|
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] |