A new revolutionary workflow for a unified collection of citations: say hello to the OpenCitations Index

Blog post by Ivan Heibi (University of Bologna), Arianna Moretti (University of Bologna) and Chiara Di Giambattista (University of Bologna).

In the past five years, the OpenCitations data has been enriched with numerous new indexes of open citation data from different sources. However, the quantity and diversification of the ingested information have raised several issues, which recently made it essential to conduct a complete revision of the ingestion workflow. The result was a revolution in the way OpenCitations data is delivered. In this blog post, we will explain the context and challenges raised by the old procedure. Then, we will present the new ingestion workflow, designed to produce just two comprehensive collections: OpenCitations Index, collecting open citation data, and OpenCitations Meta, for the open bibliographical metadata. 

Once upon a time, there were five OpenCitations indexes…

In 2018, OpenCitations released the kickoff version of its first citation index, COCI (citations from Crossref), which contained around 300 million citation links derived from the subset of the reference lists in the Crossref database, where citing and cited entities were identified using Digital Object Identifiers (DOIs). COCI gathered citations with associated metadata in compliance with the recommendations from the Initiative for Open Citations (I4OC) that citation data should be structured, separable, and open, thus marking a turning point by providing a disruptive and free and open alternative to earlier sources such as Google Scholar, which provided freely accessible data although not downloadable, and Web of Science or Scopus, which demanded paid access. 

In a short time, COCI became a competitive and trusted index of citation data, used by numerous institutional repositories, including B!son and Optimeta. In 2021, COCI was taken into account in a comparative study with the most relevant sources in the landscape, including the proprietary ones, which showed its coverage approaching parity with those of the other sources involved in the analysis (Microsoft Academic, Scopus, Dimensions, and Web of Science). At the time of its most recent update in January 2023, COCI counted more than 1.4 billion citations. The reason behind this outstanding number lies in several factors, including Elsevier’s endorsement of the Declaration on Research Assessment (DORA) in December 2020, leading to the open release via Crossref of the reference lists of the articles published in all its journals, and confirming the value of initiatives such as the Initiative for Open Citations (I4OC)

However, before this change of heart, in 2019 OpenCitations had tried to narrow the open citations coverage gap by launching its second index, the Crowdsourced Open Citations Index (CROCI). This index allowed publishers and scholars to contribute directly by uploading crowdsourced open citations into the OpenCitations infrastructure.

In December 2022, a new concrete step towards a factual plurality of OpenCitations indexes was taken by the ingestion of new data sources into the infrastructure, with the publication of the inaugural dumps of DOCI (citations from DataCite) and POCI (citations from PubMed). In June 2023, the first version of the OROCI (citations from OpenAIRE) dump was released too, and JOCI (citations from JALC) is expected to be available by the end of November 2023, for a total of five collections from different sources. 

Why a new workflow? The issues with multiple sources management and new challenges

While having such a variety and richness of indexes helped present the extent of OpenCitations sources, the recent increment in the number of sources and the diversification of data integrated led to two primary issues:

    1. the necessity to handle the ingestion of new identifier types in a DOI-based software infrastructure, and
    2. the consequent possibility of encountering the same citation expressed by several sources with different identifiers.

Moreover, it soon became evident the need to optimize the reuse of the already developed software components to facilitate the metadata crosswalk processes between the new sources’ data models and the OpenCitations Data Model, with the aim to define a functional and easily extendable workflow to be easily reused when it comes to incorporating new data sources, which should be: 

    1. sufficiently generic to establish a globally unique procedure; 
    2. customizable enough to capture the necessary information within each of the specific data models and formats. 

As a solution, we decided to use OpenCitations Meta, the new OpenCitations database and tool for managing bibliographic data related to the publications involved in the citations. OpenCitations Meta makes it possible to assign each entity involved in a citation an internal identifier, nominally the OpenCitations Meta Identifier (OMID), to which all the associated persistent identifiers of the same publication are redirected.

As a result, the allocation of an OMID for each bibliographic resource also enabled the unambiguous identification of each citation, regardless of the persistent identifier schema originally used by the data source to identify the resources. This approach allowed us to perform data deduplication and finally make all the sources’ contributions converge into a unified index containing all the unique citations managed by OpenCitations, expressed as OMID to OMID citation links.

The revised workflow

The new workflow is based on three main components with the benefit of optimizing the process both in terms of computational cost and in terms of flexibility. As shown in Fig. 1, in a preliminary step, source-specific software converts the input dataset – structured according to the source data model – to extract two OpenCitations Data Model compliant data collections in tabular format for bibliographic metadata and citation data, respectively.

The following steps are common to the process of each dataset.  

STEP 1: The bibliographic metadata collection is used as input for the META software. At this stage, it is checked whether or not the bibliographic entities have been previously integrated into our infrastructure (coming from other data sources). If so, the existing OMID is linked also to the new alternative identifiers of the new bibliographic resources. New metadata values, if any, are also integrated. A new OMID identifier is produced for entities never previously encountered, uniquely representing the bibliographic resource in OpenCitations. The outputs of the process are: (I) an updated version of the OpenCitations Meta collection that also includes the metadata of the bibliographic entities provided by the new source, and (II) a collection of provenance data. An internal database is constantly refreshed to preserve correspondence between IDs and the associated internal OMIDs.

STEP 2: Starting from the collection of citations expressed as directional links between identifiers of potentially any type (e.g., DOI-DOI, PMID-PMID, PMC-PMID, etc.), the INDEX software queries the internal database mapping IDs to OMIDs to produce an updated version of the OpenCitations Index: unique citations expressed as OMID-OMID links in different formats, accompanied by their corresponding provenance data.

Fig. 1: An overview of the data ingestion workflow, starting from the data source-specific conversion and production of citations and bibliographic metadata tables, progressing through the META process and the assignation of an OMID identifier to each bibliographic record involved in a citation, and culminating with the exposition of the OpenCitations Index collection of OMID-OMID unique citations.

What we have now: The OpenCitations Index 

From now on, OpenCitations will no longer display an index of citation data for each source. Instead, we will publish a single collection of citations into which the contributions from each of the sources will flow, which we will simply call ‘The OpenCitations Index‘. The first version of this unified index of OMID-OMID citations is posted on Figshare. It was produced in RDF, CSV, and SCHOLIX formats, together with a collection of its provenance information, provided in RDF and CSV formats. For each citation, it is possible to trace the source of the information by consulting the Provenance data collection, thanks to the http://www.w3.org/ns/prov#atLocation property, which defines the location of each citation.

This new solution has the benefit of simplifying the consultation of the data maintained by our infrastructure without reducing the information content. In addition, by including efficient handling of the deduplication problem, the new Index not only provides accurate data on the exact number of unique citations exposed by the framework but also verifies the individual contribution of each source, as well as their overlapping data (Fig. 2).

Fig. 2: An overview of the number of citations stored in the OpenCitations Index as of October 31, 2023. The diagonal cells in the table (highlighted in yellow) show the unique contribution of each collection to the OpenCitations Index, while the other cells represent the citations that are shared between the collections. More in detail, the green cells show the overall input of each source, while the pink cells represent the number of overlapping citations between two data sources.

Currently, the Index contains almost 2 billion unique citations. By the end of November, a new version of the collection will be published, including the contribution of the new Japan Link Centre (JaLC) source. 

How to access the OpenCitations Index data

To maximize the reuse of the exposed information and to ensure the greatest possible interoperability, the collection will always be published on Figshare in all formats listed above. In addition, the data will be accessible via an API, a SPARQL endpoint, and a web interface.

The redesign of the ingestion workflow marks a fundamental step for OpenCitations towards a more intuitive and simple access to our services while always preserving and improving the quality of our data. If you need further information on how the new workflow works, please visit our website, contact us at contact@opencitations.net  or leave feedback and/or suggestions in the dedicated card on our public roadmap to help us improve our services and communications. Thank you!

Discover DOCI, the index of open citations from DataCite

We’re excited to introduce DOCI, the OpenCitations Index of Datacite open DOI-to-DOI citations, a new tool containing citations derived from publications bearing DataCite DOIs to other DOI-identified publications, harvested from DataCite. The citations available in DOCI are treated as first-class data entities, with accompanying properties including the citations timespan, modelled according to the OpenCitations Data Model

Currently, DOCI’s December 2022 release contains 169,822,752 citations from 1,753,860  citing resources, and is based on the last dump of DataCite dated 22 October 2021 provided by the Internet Archive

Citation URLs

Each citation (i.e. an individual of the class cito:Citation) is identified by an URL structured as follows:

 https://w3id.org/oc/index/doci/ci/[[OCI]].

Open Citation Identifiers

Each Open Citation Identifier [[OCI]] has a simple structure: the lower-case letters “oci” followed by a colon, followed by two numbers separated by a dash (e.g. https://opencitations.net/index/doci/ci/080010504060836132137200707121027-080010504060836161221130313.html), in which the first number identifies the citing work and the second number identifies the cited work.

For citations in which the citing and cited works are identified by DOIs, which includes all the DOCI citations, the OCI is created in the following manner, as explained more fully here. Each case-insensitive DOI is first normalized to lower case letters. Then, after omitting the initial doi:10. prefix, the alphanumeric string of the DOI is converted reversibly to a pure numerical string using the simple two-numeral lookup table for numerals, lower case letters and other characters presented at https://github.com/opencitations/oci/blob/master/lookup.csv. Finally, each converted numeral is prefixes by a 080, which indicates that DataCite is the supplier of the original metadata of the citation (as indicated at http://opencitations.net/oci).

OCIs can be resolved using the OpenCitations OCI Resolution Service.

Access to DOCI data

All the data in DOCI:

More information is available at https://opencitations.net/index/doci. 

What is an Open Citation Index? 

A citation index is a bibliographic index recording citations between publications, allowing the user to establish which later documents cite earlier documents. The current indexes available in OpenCitations are: 

All the OpenCitations Indexes have six characteristics in common, summarized here: https://opencitations.net/index  

The OpenCitations Roadmap is now publicly available on Trello

Want to keep yourself updated about the ongoing activities of OpenCitations? We have now publicly released the OpenCitations Roadmap, available on Trello.com:

https://trello.com/b/RprHYoKL/opencitations

The OpenCitations Roadmap consists of a board fulfilled with colour-labelled cards which present the goals so far reached, the present projects and activities, and the future plans. By clicking on the cards, it is possible to visualize a description for each activity, the progress state, and who in the OpenCitations team is working on it.

The OpenCitations Roadmap covers all kinds of activities divided according to the scope, identified by the coloured labels, in particular:

  • light blue for the technical development, such as the development of the software for the creation of the new database OpenCitations Meta and of DOCI, the OpenCitations Index of DataCite open DOI-to-DOI citations, and the re-engineering of the infrastructure and the website;
  • green for the data model implementation;
  • yellow for the data development, such as the bi-monthly COCI releases;
  • purple for the events and outreach activities.

The cards also highlight the activities related to the two EC-funded projects OpenCitations is involved in, OpenAIRE Nexus (blue label) and RISIS2 (orange label). We thank the OpenAIRE team for the help and suggestions during the Roadmap review process.

The OpenCitations Roadmap is an open work in progress that will reflect the developments and growth of OpenCitations. At OpenCitations, we don’t want this Roadmap to be just an online ‘showcase’, but a room in which to share ideas and opinions. We invite you – the members of our community, our stakeholders, the other Open Science actors, researchers, and librarians, and anyone who is interested in OpenCitations activities – to add a comment or a question in the ‘Leave feedback‘ card. This will help us to better understand our strong and weak points, and to stay in touch with the needs and thoughts of the community.

In this way, supplementing the conventional communications channels of email and the social platforms (our blog, Twitter, LinkedIn), the OpenCitations Roadmap will become a new virtual place for dialogue, where you can directly contribute to improve OpenCitations.

OpenCitations and EC funding: OpenAIRE Nexus and RISIS2

The incentives for new OpenCitations innovative solutions

Two years ago, in their canonical 2020 QSS paper on OpenCitations, Silvio Peroni and David Shotton anticipated the creation of the new database, OpenCitations Meta, able to “offer a faster and richer service” by storing bibliographic metadata “in house”. Meta would “avoid duplication of data by efficiently permitting us to keep […] a single copy of the metadata for each of the bibliographic entities involved as citing or cited entities in the different OpenCitations’ citation indexes”, would remove the requirement for potentially slow API calls to external metadata sources such as Crossref and ORCID, and would enable us to index citations involving entities lacking DOIs.

Important synergies to achieve goals

Today, thanks to the recent involvement of OpenCitations in two EC-funded projects, the OpenAIRE-Nexus Project (Horizon 2020 EU funded project, GA: 101017452) and the RISIS2 Project (Horizon 2020 EU funded project, GA: 824091), the development of OpenCitations Meta has commenced, with a planned release date later in 2022.

The OpenAIRE-Nexus project started in January 2021 to embrace and expand the operation of a portfolio of thirteen services, provided by OpenAIRE infrastructure, public institutions, organisations and universities, classified into three portfolios entitled PUBLISH, MONITOR, and DISCOVER. The OpenAIRE-Nexus portfolios focus on the demands of the three main categories of the research lifecycle.  Therefore, OpenAIRE-Nexus makes sure such services are integrated to provide a uniform Open Science Scholarly Communication package for the European Open Science Cloud (EOSC). Within the OpenAIRE Nexus project there is scope for producing not only support materials (factsheet, guides, video tutorials, demos) but also training sessions where the services in the three portfolios will be showcased, anticipating the EOSC onboarding process. The role of OpenCitations in the project is to provide open bibliographic citations, and interconnect and integrate (and vice versa) functionalities with the  OpenAIRE Research Graph and more OpenAIRE-Nexus services such as EpiSciences, OpenAIRE MONITOR) the core component of OpenAIRE infrastructure and services and of the EOSC Resource Catalogue. 

Additionally, we are happy to announce our recent involvement in the RISIS2 Project. The Research Infrastructure for Science and Innovation Policy Studies (RISIS) is a project funded by the European Union under a Horizon2020 Research and Innovation Programme. RISIS2 involves 18 partners working together to create and maintain a research infrastructure for the field of Science, Technology, and Industry (STI) Studies, and to build an advanced research community in this field. OpenCitations’ contributions to RISIS2 will include not only the creation of OpenCitations Meta but also the development of a new citation index of open references, the OpenCitations Index of DataCite Open Citations (DOCI), which will be based on the open reference holdings of DataCite and, together with COCI, will be cross-searchable through our unified OpenCitations API.

Lessons learnt so far

A year into the OpenAIRE-Nexus project, we have found that one of the most significant benefits for OpenCitations is our involvement with this wide cooperative network of European research infrastructures, services, and communities, within which we can exchange experiences, ideas, and knowledge, and discuss any challenges and outcomes with our colleagues. More importantly, OpenCitations becomes positioned within the Open Science ecosystem, as a valuable innovative infrastructure with strong proof of integration and interoperable operations. Being part of the OpenAIRE-Nexus team has opened up more future challenges and expectations, and raised the bar for the inclusion of more functionalities of value. Thanks to the dedication of its efficient communication team, OpenAIRE is also helping us by communicating OpenCitations services to additional users and stakeholders, by inclusion within the comprehensive OpenAIRE services catalogue, by releasing an OpenCitations factsheet and by permitting us to present the latest information on OpenCitations through established events (i.e. Open Science FAIR 2022). FAIR and openness of information is our motto, and we strongly promote this through all our activities.

Expanding our team

As announced in our previous blog post “Five reasons why 2021 has been a great year for OpenCitations”, the support we receive from the EU as part of OpenAIRE-Nexus has enabled our recent appointment of Arcangelo Massari, a software developer who is now playing a crucial role in the creation and development of OpenCitations Meta.

As the year 2022 progresses, we look forward to bringing you further information about other new goals for OpenCitations, made possible by the support we receive from our numerous partnerships.

Open citations in Informatics: current status and lines of research

This post was first published on QWERTY: musings from the rabbit hole, a blog by Silvio Peroni

A few months ago, I was invited to have a talk at the European Computer Science Symposium on an aspect of my research I particularly care about, that of open citations. What I tried to address during the presentation concerned the current status of open citation availability in a particular domain, Informatics, by using two open datasets, i.e. DBLP for gathering bibliographic metadata about relevant publications and OpenCitations’ COCI for identifying citations where such publications are involved. This post briefly introduces the preliminaries and results obtained from the material used to prepare the talk.

Open citations and where to find them

A citation is a conceptual directional link between a citing entity and a cited entity which is defined by means of specific textual devices contained in the text of the citing entity, e.g. a bibliographic reference denoted by an in-text reference pointer (e.g. “[3]” or “(Doe et al, 2021)”). While reasons for citing may vary, citations are used in academia for acknowledging others’ work and enabling building trails of relations defining how science evolves in time.

The data needed to describe a citation should include, at least, a representation of such a conceptual link and the basic bibliographic metadata to identify the citing and cited entities, i.e. those typically used for defining bibliographic references such as authors’ names, year of publication, the title of the work, venue of publication, pages, identifiers, etc. We say that a citation is open when these citation data are in the public domain and can be retrieved freely (via the HTTP protocol) in a structured and machine-readable format (e.g. JSON or RDFwithout accessing the source of citing article defining it, which, potentially, could be behind a paywall.

OpenCitations [full disclosure: I am one of its directors] is one of the founders of the Initiative for Open Citations (I4OC) and one of the open scholarly infrastructures providing open citation data through several channels (REST APIs, SPARQL endpoints, Web interfaces, full dumps in different formats). As of 31 December 2021, it makes available more than 1.2 billion open DOI-to-DOI citation links between more than 69.5 million bibliographic resources, which are mainly journal articles but also include books, book chapters, datasets, and other DOI-identified resources. The entities involved in such citations come from different domains, spanning from Medicine articles to Humanities publications, and have recently approached parity with those included in well-known proprietary services such as Web of Science and Scopus.

What about Informatics

Such a huge mass of open citations available enables us to analyse citation coverage in different scholarly disciplines, e.g. to understand which publishers contributed to the availability of open citation data in a discipline and to check what are the citation trails between different disciplines. However, to compute such citation coverage, we need to have some information that allows us to identify when a particular bibliographic resource involved in a citation belongs to the particular discipline we want to analyse. We can use information about the subject categories of publications (e.g. that of Web of Science), if included in citation indexes, to identify the discipline(s) of a given bibliographic resource. Unluckily, OpenCitations does not provide this information and, as such, we need to rely on external repositories for gathering subject categories of publications, e.g. collections of bibliographic metadata of disciplinary publications.

In the context of Informatics, there is at least one well-known resource gathering and exposing bibliographic metadata of a large part of Computer Science publications, i.e. DBLP. As of 30 December 2021, DBLP contains more than 5.9 million publications published in 1,781 journals and in the proceedings of 5,621 conferences, involving more than 2.9 million authors that are manually curated (and disambiguated) by the DBLP team.

DBLP can be used as a proxy to understand if a particular publication belongs to the Computer Science subject category. Through it, it is possible to understand how many citations in OpenCitations involve Computer Science publications by comparing the DOIs of citing and cited entities with those available in DBLP. In particular, using the OpenCitations’ COCI September 2021 dump and DBLP October dump, I found that more than 80 million citations in COCI involved at least one of the 4,637,865 entities in DBLP (considering only journal articles, conference proceedings papers, books and book chapters). As shown in Figure 1, only 39% of these citations are between citing and cited entities both included in DBLP, while the rest of them either come from or go to publications not listed in DBLP – that, potentially, could not be Computer Science publications.

Figure 1. A Venn diagram showing how many citations involving Computer Science publications (obtained from DBLP) are included in OpenCitations.

Additional information about the publishers of such DBLP entities, retrieved by querying the Crossref API and the DataCite API with entities’ DOIs, are shown in Table 1. IEEE is the publisher with the biggest number of entities of those considered for this study, and its entities are involved in more than 18.9 million incoming and 21.5 million outgoing citations. The other bigger publishers, in terms of entities and citations, are Springer, Elsevier, ACM and Wiley. It is worth mentioning that the two publishers responsible for publishing mainly Computer Science journals and a relatively low number of conference proceedings (if any), i.e. Elsevier and Wiley, are those providing the highest number of openly-available references per publication (on average, around 29 and 37 cited works for each publication respectively).

PublisherDBLP entitiesCOCI incoming citationsCOCI outgoing citations
IEEE1,730,48518,930,05521,582,093
Springer1,012,53418,482,13211,179,566
Elsevier574,86015,536,20717,019,716
ACM433,1883,695,2556,050,342
Wiley89,6623,350,1833,357,065
Table 1. The DBLP entities retrieved in the study grouped by their publisher and their incoming and outgoing citations according to COCI.

Future developments

Of course, this study does not provide full coverage of open citations in Computer Science but just a preliminary insight. First, as anticipated below, DBLP does not have the complete coverage of all CS-related publications since there are some venues that are not listed there (yet). Thus, some relevant open citations could not be extracted from COCI if these involve as citing and cited entity non-DBLP publications that belong to the CS domain. However, it is worth mentioning that no bibliographic and citation database (including commercial and proprietary ones) has a full disciplinary coverage anyway and DBLP is, probably, the most comprehensive collection of Computer Science publications metadata (something that could be assessed in future analysis).

Along the same lines, the index of open citations used, i.e. COCI, does not contain all the citations defined in CS publications, but only DOI-to-DOI citations as retrievable from Crossref data. Although Crossref is the biggest DOI provider and it is used by the majority of the big publishers,citations defined in publications with a non-Crossref DOI (e.g. DataCite) and those not having any DOI assigned (e.g. the papers published in CEUR Workshop Proceedings) are not included in COCI and, consequently, have not been used in the analysis. However, OpenCitations plans to extend its data coverage adding more sources in the next years. Thus, it would be interesting to replicate the same analysis in the future to see if and how much the coverage increase, at least in the context of Computer Science publications.

Still about coverage, currently (i.e. 31 December 2021) the only publisher of those included in Table 1 which is not providing open references through Crossref is IEEE. Indeed, while COCI includes several citations involving IEEE publications as citing entities, there is no availability of such citation after October 2018, when IEEE decided not to allow anymore Crossref Metadata Plus users to access these reference data.

Finally, analysing the preliminary results of this study, it would be interesting to understand which are the main subject categories of non-DBLP publications included in the 61% of citations shown in Figure 1 (e.g. by using the Scimago Journal and Country Rank database to retrieve their subject categories) to understand what are the citation dynamics between Informatics and other disciplines. However, I will leave the answer to this question to future analysis.

A final remark on reproducibility

Since several of the suggestions provided above start from the idea of either replicating or extending this study with additional materials and insights, it is important that all data and software used to perform the analysis are available online to permit its reproducibility. To this end, I have published both the software and the data retrieved online with open licenses to enable anyone to reuse it freely for any purpose.

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