In this paper, we present COCI, the OpenCitations Index of Crossref open DOI-to-DOI citations (this http URL). 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 in RDF 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.
Biotea ( https: biotea.github.io ) @cite_15 is an RDF datasets containing information about some of the articles available in the Open Access subset of PubMed Central, that have been enhanced with specialized annotation pipelines. The last released dataset includes information extracted from 2,811 articles, including data on their citations.
@cite_15
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A significant portion of biomedical literature is represented in a manner that makes it difficult for consumers to find or aggregate content through a computational query. One approach to facilitate reuse of the scientific literature is to structure this information as linked data using standardized web technologies. In this paper we present the second version of Biotea, a semantic, linked data version of the open-access subset of PubMed Central that has been enhanced with specialized annotation pipelines that uses existing infrastructure from the National Center for Biomedical Ontology. We expose our models, services, software and datasets. Our infrastructure enables manual and semi-automatic annotation, resulting data are represented as RDF-based linked data and can be readily queried using the SPARQL query language. We illustrate the utility of our system with several use cases. Our datasets, methods and techniques are available at http: biotea.github.io. Bio2RDF is an open source project to generate and provide Linked Data for the Life Sciences. Here, we report on a third coordinated release of ∼11 billion triples across 30 biomedical databases and datasets, representing a 10 fold increase in the number of triples since Bio2RDF Release 2 (Jan 2013). New clinically relevant datasets have been added. New features in this release include improved data quality, typing of every URI, extended dataset statistics, tighter integration, and a refactored linked data platform. Bio2RDF data is available via REST services, SPARQL endpoints, and downloadable files. Over the last decades, several billion Web pages have been made available on the Web. The ongoing transition from the current Web of unstructured data to the Web of Data yet requires scalable and accurate approaches for the extraction of structured data in RDF (Resource Description Framework) from these websites. One of the key steps towards extracting RDF from text is the disambiguation of named entities. While several approaches aim to tackle this problem, they still achieve poor accuracy. We address this drawback by presenting AGDISTIS, a novel knowledge-base-agnostic approach for named entity disambiguation. Our approach combines the Hypertext-Induced Topic Search (HITS) algorithm with label expansion strategies and string similarity measures. Based on this combination, AGDISTIS can efficiently detect the correct URIs for a given set of named entities within an input text. We evaluate our approach on eight different datasets against state-of-the-art named entity disambiguation frameworks. Our results indicate that we outperform the state-of-the-art approach by up to 29 F-measure. This article reports on a corpus annotation project that has produced a freely available resource for research on handling negation and uncertainty in biomedical texts (we call this corpus the BioScope corpus). The corpus consists of three parts, namely medical free texts, biological full papers and biological scientific abstracts. The dataset contains annotations at the token level for negative and speculative keywords and at the sentence level for their linguistic scope. The annotation process was carried out by two independent linguist annotators and a chief annotator -- also responsible for setting up the annotation guidelines -- who resolved cases where the annotators disagreed. We will report our statistics on corpus size, ambiguity levels and the consistency of annotations.