FAIR Bioinformatics computation and data management: FAIRDOM and the Norwegian Digital Life initiative

Natalie Stanford, Finn Bacall, Fatemeh Zamanzad Ghavidel, Martin Golebiewski, Inge Jonassen, Rune Kleppe, Olga Krebs, Hadas Leonov, Stuart Owen, Kjell Peterson, Maja Rey, Stian Soiland-Reyes, Kidane Tekle, Andreas Weiderman, Alan Williams, Ulrike Wittig, Katherine Wolstencroft, Anders Goksøyr, Jacky Snoep, Jon Olav VikWolfgang Müller, Carole Goble

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Abstract

The FAIR data principles state that data should be Findable (and citable), Accessible (with appropriate caveats for sensitive data), Interoperable (able to be exchanged or combined, typically as a result of using community standards) and Reusable (can be reused later or reproduced from a publication). The FAIRDOM Research Infrastructure (http://fair-dom.org) has been fostering software and community activities to support the adoption of FAIR data management practices since 2008. The SEEK software component of FAIRDOM provides a web-based yellow pages (of programmes, projects, institutions and people), a catalogue of their research assets (data, models, SOPs, samples, organisms, publications etc), and the metadata associated with them. A common, related view of the assets is organised using ISA (Investigation, Study, Assay/Analysis).

The Norwegian e-Infrastructure for Life Sciences (NeLS) is developed and supported by ELIXIR-Norway as a national infrastructure for bioinformatics, providing storage, data sharing and analysis tools (using Galaxy) and connecting to the national data storage platform, NIRD, for long term storage.

FAIRDOM, DLN and ELIXIR-Norway teamed up to support projects in the Digital Life initiative with their FAIR data management. The SEEK and NeLS platforms were adapted to provide functional linking for storing and sharing data sets from NeLS to SEEK. Linking up bioinformatics compute capabilities, with long-term storage and publication of the data.
Original languageEnglish
Number of pages4
Publication statusAccepted/In press - 4 Sep 2018
EventNETTAB 2018 Network Tools and Applications in Biology : Building a FAIR Bioinformatics environment - Genova, Genova, Italy
Duration: 22 Oct 201826 Oct 2018
Conference number: 2018
http://www.igst.it/nettab/2018/

Workshop

WorkshopNETTAB 2018 Network Tools and Applications in Biology
Abbreviated titleNETTAB
Country/TerritoryItaly
CityGenova
Period22/10/1826/10/18
Internet address

Keywords

  • Bioinformatics
  • FAIR
  • Data management
  • Research Infrastructure
  • Publication
  • system biology
  • life science
  • digital life initiative
  • digital life norway
  • digital salmon
  • elixir norway

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  • FAIRDOMHub: a repository and collaboration environment for sharing systems biology research

    Wolstencroft, K., Krebs, O., Snoep, J., Stanford, N. J., Bacall, F., Golebiewski, M., Kuzyakiv, R., Nguyen, Q., Owen, S., Soiland-Reyes, S., Straszewski, J., van Niekerk, D. D., Williams, A., Malmström, L., Rinn, B., Müller, W. & Goble, C., 2016, In: Nucleic acids research. 45, D1, p. D404-D407 4 p.

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    Open Access
  • The FAIR Guiding Principles for scientific data management and stewardship

    Wilkinson, M. D., Dumontier, M., Aalbersberg, IJ. J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J. W., da Silva Santos, L. B., Bourne, P. E., Bouwman, J., Brookes, A. J., Clark, T., Crosas, M., Dillo, I., Dumon, O., Edmunds, S., Evelo, C. T., Finkers, R., Gonzalez-Beltran, A., & 33 othersGray, A. J. G., Groth, P., Goble, C., Grethe, J. S., Heringa, J., 't Hoen, P. A. C., Hooft, R., Kuhn, T., Kok, R., Kok, J., Lusher, S. J., Martone, M. E., Mons, A., Packer, A. L., Persson, B., Rocca-Serra, P., Roos, M., van Schaik, R., Sansone, S. A., Schultes, E., Sengstag, T., Slater, T., Strawn, G., Swertz, M. A., Thompson, M., Van Der Lei, J., Van Mulligen, E., Velterop, J., Waagmeester, A., Wittenburg, P., Wolstencroft, K., Zhao, J. & Mons, B., 2016, In: Scientific Data. 3, 160018.

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  • SEEK: a systems biology data and model management platform.

    Wolstencroft, K., Owen, S., Krebs, O., Nguyen, Q., Stanford, N. J., Golebiewski, M., Weidemann, A., Bittkowski, M., An, L., Shockley, D., Snoep, J. L., Mueller, W. & Goble, C., Jun 2015, In: BMC Systems Biology. 9, 33, 33 p.

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