| --- |
| configs: |
| - config_name: commercial |
| data_files: |
| - split: train |
| path: "data/commercial/*.arrow" |
| - config_name: non_commercial |
| data_files: |
| - split: train |
| path: "data/non_commercial/*.arrow" |
| - config_name: other |
| data_files: |
| - split: train |
| path: "data/other/*.arrow" |
| pretty_name: XML-parsed PMC |
| task_categories: |
| - text-classification |
| - summarization |
| - other |
| annotations_creators: |
| - no-annotation |
| language_creators: |
| - expert-generated |
| language: |
| - en |
| size_categories: |
| - 1M<n<10M |
| source_datasets: |
| - original |
| license: |
| - cc0-1.0 |
| - cc-by-4.0 |
| - cc-by-sa-4.0 |
| - cc-by-nc-4.0 |
| - cc-by-nd-4.0 |
| - cc-by-nc-nd-4.0 |
| - cc-by-nc-sa-4.0 |
| - unknown |
| - other |
| multilinguality: |
| - monolingual |
| task_ids: [] |
| tags: |
| - research papers |
| - biology |
| - medecine |
| --- |
| |
| # 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 reference 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 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. |
| - "chemical": 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. |
| - "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 (to append to the base URL: ftp.ncbi.nlm.nih.gov/pub/pmc/) |
| |
| In text, the references are in the form ##KEYWORD##IDX_REF##OLD_TEXT##, with keywords (REF, UREF, FIG, TAB, FORMU, BOX, CODE, QUOTE, CHEM, SUPPL, FOOTN, GRAPH, MEDIA) referencing respectively to "pubmed articles" (external), "unknown_references", "figure", "table", "formula", "box", "code", "quote", "chem", "supplementary", "footnote", "graphic" and "media". |
| ### 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 |
|
|
| Data was obtained from: |
| - ftp.ncbi.nlm.nih.gov/pub/pmc/oa_bulk/oa_noncomm/xml/ |
| - ftp.ncbi.nlm.nih.gov/pub/pmc/oa_bulk/oa_comm/xml/ |
| - ftp.ncbi.nlm.nih.gov/pub/pmc/oa_bulk/oa_other/xml/ |
|
|
| Additional content for individual articles (graphics, media) can be obtained from: |
| - ftp.ncbi.nlm.nih.gov/pub/pmc + "package_file" |
| |
| #### 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] |
| |
| ### Preprocessing recommendations |
| |
| - Filter out empty contents. |
| - Remove unwanted references from the text, and replace either by the "references_text" or by the reference content itself. |
| - Unescape HTML special characters: `import html; html.unescape(my_text)` |
| - Remove superfluous line break in text. |
| - Remove XML tags (\<italic\>, \<sup\>, \<sub\>, ...), replace by special tokens? |
| - Join the items of the contents' lists. |
|
|
| ## 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] |
