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Tag: Open Biomedical Citations in Context Corpus

OpenCitations and SCOSS: one year of support

At the end of 2019, OpenCitations was selected by The Global Sustainability Coalition for Open Science Service (SCOSS) for presentation to the international scholarly community for crowd-sourced sustainability funding, along with the Public Knowledge Project (PKP) and the Directory of Open Access Books (DOAB). Since 2017, SCOSS has been helping identify non-commercial services essential to Open Science, and making recommendations that these services should be considered for funding support by the global OA/OS community of stakeholders (academic institutions and their libraries, research institutes, publishers, funding organisations, national and regional governments, international organisations, learned societies and service providers worldwide, and everyone who is invested in Open Access and Open Science).

Since OpenCitations is not-for-profit and all our data and services are free, the relationship with SCOSS is crucial in maintaining and developing OpenCitations’ infrastructure and continuing to make our data and service freely available.

Thanks to the renewed engagement and support from the OA/OS Community, 2020 has been a year of great achievements for OpenCitations.

As first described here, the starting point has been the set-up of an initial open governance structure. For administrative convenience, OpenCitations is managed by the Research Centre for Open Scholarly Metadata at the University of Bologna. Currently, the organizational bodies included in the OpenCitations governance are three: the Directors, the International Advisory Board, and the Council. All these bodies are regulated and described in two documents, “Organizational Bodies and Finances”, and “Rules for Membership” that specifically describes the criteria for Membership of OpenCitations.

The generous support received from OpenCitations’ donors and members during 2020 is making it possible to pay for necessary services and the salaries of personnel to support the daily activities of OpenCitations, thus enhancing the administration of OpenCitations and communication with new supporters and collaborators.

Separately, the involvement of OpenCitations in different funding applications throughout 2020 has led to the successful development of two projects.

The first one, OpenAIRE Nexus, started on 1 January 2021 with the aim to create a framework of services for assisting in publishing research, monitoring its impact, helping promote its discovery, and integrating it into the European Open Science Cloud (EOSC) for the benefit of the open science community worldwide. OpenCitations’ role in this will be to provide open bibliographic citations as part of the open data components of OpenAIRE and the EOSC.

The second project, the Open Biomedical Citations in Context Corpus, funded by the Wellcome Trust from July 2019 to December 2020, had the aim to expand the types of citation data provided by OpenCitations to include information about each individual in-text reference and its semantic context. This makes it possible, for example, to distinguish references that are cited only once from those that are cited multiple times, to see which references are cited together (e.g. in the same sentence), to determine in which section of the article references are cited (e.g. Introduction, Methods), and to specify the textual context of each citation, thus potentially making it possible to determine the function of the citation. Part of the grant received for this project was used to cover the salaries and expenses of developers who worked on the creation of a new persistent identifier (PID) for in-text reference pointers, the In-Text Reference Pointer Identifier (InTRePID) first described here, in the release of the new version of the OpenCitations Data Model (OCDM), and the creation of a new database, the Open Biomedical Citations in Context Corpus (CCC) containing the metadata describing the in-text references that we processed, drawn from the open biomedical literature.

Through its projects, OpenCitations has strengthened its connections with data of topical urgency. A relevant and timely output, for instance, was the creation of the Coronavirus Open Citations Dataset, which contains (as of 16 May 2020) information about 189,697 citations and about the 49,719 citing or cited articles involved in these citations related to the COVID-19 pandemic.

The involvement of OpenCitations in the SCOSS community has included our participation to several SCOSS-related events (amongst others, the SCOSS Webinar for the Couperin Consortium, the JROST Conference 2020), and the Jisc Webinar Sustaining the future of key open research infrastructure services (SCOSS) in order to present OpenCitations to the OA/OS community, together with the other Open Infrastructures selected in the first and second funding cycles. In addition, during 2020 OpenCitations participated in several international conferences, talks and meetups, including PIDapalooza 2020 and the International Semantic Web Conference 2020, and organized and co-hosted the Workshop on Open Citations and Scholarly Metadata 2020 (September 2020), gathering scholars, policy makers, publishers, and open scholarly data advocates.

Being part of the SCOSS network during 2020 has been an enriching and stimulating opportunity. The support of the international coalition for Open Science has resulted in a massive interest from European governments and Institutions (including the French Government through its National Plan for Open Science, the AgroParisTech, the Katholieke Universiteit Leuven and the Royal Danish Library), and the involvement of the Canadian Research Knowledge Network and the Council of Australian University Librarians. So far, 2021 seems to be equally promising, as judged by the increasing support being shown by US consortia for open infrastructures. Between May 2020 and April 2021 the US was responsible for 19% of the traffic to OpenCitations services, and every month has been listed in the top 4 countries using our data.

Despite the enthusiastic results, there’s still much to be done: 2020 was the first year of a three-year-long collaborative journey, in which OpenCitations will be moving forward with SCOSS to create an open, secured and inclusive future for science and research.

OpenCitations updates: interviews, outreach, research positions, citations

Several important recent events have involved OpenCitations directly as a participant. Here we introduce some of the most significant ones:

  • Our interviews during a Fireside Chat with John Chodacki during the Open Publishing Fest;
  • The SCOSS poster about OpenCitations and the other two selected infrastructures during LIBER 2020, which won the LIBER 2020 Peoples Choice Poster Award;
  • The availability of two new short-term research positions with OpenCitations for our Wellcome Trust funded project (application closing deadline: 23 July 2020); and
  • A new release of COCI, bringing the total number of open citations available in this dataset to more than 721 million.

Open Publishing Fest

The Open Publishing Fest was a decentralized on-line public event held from 18 May to 29 May

to bring together communities supporting open source software, open content, and open publishing models.

(from the Open Publishing Fest website, last visited 4 July 2020)

Within this event, John Chodaki and Cameron Neylon organised a series of sessions named “Fireside Chats” in which they invited people from the open publishing community to discuss their careers and projects. David Shotton and Silvio Peroni were the guests in one of these chats with John Chodaki, in which we talked about the origins of OpenCitations and the plans for OpenCitations’ future. The video of our chat (see link below) is available on YouTube.

The recording of the fireside chat that David Shotton and Silvio Peroni had on May 28th 2020 with John Chodaki in the context of the Open Publishing Fest.

SCOSS at LIBER 2020: promoting open infrastructures

SCOSS, the Global Sustainability Coalition for Open Science Services, which selected OpenCitations last December as worthy of community crowd-funding support as part of its second funding cycle, participated in LIBER 2020 with a poster which showcases the infrastructures that they recommend that the community financially supports.

Tweet by SCOSS on the poster presented at Liber 2020.

This poster won the People’s Choice Award and confirms the crucial activity that SCOSS is doing in making the academic community aware of the importance of providing financial support to open infrastructures like OpenCitations for the benefit of the whole of society.

A tweet by SCOSS on the document they wrote on the importance of supporting open infrastructures.

Furthermore, Giannis Tsakonas, Director in the Library & Information Center at the University of Patras (Greece), and a member of the LIBER Executive Board as head of its Innovative Scholarly Communication Steering Committee, shared a wonderful thread on Twitter about OpenCitations and the other open infrastructures (DOAB, OAPEN, and PKP) that have been selected by SCOSS in its second funding cycle.

A thread by Giannis Tsakonas about us and the other open infrastructures selected by SCOSS for their second funding cycle.

Short-term research positions open at OpenCitations in Bologna for our Wellcome Trust funded project

Wellcome Trust announced they have extended all their grants that were due to end in 2020 or 2021, including our Open Research Fund funded project entitled “Open Biomedical Citations in Context Corpus”. This project aims at providing data for each individual in-text reference pointer (aka in-text citation) and its semantic context, making it possible to distinguish references that are cited only once in the text of a paper from those that are cited multiple times, to see which references are cited together (e.g. in the same sentence), to determine in which section of the article references are cited (e.g. Introduction, Methods), and, potentially, to retrieve the function of each citation.

Some preliminary outcomes of the project have already been described in a recent blog post, and a preprint describing some of the activities of the project has also been also made available on arXiv. That paper focuses on the extensions we have made to the OpenCitations Data Model, used for the storage of data in all the OpenCitations datasets, to enable the additional metadata types resulting from the Citations in Context project to be recorded.

In the context of the funding extension to this Wellcome Trust project, the Department of Classical Philology and Italian Studies (FICLIT) at the University of Bologna has just opened two new positions for short-term (5 months) research fellowships from August to December 2020 inclusive, for which the application closing deadline is 23 July 2020. The main goals of these the short-term research fellowship are (a) to develop the software for handling the data stored in the Open Biomedical Citations in Context Corpus, and (b) to develop indexing mechanisms to analyse a large number of documents simultaneously within our local computing environment, without having to use external services.

The net salary for each research fellowship is 1,600 EUR per month, tax free. The minimal requirement to apply for one of these positions is to have a Bachelor degree, although higher qualifications in Computer Science would be beneficial. Since these are University of Bologna positions, the application forms are in Italian. However, the description of the activity plan of the research fellowships is available in both Italian and English.  We would be happy to provide further information, and help in completing the application forms if necessary, so please do not hesitate to email us.

New release of COCI with an additional 18 million citations

Every two months we are able to publish additions to COCI, the OpenCitations Index of Crossref open DOI-to-DOI citations. This latest release (dated 4 July 2020) extended COCI with more than 18 million additional citations, so that COCI now contains more than 721 million DOI-to-DOI citation links between more than 58.8 million bibliographic entities.

These new citations were harvested from the most recent Crossref data dump, downloaded on 8 June 2020, which includes the references of articles deposited in Crossref between 4 April 2020 and 4 June 2020. As before, we will use this new release of COCI to update the Coronavirus Open Citations Dataset, the third release of which will include details about relevant additional references and publications.

We remind you that COCI has been fully described in our open-access article

Ivan Heibi, Silvio Peroni & David Shotton (2019). Software review: COCI, the OpenCitations Index of Crossref open DOI-to-DOI citations. Scientometrics, 121 (2): 1213-1228. DOI: https://doi.org/10.1007/s11192-019-03217-6

and that all the bibliographic and citation data in COCI:

The Open Biomedical Citations in Context Corpus: Progress Report

The creation of the Open Biomedical Citations in Context Corpus (CCC) is the goal of a one-year project funded by the Wellcome Trust. The aim is to create a new open corpus of bibliographic and citation data that contain detailed information about individual in-text reference pointers in biomedical journal articles. The project is led by Professor Silvio Peroni of the Research Centre for Open Scholarly Metadata (University of Bologna), is being undertaken by Dr Marilena Daquino (University of Bologna), and actively involves the Oxford e-Research Centre (University of Oxford), the École de Bibliothéconomie et des Sciences de l’Information (Université de Montréal), and the Centre for Science and Technology Studies (CWTS), (Leiden University).

An in-text reference pointer is a textual device (e.g. “[1]”, or “(Peroni and Shotton 2012)”) that appears in the main text of a citing work and denotes a bibliographic reference listed in the Bibliography section of the citing work. While a single in-text reference pointer uniquely denotes a single bibliographic reference, it can occur together with one or more other pointers, forming an in-text reference pointer list that denotes several references (e.g. “[5-13]”, or “(Peroni and Shotton 2012; Peroni and Shotton 2019)”). In-text reference pointers may appear in several places within the same citing publication (e.g. Introduction, Methods, Discussion), may occur within different document components (e.g. body text, figure captions, tables), and may address the cited publication for different purposes (e.g. as the source of an experimental protocol, as a data source, or for general background information).

Unfortunately, current citation indexes contain no information about in-text reference pointers, such as the number of times a particular work is referenced in the citing work, the text of the sentences in which they occur, or the rhetorical purpose of such citations.

Having data at the level of individual in-text reference pointers offers many new opportunities, enabling one: (1) to distinguish between works that are referenced just once in a citing publication and those that are referenced multiple times, and thereby (potentially) to distinguish when a citation is fundamental for the understanding or the development of the citing work, or merely incidental; (2) to see which in-text reference pointers occur together (e.g. in the same sentence or the same paragraph), thus, potentially, to infer similarities between the co-cited publications; and (3) to determine in which specific sections of the publication these in-text references occur (e.g. Introduction, Methods, Results), and thus, potentially, by means of textual analysis of the citation contexts, to retrieve the rhetorical functions of the citations – i.e. the reason why an author cites another work. 

The goal of the CCC Project is to provide stakeholders with an exemplar Linked Open Data corpus, created from the open access biomedical research literature, that is tailored for such deep citation analyses. The corpus will be a new member of the collection of OpenCitations datasets, and will be accompanied by services for accessing and querying data.

In the CCC Project, we have achieved or are currently dealing with the following developments:

  • Extending the OpenCitations Data Model (OCDM). The OpenCitations Data Model has been extended and enriched with new terms and relations to represent bibliographic entities related to in-text reference pointers, such as the in-text reference pointers themselves, in-text reference pointer lists, discourse elements (e.g. sections, paragraphs, sentences), and annotations on citations, bibliographic references and in-text reference pointers. In addition, the provenance layer of the data model has been revised to provide meaningful provenance information in a more compact way. A revised version of the OCDM including these terms was published on November 8, 2019, and it is available on Figshare [1].
  • Extending the OpenCitation harvesting and data re-engineering pipeline. The CCC Project leverages existing OpenCitations technologies for building this new corpus, using as input articles from the Open Access Subset of biomedical literature hosted by Europe PubMed Central (EPMC) and encoded in XML. The OpenCitations pipelines for knowledge extraction (i.e. the software called BEE) and for data re-engineering (i.e. the software called SPACIN) have been enhanced so as to harvest relevant information from the full-text of the XML sources provided by EPMC, rather than just the reference lists,  and to transform these data into RDF according to the revised OCDM. The source code of the new pipeline is available on GitHub.
  • Creating InTRePID, a new persistent identifier for in-text reference pointers. Different in-text reference pointers denoting the same bibliographic reference have distinct logical, rhetorical and textual contexts wherein they occur. To permit them to be identified individually and handled properly, we have recently developed a new persistent identifier, the In-Text Reference Pointer Identifier (InTRePID), for identifying individual in-text reference pointers relating to an open bibliographic citation. The InTRePID is based on the Open Citation Identifier (OCI), currently being used to identify the >624 million citations present in the new release of COCI, the OpenCitations Index of Crossref open DOI-to-DOI citations, described in the previous blog post. The formal definition of an InTRePID is available on Figshare [2]. In addition, an InTRePID Resolution Service has been developed (currently in beta-testing) to facilitate the retrieval of the metadata relating to in-text reference pointers. At the moment, a subset of the CCC corpus is available online for testing the InTRePID Resolution Service.
  • Development of services for accessing and querying the Citations in Context Corpus. Along with the development of the CCC itself, we are also developing services for querying data within the CCC. In particular, we are currently working to extend the RAMOSE software to provide an API for accessing the CCC triplestore. This CCC API will permit users to access the CCC corpus and retrieve detailed information about in-text reference pointers and their related annotations in a variety of human- and machine-readable formats. The source code of the API Manager is available on GitHub. The configuration file for querying the CCC corpus is still in the process of development.

Moreover, we are currently working to evaluate the content data quality of the CCC corpus and to develop reconciliation activities with information stored in Crossref. Specifically, by means of new validation methods, we are testing whether the extracted in-text reference pointers are complete (i.e. determining that all the in-text reference pointers for a particular bibliographic reference have been correctly extracted from the text), and that in-text reference pointer lists (e.g. “[5-13]”) have been correctly parsed to extract all the implicit pointers (in this case “[6]”, “[7]”, “[8]”, “[9]”, “[10]”, “[11]” and “[12]”), and to associate them correctly with the appropriate bibliographic references that they denote. This activity is fundamental, in order to address the diverse citation styles adopted by different journals and to overcome possible incoherencies in the publishers’ XML markup of the articles. Secondly, whenever a DOI is not specified for the citing or cited publications in the full-text of the citing publication, a text search using the Crossref API is performed in order to match possible candidates and supply the missing DOI. This reconciliation process itself can be error-prone since recommended matches are obtained by means of a non-transparent scoring mechanism. Therefore we are currently testing the application of a scoring threshold that will eliminate false positives and provide us only with correct results.

The deployment of the enhanced OpenCitations pipeline for populating the CCC corpus automatically is planned to start in the next weeks. For more details and to provide suggestions, please contact us!

References

[1] Marilena Daquino, Silvio Peroni and David Shotton (2019). The OpenCitations Data Model. Version 2.0. Figshare. DOI:  ​https://doi.org/10.6084/m9.figshare.3443876 

[2] David Shotton, Marilena Daquino and Silvio Peroni (2020). In-Text Reference Pointer Identifier: Definition. Figshare.  DOI: https://doi.org/10.6084/m9.figshare.11674032