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Items: 1 to 20 of 92

1.

DataMed - an open source discovery index for finding biomedical datasets.

Chen X, Gururaj AE, Ozyurt B, Liu R, Soysal E, Cohen T, Tiryaki F, Li Y, Zong N, Jiang M, Rogith D, Salimi M, Kim HE, Rocca-Serra P, Gonzalez-Beltran A, Farcas C, Johnson T, Margolis R, Alter G, Sansone SA, Fore IM, Ohno-Machado L, Grethe JS, Xu H.

J Am Med Inform Assoc. 2018 Jan 13. doi: 10.1093/jamia/ocx121. [Epub ahead of print]

PMID:
29346583
2.

Data discovery with DATS: exemplar adoptions and lessons learned.

Gonzalez-Beltran AN, Campbell J, Dunn P, Guijarro D, Ionescu S, Kim H, Lyle J, Wiser J, Sansone SA, Rocca-Serra P.

J Am Med Inform Assoc. 2018 Jan 1;25(1):13-16. doi: 10.1093/jamia/ocx119.

PMID:
29228196
3.

The international MAQC Society launches to enhance reproducibility of high-throughput technologies.

Shi L, Kusko R, Wolfinger RD, Haibe-Kains B, Fischer M, Sansone SA, Mason CE, Furlanello C, Jones WD, Ning B, Tong W.

Nat Biotechnol. 2017 Dec 8;35(12):1127-1128. doi: 10.1038/nbt.4029. No abstract available.

PMID:
29220036
4.

The future of metabolomics in ELIXIR.

van Rijswijk M, Beirnaert C, Caron C, Cascante M, Dominguez V, Dunn WB, Ebbels TMD, Giacomoni F, Gonzalez-Beltran A, Hankemeier T, Haug K, Izquierdo-Garcia JL, Jimenez RC, Jourdan F, Kale N, Klapa MI, Kohlbacher O, Koort K, Kultima K, Le Corguillé G, Moreno P, Moschonas NK, Neumann S, O'Donovan C, Reczko M, Rocca-Serra P, Rosato A, Salek RM, Sansone SA, Satagopam V, Schober D, Shimmo R, Spicer RA, Spjuth O, Thévenot EA, Viant MR, Weber RJM, Willighagen EL, Zanetti G, Steinbeck C.

Version 2. F1000Res. 2017 Sep 6 [revised 2017 Jan 1];6. pii: ELIXIR-1649. doi: 10.12688/f1000research.12342.2. eCollection 2017.

5.

ELIXIR-UK role in bioinformatics training at the national level and across ELIXIR.

Larcombe L, Hendricusdottir R, Attwood TK, Bacall F, Beard N, Bellis LJ, Dunn WB, Hancock JM, Nenadic A, Orengo C, Overduin B, Sansone SA, Thurston M, Viant MR, Winder CL, Goble CA, Ponting CP, Rustici G.

F1000Res. 2017 Jun 21;6. pii: ELIXIR-952. doi: 10.12688/f1000research.11837.1. eCollection 2017.

6.

Developing a strategy for computational lab skills training through Software and Data Carpentry: Experiences from the ELIXIR Pilot action.

Pawlik A, van Gelder CWG, Nenadic A, Palagi PM, Korpelainen E, Lijnzaad P, Marek D, Sansone SA, Hancock J, Goble C.

F1000Res. 2017 Jul 3;6. pii: ELIXIR-1040. doi: 10.12688/f1000research.11718.1. eCollection 2017.

7.

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data.

McMurry JA, Juty N, Blomberg N, Burdett T, Conlin T, Conte N, Courtot M, Deck J, Dumontier M, Fellows DK, Gonzalez-Beltran A, Gormanns P, Grethe J, Hastings J, Hériché JK, Hermjakob H, Ison JC, Jimenez RC, Jupp S, Kunze J, Laibe C, Le Novère N, Malone J, Martin MJ, McEntyre JR, Morris C, Muilu J, Müller W, Rocca-Serra P, Sansone SA, Sariyar M, Snoep JL, Soiland-Reyes S, Stanford NJ, Swainston N, Washington N, Williams AR, Wimalaratne SM, Winfree LM, Wolstencroft K, Goble C, Mungall CJ, Haendel MA, Parkinson H.

PLoS Biol. 2017 Jun 29;15(6):e2001414. doi: 10.1371/journal.pbio.2001414. eCollection 2017 Jun.

8.

DATS, the data tag suite to enable discoverability of datasets.

Sansone SA, Gonzalez-Beltran A, Rocca-Serra P, Alter G, Grethe JS, Xu H, Fore IM, Lyle J, Gururaj AE, Chen X, Kim HE, Zong N, Li Y, Liu R, Ozyurt IB, Ohno-Machado L.

Sci Data. 2017 Jun 6;4:170059. doi: 10.1038/sdata.2017.59.

9.

Finding useful data across multiple biomedical data repositories using DataMed.

Ohno-Machado L, Sansone SA, Alter G, Fore I, Grethe J, Xu H, Gonzalez-Beltran A, Rocca-Serra P, Gururaj AE, Bell E, Soysal E, Zong N, Kim HE.

Nat Genet. 2017 May 26;49(6):816-819. doi: 10.1038/ng.3864. No abstract available.

PMID:
28546571
10.

Discovering and linking public omics data sets using the Omics Discovery Index.

Perez-Riverol Y, Bai M, da Veiga Leprevost F, Squizzato S, Park YM, Haug K, Carroll AJ, Spalding D, Paschall J, Wang M, Del-Toro N, Ternent T, Zhang P, Buso N, Bandeira N, Deutsch EW, Campbell DS, Beavis RC, Salek RM, Sarkans U, Petryszak R, Keays M, Fahy E, Sud M, Subramaniam S, Barbera A, Jiménez RC, Nesvizhskii AI, Sansone SA, Steinbeck C, Lopez R, Vizcaíno JA, Ping P, Hermjakob H.

Nat Biotechnol. 2017 May 9;35(5):406-409. doi: 10.1038/nbt.3790. No abstract available.

PMID:
28486464
11.

Measures for interoperability of phenotypic data: minimum information requirements and formatting.

Ćwiek-Kupczyńska H, Altmann T, Arend D, Arnaud E, Chen D, Cornut G, Fiorani F, Frohmberg W, Junker A, Klukas C, Lange M, Mazurek C, Nafissi A, Neveu P, van Oeveren J, Pommier C, Poorter H, Rocca-Serra P, Sansone SA, Scholz U, van Schriek M, Seren Ü, Usadel B, Weise S, Kersey P, Krajewski P.

Plant Methods. 2016 Nov 9;12:44. eCollection 2016.

12.

Selective serotonin reuptake inhibitors for depression in pregnancy.

Susser LC, Sansone SA, Hermann AD.

Am J Obstet Gynecol. 2016 Dec;215(6):722-730. doi: 10.1016/j.ajog.2016.07.011. Epub 2016 Jul 16. Review.

PMID:
27430585
13.

Publishing descriptions of non-public clinical datasets: proposed guidance for researchers, repositories, editors and funding organisations.

Hrynaszkiewicz I, Khodiyar V, Hufton AL, Sansone SA.

Res Integr Peer Rev. 2016 Jun 22;1:6. doi: 10.1186/s41073-016-0015-6. eCollection 2016.

14.

BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences.

McQuilton P, Gonzalez-Beltran A, Rocca-Serra P, Thurston M, Lister A, Maguire E, Sansone SA.

Database (Oxford). 2016 May 17;2016. pii: baw075. doi: 10.1093/database/baw075. Print 2016.

15.

The Ontology for Biomedical Investigations.

Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B, Chibucos MC, Clancy K, Courtot M, Derom D, Dumontier M, Fan L, Fostel J, Fragoso G, Gibson F, Gonzalez-Beltran A, Haendel MA, He Y, Heiskanen M, Hernandez-Boussard T, Jensen M, Lin Y, Lister AL, Lord P, Malone J, Manduchi E, McGee M, Morrison N, Overton JA, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Schober D, Smith B, Soldatova LN, Stoeckert CJ Jr, Taylor CF, Torniai C, Turner JA, Vita R, Whetzel PL, Zheng J.

PLoS One. 2016 Apr 29;11(4):e0154556. doi: 10.1371/journal.pone.0154556. eCollection 2016.

16.

The FAIR Guiding Principles for scientific data management and stewardship.

Wilkinson MD, Dumontier M, Aalbersberg IJ, Appleton G, Axton M, Baak A, Blomberg N, Boiten JW, da Silva Santos LB, Bourne PE, Bouwman J, Brookes AJ, Clark T, Crosas M, Dillo I, Dumon O, Edmunds S, Evelo CT, Finkers R, Gonzalez-Beltran A, Gray AJ, Groth P, Goble C, Grethe JS, Heringa J, 't Hoen PA, Hooft R, Kuhn T, Kok R, Kok J, Lusher SJ, Martone ME, Mons A, Packer AL, Persson B, Rocca-Serra P, Roos M, van Schaik R, Sansone SA, Schultes E, Sengstag T, Slater T, Strawn G, Swertz MA, Thompson M, van der Lei J, van Mulligen E, Velterop J, Waagmeester A, Wittenburg P, Wolstencroft K, Zhao J, Mons B.

Sci Data. 2016 Mar 15;3:160018. doi: 10.1038/sdata.2016.18.

17.

Data standards can boost metabolomics research, and if there is a will, there is a way.

Rocca-Serra P, Salek RM, Arita M, Correa E, Dayalan S, Gonzalez-Beltran A, Ebbels T, Goodacre R, Hastings J, Haug K, Koulman A, Nikolski M, Oresic M, Sansone SA, Schober D, Smith J, Steinbeck C, Viant MR, Neumann S.

Metabolomics. 2016;12:14. doi: 10.1007/s11306-015-0879-3. Epub 2015 Nov 17. Review.

18.

COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access.

Salek RM, Neumann S, Schober D, Hummel J, Billiau K, Kopka J, Correa E, Reijmers T, Rosato A, Tenori L, Turano P, Marin S, Deborde C, Jacob D, Rolin D, Dartigues B, Conesa P, Haug K, Rocca-Serra P, O'Hagan S, Hao J, van Vliet M, Sysi-Aho M, Ludwig C, Bouwman J, Cascante M, Ebbels T, Griffin JL, Moing A, Nikolski M, Oresic M, Sansone SA, Viant MR, Goodacre R, Günther UL, Hankemeier T, Luchinat C, Walther D, Steinbeck C.

Metabolomics. 2015;11(6):1587-1597. Epub 2015 May 26.

19.

From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics.

González-Beltrán A, Li P, Zhao J, Avila-Garcia MS, Roos M, Thompson M, van der Horst E, Kaliyaperumal R, Luo R, Lee TL, Lam TW, Edmunds SC, Sansone SA, Rocca-Serra P.

PLoS One. 2015 Jul 8;10(7):e0127612. doi: 10.1371/journal.pone.0127612. eCollection 2015.

20.

The center for expanded data annotation and retrieval.

Musen MA, Bean CA, Cheung KH, Dumontier M, Durante KA, Gevaert O, Gonzalez-Beltran A, Khatri P, Kleinstein SH, O'Connor MJ, Pouliot Y, Rocca-Serra P, Sansone SA, Wiser JA; CEDAR team.

J Am Med Inform Assoc. 2015 Nov;22(6):1148-52. doi: 10.1093/jamia/ocv048. Epub 2015 Jun 25.

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