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CD2H Resource Discovery Core
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Resources of possible relevance #12

Closed kristiholmes closed 4 years ago

kristiholmes commented 4 years ago

Possible items of biomedical relevance (not an exhaustive search)

kristiholmes commented 4 years ago

1: Stanford NJ, Scharm M, Dobson PD, Golebiewski M, Hucka M, Kothamachu VB, Nickerson D, Owen S, Pahle J, Wittig U, Waltemath D, Goble C, Mendes P, Snoep J. Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices. Methods Mol Biol. 2019;2049:285-314. doi: 10.1007/978-1-4939-9736-7_17. PubMed PMID: 31602618.

2: Barba A, Dominguez S, Cobas C, Martinsen DP, Romain C, Rzepa HS, Seoane F. Workflows Allowing Creation of Journal Article Supporting Information and Findable, Accessible, Interoperable, and Reusable (FAIR)-Enabled Publication of Spectroscopic Data. ACS Omega. 2019 Feb 14;4(2):3280-3286. doi: 10.1021/acsomega.8b03005. eCollection 2019 Feb 28. PubMed PMID: 31459544; PubMed Central PMCID: PMC6648158.

3: Jansen P, van den Berg L, van Overveld P, Boiten JW. Research Data Stewardship for Healthcare Professionals. 2018 Dec 22. In: Kubben P, Dumontier M, Dekker A, editors. Fundamentals of Clinical Data Science [Internet]. Cham (CH): Springer;

  1. Chapter 4. Available from http://www.ncbi.nlm.nih.gov/books/NBK543528/ PubMed PMID: 31314246.

4: Vesteghem C, Brøndum RF, Sønderkær M, Sommer M, Schmitz A, Bødker JS, Dybkær K, El-Galaly TC, Bøgsted M. Implementing the FAIR Data Principles in precision oncology: review of supporting initiatives. Brief Bioinform. 2019 Jun 29. pii: bbz044. doi: 10.1093/bib/bbz044. [Epub ahead of print] PubMed PMID: 31263868.

5: Adler-Milstein J, Nong P, Friedman CP. Preparing healthcare delivery organizations for managing computable knowledge. Learn Health Syst. 2018 Oct 10;3(2):e10070. doi: 10.1002/lrh2.10070. eCollection 2019 Apr. PubMed PMID: 31245601; PubMed Central PMCID: PMC6508827.

6: Chevrier R, Foufi V, Gaudet-Blavignac C, Robert A, Lovis C. Use and Understanding of Anonymization and De-Identification in the Biomedical Literature: Scoping Review. J Med Internet Res. 2019 May 31;21(5):e13484. doi: 10.2196/13484. Review. PubMed PMID: 31152528; PubMed Central PMCID: PMC6658290.

7: Madduri R, Chard K, D'Arcy M, Jung SC, Rodriguez A, Sulakhe D, Deutsch E, Funk C, Heavner B, Richards M, Shannon P, Glusman G, Price N, Kesselman C, Foster I. Reproducible big data science: A case study in continuous FAIRness. PLoS One. 2019 Apr 11;14(4):e0213013. doi: 10.1371/journal.pone.0213013. eCollection 2019. PubMed PMID: 30973881; PubMed Central PMCID: PMC6459504.

8: Williams R, Brown B, Kontopantelis E, van Staa T, Peek N. Term sets: A transparent and reproducible representation of clinical code sets. PLoS One. 2019 Feb 14;14(2):e0212291. doi: 10.1371/journal.pone.0212291. eCollection 2019. PubMed PMID: 30763407; PubMed Central PMCID: PMC6375602.

9: Caufield JH, Zhou Y, Garlid AO, Setty SP, Liem DA, Cao Q, Lee JM, Murali S, Spendlove S, Wang W, Zhang L, Sun Y, Bui A, Hermjakob H, Watson KE, Ping P. A reference set of curated biomedical data and metadata from clinical case reports. Sci Data. 2018 Nov 20;5:180258. doi: 10.1038/sdata.2018.258. PubMed PMID: 30457569; PubMed Central PMCID: PMC6244181.

10: Navale V, McAuliffe M. Long-term preservation of biomedical research data. F1000Res. 2018 Aug 29;7:1353. doi: 10.12688/f1000research.16015.1. eCollection

  1. PubMed PMID: 30356367; PubMed Central PMCID: PMC6144948.

11: Reiser L, Harper L, Freeling M, Han B, Luan S. FAIR: A Call to Make Published Data More Findable, Accessible, Interoperable, and Reusable. Mol Plant. 2018 Sep 10;11(9):1105-1108. doi: 10.1016/j.molp.2018.07.005. Epub 2018 Aug 1. PubMed PMID: 30076986.

12: Stathias V, Koleti A, Vidović D, Cooper DJ, Jagodnik KM, Terryn R, Forlin M, Chung C, Torre D, Ayad N, Medvedovic M, Ma'ayan A, Pillai A, Schürer SC. Sustainable data and metadata management at the BD2K-LINCS Data Coordination and Integration Center. Sci Data. 2018 Jun 19;5:180117. doi: 10.1038/sdata.2018.117. PubMed PMID: 29917015; PubMed Central PMCID: PMC6007090.

13: Corpas M, Kovalevskaya NV, McMurray A, Nielsen FGG. A FAIR guide for data providers to maximise sharing of human genomic data. PLoS Comput Biol. 2018 Mar 15;14(3):e1005873. doi: 10.1371/journal.pcbi.1005873. eCollection 2018 Mar. PubMed PMID: 29543799; PubMed Central PMCID: PMC5854239.

14: Holub P, Kohlmayer F, Prasser F, Mayrhofer MT, Schlünder I, Martin GM, Casati S, Koumakis L, Wutte A, Kozera Ł, Strapagiel D, Anton G, Zanetti G, Sezerman OU, Mendy M, Valík D, Lavitrano M, Dagher G, Zatloukal K, van Ommen GB, Litton JE. Enhancing Reuse of Data and Biological Material in Medical Research: From FAIR to FAIR-Health. Biopreserv Biobank. 2018 Apr;16(2):97-105. doi: 10.1089/bio.2017.0110. Epub 2018 Jan 23. Review. PubMed PMID: 29359962; PubMed Central PMCID: PMC5906729.

15: Greenbaum D, Rozowsky J, Stodden V, Gerstein M. Structuring supplemental materials in support of reproducibility. Genome Biol. 2017 Apr 5;18(1):64. doi: 10.1186/s13059-017-1205-3. PubMed PMID: 28381262; PubMed Central PMCID: PMC5382465.

16: Matthews PC. Fairness in scientific publishing. Version 2. F1000Res. 2016 Dec 5 [revised 2017 Jan 1];5:2816. doi: 10.12688/f1000research.10318.2. eCollection

  1. PubMed PMID: 28163900; PubMed Central PMCID: PMC5247776.

17: Wolstencroft K, Krebs O, Snoep JL, Stanford NJ, Bacall F, Golebiewski M, Kuzyakiv R, Nguyen Q, Owen S, Soiland-Reyes S, Straszewski J, van Niekerk DD, Williams AR, Malmström L, Rinn B, Müller W, Goble C. FAIRDOMHub: a repository and collaboration environment for sharing systems biology research. Nucleic Acids Res. 2017 Jan 4;45(D1):D404-D407. doi: 10.1093/nar/gkw1032. Epub 2016 Nov 28. PubMed PMID: 27899646; PubMed Central PMCID: PMC5210530.

18: Rodríguez-Iglesias A, Rodríguez-González A, Irvine AG, Sesma A, Urban M, Hammond-Kosack KE, Wilkinson MD. Publishing FAIR Data: An Exemplar Methodology Utilizing PHI-Base. Front Plant Sci. 2016 May 12;7:641. doi: 10.3389/fpls.2016.00641. eCollection 2016. PubMed PMID: 27433158; PubMed Central PMCID: PMC4922217.

19: McQuilton P, Gonzalez-Beltran A, Rocca-Serra P, Thurston M, Lister A, Maguire E, Sansone SA. BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences. Database (Oxford). 2016 May 17;2016. pii: baw075. doi: 10.1093/database/baw075. Print 2016. PubMed PMID: 27189610; PubMed Central PMCID: PMC4869797.

20: Clarke DJB, Wang L, Jones A, Wojciechowicz ML, Torre D, Jagodnik KM, Jenkins SL, McQuilton P, Flamholz Z, Silverstein MC, Schilder BM, Robasky K, Castillo C, Idaszak R, Ahalt SC, Williams J, Schurer S, Cooper DJ, de Miranda Azevedo R, Klenk JA, Haendel MA, Nedzel J, Avillach P, Shimoyama ME, Harris RM, Gamble M, Poten R, Charbonneau AL, Larkin J, Brown CT, Bonazzi VR, Dumontier MJ, Sansone SA, Ma'ayan A. FAIRshake: Toolkit to Evaluate the FAIRness of Research Digital Resources. Cell Syst. 2019 Oct 10. pii: S2405-4712(19)30345-X. doi: 10.1016/j.cels.2019.09.011. [Epub ahead of print] PubMed PMID: 31677972.

kristiholmes commented 4 years ago

no action item