"We started by organizing a Dagstuhl meeting “Digital Scholarship and Open Science in Psychology and Behavioural Sciences”. During this meeting we discussed issues in open science related to these specific domains. The work continued by addressing some of the identified problems; in particular that of using existing semantic, NLP and data infrastructure in psychology within the framework provided by ZPID. We have built the semantic layer for Psych Open, an open access publisher in psychology. Our approach uses linked open data (LOD) technology and addresses four important aspects in the publication workflow, namely, queryability, discoverability, interoperability and user experience. In order to address the former three aspects we have developed SE4OJS to generate semantically annotated documents from the JATS/XML that comes from the OJS. We are adding semantics to our content, Psych Open, and publishing it as LOD in RDF format; this semantic enrichment adds context to the metadata of the publication, it also creates an anchor to the content. The datasets we are building for each article include i) the RDF description of article metadata, e.g. information on title, keywords, authors and editors; ii) structural information such as sections, section types, paragraphs, in-text citations; and also, iii) RDF for content and annotations. In order to enhance the user experience we are bringing the semantics to the user interface. We have extended LENS, a Java Script toolkit for scientific publications; as our content in RDF has semantically characterized entities, we have adapted LENS to expand on these entities. This enhancement delivers an experience similar to that of ""apps"" in mobile devices; characterized entities are processed by ""apps"", thus delivering an enriched user experience over the LENS interface. Also, we have added annotation capabilities to LENS by adapting hypothes.is. This annotation tool kit was also extended in order to support real time annotation with ontologies; thus facilitating conceptual navigation on the paper. Over a single environment we are supporting the annotation of the PDF as well as of the corresponding JATS/XML manifestation of the same document. We are structuring the annotations by using the Annotation Ontology. The KOPAR approach makes it possible to build concept-based queries; we are delivering a flexible, reusable and adaptable set of tools for metadata enrichment, semantic processing and enhancement of scientific documents in psychology.
A similar approach was used against the open access full content subset of PubMed Central -this is the largest digital library in the biomedical domain. A framework for generating RDF for PMC was developed. Use cases illustrating how to make practical use of semantics were also defined and implemented. 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. We have built a semantic, linked data version of the open-access subset of PubMed Central that has been enhanced with specialized annotation pipelines using existing infrastructure from the National Center for Biomedical Ontology. We expose our models, services, software and datasets. We illustrate the utility of our system with several use cases and make possible to SPARQL over the resulting datasets
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