We’re happy to announcePOCI, 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.
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).
are available as dumps on Figshare in CSV, N-Triples and Scholix.
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:
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.
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).
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:
We’re now proud to announce the September 2021 release of COCI, which is based on open references to works with DOIs within the Crossref dump dated August 2021. This new release extends COCI with more than 92 Million additional citations, giving a total number of more than 1.18 Billion DOI-to-DOI citation links.
This latest release includes citations from the most recent articles published by the American Chemical Society, whose bibliographic references were opened in February 2021. The ACS back number citations will be available in the next COCI release, when a new processing of all the Crossref data will be completed.
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;
Readers of this blog will be familiar with Open Citation Identifiers (OCIs), described in an earlier post and formally defined in [1]. OCIs enable bibliographic citations, treated as first class information entities, to be uniquely identified and referenced, and are used to identify the >624 million individual citations indexed in the latest release of COCI, the OpenCitations Index of Crossref open DOI-to-DOI citations, as described in a recent post.
However, COCI and similar citation indexes do not provide any information about where within the citing paper a citation is generated, the textual contexts of the in-text reference pointers, or the reasons for including different in-text reference pointers denoting the same reference at different points within the text.
As explained in the preceding post describing the Open Biomedical Citations in Context Corpus funded by the Wellcome Trust and under development by OpenCitations, deep citation analysis requires a more nuanced approach to citations, which acknowledges that each in-text reference pointer that denotes a bibliographic reference in the reference list of a citing publication instantiates its own citation, as shown in Figure 1.
Figure 1. Citations between a citing paper and a cited paper instantiated both by the inclusion of a bibliographic reference within the reference list of the citing paper and by the inclusion within the text of the citing paper of one or more in-text reference pointers denoting that reference.
The pointer citations clearly involve the same cited publication as does the reference citation itself, but each has its own unique characteristics: the location and textual context of its in-text reference pointer within the text of the citing publication, and its particular rhetorical function which is determined by that context.
If the reference citation is open (as defined in [2]) and identified by an OCI, each in-text reference pointer related to that citation can be identified uniquely using an In-Text Reference Pointer Identifier (InTRePID).
InTRePIDs facilitate in-depth scholarship on in-text reference pointer locations and citation functions, and fine-grained analysis of the relationships between publications, by making it possible
to identify each in-text reference pointer with a unique PID,
to distinguish references that are cited only once from those that are cited multiple times,
to see which references are cited together (e.g. in the same sentence or within an in-text reference pointer list),
to determine from which section(s) of the article references are cited (e.g. Introduction, Methods, Discussion), and, potentially,
to determine the rhetorical function of the citations from analysis of their textual contexts, by the application of natural language processing, machine learning and artificial intelligence techniques to conduct sentiment analysis on the citation contexts.
Definition of an InTRePID
An InTRePID is composed of two parts separated by an oblique stroke
intrepid:<oci-numerals>/<ordinal>–<total>
where
<oci-numerals> is the numerical part of the OCI uniquely identifying the particular open citation to which the in-text reference pointer and its denoted bibliographic reference relate. Thus an InTRePID can be assigned for any in-text reference pointer that relates to an open citation for which a valid OCI has been assigned;
<ordinal> identifies the nth occurrence of an in-text reference pointer within the text of the citing paper relating to that citation; and
<total> defines the total number of in-text reference pointers denoting that bibliographic reference within the citing paper.
For example, intrepid:070433-070475/4–6 is a valid InTRePID for an in-text reference pointer defined within the OpenCitations Citations in Context Corpus.
A formal definition document for the InTRePID is given in [3].
Exemplar in-text reference pointers
Consider the following citing paper:
Zou, J. et al. (2020). Phenotypic and genotypic correlates of penicillin susceptibility in nontoxigenic Corynebacterium diphtheriae, British Columbia, Canada, 2015–2018. Emerging Infectious Diseases, 26: 97-103. https://doi.org/10.3201/eid2601.191241
This paper contains six in-text reference pointers denoting Reference 13 in the reference list:
13. Lowe, C. et al. (2011). Cutaneous diphtheria in the urban poor population of Vancouver, British Columbia, Canada: a 10-year review. J. Clinical Microbiology49: 2664-2666. https://doi.org/10.1128/JCM.00362-11
The InTRePIDs for these pointers are recorded within the OpenCitations Biomedical Citations in Context Corpus, together with the corpus identifiers and DOIs of the citing and cited papers, as shown in the excerpt presented in Figure 2.
Figure 2. An excerpt from the OpenCitations Biomedical Citations in Context Corpus, showing highlighted the InTRePIDs for the six in-text reference pointers within Zou, J. et al. (2020) denoting Reference 13, the reference to Lowe, C. et al. (2011), together with the internal corpus identifiers for each in-text reference pointer, and the corpus identifiers and DOIs for the citing and cited papers.
Of these six in-text reference pointers, having InTRePIDs intrepid:070433-070475/1-6 to intrepid:070433-070475/6-6, the first and the fourth of these, together with their document locations, their embedding sentences, their in-text reference pointer lists, and their InTRePIDs, chosen as examples, are as follows:
Introduction. “Nontoxigenic strains have been shown to have epidemic potential, causing infections in persons afflicted by homelessness, alcohol abuse, and injection drug use (9,13–15).” (intrepid:070433-070475/1-6)
Discussion. “We also noted ST5 and ST32 in our review from downtown Vancouver during 1998–2007 (13).” (intrepid:070433-070475/4-6)
The first of these discusses those people most susceptible to diphtheria infection, while the other discusses which multilocus sequence types (STs) of C. diphtheriae were found, thus relating to the organism causing the infection rather than to the infected individuals. The rhetorical function of these two in-text reference pointers is quite distinct.
To permit this information to be recorded within the OpenCitations Citations in Context Corpus, extensions were required to the OpenCitations Data Model, a new extended version of which was recently published [4], as described in a related blog post.
The OpenCitations InTRePID Resolution Service
To support the use of InTRePIDs to identify in-text reference pointers, OpenCitations has recently developed an InTRePID Resolution Service (currently in ‘beta’ in its development cycle), which is running at http://opencitations.net/intrepid. A screenshot of this service is shown in Figure 3.
Figure 3. A screenshot of the user interface of the InTRePID Resolution Service.
In addition to using the Web user interface shown in Figure 3, InTRePIDs can be entered into this resolution service in the form of resolvable URIs, e.g.
As shown in Figure 4, the OpenCitations InTRePID Resolution service returns metadata concerning the in-text reference pointer identified by the InTRePID, and the bibliographic reference that it denotes, from which further information about the citation and the citing and cited publications may be obtained by following the links provided.
Figure 4. A screenshot of the Web page displaying metadata returned by the InTRePID Resolution Service.
Note that as well as rendering this information in HTML on a web page, the resolution service can also provide it in a variety of machine-readable formats.
Conclusion
InTRePIDs, which enable the identification of individual in-text reference pointers, and the InTRePID Resolution Service, are new services from OpenCitations that will facilitate scholarship on the textual contexts and rhetorical functions of such in-text reference pointers, and of the citations that they instantiate.
InTRePIDs were first announced on 30th January 2020 at PIDapalooza 2020 in Lisbon, the Open Festival of Persistent Identifiers.
Heibi I, Peroni S, Shotton D (2019). Software review: COCI, the OpenCitations Index of Crossref open DOI-to-DOI citations. Scientometrics 121(2): 1213-1228. https://doi.org/10.1007/s11192-019-03217-6
COCI is our first OpenCitations Index of open citations, in which we have applied the concept of citations as first-class data entities, each identified using a unique persistent Open Citation Identifier (OCI), to index the contents of one of the major databases of open scholarly citation information, namely Crossref, and to render and make available this information in machine-readable RDF.
We are now proud to announce the third release of COCI, which contains more than 624 million DOI-to-DOI citation links coming from both ‘the ‘Open’ and the ‘Limited’ sets of Crossref reference data. This represents an increase of 40% in the number of indexed citations, compared with the second release of COCI on 12th November 2018, which indexed more than 445 million citations. The data model used for this third release of COCI is the updated revision of the OpenCitation Data Model, published on 8 November 2019 and available at https://doi.org/10.6084/m9.figshare.3443876.
This new release of COCI has been created using new software developed specifically for this purpose, which is available on our GitHub repository under an open ISC license. This software automates the process of creating an OpenCitations Index compliant with the OpenCitations Data Model and creates the citation data and related provenance information in three different formats: CSV, N-Triples (RDF), and Scholix. The support for Scholix – a high-level interoperability framework supported by Crossref, DataCite, Europe PubMed Central, OpenAIRE and others – has recently been added to provide an additional format for the exchange of information about the links between scholarly literature and datasets.
A great advantage of the new software is that it will now enable us to extend COCI (and any other OpenCitations Index) by means of incremental additions, rather than having to re-create the entire index at each update. This should enable us to release index updates more frequently than hitherto, thus keeping the index more closely in synchrony with the latest reference data released by Crossref. Note that we are currently run the software on previous dumps of Crossref data so as to retrieve all the citations that involve references in citing articles that were in the ‘Limited’ set when we downloaded it, but that currently appear in the Crossref ‘Closed’ data set due to more recent restrictive policy decisions taken by their publishers.
Finally, we wish to remind you that all the bibliographic and citation data in COCI:
