Discover POCI, the index of open citations from PubMed 

We’re happy to announce POCI, the OpenCitations Index of PubMed open PMID-to-PMID citations, an RDF dataset containing details of all the citations from publications bearing PubMed Identifiers (PMIDs) to other PMID-identified publications, harvested from the National Institutes of Health Open Citations Collection (NIH-OCC). The citations available in POCI are treated as first-class data entities, with accompanying properties including the citations timespan, modelled according to the OpenCitations Data Model. 

Currently, POCI’s December 2022 release contains 717,654,703 citations from 26,024,862 bibliographic resources, and is based on the dump of NIH Open Citation Collection dated November 2022. 

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/poci/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://w3id.org/oc/index/poci/ci/01600102060800080706-016002060909030401), 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 PMIDs, which includes all the POCI citations, the OCI is created in the following manner, as explained more fully here. Each converted numeral part of OCI is prefixed by a 0160, which indicates that NIH 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 POCI data

All the data in POCI:

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   

 

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  

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"])

 

OpenCitations Access Tokens: how they work and why they are important

Since its inauguration in 2010, OpenCitations has always granted free access to its services to users throughout the world, with no requirement for registration or sign-up. Programmatic access to OpenCitations data can be obtained either via our SPARQL endpoints and our REST APIs. In addition, OpenCitations data – available in CSV, Scholix, and RDF formats – can be downloaded from data dumps made periodically and stored on Figshare, so as to enable large-scale analyses using the whole content of the data sets, and also be obtained via our user-friendly text-based search and browsing interfaces.

One of OpenCitations’ priorities is (and will always be) to keep its data globally open and available at zero cost and without restriction for third-party analysis and re-use. As a matter of sustainability, OpenCitations relies on financial support from the scholarly community, which includes those institutions that use OpenCitations data. However, OpenCitations has not so far had in place a proper system to monitor its users, and the main evidence of the impact of OpenCitations in different academic fields and countries has been incompletely obtained from direct contacts with our members and donors across the world, our collaborations with international projects, and the interactions on our social platforms (Twitter and LinkedIn).

We would now like to institute a system that enables us to follow the usage and assess the impact of OpenCitations more reliably. For this purpose, we are now happy to announce the launch of the OpenCitations Access Token System for access to the OpenCitations data and services.

An OpenCitations Access Token is an opaque character string that anonymously identifies a unique user of the OpenCitations APIs. OpenCitations assigns an access token only if authorized to do so by each user, who can request a token by inserting his/her email address into the access form and clicking “Get token”. Upon submission of such a request, each user will automatically receive a personal access token by email. Users can save their personal access token and reuse it every time calling the APIs of OpenCitations, by passing it as a value for the key access-token in the header of each API call. 

Obtaining and using an OpenCitations Access Token is thus easy. It only requires a simple form request, and then the insertion of your personal token into the API call header when using OpenCitations REST APIs. OpenCitations will not store users’ email addresses or any personal information, so that the users’ privacy will be totally safeguarded. The token system just provides a simple mechanism for identifying unique users, for which the use of IP addresses is insufficient.

Obtaining an OpenCitations Access Token will take the user only a few seconds and needs to happen only once. You can request your OpenCitations Access Token here

https://opencitations.net/accesstoken 

Use of an OpenCitations Access Token is not compulsory. However, token use will help OpenCitations incredibly, by enabling us to monitor the number of the unique users accessing our data and services, providing objective anonymized evidence of the number of institutions and researchers accessing our data either occasionally or on a regular basis, which we can then employ to demonstrate the usefulness of OpenCitations in the research environment. While the token system will initially be employed just for API calls (the most used service we offer), it will subsequently be extended to our other forms of data access.

OpenCitations exists for the people that use its data for research purposes every day, and thanks to their support. This is why obtaining precise knowledge of how many researchers and institutions are accessing our services is essential to us, since it will enable us to present the uniqueness and value of OpenCitations to new communities of stakeholders, and thus to make it possible to enlarge the already enthusiastic and diverse group of people and institutions supporting and using our Open Science Infrastructure.

To summarize: Getting and using an OpenCitations Access Token is voluntary, easy, and does not cost you anything. However, it will help OpenCitations a great deal. Please get your own token now, and use it next time you access OpenCitations. Thank you very much!

 

Additional 48 million citations in COCI, including references from IEEE 

We announce the August 2022 release of COCI, the OpenCitations Index of Crossref open DOI-to-DOI citations, which is based on open references to works with DOIs within the Crossref dump dated August 2022. This new release extends COCI with more than 48 million additional citations, giving a total number of more than 1.36 billion DOI-to-DOI citation links. 

This release includes citations from the articles published over the last four years by IEEE, whose bibliographic references were opened in June 2022. 

A fundamental role in pushing the commercial publishers to open their citation data was played by Crossref’s recent announcement to change its reference distribution policy, by making all its metadata open.  

Besides IEEE, COCI already includes the citation data derived from Elsevier (open via Crossref since December 2020) and from the last articles published by the American Chemical Society (whose references were opened in February 2021) 

You can find more information about COCI in our open-access article  

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

Finally, just a reminder that the bibliographic and citation data in COCI:  

    • can be queried using the OpenCitations Indexes SPARQL endpoint;  
    • can be retrieved by using the COCI REST API;  
    • can be searched by using the OpenCitations Indexes Search Interface;  
    • are also available as dumps on Figshare in CSV, N-Triples, and Scholix; and  
    • can be freely re-used for any purpose.

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!

Five reasons why 2021 has been a great year for OpenCitations

2021 is just behind us. Since January is “the Monday of the months”, as F. Scott Fitzgerald once wrote[1], it’s a good time to take stock of what happened at OpenCitations during the past year.

Among the numerous events, achievements and challenges that 2021 brought with it, we want to highlight five milestones which make us proud to look back:

1. We extended our coverage to well over one billion citations

During 2021, OpenCitations’ largest index COCI (the OpenCitations Index of Crossref open DOI-to-DOI citations) was able to include for the first time the citation links involving references that had been opened at Crossref by Elsevier and the American Chemical Society, thereby greatly expanding its coverage. The last release of COCI (November 2021) is based on open references to works with DOIs within the Crossref dump dated October 2021, and, as a result, COCI now contains information on more than 1.23 billion citations involving almost 70 million publications.
A recent analysis by Alberto Martìn-Martìn (Facultad de Comunicación y Documentación, Universidad de Granada, Spain), published on the OpenCitations Blog in October, shows that the citation coverage provided by OpenCitations is approaching parity with that of the leading commercial citation indexes, Web of Science and Scopus, offering a viable alternative upon which to base open and reproducible metrics of academic performance.

2. OpenCitations team grew

Last summer, we appointed Claudio Fabbri as our Administrator and Research Manager to take responsibility for the day-to-day administrative and financial activities of OpenCitations; Chiara Di Giambattista as Communications Director and Community Development Manager to take care of all communications and community interactions made on behalf of OpenCitations; and Giuseppe Grieco as our new Software and Systems Developer to take charge of technical development related to the OpenCitations services.

Thanks to the support from the OpenAIRE Nexus project, the team has also recently welcomed Arcangelo Massari as our new Software Developer to take care of the development of the new database OpenCitations Meta. We anticipate further appointments during 2022!

Our International Advisory Board met in November, and we thank its members for the valuable advice they provided. The Board will meet again later this month.

3. We participated in many international meetings

During the past year, OpenCitations’ directors Silvio Peroni and David Shotton took part in numerous international conferences, webinars and workshops, including the LIBER Annual Conference 2021, the OS Fair 2021, OASPA 2021 and FORCE2021. These provided excellent opportunities to describe and promote OpenCitations, to reach out to new potential stakeholders, and to discuss with other experts the main themes of our activities and plans as they relate to Open Science.

The year ended with a bang, with the announcement during the closing session of FORCE2021 that the 2021 Open Publishing Award for Open Data had been awarded to OpenCitations.

4. We received a world of support

In 2021, thanks to our involvement in the SCOSS funding campaign and to our commitment to reaching out to the libraries and universities potentially interested in OpenCitations, we gathered a wide international community of stakeholders and supporters around us. We are deeply thankful to the 6 consortia and 56 institutions across the globe which are now supporting us financially, thus making it possible for us to enhance our services and expand our team. You can find the full list of our supporters on the OpenCitations website and in this recent Thank You video:

Additionally, in January 2021, we started our involvement in the EC-funded OpenAIRE Nexus project, bringing us into closer collaboration with our European colleagues and infrastructures, including OpenAIRE. The main aim of the project is to create a framework of services for assisting in publishing research, monitoring its impact, helping promote its discovery, and integrating it into the European Open Science Cloud (EOSC) “for the benefit of the open science community worldwide”. In OpenCitations, we’re thrilled to be part of this collaborative project by providing open bibliographic citations as part of the open data components of OpenAIRE and the EOSC.

5. We set the stage for future developments

Thanks to the research grants and the support and endorsement we have received from the international scholarly community, we are now working on a variety of new services, thus setting our goals for the coming years. In particular, we want to enhance OpenCitations partnerships and dialogue with the scholarly community; to collaborate with colleagues to develop new services that will expand our citation coverage, including new OpenCitations indexes of NIH-OCC, of DataCite and of other sources of open references, that will all be searchable through a single API; and to create OpenCitations Meta, our new database that will hold comprehensive bibliographic metadata of the publications involved in our indexes citations, thereby enabling faster query responses and the ability to host citations involving publications lacking DOIs[2].

[1] F. Scott Fitzgerald (2002). The beautiful and damned (page 50 in the original 1922 edition); United Kingdom: Dover Publications. https://www.google.it/books/edition/The_Beautiful_and_Damned/-tUoAwAAQBAJ?hl=en&gbpv=0

[2] Silvio Peroni, David Shotton; OpenCitations, an infrastructure organization for open scholarship. Quantitative Science Studies 2020; 1 (1): 428–444. doi: https://doi.org/10.1162/qss_a_00023

OpenCitations receives the Open Publishing Award in Open Data

What role does ‘open’ play in making this project special?”

This apparently easy, but not banal, question was asked in the Open Publishing Awards nomination form, and at OpenCitations we prefaced our answer to it by stating “For OpenCitations, ‘open’ is the crucial value and the final purpose.” We consider the free availability of bibliographic citation data to be a necessary condition for the establishment of an open knowledge graph, and believe that having citations open helps achieve a more transparent, accessible and comprehensive research practice.

Since 2019, the Open Publishing Awards, founded and organized by the Coko Foundation and sponsored by OASPA, Crossref and Cloud68.Co, “celebrate software and content in publishing that use open licenses but also, importantly, provide a chance to reflect on the strategic value of openness”. The award judges considered open access projects divided into five categories: Open Publishing Lifetime Contribution, Open Content, Open Publishing Models, Open Source Software and Open Data.

It is in this final Open Data category of the Open Publishing Awardsthat OpenCitations was selected, as an infrastructure that perfectly represents the open principles, from among the few semantic web and linked open data initiatives currently available in the scholarly communication landscape. The award was announced in the Open Publishing Awards Ceremony, during the closing session of the FORCE2021 conference “Joining Forces to Advance the Future of Research Communication” (7-9 December). You can learn more about the Awards and the other projects selected here: https://openpublishingawards.org/results/2021/index.html

The greatest honour for OpenCitations was receiving the following comment given on behalf of the jury panel, which included open source and scholarly communication experts:

“At the time of writing this review, the largest database provided by OpenCitations contains more than 1.23 billion citations. Compiling this database in a license-friendly way is a feat on its own, but combine that with OpenCitations’ persistence (established 11 years ago), their active and consistent involvement with the community, and the number of works that were made possible by their effort (Google Scholar lists 1440 results), it is clear that OpenCitations is one of the fundamental projects in open publishing, specifically in open scientific publishing”.

We are proud and humbled to count the Open Publishing Award in Open Data among the acknowledgements so far received by OpenCitations. Despite the term “award”, the Open Publishing Awards, in fact, don’t aim to proclaim winners, but rather to “shake the hands” of some projects which seem to be following (and tracing) a right path towards a more open knowledge. All the projects awarded help by defining more concretely what “open”means, and at the same time their example encourages awareness on the variety of the open publishing projects, and a reflection about the common values and goals that gather so many different people, institutions and organizations.

Recognizing the commitment to the openness of knowledge and research of the not-for-profit and collaborative projects like OpenCitations is about community, not competition.

As Silvio recently stated:

OpenCitations is a plural. Together, we are OpenCitations.”

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