Academic literature on the topic 'OpenCitations'

OpenCitations is an infrastructure organization for open scholarship dedicated to the publication of open citation data as Linked Open Data using Semantic Web technologies, thereby providing a disruptive alternative to traditional proprietary citation indexes. Open citation data are valuable for bibliometric analysis, increasing the reproducibility of large-scale analyses by enabling publication of the source data. Following brief introductions to the development and benefits of open scholarship and to Semantic Web technologies, this paper describes OpenCitations and its data sets, tools, services, and activities. These include the OpenCitations Data Model; the SPAR (Semantic Publishing and Referencing) Ontologies; OpenCitations’ open software of generic applicability for searching, browsing, and providing REST APIs over resource description framework (RDF) triplestores; Open Citation Identifiers (OCIs) and the OpenCitations OCI Resolution Service; the OpenCitations Corpus (OCC), a database of open downloadable bibliographic and citation data made available in RDF under a Creative Commons public domain dedication; and the OpenCitations Indexes of open citation data, of which the first and largest is COCI, the OpenCitations Index of Crossref Open DOI-to-DOI Citations, which currently contains over 624 million bibliographic citations and is receiving considerable usage by the scholarly community.

Abstract In this paper, we present COCI, the OpenCitations Index of Crossref open DOI-to-DOI citations (http://opencitations.net/index/coci). COCI is the first open citation index created by OpenCitations, in which we have applied the concept of citations as first-class data entities, and it contains more than 445 million DOI-to-DOI citation links derived from the data available in Crossref. These citations are described using the resource description framework by means of the newly extended version of the OpenCitations Data Model (OCDM). We introduce the workflow we have developed for creating these data, and also show the additional services that facilitate the access to and querying of these data via different access points: a SPARQL endpoint, a REST API, bulk downloads, Web interfaces, and direct access to the citations via HTTP content negotiation. Finally, we present statistics regarding the use of COCI citation data, and we introduce several projects that have already started to use COCI data for different purposes.

Acesso aberto aos artigos, dados e materiais de pesquisa são alguns elementos-chave da ciência aberta, um movimento plural que visa a transformar a criação e a comunicação do conhecimento científico. Graças à publicação de artigos em acesso aberto e à adoção de boas práticas editoriais, a RBMFC tem seus artigos indexados na LILACS e, mais recentemente, no DOAJ. A RBMFC também adota as diretrizes Transparency and Openness Promotion do Center for Open Science, e disponibiliza suas referências na CrossRef em domínio público, graças ao que a revista foi incluída no índice de citações OpenCitations. Com isso, a RBMFC espera tornar mais acessível, democrática e eficiente a pesquisa em medicina de família e comunidade e atenção primária à saúde.

Semantic Web technologies are widely used for storing RDF data and making them available on the Web through SPARQL endpoints, queryable using the SPARQL query language. While the use of SPARQL endpoints is strongly supported by Semantic Web experts, it hinders broader use of RDF data by common Web users, engineers and developers unfamiliar with Semantic Web technologies, who normally rely on Web RESTful APIs for querying Web-available data and creating applications over them. To solve this problem, we have developed RAMOSE, a generic tool developed in Python to create REST APIs over SPARQL endpoints. Through the creation of source-specific textual configuration files, RAMOSE enables the querying of SPARQL endpoints via simple Web RESTful API calls that return either JSON or CSV-formatted data, thus hiding all the intrinsic complexities of SPARQL and RDF from common Web users. We provide evidence that the use of RAMOSE to provide REST API access to RDF data within OpenCitations triplestores is beneficial in terms of the number of queries made by external users of such RDF data using the RAMOSE API, compared with the direct access via the SPARQL endpoint. Our findings show the importance for suppliers of RDF data of having an alternative API access service, which enables its use by those with no (or little) experience in Semantic Web technologies and the SPARQL query language. RAMOSE can be used both to query any SPARQL endpoint and to query any other Web API, and thus it represents an easy generic technical solution for service providers who wish to create an API service to access Linked Data stored as RDF in a triplestore.

Twenty years ago, open access emerged out of a crisis within scholarly communications. Back then, it was about solving the issue of cost as a barrier to accessing scholarly content, due to the increasing concentration of commercial publishing. Today, another crisis is relying on open access to remove barriers to creating and consuming scholarship. This time, however, our sights are set on increasing public access as a means to solve a global pandemic. While open scholarship requires information to be freely available, it costs money to create and sustain high quality books and articles, discovery services that provide access to them, and software that enables their creation. We have seen this in discussions and developments surrounding open access business models, including article processing changes (APCs), open access funds, and “subscribe-to-open.” Where such infrastructures do not generate commercial profits, they require financial support from the communities they serve, including authors, publishers, libraries, funders, scholarly institutions and other stakeholders, to make open access a reality. As we set up national networks, mandates, and other initiatives to support and promote open access, we must not forget another critical element: open infrastructure. In the open access context, “infrastructure” -- the "structures and facilities" -- refers to the scholarly communication resources and services, including software, that we depend upon to enable the scientific and scholarly community to collect, store, organise, access, share, and assess research. Open infrastructure provides the foundation for keeping costs down and quality high, ensuring community-driven development. But who funds open infrastructure? And how do we create a sustainable future for the services that many of us have come to rely on? This 20 minute session will examine three open infrastructure case studies: OpenCitations, OAPEN/DOAB, and the Public Knowledge Project. These three initiatives are currently being promoted by the Global Sustainability Coalition for Open Science Services (SCOSS), a network of influential organisations committed to helping secure open access infrastructure well into the future. Our panel of services will explore how the current round of SCOSS-supported projects are ensuring a sustainable future for open access scholarly publishing, and will discuss the essential role that governments, libraries, publishers and others are playing - and need to play - in making this a reality. Following the growth of open access publishing, scholar-led and community-driven open infrastructure and innovations have supported and facilitated the vital (and now urgent) need for open knowledge. What does the next twenty years look like for these services? And how can we work together to ensure open access isn’t just a response to crises, but rather the “new normal”?

Scientists frequently collect biological and environmental information over years and store it in database systems to answer their own research questions without exposing it in repositories that make it easy to find and retrieve. While in recent years the community working on biodiversity informatics has made significant strides by creating common shared vocabularies such as the Darwin Core (DwC, Wieczorek et al. 2012) and publishing mechanisms such as the Integrated Publishing Toolkit (IPT, Robertson et al. 2014), integration is largely limited to the aggregation of datasets and full interoperability has still not been achieved. In this context, The Semantic Web (SW) aims to represent information in a way that, in addition to the human-centered display purposes, it can be used autonomously by machines for integration and reuse across applications. From the biodiversity informatics point of view, interoperability and links among data sources would allow integration of information that is otherwise disconnected, enabling scientists to answer broader questions. These considerations provide strong motivations to formulate a web application considering the semantic interoperability that may provide answers to questions such as the following: (Q1) Is it possible to complement taxonomic, bibliographic and environmental information of a particular species without relying on specific Application Programming Interfaces (APIs)? (Q2) How to relate occurrences of species with environmental variables within a specific region? (Q3) What are the bibliographic references associated with a given species? (Q1) Is it possible to complement taxonomic, bibliographic and environmental information of a particular species without relying on specific Application Programming Interfaces (APIs)? (Q2) How to relate occurrences of species with environmental variables within a specific region? (Q3) What are the bibliographic references associated with a given species? With questions such as these in mind, we present the design of a proof-of-concept application: Linked Open Biodiversity Data (LOBD). LOBD uses Linked Data (LD) (Heath and Bizer 2011) to complement species occurrence information previously extracted from GBIF and converted to Resource Description Framework (RDF) (Zárate et al. 2020) with information about the taxa in question from different RDF datasets, such as Wikidata, NCBI Taxonomy, Springer Nature SciGraph and OpenCitation corpus. A simplified view of the architecture is shown in Fig. 1. To achieve semantic interoperability, we use the SPARQL query language, which allows us not to depend on specific APIs to retrieve information. The application consists of three modules: General information, where the Wikidata endpoint is used to retrieve additional information about the selected species, including links to other databases and information about the species extracted from National Center for Biotechnology Information (NCBI) Taxonomy. Bibliography, where all publications related to the species are retrieved and extracted from OpenCitation. Environment, where users can plot species on a map and add layers related to marine regions as well as environmental layers (e.g., temperature, salinity, etc). General information, where the Wikidata endpoint is used to retrieve additional information about the selected species, including links to other databases and information about the species extracted from National Center for Biotechnology Information (NCBI) Taxonomy. Bibliography, where all publications related to the species are retrieved and extracted from OpenCitation. Environment, where users can plot species on a map and add layers related to marine regions as well as environmental layers (e.g., temperature, salinity, etc). For the development of the application, we use the Shiny framework for R, access to SPARQL endpoints is done through the SPARQL package, marine regions are obtained from marineregion.org and the environmental layers are extracted from Bio-ORACLE. The data used for this article were collected by the Center for the Study of Marine Systems at the National Patagonian Sci-Tech Centre (CCT CENPAT-CONICET), and are published and available through the GBIF network. Linked Data is a powerful tool for scientists, as it allows generating new approaches to biodiversity informatics, which can help to address the data integration challenges. Users would benefit from complementing the current prevalent use of vocabularies that are not ontologically defined (like DwC) for sharing biodiversity data. Although this application is a proof of concept, it shows that with little effort, it is possible to achieve greater interoperability between datasets that were not initially represented as LD.

Questa dissertazione presenta OCEB (OpenCitations Entities Browser), un'applicazione web che permette la visualizzazione di metadati presenti nel database di OpenCitations. OpenCitations è un progetto il cui scopo principale è la raccolta di metadati bibliografici e citazionali provenienti dalla letteratura accademica. OCEB visualizza queste informazioni, in modo ordinato, in una pagina HTML e fornisce un meccanismo che consente all'utente di navigare tra i contenuti di OpenCitations.