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Showing 1 to 12 of 13 entries
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Modeling biomedical experimental processes with OBI.

Journal of biomedical semantics

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, Zheng J.
PMID: 20626927
J Biomed Semantics. 2010 Jun 22;1:S7. doi: 10.1186/2041-1480-1-S1-S7.

BACKGROUND: Experimental descriptions are typically stored as free text without using standardized terminology, creating challenges in comparison, reproduction and analysis. These difficulties impose limitations on data exchange and information retrieval.RESULTS: The Ontology for Biomedical Investigations (OBI), developed as a...

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Brinkman RR, Courtot M, Derom D, et al. Modeling biomedical experimental processes with OBI. J Biomed Semantics. 2010;1:S7doi: 10.1186/2041-1480-1-S1-S7.
Brinkman, R. R., Courtot, M., Derom, D., Fostel, J. M., He, Y., Lord, P., Malone, J., Parkinson, H., Peters, B., Rocca-Serra, P., Ruttenberg, A., Sansone, S. A., Soldatova, L. N., Stoeckert, C. J., Turner, J. A., Zheng, J. (2010). Modeling biomedical experimental processes with OBI. Journal of biomedical semantics, 1S7. https://doi.org/10.1186/2041-1480-1-S1-S7
Brinkman, Ryan R, et al. "Modeling biomedical experimental processes with OBI." Journal of biomedical semantics vol. 1 (2010): S7. doi: https://doi.org/10.1186/2041-1480-1-S1-S7
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, Zheng J. Modeling biomedical experimental processes with OBI. J Biomed Semantics. 2010 Jun 22;1:S7. doi: 10.1186/2041-1480-1-S1-S7. PMID: 20626927; PMCID: PMC2903726.
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Towards BioDBcore: a community-defined information specification for biological databases.

Nucleic acids research

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, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Mizrachi IK, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C.
PMID: 21097465
Nucleic Acids Res. 2011 Jan;39:D7-10. doi: 10.1093/nar/gkq1173. Epub 2010 Nov 18.

The present article proposes the adoption of a community-defined, uniform, generic description of the core attributes of biological databases, BioDBCore. The goals of these attributes are to provide a general overview of the database landscape, to encourage consistency and...

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Gaudet P, Bairoch A, Field D, et al. Towards BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Res. 2010;39:D7-10doi: 10.1093/nar/gkq1173.
Gaudet, P., Bairoch, A., Field, D., Sansone, S. A., Taylor, C., Attwood, T. K., Bateman, A., Blake, J. A., Bult, C. J., Cherry, J. M., Chisholm, R. L., Cochrane, G., Cook, C. E., Eppig, J. T., Galperin, M. Y., Gentleman, R., Goble, C. A., Gojobori, T., Hancock, J. M., Howe, D. G., Imanishi, T., Kelso, J., Landsman, D., Lewis, S. E., Mizrachi, I. K., Orchard, S., Ouellette, B. F., Ranganathan, S., Richardson, L., Rocca-Serra, P., Schofield, P. N., Smedley, D., Southan, C., Tan, T. W., Tatusova, T., Whetzel, P. L., White, O., Yamasaki, C. (2011). Towards BioDBcore: a community-defined information specification for biological databases. Nucleic acids research, 39D7-10. https://doi.org/10.1093/nar/gkq1173
Gaudet, Pascale, et al. "Towards BioDBcore: a community-defined information specification for biological databases." Nucleic acids research vol. 39 (2011): D7-10. doi: https://doi.org/10.1093/nar/gkq1173
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, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Mizrachi IK, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C. Towards BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Res. 2011 Jan;39:D7-10. doi: 10.1093/nar/gkq1173. Epub 2010 Nov 18. PMID: 21097465; PMCID: PMC3013734.
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DataMed - an open source discovery index for finding biomedical datasets.

Journal of the American Medical Informatics Association : JAMIA

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.
PMID: 29346583
J Am Med Inform Assoc. 2018 Mar 01;25(3):300-308. doi: 10.1093/jamia/ocx121.

OBJECTIVE: Finding relevant datasets is important for promoting data reuse in the biomedical domain, but it is challenging given the volume and complexity of biomedical data. Here we describe the development of an open source biomedical data discovery system...

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Chen X, Gururaj AE, Ozyurt B, et al. DataMed - an open source discovery index for finding biomedical datasets. J Am Med Inform Assoc. 2018;25(3):300-308doi: 10.1093/jamia/ocx121.
Chen, X., Gururaj, A. E., Ozyurt, B., Liu, R., Soysal, E., Cohen, T., Tiryaki, F., Li, Y., Zong, N., Jiang, M., Rogith, D., Salimi, M., Kim, H. E., Rocca-Serra, P., Gonzalez-Beltran, A., Farcas, C., Johnson, T., Margolis, R., Alter, G., Sansone, S. A., Fore, I. M., Ohno-Machado, L., Grethe, J. S., & Xu, H. (2018). DataMed - an open source discovery index for finding biomedical datasets. Journal of the American Medical Informatics Association : JAMIA, 25(3), 300-308. https://doi.org/10.1093/jamia/ocx121
Chen, Xiaoling, et al. "DataMed - an open source discovery index for finding biomedical datasets." Journal of the American Medical Informatics Association : JAMIA vol. 25,3 (2018): 300-308. doi: https://doi.org/10.1093/jamia/ocx121
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. DataMed - an open source discovery index for finding biomedical datasets. J Am Med Inform Assoc. 2018 Mar 01;25(3):300-308. doi: 10.1093/jamia/ocx121. PMID: 29346583; PMCID: PMC7378878.
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Consent insufficient for data release-Response.

Science (New York, N.Y.)

Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I.
PMID: 31048484
Science. 2019 May 03;364(6439):446. doi: 10.1126/science.aax7509.

No abstract available.

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Amann RI, Baichoo S, Blencowe BJ, et al. Consent insufficient for data release-Response. Science. 2019;364(6439):446doi: 10.1126/science.aax7509.
Amann, R. I., Baichoo, S., Blencowe, B. J., Bork, P., Borodovsky, M., Brooksbank, C., Chain, P. S. G., Colwell, R. R., Daffonchio, D. G., Danchin, A., de Lorenzo, V., Dorrestein, P. C., Finn, R. D., Fraser, C. M., Gilbert, J. A., Hallam, S. J., Hugenholtz, P., Ioannidis, J. P. A., Jansson, J. K., Kim, J. F., Klenk, H. P., Klotz, M. G., Knight, R., Konstantinidis, K. T., Kyrpides, N. C., Mason, C. E., McHardy, A. C., Meyer, F., Ouzounis, C. A., Patrinos, A. A. N., Podar, M., Pollard, K. S., Ravel, J., Muñoz, A. R., Roberts, R. J., Rosselló-Móra, R., Sansone, S. A., Schloss, P. D., Schriml, L. M., Setubal, J. C., Sorek, R., Stevens, R. L., Tiedje, J. M., Turjanski, A., Tyson, G. W., Ussery, D. W., Weinstock, G. M., White, O., Whitman, W. B., & Xenarios, I. (2019). Consent insufficient for data release-Response. Science (New York, N.Y.), 364(6439), 446. https://doi.org/10.1126/science.aax7509
Amann, Rudolf I, et al. "Consent insufficient for data release-Response." Science (New York, N.Y.) vol. 364,6439 (2019): 446. doi: https://doi.org/10.1126/science.aax7509
Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I. Consent insufficient for data release-Response. Science. 2019 May 03;364(6439):446. doi: 10.1126/science.aax7509. PMID: 31048484.
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Semantic concept schema of the linear mixed model of experimental observations.

Scientific data

Ćwiek-Kupczyńska H, Filipiak K, Markiewicz A, Rocca-Serra P, Gonzalez-Beltran AN, Sansone SA, Millet EJ, van Eeuwijk F, Ławrynowicz A, Krajewski P.
PMID: 32109232
Sci Data. 2020 Feb 27;7(1):70. doi: 10.1038/s41597-020-0409-7.

In the information age, smart data modelling and data management can be carried out to address the wealth of data produced in scientific experiments. In this paper, we propose a semantic model for the statistical analysis of datasets by...

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Ćwiek-Kupczyńska H, Filipiak K, Markiewicz A, et al. Semantic concept schema of the linear mixed model of experimental observations. Sci Data. 2020;7(1):70doi: 10.1038/s41597-020-0409-7.
Ćwiek-Kupczyńska, H., Filipiak, K., Markiewicz, A., Rocca-Serra, P., Gonzalez-Beltran, A. N., Sansone, S. A., Millet, E. J., van Eeuwijk, F., Ławrynowicz, A., & Krajewski, P. (2020). Semantic concept schema of the linear mixed model of experimental observations. Scientific data, 7(1), 70. https://doi.org/10.1038/s41597-020-0409-7
Ćwiek-Kupczyńska, Hanna, et al. "Semantic concept schema of the linear mixed model of experimental observations." Scientific data vol. 7,1 (2020): 70. doi: https://doi.org/10.1038/s41597-020-0409-7
Ćwiek-Kupczyńska H, Filipiak K, Markiewicz A, Rocca-Serra P, Gonzalez-Beltran AN, Sansone SA, Millet EJ, van Eeuwijk F, Ławrynowicz A, Krajewski P. Semantic concept schema of the linear mixed model of experimental observations. Sci Data. 2020 Feb 27;7(1):70. doi: 10.1038/s41597-020-0409-7. PMID: 32109232; PMCID: PMC7046786.
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Road to effective data curation for translational research.

Drug discovery today

Gu W, Hasan S, Rocca-Serra P, Satagopam VP.
PMID: 33338655
Drug Discov Today. 2021 Mar;26(3):626-630. doi: 10.1016/j.drudis.2020.12.007. Epub 2020 Dec 15.

Translational research today is data-intensive and requires multi-stakeholder collaborations to generate and pool data together for integrated analysis. This leads to the challenge of harmonization of data from different sources with different formats and standards, which is often overlooked...

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Gu W, Hasan S, Rocca-Serra P, et al. Road to effective data curation for translational research. Drug Discov Today. 2020;26(3):626-630doi: 10.1016/j.drudis.2020.12.007.
Gu, W., Hasan, S., Rocca-Serra, P., & Satagopam, V. P. (2021). Road to effective data curation for translational research. Drug discovery today, 26(3), 626-630. https://doi.org/10.1016/j.drudis.2020.12.007
Gu, Wei, et al. "Road to effective data curation for translational research." Drug discovery today vol. 26,3 (2021): 626-630. doi: https://doi.org/10.1016/j.drudis.2020.12.007
Gu W, Hasan S, Rocca-Serra P, Satagopam VP. Road to effective data curation for translational research. Drug Discov Today. 2021 Mar;26(3):626-630. doi: 10.1016/j.drudis.2020.12.007. Epub 2020 Dec 15. PMID: 33338655.
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Metabolomics: The Stethoscope for the Twenty-First Century.

Medical principles and practice : international journal of the Kuwait University, Health Science Centre

Ashrafian H, Sounderajah V, Glen R, Ebbels T, Blaise BJ, Kalra D, Kultima K, Spjuth O, Tenori L, Salek RM, Kale N, Haug K, Schober D, Rocca-Serra P, O'Donovan C, Steinbeck C, Cano I, de Atauri P, Cascante M.
PMID: 33271569
Med Princ Pract. 2021;30(4):301-310. doi: 10.1159/000513545. Epub 2020 Dec 03.

Metabolomics encompasses the systematic identification and quantification of all metabolic products in the human body. This field could provide clinicians with novel sets of diagnostic biomarkers for disease states in addition to quantifying treatment response to medications at an...

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Ashrafian H, Sounderajah V, Glen R, et al. Metabolomics: The Stethoscope for the Twenty-First Century. Med Princ Pract. 2020;30(4):301-310doi: 10.1159/000513545.
Ashrafian, H., Sounderajah, V., Glen, R., Ebbels, T., Blaise, B. J., Kalra, D., Kultima, K., Spjuth, O., Tenori, L., Salek, R. M., Kale, N., Haug, K., Schober, D., Rocca-Serra, P., O'Donovan, C., Steinbeck, C., Cano, I., de Atauri, P., & Cascante, M. (2021). Metabolomics: The Stethoscope for the Twenty-First Century. Medical principles and practice : international journal of the Kuwait University, Health Science Centre, 30(4), 301-310. https://doi.org/10.1159/000513545
Ashrafian, Hutan, et al. "Metabolomics: The Stethoscope for the Twenty-First Century." Medical principles and practice : international journal of the Kuwait University, Health Science Centre vol. 30,4 (2021): 301-310. doi: https://doi.org/10.1159/000513545
Ashrafian H, Sounderajah V, Glen R, Ebbels T, Blaise BJ, Kalra D, Kultima K, Spjuth O, Tenori L, Salek RM, Kale N, Haug K, Schober D, Rocca-Serra P, O'Donovan C, Steinbeck C, Cano I, de Atauri P, Cascante M. Metabolomics: The Stethoscope for the Twenty-First Century. Med Princ Pract. 2021;30(4):301-310. doi: 10.1159/000513545. Epub 2020 Dec 03. PMID: 33271569; PMCID: PMC8436726.
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Road to effective data curation for translational research.

Drug discovery today

Gu W, Hasan S, Rocca-Serra P, Satagopam VP.
PMID: 33338655
Drug Discov Today. 2021 Mar;26(3):626-630. doi: 10.1016/j.drudis.2020.12.007. Epub 2020 Dec 15.

Translational research today is data-intensive and requires multi-stakeholder collaborations to generate and pool data together for integrated analysis. This leads to the challenge of harmonization of data from different sources with different formats and standards, which is often overlooked...

Cite
Gu W, Hasan S, Rocca-Serra P, et al. Road to effective data curation for translational research. Drug Discov Today. 2020;26(3):626-630doi: 10.1016/j.drudis.2020.12.007.
Gu, W., Hasan, S., Rocca-Serra, P., & Satagopam, V. P. (2021). Road to effective data curation for translational research. Drug discovery today, 26(3), 626-630. https://doi.org/10.1016/j.drudis.2020.12.007
Gu, Wei, et al. "Road to effective data curation for translational research." Drug discovery today vol. 26,3 (2021): 626-630. doi: https://doi.org/10.1016/j.drudis.2020.12.007
Gu W, Hasan S, Rocca-Serra P, Satagopam VP. Road to effective data curation for translational research. Drug Discov Today. 2021 Mar;26(3):626-630. doi: 10.1016/j.drudis.2020.12.007. Epub 2020 Dec 15. PMID: 33338655.
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Towards BioDBcore: a community-defined information specification for biological databases.

Database : the journal of biological databases and curation

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, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Karsch Mizrachi I, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C.
PMID: 21205783
Database (Oxford). 2011 Jan 04;2011:baq027. doi: 10.1093/database/baq027. Print 2011.

The present article proposes the adoption of a community-defined, uniform, generic description of the core attributes of biological databases, BioDBCore. The goals of these attributes are to provide a general overview of the database landscape, to encourage consistency and...

Cite
Gaudet P, Bairoch A, Field D, et al. Towards BioDBcore: a community-defined information specification for biological databases. Database (Oxford). 2011;2011:baq027doi: 10.1093/database/baq027.
Gaudet, P., Bairoch, A., Field, D., Sansone, S. A., Taylor, C., Attwood, T. K., Bateman, A., Blake, J. A., Bult, C. J., Cherry, J. M., Chisholm, R. L., Cochrane, G., Cook, C. E., Eppig, J. T., Galperin, M. Y., Gentleman, R., Goble, C. A., Gojobori, T., Hancock, J. M., Howe, D. G., Imanishi, T., Kelso, J., Landsman, D., Lewis, S. E., Karsch Mizrachi, I., Orchard, S., Ouellette, B. F., Ranganathan, S., Richardson, L., Rocca-Serra, P., Schofield, P. N., Smedley, D., Southan, C., Tan, T. W., Tatusova, T., Whetzel, P. L., White, O., Yamasaki, C. (2011). Towards BioDBcore: a community-defined information specification for biological databases. Database : the journal of biological databases and curation, 2011baq027. https://doi.org/10.1093/database/baq027
Gaudet, Pascale, et al. "Towards BioDBcore: a community-defined information specification for biological databases." Database : the journal of biological databases and curation vol. 2011 (2011): baq027. doi: https://doi.org/10.1093/database/baq027
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, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Karsch Mizrachi I, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C. Towards BioDBcore: a community-defined information specification for biological databases. Database (Oxford). 2011 Jan 04;2011:baq027. doi: 10.1093/database/baq027. Print 2011. PMID: 21205783; PMCID: PMC3017395.
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MetaboLights: towards a new COSMOS of metabolomics data management.

Metabolomics : Official journal of the Metabolomic Society

Steinbeck C, Conesa P, Haug K, Mahendraker T, Williams M, Maguire E, Rocca-Serra P, Sansone SA, Salek RM, Griffin JL.
PMID: 23060735
Metabolomics. 2012 Oct;8(5):757-760. doi: 10.1007/s11306-012-0462-0. Epub 2012 Sep 25.

Exciting funding initiatives are emerging in Europe and the US for metabolomics data production, storage, dissemination and analysis. This is based on a rich ecosystem of resources around the world, which has been build during the past ten years,...

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Steinbeck C, Conesa P, Haug K, et al. MetaboLights: towards a new COSMOS of metabolomics data management. Metabolomics. 2012;8(5):757-760doi: 10.1007/s11306-012-0462-0.
Steinbeck, C., Conesa, P., Haug, K., Mahendraker, T., Williams, M., Maguire, E., Rocca-Serra, P., Sansone, S. A., Salek, R. M., & Griffin, J. L. (2012). MetaboLights: towards a new COSMOS of metabolomics data management. Metabolomics : Official journal of the Metabolomic Society, 8(5), 757-760. https://doi.org/10.1007/s11306-012-0462-0
Steinbeck, Christoph, et al. "MetaboLights: towards a new COSMOS of metabolomics data management." Metabolomics : Official journal of the Metabolomic Society vol. 8,5 (2012): 757-760. doi: https://doi.org/10.1007/s11306-012-0462-0
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. 2012 Oct;8(5):757-760. doi: 10.1007/s11306-012-0462-0. Epub 2012 Sep 25. PMID: 23060735; PMCID: PMC3465651.
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The Data Tags Suite (DATS) model for discovering data access and use requirements.

GigaScience

Alter G, Gonzalez-Beltran A, Ohno-Machado L, Rocca-Serra P.
PMID: 32031623
Gigascience. 2020 Feb 01;9(2). doi: 10.1093/gigascience/giz165.

BACKGROUND: Data reuse is often controlled to protect the privacy of subjects and patients. Data discovery tools need ways to inform researchers about restrictions on data access and re-use.RESULTS: We present elements in the Data Tags Suite (DATS) metadata...

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Alter G, Gonzalez-Beltran A, Ohno-Machado L, et al. The Data Tags Suite (DATS) model for discovering data access and use requirements. Gigascience. 2020;9(2)doi: 10.1093/gigascience/giz165.
Alter, G., Gonzalez-Beltran, A., Ohno-Machado, L., & Rocca-Serra, P. (2020). The Data Tags Suite (DATS) model for discovering data access and use requirements. GigaScience, 9(2), . https://doi.org/10.1093/gigascience/giz165
Alter, George, et al. "The Data Tags Suite (DATS) model for discovering data access and use requirements." GigaScience vol. 9,2 (2020). doi: https://doi.org/10.1093/gigascience/giz165
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. 2020 Feb 01;9(2). doi: 10.1093/gigascience/giz165. PMID: 32031623; PMCID: PMC7006671.
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Interoperable and scalable data analysis with microservices: applications in metabolomics.

Bioinformatics (Oxford, England)

Emami Khoonsari P, Moreno P, Bergmann S, Burman J, Capuccini M, Carone M, Cascante M, de Atauri P, Foguet C, Gonzalez-Beltran AN, 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.
PMID: 30851093
Bioinformatics. 2019 Oct 01;35(19):3752-3760. doi: 10.1093/bioinformatics/btz160.

MOTIVATION: Developing a robust and performant data analysis workflow that integrates all necessary components whilst still being able to scale over multiple compute nodes is a challenging task. We introduce a generic method based on the microservice architecture, where...

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Emami Khoonsari P, Moreno P, Bergmann S, et al. Interoperable and scalable data analysis with microservices: applications in metabolomics. Bioinformatics. 2019;35(19):3752-3760doi: 10.1093/bioinformatics/btz160.
Emami Khoonsari, P., Moreno, P., Bergmann, S., Burman, J., Capuccini, M., Carone, M., Cascante, M., de Atauri, P., Foguet, C., Gonzalez-Beltran, A. N., 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, R. M., Sansone, S. A., Schober, D., Selivanov, V., Thévenot, E. A., van Vliet, M., Zanetti, G., Steinbeck, C., Kultima, K., & Spjuth, O. (2019). Interoperable and scalable data analysis with microservices: applications in metabolomics. Bioinformatics (Oxford, England), 35(19), 3752-3760. https://doi.org/10.1093/bioinformatics/btz160
Emami Khoonsari, Payam, et al. "Interoperable and scalable data analysis with microservices: applications in metabolomics." Bioinformatics (Oxford, England) vol. 35,19 (2019): 3752-3760. doi: https://doi.org/10.1093/bioinformatics/btz160
Emami Khoonsari P, Moreno P, Bergmann S, Burman J, Capuccini M, Carone M, Cascante M, de Atauri P, Foguet C, Gonzalez-Beltran AN, 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. Interoperable and scalable data analysis with microservices: applications in metabolomics. Bioinformatics. 2019 Oct 01;35(19):3752-3760. doi: 10.1093/bioinformatics/btz160. PMID: 30851093; PMCID: PMC6761976.
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