Assessment of transparency indicators across the biomedical literature: how open is open? release_w57ueehcmvegrdf22i563powtq

by Stylianos Serghiou, Despina Contopoulos-Ioannidis, Kevin Boyack, Nico Riedel, Joshua D Wallach, John Ioannidis

Entity Metadata (schema)

abstracts [{'sha1': '04ff0af536184d04010c358fea2d50afd383007b', 'content': 'Recent concerns about the reproducibility of science have led to several calls for more open and transparent research practices and for the monitoring of potential improvements over time. However, with tens of thousands of new biomedical articles published per week, manually mapping and monitoring changes in transparency is unrealistic. We present an open-source, automated approach to identify five indicators of transparency (data sharing, code sharing, conflicts of interest disclosures, funding disclosures and protocol registration) and apply it across the entire open access biomedical literature of 2.75 million articles on PubMed Central. Our results indicate remarkable improvements in some (e.g. conflict of interest disclosures, funding disclosures), but not other (e.g. protocol registration, code sharing) areas of transparency over time, and map transparency across fields of science, countries, journals and publishers. This work has enabled the creation of a large, integrated, and openly available database to expedite further efforts to monitor, understand and promote transparency and reproducibility in science.', 'mimetype': 'application/xml+jats', 'lang': None}]
container
container_id
contribs [{'index': 0, 'creator_id': '5rmcpnghrrdmfoxjuzvdyaaosq', 'creator': {'state': 'active', 'ident': '5rmcpnghrrdmfoxjuzvdyaaosq', 'revision': '49aab570-3b5a-425c-a8b6-37800601010f', 'redirect': None, 'extra': None, 'edit_extra': None, 'display_name': 'Stylianos Serghiou', 'given_name': 'Stylianos', 'surname': 'Serghiou', 'orcid': '0000-0002-2477-6060', 'wikidata_qid': None}, 'raw_name': 'Stylianos Serghiou', 'given_name': 'Stylianos', 'surname': 'Serghiou', 'role': 'author', 'raw_affiliation': None, 'extra': {'seq': 'first'}}, {'index': 1, 'creator_id': 'q2o4jntiujdxxiiimcykjcqqwm', 'creator': {'state': 'active', 'ident': 'q2o4jntiujdxxiiimcykjcqqwm', 'revision': 'a10cfda1-d715-482d-ba04-7f2644fcc7a8', 'redirect': None, 'extra': None, 'edit_extra': None, 'display_name': 'Despina Contopoulos-Ioannidis', 'given_name': 'Despina', 'surname': 'Contopoulos-Ioannidis', 'orcid': '0000-0002-1918-8918', 'wikidata_qid': None}, 'raw_name': 'Despina G Contopoulos-Ioannidis', 'given_name': 'Despina G', 'surname': 'Contopoulos-Ioannidis', 'role': 'author', 'raw_affiliation': None, 'extra': None}, {'index': 2, 'creator_id': 'vzy6ofynwraezplazab5rhtw7m', 'creator': {'state': 'active', 'ident': 'vzy6ofynwraezplazab5rhtw7m', 'revision': 'c7c295d0-9fe1-4c43-a5ce-d8463e2a3e00', 'redirect': None, 'extra': None, 'edit_extra': None, 'display_name': 'Kevin Boyack', 'given_name': 'Kevin', 'surname': 'Boyack', 'orcid': '0000-0001-7814-8951', 'wikidata_qid': None}, 'raw_name': 'Kevin W Boyack', 'given_name': 'Kevin W', 'surname': 'Boyack', 'role': 'author', 'raw_affiliation': None, 'extra': None}, {'index': 3, 'creator_id': 'fb4y72yfejhpvnq5iu7abu5lbe', 'creator': {'state': 'active', 'ident': 'fb4y72yfejhpvnq5iu7abu5lbe', 'revision': 'c8a648af-b15d-4d0f-b6e6-a67cdce3568d', 'redirect': None, 'extra': None, 'edit_extra': None, 'display_name': 'Nico Riedel', 'given_name': 'Nico', 'surname': 'Riedel', 'orcid': '0000-0002-3808-1163', 'wikidata_qid': None}, 'raw_name': 'Nico Riedel', 'given_name': 'Nico', 'surname': 'Riedel', 'role': 'author', 'raw_affiliation': None, 'extra': None}, {'index': 4, 'creator_id': 'adz5tulcyncwhbr5mwlmx6rbaa', 'creator': {'state': 'active', 'ident': 'adz5tulcyncwhbr5mwlmx6rbaa', 'revision': '7bfc3474-13cf-453c-8d47-afb1606cb83f', 'redirect': None, 'extra': None, 'edit_extra': None, 'display_name': 'Joshua D Wallach', 'given_name': 'Joshua', 'surname': 'Wallach', 'orcid': '0000-0002-2816-6905', 'wikidata_qid': None}, 'raw_name': 'Joshua David Wallach', 'given_name': 'Joshua David', 'surname': 'Wallach', 'role': 'author', 'raw_affiliation': None, 'extra': None}, {'index': 5, 'creator_id': 'iimvc523xbhqlav6j3sbthuehu', 'creator': {'state': 'active', 'ident': 'iimvc523xbhqlav6j3sbthuehu', 'revision': '52444283-850c-41d5-945b-bd7c6112cb89', 'redirect': None, 'extra': None, 'edit_extra': None, 'display_name': 'John Ioannidis', 'given_name': 'John', 'surname': 'Ioannidis', 'orcid': '0000-0003-3118-6859', 'wikidata_qid': 'Q6251482'}, 'raw_name': 'John P. A. Ioannidis', 'given_name': 'John P. A.', 'surname': 'Ioannidis', 'role': 'author', 'raw_affiliation': None, 'extra': None}]
edit_extra
ext_ids {'doi': '10.1101/2020.10.30.361618', 'wikidata_qid': None, 'isbn13': None, 'pmid': None, 'pmcid': None, 'core': None, 'arxiv': None, 'jstor': None, 'ark': None, 'mag': None, 'doaj': None, 'dblp': None, 'oai': None}
files [{'state': 'active', 'ident': 'i3j76a4kf5bmnakktul25hhwrm', 'revision': '1eee62fe-b638-4e12-a51f-4d3038df37c7', 'redirect': None, 'extra': None, 'edit_extra': None, 'size': 2239683, 'md5': '9656ae3a0cb208e3e0312a6c0e52f86a', 'sha1': 'a9e870ed1d351ac7f05a8e63a28df29d18640f43', 'sha256': 'f4e7c6b6fd3e0dbf6e15c35d13895d0e9e62127436a51a020cb046816a5a62e5', 'urls': [{'url': 'https://web.archive.org/web/20201229173015/https://www.biorxiv.org/content/biorxiv/early/2020/10/30/2020.10.30.361618.full.pdf', 'rel': 'webarchive'}, {'url': 'https://www.biorxiv.org/content/biorxiv/early/2020/10/30/2020.10.30.361618.full.pdf', 'rel': 'repository'}], 'mimetype': 'application/pdf', 'release_ids': ['w57ueehcmvegrdf22i563powtq'], 'releases': None}]
filesets []
ident w57ueehcmvegrdf22i563powtq
issue
language
license_slug
number
original_title
pages
publisher Cold Spring Harbor Laboratory
redirect
refs []
release_date 2020-10-30
release_stage
release_type post
release_year 2020
revision 59eb92f5-1d6a-4aa5-a7ea-c896b0124610
state active
subtitle
title Assessment of transparency indicators across the biomedical literature: how open is open?
version
volume
webcaptures []
withdrawn_date
withdrawn_status
withdrawn_year
work_id 6ctrx5p6djebdgwlcn7sa3c7mm
As JSON via API

Extra Metadata (raw JSON)

crossref.type posted-content