Perspectives on automated composition of workflows in the life sciences [version 1; peer review: 2 approved]

Autor: Anna-Lena Lamprecht, Magnus Palmblad, Jon Ison, Veit Schwämmle, Mohammad Sadnan Al Manir, Ilkay Altintas, Christopher J. O. Baker, Ammar Ben Hadj Amor, Salvador Capella-Gutierrez, Paulos Charonyktakis, Michael R. Crusoe, Yolanda Gil, Carole Goble, Timothy J. Griffin, Paul Groth, Hans Ienasescu, Pratik Jagtap, Matúš Kalaš, Vedran Kasalica, Alireza Khanteymoori, Tobias Kuhn, Hailiang Mei, Hervé Ménager, Steffen Möller, Robin A. Richardson, Vincent Robert, Stian Soiland-Reyes, Robert Stevens, Szoke Szaniszlo, Suzan Verberne, Aswin Verhoeven, Katherine Wolstencroft

Publikováno v: F1000Research, Vol 10 (2021)

Scientific data analyses often combine several computational tools in automated pipelines, or workflows. Thousands of such workflows have been used in the life sciences, though their composition has remained a cumbersome manual process due to a lack

Externí odkaz: https://doaj.org/article/e9b280176ab24646b8b7d023b327e100

A Malaria Analytics Framework to Support Evolution and Interoperability of Global Health Surveillance Systems

Autor: Jon Hael Brenas, Mohammad Sadnan Al-Manir, Christopher J. O. Baker, Arash Shaban-Nejad

Publikováno v: IEEE Access, Vol 5, Pp 21605-21619 (2017)

Malaria is a leading cause of death in Africa. Many organizations, NGO's, and government agencies are collaborating to prevent, control, and eliminate malaria. In order to succeed in these shared goals, an integrated, consistent knowledge source to e

Externí odkaz: https://doaj.org/article/2a5439ccdfb84055aed7a48068240b75

Automated Coding of Job Descriptions From a General Population Study: Overview of Existing Tools, Their Application and Comparison

Autor: Wenxin Wan, Calvin B Ge, Melissa C Friesen, Sarah J Locke, Daniel E Russ, Igor Burstyn, Christopher J O Baker, Anil Adisesh, Qing Lan, Nathaniel Rothman, Anke Huss, Martie van Tongeren, Roel Vermeulen, Susan Peters

Objectives Automatic job coding tools were developed to reduce the laborious task of manually assigning job codes based on free-text job descriptions in census and survey data sources, including large occupational health studies. The objective of thi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f639448593f8f32665973ea14f16a631
https://dspace.library.uu.nl/handle/1874/429394

Perspectives on automated composition of workflows in the life sciences

Autor: Robin A. Richardson, Timothy J. Griffin, Hailiang Mei, Jon Ison, Pratik D. Jagtap, A. Amor, Ilkay Altintas, Christopher J. O. Baker, Magnus Palmblad, Szoke Szaniszlo, Tobias Kuhn, Carole Goble, Suzan Verberne, Anna-Lena Lamprecht, Paulos Charonyktakis, Hans Ienasescu, Salvador Capella-Gutierrez, Matúš Kalaš, Michael R. Crusoe, Aswin Verhoeven, Steffen Möller, Katherine Wolstencroft, Yolanda Gil, Vedran Kasalica, Hervé Ménager, Vincent Robert, Stian Soiland-Reyes, Alireza Khanteymoori, Paul Groth, Robert Stevens, Mohammad Sadnan Al Manir, Veit Schwämmle

Publikováno v: F1000Research, 10:897. F1000 Research Ltd.
F1000Research, 10, 1. F1000 Research Ltd.
F1000Research
F1000Research, 2021, 10, pp.897. ⟨10.12688/f1000research.54159.1⟩
Lamprecht, A-L, Palmblad, M, Ison, J, Schwämmle, V S, Sadnan Al Manir, M, Altintas, I, Baker, C J O, Amor, A B H, Capella-Gutierrez, S, Charonyktakis, P, Crusoe, M R, Gil, Y, Goble, C, Griffin, T J, Groth, P, Ienasescu, H, Jagtap, P, Kalaš, M, Kasalica, V, Khanteymoori, A, Kuhn, T, Mei, H, Ménager, H, Möller, S, Richardson, R A, Robert, V, Soiland-Reyes, S, Stevens, R K, Szaniszlo, S, Verberne, S & Verhoeven, A 2021, ' Perspectives on automated composition of workflows in the life sciences ', F1000Research, vol. 10, 897 . https://doi.org/10.12688/f1000research.54159.1
F1000Research, 10
Lamprecht, A L, Palmblad, M, Ison, J, Schwämmle, V, Al Manir, M S, Altintas, I, Baker, C J O, Ben Hadj Amor, A, Capella-Gutierrez, S, Charonyktakis, P, Crusoe, M R, Gil, Y, Goble, C, Griffin, T J, Groth, P, Ienasescu, H, Jagtap, P, Kalaš, M, Kasalica, V, Khanteymoori, A, Kuhn, T, Mei, H, Ménager, H, Möller, S, Richardson, R A, Robert, V, Soiland-Reyes, S, Stevens, R, Szaniszlo, S, Verberne, S, Verhoeven, A & Wolstencroft, K 2021, ' Perspectives on automated composition of workflows in the life sciences ', F1000Research, vol. 10, 897, pp. 1-28 . https://doi.org/10.12688/f1000research.54159.1
F1000Research, 10:897, 1-28. F1000 Research Ltd.
F1000Research, 10. F1000 Research Ltd.
Lamprecht, A-L, Palmblad, M, Ison, J, Schwämmle, V, Al Manir, M S, Altintas, I, Baker, C J O, Ben Hadj Amor, A, Capella-Gutierrez, S, Charonyktakis, P, Crusoe, M R, Gil, Y, Goble, C, Griffin, T J, Groth, P, Ienasescu, H, Jagtap, P, Kalaš, M, Kasalica, V, Khanteymoori, A, Kuhn, T, Mei, H, Ménager, H, Möller, S, Richardson, R A, Robert, V, Soiland-Reyes, S, Stevens, R, Szaniszlo, S, Verberne, S, Verhoeven, A & Wolstencroft, K 2021, ' Perspectives on automated composition of workflows in the life sciences ', F1000Research, vol. 10, 897 . https://doi.org/10.12688/f1000research.54159.1

Scientific data analyses often combine several computational tools in automated pipelines, or workflows. Thousands of such workflows have been used in the life sciences, though their composition has remained a cumbersome manual process due to a lack

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::17f6f7b52a69eeff5cdcf069034bb015
https://doi.org/10.12688/f1000research.54159.1

O-15 Occupational Health: A Multi-Cohort Job Title Cleaning Project by Algorithm

Autor: Christopher J. O. Baker, Mohammad Sadnan Al Manir, Ellen Sweeney, Deobrah Addey, Cheryl Peters, Hicks Jason, Anil Adisesh, Jennifer Vena, Grace Shen Tu, Yunsong Cui

Publikováno v: Oral Presentations.

Introduction Occupational data in prospective cohort studies is often underutilized due to the human and financial resources required to code open-ended text, such as job titles. Recognizing the value of occupational data in health research, as well

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::4bc402b5c4b0f5c4f47e963e0e5519a4
https://doi.org/10.1136/oem-2021-epi.80