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--- |
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pretty_name: XML-parsed PMC |
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task_categories: |
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- text-classification |
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- summarization |
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- other |
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annotations_creators: |
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- no-annotation |
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language_creators: |
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- expert-generated |
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language: |
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- en |
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size_categories: |
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- 1M<n<10M |
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source_datasets: |
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- original |
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license: |
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- cc0-1.0 |
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- cc-by-4.0 |
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- cc-by-sa-4.0 |
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- cc-by-nc-4.0 |
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- cc-by-nd-4.0 |
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- cc-by-nc-nd-4.0 |
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- cc-by-nc-sa-4.0 |
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- unknown |
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- other |
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multilinguality: |
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- monolingual |
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task_ids: [] |
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tags: |
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- research papers |
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- biology |
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- medecine |
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--- |
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# Dataset Card for PMC Open Access XML |
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## Table of Contents |
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- [Dataset Description](#dataset-description) |
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- [Dataset Summary](#dataset-summary) |
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- [Supported Tasks](#supported-tasks-and-leaderboards) |
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- [Languages](#languages) |
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- [Dataset Structure](#dataset-structure) |
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- [Data Instances](#data-instances) |
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- [Data Fields](#data-instances) |
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- [Data Splits](#data-instances) |
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- [Dataset Creation](#dataset-creation) |
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- [Curation Rationale](#curation-rationale) |
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- [Source Data](#source-data) |
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- [Annotations](#annotations) |
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- [Personal and Sensitive Information](#personal-and-sensitive-information) |
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- [Considerations for Using the Data](#considerations-for-using-the-data) |
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- [Social Impact of Dataset](#social-impact-of-dataset) |
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- [Discussion of Biases](#discussion-of-biases) |
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- [Other Known Limitations](#other-known-limitations) |
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- [Additional Information](#additional-information) |
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- [Dataset Curators](#dataset-curators) |
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- [Licensing Information](#licensing-information) |
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- [Citation Information](#citation-information) |
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## Dataset Description |
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- **Homepage:** https://www.ncbi.nlm.nih.gov/pmc/tools/openftlist/ |
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- **Repository:** [Needs More Information] |
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- **Paper:** [Needs More Information] |
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- **Leaderboard:** [Needs More Information] |
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- **Point of Contact:** [Needs More Information] |
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### Dataset Summary |
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The XML Open Access includes more than 3.4 million journal articles and preprints that are made available under |
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license terms that allow reuse. |
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Not all articles in PMC are available for text mining and other reuse, many have copyright protection, however articles |
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in the PMC Open Access Subset are made available under Creative Commons or similar licenses that generally allow more |
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liberal redistribution and reuse than a traditional copyrighted work. |
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The PMC Open Access Subset is one part of the PMC Article Datasets |
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This version takes XML version as source, benefiting from the structured text |
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to split the articles in parts, naming the introduction, methods, results, |
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discussion and conclusion, and refers with keywords in the text to external or internal |
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resources (articles, figures, tables, formulas, boxed-text, quotes, code, footnotes, chemicals, graphics, medias). |
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The dataset was initially created with relation-extraction tasks in mind, between the references in text and the content of the |
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references (e.g. for PMID, by joining the refered article abstract from the pubmed dataset), but aims in a larger extent to provide |
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a corpus of pre-annotated text for other tasks (e.g. figure caption to graphic, glossary definition detection, summarization). |
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### Supported Tasks and Leaderboards |
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[Needs More Information] |
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### Languages |
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[Needs More Information] |
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## Dataset Structure |
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### Data Fields |
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- "accession_id": The PMC ID of the article |
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- "pmid": The PubMed ID of the article |
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- "introduction": List of \<title\> and \<p\> elements in \<body\>, sharing their root with a \<title\> containing "introduction" or "background". |
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- "methods": Same as introduction with "method" keyword. |
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- "results": Same as introduction with "result" keyword. |
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- "discussion": Same as introduction with "discussion" keyword. |
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- "conclusion": Same as introduction with "conclusion" keyword. |
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- "front": List of \<title\> and \<p\> elements in \<front\> after everything else has been searched. |
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- "body": List of \<title\> and \<p\> elements in \<body\> after everything else has been searched. |
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- "back": List of \<title\> and \<p\> elements in \<back\> after everything else has been searched. |
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- "figure": List of \<fig\> elements of the article. |
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- "table": List of \<table-wrap\> and \<array\> elements of the article. |
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- "formula": List of \<disp-formula\> and \<inline-formula\> elements of the article. |
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- "box": List of \<boxed-text\> elements of the article. |
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- "code": List of \<code\> elements of the article. |
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- "quote": List of \<disp-quote\> and \<speech\> elements of the article. |
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- "chem": List of \<chem-struct-wrap\> elements of the article. |
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- "supplementary": List of \<supplementary-material\> and \<inline-supplementary-material\> elements of the article. |
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- "footnote": List of \<fn-group\> and \<table-wrap-foot\> elements of the article. |
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- "graphic": List of \<graphic\> and \<inline-graphic\> elements of the article. |
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- "media": List of \<media\> and \<inline-media\> elements of the article. |
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- "references": Lists of references in the order found in the corresponding categories |
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- "pmid_ref": PMIDs of other articles. In text, replaced by " ##REF## " |
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- "unknown_pub_ref": 0-indexed idx of the article in "unknown_pub". In text, replaced by " ##UREF## " |
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- "figure_ref": 0-indexed idx of the figures in "figure" In text, replaced by " ##FIG## " |
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- "table_ref": 0-indexed idx of the tables in "table" In text, replaced by " ##TAB## " |
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- "formula_ref": 0-indexed idx of the formulas in "formula" In text, replaced by " ##FORMU## " |
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- "box_ref": 0-indexed idx of the box in "box" In text, replaced by " ##BOX## " |
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- "code_ref": 0-indexed idx of the code in "code" In text, replaced by " ##CODE## " |
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- "quote_ref": 0-indexed idx of the quote in "quote" In text, replaced by " ##QUOTE## " |
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- "chem_ref": 0-indexed idx of the chemical in "chem" In text, replaced by " ##CHEM## " |
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- "supplementary_ref": 0-indexed idx of the figure in "supplementary" In text, replaced by " ##SUPPL## " |
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- "footnote_ref": 0-indexed idx of the footnote in "footnote" In text, replaced by " ##FOOTN## " |
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- "graphic_ref": 0-indexed idx of the graphics in "graphics" In text, replaced by " ##GRAPH## " |
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- "media_ref": 0-indexed idx of the medias in "medias" In text, replaced by " ##MEDIA## " |
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- "references_text": For each reference in "references", the corresponding text that the reference keywords replaced. |
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- "glossary": Glossary if found in the XML |
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- "unknown_references": JSON of a dictionnary of each "tag":"text" for the reference that did not indicate a PMID |
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- "n_references": Total number of references and unknown references |
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- "license": The licence of the article |
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- "retracted": If the article was retracted or not |
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- "last_updated": Last update of the article |
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- "citation": Citation of the article |
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- "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/) |
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### Data Splits |
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[Needs More Information] |
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## Dataset Creation |
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### Curation Rationale |
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Internal references (figures, tables, ...) were found using specific tags. Deciding on those tags was done by testing and by looking in the documentation |
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for the different kind of possible usage. |
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Then, to split the article into introduction, methods, results, discussion and conclusion, specific keywords in titles were used. Because there are no rules |
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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 |
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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 |
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work of further versions of this dataset. |
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### Source Data |
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#### Initial Data Collection and Normalization |
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Data was obtained from: |
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- ftp.ncbi.nlm.nih.gov/pub/pmc/oa_bulk/oa_noncomm/xml/ |
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- ftp.ncbi.nlm.nih.gov/pub/pmc/oa_bulk/oa_comm/xml/ |
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- ftp.ncbi.nlm.nih.gov/pub/pmc/oa_bulk/oa_other/xml/ |
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Additional content for individual articles (graphics, media) can be obtained from: |
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- ftp.ncbi.nlm.nih.gov/pub/pmc + "package_file" |
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#### Who are the source language producers? |
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[Needs More Information] |
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### Annotations |
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#### Annotation process |
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[Needs More Information] |
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#### Who are the annotators? |
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[Needs More Information] |
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### Personal and Sensitive Information |
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[Needs More Information] |
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## Considerations for Using the Data |
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### Social Impact of Dataset |
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[Needs More Information] |
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### Discussion of Biases |
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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 |
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well annotated than others. This concerns all the sections (intro, methods, ...), the external references (pmids) and the internal references (tables, figures, ...). |
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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 |
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future version. |
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### Other Known Limitations |
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[Needs More Information] |
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### Preprocessing advices |
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- Filter out empty contents. |
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- Remove unwanted references from the text, and replace either by the "references_text" or by the reference content itself. |
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- Unescape HTML special characters: `import html; html.unescape(my_text)` |
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- Remove superfluous line break in text. |
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- Remove XML tags / replace by special tokens (\<italic\>, \<sup\>, \<sub\>, ...). |
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- Join the items of the contents' lists. |
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## Additional Information |
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### Dataset Curators |
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[Needs More Information] |
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### Licensing Information |
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https://www.ncbi.nlm.nih.gov/pmc/about/copyright/ |
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Within the PMC Open Access Subset, there are three groupings: |
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Commercial Use Allowed - CC0, CC BY, CC BY-SA, CC BY-ND licenses |
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Non-Commercial Use Only - CC BY-NC, CC BY-NC-SA, CC BY-NC-ND licenses; and |
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Other - no machine-readable Creative Commons license, no license, or a custom license. |
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### Citation Information |
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[Needs More Information] |
