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!

The OpenCitations blog posts are now archived on Rogue Scholar with DOIs

Last April, Martin Fenner launched Rogue Scholar, an archive of science blogs aiming to index full-text of blog posts, establish a full-text search, and register DOIs and metadata for all posts. Rogue Scholar works with all blogging platforms that publish scholarly content and have an RSS or Atom feed with full-text content distributed under a Creative Commons Attribution (CC-BY 4.0) license.    

Rogue Scholar currently features 40 blogs, including the OpenCitations blog, with more than 1,000 blog posts that are available via full-text search, with DOIs linking to the original post on one of 40 science blogs. By exploring the OpenCitations blog’s profile on Rogue Scholar, you will find the last 40 posts with summaries (derived from the information you get in the RSS feed), and by clicking on the DOI you will be redirected to the full post on the blog. The DOI metadata include abstract, language, license, and (OECD Fields of Science) subject category for all posts.  

Rogue Scholar is growing day by day, and the increasing involvement of science blogs – from different disciplines and various languages – demonstrates that a central archive of science blogs with full-text content, and DOIs for all blog posts with relevant metadata is feasible, making an important contribution to Open Scholarly infrastructure”. 

Thanks to a recently launched Mastodon instance at Rogue Scholar Social, the OpenCitations blog has now its own Mastodon feed, where you can keep yourself updated about the last posts of the OpenCitations blog, by finding summaries and the related DOIs linking to the full post – and you can also boost and comment, of course! Please follow us at https://rogue-scholar.social/@opencitations  to not miss anything.  

If you are managing a Science Blog and are interested in adding it to the Rogue Scholar archive, or if you are just interested in the topic of metadata for scholarly blogs, please contact info@front-matter.io  

 

Follow OpenCitations on Mastodon

OpenCitations has happily joined the open-source social media platform joinmastodon.org.

Mastodon is “a free and open-source software developed by a non-profit organization”, with the aim of favouring interoperability and bringing social media interaction “back in the hands of the people”.

We look forward to recreating there our wide network of connections, and getting in touch with new people, projects and institutions in a different virtual environment.

Follow us at https://scicomm.xyz/@opencitations !

Tutorial: how to process COCI’s zipped CSV dump without decompressing it

Blog post by Ivan Heibi (Universiy of Bologna) and Arcangelo Massari (University of Bologna).

OpenCitations publishes the COCI dataset after each new release in three main formats: CSV, N-Triples, and Scholix (see https://opencitations.net/download#coci). The CSV format is the most popular and downloaded one due to its comprehensive data organization (i.e. tabular format) and smaller size (compared to the other formats provided). Therefore, this is also the format we suggest using for a local process of the entire COCI dataset. 

The CSV dumps of COCI are uploaded on Figshare. You can check and download the last dump released from https://doi.org/10.6084/m9.figshare.6741422. The dump consists of one main ZIP file, including other smaller ZIP archives (one for each release) containing the actual CSV files (Figure 1).

Figure 1. The contents of the COCI CSV dataset (after the August 2022 release)

It is possible to process this data without unzipping the internal archives, thus saving a lot of disk space. In this tutorial, we will see how to achieve this in Python. Same process could be done in other programming languages.

Processing the COCI dump using Python

Step 1) Downloading the COCI dump

First, you need to download the last CSV dump release of COCI from https://doi.org/10.6084/m9.figshare.6741422 and decompress only the external archive. After this operation, you should have a folder containing the internal ZIP files such as in Figure 1.

Note: It is beneficial to decompress the external archive because doing so does not increase the space occupied on the disk (compressing archives results in a compression rate of 0%) and because working on nested archives would significantly increase RAM requirements. 

Step 2) Working with the ZIP files

Python provides the built-in zipfile module, whose ZipFile class allows you to create, read, write, edit and list the contents of a ZIP file. Given as input the path of the root directory containing all the ZIP files (FOLDER_PATH), the process elaborates each of these files on a different iteration. Each cycle initializes a ZipFile object by specifying the path to the ZIP file (archive_path).

from zipfile import ZipFile
import os

for archive_name in os.listdir(FOLDER_PATH):        
archive_path = os.path.join(FOLDER_PATH, archive_name)
with ZipFile(archive_path) as archive:     # ...

Step 3) Accessing the ZIP files

Use the namelist() method to return the list of CSV files contained in each archive. Then to open the inner CSV files, simply cycle through the list of names and feed them to the open() method of the ZipFile instance, i.e. archive in the example below.

from zipfile import ZipFile
import os

for archive_name in os.listdir(FOLDER_PATH):
    archive_path = os.path.join(FOLDER_PATH, archive_name)
    with ZipFile(archive_path) as archive:
        for csv_name in archive.namelist():
with archive.open(csv_name) as csv_file:       # ...

Step 4) Reading the CSVs

The .open() method returns a buffer. To read the CSV file as a list of dictionaries (i.e. represent each row of the CSV in dictionary format, e.g., {“column1″:”val1”, “column2″:”val2”}) we need to transform the buffer using the TextIOWrapper class and read it using the DictReader class of csv. Then we convert the result of DictReader into a list. 

from io import TextIOWrapper
from zipfile import ZipFile
import os

for archive_name in os.listdir(FOLDER_PATH):
    archive_path = os.path.join(FOLDER_PATH, archive_name)
    with ZipFile(archive_path) as archive:
        for csv_name in archive.namelist():
with archive.open(csv_name) as csv_file:
reader = csv.DictReader(io.TextIOWrapper(csv_file))
rows = list(reader)
# ...

Step 5) Processing the CSVs content

Now you can go through each row of the list and process the citation data as you want. The following example prints the citing and cited entity of each citation in the dump. 

from io import TextIOWrapper
from zipfile import ZipFile
import os

for archive_name in os.listdir(FOLDER_PATH):
    archive_path = os.path.join(FOLDER_PATH, archive_name)
    with ZipFile(archive_path) as archive:
        for csv_name in archive.namelist():
with archive.open(csv_name) as csv_file:
reader = csv.DictReader(io.TextIOWrapper(csv_file))
rows = list(reader)
# Process the CSV here
for r in rows:
print("Citing entity:",r["citing"])
print("Cited entity:",r["cited"])

 

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!

Reflections on the global citation graph

In his call for open citations, Dario Taraborelli hailed the scholarly citation graph (in which the nodes (vertices) are individual academic publications and the links (edges) represent bibliographic citations from one publication to another) as one of humankind’s most important intellectual achievements.

We all understand that the inclusion within our own academic publications of bibliographic references to the works of others is one of the most explicit ways of acknowledging the thoughts, discoveries, achievements and influences of other scholars, and their contributions to our own work. Not only does what we gain from their publications enable us to make intellectual progress, by “standing on the shoulders of giants” as Newton once famously observed [1], but the influence of these publications extends forward in time across the entire intellectual landscape, like gigantic shadows cast at sunset, whether or not those influenced by these publications have occasion to reference them in their own works.

A bibliographic citation is not only “a conceptual directional link from a citing entity to a cited entity, created by a human performative act of making a citation”, but it is additionally both enduring and retrospective. Enduring, because once made it persists for ever within the global corpus of scholarly literature, and retrospective because (with the exception of occasional contemporaneous citations) the cited publication predates the citing publication.

At the anterior margin of a crawling cell, cellular protrusive extension (for example of a pseudopodium) is achieved by the catalysed polymerization of new filaments of the cytoskeletal protein actin from attachment sites on an existing stationary actin filament network, pushing the cell margin forward [2]. The scholarly citation network (or citation graph, the two terms here being used interchangeably) is similarly dynamic and temporally directional, being extended forward as new works of scholarship are published. Extension of knowledge is achieved by the catalytic inspiration provided by existing academic publications, themselves temporally stationary within the expanding citation network, leading to the publication of new works of scholarship that cite these previous publications and thus extend the citation network further into the future. The citation graph is thus not just an acyclic directed graph, but an acyclic temporally directed graph. Indeed, it is this temporal aspect of the citation network that is one of its most important features.

To use another analogy, the human genealogical tree is inherently multidimensional and difficult to represent pictorially in its entirety, because each new birth brings together the family trees of the child’s two parents. However, unless the parents are seriously promiscuous, the resulting genealogical tree is not impossibly complex. In contrast, the scholarly citation network is much more highly interlinked, since each new publication cites not just two but many preceding (‘parent’) publications, which themselves may beget many other citations.

Visualization of the global scholarly citation graph, or portions of it, is thus inherently difficult, and the important temporal aspect of the graph is the one ignored by almost every method used for visualizing aspects of that graph. Existing methods may take the broad view, showing the links, and the strength of those links, between one scholarly domain and another, thus visualizing the ‘structure of science’. Alternatively, they may take a more detailed view of a small section of the graph, visualize the proximity of individual publications to one another. Often a radial display is chosen for this, that shows in closest proximity those papers directly referenced by the selected publication in the centre, then at a greater radius those papers referenced by the cited papers shown in the inner circle, and so on. Because of the graph’s complexity, such displays quickly looses intelligibility after two citation links.

Among a small number of visualization applications that do not ignore the temporal aspect of the graph is Citeology, a temporally based citation network visualization tool developed some years ago by Justin Matejka and colleagues at the design software company Autodesk [3]. Unfortunately, this innovative software prototype was not central to that company’s mission, development ceased, and the Citeology Java app is no longer available. However, in his last email to me, Justin Matejka kindly offered to help others re-create this application.

There is thus an urgent need for innovative new open-source visualization tools that will clearly and dynamically display portions of the global citation graph, for example the direct and indirect citation connections between any two publications or any two individuals, along the temporal axis of publication date. Developers within the open science community please step forward!

References

[1] Isaac Newton, in a 1675 letter to Robert Hooke, wrote “If I have seen further it is by standing on the shoulders of Giants.” https://discover.hsp.org/Record/dc-9792/

[2] Bruce Alberts et al. (2014). Molecular Biology of the Cell. 6th Edition. Garland Science. Chapter 16, The Cytoskeleton.

[3] Justin Matejka, Tovi Grossman, George Fitzmaurice (2012). Citeology: Visualizing Paper Genealogy. ACM Extended Abstracts on Human Factors in Computing Systems. https://www.autodesk.com/research/publications/citeology https://d2f99xq7vri1nk.cloudfront.net/CiteologyVideo.mp4

Crossing a significant threshold: more than one billion citations now available in COCI!

“The competitive benefits of closing access to citation data diminish with each new citation released to the public domain, but the benefits of open data remain. Going forward, citation data is almost completely public domain”.

With these words, from the article “A tipping point for open citations data” (July 15, 2021), Ian Hutchins celebrated the threshold crossing of one billion citations on public-domain databases in February 2021.

Now, a new significant milestone has been reached. We are enthusiastic to announce that COCI, the OpenCitations Index of Crossref open DOI-to-DOI citations has just been extended with 334 million additional citations. Its most recent release, the COCI July 2021 release, now contains a total of 1.09 billion DOI-to-DOI citation links derived from open references within Crossref,which includes the references of articles deposited or opened in Crossref between November 2020 and January 2021.

These numbers make us proud, and confirm the essential value of the Initiative for Open Citations (I4OC). Since 2018, the mission of I4OC has been to persuade publishers to provide open citation data by means of the Crossref platform. The I4OC untiring commitment has led the major academic publishers to a progressive change of heart regarding open citations, and the scholarly community to a deeper interest in this openness.

These factors contributed to the creation of COCI in 2018, the first open citation index created by OpenCitations, in which we applied the concept of citations as first-class data entities (Heibi I., Peroni S., Shotton D., 2019). Over the last three years, COCI has been extended in a series of releases, by harvesting citations mostly from Crossref data dumps, starting from an initial coverage of 300 million citations (First release).

A crucial event that preceded (and delayed!) this latest COCI release was Elsevier’s endorsement in the DORA Declaration on Research Assessment in December 2020, thereby making “reference lists for all articles published in Elsevier journals openly available via Crossref so they can be available for reuse. This means other important initiatives like I4OC can draw on this metadata”. As described in our previous post, Elsevier’s welcome commitment led to the opening of many previously closed references from its numerous academic journals submitted to Crossref. Now, after an extended period of data ingestion and processing, all these newly opened Elsevier references are available at OpenCitations within COCI.

Elsevier’s involvement has both an effective and a symbolical value. Even if publishing more than one billion citations is a thrilling achievement, and – as Hutchins wrote – we are now at a tipping point with regard to open citations data, this milestone is not the last stop. Together with the other organizations and projects that participate in the Initiative for Open Citations, we will keep claiming the urgency for the remaining academic publishers to join our cause, and sharing our values with the whole academic community to make all existing citations data freely open and accessible. Recalling what Dario Taraborelli wrote in the conclusion of his article “The citation graph is one of humankind’s most important intellectual achievements“, “the world is waiting for the citation graph to become a public good”.

COCI has surpassed 700M citations

We are excited to share that COCI, the OpenCitations Index of Crossref open DOI-to-DOI citations, was on 12 May 2020 extended with more than 47 million additional citations, and has reached a total number of more than 702 million DOI-to-DOI citation links between more than 58 million bibliographic entities.

The citations added in this the fifth release of COCI came from the most recent Crossref dump downloaded on 22 April 2020, which includes the references of the articles deposited in Crossref between 4 October 2019 and 4 April 2020. Such updates to COCI will now occur regularly at bimonthly intervals.

As a consequence, COCI now contains 702,772,530 citations, and also includes publications about the COVID-19 pandemic. We will use this new release of COCI to update the Coronavirus Open Citations Dataset, the second release of which will include details about these additional references and publications.

COCI, which is fully described in our open-access article, was one of the subjects of a multidisciplinary comparison between the major citation indexes recently published on arXiv. In addition, it has been recently mentioned on the Scholix web site as one of the implementors of the Scholix citation data format.

Finally, we wish to remind you that all the bibliographic and citation data in COCI:

The OpenCitations Enhancement Project – final report

The OpenCitations Enhancement Project
Final report for the Alfred P. Sloan Foundation

Report period: 1st May 2017 – 30 November 2018.
Report written: 30th December 2018

Background

OpenCitations (http://opencitations.net) is a scholarly infrastructure organization dedicated to open scholarship and the publication of open bibliographic and citation data by the use of Semantic Web (Linked Data) technologies, and engaged in advocacy for semantic publishing and open citations [Peroni and Shotton, 2018b]. It provides the OpenCitations Data Model [Peroni and Shotton, 2018d], the SPAR (Semantic Publishing and Referencing) Ontologies [Peroni and Shotton, 2018e] for encoding scholarly bibliographic and citation data in RDF, and open software of generic applicability for searching, browsing and providing APIs over RDF triplestores. It has developed the OpenCitations Corpus (OCC) [Peroni et al., 2017] of open downloadable bibliographic and citation data recorded in RDF, and a system and resolution service for Open Citation Identifiers (OCIs) [Peroni and Shotton, 2018c], and it is currently developing a number of Open Citation Indexes using the data openly available in third-party bibliographic databases.

The Directors of OpenCitations are David Shotton, Oxford e-Research Centre, University of Oxford (david.shotton@opencitations.net), and Silvio Peroni, Digital Humanities Advanced Research Centre, Department of Classical Philology and Italian Studies, University of Bologna (silvio.peroni@opencitations.net). We are committed to open scholarship, open data, open access publication, and open source software. We espouse the FAIR data principles developed by Force11, of which David Shotton was a founding member (https://www.force11.org/group/fairgroup/fairprinciples), and the aim of the Initiative for OpenCitations (I4OC, https://i4oc.org), of which both David Shotton and Silvio Peroni were founding members, to promote the availability of citation data that is structured, separable, and open.

Project personnel and roles

Ivan Heibi – Research Fellow

Ivan Heibi was appointed to the 12 months Research Fellowship position funded by the Sloan Foundation.

Ivan has been responsible for the development of new visualization and programming interfaces for exploring and making sense of the citation data included in the OCC and in the new OpenCitations Indexes, for the main part of the scripts related to the population and regular maintenance of COCI (The OpenCitations Index of Crossref open DOI-to-DOI citations, the first of the OpenCitations Indexes), and for conference presentations and paper writing.

Silvio Peroni – Lead Applicant and Principal Investigator

Silvio has been responsible for project management, for interview, appointment and supervision of the work of Ivan Heibi, for all aspects of software coding and technical developments required for the OpenCitations Corpus (OCC), the OpenCitations Indexes, and the Open Citation Identifier Resolution Service, for the ordering and management of new Sloan-funded hardware, and for conference presentations, paper writing and other forms of outreach and dissemination (e.g. blog and social networks).

David Shotton – Consultant Co-Investigator

David has been responsible for project management, interaction with publishers, conference presentations, paper writing, other forms of outreach and dissemination (e.g. blog and social networks), for web site and data model revision, and for independent usability evaluation, stress-testing and design feedback of new user interfaces and applications.

Project management

Project management has been straightforward, as should be the case, given the small size of our team. It has involved more than 1500 e-mail exchanges between David Shotton and Silvio Peroni, about 500 e-mail exchanges between Silvio Peroni and Ivan Heibi since November 2017, two dozen or so video conferences, some of which have involved collaborators, and an extended face-to-face meeting during the WikiCite 2017 Conference in Vienna at the start of the project and the Workshop on Open Citations 2018 in Bologna.

We have together harmoniously developed the concept of and vision for OpenCitations as an infrastructure organization, the structure and content of the OpenCitations web site (http://opencitaitons.net), the classes and properties of our supporting SPAR ontologies (http://www.sparontologies.net), and the community of collaborators and users of our developments. This has involved outreach and dissemination at a number of international research conferences, involvement with publishers through the Initiative for Open Citations, and associated publications.

We have studied and preliminarily tested a new scalable architecture centred on one powerful independent physical server, that both stores and handles all the data in the Corpus and in the new OpenCitations Indexes, and also offers adequate performance for query services. This server is supplemented by 30 additional small physical machines, Raspberry Pi 3Bs, working in parallel, each in charge of ingesting a defined set of reference lists and feeding the ingested data to the central server for further processing and storage as RDF in our Blazegraph triplestore.

Current status of the OpenCitations services

Currently, we release two different datasets – the OpenCitations Corpus and COCI, the OpenCitations Index of Crossref open DOI-to-DOI citations – and several interfaces so as to make these data queryable from different access points.

Functionality and holdings

As of 29th December 2018, the OpenCitations Corpus (OCC) contains information about 13,964,148 citation links to 7,565,367 cited resources, ingested from 326,743 citing bibliographic resources obtained from the Open Access corpus of Europe PubMed Central and from the citation data imported from the EXCITE project. The main part of the development effort in the past months has been spent in implementing ingestion strategies that allow partners to provide us citation data, stored according the OpenCitations Data Model [Peroni and Shoton, 2018b], so as to be added directly into the Corpus. In September 2018, we successfully completed the ingestion of the initial data coming from the EXCITE project (citations from social sciences scholarly papers published by German publishers), and we are actively interacting with the LOC-DB project and the Venice Scholar Index so as to add their data to the OCC as well. In ongoing work, we are also collaborating with arXiv and EXCITE to harvest all the references from all PDF documents in the arXiv ePrints collection, to record these in RDF according to the OpenCitations Data Model, and to ingest them into the OpenCitations Corpus, as well as creating a new Index of these citations.

The first of these OpenCitations Indexes is COCI, the OpenCitations Index of Crossref open DOI-to-DOI citations, an RDF dataset containing details of all the citations that are specified by the open references to DOI-identified works present in Crossref, as of the latest COCI update. COCI does not index Crossref references that are closed, nor Crossref references to entities that lack DOIs. These citations are treated as first-class data entities, with accompanying properties including the citations timespan and possible kinds of self-citation characteristics, modelled according to the index data model described in the OpenCitations Indexes page. COCI was launched in July 2018, and the most recent update of COCI is dated 12 November 2018. It presently contains 449,840,503 citations between 46,534,705 bibliographic resources. COCI is the first citation index released by OpenCitations, being a bibliographic index recording citations between publications that permits the user to establish which later documents cite earlier documents, and to create citation graphs of these citations.).

While full coverage of the scholarly citation graph depicted by the aforementioned datasets (or as full as practically possible) is required for the calculation of certain bibliometric indicators such as journal impact factors and individual h-indexes (Hirsch numbers), partial coverage while OCC grows is still of value, since it includes citations of all the most important biomedical papers obtained from the Open Access Subset off PubMed Central. These can be easily recognized by their large number of inward citation links, and can be used to explore the development of disciplines and research trends. In addition, COCI, with its wider scope, has sufficient coverage to be used for large-scale bibliometrics analysis.

Purchase of new hardware, and testing and development of new software

Because of unavoidable academic teaching commitments for Silvio Peroni, the installation of the new Sloan-funded hardware for OCC, purchased in autumn 2017, had to be postponed. All the services (old and new) of OpenCitations were successfully transferred to our new server in October 2018. In order to implement such transition, the ingestion process of the OCC was halted, so as to allow Silvio Peroni to properly test the new hardware and to extend the existing ingestion software so as to be usable within the new parallel processing architecture. The final tests are currently running, and we will recommence the full ingestion process of the OCC using the new hardware configuration, with its greatly enhanced ingest rate, in January 2019. In the meantime, the new infrastructure has been used to allow us to create COCI, so far the largest RDF dataset of open citation data available worldwide.

In addition, we have completed the transition of all the OpenCitations software from the old GitHub repository (i.e. https://github.com/essepuntato/opencitations) to a new GitHub organization, namely https://github.com/opencitations. This organisation includes several repositories which permit third parties to initiate the whole suite of OpenCitations software on a local machine. This is of key importance for the resilience of this open source project.

User interfaces

SPARQL, the query language used to interrogate RDF triplestores, is a quite powerful language. However, one needs appropriate skills with Semantic Web technologies to master it for solving even easy search tasks. Thus normal web users are unable to use appropriately such technologies if not appropriately instructed, leaving all these technologies in the hands of a limited number of experts. The datasets made available by OpenCitations suffered similar issues.

Initially, the goal we had was to develop ad-hoc user interfaces to abstract the complexities of the SPARQL endpoints into well-designed Web interfaces that anyone could use. During the development, though, we thought it would be better to develop generic frameworks for building customizable interfaces that allow one to expose, in a more human-understandable way, RDF data stored in any RDF triplestore and accessible through any SPARQL-endpoint, so as to forster reuse of such software in contexts that, in principle, might go far beyond the OpenCitations domain.

To this end we developed three different open software applications:

  • OSCAR [Heibi et al., 2018a] [Heibi et al., 2018b], a Javascript application for creating textual search interfaces to RDF data;
  • LUCINDA, another Javascript application for creating Web browsers over RDF data;
  • RAMOSE, a Python application that permits one to easily create and serve a conventional HTTP REST API over a SPARQL endpoint.

All these tools provide a configurable mechanism – by means of one single textual configuration file – that allows one to generate Web-based interfaces to any SPARQL endpoint. In practice, these tools are flexible Web-interface makers to RDF data, and as such represent a significant advance available to the entire community.

All these applications have been used to produce several interfaces to all the datasets released by OpenCitations. In particular, we have created user-friendly textual search interfaces (via OSCAR) both for the OCC (see the search box now on the OpenCitations home page, and the related search page) and for COCI (see the related search page). We have additionally developed browsing applications (via LUCINDA) to permit humans an easier navigation of all the entities included in the OCC (e.g. see the bibliographic resource br/1791056) and in COCI (e.g. see the citation oci:02001010806360107050663080702026306630509-02001010806360107050663080702026305630301). Finally, we have also implemented REST HTTP APIs (via RAMOSE) for simplifying the queries to both datasets, the OCC and COCI, by Web developers with no expertise in Semantic Web technologies.

In addition, in order to demonstrate its flexibility, we have also created two web pages using OSCAR, LUCINDA, and RAMOSE for permitting similar tasks (text query, browsing, and REST APIs) on the scholarly data in Wikidata / WikiCite – another project recently funded by the Alfred P. Sloan Foundation. These interfaces have been introduced in two distinct event: during the hack day of the Workshop on Open Citations 2018 and during the WikiCite 2018 Conference.

A further prototypical interface / service has been recently proposed so as to try to gather additional open citation data to include in the OCC, involving users of the scholarly domain such as editors and researchers. This application is called BCite [Daquino et al., 2018]. BCite is designed to provide a full workflow for citation discovery, allowing users to specify the references as provided by the authors of an article, to retrieve them in the required format and style, to double-check their correctness, and, finally, to create new open citation data according to the OpenCitations Data Model [Peroni and Shotton, 2018d], so as to permit their future integration into the OCC. While presently only a prototype, we received several commendations for this tool, and we are currently studying funding strategies to develop a full standalone application that can be used by anyone and that allows users to directly interact with the OCC, so as to upload new data into the Corpus.

Open Citation Identifiers

During the reporting period, it became increasingly evident to us that citations deserved treating as First Class Data Entities, which would give the following advantages:

  • All the information regarding each citation would be available in one place.
  • Citations become easier to describe, distinguish, count and process.
  • If available in aggregate, citations become easier to analyze using bibliometric methods, for example to determine how citation time spans vary by discipline.

Four developments were required to make this possible:

  • The metadata describing the citation must be definable in a machine-readable manner.
  • Such metadata must be storable, searchable and retrievable.
  • Each citation must be identifiable, using a globally unique Persistent Identifier.
  • There must be a Web-based resolution service that takes the identifier as input and returns a description of the citation.

To this end, we have achieved:

  • the first requirement by the addition of appropriate classes and properties to CiTO, the Citation Typing Ontology, and by the addition of a new member of the class datacite:ResourceIdentifierScheme in the DataCite Ontology, namely Open Citation Identifier;
  • the second requirement by modifying the OpenCitations Data Model [Peroni and Shotton, 2018d] so that citations can be properly described using these new ontology terms within the OpenCitations Corpus;
  • the third requirement by creating the syntax for this new Open Citation Identifier (OCI) [Peroni and Shotton, 2018c], and enabling the creation of such identifiers, both to specify citations within the OpenCitations Corpus, and also (importantly) to specify citations described in Wikidata (by QIDs) and in Crossref (by DOIs); and
  • the fourth requirement by creating a resolving service for OCIs at http://opencitations.net/oci and additional software (in Python) for retrieving information about a particular citation identified by an OCI.

To date, OCIs have been actively used both in the OCC and in COCI to identify all the citations they contain. In addition, we now plan to create and publish additional OpenCitations Indexes of all the citations DataCite, Wikidata and (of course) the OCC, which we hope will be of great benefit to bibliometricians in their analysis of citation networks, self-citation, etc., and in the calculation of citation metrics. OCIs have been recognised by the EU Project FREYA as unique global identifiers for bibliographic citations.

Collaborations and Users

OpenCitations Data Model

We are collaborating with the following groups and academic projects, both to promote the use of the OpenCitations Data Model (OCDM), and to provide a publication venue for the citation data that they are liberating from the scholarly literature:

  • Matteo Romanello of the Digital Humanities Laboratory at the University of Lausanne is using OCDM for modelling citations of the classical literature within ancient Venetian documents in the context of the Venice Scholar Index, and is currently working on producing a dataset of citation data compliant with OCDM so as to be ingested in the OCC.
  • Two DFG-funded German projects that are extracting citations from Social Science publications:
    • The Linked Open Citations Database (LOC-DB) at the University of Mannheim is using OCDM to model their data, with the aim of producing them accordigly with such model so as to be ingested in the OCC.
    • Steffen Staab (University of Koblenz) and Philipp Mayr (GESIS) are running the EXCITE Project, which uses OCDM to model their citation data, and already adopted the OCC as their publication platform. In fact, in September 2018, ~1 million citations coming from the EXCITE Project were successfully ingested in the OCC.
  • Sergey Parinov is technically leading CitEcCyr, which is an open repository of citation relationships obtained from research papers in the Russian language and Cyrillic script. This project intends to model its citations using the OCDM, and will use the OpenCitations Corpus as its publication platform.

Users of OpenCitations data

The following project and organizations have let us know that they are using data from the OCC and COCI:

  • Wikidata includes alignments between several bibliographic entries with OCC resources;
  • OpenAIRE imported OCC metadata about articles into their LOD database;
  • Daniel Ecer and Lisa Knoll of eLife performed analytics on the OCC data;
  • Ontotext demonstrated SPARQL query federation between Springer Nature LOD and OCC;
  • Anna Kamińska published a bibliometrics case study of PLOS ONE articles in OCC;
  • Daniel Himmelstein processed OpenCitations data to create DOI-to-DOI citation tables;
  • Thiago Nunes and Daniel Schwabe are using OCC to exemplify their XPlain framework;
  • Antonina Dattolo and Marco Corbatto are using the OCC as source for VisualBib framework;
  • Nees Jan van Eck and Ludo Waltman extended VOSviewer so as to use data in the OCC + COCI, that will be officially published in the next release of the tool;
  • Barney Walker developed Citation Gecko, a graph-based citation discovery tool based on the OCC and COCI for retrieving citation data about the papers;
  • Philipp Zumstein developed a Zotero plugin that gives information about open citations using COCI;
  • Dominique Rouger developed a Web application that provides a visual graph representation of citation links in COCI.

Website statistics

From May 2017 to November 2018, the official OpenCitations website has been accessed ~5.8M times – we have excluded from this list the hits done by well-known spiders and crawlers. It is worth mentioning that the pages related to the data available and the services for querying them (i.e. “/corpus”, “/sparql”, and “/index” in the following diagram) have together gained a very high percentage of the overall accesses, showing that the main reason people access the OpenCitations website is to explore and use the data in the OCC and in COCI. It is also clear how the introduction of COCI brought additional accesses to the OpenCitations services, and the trend is increasing – e.g. in December 2018 (not shown in the following diagram) we got more than 200M accesses to “/index”, mainly related to the use of the COCI REST APIs.

Community outreach

From May 2017 to November 2018, the documents (i.e. [Peroni and Shotton, 2018b] [Peroni and Shotton, 2018c] [Peroni and Shotton, 2018d]) and the dumps of the OCC and of COCI available on Figshare (see http://opencitations.net/download) have been viewed 37,960 times and downloaded 3,842 times. The figure below summarizes how many views and downloads such resources have received month by month. For example, the latest version of COCI in CSV has been downloaded 239 times since its release in November (see https://doi.org/10.6084/m9.figshare.6741422.v3).

In the past nineteen months, the posts published by the official Twitter account of OpenCitations have been engaged by 599,200 distinct Twitter accounts, the Twitter profile (@opencitations) has been visited 12,719 times and has been mentioned in 565 tweets written by others, and it has collected an additional 1,925 followers. The diagram below shows all these statistics month by month.

Although we made relatively few new blog posts in the reporting period (there have been twenty more since then), from May to November 2018, the blog dedicated to OpenCitations (http://opencitations.wordpress.com) received 19,454 visits by 15,184 distinct users. As shown in the diagram below, the biggest peaks in terms of visits has been in July 2018 (the month when we launched COCI) and in September 2018 (the month of the Workshop on Open Citations).

Users of the SPAR Ontologies

The SPAR Ontologies [Peroni and Shotton, 2018e] are in use by about 40 other projects and organizations, including:

  • The United States Global Change Information System, which encodes federal information relating to climate change, makes extensive use of SPAR ontology terms.
  • The United Nations Document Ontology (UNDO) has been specifically aligned with FaBiO.
  • Wikidata has many classes that have been alighted with FaBiO or CiTO.
  • DBPedia’s DataID ontology uses the FaBiO and DataCite ontologies.
  • W3C’s Data on the Web Best Practices: Dataset Usage Vocabulary uses SPAR Ontologies.

For the full list, see http://www.sparontologies.net/uptake.

To date, as far as we are aware, more than 677 papers have been published that cite or use one or more of the SPAR ontologies. For the full list, see http://www.sparontologies.net/uptake#publications.

OpenCitations and the Initiative for Open Citations

OpenCitations and the Initiative for Open Citations, despite the similarity of title, are two distinct organizations. The primary purpose of OpenCitations is to host and build the OpenCitations Corpus (OCC) and the OpenCitations Indexes, as long as additional service to browse, query, and analyse citation data. In contrast, the Initiative for Open Citations (I4OC, https://i4oc.org) is separate and independent organization, whose founding was spearheaded by Dario Taraborelli of the WikiMedia Foundation. OpenCitations is one of several founding members of the Initiative for Open Citations, as documented at https://i4oc.org/#founders. I4OC is a pressure group to promote the unrestricted availability of scholarly citation data, but does not itself host citation data.

Because open reference lists are necessary for the population of OCC, we at OpenCitations have devoted considerable effort to promoting I4OC’s aims, and we host the I4OC web site on behalf of that community.

Within a short space of time, I4OC has persuaded most of the major scholarly publishers to open their reference lists submitted to Crossref, so that the proportion of all references submitted to Crossref that are now open has risen from 1% to over 50%. These are now available for OpenCitations to harvest into the OpenCitations Corpus and publish in RDF, as well as for others to harvest and use as they wish [Shotton, 2018].

Publications during the reporting period

Scholarly papers

Marilena Daquino, Ilaria Tiddi, Silvio Peroni, David Shotton (2018). Creating Open Citation Data with BCite. In Emerging Topics in Semantic Technologies – ISWC 2018 Satellite Events: 83-93. DOI: https://doi.org/10.3233/978-1-61499-894-5-83, OA at http://ceur-ws.org/Vol-2184/paper-01.pdf

Ivan Heibi, Silvio Peroni, David Shotton (2018). Enabling text search on SPARQL-endpoints through OSCAR. Submitted for publication to Data Science – Methods, Infrastructure, and Applications. OA at at https://w3id.org/people/essepuntato/papers/oscar-datascience2019/

Ivan Heibi, Silvio Peroni, David Shotton (2018). OSCAR: A Customisable Tool for Free-Text Search over SPARQL Endpoints. In Semantics, Analytics, Visualization – 3rd International Workshop, SAVE-SD 2017, and 4th International Workshop, SAVE-SD 2018, Revised Selected Papers: 121-137. DOI: https://doi.org/10.1007/978-3-030-01379-0_9, OA at https://w3id.org/people/essepuntato/papers/oscar-savesd2018.html

Silvio Peroni, David Shotton (2018). OpenCitations: enabling the FAIR use of open citation data. In Proceedings of the GARR Conference 2017 – The data way to Science – Selected Papers. DOI: https://doi.org/10.26314/GARR-Conf17-proceedings-19

Silvio Peroni, David Shotton (2018). The SPAR Ontologies. In Proceedings of the 17th International Semantic Web Conference (ISWC 2018): 119-136. DOI: https://doi.org/10.1007/978-3-030-00668-6_8

Silvio Peroni, David Shotton, Fabio Vitali (2017). One year of the OpenCitations Corpus: Releasing RDF-based scholarly citation data into the Public Domain. In Proceedings of the 16th International Semantic Web Conference (ISWC 2017): 184-192. DOI: https://doi.org/10.1007/978-3-319-68204-4_19, OA at https://w3id.org/people/essepuntato/papers/oc-iswc2017.html

David Shotton (2018). Funders should mandate open citations. Nature 553: 129. https://doi.org/10.1038/d41586-018-00104-7

Additional documents

Silvio Peroni, David Shotton (2018). Open Citation: Definition. Figshare. DOI: https://doi.org/10.6084/m9.figshare.6683855.v1

Silvio Peroni, David Shotton (2018). Open Citation Identifier: Definition. Figshare. DOI: https://doi.org/10.6084/m9.figshare.7127816.v1

Silvio Peroni, David Shotton (2018). The OpenCitations Data Model. Figshare. DOI: https://doi.org/10.6084/m9.figshare.3443876.v5

Blog posts

6 May 2017: Querying the OpenCitations Corpus

15 May 2017: The Sloan Foundation funds OpenCitations

24 Nov 2017: Milestone for I4OC – open references at Crossref exceed 50%

24 Nov 2017: Elsevier references dominate those that are not open at Crossref

28 Nov 2017: Openness of non-Elsevier references

9 Jan 2018: The new Crossref reference distribution policy

9 Jan 2018: Barriers to comprehensive reference availability

15 Jan 2018: Funders should mandate open citations

16 Jan 2018: Oxford University Press opens its references!

29 Jan 2018: OpenCitations and the Initiative for Open Citations: A Clarification

19 Feb 2018: Citations as First-Class Data Entities: Introduction

22 Feb 2018: Citations as First-Class Data Entities: Citation Descriptions

25 Feb 2018: Citations as First-Class Data Entities: The OpenCitations Data Model

4 Mar 2018: Citations as First-Class Data Entities: The OpenCitations Corpus

12 Mar 2018: Citations as First-Class Data Entities: Open Citation Identifiers

15 Mar 2018: Citations as First-Class Data Entities: The Open Citation Identifier Resolution Service

23 Mar 2018: Early adopters of the OpenCitations Data Model

17 Apr 2018: Workshop on Open Citations

12 Jul 2018: COCI, the OpenCitations Index of Crossref open DOI-to-DOI references

19 Nov 2018: New release of COCI: 450M DOI-to-DOI citation links now available

Conference presentations and other outreach

Workshop on Open Citations 2018

OpenCitations, the EXCITE Project and Europe PubMed Central ran the first Workshop on Open Citations (Twitter: @workshop_oc) at the University of Bologna in Bologna, Italy, on 3-5 September 2018. It was organised as follows:

  • Day One and Day Two: Formal presentations and discussions on the creation, availability, uses and applications of open bibliographic citations, and of bibliometric studies based upon them;
  • Day Three: A Hack Day on Open Citations to see what services can be prototyped using large volumes of open citation data.

The workshop involved 60 participants, including researchers, computer scientists, scholarly publishers, academic administrators, research funders and policy makers. The workshop was organised around the following topics:

  • Opening up citations: Initiatives, collaborations, methods and approaches for the creation of open access to bibliographic citations;
  • Policies and funding: Strategies, policies and mandates for promoting open access to citations, and transparency and reproducibility of research and research evaluation;
  • Publishers and learned societies: Approaches to, benefits of, and issues surrounding the deposit, distribution, and services for open bibliographic metadata and citations;
  • Projects: Metrics, visualizations and other projects. The uses and applications of open citations, and bibliometric analyses and metrics based upon them.

All the sessions were recorded and are available on the official YouTube channel of the University of Bologna, and are linked (together with slides) at the website of the workshop – https://workshop-oc.github.io.

A further Workshop on Open Citations is being planned for autumn 2019.

Presentations

We have made conference presentations on OpenCitations, the Initiative for Open Citations, and Open Citation Identifiers at the following international conferences and workshops:

WikiCite Conference 2017, Vienna, 23 May 2017, https://www.slideshare.net/essepuntato/opencitations (Silvio Peroni and David Shotton)

COASP 9, 9th Conference of Open Access Scholarly Publishing, Lisbon, 20 September 2017, https://www.slideshare.net/essepuntato/the-initiative-for-open-citations-and-the-opencitations-corpus (David Shotton)

SemSci 2017, 1st International Workshop on Enabling Open Semantic Science, Vienna, 21 October 2017, https://w3id.org/people/essepuntato/presentations/the-open-citations-revolution.html (Silvio Peroni)

ISWC 2017, 16th International Semantic Web Conference, Vienna, 24 October 2017, https://w3id.org/people/essepuntato/presentations/oc-iswc2017.html (Silvio Peroni)

FORCE 2017, Research Communication and e-Scholarship Conference, Berlin, 27 October 2017, http://w3id.org/people/essepuntato/presentations/oc-force2017.html (Silvio Peroni)

Linked Open Citation Database (LOC-DB) Workshop, Mannheim, 7 November 2017, https://locdb.bib.uni-mannheim.de/wordpress/wp-content/uploads/2017/10/Shotton-LOC-DB-Mannheim.pdf (David Shotton)

GARR Conference 2017, Venice, 16 November 2017, https://www.eventi.garr.it/it/documenti/conferenza-garr-2017/presentazioni-2/232-conf2017-presentazione-peroni/file (Silvio Peroni)

OpenCon 2017, Oxford, 1 December 2017, https://doi.org/10.6084/m9.figshare.5844981.v1 (David Shotton)

PIDapalooza Conference of Persistent Identifiers, Girona, 24 January 2018, https://doi.org/10.6084/m9.figshare.5844972.v2 (David Shotton)

2018 International Workshop on Semantics, Analytics, Visualisation: Enhancing Scholarly Dissemination, Lyon, 24 April 2018, https://doi.org/10.6084/m9.figshare.7531577.v1 (Ivan Heibi)

Workshop on Open Citations 2018, Bologna, 3 September 2018, https://workshop-oc.github.io/presentations/D1S3_David_Shotton.pdf (David Shotton)

Workshop on Open Citations 2018, Bologna, 4 September 2018, https://docs.google.com/presentation/d/1mybQmjhFY6kLtTE1TdONaxsl0nSjmRGOSCnFMTwfzWQ/edit?usp=sharing (Silvio Peroni)

The 5th Conference on Scholarly Publishing in the Context of Open Science (PUBMET 2018), Zadar, 20 September 2018, https://doi.org/10.6084/m9.figshare.7110653.v3 (Silvio Peroni)

The 17th International Semantic Web Conference (ISWC 2018), Monterey, 12 October 2018, https://doi.org/10.6084/m9.figshare.7151759.v1 (Silvio Peroni)

WikiCite Conference 2018, Berkeley, 27 November 2018, https://doi.org/10.6084/m9.figshare.7396667.v1 (Ivan Heibi)

A further presentation on Open Citation Identifiers will be given at the 2019 PIDapalooza Conference of Persistent Identifiers in Dublin in January 2019.

Tweets

We have tweeted about the project and related matters under the names @opencitations, @dshotton, @essepuntato, @ivanHeiB, @workshop_oc, and @i4oc_org.

Future sustainability

While presently the OpenCitations Corpus has only partial coverage, our aim is that OpenCitations should become a comprehensive source of open citation information from all disciplines of scholarly endeavour, used on a daily basis by scholars worldwide, to equal or better the commercial offerings from Clarivate Analytics (Web of Science) and Elsevier (Scopus).

We also wish to develop effective graphical user interfaces to explore the citation network, and analytical tools over our open data. Since the OCC and COCI data are all open and available for others also to build such tools, we anticipate that such developments will best be undertaken collaboratively, under some open community organization, and indeed such development is currently being undertaken in collaboration with colleagues from CWTS at the University of Leiden, famous for their development of VOSviewer.

In order to fully support open scholarship, OpenCitations need to mature from being an academic research and development project to become a recognised scholarly infrastructure service such as PubMed. We wish to avoid becoming a commercial company, and see our development better served by being ‘adopted’ by a major established scholarly institution such as national or university library or an internationally recognised centre providing scholarly bibliographic services, that has already shown a commitment to open scholarship, where the interaction between that institution and OpenCitations would be mutually beneficial. To this end, we are currently in the mid-phase of negotiations with two institutions.

Conclusions

The grantees wish to express their deep gratitude to the Alfred P. Sloan Foundation for financial support enabling them to undertake the OpenCitations Enhancement Project, without which the rapid developments reported here would not have been possible.

References

Marilena Daquino, Ilaria Tiddi, Silvio Peroni, David Shotton (2018). Creating Open Citation Data with BCite. In Emerging Topics in Semantic Technologies – ISWC 2018 Satellite Events: 83-93. DOI: https://doi.org/10.3233/978-1-61499-894-5-83, OA at http://ceur-ws.org/Vol-2184/paper-01.pdf

Ivan Heibi, Silvio Peroni, David Shotton (2018a). Enabling text search on SPARQL-endpoints through OSCAR. Submitted for publication to Data Science – Methods, Infrastructure, and Applications. OA at at https://w3id.org/people/essepuntato/papers/oscar-datascience2019/

Ivan Heibi, Silvio Peroni, David Shotton (2018b). OSCAR: A Customisable Tool for Free-Text Search over SPARQL Endpoints. In Semantics, Analytics, Visualization – 3rd International Workshop, SAVE-SD 2017, and 4th International Workshop, SAVE-SD 2018, Revised Selected Papers: 121-137. DOI: https://doi.org/10.1007/978-3-030-01379-0_9, OA at https://w3id.org/people/essepuntato/papers/oscar-savesd2018.html

Silvio Peroni, Alexander Dutton, Tanya Gray, David Shotton (2015). Setting our bibliographic references free: towards open citation data. Journal of Documentation, 71: 253-77. DOI: https://doi.org/10.1108/JD-12-2013-0166, OA at http://speroni.web.cs.unibo.it/publications/peroni-2015-setting-bibliographic-references.pdf

Silvio Peroni, David Shotton (2018a). OpenCitations: enabling the FAIR use of open citation data. In Proceedings of the GARR Conference 2017 – The data way to Science – Selected Papers. DOI: https://doi.org/10.26314/GARR-Conf17-proceedings-19

Silvio Peroni, David Shotton (2018b). Open Citation: Definition. Figshare. DOI: https://doi.org/10.6084/m9.figshare.6683855.v1

Silvio Peroni, David Shotton (2018c). Open Citation Identifier: Definition. Figshare. DOI: https://doi.org/10.6084/m9.figshare.7127816.v1

Silvio Peroni, David Shotton (2018d). The OpenCitations Data Model. Figshare. DOI: https://doi.org/10.6084/m9.figshare.3443876.v5

Silvio Peroni, David Shotton (2018e). The SPAR Ontologies. In Proceedings of the 17th International Semantic Web Conference (ISWC 2018): 119-136. DOI: https://doi.org/10.1007/978-3-030-00668-6_8

Silvio Peroni, David Shotton, Fabio Vitali (2016a). Building Citation Networks with SPACIN. Knowledge Engineering and Knowledge Management – EKAW 2016 Satellite Events, EKM and Drift-an-LOD, Revised Selected Papers: 162-166. DOI: https://doi.org/10.1007/978-3-319-58694-6_23, OA at https://w3id.org/oc/paper/spacin-demo-ekaw2016.html

Silvio Peroni, David Shotton, Fabio Vitali (2016b). Freedom for bibliographic references: OpenCitations arise. In Proceedings of 2016 International Workshop on Linked Data for Information Extraction (LD4IE 2016): 32-43. http://ceur-ws.org/Vol-1699/paper-05.pdf

Silvio Peroni, David Shotton, Fabio Vitali (2017). One year of the OpenCitations Corpus: Releasing RDF-based scholarly citation data into the Public Domain. In Proceedings of the 16th International Semantic Web Conference (ISWC 2017): 184-192. DOI: https://doi.org/10.1007/978-3-319-68204-4_19, OA at https://w3id.org/people/essepuntato/papers/oc-iswc2017.html

David Shotton (2013). Open citations. Nature, 502: 295-297. https://doi.org/10.1038/502295a

David Shotton (2018). Funders should mandate open citations. Nature 553: 129. https://doi.org/10.1038/d41586-018-00104-7

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 19th 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

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