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Items: 31

1.

Addendum: The FAIR Guiding Principles for scientific data management and stewardship.

Wilkinson MD, Dumontier M, Jan Aalbersberg I, 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 AJG, Groth P, Goble C, Grethe JS, Heringa J, Hoen PAC', 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, Jan Velterop, Waagmeester A, Wittenburg P, Wolstencroft K, Zhao J, Mons B.

Sci Data. 2019 Mar 19;6(1):6. doi: 10.1038/s41597-019-0009-6. No abstract available.

2.

Interoperable and scalable data analysis with microservices: Applications in Metabolomics.

Emami Khoonsari P, Moreno P, Bergmann S, Burman J, Capuccini M, Carone M, Cascante M, de Atauri P, Foguet C, Gonzalez-Beltran A, Hankemeier T, Haug K, He S, Herman S, Johnson D, Kale N, Larsson A, Neumann S, Peters K, Pireddu L, Rocca-Serra P, Roger P, Rueedi R, Ruttkies C, Sadawi N, Salek RM, Sansone SA, Schober D, Selivanov V, Thévenot EA, van Vliet M, Zanetti G, Steinbeck C, Kultima K, Spjuth O.

Bioinformatics. 2019 Mar 9. pii: btz160. doi: 10.1093/bioinformatics/btz160. [Epub ahead of print]

PMID:
30851093
3.

PhenoMeNal: processing and analysis of metabolomics data in the cloud.

Peters K, Bradbury J, Bergmann S, Capuccini M, Cascante M, de Atauri P, Ebbels TMD, Foguet C, Glen R, Gonzalez-Beltran A, Günther UL, Handakas E, Hankemeier T, Haug K, Herman S, Holub P, Izzo M, Jacob D, Johnson D, Jourdan F, Kale N, Karaman I, Khalili B, Emami Khonsari P, Kultima K, Lampa S, Larsson A, Ludwig C, Moreno P, Neumann S, Novella JA, O'Donovan C, Pearce JTM, Peluso A, Piras ME, Pireddu L, Reed MAC, Rocca-Serra P, Roger P, Rosato A, Rueedi R, Ruttkies C, Sadawi N, Salek RM, Sansone SA, Selivanov V, Spjuth O, Schober D, Thévenot EA, Tomasoni M, van Rijswijk M, van Vliet M, Viant MR, Weber RJM, Zanetti G, Steinbeck C.

Gigascience. 2019 Feb 1;8(2). pii: giy149. doi: 10.1093/gigascience/giy149.

4.

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
5.

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
6.

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.

7.

Four simple recommendations to encourage best practices in research software.

Jiménez RC, Kuzak M, Alhamdoosh M, Barker M, Batut B, Borg M, Capella-Gutierrez S, Chue Hong N, Cook M, Corpas M, Flannery M, Garcia L, Gelpí JL, Gladman S, Goble C, González Ferreiro M, Gonzalez-Beltran A, Griffin PC, Grüning B, Hagberg J, Holub P, Hooft R, Ison J, Katz DS, Leskošek B, López Gómez F, Oliveira LJ, Mellor D, Mosbergen R, Mulder N, Perez-Riverol Y, Pergl R, Pichler H, Pope B, Sanz F, Schneider MV, Stodden V, Suchecki R, Svobodová Vařeková R, Talvik HA, Todorov I, Treloar A, Tyagi S, van Gompel M, Vaughan D, Via A, Wang X, Watson-Haigh NS, Crouch S.

F1000Res. 2017 Jun 13;6. pii: ELIXIR-876. doi: 10.12688/f1000research.11407.1. eCollection 2017.

8.

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.

9.

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.

10.

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
11.

The health care and life sciences community profile for dataset descriptions.

Dumontier M, Gray AJG, Marshall MS, Alexiev V, Ansell P, Bader G, Baran J, Bolleman JT, Callahan A, Cruz-Toledo J, Gaudet P, Gombocz EA, Gonzalez-Beltran AN, Groth P, Haendel M, Ito M, Jupp S, Juty N, Katayama T, Kobayashi N, Krishnaswami K, Laibe C, Le Novère N, Lin S, Malone J, Miller M, Mungall CJ, Rietveld L, Wimalaratne SM, Yamaguchi A.

PeerJ. 2016 Aug 16;4:e2331. doi: 10.7717/peerj.2331. eCollection 2016.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach.

Rocca-Serra P, Walls R, Parnell J, Gallery R, Zheng J, Sansone SA, Gonzalez-Beltran A.

Database (Oxford). 2015 Jan 28;2015. pii: bau132. doi: 10.1093/database/bau132. Print 2015.

19.

linkedISA: semantic representation of ISA-Tab experimental metadata.

González-Beltrán A, Maguire E, Sansone SA, Rocca-Serra P.

BMC Bioinformatics. 2014;15 Suppl 14:S4. doi: 10.1186/1471-2105-15-S14-S4. Epub 2014 Nov 27.

20.

The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again.

González-Beltrán A, Neumann S, Maguire E, Sansone SA, Rocca-Serra P.

BMC Bioinformatics. 2014;15 Suppl 1:S11. doi: 10.1186/1471-2105-15-S1-S11. Epub 2014 Jan 10.

21.

The Stem Cell Commons: an exemplar for data integration in the biomedical domain driven by the ISA framework.

Ho Sui S, Merrill E, Gehlenborg N, Haseley P, Sytchev I, Park R, Rocca-Serra P, Corlosquet S, Gonzalez-Beltran A, Maguire E, Hofmann O, Park P, Das S, Sansone SA, Hide W.

AMIA Jt Summits Transl Sci Proc. 2013 Mar 18;2013:70. eCollection 2013.

PMID:
24303302
22.

EBI metagenomics--a new resource for the analysis and archiving of metagenomic data.

Hunter S, Corbett M, Denise H, Fraser M, Gonzalez-Beltran A, Hunter C, Jones P, Leinonen R, McAnulla C, Maguire E, Maslen J, Mitchell A, Nuka G, Oisel A, Pesseat S, Radhakrishnan R, Rocca-Serra P, Scheremetjew M, Sterk P, Vaughan D, Cochrane G, Field D, Sansone SA.

Nucleic Acids Res. 2014 Jan;42(Database issue):D600-6. doi: 10.1093/nar/gkt961. Epub 2013 Oct 27.

23.

The MetaboLights repository: curation challenges in metabolomics.

Salek RM, Haug K, Conesa P, Hastings J, Williams M, Mahendraker T, Maguire E, González-Beltrán AN, Rocca-Serra P, Sansone SA, Steinbeck C.

Database (Oxford). 2013 Apr 29;2013:bat029. doi: 10.1093/database/bat029. Print 2013.

24.

OntoMaton: a bioportal powered ontology widget for Google Spreadsheets.

Maguire E, González-Beltrán A, Whetzel PL, Sansone SA, Rocca-Serra P.

Bioinformatics. 2013 Feb 15;29(4):525-7. doi: 10.1093/bioinformatics/bts718. Epub 2012 Dec 24.

25.

MetaboLights--an open-access general-purpose repository for metabolomics studies and associated meta-data.

Haug K, Salek RM, Conesa P, Hastings J, de Matos P, Rijnbeek M, Mahendraker T, Williams M, Neumann S, Rocca-Serra P, Maguire E, González-Beltrán A, Sansone SA, Griffin JL, Steinbeck C.

Nucleic Acids Res. 2013 Jan;41(Database issue):D781-6. doi: 10.1093/nar/gks1004. Epub 2012 Oct 29.

26.

Federated ontology-based queries over cancer data.

González-Beltrán A, Tagger B, Finkelstein A.

BMC Bioinformatics. 2012 Jan 25;13 Suppl 1:S9. doi: 10.1186/1471-2105-13-S1-S9.

27.

Guidelines for information about therapy experiments: a proposal on best practice for recording experimental data on cancer therapy.

González-Beltrán AN, Yong MY, Dancey G, Begent R.

BMC Res Notes. 2012 Jan 6;5:10. doi: 10.1186/1756-0500-5-10.

28.

Establishing a knowledge trail from molecular experiments to clinical trials.

Yong MY, González-Beltrán A, Begent R.

N Biotechnol. 2011 Sep;28(5):464-80. doi: 10.1016/j.nbt.2011.03.016. Epub 2011 Apr 5. Review.

PMID:
21473938
29.

Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop.

Kettner C, Field D, Sansone SA, Taylor C, Aerts J, Binns N, Blake A, Britten CM, de Marco A, Fostel J, Gaudet P, González-Beltrán A, Hardy N, Hellemans J, Hermjakob H, Juty N, Leebens-Mack J, Maguire E, Neumann S, Orchard S, Parkinson H, Piel W, Ranganathan S, Rocca-Serra P, Santarsiero A, Shotton D, Sterk P, Untergasser A, Whetzel PL.

Stand Genomic Sci. 2010 Dec 25;3(3):259-66. doi: 10.4056/sigs.147362.

30.

[Risk factors associated with preeclampsia: case-control study].

Morgan-Ortiz F, Calderón-Lara SA, Martínez-Félix JI, González-Beltrán A, Quevedo-Castro E.

Ginecol Obstet Mex. 2010 Mar;78(3):153-9. Spanish.

PMID:
20939219
31.

Semantic web data warehousing for caGrid.

McCusker JP, Phillips JA, González Beltrán A, Finkelstein A, Krauthammer M.

BMC Bioinformatics. 2009 Oct 1;10 Suppl 10:S2. doi: 10.1186/1471-2105-10-S10-S2.

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