Pattern Functional Dependencies for Data Cleaning

Patterns (or regex-based expressions) are widely used to constrain the format of a domain (or a column), e.g., a Year column should contain only four digits, and thus a value like "1980-" might be a typo. Moreover, integrity constraints (ICs) defined over multiple columns, such as (conditional) functional dependencies and denial constraints, e.g., a ZIP code uniquely determines a city in the UK, have been widely used in data cleaning. However, a promising, but not yet explored, direction is to combine regex- and IC-based theories to capture data dependencies involving partial attribute values. For example, in an employee ID such as"F-9-107", "F" is sufficient to determine the finance department. Inspired by the above observation, we propose a novel class of ICs, called pattern functional dependencies (PFDs), to model fine-grained data dependencies gleaned from partial attribute values. These dependencies cannot be modeled using traditional ICs, such as (conditional) functional dependencies, which work on entire attribute values. We also present a set of axioms for the inference of PFDs, analogous to Armstrong's axioms for FDs, and study the complexity of consistency and implication analysis of PFDs. Moreover, we devise an effective algorithm to automatically discover PFDs even in the presence of errors in the data. Our extensive experiments on 15 real-world datasets show that our approach can effectively discover valid and useful PFDs over dirty data, which can then be used to detect data errors that are hard to capture by other types of ICs

Incorporating Social Context and Domain Knowledge for Entity Recognition

Recognizing entity instances in documents according to a knowl-edge base is a fundamental problem in many data mining applica-tions. The problem is extremely challenging for short documents in complex domains such as social media and biomedical domains. Large concept spaces and instance ambiguity are key issues that need to be addressed. Most of the documents are created in a social context by common authors via social interactions, such as reply and citations. Such social contexts are largely ignored in the instance-recognition liter-ature. How can users ’ interactions help entity instance recognition? How can the social context be modeled so as to resolve the ambi-guity of different instances? In this paper, we propose the SOCINST model to formalize the problem into a probabilistic model. Given a set of short document

A unified framework for managing provenance information in translational research

<p>Abstract</p> <p>Background</p> <p>A critical aspect of the NIH <it>Translational Research </it>roadmap, which seeks to accelerate the delivery of "bench-side" discoveries to patient's "bedside," is the management of the <it>provenance </it>metadata that keeps track of the origin and history of data resources as they traverse the path from the bench to the bedside and back. A comprehensive provenance framework is essential for researchers to verify the quality of data, reproduce scientific results published in peer-reviewed literature, validate scientific process, and associate trust value with data and results. Traditional approaches to provenance management have focused on only partial sections of the translational research life cycle and they do not incorporate "domain semantics", which is essential to support domain-specific querying and analysis by scientists.</p> <p>Results</p> <p>We identify a common set of challenges in managing provenance information across the <it>pre-publication </it>and <it>post-publication </it>phases of data in the translational research lifecycle. We define the semantic provenance framework (SPF), underpinned by the Provenir upper-level provenance ontology, to address these challenges in the four stages of provenance metadata:</p> <p>(a) Provenance <b>collection </b>- during data generation</p> <p>(b) Provenance <b>representation </b>- to support interoperability, reasoning, and incorporate domain semantics</p> <p>(c) Provenance <b>storage </b>and <b>propagation </b>- to allow efficient storage and seamless propagation of provenance as the data is transferred across applications</p> <p>(d) Provenance <b>query </b>- to support queries with increasing complexity over large data size and also support knowledge discovery applications</p> <p>We apply the SPF to two exemplar translational research projects, namely the Semantic Problem Solving Environment for <it>Trypanosoma cruzi </it>(<it>T.cruzi </it>SPSE) and the Biomedical Knowledge Repository (BKR) project, to demonstrate its effectiveness.</p> <p>Conclusions</p> <p>The SPF provides a unified framework to effectively manage provenance of translational research data during pre and post-publication phases. This framework is underpinned by an upper-level provenance ontology called Provenir that is extended to create domain-specific provenance ontologies to facilitate provenance interoperability, seamless propagation of provenance, automated querying, and analysis.</p

Information retrieval and text mining technologies for chemistry

Efficient access to chemical information contained in scientific literature, patents, technical reports, or the web is a pressing need shared by researchers and patent attorneys from different chemical disciplines. Retrieval of important chemical information in most cases starts with finding relevant documents for a particular chemical compound or family. Targeted retrieval of chemical documents is closely connected to the automatic recognition of chemical entities in the text, which commonly involves the extraction of the entire list of chemicals mentioned in a document, including any associated information. In this Review, we provide a comprehensive and in-depth description of fundamental concepts, technical implementations, and current technologies for meeting these information demands. A strong focus is placed on community challenges addressing systems performance, more particularly CHEMDNER and CHEMDNER patents tasks of BioCreative IV and V, respectively. Considering the growing interest in the construction of automatically annotated chemical knowledge bases that integrate chemical information and biological data, cheminformatics approaches for mapping the extracted chemical names into chemical structures and their subsequent annotation together with text mining applications for linking chemistry with biological information are also presented. Finally, future trends and current challenges are highlighted as a roadmap proposal for research in this emerging field.A.V. and M.K. acknowledge funding from the European Community’s Horizon 2020 Program (project reference: 654021 - OpenMinted). M.K. additionally acknowledges the Encomienda MINETAD-CNIO as part of the Plan for the Advancement of Language Technology. O.R. and J.O. thank the Foundation for Applied Medical Research (FIMA), University of Navarra (Pamplona, Spain). This work was partially funded by Consellería de Cultura, Educación e Ordenación Universitaria (Xunta de Galicia), and FEDER (European Union), and the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684). We thank Iñigo Garciá -Yoldi for useful feedback and discussions during the preparation of the manuscript.info:eu-repo/semantics/publishedVersio

Palmoplantar Keratoderma with Leukokeratosis Anogenitalis Caused by KDSR Mutations.

No abstract available

PrIMe: a methodology for developing provenance-aware applications

Provenance refers to the past processes that brought about a given (version of an) object, item or entity. By knowing the provenance of data, users can often better understand, trust, reproduce, and validate it. A provenance-aware application has the functionality to answer questions regarding the provenance of the data it produces, by using documentation of past processes. PrIMe is a software engineering technique for adapting application designs to enable them to interact with a provenance middleware layer, thereby making them provenance-aware. In this article, we specify the steps involved in applying PrIMe, analyse its effectiveness, and illustrate its use with two case studies, in bioinformatics and medicine