Moussab/ORKG-training-evaluation-set huggingface dataset:
Research field: Information Science
Title: A streamlined workflow for conversion, peer review, and publication of genomics metadata as omics data papers 
Abstract: Abstract Background Data papers have emerged as a powerful instrument for open data publishing, obtaining credit, and establishing priority for datasets generated in scientific experiments. Academic publishing improves data and metadata quality through peer review and increases the impact of datasets by enhancing their visibility, accessibility, and reusability. Objective We aimed to establish a new type of article structure and template for omics studies: the omics data paper. To improve data interoperability and further incentivize researchers to publish well-described datasets, we created a prototype workflow for streamlined import of genomics metadata from the European Nucleotide Archive directly into a data paper manuscript. Methods An omics data paper template was designed by defining key article sections that encourage the description of omics datasets and methodologies. A metadata import workflow, based on REpresentational State Transfer services and Xpath, was prototyped to extract information from the European Nucleotide Archive, ArrayExpress, and BioSamples databases. Findings The template and workflow for automatic import of standard-compliant metadata into an omics data paper manuscript provide a mechanism for enhancing existing metadata through publishing. Conclusion The omics data paper structure and workflow for import of genomics metadata will help to bring genomic and other omics datasets into the spotlight. Promoting enhanced metadata descriptions and enforcing manuscript peer review and data auditing of the underlying datasets brings additional quality to datasets. We hope that streamlined metadata reuse for scholarly publishing encourages authors to create enhanced metadata descriptions in the form of data papers to improve both the quality of their metadata and its findability and accessibility.
Extracted statement — Process: open data publishing
Research field: Information Science
Title: OpenBiodiv: A Knowledge Graph for Literature-Extracted Linked Open Data in Biodiversity Science
Abstract: Hundreds of years of biodiversity research have resulted in the accumulation of a substantial pool of communal knowledge; however, most of it is stored in silos isolated from each other, such as published articles or monographs. The need for a system to store and manage collective biodiversity knowledge in a community-agreed and interoperable open format has evolved into the concept of the Open Biodiversity Knowledge Management System (OBKMS). This paper presents OpenBiodiv: An OBKMS that utilizes semantic publishing workflows, text and data mining, common standards, ontology modelling and graph database technologies to establish a robust infrastructure for managing biodiversity knowledge. It is presented as a Linked Open Dataset generated from scientific literature. OpenBiodiv encompasses data extracted from more than 5000 scholarly articles published by Pensoft and many more taxonomic treatments extracted by Plazi from journals of other publishers. The data from both sources are converted to Resource Description Framework (RDF) and integrated in a graph database using the OpenBiodiv-O ontology and an RDF version of the Global Biodiversity Information Facility (GBIF) taxonomic backbone. Through the application of semantic technologies, the project showcases the value of open publishing of Findable, Accessible, Interoperable, Reusable (FAIR) data towards the establishment of open science practices in the biodiversity domain.
Extracted statement — Data: OpenBiodiv encompasses data
Research field: Information Science
Title: ORCID: a system to uniquely identify researchers
Abstract: The Open Researcher & Contributor ID (ORCID) registry presents a unique opportunity to solve the problem of author name ambiguity. At its core the value of the ORCID registry is that it crosses disciplines, organizations, and countries, linking ORCID with both existing identifier schemes as well as publications and other research activities. By supporting linkages across multiple datasets – clinical trials, publications, patents, datasets – such a registry becomes a switchboard for researchers and publishers alike in managing the dissemination of research findings. We describe use cases for embedding ORCID identifiers in manuscript submission workflows, prior work searches, manuscript citations, and repository deposition. We make recommendations for storing and displaying ORCID identifiers in publication metadata to include ORCID identifiers, with CrossRef integration as a specific example. Finally, we provide an overview of ORCID membership and integration tools and resources.
Extracted statement — uses identifier system: ORCID Identifiers
Research field: Information Science
Title: The Pattern of Patterns: What is a pattern in conceptual modeling?
Abstract: It has been proven that using structured methods to represent the domain reduces human errors in the process of creating models and also in the process of using them. Using modeling patterns is a proven structural method in this regard. A pattern is a generalizable reusable solution to a design problem. Positive effects of using patterns were demonstrated in several experimental studies and explained using theories. However, detailed knowledge about how properties of patterns lead to increased performance in writing and reading conceptual models is currently lacking. This paper proposes a theoretical framework to characterize the properties of ontology-driven conceptual model patterns. The development of such framework is the first step in investigating the effects of pattern properties and devising rules to compose patterns based on well-understood properties.
Extracted statement — Data: pattern properties
Research field: Information Science
Title: Ontology-based E-learning Content Recommender System for Addressing the Pure Cold-start Problem
Abstract: E-learning recommender systems are gaining significance nowadays due to its ability to enhance the learning experience by providing tailor-made services based on learner preferences. A Personalized Learning Environment (PLE) that automatically adapts to learner characteristics such as learning styles and knowledge level can recommend appropriate learning resources that would favor the learning process and improve learning outcomes. The pure cold-start problem is a relevant issue in PLEs, which arises due to the lack of prior information about the new learner in the PLE to create appropriate recommendations. This article introduces a semantic framework based on ontology to address the pure cold-start problem in content recommenders. The ontology encapsulates the domain knowledge about the learners as well as Learning Objects (LOs). The semantic model that we built has been experimented with different combinations of the key learner parameters such as learning style, knowledge level, and background knowledge. The proposed framework utilizes these parameters to build natural learner groups from the learner ontology using SPARQL queries. The ontology holds 480 learners’ data, 468 annotated learning objects with 5,600 learner ratings. A multivariate k-means clustering algorithm, an unsupervised machine learning technique for grouping similar data, is used to evaluate the learner similarity computation accuracy. The learner satisfaction achieved with the proposed model is measured based on the ratings given by the 40 participants of the experiments. From the evaluation perspective, it is evident that 79% of the learners are satisfied with the recommendations generated by the proposed model in pure cold-start condition.
Extracted statement — keywords: personalized learning environment
Research field: Information Science
Title: Expanding horizons in historical linguistics with the 400-million word Corpus of Historical American English
Abstract: The Corpus of Historical American English (COHA) contains 400 million words in more than 100,000 texts which date from the 1810s to the 2000s. The corpus contains texts from fiction, popular magazines, newspapers and non-fiction books, and is balanced by genre from decade to decade. It has been carefully lemmatised and tagged for part-of-speech, and uses the same architecture as the Corpus of Contemporary American English (COCA), BYU-BNC, the TIME Corpus and other corpora. COHA allows for a wide range of research on changes in lexis, morphology, syntax, semantics, and American culture and society (as viewed through language change), in ways that are probably not possible with any text archive (e.g., Google Books) or any other corpus of historical American English.
Extracted statement — Corpus genres: popular magazines
Research field: Information Science
Title: The Pattern of Patterns: What is a pattern in conceptual modeling?
Abstract: It has been proven that using structured methods to represent the domain reduces human errors in the process of creating models and also in the process of using them. Using modeling patterns is a proven structural method in this regard. A pattern is a generalizable reusable solution to a design problem. Positive effects of using patterns were demonstrated in several experimental studies and explained using theories. However, detailed knowledge about how properties of patterns lead to increased performance in writing and reading conceptual models is currently lacking. This paper proposes a theoretical framework to characterize the properties of ontology-driven conceptual model patterns. The development of such framework is the first step in investigating the effects of pattern properties and devising rules to compose patterns based on well-understood properties.
Extracted statement — Process: Positive effects
Research field: Information Science
Title: The Pattern of Patterns: What is a pattern in conceptual modeling?
Abstract: It has been proven that using structured methods to represent the domain reduces human errors in the process of creating models and also in the process of using them. Using modeling patterns is a proven structural method in this regard. A pattern is a generalizable reusable solution to a design problem. Positive effects of using patterns were demonstrated in several experimental studies and explained using theories. However, detailed knowledge about how properties of patterns lead to increased performance in writing and reading conceptual models is currently lacking. This paper proposes a theoretical framework to characterize the properties of ontology-driven conceptual model patterns. The development of such framework is the first step in investigating the effects of pattern properties and devising rules to compose patterns based on well-understood properties.
Extracted statement — Process: process of creating
Research field: Information Science
Title: The Pattern of Patterns: What is a pattern in conceptual modeling?
Abstract: It has been proven that using structured methods to represent the domain reduces human errors in the process of creating models and also in the process of using them. Using modeling patterns is a proven structural method in this regard. A pattern is a generalizable reusable solution to a design problem. Positive effects of using patterns were demonstrated in several experimental studies and explained using theories. However, detailed knowledge about how properties of patterns lead to increased performance in writing and reading conceptual models is currently lacking. This paper proposes a theoretical framework to characterize the properties of ontology-driven conceptual model patterns. The development of such framework is the first step in investigating the effects of pattern properties and devising rules to compose patterns based on well-understood properties.
Extracted statement — Data: properties of patterns
Research field: Information Science
Title: The MIPS mammalian protein–protein interaction database
Abstract: SUMMARY The MIPS mammalian protein-protein interaction database (MPPI) is a new resource of high-quality experimental protein interaction data in mammals. The content is based on published experimental evidence that has been processed by human expert curators. We provide the full dataset for download and a flexible and powerful web interface for users with various requirements.
Extracted statement — Domain: Protein-protein interaction
Research field: Information Science
Title: OpenBiodiv: A Knowledge Graph for Literature-Extracted Linked Open Data in Biodiversity Science
Abstract: Hundreds of years of biodiversity research have resulted in the accumulation of a substantial pool of communal knowledge; however, most of it is stored in silos isolated from each other, such as published articles or monographs. The need for a system to store and manage collective biodiversity knowledge in a community-agreed and interoperable open format has evolved into the concept of the Open Biodiversity Knowledge Management System (OBKMS). This paper presents OpenBiodiv: An OBKMS that utilizes semantic publishing workflows, text and data mining, common standards, ontology modelling and graph database technologies to establish a robust infrastructure for managing biodiversity knowledge. It is presented as a Linked Open Dataset generated from scientific literature. OpenBiodiv encompasses data extracted from more than 5000 scholarly articles published by Pensoft and many more taxonomic treatments extracted by Plazi from journals of other publishers. The data from both sources are converted to Resource Description Framework (RDF) and integrated in a graph database using the OpenBiodiv-O ontology and an RDF version of the Global Biodiversity Information Facility (GBIF) taxonomic backbone. Through the application of semantic technologies, the project showcases the value of open publishing of Findable, Accessible, Interoperable, Reusable (FAIR) data towards the establishment of open science practices in the biodiversity domain.
Extracted statement — Data: published articles or monographs
Research field: Information Science
Title: OpenBiodiv: A Knowledge Graph for Literature-Extracted Linked Open Data in Biodiversity Science
Abstract: Hundreds of years of biodiversity research have resulted in the accumulation of a substantial pool of communal knowledge; however, most of it is stored in silos isolated from each other, such as published articles or monographs. The need for a system to store and manage collective biodiversity knowledge in a community-agreed and interoperable open format has evolved into the concept of the Open Biodiversity Knowledge Management System (OBKMS). This paper presents OpenBiodiv: An OBKMS that utilizes semantic publishing workflows, text and data mining, common standards, ontology modelling and graph database technologies to establish a robust infrastructure for managing biodiversity knowledge. It is presented as a Linked Open Dataset generated from scientific literature. OpenBiodiv encompasses data extracted from more than 5000 scholarly articles published by Pensoft and many more taxonomic treatments extracted by Plazi from journals of other publishers. The data from both sources are converted to Resource Description Framework (RDF) and integrated in a graph database using the OpenBiodiv-O ontology and an RDF version of the Global Biodiversity Information Facility (GBIF) taxonomic backbone. Through the application of semantic technologies, the project showcases the value of open publishing of Findable, Accessible, Interoperable, Reusable (FAIR) data towards the establishment of open science practices in the biodiversity domain.
Extracted statement — Material: published articles or monographs
Research field: Information Science
Title: Ontology-based E-learning Content Recommender System for Addressing the Pure Cold-start Problem
Abstract: E-learning recommender systems are gaining significance nowadays due to its ability to enhance the learning experience by providing tailor-made services based on learner preferences. A Personalized Learning Environment (PLE) that automatically adapts to learner characteristics such as learning styles and knowledge level can recommend appropriate learning resources that would favor the learning process and improve learning outcomes. The pure cold-start problem is a relevant issue in PLEs, which arises due to the lack of prior information about the new learner in the PLE to create appropriate recommendations. This article introduces a semantic framework based on ontology to address the pure cold-start problem in content recommenders. The ontology encapsulates the domain knowledge about the learners as well as Learning Objects (LOs). The semantic model that we built has been experimented with different combinations of the key learner parameters such as learning style, knowledge level, and background knowledge. The proposed framework utilizes these parameters to build natural learner groups from the learner ontology using SPARQL queries. The ontology holds 480 learners’ data, 468 annotated learning objects with 5,600 learner ratings. A multivariate k-means clustering algorithm, an unsupervised machine learning technique for grouping similar data, is used to evaluate the learner similarity computation accuracy. The learner satisfaction achieved with the proposed model is measured based on the ratings given by the 40 participants of the experiments. From the evaluation perspective, it is evident that 79% of the learners are satisfied with the recommendations generated by the proposed model in pure cold-start condition.
Extracted statement — keywords: pure cold-start problem
Research field: Information Science
Title: Scalable SPARQL querying of large RDF graphs
Abstract: The generation of RDF data has accelerated to the point where many data sets need to be partitioned across multiple machines in order to achieve reasonable performance when querying the data. Although tremendous progress has been made in the Semantic Web community for achieving high performance data management on a single node, current solutions that allow the data to be partitioned across multiple machines are highly inefficient. In this paper, we introduce a scalable RDF data management system that is up to three orders of magnitude more efficient than popular multi-node RDF data management systems. In so doing, we introduce techniques for (1) leveraging state-of-the-art single node RDF-store technology (2) partitioning the data across nodes in a manner that helps accelerate query processing through locality optimizations and (3) decomposing SPARQL queries into high performance fragments that take advantage of how data is partitioned in a cluster.
Extracted statement — Material: RDF data
Research field: Information Science
Title: A Hybrid Knowlegde-Based Approach for Recommending Massive Learning Activities
Abstract: In recent years, the development of recommender systems has attracted increased interest in several domains, especially in e-learning. Massive Open Online Courses have brought a revolution. However, deficiency in support and personalization in this context drive learners to lose their motivation and leave the learning process. To overcome this problem we focus on adapting learning activities to learners' needs using a recommender system.This paper attempts to provide an introduction to different recommender systems for e-learning settings, as well as to present our proposed recommender system for massive learning activities in order to provide learners with the suitable learning activities to follow the learning process and maintain their motivation. We propose a hybrid knowledge-based recommender system based on ontology for recommendation of e-learning activities to learners in the context of MOOCs. In the proposed recommendation approach, ontology is used to model and represent the knowledge about the domain model, learners and learning activities.
Extracted statement — keywords: recommender system
Research field: Information Science
Title: The New DBpedia Release Cycle: Increasing Agility and Efficiency in Knowledge Extraction Workflows
Abstract: Abstract Since its inception in 2007, DBpedia has been constantly releasing open data in RDF, extracted from various Wikimedia projects using a complex software system called the DBpedia Information Extraction Framework (DIEF). For the past 12 years, the software received a plethora of extensions by the community, which positively affected the size and data quality. Due to the increase in size and complexity, the release process was facing huge delays (from 12 to 17 months cycle), thus impacting the agility of the development. In this paper, we describe the new DBpedia release cycle including our innovative release workflow, which allows development teams (in particular those who publish large, open data) to implement agile, cost-efficient processes and scale up productivity. The DBpedia release workflow has been re-engineered, its new primary focus is on productivity and agility , to address the challenges of size and complexity. At the same time, quality is assured by implementing a comprehensive testing methodology. We run an experimental evaluation and argue that the implemented measures increase agility and allow for cost-effective quality-control and debugging and thus achieve a higher level of maintainability. As a result, DBpedia now publishes regular (i.e. monthly) releases with over 21 billion triples with minimal publishing effort .
Extracted statement — Method: Release cycle
Research field: Information Science
Title: Curating Scientific Information in Knowledge Infrastructures
Abstract: Interpreting observational data is a fundamental task in the sciences, specifically in earth and environmental science where observational data are increasingly acquired, curated, and published systematically by environmental research infrastructures. Typically subject to substantial processing, observational data are used by research communities, their research groups and individual scientists, who interpret such primary data for their meaning in the context of research investigations. The result of interpretation is information – meaningful secondary or derived data – about the observed environment. Research infrastructures and research communities are thus essential to evolving uninterpreted observational data to information. In digital form, the classical bearer of information are the commonly known “(elaborated) data products,” for instance maps. In such form, meaning is generally implicit e.g., in map colour coding, and thus largely inaccessible to machines. The systematic acquisition, curation, possible publishing and further processing of information gained in observational data interpretation – as machine readable data and their machine-readable meaning – is not common practice among environmental research infrastructures. For a use case in aerosol science, we elucidate these problems and present a Jupyter based prototype infrastructure that exploits a machine learning approach to interpretation and could support a research community in interpreting observational data and, more importantly, in curating and further using resulting information about a studied natural phenomenon.
Extracted statement — Material: Research infrastructures and research communities