| Year |
Citation |
Score |
| 2023 |
Welter D, Rocca-Serra P, Grouès V, Sallam N, Ancien F, Shabani A, Asariardakani S, Alper P, Ghosh S, Burdett T, Sansone SA, Gu W, Satagopam V. The Translational Data Catalog - discoverable biomedical datasets. Scientific Data. 10: 470. PMID 37474618 DOI: 10.1038/s41597-023-02258-0 |
0.318 |
|
| 2023 |
Rocca-Serra P, Gu W, Ioannidis V, Abbassi-Daloii T, Capella-Gutierrez S, Chandramouliswaran I, Splendiani A, Burdett T, Giessmann RT, Henderson D, Batista D, Emam I, Gadiya Y, Giovanni L, Willighagen E, et al. The FAIR Cookbook - the essential resource for and by FAIR doers. Scientific Data. 10: 292. PMID 37208467 DOI: 10.1038/s41597-023-02166-3 |
0.38 |
|
| 2023 |
Welter D, Juty N, Rocca-Serra P, Xu F, Henderson D, Gu W, Strubel J, Giessmann RT, Emam I, Gadiya Y, Abbassi-Daloii T, Alharbi E, Gray AJG, Courtot M, Gribbon P, et al. FAIR in action - a flexible framework to guide FAIRification. Scientific Data. 10: 291. PMID 37208349 DOI: 10.1038/s41597-023-02167-2 |
0.313 |
|
| 2022 |
Charbonneau AL, Brady A, Czajkowski K, Aluvathingal J, Canchi S, Carter R, Chard K, Clarke DJB, Crabtree J, Creasy HH, D'Arcy M, Felix V, Giglio M, Gingrich A, Harris RM, ... ... Rocca-Serra P, et al. Making Common Fund data more findable: catalyzing a data ecosystem. Gigascience. 11. PMID 36409836 DOI: 10.1093/gigascience/giac105 |
0.388 |
|
| 2022 |
Batista D, Gonzalez-Beltran A, Sansone SA, Rocca-Serra P. Machine actionable metadata models. Scientific Data. 9: 592. PMID 36180441 DOI: 10.1038/s41597-022-01707-6 |
0.301 |
|
| 2022 |
Liyanage I, Burdett T, Droesbeke B, Erdos K, Fernandez R, Gray A, Haseeb M, Penim F, Pommier C, Rocca-Serra P, Courtot M, Coppens F. ELIXIR biovalidator for semantic validation of life science metadata. Bioinformatics (Oxford, England). PMID 35380605 DOI: 10.1093/bioinformatics/btac195 |
0.332 |
|
| 2021 |
Johnson D, Batista D, Cochrane K, Davey RP, Etuk A, Gonzalez-Beltran A, Haug K, Izzo M, Larralde M, Lawson TN, Minotto A, Moreno P, Nainala VC, O'Donovan C, Pireddu L, ... ... Rocca-Serra P, et al. ISA API: An open platform for interoperable life science experimental metadata. Gigascience. 10. PMID 34528664 DOI: 10.1093/gigascience/giab060 |
0.32 |
|
| 2020 |
Gu W, Hasan S, Rocca-Serra P, Satagopam VP. Road to effective data curation for translational research. Drug Discovery Today. PMID 33338655 DOI: 10.1016/j.drudis.2020.12.007 |
0.303 |
|
| 2020 |
Gonzalez-Beltran AN, Masuzzo P, Ampe C, Bakker GJ, Besson S, Eibl RH, Friedl P, Gunzer M, Kittisopikul M, Dévédec SEL, Leo S, Moore J, Paran Y, Prilusky J, Rocca-Serra P, et al. Community standards for open cell migration data. Gigascience. 9. PMID 32396199 DOI: 10.1093/Gigascience/Giaa041 |
0.473 |
|
| 2020 |
Papoutsoglou EA, Faria D, Arend D, Arnaud E, Athanasiadis IN, Chaves I, Coppens F, Cornut G, Costa BV, Ćwiek-Kupczyńska H, Droesbeke B, Finkers R, Gruden K, Junker A, King GJ, ... ... Rocca-Serra P, et al. Enabling reusability of plant phenomic datasets with MIAPPE 1.1. The New Phytologist. PMID 32171029 DOI: 10.1111/Nph.16544 |
0.454 |
|
| 2020 |
Ćwiek-Kupczyńska H, Filipiak K, Markiewicz A, Rocca-Serra P, Gonzalez-Beltran AN, Sansone SA, Millet EJ, Eeuwijk Fv, Ławrynowicz A, Krajewski P. Semantic concept schema of the linear mixed model of experimental observations. Scientific Data. 7: 1-13. PMID 32109232 DOI: 10.1038/S41597-020-0409-7 |
0.442 |
|
| 2020 |
Alter G, Gonzalez-Beltran A, Ohno-Machado L, Rocca-Serra P. The Data Tags Suite (DATS) model for discovering data access and use requirements. Gigascience. 9. PMID 32031623 DOI: 10.1093/Gigascience/Giz165 |
0.49 |
|
| 2019 |
Rocca-Serra P, Sansone S. Experiment design driven FAIRification of omics data matrices, an exemplar Scientific Data. 6: 271. PMID 31831744 DOI: 10.1038/S41597-019-0286-0 |
0.492 |
|
| 2019 |
Wilkinson MD, Dumontier M, Sansone SA, Bonino da Silva Santos LO, Prieto M, Batista D, McQuilton P, Kuhn T, Rocca-Serra P, Crosas M, Schultes E. Author Correction: Evaluating FAIR maturity through a scalable, automated, community-governed framework. Scientific Data. 6: 230. PMID 31636272 DOI: 10.1038/S41597-019-0248-6 |
0.338 |
|
| 2019 |
Wilkinson MD, Dumontier M, Sansone SA, Bonino da Silva Santos LO, Prieto M, Batista D, McQuilton P, Kuhn T, Rocca-Serra P, Crosas M, Schultes E. Evaluating FAIR maturity through a scalable, automated, community-governed framework. Scientific Data. 6: 174. PMID 31541130 DOI: 10.1038/S41597-019-0184-5 |
0.402 |
|
| 2019 |
Emam I, Elyasigomari V, Matthews A, Pavlidis S, Rocca-Serra P, Guitton F, Verbeeck D, Grainger L, Borgogni E, Del Giudice G, Saqi M, Houston P, Guo Y. PlatformTM, a standards-based data custodianship platform for translational medicine research. Scientific Data. 6: 149. PMID 31409798 DOI: 10.1038/S41597-019-0156-9 |
0.505 |
|
| 2019 |
Viant MR, Ebbels TMD, Beger RD, Ekman DR, Epps DJT, Kamp H, Leonards PEG, Loizou GD, MacRae JI, van Ravenzwaay B, Rocca-Serra P, Salek RM, Walk T, Weber RJM. Use cases, best practice and reporting standards for metabolomics in regulatory toxicology. Nature Communications. 10: 3041. PMID 31292445 DOI: 10.1038/S41467-019-10900-Y |
0.384 |
|
| 2019 |
Fenner M, Crosas M, Grethe JS, Kennedy D, Hermjakob H, Rocca-Serra P, Durand G, Berjon R, Karcher S, Martone M, Clark T. A data citation roadmap for scholarly data repositories. Scientific Data. 6: 28. PMID 30971690 DOI: 10.1038/S41597-019-0031-8 |
0.476 |
|
| 2019 |
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, ... ... Rocca-Serra P, et al. Addendum: The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data. 6: 6. PMID 30890711 DOI: 10.1038/S41597-019-0009-6 |
0.371 |
|
| 2019 |
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, ... ... Rocca-Serra P, et al. Interoperable and scalable data analysis with microservices: Applications in Metabolomics. Bioinformatics (Oxford, England). PMID 30851093 DOI: 10.1093/Bioinformatics/Btz160 |
0.398 |
|
| 2019 |
Hoffmann N, Rein J, Sachsenberg TT, Hartler J, Haug K, Mayer G, Alka O, Dayalan S, Pearce JTM, Rocca-Serra P, Qi D, Eisenacher M, Perez-Riverol Y, Vizcaíno JA, Salek RM, et al. mzTab-M: a data standard for sharing quantitative results in mass spectrometry metabolomics. Analytical Chemistry. PMID 30688441 DOI: 10.1021/Acs.Analchem.8B04310 |
0.355 |
|
| 2019 |
McQuilton P, Thurston M, Izzo M, Granell R, Batista D, Lister AL, Dauga D, Adekale M, Gonzalez-Beltran A, Rocca-Serra P, Sansone S. FAIRsharing: Mapping the landscape of biocuration – what standards should you use, what kind of data is in each database, which resources are FAIR? F1000research. 8. DOI: 10.7490/F1000Research.1116783.1 |
0.398 |
|
| 2018 |
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, ... ... Rocca-Serra P, et al. PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud. Gigascience. PMID 30535405 DOI: 10.1093/Gigascience/Giy149 |
0.457 |
|
| 2018 |
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, et al. DataMed - an open source discovery index for finding biomedical datasets. Journal of the American Medical Informatics Association : Jamia. PMID 29346583 DOI: 10.1093/Jamia/Ocx121 |
0.438 |
|
| 2018 |
Mahurkar A, Crabtree J, Nadendla S, Gonzalez-Beltran A, Rocca-Serra P, Felix V, Ifeonu O, Giglio M, Kesselman C, Foster I, Sansone S, White O. NIH Data Commons Pilot Phase Consortium (DCPPC) Crosscut Metadata Model: a generalized model to represent genomic datasets in the Commons F1000research. 7. DOI: 10.7490/F1000Research.1116159.1 |
0.337 |
|
| 2018 |
Rocca-Serra P, Johnson D, Weber R, Pireddu L, Roger P, Gonzalez-Beltran A, Izzo M, Piras E, Moreno P, Sansone S. ISAcreate Galaxy tool for prospective data management with ISA format support – application to metabolomics datasets F1000research. 7. DOI: 10.7490/F1000Research.1115757.1 |
0.367 |
|
| 2017 |
Gonzalez-Beltran AN, Campbell J, Dunn P, Guijarro D, Ionescu S, Kim H, Lyle J, Wiser J, Sansone SA, Rocca-Serra P. Data discovery with DATS: exemplar adoptions and lessons learned. Journal of the American Medical Informatics Association : Jamia. PMID 29228196 DOI: 10.1093/Jamia/Ocx119 |
0.502 |
|
| 2017 |
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, ... ... Rocca-Serra P, et al. The future of metabolomics in ELIXIR. F1000research. 6. PMID 29043062 DOI: 10.12688/F1000Research.12342.2 |
0.411 |
|
| 2017 |
Schober D, Jacob D, Wilson M, Cruz JA, Marcu A, Grant JR, Moing A, Deborde C, de Figueiredo LF, Haug K, Rocca-Serra P, Easton JM, Ebbels TMD, Hao J, Ludwig C, et al. nmrML: a community supported open data standard for the description, storage, and exchange of NMR data. Analytical Chemistry. PMID 29035042 DOI: 10.1021/Acs.Analchem.7B02795 |
0.48 |
|
| 2017 |
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, ... ... Rocca-Serra P, et al. Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. Plos Biology. 15: e2001414. PMID 28662064 DOI: 10.1371/Journal.Pbio.2001414 |
0.482 |
|
| 2017 |
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, et al. DATS, the data tag suite to enable discoverability of datasets. Scientific Data. 4: 170059. PMID 28585923 DOI: 10.1038/Sdata.2017.59 |
0.494 |
|
| 2017 |
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. Finding useful data across multiple biomedical data repositories using DataMed. Nature Genetics. 49: 816-819. PMID 28546571 DOI: 10.1038/Ng.3864 |
0.506 |
|
| 2017 |
Larralde M, Lawson TN, Weber RJ, Moreno P, Haug K, Rocca-Serra P, Viant MR, Steinbeck C, Salek RM. mzML2ISA & nmrML2ISA: generating enriched ISA-Tab metadata files from metabolomics XML data. Bioinformatics (Oxford, England). PMID 28402395 DOI: 10.1093/Bioinformatics/Btx169 |
0.434 |
|
| 2016 |
Verspoor K, Oellrich A, Collier N, Groza T, Rocca-Serra P, Soldatova L, Dumontier M, Shah N. Thematic issue of the Second combined Bio-ontologies and Phenotypes Workshop. Journal of Biomedical Semantics. 7: 66. PMID 27955708 DOI: 10.1186/S13326-016-0108-7 |
0.42 |
|
| 2016 |
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, ... ... Rocca-Serra P, et al. Measures for interoperability of phenotypic data: minimum information requirements and formatting. Plant Methods. 12: 44. PMID 27843484 DOI: 10.1186/S13007-016-0144-4 |
0.479 |
|
| 2016 |
McQuilton P, González-Beltrán AN, Rocca-Serra P, Thurston M, Lister AL, Maguire E, Sansone S. BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences Database. 2016. PMID 27189610 DOI: 10.1093/Database/Baw075 |
0.463 |
|
| 2016 |
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, ... ... Rocca-Serra P, et al. The Ontology for Biomedical Investigations. Plos One. 11: e0154556. PMID 27128319 DOI: 10.1371/Journal.Pone.0154556 |
0.454 |
|
| 2016 |
Kale NS, Haug K, Conesa P, Jayseelan K, Moreno P, Rocca-Serra P, Nainala VC, Spicer RA, Williams M, Li X, Salek RM, Griffin JL, Steinbeck C. MetaboLights: An Open-Access Database Repository for Metabolomics Data. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. 53: 14.13.1-14.13.18. PMID 27010336 DOI: 10.1002/0471250953.Bi1413S53 |
0.352 |
|
| 2016 |
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, ... ... Rocca-Serra P, et al. The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data. 3: 160018. PMID 26978244 DOI: 10.1038/Sdata.2016.18 |
0.489 |
|
| 2016 |
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, et al. Data standards can boost metabolomics research, and if there is a will, there is a way. Metabolomics : Official Journal of the Metabolomic Society. 12: 14. PMID 26612985 DOI: 10.1007/S11306-015-0879-3 |
0.52 |
|
| 2016 |
McQuilton P, Gonzalez-Beltran A, Izzo M, Lister A, Maguire E, Rocca-Serra P, Thurston M, Sansone S. BioSharing: Mapping the landscape of standard and database resources in the life sciences F1000research. 5. DOI: 10.7490/F1000Research.1113103.1 |
0.308 |
|
| 2015 |
Soldatova LN, Collier N, Oellrich A, Groza T, Verspoor K, Rocca-Serra P, Dumontier M, Shah NH. Special issue on bio-ontologies and phenotypes. Journal of Biomedical Semantics. 6: 40. PMID 26682035 DOI: 10.1186/S13326-015-0040-2 |
0.35 |
|
| 2015 |
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, ... ... Rocca-Serra P, et al. COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access. Metabolomics : Official Journal of the Metabolomic Society. 11: 1587-1597. PMID 26491418 DOI: 10.1007/S11306-015-0810-Y |
0.515 |
|
| 2015 |
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. From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics. Plos One. 10: e0127612. PMID 26154165 DOI: 10.1371/Journal.Pone.0127612 |
0.442 |
|
| 2015 |
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. The center for expanded data annotation and retrieval. Journal of the American Medical Informatics Association : Jamia. PMID 26112029 DOI: 10.1093/Jamia/Ocv048 |
0.529 |
|
| 2015 |
Davey R, Etuk A, Shaw F, Gonzalez-Beltran A, Rocca-Serra P, Sansone S. COPO: Aiding the journey from data to publication in the plant sciences F1000research. 4. DOI: 10.7490/F1000Research.1110111.1 |
0.309 |
|
| 2015 |
Salek RM, Arita M, Dayalan S, Ebbels T, Jones AR, Neumann S, Rocca-Serra P, Viant MR, Vizcaíno JA. Embedding standards in metabolomics: the Metabolomics Society data standards task group Metabolomics. 11: 782-783. DOI: 10.1007/S11306-015-0821-8 |
0.321 |
|
| 2014 |
González-Beltrán A, Maguire E, Sansone SA, Rocca-Serra P. linkedISA: semantic representation of ISA-Tab experimental metadata. Bmc Bioinformatics. 15: S4. PMID 25472428 DOI: 10.1186/1471-2105-15-S14-S4 |
0.457 |
|
| 2014 |
González-Beltrán A, Neumann S, Maguire E, Sansone SA, Rocca-Serra P. The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again. Bmc Bioinformatics. 15: S11. PMID 24564732 DOI: 10.1186/1471-2105-15-S1-S11 |
0.451 |
|
| 2014 |
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, ... ... Rocca-Serra P, et al. BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. Journal of Biomedical Semantics. 5: 5. PMID 24495517 DOI: 10.1186/2041-1480-5-5 |
0.436 |
|
| 2014 |
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, ... ... Rocca-Serra P, et al. EBI metagenomics--a new resource for the analysis and archiving of metagenomic data. Nucleic Acids Research. 42: D600-6. PMID 24165880 DOI: 10.1093/Nar/Gkt961 |
0.44 |
|
| 2014 |
Soldatova LN, Rocca-Serra P, Dumontier M, Shah NH. Selected papers from the 16th annual Bio-Ontologies Special Interest Group Meeting Journal of Biomedical Semantics. 5. DOI: 10.1186/2041-1480-5-S1-I1 |
0.438 |
|
| 2014 |
Walls RL, Guralnick R, Deck J, Buntzman A, Buttigieg PL, Davies N, Denslow MW, Gallery RE, Parnell JJ, Osumi-Sutherland D, Robbins RJ, Rocca-Serra P, Wieczorek J, Zheng J. Meeting report: Advancing practical applications of biodiversity ontologies Standards in Genomic Sciences. 9. DOI: 10.1186/1944-3277-9-17 |
0.465 |
|
| 2013 |
Maguire E, Rocca-Serra P, Sansone SA, Davies J, Chen M. Visual compression of workflow visualizations with automated detection of macro motifs. Ieee Transactions On Visualization and Computer Graphics. 19: 2576-85. PMID 24051824 DOI: 10.1109/Tvcg.2013.225 |
0.365 |
|
| 2013 |
Salek RM, Haug K, Conesa P, Hastings J, Williams M, Mahendraker T, Maguire E, González-Beltrán AN, Rocca-Serra P, Sansone SA, Steinbeck C. The MetaboLights repository: curation challenges in metabolomics. Database : the Journal of Biological Databases and Curation. 2013: bat029. PMID 23630246 DOI: 10.1093/Database/Bat029 |
0.478 |
|
| 2013 |
Baker NA, Klemm JD, Harper SL, Gaheen S, Heiskanen M, Rocca-Serra P, Sansone SA. Standardizing data. Nature Nanotechnology. 8: 73-4. PMID 23380926 DOI: 10.1038/nnano.2013.12 |
0.342 |
|
| 2013 |
Maguire E, González-Beltrán A, Whetzel PL, Sansone SA, Rocca-Serra P. OntoMaton: a bioportal powered ontology widget for Google Spreadsheets. Bioinformatics (Oxford, England). 29: 525-7. PMID 23267176 DOI: 10.1093/Bioinformatics/Bts718 |
0.374 |
|
| 2013 |
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. MetaboLights--an open-access general-purpose repository for metabolomics studies and associated meta-data. Nucleic Acids Research. 41: D781-6. PMID 23109552 DOI: 10.1093/Nar/Gks1004 |
0.455 |
|
| 2013 |
Gonzalez-Beltran A, Maguire E, Georgiou P, Sansone S, Rocca-Serra P. Bio-GraphIIn: a graph-based, integrative and semantically-enabled repository for life science experimental data Embnet.Journal. 19: 46-50. DOI: 10.14806/Ej.19.B.728 |
0.351 |
|
| 2012 |
Sansone SA, Rocca-Serra P. On the evolving portfolio of community-standards and data sharing policies: turning challenges into new opportunities. Gigascience. 1: 10. PMID 23587326 DOI: 10.1186/2047-217X-1-10 |
0.491 |
|
| 2012 |
Davies N, Meyer C, Gilbert JA, Amaral-Zettler L, Deck J, Bicak M, Rocca-Serra P, Assunta-Sansone S, Willis K, Field D. A call for an international network of genomic observatories (GOs). Gigascience. 1: 5. PMID 23587188 DOI: 10.1186/2047-217X-1-5 |
0.309 |
|
| 2012 |
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. The Metadata Coverage Index (MCI): A standardized metric for quantifying database metadata richness. Standards in Genomic Sciences. 6: 438-47. PMID 23409217 DOI: 10.4056/Sigs.2675953 |
0.399 |
|
| 2012 |
Steinbeck C, Conesa P, Haug K, Mahendraker T, Williams M, Maguire E, Rocca-Serra P, Sansone SA, Salek RM, Griffin JL. MetaboLights: towards a new COSMOS of metabolomics data management. Metabolomics : Official Journal of the Metabolomic Society. 8: 757-760. PMID 23060735 DOI: 10.1007/S11306-012-0462-0 |
0.488 |
|
| 2012 |
Brandizi M, Kurbatova N, Sarkans U, Rocca-Serra P. graph2tab, a library to convert experimental workflow graphs into tabular formats. Bioinformatics (Oxford, England). 28: 1665-7. PMID 22556367 DOI: 10.1093/Bioinformatics/Bts258 |
0.403 |
|
| 2012 |
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, et al. Toward interoperable bioscience data. Nature Genetics. 44: 121-6. PMID 22281772 DOI: 10.1038/Ng.1054 |
0.458 |
|
| 2012 |
González-Beltrán A, Maguire E, Rocca-Serra P, Sansone S. The open source ISA software suite and its international user community: knowledge management of experimental data Embnet.Journal. 18: 35-37. DOI: 10.14806/Ej.18.B.542 |
0.504 |
|
| 2011 |
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, et al. Sharing and archiving nucleic acid structure mapping data. Rna (New York, N.Y.). 17: 1204-12. PMID 21610212 DOI: 10.1261/Rna.2753211 |
0.411 |
|
| 2011 |
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, et al. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nature Biotechnology. 29: 415-20. PMID 21552244 DOI: 10.1038/Nbt.1823 |
0.323 |
|
| 2011 |
Chervitz SA, Deutsch EW, Field D, Parkinson H, Quackenbush J, Rocca-Serra P, Sansone SA, Stoeckert CJ, Taylor CF, Taylor R, Ball CA. Data standards for Omics data: the basis of data sharing and reuse. Methods in Molecular Biology (Clifton, N.J.). 719: 31-69. PMID 21370078 DOI: 10.1007/978-1-61779-027-0_2 |
0.483 |
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| 2011 |
Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, ... ... Rocca-Serra P, et al. Towards BioDBcore: a community-defined information specification for biological databases. Database : the Journal of Biological Databases and Curation. 2011: baq027. PMID 21205783 DOI: 10.1093/Database/Baq027 |
0.445 |
|
| 2011 |
Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, ... ... Rocca-Serra P, et al. Towards BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Research. 39: D7-10. PMID 21097465 DOI: 10.1093/Nar/Gkq1173 |
0.445 |
|
| 2011 |
Rocca-Serra P, Ruttenberg A, O'Connor MJ, Whetzel PL, Schober D, Greenbaum J, Courtot M, Brinkman RR, Sansone SA, Scheuermann R, Peters B. Overcoming the ontology enrichment bottleneck with Quick Term Templates Applied Ontology. 6: 13-22. DOI: 10.3233/Ao-2011-0086 |
0.342 |
|
| 2011 |
Sansone S, Rocca-Serra P, Gaudet P, Field D. Agenda of the “BioSharing workshop – Unifying Bio-Resources Descriptors” Nature Precedings. 6: 1-1. DOI: 10.1038/Npre.2011.6148.1 |
0.464 |
|
| 2011 |
Sansone S, Rocca-Serra P, Field D, Gaudet P. Agenda of the "BioSharing workshop - Bringing catalogues of bio-resource and standards together" Nature Precedings. 6: 1-1. DOI: 10.1038/Npre.2011.6145.1 |
0.331 |
|
| 2010 |
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, ... ... Rocca-Serra P, et al. Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop. Standards in Genomic Sciences. 3: 259-66. PMID 21304730 DOI: 10.4056/Sigs.147362 |
0.419 |
|
| 2010 |
Field D, Sansone S, Delong EF, Sterk P, Friedberg I, Gaudet P, Lewis S, Kottmann R, Hirschman L, Garrity G, Cochrane G, Wooley J, Meyer F, Hunter S, White O, ... ... Rocca-Serra P, et al. Meeting Report: BioSharing at ISMB 2010. Standards in Genomic Sciences. 3: 254-8. PMID 21304729 DOI: 10.4056/Sigs/1403501 |
0.43 |
|
| 2010 |
van Ommen B, Bouwman J, Dragsted LO, Drevon CA, Elliott R, de Groot P, Kaput J, Mathers JC, Müller M, Pepping F, Saito J, Scalbert A, Radonjic M, Rocca-Serra P, Travis A, et al. Challenges of molecular nutrition research 6: the nutritional phenotype database to store, share and evaluate nutritional systems biology studies. Genes & Nutrition. 5: 189-203. PMID 21052526 DOI: 10.1007/S12263-010-0167-9 |
0.413 |
|
| 2010 |
Rocca-Serra P, Brandizi M, Maguire E, Sklyar N, Taylor C, Begley K, Field D, Harris S, Hide W, Hofmann O, Neumann S, Sterk P, Tong W, Sansone SA. ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level. Bioinformatics (Oxford, England). 26: 2354-6. PMID 20679334 DOI: 10.1093/Bioinformatics/Btq415 |
0.414 |
|
| 2010 |
Brinkman RR, Courtot M, Derom D, Fostel JM, He Y, Lord P, Malone J, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Soldatova LN, Stoeckert CJ, Turner JA, et al. Modeling biomedical experimental processes with OBI. Journal of Biomedical Semantics. 1: S7. PMID 20626927 DOI: 10.1186/2041-1480-1-S1-S7 |
0.447 |
|
| 2009 |
Sansone SA, Rocca-Serra P, Field D, Taylor CF, Tong W, Brandizi M, Maguire E, Sklyar N. Towards interoperable reporting standards for omics data: hopes and hurdles. Summit On Translational Bioinformatics. 2009: 112-5. PMID 21347181 |
0.337 |
|
| 2009 |
Field D, Sansone SA, Collis A, Booth T, Dukes P, Gregurick SK, Kennedy K, Kolar P, Kolker E, Maxon M, Millard S, Mugabushaka AM, Perrin N, Remacle JE, Remington K, ... Rocca-Serra P, et al. Megascience. 'Omics data sharing. Science (New York, N.Y.). 326: 234-6. PMID 19815759 DOI: 10.1126/Science.1180598 |
0.411 |
|
| 2009 |
Harttig U, Travis AJ, Rocca-Serra P, Renkema M, van Ommen B, Boeing H. Owner controlled data exchange in nutrigenomic collaborations: the NuGO information network. Genes & Nutrition. 4: 113-22. PMID 19408032 DOI: 10.1007/S12263-009-0123-8 |
0.435 |
|
| 2009 |
Schober D, Smith B, Lewis SE, Kusnierczyk W, Lomax J, Mungall C, Taylor CF, Rocca-Serra P, Sansone SA. Survey-based naming conventions for use in OBO Foundry ontology development. Bmc Bioinformatics. 10: 125. PMID 19397794 DOI: 10.1186/1471-2105-10-125 |
0.422 |
|
| 2009 |
Beltrame L, Rizzetto L, Paola R, Rocca-Serra P, Gambineri L, Battaglia C, Cavalieri D. Using pathway signatures as means of identifying similarities among microarray experiments. Plos One. 4: e4128. PMID 19125200 DOI: 10.1371/Journal.Pone.0004128 |
0.383 |
|
| 2009 |
Parkinson H, Kapushesky M, Kolesnikov N, Rustici G, Shojatalab M, Abeygunawardena N, Berube H, Dylag M, Emam I, Farne A, Holloway E, Lukk M, Malone J, Mani R, Pilicheva E, ... ... Rocca-Serra P, et al. ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Research. 37: D868-72. PMID 19015125 DOI: 10.1093/Nar/Gkn889 |
0.417 |
|
| 2009 |
Peters B, Ruttenberg A, Greenbaum J, Courtot M, Brinkman R, Whetzel P, Schober D, Sansone SA, Scheuerman R, Rocca-Serra P. Overcoming the Ontology Enrichment Bottleneck with Quick Term Templates Nature Precedings. 4: 1-1. DOI: 10.1038/Npre.2009.3970.1 |
0.342 |
|
| 2009 |
Sansone S, Rocca-Serra P. Standards and infrastructure for managing experimental metadata Nature Precedings. 4: 1-1. DOI: 10.1038/Npre.2009.3144.1 |
0.336 |
|
| 2008 |
Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz PA, Bogue M, Booth T, Brazma A, Brinkman RR, Michael Clark A, Deutsch EW, Fiehn O, ... ... Rocca-Serra P, et al. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nature Biotechnology. 26: 889-96. PMID 18688244 DOI: 10.1038/Nbt.1411 |
0.315 |
|
| 2008 |
Sansone SA, Rocca-Serra P, Brandizi M, Brazma A, Field D, Fostel J, Garrow AG, Gilbert J, Goodsaid F, Hardy N, Jones P, Lister A, Miller M, Morrison N, Rayner T, et al. The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?". Omics : a Journal of Integrative Biology. 12: 143-9. PMID 18447634 DOI: 10.1089/Omi.2008.0019 |
0.488 |
|
| 2007 |
Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, et al. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nature Biotechnology. 25: 1251-5. PMID 17989687 DOI: 10.1038/Nbt1346 |
0.473 |
|
| 2007 |
Griffin JL, Nicholls AW, Daykin CA, Heald S, Keun HC, Schuppe-Koistinen I, Griffiths JR, Cheng LL, Rocca-Serra P, Rubtsov DV, Robertson D. Standard reporting requirements for biological samples in metabolomics experiments: Mammalian/in vivo experiments Metabolomics. 3: 179-188. DOI: 10.1007/S11306-007-0077-Z |
0.4 |
|
| 2006 |
Rayner TF, Rocca-Serra P, Spellman PT, Causton HC, Farne A, Holloway E, Irizarry RA, Liu J, Maier DS, Miller M, Petersen K, Quackenbush J, Sherlock G, Stoeckert CJ, White J, et al. A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. Bmc Bioinformatics. 7: 489. PMID 17087822 DOI: 10.1186/1471-2105-7-489 |
0.48 |
|
| 2006 |
Whetzel PL, Brinkman RR, Causton HC, Fan L, Field D, Fostel J, Fragoso G, Gray T, Heiskanen M, Hernandez-Boussard T, Morrison N, Parkinson H, Rocca-Serra P, Sansone SA, Schober D, et al. Development of FuGO: an ontology for functional genomics investigations. Omics : a Journal of Integrative Biology. 10: 199-204. PMID 16901226 DOI: 10.1089/Omi.2006.10.199 |
0.438 |
|
| 2006 |
Morrison N, Wood AJ, Hancock D, Shah S, Hakes L, Gray T, Tiwari B, Kille P, Cossins A, Hegarty M, Allen MJ, Wilson WH, Olive P, Last K, Kramer C, ... ... Rocca-Serra P, et al. Annotation of environmental OMICS data: application to the transcriptomics domain. Omics : a Journal of Integrative Biology. 10: 172-8. PMID 16901223 DOI: 10.1089/Omi.2006.10.172 |
0.454 |
|
| 2006 |
Sansone SA, Rocca-Serra P, Tong W, Fostel J, Morrison N, Jones AR. A strategy capitalizing on synergies: the Reporting Structure for Biological Investigation (RSBI) working group. Omics : a Journal of Integrative Biology. 10: 164-71. PMID 16901222 DOI: 10.1089/Omi.2006.10.164 |
0.313 |
|
| 2006 |
Rocca-Serra P, Elliott RM. Data storage: bringing us a step closer to data sharing? The British Journal of Nutrition. 95: 1237-9. PMID 16768851 DOI: 10.1079/Bjn20061747 |
0.442 |
|
| 2006 |
Castro AG, Rocca-Serra P, Stevens R, Taylor C, Nashar K, Ragan MA, Sansone SA. The use of concept maps during knowledge elicitation in ontology development processes--the nutrigenomics use case. Bmc Bioinformatics. 7: 267. PMID 16725019 DOI: 10.1186/1471-2105-7-267 |
0.375 |
|
| 2006 |
Whetzel PL, Parkinson H, Causton HC, Fan L, Fostel J, Fragoso G, Game L, Heiskanen M, Morrison N, Rocca-Serra P, Sansone SA, Taylor C, White J, Stoeckert CJ. The MGED Ontology: a resource for semantics-based description of microarray experiments. Bioinformatics (Oxford, England). 22: 866-73. PMID 16428806 DOI: 10.1093/Bioinformatics/Btl005 |
0.512 |
|
| 2006 |
Stoeckert C, Ball C, Brazma A, Brinkman R, Causton H, Fan L, Fostel J, Fragoso G, Heiskanen M, Holstege F, Morrison N, Parkinson H, Quackenbush J, Rocca-Serra P, Sansone SA, et al. Wrestling with SUMO and bio-ontologies. Nature Biotechnology. 24: 21-2; author reply 2. PMID 16404382 DOI: 10.1038/Nbt0106-21A |
0.368 |
|
| 2005 |
Fostel J, Choi D, Zwickl C, Morrison N, Rashid A, Hasan A, Bao W, Richard A, Tong W, Bushel PR, Brown R, Bruno M, Cunningham ML, Dix D, Eastin W, ... ... Rocca-Serra P, et al. Chemical effects in biological systems--data dictionary (CEBS-DD): a compendium of terms for the capture and integration of biological study design description, conventional phenotypes, and 'omics data. Toxicological Sciences : An Official Journal of the Society of Toxicology. 88: 585-601. PMID 16150882 DOI: 10.1093/Toxsci/Kfi315 |
0.446 |
|
| 2005 |
Garosi P, De Filippo C, van Erk M, Rocca-Serra P, Sansone SA, Elliott R. Defining best practice for microarray analyses in nutrigenomic studies. The British Journal of Nutrition. 93: 425-32. PMID 15946403 DOI: 10.1079/Bjn20041385 |
0.361 |
|
| 2005 |
Parkinson H, Sarkans U, Shojatalab M, Abeygunawardena N, Contrino S, Coulson R, Farne A, Lara GG, Holloway E, Kapushesky M, Lilja P, Mukherjee G, Oezcimen A, Rayner T, Rocca-Serra P, et al. ArrayExpress--a public repository for microarray gene expression data at the EBI. Nucleic Acids Research. 33: D553-5. PMID 15608260 DOI: 10.1093/Nar/Gki056 |
0.49 |
|
| 2005 |
Sarkans U, Parkinson H, Lara GG, Oezcimen A, Sharma A, Abeygunawardena N, Contrino S, Holloway E, Rocca-Serra P, Mukherjee G, Shojatalab M, Kapushesky M, Sansone SA, Farne A, Rayner T, et al. The ArrayExpress gene expression database: a software engineering and implementation perspective. Bioinformatics (Oxford, England). 21: 1495-501. PMID 15564302 DOI: 10.1093/Bioinformatics/Bti157 |
0.452 |
|
| 2004 |
Sansone SA, Morrison N, Rocca-Serra P, Fostel J. Standardization Initiatives in the (eco)toxicogenomics domain: a review. Comparative and Functional Genomics. 5: 633-41. PMID 18629184 DOI: 10.1002/Cfg.447 |
0.47 |
|
| 2004 |
Kasprzyk A, Keefe D, Smedley D, London D, Spooner W, Melsopp C, Hammond M, Rocca-Serra P, Cox T, Birney E. EnsMart: a generic system for fast and flexible access to biological data. Genome Research. 14: 160-9. PMID 14707178 DOI: 10.1101/Gr.1645104 |
0.466 |
|
| 2004 |
Sansone SA, Morrison N, Rocca-Serra P, Fostel J. Standardization initiatives in the (eco)toxicogenomics domain: a review: Conference Papers Comparative and Functional Genomics. 5: 633-641. DOI: 10.1002/Cfg.V5:8 |
0.405 |
|
| 2003 |
Rocca-Serra P, Brazma A, Parkinson H, Sarkans U, Shojatalab M, Contrino S, Vilo J, Abeygunawardena N, Mukherjee G, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Sansone SA. ArrayExpress: a public database of gene expression data at EBI. Comptes Rendus Biologies. 326: 1075-8. PMID 14744115 DOI: 10.1016/J.Crvi.2003.09.026 |
0.497 |
|
| 2003 |
Brazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J, Abeygunawardena N, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Rocca-Serra P, Sansone SA. ArrayExpress--a public repository for microarray gene expression data at the EBI. Nucleic Acids Research. 31: 68-71. PMID 12519949 DOI: 10.1093/nar/gkg091 |
0.368 |
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