stored in a standard RDBMS. In this paper, we present a framework for discovery of semantic links from relational data. Our framework is based on declarative specification of linkage requirements by a user. We illustrate the use of our framework using several link discovery algorithms on a real world scenario. Our framework allows data publishers to easily find and publish high-quality links to other data sources, and therefore could significantly enhance the value of the data in the next generation of web.

Toward a complete dataset of drug-drug interaction information from publicly available sources

Although potential drug-drug interactions (PDDIs) are a significant source of preventable drug-related harm, there is currently no single complete source of PDDI information. In the current study, all publically available sources of PDDI information that could be identified using a comprehensive and broad search were combined into a single dataset. The combined dataset merged fourteen different sources including 5 clinically-oriented information sources, 4 Natural Language Processing (NLP) Corpora, and 5 Bioinformatics/Pharmacovigilance information sources. As a comprehensive PDDI source, the merged dataset might benefit the pharmacovigilance text mining community by making it possible to compare the representativeness of NLP corpora for PDDI text extraction tasks, and specifying elements that can be useful for future PDDI extraction purposes. An analysis of the overlap between and across the data sources showed that there was little overlap. Even comprehensive PDDI lists such as DrugBank, KEGG, and the NDF-RT had less than 50% overlap with each other. Moreover, all of the comprehensive lists had incomplete coverage of two data sources that focus on PDDIs of interest in most clinical settings. Based on this information, we think that systems that provide access to the comprehensive lists, such as APIs into RxNorm, should be careful to inform users that the lists may be incomplete with respect to PDDIs that drug experts suggest clinicians be aware of. In spite of the low degree of overlap, several dozen cases were identified where PDDI information provided in drug product labeling might be augmented by the merged dataset. Moreover, the combined dataset was also shown to improve the performance of an existing PDDI NLP pipeline and a recently published PDDI pharmacovigilance protocol. Future work will focus on improvement of the methods for mapping between PDDI information sources, identifying methods to improve the use of the merged dataset in PDDI NLP algorithms, integrating high-quality PDDI information from the merged dataset into Wikidata, and making the combined dataset accessible as Semantic Web Linked Data.

Instance-Based matching of large ontologies using locality-sensitive hashing

In this paper, we describe a mechanism for ontology alignment using instance based matching of types (or classes). Instance-based matching is known to be a useful technique for matching ontologies that have different names and different structures. A key problem in instance matching of types, however, is scaling the matching algorithm to (a) handle types with a large number of instances, and (b) efficiently match a large number of type pairs. We propose the use of state-of-the art locality-sensitive hashing (LSH) techniques to vastly improve the scalability of instance matching across multiple types. We show the feasibility of our approach with DBpedia and Freebase, two different type systems with hundreds and thousands of types, respectively. We describe how these techniques can be used to estimate containment or equivalence relations between two type systems, and we compare two different LSH techniques for computing instance similarity.

A declarative framework for semantic link discovery over relational data

In this paper, we present a framework for online discovery of semantic links from relational data. Our framework is based on declarative specification of the linkage requirements by the user, that allows matching data items in many real-world scenarios. These requirements are translated to queries that can run over the relational data source, potentially using the semantic knowledge to enhance the accuracy of link discovery. Our framework lets data publishers to easily find and publish high-quality links to other data sources, and therefore could significantly enhance the value of the data in the next generation of web.

Discovering linkage points over web data

A basic step in integration is the identification of linkage points, i.e., finding attributes that are shared (or related) between data sources, and that can be used to match records or entities across sources. This is usually performed using a match operator, that associates attributes of one database to another. However, the massive growth in the amount and variety of unstructured and semi-structured data on the Web has created new challenges for this task. Such data sources often do not have a fixed pre-defined schema and contain large numbers of diverse attributes. Furthermore, the end goal is not schema alignment as these schemas may be too heterogeneous (and dynamic) to meaningfully align. Rather, the goal is to align any overlapping data shared by these sources. We will show that even attributes with different meanings (that would not qualify as schema matches) can sometimes be useful in aligning data. The solution we propose in this paper replaces the basic schema-matching step with a more complex instance-based schema analysis and linkage discovery. We present a framework consisting of a library of efficient lexical analyzers and similarity functions, and a set of search algorithms for effective and efficient identification of linkage points over Web data. We experimentally evaluate the effectiveness of our proposed algorithms in real-world integration scenarios in several domains.

Linkage Query Writer

We present Linkage Query Writer (LinQuer), a system for generating SQL queries for semantic link discovery over relational data. The LinQuer framework consists of (a) LinQL, a language for specification of linkage requirements; (b) a web interface and an API for translating LinQL queries to standard SQL queries; (c) an interface that assists users in writing LinQL queries. We discuss the challenges involved in the design and implementation of a declarative and easy to use framework for discovering links between different data items in a single data source or across different data sources. We demonstrate different steps of the linkage requirements specification and discovery process in several real world scenarios and show how the LinQuer system can be used to create high-quality linked data sources.