semantic publishing – OpenCitations blog

New documents that present OpenCitations’ mission, unique benefits, present status and future plans

Posted on August 10th 2022 by Chiara Di Giambattista

More than a year ago, Ginny Hendricks, Director of Member & Community Outreach for Crossref, and a valued member of the OpenCitations International Advisory Board, published on the Crossref blog the post “The road ahead: our strategy through 2025”. In order to describe all Crossref’s principles and activities, Ginny presented the Crossref strategic planning framework as a diagram summarizing Crossref’s statements, key messages and truths. The clarity and immediacy of the diagram were such that we adapted it to present OpenCitations’ own statements and goals. The resulting poster “OpenCitations – what does the future hold?” was presented by our Director David Shotton at the OASPA2021 conference, and can be found in this blog post.

Although the poster offered a wide overview of OpenCitations values, unique traits, benefits and plans, it differed slightly from Ginny’s original diagram, in particular because it lacked a “Mission Statement”, scattering the relevant information within the “Values” and “Principles” boxes. Indeed, at that time (September 2021), we didn’t have a clearly defined Mission Statement.

Nevertheless, the creation of that poster was crucial in helping us start to articulate more clearly the purpose and meaning of OpenCitations. As David underlined in his post “From little acorns…a retrospective on OpenCitations”, since 2018 OpenCitations activities have progressively increased and, with them, the number of related journal articles, conference papers and technical definitions. OpenCitations’ involvement in international networks and collaborations (such as SCOSS and the OpenAIRE-Nexus project), together with our need of identifying and reaching out to new stakeholders to assure OpenCitations’ development and sustainability, has made it necessary to publicly define OpenCitations’ mission, unique strengths and next developmental steps.

After numerous revisions, aided by wise advice from members of the OpenCitations Advisory Board members, we’re now happy to publish the following three OpenCitations documents:

OpenCitations Mission Statement,

The Uniqueness of OpenCitations and

OpenCitations – Present Status and Future Plans,

which together provide a summary of why we exist and where we are heading.

We are particularly proud of the definition of OpenCitations’ primary mission, namely

“to harvest and openly publish accurate and comprehensive metadata describing the world’s academic publications and the scholarly citations that link them, and to preserve ongoing access to this information by secure archiving.”

The Mission Statement also presents brief descriptions of the OpenCitations context, our vision, our value proposition and our relationship with the community and stakeholders.

The Uniqueness of OpenCitations provides the answer to the question ‘Why choose to use OpenCitations?’, and is a detailed presentation of OpenCitations’ benefits.

OpenCitations – Present Status and Future Plans summarizes OpenCitations’ ongoing activities, that can be quickly visualized on our public roadmap. It also introduces the OpenCitations Working Groups, served by the members of the OpenCitations International Advisory Board, which are currently working on the themes of governance evolution and community building, with the common purpose of driving OpenCitations along the path from being a ‘sustainable infrastructure’ (in POSI terms) to being an enduring community led and financially sustained infrastructure.

In fulfilling our mission and reaching our goals, the support and vital interest of our community members is fundamental. We request that you, as a member of our community, provide us with feedback on these documents and the ideas they contain, or indeed to ask for clarifications, to help us improving our mission and our communications to explain it. You can reach us here: contact@opencitations.net.

Thank you!

Early adopters of the OpenCitations Data Model

OpenCitations is very pleased to announce its collaboration with four new scholarly Research and Development projects that are early adopters of the recently updated OpenCitations Data Model, described in this blog post.

The four projects are similar, in that they each are independently using text mining and optical character recognition or PDF extraction techniques to extract citation information from the reference lists of published works, and are making these citations available as Linked Open Data. Three of the four will also use the OpenCitations Corpus as publication platform for their citation data. The academic disciplines from which these citation data are being extracted are social science, humanities and economics.

1 Linked Open Citation Database (LOC-DB)

The Linked Open Citation Database, with partners in Mannheim, Stuttgart, Kiel, and Kaiserslautern (LOC-DB, https://locdb.bib.uni-mannheim.de/blog/en/), is the first of two German projects funded by the Deutsche Forschungsgemeinschaft (DFG) that are extracting citations from Social Science publications. Dr. Annette Klein, Deputy Director of the Mannheim University Library, is the project manager.

The project is using Deep Neural Networks based approaches for reference detection and state-of-the-art methods for information extraction and semantic labelling of reference lists from electronic and print media with arbitrary layouts [3]. The raw data obtained will be manually checked against and linked with existing bibliographic metadata sources in an editorial system. They will then be structured in RDF using the OpenCitations Data Model, and published in the Linked Open Citations Database under a CC0 waiver. Using its libraries’ own Social Science print holdings and licensed electronic journals as subject material, this project will demonstrate how these citation extraction processes can be applied to the holdings of individual academic libraries, and can be integrated with library catalogues [1, 2, 3].

References

[1] Kai Eckert, Anne Lauscher and Akansha Bhardwaj (2017) LOC-DB: A Linked Open Citation Database provided by Libraries. Motivation and Challenges. EXCITE Workshop 2017: “Challenges in Extracting and Managing References”. https://locdb.bib.uni-mannheim.de/wordpress/wp-content/uploads/2016/11/LOC-DB@EXCITE.pdf

[2] Lauscher, Anne; Eckert, Kai; Galke, Lukas; Scherp, Ansgar; Rizvi, Syed Tahseen Raza; Ahmed, Sheraz; Dengel, Andreas; Zumstein, Philipp; Klein, Annette (2018) Linked Open Citation Database: Enabling libraries to contribute to an open and interconnected citation graph. Accepted for the JCDL 2018: Joint Conference on Digital Libraries 2018, June 3-6, 2018 in Fort Worth, Texas [Preprint of the conference publication].
https://locdb.bib.uni-mannheim.de/wordpress/wp-content/uploads/2018/04/LOCDB-JCDL2018-paper-camera-ready.pdf

[3] Bhardwaj A., Mercier D., Dengel A., Ahmed S. (2017). DeepBIBX: deep learning for image based bibliographic data extraction. In: Liu D., Xie S., Li Y., Zhao D., El-Alfy ES. (eds) Neural Information Processing. ICONIP 2017. Lecture Notes in Computer Science, vol 10635. Springer, Cham [Conference publication].

2 The EXCITE (Extraction of Citations from PDF Documents) Project

The EXCITE Project (http://west.uni-koblenz.de/en/research/excite/), run jointly at the University of Koblenz-Landau and GESIS (Leibniz Institute for Social Sciences), is the second project funded by the Deutsche Forschungsgemeinschaft (DFG) that is extracting citations from Social Science publications. It is headed by Steffen Staab, head of the Institute for Web Science and Technologies at the University of Koblenz-Landau, and Philipp Mayr of GESIS.

Since the social sciences are given only marginal coverage in the main bibliographic databases, this project aims to make more citation data available to researchers, with a particular focus on the German language social sciences. It has developed a set of algorithms for the extraction of reference information from PDF documents and for matching the reference entry strings thus obtained against bibliographic databases (see EXCITE git https://github.com/exciteproject/). It is using as its data sources the following Social Science collections: full texts from SSOAR, the Gesis Social Science Open Access Repository (https://www.gesis.org/ssoar/home/) and scattered pdf stocks from other social science collections including SOLIS, Springer Online Journals and CSA Sociological Abstracts [4, 5].

The EXCITE project organized an international developer and researcher workshop “Challenges in Extracting and Managing References” in March 2017 in Cologne. http://west.uni-koblenz.de/en/research/excite/workshop-2017

EXCITE will then structure the extracted bibliographic and citation data in RDF using the OpenCitations Data Model, and will use the OpenCitations Corpus as its publication platform, employing the OCC EXCITE supplier prefix 0110, described here, to identify the provenance of these citations.

References

[4] Martin Körner (2016). Extraction from social science research papers using conditional random fields and distant supervision, Master’s Thesis, University of Koblenz-Landau, 2016.

[5] Körner, M., Ghavimi, B., Mayr, P., Hartmann, H., & Staab, S. (2017). Evaluating reference string extraction using line-based conditional random fields: a case study with german language publications. In M. Kirikova, K. Nørvåg, G. A. Papadopoulos, J. Gamper, R. Wrembel, J. Darmont, & S. Rizzi (Hrsg.), New Trends in Databases and Information Systems (Bd. 767, S. 137–145). Springer International Publishing. https://doi.org/10.1007/978-3-319-67162-8_15 Preprint: https://philippmayr.github.io/papers/Koerner-et-al2017.pdf

3 The Venice Scholar Index

The Venice Scholar Index is a citation index of literature on the history of Venice, indexing nearly 3000 volumes of scholarship from the mid 19^th century to 2013, from which some 4 million bibliographic references have been extracted.

The Venice Scholar Index is the first prototype resulting from Linked Books Project (https://dhlab.epfl.ch/page-127959-en.html), a project spearheaded by Giovanni Colavizza and Matteo Romanello of the Digital Humanities Laboratory at EPFL (École Polytechnique Fédérale de Lausanne), with partners in Venice, Milan and Rome.

The project is exploring the history of Venice through references to scholarly literature as well as archival documents found within publications. To achieve this goal, the project has developed a system to automatically extract bibliographic references found within a large set of digitized books and journals, which has then been applied to the publications on the history of Venice, its main use case [6].

The Linked Books Project is specifically interested in analysing the interplay between citations to primary (e.g. archival) documents and those to secondary sources (scholarly literature), and the citation profiles of publications through time. To this end, it developed the Venice Scholar Index, a rich search interface to navigate through the resulting network of citations, with the final aim of interlinking digital archives and digital libraries.

The citation data underlying the Venice Scholar Index are modelled using the OpenCitations Data Model, and will use the OpenCitations Corpus as its publication platform, using the OCC Venice Scholar Index supplier prefix 0120 to identify the provenance of these citations.

Reference

[6] Giovanni Colavizza, Matteo Romanello, and Frédéric Kaplan (2017). The references of references: a method to enrich humanities library catalogs with citation data. In International Journal on Digital Libraries 18 (March 8, 2017): 1–11. https://doi.org/10.1007/s00799-017-0210-1.

4 CitEcCyr – Citations in Economics published in CyrillicCitEcCyr (https://github.com/citeccyr/CitEcCyr) is an open repository of citation relationships obtained from research papers in the Russian language and Cyrillic script from Socionet (https://socionet.ru/) and RePEc (http://repec.org/) [7, 8]. The CitEcCyr project is headed by Oxana Medvedeva, is technically led by Sergey Parinov, and is funded by RANEPA (http://www.ranepa.ru/eng/), the Russian Presidential Academy of National Economy and Public. CitEcCyr is also developing a suite of open software for the citation content analysis of these papers. This project intends to model its citations using the OpenCitations Data Model, and will use the OpenCitations Corpus as its publication platform, using the OCC CitEcCyr supplier prefix 0140 to identify the provenance of these citations.

However, since this is the first project from which OpenCitations will be importing bibliographic metadata and citations in a language other than English and in a script other than the Latin script, we at OpenCitations are going to have to crawl out of our comfortable ‘Western’ shells and learn to handle foreign languages and scripts other than Latin scripts.

For Russian language papers written using Cyrillic script, we at OpenCitations will to decide how best to handle Russian language written using Cyrillic script, Cyrillic script transliterated into Latin script, and Russian language translated into English and rendered using Latin script. In particular, since in the OpenCitations Corpus our reference entry records are the uncorrected literal texts of the references in the reference lists of the citing papers, these will need to be recorded as given in Cyrillic.

We will need to develop a policy for when to provide Latin script translations of (for example) titles and abstracts, if these are not provided by the data supplier. To facilitate use of the OpenCitations Corpus by Russian scholars, we will also need to modify the OpenCitations web site, so as to render the static information displayed in the web pages in the language and script appropriate to the language setting on the user’s web browser.

Unfortunately, all this will take time, so we do not anticipate publishing citation data from the CitEcCyr project within OCC any time soon. However, this collaboration will be of tremendous value to OpenCitations as well as to CitEcCyr, since the lessons learned by our collaboration with the CitEcCyr project will enable the OpenCitations Corpus to handle citation data not just in Russian, but also in Arabic, Chinese, Japanese and other languages where the Latin script is not used, something that is not found in other major bibliographic databases.

Watch this space!

References

[7] Jose Manuel Barrueco, Thomas Krichel, Sergey Parinov, Victor Lyapunov, Oxana Medvedeva and Varvara Sergeeva (2017). Towards open data for the citation content analysis. https://arxiv.org/abs/1710.00302

[8] Thomas Krichel (2017). CitEc to CitEcCyr – A stab at distributed citation systems. Presented at the 2017 EXCITE workshop. http://west.uni-koblenz.de/sites/default/files/research/projects/excite/workshop-2017/slides/excite-workshop-2017_krichel_citec-to-citeccyr.pdf

Three publications describing the Open Citations Corpus

Last September, I attended the Fifth Annual Conference on Open Access Scholarly Publishing, held in Riga, at which I had been invited to give a paper entitled The Open Citations Corpus – freeing scholarly citation data. A recording of my talk is available here, and my PowerPoint presentation is separately available here. My own reflections on the major themes of the conference are given in a separate Semantic Publishing Blog post.

While in Riga preparing to give that talk about the importance of open citation data, I received an invitation from Sara Abdulla, Chief Commissioning Editor at Nature, to write a Comment piece for their forthcoming special issue on Impact. My immediate reaction was that this should be on the same theme, an idea to which Sara readily agreed. The deadline for delivery of the article was 10 days later!

As soon as the Riga conference was over, I first assembled all the material I had to hand that could be relevant to describing the Open Citations Corpus (OCC) in the context of conventional access to academic citation data from commercial sources. That gave me a raw manuscript of some five thousand words, from which I had to distil an article of less than 1,300 words. I then started editing, and asked my colleagues Silvio Peroni and Tanya Gray for their comments.

The end result, enriched by some imaginative art work by the Nature team, was published a couple of weeks later on 16th October [1], and presents both the intellectual argument for open citation data, and the practical obstacles to be overcome in achieving the goal of a substantial corpus of such data, as well as giving a general description of the Open Citations Corpus itself and of the development work we have planned for it.

Because of the drastic editing required to reduce the original draft to about a quarter of its size, all material not crucial to the central theme had to be cut. I thus had the idea of developing the original draft subsequently into a full journal article that would include these additional themes, particularly Silvio’s work on the SPAR ontologies described in this Semantic Publishing Blog post [2], Tanya’s work on the CiTO Reference Annotation Tools described in this Semantic Publishing Blog post, and a wonderful analogy between the scholarly citation network and Venice devised by Silvio. I also wanted to give authorship credit to Alex Dutton, who had undertaken almost all of the original software development work for the OCC. For this reason, instead of assigning copyright to Nature for the Comment piece, I gave them a license to publish, retaining copyright to myself so I could re-use the text. I am pleased to say that they accepted this without comment.

Silvio and I then set to work to develop the draft into a proper article. The result was a ten-thousand word paper submitted to the Journal of Documentation a week before Christmas [3]. We await the referees’ comments!

References

[1] Shotton D. (2013). Open citations. Nature 502: 295–297. http://www.nature.com/news/publishing-open-citations-1.13937. doi:10.1038/502295a.

[2] Peroni S and Shotton D (2012). FaBiO and CiTO: ontologies for describing bibliographic resources and citations. Web Semantics: Science, Services and Agents on the World Wide Web. 17: 33-34. doi:10.1016/j.websem.2012.08.001.

[3] Silvio Peroni, Alexander Dutton, Tanya Gray, David Shotton (2015). Setting our bibliographic references free: towards open citation data. Journal of Documentation, 71 (2): 253-277. http://dx.doi.org/10.1108/JD-12-2013-0166; OA at http://speroni.web.cs.unibo.it/publications/peroni-2015-setting-bibliographic-references.pdf

This is the main article about OpenCitations, which includes several background information and the main ideas and works supporting the whole project, the Corpus, and some possible future developments in terms of new kinds of data to be included, e.g. citation functions.

Open letter to publishers

[The text of this post was updated on 27-09-2013 and 04-04-2017 to reflect a new CrossRef metadata best practice document and a change in their URI.]

Today I wrote an open letter to all scholarly journal publishers, available online here, entitled:

Open your article reference lists for inclusion in the Open Citations Corpus.

In this letter, I request that publishers open the bibliographic citation data in their journal article reference lists. There is a growing movement to make such bibliographic citation data open – for example, Nature Publishing Group’s open Linked Data Platform now includes citation metadata for all published article references.

Provided a publisher is already depositing article references with CrossRef as part of the CrossRef CitedBy Linking service, all the publisher need to do is to inform CrossRef that it is willing for CrossRef to freely distribute these reference, for example in response to queries against the CrossRef XML API. We will then harvest them from CrossRef and incorporate them as open linked data in the Open Citations Corpus.

Nature Publishing Group, Taylor & Francis, the American Association for the Advancement of Science (who publish Science) and Oxford University Press, as well as a number of open-access publishers, have already given their consent to CrossRef to do this for some or all of their journals.

If not already a subscriber to the CrossRef CitedBy Linking service, a publisher can register for this useful service free of charge. Having done so, there is nothing further the publisher needs to do to ‘open’ its reference data, other than to give its consent to CrossRef. This can be done automatically, in the submitted article metadata, or (for back numbers) by informing CrossRef directly.

Even Open Access publishers, publishing articles under a CC-By open license, need to give this specific permission to CrossRef for this to occur, because CrossRef policy is that all publishers, including open access publishers, have to opt in to any distribution of references that CrossRef makes.

For new submissions, publishers should follow instructions detailed in the CrossRef blog at https://www.crossref.org/blog/distributing-references-via-crossref/, which contains the following key instruction:

“In order for publishers to distribute references along with standard bibliographic metadata, publishers need to set the <reference_distribution_opt> metadata element to “any" for each DOI deposit where they want to make references openly available.”

In this way, publishers can choose to open the reference lists for all their journals, or to do so on a journal-by-journal or on an article-by-article basis (useful for ‘hybrid’ subscription-access journals in which only some articles are open access).

To open reference lists for back numbers, publisher needs to e-mail CrossRef to express their intent,using the template shown at the foot of this post, as detailed in my Open Letter to Publishers.

I have copied this open letter to the CEOs of the Open Access Scholarly Publishers Association (OASPA), of the Association of Learned and Professional Society Publishers (ALPSP), and of the International Association of Scientific, Technical & Medical Publishers (STM), asking them to distribute it to their members, perhaps in association with their next Members News Letter, as CrossRef itself is planning to do later this month.

Please spread the word about this, particularly to publishers who may not be members of these professional associations. Thanks.

= = =

Template for an e-mail to CrossRef expressing willingness to open reference lists in previously published and future journal articles.

To support@crossref.org

I am writing on behalf of *** [name of publisher] to confirm that *** [name of publisher] is willing for the bibliographic reference lists within the articles in [delete as necessary:] all our journals [or] the attached list of journals be made freely available by CrossRef, for inclusion in the Open Citations Corpus. These journals are associated with the following DOI prefix(es): 10.**** [Please complete DOI prefix(es) – see footnote].
Yours sincerely [name, position, date]
= = =
Footnote: Publisher’s DOI prefixes are listed at http://www.crossref.org/06members/50go-live.html by name of publisher.

Taylor & Francis to open article reference lists

I am very pleased to announce that last year Ian Bannerman, Managing Director for Journals at Taylor & Francis, confirmed this publisher’s willingness to pilot the opening of the reference lists from articles in 29 of their subscription access journals, as well as from all of their current list of 15 Open Access journals, for inclusion in the Open Citations Corpus. The reference lists for these journals are already being supplied to CrossRef as part of the CrossRef CitedBy Linking service, and will be made available publicly via the CrossRef XML query API.

Taylor & Francis is a major international publisher of over 1,000 academic journals and more than 1,800 books per year, incorporating well-known publishing names including Bios Scientific Publishing, CRC Press, Garland Science, Marcel Decker and Routledge. It is the largest publisher of subscription access journals yet to agree to make reference lists available from its journal articles, and I welcome them warmly into the Open Citations fold.

Incorporation of new reference data from Taylor and Frances journals into the Open Citations Corpus will commence in the near future.

An entry form for JATS metadata

JATS, the Journal Article Tag Suite, defines a vocabulary of XML elements and attributes used to describe the content and metadata of journal articles. As described in the previous post, we have mapped the metadata elements of the JATS Journal Publishing Tag Set to RDF, so that publishers’ XML article metadata encoded using JATS might become part of the web of linked data. Our JATS2RDF mapping document is available here in PDF format. We also created an XSLT to automate the creation of RDF metadata from documents marked up in XML using the NISO-JATS Journal Publishing Tag Library v1.0, enabling this information to be published to the Semantic Web as linked open data in a manner that is unambiguous and universally understood.

Most XML markup applied to journal articles is created by specialist companies employed by publishers for this purpose. However, to facilitate the creation of JATS-compliant metadata by others, Tanya Gray and I have separately created a JATS Metadata Input Form, by adapting the metadata input system that she had previously created to permit entry of MIIDI metadata (Minimal Information to record an Infectious Disease Investigation), as we also repurposed to create the DataCite metadata input form described in a recent post.

The JATS Metadata Input Form is freely available on the Web at http://www.miidi.org/jats. Backed by an XML model that is interpreted by XForms and Orbeon Forms to create the displayed Web form dynamically, this form contains an input tab for the five principal metadata elements that we mapped, <article> <article-meta> <journal-meta> <contrib> and <ref-list>, with an input field in each tab for the various relevant JATS metadata elements and attributes. Where appropriate, each element is accompanied by a drop-down menu that permits the user to choose one from the list of suggested input values given in the JATS specification, as shown for the element <article-type> in the following screen shot of the <article> tab:

Screen shot of the initial metadata entry fields in the tab of the JATS Metadata Entry Form, showing the drop-down menu for the element . — Screen shot of the metadata entry fields in the article tab of the JATS Metadata Entry Form

The entered JATS metadata are saved as an XML file on the user’s local hard drive, with a name and directory location of the user’s choosing. Optionally, the metadata can also be saved in other formats including HTML, PDF and Kipling XML (a subset of the NLM Journal Publishing DTD version 3.0 that is the input format for Annotum, a publishing system based on the WordPress blogging platform). Additionally, the metadata can also be converted to RDF using the XSLT transformation described in the previous blog post.

We welcome feedback about the usefulness and functionality of this service.

David Shotton (david.shotton@zoo.ox.ac.uk)

Tanya Gray (tanya.gray@zoo.ox.ac.uk)

Mapping JATS to RDF

JATS, the Journal Article Tag Suite, defines a vocabulary of XML elements and attributes used to describe the content and metadata of journal articles. In this post, I describe the mapping of JATS to RDF, so that publishers’ XML article metadata encoded using JATS might become part of the web of linked data.

This work, that makes extensive use of the SPAR (Semantic Publishing and Referencing) Ontologies, was undertaken by Silvio Peroni and myself over the past summer, guided by Deborah Aleyne Lapeyre of Mulberry Technologies Inc., Maryland, the company that wrote the JATS specification on behalf of the National Library of Medicine.

Background

JATS was officially published on 22 August 2012 as ANSI/NISO Z39.96-2012, JATS: Journal Article Tag Suite (version 1.0), with the public URL http://www.niso.org/apps/group_public/document.php?document_id=8975.

It is the successor to the National Library of Medicine (NLM) DTD, which for many years has been a de facto standard for the XML markup of scholarly journal articles, widely used by many academic publishers within their routine publication workflows, and also used as the ingest format for PubMed Central. The last version of the NLM DTD, Version 3.0, was released in 2008, and JATS, although rebranded and now an official NISO standard, can be thought of simply as the next version of it.

As did the NLM DTD, JATS contains three tag sets, the Journal Archiving and Interchange Tag Set, the Journal Publishing Tag Set, and the Article Authoring Tag Set, intended for slightly different purposes. The Journal Publishing Tag Set is a moderately prescriptive Tag Set, optimized to regularize and control the sequence of the XML content.

As regular readers of this blog will know, the Resource Description Framework (RDF) is the key enabling technology for the Semantic Web, also know as the web of linked data. By defining statements about entities and their relationships in RDF syntax using publicly available ontologies, such statements can be combined into interconnected information networks (RDF graphs) in which the truth content of each original statement is maintained, thereby creating a web of linked data, the Semantic Web.

The SPAR (Semantic Publishing and Referencing) Ontologies are a suite of complementary and orthogonal OWL 2 DL ontologies described in this and subsequent posts in this blog. These ontologies were created specifically to permit RDF descriptions of bibliographic entities, citations, reference collections and library catalogues, the structural and rhetorical component parts of documents, and roles, statuses and workflows in publishing.

Mapping JATS to RDF

Silvio Peroni and I decided to map the metadata elements of the JATS Journal Publishing Tag Set to RDF. For this purpose, we were given pre-publication access to JATS v1.0, enabling us to undertake our mapping work in July, and to revise it during August and September 2012. I present this work at the 2012 JATS Conference at the National Library of Medicine on the NIH campus in Bethesda, Maryland on 16th October 2012.

In our mapping of JATS, we employed the SPAR ontologies as appropriate, and also used elements from other well-known vocabularies such as the Dublin Core Metadata Initiative (DCMI) Metadata Terms and the Friend of a Friend (FOAF) Vocabulary.

Since JATS is a large standard, containing 246 elements and 134 attributes, we chose to map only the JATS metadata entities that describe an article (e.g. <journal-meta> for metadata about the journal in which the article was published, such as the name of the journal), and to leave aside (possibly for a later mapping exercise using DoCO, the Document Components Ontology) those entities describing the textual and graphical structure and content of the article (e.g. <title>, <body>, <fig>, <table>).

Detailed description and examples

Within the JATS2RDF mapping document we created, our mappings are presented in tabular form, with one table for each of the principle JATS metadata elements <article>, <article-meta>, <journal-meta>, <contrib>, and <ref-list>, plus their principle contained elements and attributes. In all, we created 242 separate XML to RDF mapping statements.

Within each table there are three columns, the first giving the JATS element or attribute name, the second showing an exemplar XML usage from the JATS specification, and the third documenting our mapping of that usage to RDF.

We provide specific examples of each mapping, giving alternatives where appropriate. To show the style employed, the mappings for the first four elements in the JATS <ref-list> element table:

Screenshot of the first four mapped elements in the JATS <ref-list> table — Screenshot of the first four mapped elements in the JATS table

Automating the mapping to RDF

By means of an Extensible Stylesheet Language Transformation (XSLT) transform that we have also created (downloadable from http://purl.org/spar/jats2rdf/xslt), this JATS2RDF mapping now permit the JATS metadata elements and their attributes, from documents marked up in XML using the NISO-JATS Journal Publishing Tag Library v1.0, to be converted automatically to RDF, enabling this information to be published to the Semantic Web as linked open data in a manner that is unambiguous and universally understood.

We hope that this ability to express JATS metadata descriptions in RDF will promote the use of JATS to a wider community.

Publications arising from this work

Our paper describing our JATS to RDF mapping is available from the National Library of Medicine:

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. Proc. 2012 JATS Conference, National Library of Medicine, Bethesda, Maryland, USA, 16-17 October 2012. http://www.ncbi.nlm.nih.gov/books/NBK100491/.

Our JATS2RDF mapping document, entitled JATS2RDF (v1.2): a mapping of JATS metadata to RDF, is available in PDF format from http://purl.org/spar/jats2rdf.

Our XSLT transform to automate the creation of RDF metadata from a JATS-marked up document is available from http://purl.org/spar/jats2rdf/xslt.

An entry form for DataCite metadata

DataCite is an international organization responsible for the DOIs (Digital Object Identifiers) issued for research datasets. For each DOI issued, DataCite requires the data publisher to create and submit to DataCite descriptive metadata that can aid resource discovery. These metadata elements, divided into mandatory and option ones, are specified in a document that is periodically updated by DataCite, the most recent version of which is the DataCite Metadata Kernel, v2.2.

In July 2012, Silvio Peroni and I revised and expanded the DataCite Ontology, as described in an earlier blog post, and then used it to map include all the mandatory and optional DataCite metadata terms from the DataCite Metadata Kernel, v2.2 to RDF, as described in the previous blog post.

To facilitate the creation of metadata compliant with the DataCite Metadata Kernel v2.2, Tanya Gray and I have separately created a DataCite Metadata Input Form, by adapting the metadata input system that she had previously created to permit entry of MIIDI metadata (Minimal Information to record an Infectious Disease Investigation).

The DataCite Metadata Input Form is freely available on the Web at http://www.miidi.org/datacite. Backed by an XML model that is interpreted by XForms and Orbeon Forms to create the displayed Web form dynamically, this form contains an input field for each of the DataCite metadata elements, both the main terms and their sub-terms, in numerical order. Where appropriate, each element contains a drop-down menu that permits the user to choose one from the list of allowed input values specified by the DataCite Metadata Kernel v2.2, as shown in the following screen shot:

Screen shot of the initial metadata entry fields in the DataCite Metadata Entry Form

The entered DataCite metadata are saved as an XML file on the user’s local hard drive, with a name and directory location of the user’s choosing. Optionally, the metadata can also be saved in other formats including HTML, PDF and Kipling XML (a subset of the NLM Journal Publishing DTD version 3.0 that is the input format for Annotum, a publishing system based on the WordPress blogging platform). Additionally, the metadata can also be converted to RDF using an XSLT transformation based on the mapping of the DataCite Metadata Kernel, v2.2 to RDF described in the previous blog post.

We commend use of this service to researchers wishing to create DataCite metadata to accompany datasets sent to data repositories, and to repository creators wishing to create or supplement DataCite metadata for a newly submitted dataset they will archive and publish, to send to DataCite when registering a DOI for that dataset.

Our system uses a server-client software system that is more fully described here. Because of this, there is a possibility that our server could potentially suffer from usage overload that might lead to unacceptably slow response times. We have not experienced such slow response times while testing, but would like to hear from users both about any performance issues experienced, and about suggestions for improvement.

David Shotton (david.shotton@zoo.ox.ac.uk)

Tanya Gray (tanya.gray@zoo.ox.ac.uk)

Revising the DataCite2RDF mapping document

The purpose of mapping DataCite metadata elements to ontology terms is to enable DataCite metadata to be published in RDF as Open Linked Data, enabling these metadata to be understood programmatically and integrated automatically with similar data from elsewhere.

In the previous blog post, I described the updated and expanded version of the DataCite Ontology, version 0.6.1, that I created with Silvio Peroni to conform to the DataCite Metadata Kernel, v2.2 published in July 2012. The revised ontology now provides the eleven classes and five properties required to cover all the items in v2.2 of the DataCite Metadata Schema – not just the core DataCite metadata elements, but all of them – that were not conveniently covered by terms in other ontologies.

In this post, I describe how we have used this revised DataCite Ontology to create a new revised DataCite2RDF mapping document. This now replaces the previous mapping document, described in an earlier post, that was a partial mapping of the DataCite Metadata Kernel v2.0 using the original version of the DataCite Ontology.

Wherever possible in this new DataCite2RDF mapping, we have used commonly used vocabularies, including:

DCMI (Dublin Core Metadata Initiative),

FOAF (Friend of a Friend Vocabulary),

SKOS (Simple Knowledge Organization System), and

PRISM (Publishing Requirements for Industry Standard Metadata) terms,

supplemented by terms from FRBR (Functional Requirements for Bibliographic Records), and from the following SPAR (Semantic Publishing and Referencing) Ontologies:

CiTO, Citation Typing Ontology,

FaBiO, FRBR-aligned Bibliographic Ontology,

FRAPO, the Funding, Research Administration and Projects Ontology,

PRO, Publishing Roles Ontology,

SCORO, Scholarly Contributions and Roles Ontology, and, of course,

theDataCite Ontology itself.

The mapping document is structured in tabular form, with three columns: the first containing the DataCite ID, the second containing the name of the DataCite property, and the third containing the ontology entities used in mapping each of the DataCite metadata elements. All the metadata elements of the DataCite Metadata Kernel version 2.2 are included, both mandatory and optional, and both major and supplementary. For each, we provide not only the ontology terms, but also a specific exemplar of the usage of that term in an RDF statement, giving alternatives where appropriate. To show the style employed, the mappings for the first three DataCite metadata elements are shown in the following table:

ID	DataCite property	Equivalent ontology class or property
1	Identifier	datacite:PrimaryIdentifier (A sub-class of datacite:ResourceIdentifier that uses a datacite:IdentiferScheme that is restricted to datacite:doi, an individual in the datacite:ResourceIdentifierScheme)Exemplar usage: :my-dataset rdf:type fabio:Dataset ; datacite:hasIdentifier [ rdf:type datacite:PrimaryResourceIdentifier ; literal:hasLiteralValue "doi:10.1371/journal.pntd.0000228.g002.x001" ] .
1.1	IdentifierType	Restricted to datacite:doi, an individual in the datacite:ResourceIdentifierSchemeExemplar usage: :my-dataset rdf:type fabio:Dataset ; datacite:hasIdentifier [ rdf:type datacite:PrimaryResourceIdentifier ; literal:hasLiteralValue "doi:10.1371/journal.pntd.0000228.g002.x001" ; datacite:usesIdentifierScheme datacite:doi ] .
2	Creator	dc:creator (data property)Exemplar usage: :my-dataset rdf:type fabio:Dataset ; dc:creator "Shotton, David" . or dcterms:creator (object property) Exemplar usage: :my-dataset rdf:type fabio:Dataset ; dcterms:creator [rdf:type foaf:Person ; foaf:familyName "Shotton" ; foaf:givenName "David" ] .

To facilitate our mapping, the object properties compiles and isCompiledBy, that are required for the DataCite relationType controlled list, have now been included in version 2.2 of CiTO (created 3 July 2012) as cito:compiles and cito:isCompiledBy. The use of the mini-ontology CiTO4Data, that contained only those properties, has consequently been deprecated.

In several instances, we propose alternative mappings, depending upon whether one wishes to use a data property that has a literal (e.g. text, number, date) as its object, or to use an object property that has a URI as its object. As explained more fully in the mapping document itself, our recommended best practice is to use DCMI metadata terms (dcterms:) as object properties in preference over Dublin Core metadata elements (dc:) as data properties, unless one specifically needs to use a literal as the object of an RDF triple.

The new mapping document, DataCite2RDF, is available in PDF format from http://purl.org/spar/datacite/datacite2rdf.

A presentation related to this work, that was given at a DataCite meeting held at the British Library on 6 July 2012, is available here.

The next blog post describes a DataCite Metadata Input Form based on this new DataCite2RDF mapping that Tanya Gray and I have created. This is a Web input tool that permits easy entry of metadata compliant with the DataCite Metadata Kernel v2.2. The metadata can be saved in an XML file, and can be automatically mapped to RDF by employing an XSLT that uses this mapping.

We commend the use of this mapping to all who wish to encode DataCite metadata in RDF, and welcome feedback on this work.

David Shotton (david.shotton@zoo.ox.ac..uk)

Silvio Peroni (essepuntato@cs.unibo.it)

1 Linked Open Citation Database (LOC-DB)

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2 The EXCITE (Extraction of Citations from PDF Documents) Project

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3 The Venice Scholar Index

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Postscript