scholarly journals BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 1677
Author(s):  
Toshiaki Katayama ◽  
Shuichi Kawashima ◽  
Gos Micklem ◽  
Shin Kawano ◽  
Jin-Dong Kim ◽  
...  
Keyword(s):  
Service Discovery ◽  
Query Language ◽  
Life Sciences ◽  
Open Data ◽  
Semantic Interoperability ◽  
Science Data ◽  
Rdf Data ◽  
Description Framework ◽  
Machine Readable

Publishing databases in the Resource Description Framework (RDF) model is becoming widely accepted to maximize the syntactic and semantic interoperability of open data in life sciences. Here we report advancements made in the 6th and 7th annual BioHackathons which were held in Tokyo and Miyagi respectively. This review consists of two major sections covering: 1) improvement and utilization of RDF data in various domains of the life sciences and 2) meta-data about these RDF data, the resources that store them, and the service quality of SPARQL Protocol and RDF Query Language (SPARQL) endpoints. The first section describes how we developed RDF data, ontologies and tools in genomics, proteomics, metabolomics, glycomics and by literature text mining. The second section describes how we defined descriptions of datasets, the provenance of data, and quality assessment of services and service discovery. By enhancing the harmonization of these two layers of machine-readable data and knowledge, we improve the way community wide resources are developed and published.  Moreover, we outline best practices for the future, and prepare ourselves for an exciting and unanticipatable variety of real world applications in coming years.

Characterising RDF data sets

2017 ◽  
Vol 44 (2) ◽  
pp. 203-229 ◽  
Author(s):  
Javier D Fernández ◽  
Miguel A Martínez-Prieto ◽  
Pablo de la Fuente Redondo ◽  
Claudio Gutiérrez
Keyword(s):  
Data Structures ◽  
Large Scale ◽  
Open Data ◽  
Structural Features ◽  
Data Sets ◽  
Data Set ◽  
Wide Range ◽  
Rdf Data ◽  
Description Framework ◽  
Resource Description

The publication of semantic web data, commonly represented in Resource Description Framework (RDF), has experienced outstanding growth over the last few years. Data from all fields of knowledge are shared publicly and interconnected in active initiatives such as Linked Open Data. However, despite the increasing availability of applications managing large-scale RDF information such as RDF stores and reasoning tools, little attention has been given to the structural features emerging in real-world RDF data. Our work addresses this issue by proposing specific metrics to characterise RDF data. We specifically focus on revealing the redundancy of each data set, as well as common structural patterns. We evaluate the proposed metrics on several data sets, which cover a wide range of designs and models. Our findings provide a basis for more efficient RDF data structures, indexes and compressors.

scholarly journals Corruption of the Pearson correlation coefficient by measurement error: estimation, bias, and correction under different error models

2019 ◽  
Author(s):  
Edoardo Saccenti ◽  
Margriet H. W. B. Hendriks ◽  
Age K. Smilde
Keyword(s):  
Pearson Correlation ◽  
Measurement Techniques ◽  
Life Sciences ◽  
Real Life ◽  
Correlation Coefficients ◽  
Gene Expressions ◽  
Science Data ◽  
Real Life Data ◽  
Comprehensive Measurement

ABSTRACTCorrelation coefficients are abundantly used in the life sciences. Their use can be limited to simple exploratory analysis or to construct association networks for visualization but they are also basic ingredients for sophisticated multivariate data analysis methods. It is therefore important to have reliable estimates for correlation coefficients. In modern life sciences, comprehensive measurement techniques are used to measure metabolites, proteins, gene-expressions and other types of data. All these measurement techniques have errors. Whereas in the old days, with simple measurements, the errors were also simple, that is not the case anymore. Errors are heterogeneous, non-constant and not independent. This hampers the quality of the estimated correlation coefficients seriously. We will discuss the different types of errors as present in modern comprehensive life science data and show with theory, simulations and real-life data how these affect the correlation coefficients. We will briefly discuss ways to improve the estimation of such coefficients.

scholarly journals Modern Users of Libraries and the Linked Open Data Environment

2020 ◽  
Vol 69 (3) ◽  
pp. 243-260
Author(s):  
Olga A. Lavrenova ◽  
Andrey A. Vinberg
Keyword(s):  
Classification System ◽  
Query Language ◽  
Open Data ◽  
Basic Research ◽  
Linked Open Data ◽  
Knowledge Organization ◽  
Global Network ◽  
Knowledge Organization System ◽  
Description Framework ◽  
State Library

The goal of any library is to ensure high quality and general availability of information retrieval tools. The paper describes the project implemented by the Russian State Library (RSL) to present Library Bibliographic Classification as a Networked Knowledge Organization System. The project goal is to support content and provide tools for ensuring system’s interoperability with other resources of the same nature (i.e. with Linked Data Vocabularies) in the global network environment. The project was partially supported by the Russian Foundation for Basic Research (RFBR).The RSL General Classified Catalogue (GCC) was selected as the main data source for the Classification system of knowledge organization. The meaning of each classification number is expressed by complete string of wordings (captions), rather than the last level caption alone. Data converted to the Resource Description Framework (RDF) files based on the standard set of properties defined in the Simple Knowledge Organization System (SKOS) model was loaded into the semantic storage for subsequent data processing using the SPARQL query language. In order to enrich user queries for search of resources, the RSL has published its Classification System in the form of Linked Open Data (https://lod.rsl.ru) for searching in the RSL electronic catalogue. Currently, the work is underway to enable its smooth integration with other LOD vocabularies. The SKOS mapping tags are used to differentiate the types of connections between SKOS elements (concepts) existing in different concept schemes, for example, UDC, MeSH, authority data.The conceptual schemes of the leading classifications are fundamentally different from each other. Establishing correspondence between concepts is possible only on the basis of lexical and structural analysis to compute the concept similarity as a combination of attributes.The authors are looking forward to working with libraries in Russia and other countries to create a common space of Linked Open Data vocabularies.

scholarly journals The health care and life sciences community profile for dataset descriptions

2016 ◽  
Author(s):  
Michel Dumontier ◽  
Alasdair J G Gray ◽  
M. Scott Marshall ◽  
Vladimir Alexiev ◽  
Peter Ansell ◽  
...  
Keyword(s):  
Health Care ◽  
Life Sciences ◽  
Scientific Data ◽  
Functional Requirements ◽  
High Quality ◽  
Community Profile ◽  
Value Sets ◽  
Description Framework ◽  
Machine Readable ◽  
Resource Description

Access to consistent, high-quality metadata is critical to finding, understanding, and reusing scientific data. However, while there are many relevant vocabularies for the annotation of a dataset, none sufficiently captures all the necessary metadata. This prevents uniform indexing and querying of dataset repositories. Towards providing a practical guide for producing a high quality description of biomedical datasets, the W3C Semantic Web for Health Care and the Life Sciences Interest Group (HCLSIG) identified Resource Description Framework (RDF) vocabularies that could be used to specify common metadata elements and their value sets. The resulting guideline covers elements of description, identification, attribution, versioning, provenance, and content summarization. This guideline reuses existing vocabularies, and is intended to meet key functional requirements including indexing, discovery, exchange, query, and retrieval of datasets, thereby enabling the publication of FAIR data. The resulting metadata profile is generic and could be used by other domains with an interest in providing machine readable descriptions of versioned datasets.

scholarly journals Towards Interactive Analytics over RDF Graphs

Algorithms ◽  
2021 ◽  
Vol 14 (2) ◽  
pp. 34 ◽  
Author(s):  
Maria-Evangelia Papadaki ◽  
Nicolas Spyratos ◽  
Yannis Tzitzikas
Keyword(s):  
Query Language ◽  
Proposed Model ◽  
Aggregate Queries ◽  
Rdf Data ◽  
Description Framework ◽  
Rdf Graphs ◽  
High Level ◽  
Resource Description ◽  
Functional Algebra ◽  
Continuous Accumulation

The continuous accumulation of multi-dimensional data and the development of Semantic Web and Linked Data published in the Resource Description Framework (RDF) bring new requirements for data analytics tools. Such tools should take into account the special features of RDF graphs, exploit the semantics of RDF and support flexible aggregate queries. In this paper, we present an approach for applying analytics to RDF data based on a high-level functional query language, called HIFUN. According to that language, each analytical query is considered to be a well-formed expression of a functional algebra and its definition is independent of the nature and structure of the data. In this paper, we investigate how HIFUN can be used for easing the formulation of analytic queries over RDF data. We detail the applicability of HIFUN over RDF, as well as the transformations of data that may be required, we introduce the translation rules of HIFUN queries to SPARQL and we describe a first implementation of the proposed model.

scholarly journals Evaluating the quality of linked open data in digital libraries

2020 ◽  
pp. 016555152093095
Author(s):  
Gustavo Candela ◽  
Pilar Escobar ◽  
Rafael C Carrasco ◽  
Manuel Marco-Such
Keyword(s):  
Digital Libraries ◽  
Open Data ◽  
Quality Measures ◽  
Linked Open Data ◽  
Data Sets ◽  
Design And Implementation ◽  
Bibliographic Data ◽  
Description Framework ◽  
Resource Description

Cultural heritage institutions have recently started to share their metadata as Linked Open Data (LOD) in order to disseminate and enrich them. The publication of large bibliographic data sets as LOD is a challenge that requires the design and implementation of custom methods for the transformation, management, querying and enrichment of the data. In this report, the methodology defined by previous research for the evaluation of the quality of LOD is analysed and adapted to the specific case of Resource Description Framework (RDF) triples containing standard bibliographic information. The specified quality measures are reported in the case of four highly relevant libraries.

scholarly journals Synospecies, an application to reflect changes in taxonomic names based on a triple store based on taxonomic data liberated from publication 

2021 ◽  
Vol 5 ◽  
Author(s):  
Reto Gmür ◽  
Donat Agosti
Keyword(s):  
Query Language ◽  
Building Blocks ◽  
Individual Treatment ◽  
Knowledge Graph ◽  
Triple Store ◽  
Related Group ◽  
Description Framework ◽  
Basic Vocabulary ◽  
User Friendly ◽  
Machine Readable

Taxonomic treatments, sections of publications documenting the features or distribution of a related group of organisms (called a “taxon”, plural “taxa”) in ways adhering to highly formalized conventions, and published in scientific journals, shape our understanding of global biodiversity (Catapano 2019). Treatments are the building blocks of the evolving scientific consensus on taxonomic entities. The semantics of these treatments and their relationships are highly structured: taxa are introduced, merged, made obsolete, split, renamed, associated with specimens and so on. Plazi makes this content available in machine-readable form using Resource Description Framework (RDF) . RDF is the standard model for Linked Data and the Semantic Web. RDF can be exchanged in different formats (aka concrete syntaxes) such as RDF/XML or Turtle. The data model describes graph structures and relies on Internationalized Resource Identifiers (IRIs) , ontologies such as Darwin Core basic vocabulary are used to assign meaning to the identifiers. For Synospecies, we unite all treatments into one large knowledge graph, modelling taxonomic knowledge and its evolution with complete references to quotable treatments. However, this knowledge graph expresses much more than any individual treatment could convey because every referenced entity is linked to every other relevant treatment. On synospecies.plazi.org, we provide a user-friendly interface to find the names and treatments related to a taxon. An advanced mode allows execution of queries using the SPARQL query language.

scholarly journals Standardised Globally Unique Specimen Identifiers

2018 ◽  
Vol 2 ◽  
pp. e26658 ◽  
Author(s):  
Anton Güntsch ◽  
Quentin Groom ◽  
Roger Hyam ◽  
Simon Chagnoux ◽  
Dominik Röpert ◽  
...  
Keyword(s):  
Open Data ◽  
Source Information ◽  
New Era ◽  
Semantic Inference ◽  
Description Framework ◽  
Data Objects ◽  
Machine Readable ◽  
Resource Description ◽  
Local Identifier ◽  
Correct Implementation

A simple, permanent and reliable specimen identifier system is needed to take the informatics of collections into a new era of interoperability. A system of identifiers based on HTTP URI (Uniform Resource Identifiers), endorsed by the Consortium of European Taxonomic Facilities (CETAF), has now been rolled out to 14 member organisations (Güntsch et al. 2017). CETAF-Identifiers have a Linked Open Data redirection mechanism for both human- and machine-readable access and, if fully implemented, provide Resource Description Framework (RDF) -encoded specimen data following best practices continuously improved by members of the initiative. To date, more than 20 million physical collection objects have been equipped with CETAF Identifiers (Groom et al. 2017). To facilitate the implementation of stable identifiers, simple redirection scripts and guidelines for deciding on the local identifier syntax have been compiled (http://cetafidentifiers.biowikifarm.net/wiki/Main_Page). Furthermore, a capable "CETAF Specimen URI Tester" (http://herbal.rbge.info/) provides an easy-to-use service for testing whether the existing identifiers are operational. For the usability and potential of any identifier system associated with evolving data objects, active links to the source information are critically important. This is particularly true for natural history collections facing the next wave of industrialised mass digitisation, where specimens come online with only basic, but rapidly evolving label data. Specimen identifier systems must therefore have components for monitoring the availability and correct implementation of individual data objects. Our next implementation steps will involve the development of a "Semantic Specimen Catalogue", which has a list of all existing specimen identifiers together with the latest RDF metadata snapshot. The catalogue will be used for semantic inference across collections as well as the basis for periodic testing of identifiers.

Storing massive Resource Description Framework (RDF) data: a survey

2016 ◽  
Vol 31 (4) ◽  
pp. 391-413 ◽  
Author(s):  
Zongmin Ma ◽  
Miriam A. M. Capretz ◽  
Li Yan
Keyword(s):  
Data Storage ◽  
Resource Description Framework ◽  
Relational Databases ◽  
Query Language ◽  
Current State ◽  
Rdf Data ◽  
Description Framework ◽  
Resource Description ◽  
Flexible Model ◽  
The Web

AbstractThe Resource Description Framework (RDF) is a flexible model for representing information about resources on the Web. As a W3C (World Wide Web Consortium) Recommendation, RDF has rapidly gained popularity. With the widespread acceptance of RDF on the Web and in the enterprise, a huge amount of RDF data is being proliferated and becoming available. Efficient and scalable management of RDF data is therefore of increasing importance. RDF data management has attracted attention in the database and Semantic Web communities. Much work has been devoted to proposing different solutions to store RDF data efficiently. This paper focusses on using relational databases and NoSQL (for ‘not only SQL (Structured Query Language)’) databases to store massive RDF data. A full up-to-date overview of the current state of the art in RDF data storage is provided in the paper.

scholarly journals Using superimposed multidimensional schemas and OLAP patterns for RDF data analysis

2018 ◽  
Vol 8 (1) ◽  
pp. 18-37 ◽  
Author(s):  
Median Hilal ◽  
Christoph G. Schuetz ◽  
Michael Schrefl
Keyword(s):  
Data Analysis ◽  
Semantic Web ◽  
Query Language ◽  
Query Languages ◽  
Sparql Query ◽  
Semantic Web Technologies ◽  
Rdf Data ◽  
Self Service ◽  
Description Framework ◽  
Definition Of

Abstract The foundations for traditional data analysis are Online Analytical Processing (OLAP) systems that operate on multidimensional (MD) data. The Resource Description Framework (RDF) serves as the foundation for the publication of a growing amount of semantic web data still largely untapped by companies for data analysis. Most RDF data sources, however, do not correspond to the MD modeling paradigm and, as a consequence, elude traditional OLAP. The complexity of RDF data in terms of structure, semantics, and query languages renders RDF data analysis challenging for a typical analyst not familiar with the underlying data model or the SPARQL query language. Hence, conducting RDF data analysis is not a straightforward task. We propose an approach for the definition of superimposed MD schemas over arbitrary RDF datasets and show how to represent the superimposed MD schemas using well-known semantic web technologies. On top of that, we introduce OLAP patterns for RDF data analysis, which are recurring, domain-independent elements of data analysis. Analysts may compose queries by instantiating a pattern using only the MD concepts and business terms. Upon pattern instantiation, the corresponding SPARQL query over the source data can be automatically generated, sparing analysts from technical details and fostering self-service capabilities.

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