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TIGA: Target illumination GWAS analytics
Jeremy J. Yang, Dhouha Grissa, Christophe G. Lambert, Cristian G. Bologa, Stephen L. Mathias, Anna Waller, David J. Wild, Lars Juhl Jensen, Tudor I. Oprea
bioRxiv (2020-11-12) https://www.biorxiv.org/content/10.1101/2020.11.11.378596v1
DOI: 10.1101/2020.11.11.378596
Related links:
Review of version 2 of the following preprint:
Rigor and Transparency Index, a new metric of quality for assessing biological and medical science methods
Joe Menke, Martijn Roelandse, Burak Ozyurt, Maryann Martone, Anita Bandrowski
bioRxiv (2020-01-18) https://doi.org/dkg6
DOI: 10.1101/2020.01.15.908111
The study introduces an automated method called SciScore to detect whether an article's methods section mentions any of 15 categories, such as a consent statement or an organism. These metrics are combined to create a single score for each article called the "Rigor and Transparency Index". The authors applied the method to the PubMed Central Open Access subset with over 1 million articles to identify trends in the level of details provided by method sections.
| metaedge | abbreviation | n_edges | n_connected_source_nodes | n_connected_target_nodes | n_source_wedges | n_target_wedges | n_wedges | n_valid_xswaps | |
|---|---|---|---|---|---|---|---|---|---|
| Anatomy–downregulates–Gene | AdG | 102240 | 36 | 15097 | 173440264 | 493897 | 173934161 | 5052523519 | |
| Anatomy–expresses–Gene | AeG | 526407 | 241 | 18094 | 2290279787 | 10749138 | 2301028925 | 136250872696 | |
| Anatomy–upregulates–Gene | AuG | 97848 | 36 | 15929 | 149352969 | 359661 | 149712630 | 4637353998 | |
| Compound–binds–Gene | CbG | 11571 | 1389 | 1689 | 104024 | 476540 | 580564 | 66357671 | |
| Compound–causes–Side Effect | CcSE | 138944 | 1071 | 5701 | 16998055 | 16764774 | 33762829 | 9618885267 | |
| Compound–downregulates–Gene | CdG | 21102 | 734 | 2880 | 1683615 | 291789 | 1975404 | 220661247 | |
| Compound–palliates–Disease | CpD | 390 | 221 | 50 | 326 | 2857 | 3183 | 72672 | |
| Compound–resembles–Compound | CrC | 12972 | 1281 | 1281 | 120047 | 120047 | 240094 | 83889812 | |
| Compound–treats–Disease | CtD | 755 | 387 | 77 | 1420 | 8070 | 9490 | 275145 |
From In survey, most give thumbs-up to pirated papers by John Travis on 2016-05-06 in Science, question 5 was:
What’s the primary reason you use Sci-Hub or other pirated article repositories?
The possible answers were:
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