Softcite software mention extraction from the CORD-19 publications

Softcite software mention extraction from the CORD-19 publications This dataset is the first result of the extraction of software mentions from the set of publications of the CORD-19 corpus (https://allenai.org/data/cord-19) by the Softcite software recognizer, see https://github.com/ourresearch/software-mentions. The CORD-19 version used for this dataset is the one dated 2020-09-11, using the metadata.csv file only. We re-harvested the PDF with https://github.com/kermitt2/article-dataset-builder in order to also extract coordinates of software mentions in the PDF and to take advantage of the latest version of GROBID to produce better full text extraction from PDF. Note: We are working on a new version of this dataset with the CORD-19 version dated 2021-03-22, using an improved version of the Softcite software recognizer. Data format The extraction consists of 3 JSON files: annotations.json contains the individual software annotations including software name and possible attached attributes (publisher, URL and version). Each annotation is associated with coordinates expressed as bounding boxes in the original PDF. See Coordinates of structures in the original PDF for more details on the coordinate format. The context of citation is the sentence where the software name and its attributes are extracted. It is added to the JSON structure (field context), as well as the identifier of the document where the annotation belongs (field document, pointing to entries available in documents.json) and a list of bibliographical references attached to the software name (field references, pointing to entries available in references.json, with the used reference marker string). See https://github.com/ourresearch/software-mentions for more details on the extracted attributes. If the software name was sucessfully disambiguated against WikiData ("entity linking"), it appears in the field wikidataId as Wikidata entity identifier and in the field wikipediaExternalRef as a Wikipedia PageID from the English Wikipedia. Entity linking is realized with entity-fishing. documents.json contains the metadata of the all the CORD-19 documents containing at least one software annotation. The metadata are given as a CrossRef JSON structure. The abstract should be included in the metadata most of the time, as well as some complements extracted by GROBID directly from the PDF. In addition, the size of the pages and the unique file path to the PDF can be found to allow annotations directly on the PDF (see Coordinates of structures in the original PDF for more details on the PDF annotation display mechanism). references.json contains the parsed reference entries associated to software mentions. These references are given in the field tei encoded in the XML TEI format of GROBID extraction. The extracted raw references have been matched against CrossRef to get a DOI and more complete metadata with biblio-glutton. Statistics See the included Readme.md file. License and acknowledgements This dataset is licensed under a Creative Commons Attribution 4.0 International License. We thank Alfred P. Sloan Foundation for supporting this work