README.md

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 Summary
  • Supported Tasks
  • Languages
• Dataset Structure
  • Data Instances
  • Data Fields
  • Data Splits
• Dataset Creation
  • Curation Rationale
  • Source Data
  • Annotations
  • Personal and Sensitive Information
• Considerations for Using the Data
  • Social Impact of Dataset
  • Discussion of Biases
  • Other Known Limitations
• Additional Information
  • Dataset Curators
  • Licensing 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

{
    "accession_id": "PMC8515580",
    "pmid": "34661004",
    "introduction": [
        "<title>Introduction</title>",
        "<p>Medicinal plants are\nknown to possess several primary and secondary\nmetabolites. The secondary metabolites ..."
    ],
    "methods": [
        "<title>DPPH Method</title>",
        "<p>The most effective and popular method of\nantioxidant evaluation is the DPPH radical scavenging method. ..."
    ],
    "results": [
        "<title>Results</title>",
        "<p>The phytochemical screening of the flower extract indicated the\npresence of carbohydrates, tannins, ..."
    ],
    "discussion": [
        "<title>Discussion</title>",
        "<p>The\nliver, the major metabolic organ of our body, may have toxicity\ndue to various drugs like alcohol, ..."
    ],
    "conclusion": [
        "<title>Conclusions</title>",
        "<p>The implication on the\npharmacological properties from the flower\nextract of <italic>C. paniculatum</italic>, ..."
    ],
    "front": [
        "<p content-type=\"toc-graphic\"> ##GRAPH## </p>",
        "<p>The aim of the presented\nwork involves the isolation, characterization,\nand evaluation of hepatoprotective ..."
    ],
    "body": [
        "<title>Experimental\nSection</title>",
        "<title>Chemicals and Reagents</title>",
        "<p>The chemicals and reagents used\nfor the experiments carried out ...
    ],
    "back": [
        "<title>Supporting Information Available</title>",
        "<p>The Supporting Information is\navailable free of charge at ..."
    ],
    "figure": [
        "<fig id=\"fig1\" position=\"float\"><label>Figure 1</label><caption><p>Determination\nof reducing power for various ..."
    ],
    "table": [
        "<table-wrap id=\"tbl1\" position=\"float\"><label>Table 1</label><caption><title>Phytochemical Screening for the Flower..."
    ],
    "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>..."
    ],
    "code": [
        "EXAMPLE FROM ANOTHER ARTICLE",
        "<code xml:space=\"preserve\" position=\"float\" orientation=\"portrait\">\n<monospace>\n\nLupe.dat$w &lt;\u2013 ifelse..."
    ],
    "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..."
    ],
    "chem": [
        "EXAMPLE FROM ANOTHER ARTICLE",
        "<chem-struct-wrap id=\"open202000358-disp-0001\" 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 -: ..."
    ],
    "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\"/>",
        "<graphic xlink:href=\"ao1c03722_0004\" id=\"gr3\" position=\"float\"/>",
        "<graphic xlink:href=\"ao1c03722_0005\" id=\"gr4\" position=\"float\"/>",
        "<graphic xlink:href=\"ao1c03722_m001\" position=\"anchor\"/>"
    ],
    "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.\"], ...."]}]",
    "glossary": {
        "acronym": [
            "CPFP",
            "CPFC",
            "CPFE",
            "CPFA",
            "CPFW",
            "DPPH",
            "ABTS",
            "NO",
            "GAE",
            "QE",
            "SGOT",
            "SGPT",
            "ALP",
            "\u03b3-GT",
            "CMC",
            "b.w.",
            "s.c"
        ],
        "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)",
            "nitric\noxide",
            "gallic\nacid equivalent",
            "quercetin equivalent",
            "serum glutamate oxaloacetate transaminase",
            "serum glutamate pyruvate transaminase",
            "alkaline phospahtase",
            "gamma glutamyl\ntransferase",
            "carboxy methyl cellulose",
            "body weight",
            "subcutaneous"
        ]
    },
    "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,
                5,
                6,
                7,
                7,
                8
            ],
            "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",
                "Table 5",
                "Table 6",
                "Table 7",
                "Table 8",
                "Table 8",
                "Table 9"
            ],
            "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