Preserving Comments from PubMed Commons – Hypothesis | Jon Udell
ab1630's bookmarks 2018-02-10
"On 1 February 2018, the National Center for Biotechnology Information (NCBI) announced the discontinuation of PubMed Commons, citing usage that had been “minimal, with comments submitted on only 6,000 of the 28 million articles indexed in PubMed.” Although sparse, these comments are a valuable part of the scholarly record: contributors asked questions, gave answers and provided additional insight into published articles. Many in the biomedical community questioned the decision and mourned their impending loss...On Twitter, several observers suggested Hypothesis might help carry those comments forward...
So we rolled up our sleeves and began our investigation, led by Jon Udell, Director of Integrations at Hypothesis, who so often creates connections between open, standards-based annotation and real-world needs like these. There’s no formal API for retrieving the PubMed comments, but Alf Eaton kindly provided a screenscraper that jump-started our effort. Alf’s code queries PubMed for the roughly 6K articles with comments, downloads them, and extracts the the comments. ...But what about the licensing?..."