SPARQL Research Articles

FAIR-compliant clinical, radiomics and DICOM metadata of RIDER, interobserver, Lung1 and head-Neck1 TCIA collections.

PurposeOne of the most frequently cited radiomics investigations showed that features automatically extracted from routine clinical images could be used in prognostic modeling. These images have been made publicly accessible via The Cancer Imaging Archive (TCIA). There have been numerous requests for additional explanatory metadata on the following datasets — RIDER, Interobserver, Lung1, and Head–Neck1. To support repeatability, reproducibility, generalizability, and transparency in radiomics research, we publish the subjects’ clinical data, extracted radiomics features, and digital imaging and communications in medicine (DICOM) headers of these four datasets with descriptive metadata, in order to be more compliant with findable, accessible, interoperable, and reusable (FAIR) data management principles.Acquisition and validation methodsOverall survival time intervals were updated using a national citizens registry after internal ethics board approval. Spatial offsets of the primary gross tumor volume (GTV) regions of interest (ROIs) associated with the Lung1 CT series were improved on the TCIA. GTV radiomics features were extracted using the open‐source Ontology‐Guided Radiomics Analysis Workflow (O‐RAW). We reshaped the output of O‐RAW to map features and extraction settings to the latest version of Radiomics Ontology, so as to be consistent with the Image Biomarker Standardization Initiative (IBSI). Digital imaging and communications in medicine metadata was extracted using a research version of Semantic DICOM (SOHARD, GmbH, Fuerth; Germany). Subjects’ clinical data were described with metadata using the Radiation Oncology Ontology. All of the above were published in Resource Descriptor Format (RDF), that is, triples. Example SPARQL queries are shared with the reader to use on the online triples archive, which are intended to illustrate how to exploit this data submission.Data formatThe accumulated RDF data are publicly accessible through a SPARQL endpoint where the triples are archived. The endpoint is remotely queried through a graph database web application at http://sparql.cancerdata.org. SPARQL queries are intrinsically federated, such that we can efficiently cross‐reference clinical, DICOM, and radiomics data within a single query, while being agnostic to the original data format and coding system. The federated queries work in the same way even if the RDF data were partitioned across multiple servers and dispersed physical locations.Potential applicationsThe public availability of these data resources is intended to support radiomics features replication, repeatability, and reproducibility studies by the academic community. The example SPARQL queries may be freely used and modified by readers depending on their research question. Data interoperability and reusability are supported by referencing existing public ontologies. The RDF data are readily findable and accessible through the aforementioned link. Scripts used to create the RDF are made available at a code repository linked to this submission: https://gitlab.com/UM‐CDS/FAIR‐compliant_clinical_radiomics_and_DICOM_metadata.

Semantic Querying of Hospital Data Using an Ontology-Based Model of Discharge Summaries and ICD 10.

This paper focusses on the question of knowledge-based modeling of discharge summaries for semantic requesting in the context of hospital reporting process. An ontology was designed and implemented to capture patient data and required expert knowledge. The modeling process was carried out manually using Protégé after an initial reverse engineering of the official format of discharge summaries. An OWL 2 model was built integrating discharge summaries ontology and ICD 10 hierarchy. The framework is operationalized using the OpenLink Virtuoso database system (RDF store), enabling SPARQL queries and basic reasoning features. The evaluation was performed by implementing a use case based on patient comorbidities.

Mapping Manuscript Migrations Knowledge Graph: Data for Tracing the History and Provenance of Medieval and Renaissance Manuscripts

The Mapping Manuscript Migrations (MMM) project transformed three separate datasets relating to the history and provenance of medieval and Renaissance manuscripts into a unified knowledge graph. The source databases are: Schoenberg Database of Manuscripts, from the Schoenberg Institute for Manuscript Studies, University of Pennsylvania; Bibale, from the Institut de recherche et d’histoire des textes (IRHT-CNRS, Paris); and Medieval Manuscripts in Oxford Libraries, from the Bodleian Libraries, University of Oxford. The data consist of more than 20 million RDF triples which have been mapped to the MMM Data Model. The model combines classes and properties from CIDOC-CRM and FRBR, together with some specific MMM elements. The Knowledge Graph was created using the MMM data transformation pipeline. The MMM dataset is available from the Zenodo repository, and can be directly deployed on a SPARQL endpoint using a docker recipe. To test and demonstrate its usefulness, the MMM Knowledge Graph is in use in the MMM Semantic Portal: https://mappingmanuscriptmigrations.org.

Autonomous search in a social and ubiquitous Web

Recent W3C recommendations for the Web of Things (WoT) and the Social Web are turning hypermedia into a homogeneous information fabric that interconnects heterogeneous resources: devices, people, information resources, abstract concepts, etc. The integration of multi-agent systems with such hypermedia environments now provides a means to distribute autonomous behavior in worldwide pervasive systems. A central problem then is to enable autonomous agents to discover heterogeneous resources in worldwide and dynamic hypermedia environments. This is a problem in particular in WoT environments that rely on open standards and evolve rapidly—thus requiring agents to adapt their behavior at run time in pursuit of their design objectives. To this end, we developed a hypermedia search engine for the WoT that allows autonomous agents to perform approximate search queries in order to retrieve relevant resources in their environment in (weak) real time. The search engine crawls dynamic WoT environments to discover and index device metadata described with the W3C WoT Thing Description, and exposes a SPARQL endpoint that agents can use for approximate search. To demonstrate the feasibility of our approach, we implemented a prototype application for the maintenance of industrial robots in worldwide manufacturing systems. The prototype demonstrates that our semantic hypermedia search engine enhances the flexibility and agility of autonomous agents in a social and ubiquitous Web.

“Sampo” Model and Semantic Portals for Digital Humanities on the Semantic Web

This paper presents the vision and longstanding work in Finland on creating a national Cultural Heritage ontology infrastructure and semantic portals based on Linked Data on the Semantic Web. In particular, the “Sampo” series of semantic portals is considered, including CultureSampo (2009), TravelSampo (2011), BookSampo (2011), WarSampo (2015), BiographySampo (2018), NameSampo (2019), WarWictimSampo (2019), FindSampo (2019), MMM (2020), LawSampo (2020), AcademySampo (2020), and ParliamentSampo (2022). They all share the “Sampo model” for publishing Cultural Heritage content the Semantic Web that typically involves three components: 1) A “business model” for harmonizing, aggregating, and publishing heterogeneous, distributed contents based on a shared ontology infrastructure. 2) An approach to interface design, where the data can be re-used and accessed independently from multiple application perspectives, while the data resides in a single SPARQL endpoint. 3) A two-step model for accessing and analyzing the data where the focus of interest is first filtered out using faceted semantic search, and then visualized or analyzed by ready-to-use Digital Humanities tools of the portal. This model has been proven useful in practise: Sampo portals have attracted lots users from tens of thousands to millions depending on the Sampo. It is argued that the next step ahead could be portals for serendipitous knowledge discovery where the tools, based on AI techniques, are able to find automatically serendipitous, “interesting” phenomena and research questions in the data, and even solve problems with explanations.

GlyGen data model and processing workflow.

SummaryGlycoinformatics plays a major role in glycobiology research, and the development of a comprehensive glycoinformatics knowledgebase is critical. This application note describes the GlyGen data model, processing workflow and the data access interfaces featuring programmatic use case example queries based on specific biological questions. The GlyGen project is a data integration, harmonization and dissemination project for carbohydrate and glycoconjugate-related data retrieved from multiple international data sources including UniProtKB, GlyTouCan, UniCarbKB and other key resources.Availability and implementationGlyGen web portal is freely available to access at https://glygen.org. The data portal, web services, SPARQL endpoint and GitHub repository are also freely available at https://data.glygen.org, https://api.glygen.org, https://sparql.glygen.org and https://github.com/glygener, respectively. All code is released under license GNU General Public License version 3 (GNU GPLv3) and is available on GitHub https://github.com/glygener. The datasets are made available under Creative Commons Attribution 4.0 International (CC BY 4.0) license.Supplementary information Supplementary data are available at Bioinformatics online.

Combining RDF and SPARQL with CP-theories to reason about preferences in a Linked Data setting

Combining RDF and SPARQL with CP-theories to reason about preferences in a Linked Data setting

Artificial Intelligence for Content and Context Metadata Retrieval in Photographs and Image Groups

In the age of the WWW consistent efforts have been made to make information from the archives available for the general public to facilitate access to the wealth of documentary history for research, consultation or education purposes. Linked Open Data (LOD)[1] provide a well suited framework to expose archival content to the general public while enriching it with content from other sources. This paper describes the creation of the first of its kind linked open data prototype to access data from the Historical Archive of the European Commission (HAS), carried out within ISA2 programme of the European Commission [2]. We present the designed ontology based on ISAD(G)[3], ISAAR(CPF)[4] and RIC-CM [5] models and the business processes of HAS, and the created knowledge base from a sample of HAS data, re-using authority lists from the Publication Office [6] and EuroVoc [7] and allowing querying via SPARQL endpoint [8].

GlyGen ‐ Computational Resources for Glycoscience

Advancing our understanding of the roles that glycosylation plays in development and disease is frequently hindered by the diversity of the data that must be integrated to gain insight into these complex phenomena. GlyGen is a maturing initiative, supported by the NIH Common Fund, with the goal of democratizing glycoscience research by developing and implementing a comprehensive data repository that integrates diverse types of data, including glycan structures, glycan biosynthesis enzymes, glycoproteins, three‐dimensional glycoprotein structures, along with genomic and proteomic knowledge. To achieve the highest possible integration and impact, GlyGen has established international collaborations with database providers from different domains (including but not limited to EBI, NCBI, PDB, GlyTouCan and UniCarbKB) and glycoscience researchers. Information from these resources and groups are standardized and cross‐linked to allow queries across multiple domains. To facilitate easy access to this information, an intuitive, web based interface ( http://glygen.org/) has been developed to visually represent the data and the connections between datasets. In addition to the browser‐based interface we are also developing RESTful webservice‐based APIs and SPARQL endpoints, allowing programmatic access to integrated datasets. For each glycan and glycoprotein in the dataset, GlyGen provides a details page that integrates available information. Individual details pages are interlinked with each other allowing easy data exploration across multiple domains. For example, users can browse from the webpage of a glycosylated protein to the glycan structures that have been described to be attached to this protein, and, from there, to other proteins that carry the same glycan. All information accessed through GlyGen is linked back to original sources, allowing users to browse through information pages in other resources. Our goal is to provide scientists with an easy way to access the complex information underlying state‐of‐the‐art knowledge that describes the biology of glycans and glycoproteins. To maximize usefulness of the GlyGen resource by the broadest possible user population, we have implemented a query interface that suggests likely “use‐case” questions. For instance, a question such as “What are the enzymes involved in the biosynthesis of glycan X in humans?” can be posed simply by providing minimal information (e.g. glycan X in the example). Answers are then returned following the completion of a query across multiple datasets and domains; the complexity of the query remains invisible to the user. Importantly, use‐case questions were developed as a result of outreach to potential users through community meetings and directed contacts. To schedule a demo of GlyGen or add your data to GlyGen contact Michael Tiemeyer ( mtiemeyer@ccrc.uga.edu) or Raja Mazumder ( mazumder@gwu.edu).Support or Funding InformationSupported by NIH Common Fund U01 GM124267‐01

Comparative Analysis of Information Retrieval using Ontology Based vs Traditional Information Systems in Food Science Domain

The current methods of searching and information retrieval are imprecise, often yielding results in tens of thousands of web pages. Extraction of the actual information needed often requires extensive manual browsing of retrieved documents. In order to address these drawbacks, this paper introduces an implementation in the field of food science of the ontology-based information retrieval system, and comparison is made with conventional information systems. The ontology of Food Semantic Web Knowledge Base (FSWKB) was built using the Protégé framework which supports two main models of ontology through the editors Protégé-Frames and Protégé-OWL. The FSWKB is composed of two heterogeneous ontologies, and these are merged and processed on a separate server application making use of the Apache Jena Fuseki an SPARQL server offering SPARQL endpoint. The experimental results indicated that ontology-based information systems are more effective in terms of their retrieval capability compared to the more conventional information retrieval systems. The retrieval effectiveness was measured in terms of precision and recall. The results of the work showed that traditional search results in average precision and recall levels of 0.92 and 0.18. The ontology-based test for precision and recall has average rates of 0.96 and 0.97.

A Framework for Exploration and Visualization of SPARQL Endpoint Information

Widely accepted standards, such as the Resource Description Framework, have provided unified ways for data provision aiming to facilitate the exchange of information between machines. This information became of interest to a wider audience due to its volume and variety but the available formats are posing significant challenges to users with limited knowledge of the Semantic Web. The SPARQL query language alleviates this barrier by facilitating the exploration of this information and many data providers have created dedicated SPARQL endpoints for their data. Many efforts have been dedicated to the development of systems that will provide access and support the exploration of these endpoints in a semantically correct and user friendly way. The main challenge of such approaches is the diversity of the information contained in the endpoints, which renders holistic or schema specific solutions obsolete. We present here an integrated platform that supports the users to the querying, exploration and visualization of information contained in SPARQL endpoints. The platform handles each query result independently based only on its characteristics, offering an endpoint and data schema agnostic solution. This is achieved through a Decision Support System, developed based on a knowledge base containing information experimentally collected from many endpoints, that allows us to provide case-specific visualization strategies for SPARQL query results based exclusively on features extracted from the result.

FAIR + FIT: Guiding Principles and Functional Metrics for Linked Open Data (LOD) KOS Products

AbstractPurposeTo develop a set of metrics and identify criteria for assessing the functionality of LOD KOS products while providing common guiding principles that can be used by LOD KOS producers and users to maximize the functions and usages of LOD KOS products.Design/methodology/approachData collection and analysis were conducted at three time periods in 2015–16, 2017 and 2019. The sample data used in the comprehensive data analysis comprises all datasets tagged as types of KOS in the Datahub and extracted through their respective SPARQL endpoints. A comparative study of the LOD KOS collected from terminology services Linked Open Vocabularies (LOV) and BioPortal was also performed.FindingsThe study proposes a set of Functional, Impactful and Transformable (FIT) metrics for LOD KOS as value vocabularies. The FAIR principles, with additional recommendations, are presented for LOD KOS as open data.Research limitationsThe metrics need to be further tested and aligned with the best practices and international standards of both open data and various types of KOS.Practical implicationsAssessment performed with FAIR and FIT metrics support the creation and delivery of user-friendly, discoverable and interoperable LOD KOS datasets which can be used for innovative applications, act as a knowledge base, become a foundation of semantic analysis and entity extractions and enhance research in science and the humanities.Originality/valueOur research provides best practice guidelines for LOD KOS as value vocabularies.

BiGe-Onto: An ontology-based system for managing biodiversity and biogeography data1

Great progress to digitize the world’s available Biodiversity and Biogeography data have been made recently, but managing data from many different providers and research domains still remains a challenge. A review of the current landscape of metadata standards and ontologies in Biodiversity sciences suggests that existing standards, such as the Darwin Core terminology, are inadequate for describing Biodiversity data in a semantically meaningful and computationally useful way. As a contribution to fill this gap, we present an ontology-based system, called BiGe-Onto, designed to manage data together from Biodiversity and Biogeography. As data sources, we use two internationally recognized repositories: the Global Biodiversity Information Facility (GBIF) and the Ocean Biogeographic Information System (OBIS). BiGe-Onto system is composed of (i) BiGe-Onto Architecture (ii) a conceptual model called BiGe-Onto specified in OntoUML, (iii) an operational version of BiGe-Onto encoded in OWL 2, and (iv) an integrated dataset for its exploitation through a SPARQL endpoint. We will show use cases that allow researchers to answer questions that manage information from both domains.

Enabling text search on SPARQL endpoints through OSCAR

Enabling text search on SPARQL endpoints through OSCAR

Fast and Practical Snippet Generation for RDF Datasets

Triple-structured open data creates value in many ways. However, the reuse of datasets is still challenging. Users feel difficult to assess the usefulness of a large dataset containing thousands or millions of triples. To satisfy the needs, existing abstractive methods produce a concise high-level abstraction of data. Complementary to that, we adopt the extractive strategy and aim to select the optimum small subset of data from a dataset as a snippet to compactly illustrate the content of the dataset. This has been formulated as a combinatorial optimization problem in our previous work. In this article, we design a new algorithm for the problem, which is an order of magnitude faster than the previous one but has the same approximation ratio. We also develop an anytime algorithm that can generate empirically better solutions using additional time. To suit datasets that are partially accessible via online query services (e.g., SPARQL endpoints for RDF data), we adapt our algorithms to trade off quality of snippet for feasibility and efficiency in the Web environment. We carry out extensive experiments based on real RDF datasets and SPARQL endpoints for evaluating quality and running time. The results demonstrate the effectiveness and practicality of our proposed algorithms.

The neXtProt knowledgebase in 2020: data, tools and usability improvements.

The neXtProt knowledgebase (https://www.nextprot.org) is an integrative resource providing both data on human protein and the tools to explore these. In order to provide comprehensive and up-to-date data, we evaluate and add new data sets. We describe the incorporation of three new data sets that provide expression, function, protein-protein binary interaction, post-translational modifications (PTM) and variant information. New SPARQL query examples illustrating uses of the new data were added. neXtProt has continued to develop tools for proteomics. We have improved the peptide uniqueness checker and have implemented a new protein digestion tool. Together, these tools make it possible to determine which proteases can be used to identify trypsin-resistant proteins by mass spectrometry. In terms of usability, we have finished revamping our web interface and completely rewritten our API. Our SPARQL endpoint now supports federated queries. All the neXtProt data are available via our user interface, API, SPARQL endpoint and FTP site, including the new PEFF 1.0 format files. Finally, the data on our FTP site is now CC BY 4.0 to promote its reuse.

Enzyme annotation in UniProtKB using Rhea.

MotivationTo provide high quality computationally tractable enzyme annotation in UniProtKB using Rhea, a comprehensive expert-curated knowledgebase of biochemical reactions which describes reaction participants using the ChEBI (Chemical Entities of Biological Interest) ontology.ResultsWe replaced existing textual descriptions of biochemical reactions in UniProtKB with their equivalents from Rhea, which is now the standard for annotation of enzymatic reactions in UniProtKB. We developed improved search and query facilities for the UniProt website, REST API and SPARQL endpoint that leverage the chemical structure data, nomenclature and classification that Rhea and ChEBI provide.Availability and implementationUniProtKB at https://www.uniprot.org; UniProt REST API at https://www.uniprot.org/help/api; UniProt SPARQL endpoint at https://sparql.uniprot.org/; Rhea at https://www.rhea-db.org.

Building a Semantic RESTFul API for Achieving Interoperability between a Pharmacist and a Doctor using JENA and FUSEKI

Interoperability within different healthcare systems (clinics/hospitals/pharmacies) remains an issue of further research due to a barrier in sharing of the patient’s Electronic Health Record (EHR) information. To solve this problem, cross healthcare system collaboration is required. This paper proposes an interoperability framework that enables a pharmacist to access an electronic version of the patient’s prescription from the doctor using a RESTFul API with ease. Semantic technology standards like Web Ontology Language (OWL), RDF (Resource Description Framework) and SPARQL (SPARQL Protocol and RDF Query Language) were used to implement the framework using JENA semantic framework tool to demonstrate how interoperability is achieved between a pharmacy and a clinic JENA was used to generate the ontology models for the pharmacy called pharmacy.rdf and clinic called clinic.rdf. The two models contain all the information from the two isolated systems. The JENA reasoner was used to merge the two ontology models into a single model.rdf file for easy querying with SPARQL. The model.rdf file was uploaded into a triple store database created using FUSEKI server. SPARQL Endpoint generated from FUSEKI was used to query the triple store database using a RESTFul API. The system was able to query the triple store database and output the results containing the prescription name and its details in JSON and XML formats which can be read by both machines and humans.

Technical Note: Ontology-guided radiomics analysis workflow (O-RAW).

PurposeRadiomics is the process to automate tumor feature extraction from medical images. This has shown potential for quantifying the tumor phenotype and predicting treatment response. The three major challenges of radiomics research and clinical adoption are: (a) lack of standardized methodology for radiomics analyses, (b) lack of a universal lexicon to denote features that are semantically equivalent, and (c) lists of feature values alone do not sufficiently capture the details of feature extraction that might nonetheless strongly affect feature values (e.g. image normalization or interpolation parameters). These barriers hamper multicenter validation studies applying subtly different imaging protocols, preprocessing steps and radiomics software. We propose an open‐source ontology‐guided radiomics analysis workflow (O‐RAW) to address the above challenges in the following manner: (a) distributing a free and open‐source software package for radiomics analysis, (b) deploying a standard lexicon to uniquely describe features in common usage and (c) provide methods to publish radiomic features as a semantically interoperable data graph object complying to FAIR (findable accessible interoperable reusable) data principles.MethodsO‐RAW was developed in Python, and has three major modules using open‐source component libraries (PyRadiomics Extension and PyRadiomics). First, PyRadiomics Extension takes standard DICOM‐RT (Radiotherapy) input objects (i.e. a DICOM series and an RTSTRUCT file) and parses them as arrays of voxel intensities and a binary mask corresponding to a volume of interest (VOI). Next, these arrays are passed into PyRadiomics, which performs the feature extraction procedure and returns a Python dictionary object. Lastly, PyRadiomics Extension parses this dictionary as a W3C‐compliant Semantic Web “triple store” (i.e., list of subject‐predicate‐object statements) with relevant semantic meta‐labels drawn from the radiation oncology ontology and radiomics ontology. The output can be published on an SPARQL endpoint, and can be remotely examined via SPARQL queries or to a comma separated file for further analysis.ResultsWe showed that O‐RAW executed efficiently on four datasets with different modalities, RIDER (CT), MMD (CT), CROSS (PET) and THUNDER (MR). The test was performed on an HP laptop running Windows 7 operating system and 8GB RAM on which we noted execution time including DICOM images and associated RTSTRUCT matching, binary mask conversion of a single VOI, batch‐processing of feature extraction (105 basic features in PyRadiomics), and the conversion to an resource description framework (RDF) object. The results were (RIDER) 407.3, (MMD) 123.5, (CROSS) 513.2 and (THUNDER) 128.9 s for a single VOI. In addition, we demonstrated a use case, taking images from a public repository and publishing the radiomics results as FAIR data in this study on http://www.radiomics.org. Finally, we provided a practical instance to show how a user could query radiomic features and track the calculation details based on the RDF graph object created by O‐RAW via a simple SPARQL query.ConclusionsWe implemented O‐RAW for FAIR radiomics analysis, and successfully published radiomic features from DICOM‐RT objects as semantic web triples. Its practicability and flexibility can greatly increase the development of radiomics research and ease transfer to clinical practice.

Ontology based mining of pathogen\u2013disease associations from literature

BackgroundInfectious diseases claim millions of lives especially in the developing countries each year. Identification of causative pathogens accurately and rapidly plays a key role in the success of treatment. To support infectious disease research and mechanisms of infection, there is a need for an open resource on pathogen–disease associations that can be utilized in computational studies. A large number of pathogen–disease associations is available from the literature in unstructured form and we need automated methods to extract the data.ResultsWe developed a text mining system designed for extracting pathogen–disease relations from literature. Our approach utilizes background knowledge from an ontology and statistical methods for extracting associations between pathogens and diseases. In total, we extracted a total of 3420 pathogen–disease associations from literature. We integrated our literature-derived associations into a database which links pathogens to their phenotypes for supporting infectious disease research.ConclusionsTo the best of our knowledge, we present the first study focusing on extracting pathogen–disease associations from publications. We believe the text mined data can be utilized as a valuable resource for infectious disease research. All the data is publicly available from https://github.com/bio-ontology-research-group/padimiand through a public SPARQL endpoint from http://patho.phenomebrowser.net/.