commonmeta-ruby 3.3.12 → 3.3.13
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- checksums.yaml +4 -4
- data/Gemfile.lock +1 -1
- data/lib/commonmeta/readers/json_feed_reader.rb +5 -1
- data/lib/commonmeta/version.rb +1 -1
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/substack_post_with_broken_reference.yml +2566 -1
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/syldavia_gazette_post_with_references.yml +323 -1
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/upstream_post_with_references.yml +1777 -1
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/wordpress_post_with_many_references.yml +6465 -0
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/json_feed_item_with_references.yml +1777 -1
- data/spec/readers/json_feed_reader_spec.rb +4 -3
- metadata +2 -2
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Ventures","doi-asserted-by":"crossref"}],"content-domain":{"domain":["elifesciences.org"],"crossmark-restriction":false},"accepted":{"date-parts":[[2021,7,20]]},"abstract":"<jats:p>We
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conducted the <jats:ext-link ext-link-type=\"uri\" xlink:href=\"https:\/\/elifesciences.org\/collections\/9b1e83d1\/reproducibility-project-cancer-biology\">Reproducibility
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Project: Cancer Biology<\/jats:ext-link> to investigate the replicability
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of preclinical research in cancer biology. The initial aim of the project
|
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was to repeat 193 experiments from 53 high-impact papers, using an approach
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in which the experimental protocols and plans for data analysis had to be
|
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2409
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peer reviewed and accepted for publication before experimental work could
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begin. However, the various barriers and challenges we encountered while designing
|
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and conducting the experiments meant that we were only able to repeat 50 experiments
|
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from 23 papers. Here we report these barriers and challenges. First, many
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original papers failed to report key descriptive and inferential statistics:
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the data needed to compute effect sizes and conduct power analyses was publicly
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accessible for just 4 of 193 experiments. Moreover, despite contacting the
|
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authors of the original papers, we were unable to obtain these data for 68%
|
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of the experiments. Second, none of the 193 experiments were described in
|
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sufficient detail in the original paper to enable us to design protocols to
|
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repeat the experiments, so we had to seek clarifications from the original
|
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authors. While authors were <jats:italic>extremely<\/jats:italic> or <jats:italic>very
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helpful<\/jats:italic> for 41% of experiments, they were <jats:italic>minimally
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helpful<\/jats:italic> for 9% of experiments, and <jats:italic>not at all
|
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2423
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helpful<\/jats:italic> (or did not respond to us) for 32% of experiments.
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|
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required modifications to complete the research and just 41% of those modifications
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could be implemented. Cumulatively, these three factors limited the number
|
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of experiments that could be repeated. This experience draws attention to
|
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a basic and fundamental concern about replication \u2013 it is hard to assess
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whether reported findings are credible.<\/jats:p>","DOI":"10.7554\/elife.67995","type":"journal-article","created":{"date-parts":[[2021,12,7]],"date-time":"2021-12-07T00:00:20Z","timestamp":1638835220000},"update-policy":"http:\/\/dx.doi.org\/10.7554\/elife.67995","source":"Crossref","is-referenced-by-count":75,"title":"Challenges
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for Open Science","place":["Charlottesville, United States"]}]},{"given":"Alexandria","family":"Denis","sequence":"additional","affiliation":[{"name":"Center
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science practices are on the rise: The State of Social Science (3S) Survey","volume-title":"OSF
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hindsight bias: A meta-analysis","volume":"48","author":"Christensen-Szalanski","year":"1991","journal-title":"Organizational
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target for human solid tumors","volume":"4","author":"Chroscinski","year":"2015","journal-title":"eLife"},{"key":"bib28","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.04363","article-title":"Registered
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breaks and chromosome pulverization from errors in mitosis","volume":"482","author":"Crasta","year":"2012","journal-title":"Nature"},{"key":"bib32","doi-asserted-by":"publisher","first-page":"529","DOI":"10.1038\/nature10509","article-title":"Inhibition
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of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia","volume":"478","author":"Dawson","year":"2011","journal-title":"Nature"},{"key":"bib33","doi-asserted-by":"publisher","first-page":"904","DOI":"10.1016\/j.cell.2011.08.017","article-title":"BET
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bromodomain inhibition as a therapeutic strategy to target c-Myc","volume":"146","author":"Delmore","year":"2011","journal-title":"Cell"},{"key":"bib34","doi-asserted-by":"publisher","first-page":"106","DOI":"10.1038\/nature10189","article-title":"Oncogene-induced
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Labs 3: Evaluating participant pool quality across the academic semester via
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from unfinished Registered Reports in the Reproducibility Project: Cancer
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the replicability of preclinical cancer biology","volume":"10","author":"Errington","year":"2021","journal-title":"eLife"},{"key":"bib44","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.45426","article-title":"Replication
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report: Wnt activity defines colon cancer stem cells and is regulated by the
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results increase down the hierarchy of the sciences","volume":"5","author":"Fanelli","year":"2010","journal-title":"PLOS
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Be a Problem, Even When There Is No \u201cFishing Expedition\u201d or \u201cp-Hacking\u201d
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and the Research Hypothesis Was Posited Ahead of Time. Department of Statistics,
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[Accessed August 5, 2021]."},{"key":"bib56","doi-asserted-by":"publisher","first-page":"562","DOI":"10.1177\/1745691612457576","article-title":"Science
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[Accessed August 5, 2021]."},{"key":"bib129","doi-asserted-by":"publisher","first-page":"815","DOI":"10.1016\/j.tics.2019.07.009","article-title":"Preregistration
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endogenous tumour-promoting ligand of the human aryl hydrocarbon receptor","volume":"478","author":"Opitz","year":"2011","journal-title":"Nature"},{"key":"bib134","doi-asserted-by":"publisher","first-page":"883","DOI":"10.1038\/nm.2753","article-title":"Melanoma
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microRNA regulon that mediates endothelial recruitment and metastasis by cancer
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genomics reveal that the serine synthesis pathway is essential in breast cancer","volume":"476","author":"Possemato","year":"2011","journal-title":"Nature"},{"key":"bib142","doi-asserted-by":"publisher","first-page":"427","DOI":"10.1038\/nature08902","article-title":"RAF
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recruits inflammatory monocytes to facilitate breast-tumour metastasis","volume":"475","author":"Qian","year":"2011","journal-title":"Nature"},{"key":"bib148","article-title":"R:
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A Language and Environment for Statistical Computing","author":"R Development
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killing of cancer cells by a small molecule targeting the stress response
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carcinoma","volume":"5","author":"Repass","year":"2016","journal-title":"eLife"},{"key":"bib154","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.25801","article-title":"Replication
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2715
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vascularization via endothelial differentiation of glioblastoma stem-like
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2719
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excess of positive results: Comparing the standard psychology literature with
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2723
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2726
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we really do it again? The powerful concept of replication is neglected in
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2727
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2728
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2729
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of transparency indicators across the biomedical literature: How open is open","volume":"19","author":"Serghiou","year":"2021","journal-title":"PLOS
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2730
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2731
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2732
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for MLL-fusion leukaemia","volume":"6","author":"Shan","year":"2017","journal-title":"eLife"},{"key":"bib163","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1016\/j.cell.2010.02.027","article-title":"A
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chromatin-mediated reversible drug-tolerant state in cancer cell subpopulations","volume":"141","author":"Sharma","year":"2010","journal-title":"Cell"},{"key":"bib164","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.11566","article-title":"Registered
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Report: Diverse somatic mutation patterns and pathway alterations in human
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2735
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Report: COT drives resistance to RAF inhibition through MAP kinase pathway
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2737
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reactivation","volume":"5","author":"Sharma","year":"2016","journal-title":"eLife"},{"key":"bib166","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.45120","article-title":"Replication
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2739
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favors tumor invasion and metastasis","volume":"8","author":"Sheen","year":"2019","journal-title":"eLife"},{"key":"bib167","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.26030","article-title":"Replication
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2741
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a neomorphic enzyme activity converting alpha-ketoglutarate to 2-hydroxyglutarate","volume":"6","author":"Showalter","year":"2017","journal-title":"eLife"},{"key":"bib168","doi-asserted-by":"publisher","first-page":"1359","DOI":"10.1177\/0956797611417632","article-title":"False-positive
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2742
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psychology: undisclosed flexibility in data collection and analysis allows
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evidence of research quality of registered reports compared with the standard
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enzyme activity converting alpha-ketoglutarate to 2-hydroxyglutarate","volume":"17","author":"Ward","year":"2010","journal-title":"Cancer
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FAIR Guiding Principles for scientific data management and stewardship","volume":"3","author":"Wilkinson","year":"2016","journal-title":"Scientific
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V, Mathis KW, Nusser S, Nuzzo R, Prager E, Ramirez FD, Svenson K, Berridge
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B, Brown P, Clayton J, Gordon JA, Lauer M, Wolinetz C. 2021. ACD Working Group
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2800
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on Enhancing Rigor, Transparency, and Translatability in Animal Research.
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