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task_categories:
- text-classification
- summarization
- other
annotations_creators:
- no-annotation
language_creators:
- expert-generated
languages:
- en
size_categories:
- 1M<n<10M
source_datasets:
- original
licenses:
- cc0-1.0
- cc-by-4.0
- cc-by-sa-4.0
- cc-by-nd-4.0
- cc-by-nc-4.0
- cc-by-nc-sa-4.0
- cc-by-nc-nd-4.0
- other-custom
- unknown
# Dataset Card for PMC Open Access XML
## Table of Contents
- [Dataset Description](#dataset-description)
- [Dataset Summary](#dataset-summary)
- [Supported Tasks](#supported-tasks-and-leaderboards)
- [Languages](#languages)
- [Dataset Structure](#dataset-structure)
- [Data Instances](#data-instances)
- [Data Fields](#data-instances)
- [Data Splits](#data-instances)
- [Dataset Creation](#dataset-creation)
- [Curation Rationale](#curation-rationale)
- [Source Data](#source-data)
- [Annotations](#annotations)
- [Personal and Sensitive Information](#personal-and-sensitive-information)
- [Considerations for Using the Data](#considerations-for-using-the-data)
- [Social Impact of Dataset](#social-impact-of-dataset)
- [Discussion of Biases](#discussion-of-biases)
- [Other Known Limitations](#other-known-limitations)
- [Additional Information](#additional-information)
- [Dataset Curators](#dataset-curators)
- [Licensing Information](#licensing-information)
- [Citation Information](#citation-information)
## Dataset Description
- **Homepage:** https://www.ncbi.nlm.nih.gov/pmc/tools/openftlist/
- **Repository:** [Needs More Information]
- **Paper:** [Needs More Information]
- **Leaderboard:** [Needs More Information]
- **Point of Contact:** [Needs More Information]
### Dataset Summary
The XML Open Access includes more than 3.4 million journal articles and preprints that are made available under
license terms that allow reuse.
Not all articles in PMC are available for text mining and other reuse, many have copyright protection, however articles
in the PMC Open Access Subset are made available under Creative Commons or similar licenses that generally allow more
liberal redistribution and reuse than a traditional copyrighted work.
The PMC Open Access Subset is one part of the PMC Article Datasets
This version takes XML version as source, benefiting from the structured text
to split the articles in parts, naming the introduction, methods, results,
discussion and conclusion, and refers with keywords in the text to external or internal
resources (articles, figures, tables, formulas, boxed-text, quotes, code, footnotes, chemicals, graphics, medias).
The dataset was initially created with relation-extraction tasks in mind, between the references in text and the content of the
references (e.g. for PMID, by joining the refered article abstract from the pubmed dataset), but aims in a larger extent to provide
a corpus of pre-annotated text for other tasks (e.g. figure caption to graphic, glossary definition detection, summarization).
### Supported Tasks and Leaderboards
[Needs More Information]
### Languages
[Needs More Information]
## Dataset Structure
### Data Instances
```json
{
"accession_id": "PMC8515580",
"pmid": "34661004",
"introduction": [
"<title>Introduction</title>",
"<p>Medicinal plants are\nknown to possess several primary and secondary\nmetabolites. The secondary metabolites ...",
"<p>Genus <italic>Clerodendrum</italic> belonging to\nfamily Verbenaceae or Lamiaceae has more than 500 species. ..."
],
"methods": [
"<title>DPPH Method</title>",
"<p>The most effective and popular method of\nantioxidant evaluation is the DPPH radical scavenging method. Better..."
],
"results": [
"<title>Results</title>",
"<p>The phytochemical screening of the flower extract indicated the\npresence of carbohydrates, tannins, phenolics, ...",
"<p>The total phenolic content,<sup> ##REF## </sup> as quantified\nby Folin-Ciocalteu\u2019s method, indicates the highest ...",
"<p>Antioxidant activity of the extracts was evaluated by four different\nmethods.<sup> ##REF## </sup> Antioxidants have a high...",
"<p>DPPH is widely used as an evaluation technique due\nto its ease\nof reaction. In the ABTS assay method, radical scavenging ...",
"<p>Nitric oxide radical scavenging activity results of\nthe extract\nwere evaluated by comparing with standard gallic acid. Nitric ...",
"<p>Reducing power ability of the extracts was determined\nusing potassium\nferricyanide. The ability of the extract to reduce potassium ...",
],
"discussion": [
"<title>Discussion</title>",
"<p>The\nliver, the major metabolic organ of our body, may have toxicity\ndue to various drugs like alcohol, anabolic steroids,...",
"<p>Internal antioxidant deficiency can be overcome by\nsupplementing\nwith external sources. Since polyphenolics are known to have ..."
],
"conclusion": [
"<title>Conclusions</title>",
"<p>The implication on the\npharmacological properties from the flower\nextract ..."
],
"front": [
"<p content-type=\"toc-graphic\"> ##GRAPH## </p>",
"<p>The aim of the presented\nwork involves the isolation, characterization,\nand evaluation of hepatoprotective potential of ...",
],
"body": [
"<title>Experimental\nSection</title>",
"<title>Chemicals and Reagents</title>",
"<p>The chemicals and reagents used\nfor the experiments carried out for the present investigation were\npurchased from ...",
"<title>Plant Collection</title>",
"<p><italic>C. paniculatum</italic> flowers were collected from Malappuram, Kerala during August to\nOctober. ...",
"<title>Preparation of Plant Extracts</title>",
"<p>The flowers weighing\n\u223c300 g were collected and dried under shade. Successively,\nsolvent extraction was carried out using ...",
"<title>Preliminary Phytochemical Screening</title>",
"<p>Preliminary qualitative\nanalysis was carried out for detecting the presence of various classes\nof compounds like alkaloids, ...",],
"back": [
"<title>Supporting Information Available</title>",
"<p>The Supporting Information is\navailable free of charge at <ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" ...",
"<title>Supplementary Material</title>",
"<p>This research\ndid not receive any specific grant from funding agencies in the public,\ncommercial, or not-for-profit sectors.</p>",
"<p>The authors declare no\ncompeting financial interest.</p>",
"<title>Acknowledgments</title>",
"<p>The authors would like to express their sincere\nthanks to the Management of Vellore Institute of Technology, Vellore\nand ..."
],
"figure": [
"<fig id=\"fig1\" position=\"float\"><label>Figure 1</label><caption><p>Determination\nof reducing power for various solvent...",
"<fig id=\"fig2\" position=\"float\"><label>Figure 2</label><caption><p>Photographs of hematoxylin/eosin-stained liver sections....",
"<fig id=\"fig3\" position=\"float\"><label>Figure 3</label><caption><p>GC\u2013MS chromatogram of fraction 9.</p></caption> ##GRAPH## </fig>",
"<fig id=\"fig4\" position=\"float\"><label>Figure 4</label><caption><p>HPTLC\nplates observed under (a) normal light and (b) 254 and (c)\n366 nm.</p></caption> ##GRAPH## </fig>"
],
"table": [
"<table-wrap id=\"tbl1\" position=\"float\"><label>Table 1</label><caption><title>Phytochemical Screening for the Flower\nExtract ...",
"<table-wrap id=\"tbl2\" position=\"float\"><label>Table 2</label><caption><title>Quantification of Total Phenolics\nand Flavonoids in ...",
"<table-wrap id=\"tbl3\" position=\"float\"><label>Table 3</label><caption><title>Antioxidant\nPotential, as Determined\nby DPPH Assay with the...",
"<table-wrap id=\"tbl4\" position=\"float\"><label>Table 4</label><caption><title>Antioxidant Activity, as Evaluated\nby ABTS Assay with the Alcoholic...",
"<table-wrap id=\"tbl5\" position=\"float\"><label>Table 5</label><caption><title>Antioxidant Activity, as Determined\nby Nitric Oxide Radical Scavenging Assay...",
],
"formula": [
"<disp-formula id=\"ueq1\"> ##GRAPH## </disp-formula>"
],
"box": [
"EXAMPLE FROM ANOTHER ARTICLE",
"<boxed-text id=\"BX1\" position=\"float\" orientation=\"portrait\"><caption><title>Key messages</title></caption><list list-type=\"bullet\">...",
],
"code": [
"EXAMPLE FROM ANOTHER ARTICLE",
"<code xml:space=\"preserve\" position=\"float\" orientation=\"portrait\">\n<monospace>\n\nLupe.dat$w <\u2013 ifelse(Lupe.dat$case_...",
"<code xml:space=\"preserve\" position=\"float\" orientation=\"portrait\">\n<monospace>\n\nLupe.dat <\u2010 within(Lupe.dat,\n\n\n landuseC1...",
"<code xml:space=\"preserve\" position=\"float\" orientation=\"portrait\">\n<monospace>\n\nLupe.dat <\u2010 within(Lupe.dat, landuseC <\u2010...",
],
"quote": [
"EXAMPLE FROM ANOTHER ARTICLE",
"<disp-quote><p id=\"Par20\">I constantly feel like I am fighting some system or individual to get my medical needs met...",
"<disp-quote><p id=\"Par25\">Generally, there is a neurological exam performed, but it is subjective and by no means inclusive ...",
],
"chem": [
"EXAMPLE FROM ANOTHER ARTICLE",
"<chem-struct-wrap id=\"open202000358-disp-0001\" position=\"float\" orientation=\"portrait\"><chem-struct> ##GRAPH## </chem-struct></chem-struct-wrap>",
"<chem-struct-wrap id=\"open202000358-disp-0002\" position=\"float\" orientation=\"portrait\"><chem-struct> ##GRAPH## </chem-struct></chem-struct-wrap>"
],
"supplementary": [
"<supplementary-material content-type=\"local-data\" id=\"sifile1\"> ##MEDIA## </supplementary-material>"
],
"footnote": [
"<table-wrap-foot><fn id=\"t1fn1\"><label>a</label><p>+++: highly present, ++: moderately\npresent, +: low, and -: absent.</p></fn></table-wrap-foot>",
"<table-wrap-foot><fn id=\"t3fn1\"><label>a</label><p><italic>p</italic> < 0.01, as\ncompared with the standard group.</p></fn></table-wrap-foot>",
"<table-wrap-foot><fn id=\"t4fn1\"><label>a</label><p><italic>p</italic> < 0.01, as\ncompared with the standard group.</p></fn></table-wrap-foot>"
],
"graphic": [
"<graphic xlink:href=\"ao1c03722_0006\" id=\"ab-tgr1\"/>",
"<graphic xlink:href=\"ao1c03722_0002\" id=\"gr1\" position=\"float\"/>",
"<graphic xlink:href=\"ao1c03722_0003\" id=\"gr2\" position=\"float\"/>"
],
"media": [
"<media xlink:href=\"ao1c03722_si_001.pdf\"><caption><p>ao1c03722_si_001.pdf</p></caption></media>"
],
"unknown_pub": "[{\"surname\": [\"Anand\", \"Jacobo-Herrera\", \"Altemimi\", \"Lakhssassi\"], \"given-names\": [\"U.\", \"N.\", \"A.\", \"N.\"], \"article-title\": [\"A comprehensive\\nreview on medicinal plants as antimicrobial therapeutics: Potential\\navenues of biocompatible drug discovery\"], \"source\": [\"Metabolites\"], \"year\": [\"2019\"], \"volume\": [\"9\"], \"fpage\": [\"258\"], \"pub-id\": [\"10.3390/metabo9110258\"]}, {\"surname\": [\"Kopilakkal\", \"Rani\", \"Rasheed\", \"Bency\", \"Azeem\"], \"given-names\": [\"R.\", \"S.\", \"S. P.\", \"B. T.\", \"A. K.\"], \"article-title\": [\"Monograph\\nof Clerodendrum paniculatum\"], \"source\": [\"World J. Pharm.\\nRes.\"], \"year\": [\"2019\"], \"volume\": [\"8\"], \"fpage\": [\"448\"], \"pub-id\": [\"10.20959/wjpr20198-15328\"]}, {\"surname\": [\"Ekor\"], \"given-names\": [\"M.\"], \"article-title\": [\"The growing\\nuse of herbal medicines: issues relating to adverse reactions and\\nchallenges in monitoring safety\"], \"source\": [\"Front. Pharmacol.\"], \"year\": [\"2013\"], \"volume\": [\"4\"], \"fpage\": [\"177\"], \"pub-id\": [\"10.3389/fphar.2013.00177\"]}, {\"surname\": [\"Thomford\", \"Senthebane\", \"Rowe\", \"Munro\", \"Seele\", \"Maroyi\", \"Dzobo\"], \"given-names\": [\"N.\", \"D.\", \"A.\", \"D.\", \"P.\", \"A.\", \"K.\"], \"article-title\": [\"Natural Products for\\nDrug Discovery\\nin the 21st Century: Innovations for Novel Drug Discovery\"], \"source\": [\"Int. J. Mol. Sci.\"], \"year\": [\"2018\"], \"volume\": [\"19\"], \"fpage\": [\"1578\"], \"pub-id\": [\"10.3390/ijms19061578\"]}, {\"surname\": [\"Boora\", \"Chirisa\", \"Mukanganyama\"], \"given-names\": [\"F.\", \"E.\", \"S.\"], \"article-title\": [\"Evaluation\\nof nitrite radical scavenging\\nproperties of selected Zimbabwean plant extracts and their phytoconstituents\"], \"source\": [\"J. Food Process\"], \"year\": [\"2014\"], \"volume\": [\"2014\"], \"fpage\": [\"918018\"], \"pub-id\": [\"10.1155/2014/918018\"]}, {\"surname\": [\"Altemimi\", \"Lakhssassi\", \"Baharlouei\", \"Watson\", \"Lightfoot\"], \"given-names\": [\"A.\", \"N.\", \"A.\", \"D.\", \"D.\"], \"article-title\": [\"Phytochemicals:\\nExtraction, isolation, and identification of bioactive compounds from\\nplant extracts\"], \"source\": [\"Plants\"], \"year\": [\"2017\"], \"volume\": [\"6\"], \"fpage\": [\"42\"], \"pub-id\": [\"10.3390/plants6040042\"]}, {\"surname\": [\"Fernando\", \"Soysa\"], \"given-names\": [\"C. D.\", \"P.\"], \"article-title\": [\"Evaluation of Hepatoprotective\\nactivity of Eriocaulon quinquangulare\\nin vitro using porcine liver slices against ethanol induced liver\\ntoxicity and free radical scavenging capacity\"], \"source\": [\"BMC Complementary Altern. Med.\"], \"year\": [\"2016\"], \"volume\": [\"16\"], \"fpage\": [\"74\"], \"pub-id\": [\"10.1186/s12906-016-1044-x\"]}, {\"surname\": [\"Khandelwal\", \"Varunda\"], \"given-names\": [\"K. R.\", \"S.\"], \"source\": [\"Practical\\nPharmacognosy, Techniques and Experiments\"], \"edition\": [\"23\"], \"publisher-name\": [\"Nirali Prakashan publications\"], \"publisher-loc\": [\"New Delhi\"], \"year\": [\"2008\"]}, {\"surname\": [\"Trease\", \"Evans\"], \"given-names\": [\"G. E.\", \"W. C.\"], \"source\": [\"Pharmacognosy\"], \"publisher-name\": [\"ELBS Publication\"], \"publisher-loc\": [\"East Bourne\"], \"year\": [\"2002\"]}, {\"surname\": [\"Maier\", \"Basu\"], \"given-names\": [\"C.\", \"P.\"], \"article-title\": [\"In vitro antioxidant activities and polyphenol contents of seven\\ncommercially available fruits\"], \"source\": [\"Pharmacogn. Res.\"], \"year\": [\"2016\"], \"volume\": [\"8\"], \"fpage\": [\"258\"], \"pub-id\": [\"10.4103/0974-8490.188875\"]}, {\"surname\": [\"Almeida\", \"de Sousa\", \"Arriaga\", \"do Prado\", \"Magalh\\u00e3es\", \"Maia\", \"de Lemos\"], \"given-names\": [\"M. M. B.\", \"P. H. M.\", \"\\u00c2. M. C.\", \"G. M.\", \"C. E.\\nd. C.\", \"G. A.\", \"T. L. G.\"], \"article-title\": [\"Bioactive compounds and antioxidant activity of fresh\\nexotic fruits from northeastern Brazil\"], \"source\": [\"Food\\nRes. Int.\"], \"year\": [\"2011\"], \"volume\": [\"44\"], \"fpage\": [\"2155\"], \"pub-id\": [\"10.1016/j.foodres.2011.03.051\"]}, {\"surname\": [\"Junejo\", \"Gogoi\", \"Islam\", \"Rudrapal\", \"Mondal\", \"Hazarika\", \"Zaman\"], \"given-names\": [\"J. A.\", \"G.\", \"J.\", \"M.\", \"P.\", \"H.\", \"K.\"], \"article-title\": [\"Exploration\\nof antioxidant, antidiabetic\\nand hepatoprotective activity of Diplazium esculentum - A wild edible\\nplant from North Eastern India\"], \"source\": [\"Future J. Pharm.\\nSci.\"], \"year\": [\"2018\"], \"volume\": [\"4\"], \"fpage\": [\"93\"], \"pub-id\": [\"10.1016/j.fjps.2017.10.005\"]}, {\"surname\": [\"Gnanadesigan\", \"Ravikumar\", \"Anand\"], \"given-names\": [\"M.\", \"S.\", \"M.\"], \"article-title\": [\"Hepatoprotective activity\\nofCeriops\\ndecandra(Griff.) Ding Hou mangrove plant against CCl4induced liver\\ndamage\"], \"source\": [\"J. Taibah Univ. Sci.\"], \"year\": [\"2017\"], \"volume\": [\"11\"], \"fpage\": [\"450\"], \"pub-id\": [\"10.1016/j.jtusci.2016.07.004\"]}, {\"surname\": [\"Remya\", \"Balamurali\"], \"given-names\": [\"K.\", \"M. M.\"], \"article-title\": [\"In vivo and in vitro analyses to reveal the potential\\nof Solanum violaceum as efficient hepatoprotective agent\"], \"source\": [\"Eur. J. Mol. Clin. Med.\"], \"year\": [\"2020\"], \"volume\": [\"7\"], \"fpage\": [\"41\"], \"pub-id\": [\"10.1016/S2221-1691(12)60075-6\"]}, {\"surname\": [\"Ecobichon\"], \"given-names\": [\"D. J.\"], \"source\": [\"The Basis of Toxicology\\nTesting\"], \"publisher-name\": [\"CRC Press\"], \"publisher-loc\": [\"New York\"], \"year\": [\"1997\"]}, {\"surname\": [\"Bajpai\", \"Majumder\", \"Park\"], \"given-names\": [\"V. K.\", \"R.\", \"J. G.\"], \"article-title\": [\"Isolation\\nand purification of plant\\nsecondary metabolites using column-chromatographic technique\"], \"source\": [\"Bangladesh J. Pharmacol.\"], \"year\": [\"2016\"], \"volume\": [\"11\"], \"fpage\": [\"844\"], \"pub-id\": [\"10.3329/bjp.v11i4.28185\"]}, {\"surname\": [\"Gangwar\", \"Gautam\", \"Sharma\", \"Tripathi\", \"Goel\", \"Nath\"], \"given-names\": [\"M.\", \"M. K.\", \"A. K.\", \"Y. B.\", \"R. K.\", \"G.\"], \"article-title\": [\"Antioxidant Capacity\\nand Radical Scavenging Effect of Polyphenol\\nRichMallotus philippenensisFruit Extract on Human Erythrocytes: AnIn\\nVitroStudy\"], \"source\": [\"Sci. World J.\"], \"year\": [\"2014\"], \"volume\": [\"2014\"], \"fpage\": [\"279451\"], \"pub-id\": [\"10.1155/2014/279451\"]}, {\"surname\": [\"Chaudhari\", \"Mahajan\"], \"given-names\": [\"G. M.\", \"R. T.\"], \"article-title\": [\"In vitro hepatoprotective activity of Terminalia arjuna\\nstem bark and its flavonoids against CCl\"], \"sub\": [\"4\"], \"source\": [\"Asian J. Plant\\nSci. Res.\"], \"year\": [\"2016\"], \"volume\": [\"6\"], \"fpage\": [\"10\"]}, {\"surname\": [\"Rajopadhye\", \"Upadhye\"], \"given-names\": [\"A.\", \"A. S.\"], \"article-title\": [\"Estimation of Bioactive\\nCompound, Maslinic Acid by\\nHPTLC, and Evaluation of Hepatoprotective Activity on Fruit Pulp ofZiziphus\\njujubaMill. Cultivars in India\"], \"source\": [\"Evidence-Based\\nComplementary Altern.\"], \"year\": [\"2016\"], \"volume\": [\"2016\"], \"fpage\": [\"4758734\"], \"pub-id\": [\"10.1155/2016/4758734\"]}, {\"surname\": [\"Rao\", \"Rao\", \"Nitesh\", \"Raj\", \"Chandrasekhar\", \"Vijayan\", \"Dhanaraj\"], \"given-names\": [\"M.\", \"V.\", \"K.\", \"V.\", \"R.\", \"P.\", \"S.\"], \"article-title\": [\"In vitro and\\nin vivo hepatoprotective\\neffects of the total alkaloid fraction of Hygrophila auriculata leaves\"], \"source\": [\"Indian J. Pharmacol.\"], \"year\": [\"2010\"], \"volume\": [\"42\"], \"fpage\": [\"98\"], \"pub-id\": [\"10.4103/0253-7613.64500\"]}]",
"glossary": {
"acronym": [
"CPFP",
"CPFC",
"CPFE",
"CPFA",
"CPFW",
"DPPH",
"ABTS"
],
"definition": [
"Clerodendrum paniculatum flower petroleum ether extract",
"Clerodendrum paniculatum flower chloroform extract",
"Clerodendrum paniculatum flower\nethyl acetate extract",
"Clerodendrum paniculatum flower\nalcohol extract",
"Clerodendrum paniculatum flower water\nextract",
"2,2-diphenyl-2-picryl\nhydrazyl",
"2,2-azino-bis\n(3-ethyl benzothiazoline-6-sufonic\nacid)"
]
},
"references": {
"introduction": {
"pmid_ref": [
"31358053",
"31080832",
"25646037",
"23268465"
],
"unknown_pub_ref": [
0,
1,
2,
3
],
"figure_ref": [],
"table_ref": [],
"formula_ref": [],
"box_ref": [],
"code_ref": [],
"quote_ref": [],
"chem_ref": [],
"supplementary_ref": [],
"footnote_ref": [],
"graphic_ref": [],
"media_ref": []
},
"methods": {...},
"results": {
"pmid_ref": [
"34151056",
"34124456",
"28442109",
"29379645",
"28962407"
],
"unknown_pub_ref": [
4
],
"figure_ref": [
0,
1,
2,
3
],
"table_ref": [
0,
1,
2,
3,
4
],
"formula_ref": [],
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"quote_ref": [],
"chem_ref": [],
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"footnote_ref": [],
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"media_ref": []
},
"discussion": {...},
"conclusion": {...},
"front": {...},
"body": {...},
"back": {...},
"figure": {...},
"table": {...},
"formula": {...},
"box": {...},
"code": {...},
"quote": {...},
"chem": {...},
"supplementary": {...},
"footnote": {...}
},
"references_text": {
"introduction": {
"pmid_ref": [
"1",
"2",
"4",
"5"
],
"unknown_pub_ref": [
"3",
"6",
"7",
"8"
],
"figure_ref": [],
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},
"methods": {...},
"results": {
"pmid_ref": [
"9",
"10",
"11",
"12",
"14"
],
"unknown_pub_ref": [
"13"
],
"figure_ref": [
"Figure 1",
"Figure 2",
"Figure 3",
"Figure 4"
],
"table_ref": [
"Table 1",
"Table 2",
"Table 3",
"Table 4"
],
"formula_ref": [],
"box_ref": [],
"code_ref": [],
"quote_ref": [],
"chem_ref": [],
"supplementary_ref": [],
"footnote_ref": [],
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"media_ref": []
},
"discussion": {...},
"conclusion": {...},
"front": {...},
"body": {...},
"back": {...},
"figure": {...},
"table": {...},
"formula": {...},
"box": {...},
"code": {...},
"quote": {...},
"chem": {...},
"supplementary": {...},
"footnote": {...}
},
"n_references": 43,
"license": "CC BY-NC-ND",
"retracted": "no",
"last_updated": "2022-01-15 12:37:30",
"citation": "ACS Omega. 2021 Sep 29; 6(40):26489-26498",
"package_file": "oa_package/ca/94/PMC8515580.tar.gz"
}
```
### Data Fields
- "accession_id": The PMC ID of the article
- "pmid": The PubMed ID of the article
- "introduction": List of \<title\> and \<p\> elements in \<body\>, sharing their root with a \<title\> containing "introduction" or "background".
- "methods": Same as introduction with "method" keyword.
- "results": Same as introduction with "result" keyword.
- "discussion": Same as introduction with "discussion" keyword.
- "conclusion": Same as introduction with "conclusion" keyword.
- "front": List of \<title\> and \<p\> elements in \<front\> after everything else has been searched.
- "body": List of \<title\> and \<p\> elements in \<body\> after everything else has been searched.
- "back": List of \<title\> and \<p\> elements in \<back\> after everything else has been searched.
- "figure": List of \<fig\> elements of the article.
- "table": List of \<table-wrap\> and \<array\> elements of the article.
- "formula": List of \<disp-formula\> and \<inline-formula\> elements of the article.
- "box": List of \<boxed-text\> elements of the article.
- "code": List of \<code\> elements of the article.
- "quote": List of \<disp-quote\> and \<speech\> elements of the article.
- "chem": List of \<chem-struct-wrap\> elements of the article.
- "supplementary": List of \<supplementary-material\> and \<inline-supplementary-material\> elements of the article.
- "footnote": List of \<fn-group\> and \<table-wrap-foot\> elements of the article.
- "graphic": List of \<graphic\> and \<inline-graphic\> elements of the article.
- "media": List of \<media\> and \<inline-media\> elements of the article.
- "references": Lists of references in the order found in the corresponding categories
- "pmid_ref": PMIDs of other articles. In text, replaced by " ##REF## "
- "unknown_pub_ref": 0-indexed idx of the article in "unknown_pub". In text, replaced by " ##UREF## "
- "figure_ref": 0-indexed idx of the figures in "figure" In text, replaced by " ##FIG## "
- "table_ref": 0-indexed idx of the tables in "table" In text, replaced by " ##TAB## "
- "formula_ref": 0-indexed idx of the formulas in "formula" In text, replaced by " ##FORMU## "
- "box_ref": 0-indexed idx of the box in "box" In text, replaced by " ##BOX## "
- "code_ref": 0-indexed idx of the code in "code" In text, replaced by " ##CODE## "
- "quote_ref": 0-indexed idx of the quote in "quote" In text, replaced by " ##QUOTE## "
- "chem_ref": 0-indexed idx of the chemical in "chem" In text, replaced by " ##CHEM## "
- "supplementary_ref": 0-indexed idx of the figure in "supplementary" In text, replaced by " ##SUPPL## "
- "footnote_ref": 0-indexed idx of the footnote in "footnote" In text, replaced by " ##FOOTN## "
- "graphic_ref": 0-indexed idx of the graphics in "graphics" In text, replaced by " ##GRAPH## "
- "media_ref": 0-indexed idx of the medias in "medias" In text, replaced by " ##MEDIA## "
- "references_text": For each reference in "references", the corresponding text that the reference keywords replaced.
- "glossary": Glossary if found in the XML
- "unknown_references": JSON of a dictionnary of each "tag":"text" for the reference that did not indicate a PMID
- "n_references": Total number of references and unknown references
- "license": The licence of the article
- "retracted": If the article was retracted or not
- "last_updated": Last update of the article
- "citation": Citation of the article
- "package_file": path to the folder containing the graphics and media files of the article
### Data Splits
[Needs More Information]
## Dataset Creation
### Curation Rationale
Internal references (figures, tables, ...) were found using specific tags. Deciding on those tags was done by testing and by looking in the documentation
for the different kind of possible usage.
Then, to split the article into introduction, methods, results, discussion and conclusion, specific keywords in titles were used. Because there are no rules
in this xml to tag those sections, finding the keyword seemed like the most reliable approach to do so. A drawback is that many section do not have those
keywords in the titles but could be assimilated to those. However, the huge diversity in the titles makes it harder to label such sections. This could be the
work of further versions of this dataset.
### Source Data
#### Initial Data Collection and Normalization
[Needs More Information]
#### Who are the source language producers?
[Needs More Information]
### Annotations
#### Annotation process
[Needs More Information]
#### Who are the annotators?
[Needs More Information]
### Personal and Sensitive Information
[Needs More Information]
## Considerations for Using the Data
### Social Impact of Dataset
[Needs More Information]
### Discussion of Biases
The articles XML are similar accross collections. This means that if a certain collection handles the structure in unusual ways, the whole collection might not be as
well annotated than others. This concerns all the sections (intro, methods, ...), the external references (pmids) and the internal references (tables, figures, ...).
To illustrate that, references are sometime given as a range (e.g. 10-15). In that case, only reference 10 and 15 are linked. This could potentially be handled in a
future version.
### Other Known Limitations
[Needs More Information]
## Additional Information
### Dataset Curators
[Needs More Information]
### Licensing Information
https://www.ncbi.nlm.nih.gov/pmc/about/copyright/
Within the PMC Open Access Subset, there are three groupings:
Commercial Use Allowed - CC0, CC BY, CC BY-SA, CC BY-ND licenses
Non-Commercial Use Only - CC BY-NC, CC BY-NC-SA, CC BY-NC-ND licenses; and
Other - no machine-readable Creative Commons license, no license, or a custom license.
### Citation Information
[Needs More Information] |