Ingesting bibliographic and reference information from JATS-encoded journal articles into the OpenCitations corpus

Silvio Peroni and David Shotton

At JATS-Con 2012, with Deborah Aleyne Lapeyre, we presented the first mapping of JATS XML to RDF [1]. The OpenCitations Corpus (OCC) is a dataset of open citation data encoded in RDF made available by OpenCitations (http://opencitations.net). The dynamic OCC ingestion workflow of new citation data into the OCC from JATS XML articles is regulated by two scripts: the Bibliographic Entries Extractor (BEE) and the SPAR Citation Indexer (SPACIN).

While SPACIN has previously been described [2], we wish in this presentation to introduce the main features of BEE. BEE retrieves information about articles in the OA subset of PubMed Central by querying the Europe PubMed Central API so as to get their JATS XML sources. Once identified, BEE processes the JATS sources so as to extract the complete reference list of each paper under consideration, and it includes all these reference data in JSON files organised as follows:

    {
    "doi": "10.1007/s10544-016-0081-z",
    "pmid": "27299468",
    "pmcid": "PMC4908161",
    "localid": "MED-27299468",
    "curator": "BEE EuropeanPubMedCentralProcessor",
    "source": "http://www.ebi.ac.uk/europepmc/webservices/rest/PMC4908161/fullTextXML",
    "source_provider": "Europe PubMed Central",
    "references": [
    ...
    {
    "bibentry": "Svahn, HA, Berg, A. Single cells or large populations, Lab Chip, 2007,
    7, 544, 546, DOI: 10.1039/b704632b, PMID: 17476370",
    "pmid": "17476370",
    "doi": "10.1039/b704632b",
    "process_entry": "True"
    },
    ...
    ]
    }    

In particular, for each article retrieved from the EuropePMC API, BEE stores all the available bibliographic identifiers (in the example, "doi", "pmid", "pmcid", and "localid") and all the textual references as given, each enriched by its own related bibliographic identifiers if these are available. In addition, each JSON file includes provenance information about the source, its provider and the OCC curator (i.e. the particular BEE Python class responsible for the extraction of these metadata from the source). Each of the created JSON files is then processed, independently, by SPACIN into RDF according to the OpenCitations Data Model [3] for inclusion in the OCC [2].

This process demonstrates the importance of JATS as a markup standard for providing well-structured citations and other publication metadata that can be republished in alternative formats, specifically as Linked Open Data.

References

1. Peroni S, Lapeyre DA and Shotton D (2012) From Markup to Linked Data: Mapping NISO JATS v1.0 to RDF using the SPAR (Semantic Publishing and Referencing) Ontologies. A paper presented at the 2012 JATS Conference. https://www.ncbi.nlm.nih.gov/books/NBK100491/.
2. Silvio Peroni, David Shotton, Fabio Vitali (2016). Building Citation Networks with SPACIN. In Knowledge Engineering and Knowledge Management - EKAW 2016 Satellite Events: 162-166. DOI: https://doi.org/10.1007/978-3-319-58694-6_23.
3. Silvio Peroni, David Shotton (2018). The OpenCitations Data Model. Figshare. DOI: https://doi.org/10.6084/m9.figshare.3443876.v5 .

Supporting software citation in JATS

Martin Fenner on behalf of the Force11 Software Citation Implementation Working Group

Following the publication of the Force11 Software Citation Principles in 2016, the Force11 Software Citation Implementation Working Group was started in 2017 to provide guidance on implementing these principles, including software citations in scholarly publications, and specifically how this is implemented in JATS. In this presentation we will summarize the work of the Force11 Software Citation Implementation Working Group over the past two years, wich a focus on a) issues relevant for publishers, and b) metadata for software citation outside of JATS. We will then describe the current status of software citation in JATS, and the work left to do in terms of the JATS standard, documentation and adoption.

MyCites―A new concept for reporting inaccurate citations

Mohammad Hosseini

MyCites is a concept for a browser-extension that aims to streamline the process of reporting inaccurate citations in academic publications. Given the current rates of inaccurate citations (Liang et al. 2014; Gasparyan et al. 2015), the primary objective of MyCites is to promote reporting inaccurate citations and increase transparency.

Currently, reporting inaccurate citations is time-consuming as it consists of several steps and involves various stakeholders. MyCites allows readers to log in using their ORCID username and password and reflect on individual citations within an academic article. It also enables researchers and editors to create a feedback loop by subscribing to receive notifications about articles that they authored/edited or articles that they are interested to follow.

References

• Gasparyan, A. Y., Yessirkepov, M., Voronov, A. A., Gerasimov, A. N., Kostyukova, E. I., & Kitas, G. D. (2015). Preserving the Integrity of Citations and References by All Stakeholders of Science Communication. Journal of Korean Medical Science, 30(11), 1545. doi:10.3346/jkms.2015.30.11.1545.
• Liang, L., Zhong, Z., & Rousseau, R. (2014). Scientists’ referencing (mis)behavior revealed by the dissemination network of referencing errors. Scientometrics, 101(3), 1973-1986. doi:10.1007/s11192-014-1275-x.

Are current metadata ready for the FORCE11 Software Citation Guidelines?

Ted Habermann

Many communities develop recommendations for required or suggested metadata content for particular use cases and/or data types. Understanding how these recommendations are implemented, identifying high-quality examples, and providing guidance for improvement are important elements of the adoption process. The MetaDIG Project has developed approaches and tools for evaluating metadata dialects and collections for completeness with respect to community recommendations. FORCE11 is a community of scholars, librarians, archivists, publishers and research funders that recently developed a recommendation for software citation (Smith AM, Katz DS, Niemeyer KE, FORCE11 Software Citation Working Group. (2016) Software Citation Principles. PeerJ Computer Science 2:e86. DOI: 10.7717/peerj-cs.86). We discuss implementation of these guidelines in several metadata dialects and existing software repositories and examine existing metadata collections for completeness with respect to the recommended items.