REST API of the Open Biomedical Citations in Context Corpus (CCC)

Version: 1.0.0
API URL: https://w3id.org/oc/ccc/api/v1
Contact: [email protected]
License: This document is licensed with a Creative Commons Attribution 4.0 International License, while the REST API itself has been created using RAMOSE, the Restful API Manager Over SPARQL Endpoints, which is licensed with an ISC license.

Description back to top

This document describes the REST API of the Open Biomedical Citations in Context Corpus (CCC) hosted by OpenCitations. All the operations described in this document return either a JSON document (default) or a CSV document according to the mimetype specified in the Accept header of the request.

The CCC is based on the Open Access subset of XML articles served by Europe PubMed Central API. It includes information mined from the full-text of articles, such as in-text references (e.g. (Daquino et al. 2020)), structural elements (sentences, paragraphs, footnotes, captions, tables, and sections), rhetorical elements (e.g. section "Methods"), and the sequential number of the structural elements including in-text reference pointers (e.g. sentence 5, paragraph 2, section 1 "Introduction").

We extend the definition of Open Citation Identifier (OCI) in order to identify citation links that are related to a specific in-text reference pointer, that is, the textual device that references a cited resource in the full-text of the citing resource. Specifically, OCI may appear in the form <citing_id>-<cited_id>{/<nth-occurrence>}, where:

For instance 0701-0709/1 identifies the 1st in-text reference appearing in (the text of) the citing article 0701 that is related to the cited article 0709.

Moreover, CCC introduces the usage of In-Text Reference Pointer IDentifier (InTRePID) to identify in-text reference pointers. It is based on OCI, and it appears in the form <citing_id>-<cited_id>/<nth-occurrence>-<total-count>, where:

For instance, 0701-0709/1-2 and 0701-0709/2-2 represent the first and the second in-text reference pointer respectively that appear in the citing article 0701 that are related to the cited article 0709. InTrePIDs are dereferencable and the InTrePID resolution service allows one to retrieve the citation context of a given InTrePID (such as identifiers of sentences, paragraphs, and sections where an in-text reference pointer appears).

If you would like to suggest additional operations, please use the CCC issue tracker available on GitHub to contact us.

Parameters back to top

Parameters can be used to filter and control the results returned by the API. They are passed as normal HTTP parameters in the URL of the call. They are:

  1. require=<field_name>: all the rows that have an empty value in the <field_name> specified are removed from the result set - e.g. require=given_name removes all the rows that do not have any string specified in the given_name field.

  2. filter=<field_name>:<operator><value>: only the rows compliant with <value> are kept in the result set. The parameter <operation> is not mandatory. If <operation> is not specified, <value> is interpreted as a regular expression, otherwise it is compared by means of the specified operation. Possible operators are "=", "<", and ">". For instance, filter=title:semantics? returns all the rows that contain the string "semantic" or "semantics" in the field title, while filter=date:>2016-05 returns all the rows that have a date greater than May 2016.

  3. sort=<order>(<field_name>): sort in ascending (<order> set to "asc") or descending (<order> set to "desc") order the rows in the result set according to the values in <field_name>. For instance, sort=desc(date) sorts all the rows according to the value specified in the field date in descending order.

  4. format=<format_type>: the final table is returned in the format specified in <format_type> that can be either "csv" or "json" - e.g. format=csv returns the final table in CSV format. This parameter has higher priority of the type specified through the "Accept" header of the request. Thus, if the header of a request to the API specifies Accept: text/csv and the URL of such request includes format=json, the final table is returned in JSON.

  5. json=<operation_type>("<separator>",<field>,<new_field_1>,<new_field_2>,...): in case a JSON format is requested in return, tranform each row of the final JSON table according to the rule specified. If <operation_type> is set to "array", the string value associated to the field name <field> is converted into an array by splitting the various textual parts by means of <separator>. For instance, considering the JSON table [ { "names": "Doe, John; Doe, Jane" }, ... ], the execution of array("; ",names) returns [ { "names": [ "Doe, John", "Doe, Jane" ], ... ]. Instead, if <operation_type> is set to "dict", the string value associated to the field name <field> is converted into a dictionary by splitting the various textual parts by means of <separator> and by associating the new fields <new_field_1>, <new_field_2>, etc., to these new parts. For instance, considering the JSON table [ { "name": "Doe, John" }, ... ], the execution of dict(", ",name,fname,gname) returns [ { "name": { "fname": "Doe", "gname": "John" }, ... ].

It is possible to specify one or more filtering operation of the same kind (e.g. require=given_name&require=family_name). In addition, these filtering operations are applied in the order presented above - first all the require operation, then all the filter operations followed by all the sort operation, and finally the format and the json operation (if applicable). It is worth mentioning that each of the aforementioned rules is applied in order, and it works on the structure returned after the execution of the previous rule.

Example: <api_operation_url>?require=doi&filter=date:>2015&sort=desc(date).

Operations back to top

The operations that this API implements are:

/metadata/{dois} back to operations

This operation returns bibliographic metadata of one or more articles specified in input by means of their DOIs. In case multiple DOIs are specified, these must be separated with a double underscore ("__") – e.g. "10.1016/j.ejmech.2010.06.013__10.1080/14756366.2020.1740695".

For each input DOI, the fields returned by the operation are the following:

Accepted HTTP method(s) get

Parameter(s) dois: type str, regular expression shape \"?10\..+[^_\"]((__|\" \")10\..+[^_])*\"?

Result fields typeccc_id (str), author (str), year (datetime), title (str), source_title (str), volume (str), issue (str), page (str), doi (str), occ_reference (str), doi_reference (str), citation_count (int)

Example/metadata/10.1126/science.aat5031__10.1084/jem.20200891

Exemplar output (in JSON)

[
    {
        "doi_reference": "10.1016/s0143-4004(98)90001-7; 10.1038/s41586-020-2316-7; 10.1016/j.placenta.2007.11.003; 10.1002/(sici)1099-1654(199712)7:4<219::aid-rmv205>3.0.co;2-e; 10.1530/rep-09-0092; 10.1016/j.placenta.2009.02.009; 10.1038/nbt.4096; 10.1016/0143-4004(87)90040-3; 10.3389/fimmu.2017.01357; 10.1093/infdis/jir432; 10.1038/onc.2009.189; 10.1038/s41596-020-0292-x; 10.1074/mcp.m113.035600; 10.3390/pathogens4040826; 10.3791/55107; 10.3389/fimmu.2019.00188; 10.1016/j.jtbi.2019.07.003; 10.1016/j.immuni.2016.02.024; 10.1126/science.1194637; 10.1038/nature13989; 10.1038/s41467-019-14123-z; 10.1016/j.placenta.2010.03.003; 10.1186/1742-4690-9-101; 10.1095/biolreprod.103.020651; 10.3389/fimmu.2014.00461; 10.1016/j.immuni.2007.11.011; 10.1038/s41586-018-0414-6; 10.3389/fimmu.2018.00412; 10.1530/rep-16-0159; 10.1038/tpj.2014.26; 10.1038/s41593-019-0566-1; 10.1038/nature22795; 10.1016/j.placenta.2020.01.005; 10.1016/s0143-4004(03)00082-1; 10.1073/pnas.1309561110; 10.1002/jcp.22549; 10.1038/s41591-020-0761-3; 10.1038/s41586-019-1631-3; 10.1093/nar/gkw199; 10.3389/fimmu.2018.02628; 10.1182/blood.v96.1.34; 10.1016/j.cell.2006.05.035; 10.3389/fimmu.2017.00888; 10.1016/j.chom.2018.04.013; 10.1095/biolreprod60.2.355; 10.3892/ol.2015.4035; 10.3389/fimmu.2019.01300; 10.4049/jimmunol.177.4.2651; 10.1126/science.aat5031; 10.1186/s12864-018-4772-0; 10.4049/jimmunol.1901185; 10.1111/j.1749-6632.2010.05932.x; 10.1073/pnas.1710470114; 10.1242/dev.163428; 10.1182/blood-2010-04-279489; 10.1038/s41586-018-0698-6; 10.1038/jid.2013.481; 10.1074/jbc.ra118.004565; 10.4049/jimmunol.181.9.6384; 10.1111/aji.12336; 10.1038/s41422-019-0228-6",
        "doi": "10.1084/jem.20200891",
        "volume": "218",
        "title": "Phenotypic and functional characterization of first-trimester human placental macrophages, Hofbauer cells",
        "occ_reference": "br/070448; br/070452; br/070456; br/070459; br/070460; br/070461; br/070462; br/070466; br/070470; br/070473; br/070477; br/070480; br/070483; br/070487; br/070491; br/070495; br/070499; br/070503; br/070506; br/070508; br/070511; br/070515; br/070519; br/070520; br/070523; br/070524; br/070528; br/070531; br/070535; br/070539; br/070541; br/070544; br/070547; br/070549; br/070552; br/070556; br/070560; br/070563; br/070565; br/070568; br/070572; br/070576; br/070580; br/070583; br/070587; br/070588; br/070592; br/070596; br/070597; br/070601; br/070604; br/070608; br/070609; br/070613; br/070616; br/070620; br/070621; br/070624; br/070628; br/070631; br/070635; br/070638; br/070641; br/070645; br/070649; br/070652; br/070656",
        "ccc_id": "br/070444",
        "author": "Thomas, Jake R.; Appios, Anna; Zhao, Xiaohui; Dutkiewicz, Roksana; Donde, Maria; Lee, Colin Y.C.; Naidu, Praveena; Lee, Christopher; Cerveira, Joana; Liu, Bing; Ginhoux, Florent; Burton, Graham; Hamilton, Russell S.; Moffett, Ashley; Sharkey, Andrew; McGovern, Naomi",
        "page": "",
        "source_title": "Journal of Experimental Medicine",
        "citation_count": "1",
        "issue": "1",
        "year": "2020-10-19"
    },
    {
        "doi_reference": "",
        "doi": "10.1126/science.aat5031",
        "volume": "365",
        "title": "Spatiotemporal immune zonation of the human kidney",
        "occ_reference": "",
        "ccc_id": "br/070613",
        "author": "Stewart, Benjamin J.; Ferdinand, John R.; Young, Matthew D.; Mitchell, Thomas J.; Loudon, Kevin W.; Riding, Alexandra M.; Richoz, Nathan; Frazer, Gordon L.; Staniforth, Joy U. L.; Vieira Braga, Felipe A.; Botting, Rachel A.; Popescu, Dorin-Mirel; Vento-Tormo, Roser; Stephenson, Emily; Cagan, Alex; Farndon, Sarah J.; Polanski, Krzysztof; Efremova, Mirjana; Green, Kile; Del Castillo Velasco-Herrera, Martin; Guzzo, Charlotte; Collord, Grace; Mamanova, Lira; Aho, Tevita; Armitage, James N.; Riddick, Antony C. P.; Mushtaq, Imran; Farrell, Stephen; Rampling, Dyanne; Nicholson, James; Filby, Andrew; Burge, Johanna; Lisgo, Steven; Lindsay, Susan; Bajenoff, Marc; Warren, Anne Y.; Stewart, Grant D.; Sebire, Neil; Coleman, Nicholas; Haniffa, Muzlifah; Teichmann, Sarah A.; Behjati, Sam; Clatworthy, Menna R.",
        "page": "1461-1466",
        "source_title": "Science",
        "citation_count": "1",
        "issue": "6460",
        "year": "2019-09-26"
    }
]

/references/{doi} back to operations

This operation retrieves citation data of all the bibliographic resources cited by the bibliographic resource identified by the input DOI, as they appear in the reference list.

For each cited bibliographic resource, the fields returned by this operation are the following:

Accepted HTTP method(s) get

Parameter(s) doi: type str, regular expression shape 10\..+

Result fields typeciting_doi (str), cited_doi (str), oci (str), intrepids (str), reference (str)

Example/references/10.1084/jem.20200891

Exemplar output (in JSON)

[
    {
        "citing_doi": "10.1084/jem.20200891",
        "cited_doi": "10.1038/s41586-018-0698-6",
        "intrepids": "070444-070638/7-9; 070444-070638/8-9; 070444-070638/9-9; 070444-070638/1-9; 070444-070638/2-9; 070444-070638/3-9; 070444-070638/4-9; 070444-070638/5-9; 070444-070638/6-9",
        "oci": "070272",
        "reference": "Vento-Tormo, R,, Efremova, M,, Botting, R.A,, Turco, M.Y,, Vento-Tormo, M,, Meyer, K.B,, Park, J.E,, Stephenson, E,, Polański, K,, Goncalves, A,. 2018 Single-cell reconstruction of the early maternal-fetal interface in humans. Nature. 563: 347–353. DOI: 10.1038/s41586-018-0698-6 PMID: 30429548"
    },
    {
        "citing_doi": "10.1084/jem.20200891",
        "cited_doi": "10.1038/jid.2013.481",
        "intrepids": "070444-070641/1-1",
        "oci": "070273",
        "reference": "Wang, X.N,, McGovern, N,, Gunawan, M,, Richardson, C,, Windebank, M,, Siah, T.W,, Lim, H.Y,, Fink, K,, Yao Li, J.L,, Ng, L.G,. 2014 A three-dimensional atlas of human dermal leukocytes, lymphatics, and blood vessels. J. Invest. Dermatol. 134: 965–974. DOI: 10.1038/jid.2013.481 PMID: 24352044"
    },
    {
        "citing_doi": "10.1084/jem.20200891",
        "cited_doi": "10.1074/jbc.ra118.004565",
        "intrepids": "070444-070645/1-1",
        "oci": "070274",
        "reference": "Ward, M.G,, Li, G, and, Hao, M. 2018 Apoptotic β-cells induce macrophage reprogramming under diabetic conditions. J. Biol. Chem. 293: 16160–16173. DOI: 10.1074/jbc.RA118.004565 PMID: 30213857"
    },
    {
        "citing_doi": "10.1084/jem.20200891",
        "cited_doi": "10.4049/jimmunol.181.9.6384",
        "intrepids": "070444-070649/1-1",
        "oci": "070275",
        "reference": "Wu, Y,, Li, Y-Y,, Matsushima, K,, Baba, T, and, Mukaida, N. 2008 CCL3-CCR5 axis regulates intratumoral accumulation of leukocytes and fibroblasts and promotes angiogenesis in murine lung metastasis process. J. Immunol. 181: 6384–6393. DOI: 10.4049/jimmunol.181.9.6384 PMID: 18941229"
    },
    {
        "citing_doi": "10.1084/jem.20200891",
        "cited_doi": "10.1111/aji.12336",
        "intrepids": "070444-070652/1-1",
        "oci": "070276",
        "reference": "Young, O.M,, Tang, Z,, Niven-Fairchild, T,, Tadesse, S,, Krikun, G,, Norwitz, E.R,, Mor, G,, Abrahams, V.M, and, Guller, S. 2015 Toll-like receptor-mediated responses by placental Hofbauer cells (HBCs): a potential pro-inflammatory role for fetal M2 macrophages. Am. J. Reprod. Immunol. 73: 22–35. DOI: 10.1111/aji.12336 PMID: 25345551"
    },
    {
        "citing_doi": "10.1084/jem.20200891",
        "cited_doi": "10.1038/s41422-019-0228-6",
        "intrepids": "070444-070656/1-3; 070444-070656/2-3; 070444-070656/3-3",
        "oci": "070277",
        "reference": "Zeng, Y,, He, J,, Bai, Z,, Li, Z,, Gong, Y,, Liu, C,, Ni, Y,, Du, J,, Ma, C,, Bian, L,. 2019 Tracing the first hematopoietic stem cell generation in human embryo by single-cell RNA sequencing. Cell Res. 29: 881–894. DOI: 10.1038/s41422-019-0228-6 PMID: 31501518"
    },
    {
        "citing_doi": "10.1084/jem.20200891",
        "cited_doi": "10.1016/s0143-4004(98)90001-7",
        "intrepids": "070444-070448/1-1",
        "oci": "070211",
        "reference": "Arany, E, and, Hill, D.J. 1998 Fibroblast growth factor-2 and fibroblast growth factor receptor-1 mRNA expression and peptide localization in placentae from normal and diabetic pregnancies. Placenta. 19: 133–142. DOI: 10.1016/S0143-4004(98)90001-7 PMID: 9548179"
    },
    {
        "citing_doi": "10.1084/jem.20200891",
        "cited_doi": "10.1038/s41586-020-2316-7",
        "intrepids": "070444-070452/1-5; 070444-070452/2-5; 070444-070452/3-5; 070444-070452/4-5; 070444-070452/5-5",
        "oci": "070212",
        "reference": "Bian, Z,, Gong, Y,, Huang, T,, Lee, C.Z.W,, Bian, L,, Bai, Z,, Shi, H,, Zeng, Y,, Liu, C,, He, J,. 2020 Deciphering human macrophage development at single-cell resolution. Nature. 582: 571–576. DOI: 10.1038/s41586-020-2316-7 PMID: 32499656"
    },
    {
        "citing_doi": "10.1084/jem.20200891",
        "cited_doi": "10.1016/j.placenta.2007.11.003",
        "intrepids": "070444-070456/1-1",
        "oci": "070213",
        "reference": "Böckle, B.C,, Sölder, E,, Kind, S,, Romani, N, and, Sepp, N.T. 2008 DC-sign+ CD163+ macrophages expressing hyaluronan receptor LYVE-1 are located within chorion villi of the placenta. Placenta. 29: 187–192. DOI: 10.1016/j.placenta.2007.11.003 PMID: 18078989"
    },
    {
        "citing_doi": "10.1084/jem.20200891",
        "cited_doi": "",
        "intrepids": "070444-070459/1-1",
        "oci": "070214",
        "reference": "Boyd, J.D. and, Hamilton, W.J. 1970 Stroma of villi. In The Human Placenta. Heffer, Cambridge."
    },
    {
        "citing_doi": "10.1084/jem.20200891",
        "cited_doi": "",
        "intrepids": "070444-070460/1-1",
        "oci": "070215",
        "reference": "Bulmer, J.N,, Morrison, L, and, Smith, J.C. 1988 Expression of class II MHC gene products by macrophages in human uteroplacental tissue. Immunology. 63: 707–714. PMID: 3284818"
    },
    {
        "citing_doi": "10.1084/jem.20200891",
        "cited_doi": "",
        "intrepids": "070444-070461/1-1",
        "oci": "070216",
        "reference": "Burton, G.J. 1986 Scanning electron microscopy of intervillous connections in the mature human placenta. J. Anat. 147: 245–254. PMID: 3693075"
    },
    {
        "citing_doi": "10.1084/jem.20200891",
        "cited_doi": "10.1002/(sici)1099-1654(199712)7:4<219::aid-rmv205>3.0.co;2-e",
        "intrepids": "070444-070462/1-6; 070444-070462/2-6; 070444-070462/3-6; 070444-070462/4-6; 070444-070462/5-6; 070444-070462/6-6",
        "oci": "070217",
        "reference": "Burton, G.J, and, Watson, A.L. 1997 The structure of the human placenta: Implications for initiating and defending against virus infections. Rev. Med. Virol. 7: 219–228. DOI: 10.1002/(SICI)1099-1654(199712)7:4<219:AID-RMV205>3.0.CO;2-E PMID: 10398486"
    },
    {
        "citing_doi": "10.1084/jem.20200891",
        "cited_doi": "10.1530/rep-09-0092",
        "intrepids": "070444-070466/1-1",
        "oci": "070218",
        "reference": "Burton, G.J,, Charnock-Jones, D.S, and, Jauniaux, E. 2009 a Regulation of vascular growth and function in the human placenta. Reproduction. 138: 895–902. DOI: 10.1530/REP-09-0092 PMID: 19470597"
    },
    {
        "citing_doi": "10.1084/jem.20200891",
        "cited_doi": "10.1016/j.placenta.2009.02.009",
        "intrepids": "070444-070470/1-1",
        "oci": "070219",
        "reference": "Burton, G.J,, Woods, A.W,, Jauniaux, E, and, Kingdom, J.C.P. 2009 b Rheological and physiological consequences of conversion of the maternal spiral arteries for uteroplacental blood flow during human pregnancy. Placenta. 30: 473–482. DOI: 10.1016/j.placenta.2009.02.009 PMID: 19375795"
    },
    {
        "citing_doi": "10.1084/jem.20200891",
        "cited_doi": "10.1038/nbt.4096",
        "intrepids": "070444-070473/1-1",
        "oci": "070220",
        "reference": "Butler, A,, Hoffman, P,, Smibert, P,, Papalexi, E, and, Satija, R. 2018 Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat. Biotechnol. 36: 411–420. DOI: 10.1038/nbt.4096 PMID: 29608179"
    },
    {
        "citing_doi": "10.1084/jem.20200891",
        "cited_doi": "10.1016/0143-4004(87)90040-3",
        "intrepids": "070444-070477/1-1",
        "oci": "070221",
        "reference": "Castellucci, M,, Celona, A,, Bartels, H,, Steininger, B,, Benedetto, V, and, Kaufmann, P. 1987 Mitosis of the Hofbauer cell: possible implications for a fetal macrophage. Placenta. 8: 65–76. DOI: 10.1016/0143-4004(87)90040-3 PMID: 3588557"
    },
    {
        "citing_doi": "10.1084/jem.20200891",
        "cited_doi": "10.3389/fimmu.2017.01357",
        "intrepids": "070444-070480/1-1",
        "oci": "070222",
        "reference": "Costa, M.L,, Robinette, M.L,, Bugatti, M,, Longtine, M.S,, Colvin, B.N,, Lantelme, E,, Vermi, W,, Colonna, M,, Nelson, D.M, and, Cella, M. 2017 Two distinct myeloid subsets at the term human fetal-maternal interface. Front. Immunol. 8: 1357 DOI: 10.3389/fimmu.2017.01357 PMID: 29123519"
    },
    {
        "citing_doi": "10.1084/jem.20200891",
        "cited_doi": "10.1093/infdis/jir432",
        "intrepids": "070444-070483/1-1",
        "oci": "070223",
        "reference": "D’Avila, H,, Freire-de-Lima, C.G,, Roque, N.R,, Teixeira, L,, Barja-Fidalgo, C,, Silva, A.R,, Melo, R.C.N,, Dosreis, G.A,, Castro-Faria-Neto, H.C, and, Bozza, P.T. 2011 Host cell lipid bodies triggered by Trypanosoma cruzi infection and enhanced by the uptake of apoptotic cells are associated with prostaglandin E 2 generation and increased parasite growth. J. Infect. Dis. 204: 951–961. DOI: 10.1093/infdis/jir432 PMID: 21849292"
    },
    {
        "citing_doi": "10.1084/jem.20200891",
        "cited_doi": "10.1038/onc.2009.189",
        "intrepids": "070444-070487/1-2; 070444-070487/2-2",
        "oci": "070224",
        "reference": "Dai, J,, Peng, L,, Fan, K,, Wang, H,, Wei, R,, Ji, G,, Cai, J,, Lu, B,, Li, B,, Zhang, D,. 2009 Osteopontin induces angiogenesis through activation of PI3K/AKT and ERK1/2 in endothelial cells. Oncogene. 28: 3412–3422. DOI: 10.1038/onc.2009.189 PMID: 19597469"
    },
    {
        "citing_doi": "10.1084/jem.20200891",
        "cited_doi": "10.1038/s41596-020-0292-x",
        "intrepids": "070444-070491/1-1",
        "oci": "070225",
        "reference": "Efremova, M,, Vento-Tormo, M,, Teichmann, S.A, and, Vento-Tormo, R. 2020 CellPhoneDB: inferring cell-cell communication from combined expression of multi-subunit ligand-receptor complexes. Nat. Protoc. 15: 1484–1506. DOI: 10.1038/s41596-020-0292-x PMID: 32103204"
    },
    {
        "citing_doi": "10.1084/jem.20200891",
        "cited_doi": "10.1074/mcp.m113.035600",
        "intrepids": "070444-070495/1-1",
        "oci": "070226",
        "reference": "Fagerberg, L,, Hallström, B.M,, Oksvold, P,, Kampf, C,, Djureinovic, D,, Odeberg, J,, Habuka, M,, Tahmasebpoor, S,, Danielsson, A,, Edlund, K,. 2014 Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics. Mol. Cell. Proteomics. 13: 397–406. DOI: 10.1074/mcp.M113.035600 PMID: 24309898"
    },
    {
        "citing_doi": "10.1084/jem.20200891",
        "cited_doi": "10.3390/pathogens4040826",
        "intrepids": "070444-070499/1-1",
        "oci": "070227",
        "reference": "Flannagan, R.S,, Heit, B, and, Heinrichs, D.E. 2015 Antimicrobial mechanisms of macrophages and the immune evasion strategies of Staphylococcus aureus. Pathogens. 4: 826–868. DOI: 10.3390/pathogens4040826 PMID: 26633519"
    },
    {
        "citing_doi": "10.1084/jem.20200891",
        "cited_doi": "10.3791/55107",
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    {
        "citing_doi": "10.1084/jem.20200891",
        "cited_doi": "10.1182/blood-2010-04-279489",
        "intrepids": "070444-070635/1-3; 070444-070635/2-3; 070444-070635/3-3",
        "oci": "070271",
        "reference": "Van Handel, B,, Prashad, S.L,, Hassanzadeh-Kiabi, N,, Huang, A,, Magnusson, M,, Atanassova, B,, Chen, A,, Hamalainen, E.I, and, Mikkola, H.K.A. 2010 The first trimester human placenta is a site for terminal maturation of primitive erythroid cells. Blood. 116: 3321–3330. DOI: 10.1182/blood-2010-04-279489 PMID: 20628147"
    }
]

/citations/{doi} back to operations

This operation retrieves citation data for all the works citing the bibliographic resource identified by the input DOI.

For each citing resource, the fields returned by this operation are the following:

Accepted HTTP method(s) get

Parameter(s) doi: type str, regular expression shape 10\..+

Result fields typeciting_doi (str), cited_doi (str), oci (str), creation (datetime), ?journal_sc (str), ?author_sc (str)

Example/citations/10.1126/science.aat5031

Exemplar output (in JSON)

[
    {
        "cited_doi": "10.1126/science.aat5031",
        "citing_doi": "10.1084/jem.20200891",
        "author_sc": "no",
        "journal_sc": "no",
        "creation": "2020-10-19",
        "oci": "070444-070613"
    }
]

/citation/{oci} back to operations

This operation retrieves the citation metadata for the citation identified by the input Open Citation Identifier (OCI). OCI may appear in both of the forms above described, namely: <citing_id>-<cited_id> and <citing_id>-<cited_id>/<nth-occurrence>.

It is worth mentioning that, in this REST operation, the prefix "oci:" should not be specified, and only the dash-separated numbers of the OCI should be provided, as shown in the example below.

The fields returned by this operation are:

Accepted HTTP method(s) get

Parameter(s) oci: type str, regular expression shape [0-9]+[-[0-9]+]?[\/[0-9]+]?

Result fields typeciting_doi (str), cited_doi (str), oci (str), creation (datetime), ?journal_sc (str), ?author_sc (str)

Example/citation/070444-070613

Exemplar output (in JSON)

[
    {
        "cited_doi": "10.1126/science.aat5031",
        "citing_doi": "10.1084/jem.20200891",
        "author_sc": "no",
        "journal_sc": "no",
        "creation": "2020-10-19",
        "oci": "070444-070613"
    }
]

/citation-count/{doi} back to operations

This operation retrieves the number of incoming citations to the bibliographic resource identified by the input DOI.

The fields returned by this operation are the following:

Accepted HTTP method(s) get

Parameter(s) doi: type str, regular expression shape 10\..+

Result fields typecount (int)

Example/citation-count/10.1126/science.aat5031

Exemplar output (in JSON)

[
    {
        "count": "1"
    }
]

/intext-citation/{intrepid} back to operations

This operation retrieves information related to an in-text reference pointer identified by the input InTRePID.

The fields returned by this operation are the following:

Accepted HTTP method(s) get

Parameter(s) intrepid: type str, regular expression shape [0-9]+-[0-9]+\/[0-9]+-[0-9]+

Result fields typeciting_doi (str), cited_doi (str), oci (str), intext_reference (str), section_number (int), section_title (str), paragraph_number (int), footnote_number (int), caption_number (int), table_number (int), sentence_number (int), source (str), in_list (str), xpath_intext_reference (str), xpath_container (str)

Example/intext-citation/070444-070613/1-2

Exemplar output (in JSON)

[
    {
        "caption_number": "",
        "paragraph_number": "3",
        "in_list": "yes",
        "table_number": "",
        "section_title": "Introduction",
        "sentence_number": "32",
        "oci": "070444-070613/1",
        "xpath_intext_reference": "/article/body/sec[1]/p[3]/xref[1]",
        "footnote_number": "",
        "section_number": "1",
        "intext_reference": "Stewart et al., 2019",
        "citing_doi": "10.1084/jem.20200891",
        "xpath_container": "substring(string(/article/body/sec[1]/p[3]),1,153)",
        "cited_doi": "10.1126/science.aat5031",
        "source": "https://www.ebi.ac.uk/europepmc/webservices/rest/33075123/fullTextXML"
    }
]

/intext-citations/doi/{doi} back to operations

This operation retrieves information related to all the in-text reference pointers denoting the cited bibliographic resource identified by the input DOI.

For each in-text reference pointer, the fields returned by this operation are the following:

Accepted HTTP method(s) get

Parameter(s) doi: type str, regular expression shape 10\..+

Result fields typeciting_doi (str), cited_doi (str), oci (str), intext_reference (str), section_number (int), section_title (str), paragraph_number (int), footnote_number (int), caption_number (int), table_number (int), sentence_number (int), source (str), in_list (str), xpath_intext_reference (str), xpath_container (str)

Example/intext-citations/doi/10.1126/science.aat5031

Exemplar output (in JSON)

[
    {
        "caption_number": "",
        "paragraph_number": "3",
        "in_list": "yes",
        "table_number": "",
        "section_title": "Introduction",
        "sentence_number": "32",
        "oci": "070444-070613/1",
        "xpath_intext_reference": "/article/body/sec[1]/p[3]/xref[1]",
        "footnote_number": "",
        "section_number": "1",
        "intext_reference": "Stewart et al., 2019",
        "citing_doi": "10.1084/jem.20200891",
        "xpath_container": "substring(string(/article/body/sec[1]/p[3]),1,153)",
        "cited_doi": "10.1126/science.aat5031",
        "source": "https://www.ebi.ac.uk/europepmc/webservices/rest/33075123/fullTextXML"
    },
    {
        "caption_number": "",
        "paragraph_number": "61",
        "in_list": "no",
        "table_number": "",
        "section_title": "Materials and methods",
        "sentence_number": "3278",
        "oci": "070444-070613/2",
        "xpath_intext_reference": "/article/body/sec[4]/sec[16]/p[4]/xref",
        "footnote_number": "",
        "section_number": "4",
        "intext_reference": "(Stewart et al., 2019)",
        "citing_doi": "10.1084/jem.20200891",
        "xpath_container": "substring(string(/article/body/sec[4]/sec[16]/p[4]),1,168)",
        "cited_doi": "10.1126/science.aat5031",
        "source": "https://www.ebi.ac.uk/europepmc/webservices/rest/33075123/fullTextXML"
    }
]

/intext-citations/pmid/{pmid} back to operations

This operation retrieves information related to all the in-text reference pointers denoting the cited bibliographic resource identified by the input PMID.

For each in-text reference pointer, the fields returned by this operation are the following:

Accepted HTTP method(s) get

Parameter(s) pmid: type str, regular expression shape [0-9]+

Result fields typeciting_doi (str), cited_doi (str), oci (str), intext_reference (str), section_number (int), section_title (str), paragraph_number (int), footnote_number (int), caption_number (int), table_number (int), sentence_number (int), source (str), in_list (str), xpath_intext_reference (str), xpath_container (str)

Example/intext-citations/pmid/31604275

Exemplar output (in JSON)

[
    {
        "caption_number": "",
        "paragraph_number": "3",
        "in_list": "yes",
        "table_number": "",
        "section_title": "Introduction",
        "sentence_number": "32",
        "oci": "070444-070613/1",
        "xpath_intext_reference": "/article/body/sec[1]/p[3]/xref[1]",
        "footnote_number": "",
        "section_number": "1",
        "intext_reference": "Stewart et al., 2019",
        "citing_doi": "10.1084/jem.20200891",
        "xpath_container": "substring(string(/article/body/sec[1]/p[3]),1,153)",
        "cited_doi": "10.1126/science.aat5031",
        "source": "https://www.ebi.ac.uk/europepmc/webservices/rest/33075123/fullTextXML"
    },
    {
        "caption_number": "",
        "paragraph_number": "61",
        "in_list": "no",
        "table_number": "",
        "section_title": "Materials and methods",
        "sentence_number": "3278",
        "oci": "070444-070613/2",
        "xpath_intext_reference": "/article/body/sec[4]/sec[16]/p[4]/xref",
        "footnote_number": "",
        "section_number": "4",
        "intext_reference": "(Stewart et al., 2019)",
        "citing_doi": "10.1084/jem.20200891",
        "xpath_container": "substring(string(/article/body/sec[4]/sec[16]/p[4]),1,168)",
        "cited_doi": "10.1126/science.aat5031",
        "source": "https://www.ebi.ac.uk/europepmc/webservices/rest/33075123/fullTextXML"
    }
]

/in-sentence/{sentence}/{doi} back to operations

This operation retrieves all the in-text references that appear in the specified sentence of the bibliographic resource identified by DOI.

For each in-text reference pointer, the fields returned by this operation are the following:

Accepted HTTP method(s) get

Parameter(s) sentence: type str, regular expression shape [0-9]+

  • doi: type str, regular expression shape 10\..+

    Result fields typeciting_doi (str), cited_doi (str), oci (str), intext_reference (str), section_number (int), section_title (str), paragraph_number (int), source (str), in_list (str), xpath_intext_reference (str), xpath_container (str)

    Example/in-sentence/3278/10.1084/jem.20200891

    Exemplar output (in JSON)

    [
        {
            "paragraph_number": "61",
            "source": "https://www.ebi.ac.uk/europepmc/webservices/rest/33075123/fullTextXML",
            "oci": "070444-070613/2",
            "xpath_intext_reference": "/article/body/sec[4]/sec[16]/p[4]/xref",
            "intext_reference": "(Stewart et al., 2019)",
            "section_number": "4",
            "in_list": "no",
            "citing_doi": "10.1084/jem.20200891",
            "xpath_container": "substring(string(/article/body/sec[4]/sec[16]/p[4]),1,168)",
            "cited_doi": "10.1126/science.aat5031",
            "section_title": "Materials and methods"
        }
    ]
  • /in-paragraph/{paragraph}/{doi} back to operations

    This operation retrieves all the in-text references that appear in the specified paragraph of the bibliographic resource identified by DOI.

    For each in-text reference pointer, the fields returned by this operation are the following:

    Accepted HTTP method(s) get

    Parameter(s) paragraph: type str, regular expression shape [0-9]+

  • doi: type str, regular expression shape 10\..+

    Result fields typeciting_doi (str), cited_doi (str), oci (str), intext_reference (str), section_number (int), section_title (str), source (str), in_list (str), xpath_intext_reference (str), xpath_container (str)

    Example/in-paragraph/61/10.1084/jem.20200891

    Exemplar output (in JSON)

    [
        {
            "citing_doi": "10.1084/jem.20200891",
            "source": "https://www.ebi.ac.uk/europepmc/webservices/rest/33075123/fullTextXML",
            "oci": "070444-070613/2",
            "xpath_intext_reference": "/article/body/sec[4]/sec[16]/p[4]/xref",
            "intext_reference": "(Stewart et al., 2019)",
            "section_number": "4",
            "in_list": "no",
            "xpath_container": "/article/body/sec[4]/sec[16]/p[4]",
            "cited_doi": "10.1126/science.aat5031",
            "section_title": "Materials and methods"
        }
    ]
  • /in-section/{section}/{doi} back to operations

    This operation retrieves all the in-text references that appear in the specified section of the bibliographic resource identified by DOI.

    For each in-text reference pointer, the fields returned by this operation are the following:

    Accepted HTTP method(s) get

    Parameter(s) section: type str, regular expression shape [0-9]+

  • doi: type str, regular expression shape 10\..+

    Result fields typeciting_doi (str), cited_doi (str), oci (str), intext_reference (str), section_title (str), source (str), in_list (str), xpath_intext_reference (str), xpath_container (str)

    Example/in-section/4/10.1084/jem.20200891

    Exemplar output (in JSON)

    [
        {
            "citing_doi": "10.1084/jem.20200891",
            "source": "https://www.ebi.ac.uk/europepmc/webservices/rest/33075123/fullTextXML",
            "oci": "070444-070524/1",
            "xpath_intext_reference": "/article/body/sec[4]/sec[2]/p/xref",
            "intext_reference": "(Huhn et al., 2020)",
            "section_number": "4",
            "in_list": "no",
            "xpath_container": "/article/body/sec[4]",
            "cited_doi": "10.1038/s41467-019-14123-z",
            "section_title": "Materials and methods"
        },
        {
            "citing_doi": "10.1084/jem.20200891",
            "source": "https://www.ebi.ac.uk/europepmc/webservices/rest/33075123/fullTextXML",
            "oci": "070444-070641/1",
            "xpath_intext_reference": "/article/body/sec[4]/sec[4]/p/xref[1]",
            "intext_reference": "(Wang et al., 2014)",
            "section_number": "4",
            "in_list": "no",
            "xpath_container": "/article/body/sec[4]",
            "cited_doi": "10.1038/jid.2013.481",
            "section_title": "Materials and methods"
        },
        {
            "citing_doi": "10.1084/jem.20200891",
            "source": "https://www.ebi.ac.uk/europepmc/webservices/rest/33075123/fullTextXML",
            "oci": "070444-070461/1",
            "xpath_intext_reference": "/article/body/sec[4]/sec[5]/p/xref",
            "intext_reference": "(Burton, 1986)",
            "section_number": "4",
            "in_list": "no",
            "xpath_container": "/article/body/sec[4]",
            "cited_doi": "",
            "section_title": "Materials and methods"
        },
        {
            "citing_doi": "10.1084/jem.20200891",
            "source": "https://www.ebi.ac.uk/europepmc/webservices/rest/33075123/fullTextXML",
            "oci": "070444-070601/1",
            "xpath_intext_reference": "/article/body/sec[4]/sec[7]/p/xref[1]",
            "intext_reference": "(Sharkey et al., 1999)",
            "section_number": "4",
            "in_list": "no",
            "xpath_container": "/article/body/sec[4]",
            "cited_doi": "10.1095/biolreprod60.2.355",
            "section_title": "Materials and methods"
        },
        {
            "citing_doi": "10.1084/jem.20200891",
            "source": "https://www.ebi.ac.uk/europepmc/webservices/rest/33075123/fullTextXML",
            "oci": "070444-070503/2",
            "xpath_intext_reference": "/article/body/sec[4]/sec[14]/p/xref[1]",
            "intext_reference": "(Foote et al., 2017)",
            "section_number": "4",
            "in_list": "no",
            "xpath_container": "/article/body/sec[4]",
            "cited_doi": "10.3791/55107",
            "section_title": "Materials and methods"
        },
        {
            "citing_doi": "10.1084/jem.20200891",
            "source": "https://www.ebi.ac.uk/europepmc/webservices/rest/33075123/fullTextXML",
            "oci": "070444-070503/3",
            "xpath_intext_reference": "/article/body/sec[4]/sec[14]/p/xref[2]",
            "intext_reference": "(Foote et al., 2017)",
            "section_number": "4",
            "in_list": "no",
            "xpath_container": "/article/body/sec[4]",
            "cited_doi": "10.3791/55107",
            "section_title": "Materials and methods"
        },
        {
            "citing_doi": "10.1084/jem.20200891",
            "source": "https://www.ebi.ac.uk/europepmc/webservices/rest/33075123/fullTextXML",
            "oci": "070444-070638/9",
            "xpath_intext_reference": "/article/body/sec[4]/sec[16]/p[1]/xref[1]",
            "intext_reference": "(Vento-Tormo et al., 2018)",
            "section_number": "4",
            "in_list": "no",
            "xpath_container": "/article/body/sec[4]",
            "cited_doi": "10.1038/s41586-018-0698-6",
            "section_title": "Materials and methods"
        },
        {
            "citing_doi": "10.1084/jem.20200891",
            "source": "https://www.ebi.ac.uk/europepmc/webservices/rest/33075123/fullTextXML",
            "oci": "070444-070473/1",
            "xpath_intext_reference": "/article/body/sec[4]/sec[16]/p[1]/xref[2]",
            "intext_reference": "Butler et al., 2018",
            "section_number": "4",
            "in_list": "no",
            "xpath_container": "/article/body/sec[4]",
            "cited_doi": "10.1038/nbt.4096",
            "section_title": "Materials and methods"
        },
        {
            "citing_doi": "10.1084/jem.20200891",
            "source": "https://www.ebi.ac.uk/europepmc/webservices/rest/33075123/fullTextXML",
            "oci": "070444-070544/2",
            "xpath_intext_reference": "/article/body/sec[4]/sec[16]/p[3]/xref",
            "intext_reference": "La Manno et al., 2018",
            "section_number": "4",
            "in_list": "no",
            "xpath_container": "/article/body/sec[4]",
            "cited_doi": "10.1038/s41586-018-0414-6",
            "section_title": "Materials and methods"
        },
        {
            "citing_doi": "10.1084/jem.20200891",
            "source": "https://www.ebi.ac.uk/europepmc/webservices/rest/33075123/fullTextXML",
            "oci": "070444-070613/2",
            "xpath_intext_reference": "/article/body/sec[4]/sec[16]/p[4]/xref",
            "intext_reference": "(Stewart et al., 2019)",
            "section_number": "4",
            "in_list": "no",
            "xpath_container": "/article/body/sec[4]",
            "cited_doi": "10.1126/science.aat5031",
            "section_title": "Materials and methods"
        },
        {
            "citing_doi": "10.1084/jem.20200891",
            "source": "https://www.ebi.ac.uk/europepmc/webservices/rest/33075123/fullTextXML",
            "oci": "070444-070580/3",
            "xpath_intext_reference": "/article/body/sec[4]/sec[16]/p[5]/xref[1]",
            "intext_reference": "Ramachandran et al., 2019",
            "section_number": "4",
            "in_list": "no",
            "xpath_container": "/article/body/sec[4]",
            "cited_doi": "10.1038/s41586-019-1631-3",
            "section_title": "Materials and methods"
        },
        {
            "citing_doi": "10.1084/jem.20200891",
            "source": "https://www.ebi.ac.uk/europepmc/webservices/rest/33075123/fullTextXML",
            "oci": "070444-070452/5",
            "xpath_intext_reference": "/article/body/sec[4]/sec[16]/p[5]/xref[2]",
            "intext_reference": "(Bian et al., 2020)",
            "section_number": "4",
            "in_list": "no",
            "xpath_container": "/article/body/sec[4]",
            "cited_doi": "10.1038/s41586-020-2316-7",
            "section_title": "Materials and methods"
        },
        {
            "citing_doi": "10.1084/jem.20200891",
            "source": "https://www.ebi.ac.uk/europepmc/webservices/rest/33075123/fullTextXML",
            "oci": "070444-070656/3",
            "xpath_intext_reference": "/article/body/sec[4]/sec[16]/p[5]/xref[3]",
            "intext_reference": "(Zeng et al., 2019)",
            "section_number": "4",
            "in_list": "no",
            "xpath_container": "/article/body/sec[4]",
            "cited_doi": "10.1038/s41422-019-0228-6",
            "section_title": "Materials and methods"
        },
        {
            "citing_doi": "10.1084/jem.20200891",
            "source": "https://www.ebi.ac.uk/europepmc/webservices/rest/33075123/fullTextXML",
            "oci": "070444-070616/2",
            "xpath_intext_reference": "/article/body/sec[4]/sec[16]/p[6]/xref",
            "intext_reference": "(Street et al., 2018)",
            "section_number": "4",
            "in_list": "no",
            "xpath_container": "/article/body/sec[4]",
            "cited_doi": "10.1186/s12864-018-4772-0",
            "section_title": "Materials and methods"
        },
        {
            "citing_doi": "10.1084/jem.20200891",
            "source": "https://www.ebi.ac.uk/europepmc/webservices/rest/33075123/fullTextXML",
            "oci": "070444-070491/1",
            "xpath_intext_reference": "/article/body/sec[4]/sec[17]/p/xref",
            "intext_reference": "(Efremova et al., 2020)",
            "section_number": "4",
            "in_list": "no",
            "xpath_container": "/article/body/sec[4]",
            "cited_doi": "10.1038/s41596-020-0292-x",
            "section_title": "Materials and methods"
        }
    ]
  • /in-article/{doi} back to operations

    This operation retrieves all the in-text references that appear in the bibliographic resource identified by the input DOI.

    For each in-text reference pointer, the fields returned by this operation are the following:

    Accepted HTTP method(s) get

    Parameter(s) doi: type str, regular expression shape 10\..+

    Result fields typeciting_doi (str), cited_doi (str), oci (str), intext_reference (str), section_number (int), section_title (str), paragraph_number (int), footnote_number (int), caption_number (int), table_number (int), sentence_number (int), source (str), in_list (str), xpath_intext_reference (str), xpath_container (str)

    Example/in-article/10.1084/jem.20200891

    Exemplar output (in JSON)

    [
        {
            "caption_number": "",
            "paragraph_number": "1",
            "in_list": "yes",
            "table_number": "",
            "section_title": "Introduction",
            "sentence_number": "3",
            "oci": "070444-070515/1",
            "xpath_intext_reference": "/article/body/sec[1]/p[1]/xref[1]",
            "footnote_number": "",
            "section_number": "1",
            "intext_reference": "Ginhoux et al., 2010",
            "citing_doi": "10.1084/jem.20200891",
            "xpath_container": "substring(string(/article/body/sec[1]/p[1]),276,220)",
            "cited_doi": "10.1126/science.1194637",
            "source": "https://www.ebi.ac.uk/europepmc/webservices/rest/33075123/fullTextXML"
        },
        {
            "caption_number": "",
            "paragraph_number": "1",
            "in_list": "yes",
            "table_number": "",
            "section_title": "Introduction",
            "sentence_number": "3",
            "oci": "070444-070520/1",
            "xpath_intext_reference": "/article/body/sec[1]/p[1]/xref[2]",
            "footnote_number": "",
            "section_number": "1",
            "intext_reference": "Gomez Perdiguero et al., 2015",
            "citing_doi": "10.1084/jem.20200891",
            "xpath_container": "substring(string(/article/body/sec[1]/p[1]),276,220)",
            "cited_doi": "10.1038/nature13989",
            "source": "https://www.ebi.ac.uk/europepmc/webservices/rest/33075123/fullTextXML"
        },
        ...
    ]