Format
Items per page
Sort by

Send to:

Choose Destination

Results: 1 to 20 of 59

1.

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.

2.

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.

3.

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.

4.

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.

Katayama T, Wilkinson MD, Aoki-Kinoshita KF, Kawashima S, Yamamoto Y, Yamaguchi A, Okamoto S, Kawano S, Kim JD, Wang Y, Wu H, Kano Y, Ono H, Bono H, Kocbek S, Aerts J, Akune Y, Antezana E, Arakawa K, Aranda B, Baran J, Bolleman J, Bonnal RJ, Buttigieg PL, Campbell MP, Chen YA, Chiba H, Cock PJ, Cohen KB, Constantin A, Duck G, Dumontier M, Fujisawa T, Fujiwara T, Goto N, Hoehndorf R, Igarashi Y, Itaya H, Ito M, Iwasaki W, Kalaš M, Katoda T, Kim T, Kokubu A, Komiyama Y, Kotera M, Laibe C, Lapp H, Lütteke T, Marshall MS, Mori T, Mori H, Morita M, Murakami K, Nakao M, Narimatsu H, Nishide H, Nishimura Y, Nystrom-Persson J, Ogishima S, Okamura Y, Okuda S, Oshita K, Packer NH, Prins P, Ranzinger R, Rocca-Serra P, Sansone S, Sawaki H, Shin SH, Splendiani A, Strozzi F, Tadaka S, Toukach P, Uchiyama I, Umezaki M, Vos R, Whetzel PL, Yamada I, Yamasaki C, Yamashita R, York WS, Zmasek CM, Kawamoto S, Takagi T.

J Biomed Semantics. 2014 Feb 5;5(1):5. doi: 10.1186/2041-1480-5-5.

5.

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
6.

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.

7.

Visual compression of workflow visualizations with automated detection of macro motifs.

Maguire E, Rocca-Serra P, Sansone SA, Davies J, Chen M.

IEEE Trans Vis Comput Graph. 2013 Dec;19(12):2576-85. doi: 10.1109/TVCG.2013.225.

PMID:
24051824
8.

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.

9.

The Metadata Coverage Index (MCI): A standardized metric for quantifying database metadata richness.

Liolios K, Schriml L, Hirschman L, Pagani I, Nosrat B, Sterk P, White O, Rocca-Serra P, Sansone SA, Taylor C, Kyrpides NC, Field D.

Stand Genomic Sci. 2012 Jul 30;6(3):438-47. doi: 10.4056/sigs.2675953. Epub 2012 Jul 20.

10.

Standardizing data.

Baker NA, Klemm JD, Harper SL, Gaheen S, Heiskanen M, Rocca-Serra P, Sansone SA.

Nat Nanotechnol. 2013 Feb;8(2):73-4. doi: 10.1038/nnano.2013.12. No abstract available.

11.

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.

12.

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.

13.

MetaboLights: towards a new COSMOS of metabolomics data management.

Steinbeck C, Conesa P, Haug K, Mahendraker T, Williams M, Maguire E, Rocca-Serra P, Sansone SA, Salek RM, Griffin JL.

Metabolomics. 2012 Oct;8(5):757-760. Epub 2012 Sep 25.

14.

graph2tab, a library to convert experimental workflow graphs into tabular formats.

Brandizi M, Kurbatova N, Sarkans U, Rocca-Serra P.

Bioinformatics. 2012 Jun 15;28(12):1665-7. doi: 10.1093/bioinformatics/bts258. Epub 2012 May 3.

15.

Translating standards into practice - one Semantic Web API for Gene Expression.

Deus HF, Prud'hommeaux E, Miller M, Zhao J, Malone J, Adamusiak T, McCusker J, Das S, Rocca Serra P, Fox R, Marshall MS.

J Biomed Inform. 2012 Aug;45(4):782-94. doi: 10.1016/j.jbi.2012.03.002. Epub 2012 Mar 24.

16.

Toward interoperable bioscience data.

Sansone SA, Rocca-Serra P, Field D, Maguire E, Taylor C, Hofmann O, Fang H, Neumann S, Tong W, Amaral-Zettler L, Begley K, Booth T, Bougueleret L, Burns G, Chapman B, Clark T, Coleman LA, Copeland J, Das S, de Daruvar A, de Matos P, Dix I, Edmunds S, Evelo CT, Forster MJ, Gaudet P, Gilbert J, Goble C, Griffin JL, Jacob D, Kleinjans J, Harland L, Haug K, Hermjakob H, Ho Sui SJ, Laederach A, Liang S, Marshall S, McGrath A, Merrill E, Reilly D, Roux M, Shamu CE, Shang CA, Steinbeck C, Trefethen A, Williams-Jones B, Wolstencroft K, Xenarios I, Hide W.

Nat Genet. 2012 Jan 27;44(2):121-6. doi: 10.1038/ng.1054.

17.

On the evolving portfolio of community-standards and data sharing policies: turning challenges into new opportunities.

Sansone SA, Rocca-Serra P.

Gigascience. 2012 Jul 12;1(1):10. doi: 10.1186/2047-217X-1-10.

18.

A call for an international network of genomic observatories (GOs).

Davies N, Meyer C, Gilbert JA, Amaral-Zettler L, Deck J, Bicak M, Rocca-Serra P, Assunta-Sansone S, Willis K, Field D.

Gigascience. 2012 Jul 12;1(1):5. doi: 10.1186/2047-217X-1-5.

19.

Sharing and archiving nucleic acid structure mapping data.

Rocca-Serra P, Bellaousov S, Birmingham A, Chen C, Cordero P, Das R, Davis-Neulander L, Duncan CD, Halvorsen M, Knight R, Leontis NB, Mathews DH, Ritz J, Stombaugh J, Weeks KM, Zirbel CL, Laederach A.

RNA. 2011 Jul;17(7):1204-12. doi: 10.1261/rna.2753211. Epub 2011 May 24.

20.

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.

Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, Sterk P, Arumugam M, Bailey M, Baumgartner L, Birren BW, Blaser MJ, Bonazzi V, Booth T, Bork P, Bushman FD, Buttigieg PL, Chain PS, Charlson E, Costello EK, Huot-Creasy H, Dawyndt P, DeSantis T, Fierer N, Fuhrman JA, Gallery RE, Gevers D, Gibbs RA, San Gil I, Gonzalez A, Gordon JI, Guralnick R, Hankeln W, Highlander S, Hugenholtz P, Jansson J, Kau AL, Kelley ST, Kennedy J, Knights D, Koren O, Kuczynski J, Kyrpides N, Larsen R, Lauber CL, Legg T, Ley RE, Lozupone CA, Ludwig W, Lyons D, Maguire E, Methé BA, Meyer F, Muegge B, Nakielny S, Nelson KE, Nemergut D, Neufeld JD, Newbold LK, Oliver AE, Pace NR, Palanisamy G, Peplies J, Petrosino J, Proctor L, Pruesse E, Quast C, Raes J, Ratnasingham S, Ravel J, Relman DA, Assunta-Sansone S, Schloss PD, Schriml L, Sinha R, Smith MI, Sodergren E, Spo A, Stombaugh J, Tiedje JM, Ward DV, Weinstock GM, Wendel D, White O, Whiteley A, Wilke A, Wortman JR, Yatsunenko T, Glöckner FO.

Nat Biotechnol. 2011 May;29(5):415-20. doi: 10.1038/nbt.1823.

Format
Items per page
Sort by

Send to:

Choose Destination

Supplemental Content

Loading ...
Write to the Help Desk