| 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": [], |
| "box_ref": [], |
| "code_ref": [], |
| "quote_ref": [], |
| "chem_ref": [], |
| "supplementary_ref": [], |
| "footnote_ref": [], |
| "graphic_ref": [], |
| "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": [], |
| "table_ref": [], |
| "formula_ref": [], |
| "box_ref": [], |
| "code_ref": [], |
| "quote_ref": [], |
| "chem_ref": [], |
| "supplementary_ref": [], |
| "footnote_ref": [], |
| "graphic_ref": [], |
| "media_ref": [] |
| }, |
| "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": [], |
| "graphic_ref": [], |
| "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] |
