Skip to main content
SpringerLink
Log in

AUDIT: approving and tracking updates with dependencies in collaborative databases

  • Published:
Distributed and Parallel Databases Aims and scope Submit manuscript

Abstract

Collaborative databases such as genome databases, often involve extensive curation activities where collaborators need to interact to be able to converge and agree on the content of data. In a typical scenario, a member of the collaboration makes some updates and these become visible to all collaborators for possible comments and modifications. At the same time, these updates are usually pending the approval or rejection from the data custodian based on the related discussion and the content of the data. Unfortunately, the approval and authorization of updates in current databases is based solely on the identity of the user, e.g., via the SQL GRANT and REVOKE commands. In this paper, we present a scalable cloud-based collaborative database system to support collaboration and data curation scenarios. Our system is based on an Update Pending Approval model. In a nutshell, when a collaborator updates a given data item, it is marked as pending approval until the data custodian approves or rejects the update. Until then, any other collaborator can view and comment on the data, pending its approval. We fully realized our system inside HBase, a cloud-based platform. We also conducted extensive experiments showing that the system scales well under different workloads.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9
Fig. 10
Fig. 11
Fig. 12
Fig. 13
Fig. 14
Fig. 15
Fig. 16
Fig. 17
Fig. 18
Fig. 19

Similar content being viewed by others

References

  1. BLAST. http://blast.ncbi.nlm.nih.gov/Blast.cgi/

  2. Fagin, R.: On an authorization mechanism. ACM Trans. Database Syst. 3(3), 310–319 (1978)

    Article  MathSciNet  Google Scholar 

  3. Griffiths, P.P., Wade, B.W.: An authorization mechanism for a relational database system. ACM TODS 1(3), 242–255 (1976)

    Article  Google Scholar 

  4. Apache hbase. https://hbase.apache.org/

  5. Mershad, K., Malluhi, Q., Quzzani, M., Tang, M., Aref, A.: Approving updates in collaborative databases. In: Proceedings of the 3rd IEEE International Conference on Cloud Engineering. IC2E 15 (2015)

  6. Dayal, U., Hsu, M., Ladin, R.: Organizing long-running activities with triggers and transactions. SIGMOD Rec. 19(2), 204–214 (1990)

    Article  Google Scholar 

  7. Garcia-Molina, H., Salem, K.: Sagas. SIGMOD Rec. 16(3), 249–259 (1987)

    Article  Google Scholar 

  8. Aiken, A., Hellerstein, J., Widom, J.: Behavior of database production rules: termination, confluence, and observable determinism. In: SIGMOD (1992)

  9. Paton, N.W., Daz, O.: Active database systems. ACM Comput. Surv. 31(1), 63–103 (1999)

    Article  Google Scholar 

  10. Lomet, D., Barga, R., Mokbel, M., Shegalov, G.: Transaction time support inside a database engine. In: Proceedings of the 22nd International Conference on Data Engineering (ICDE 06) (2006)

  11. Oracle flashback. http://www.oracle.com/technetwork/issue-archive/2008/08-jul/o48totalrecall-092147.html/

  12. Shankar, S., Kini, A., DeWitt, D.J., Naughton, J.: Integrating databases and workflow systems. SIGMOD Rec. 34(3), 5–11 (2005)

    Article  Google Scholar 

  13. Apache subversion. http://subversion.apache.org/

  14. Git. http://git-scm.com/

  15. Bhardwaj, A., Deshpande, A., Elmore, A.J., Karger, D., Madden, S., Parameswaran, A., Subramanyam, H., Wu, E., Zhang, R.: Collaborative data analytics with DataHub. Proc. VLDB Endow. 8(12), 1916–1919 (2015)

    Article  Google Scholar 

  16. Xu, L., Huang, S., Hui, S., Elmore, A.J., Parameswaran, A.: ORPHEUSDB: a lightweight approach to relational dataset versioning. In: Proceedings of the ACM International Conference on Management of Data, ACM 2017, pp. 1655–1658 (2017)

  17. Bhagwat, D., Chiticariu, L., Tan, W.C., Vijayvargiya, G.: An annotation management system for relational databases. VLDB J. 14(4), 373–396 (2005)

    Article  Google Scholar 

  18. Buneman, P., Chapman, A., Cheney, J.: Provenance man-agement in curated databases. In: SIGMOD 06. ACM, pp. 539–550 (2006)

  19. Buneman, P., Khanna, S., Wang-Chiew, T.: Why and where: a characterization of data provenance. In: Database Theory ICDT 2001, Ser. Lecture Notes in Computer Science, vol. 1973, pp. 316–330. Springer, Heidelberg (2001)

  20. Davidson, S.B., Freire, J.: Provenance and scientific workflows: Challenges and opportunities. In: SIGMOD 08. ACM, pp. 1345–1350 (2008)

  21. Amsterdamer, Y., Davidson, S.B., Deutch, D., Milo, T., Stoyanovich, J., Tannen, V.: Putting lipstick on pig: enabling database-style workflow provenance. Proc. VLDB Endow. 5(4), 346–357 (2011)

    Article  Google Scholar 

  22. Wikipedia Page history. https://en.wikipedia.org/wiki/Help:Page_history/

  23. XWIKI Homepage. http://www.xwiki.org/xwiki/bin/view/Main/

  24. Eltabakh, M.Y., Ouzzani, M., Aref, W.G.: DBMS—a database management system for biological data. CIDR 2007, 196–206 (2007)

    Google Scholar 

  25. Eltabakh, M., Aref, W.G., Elmagarmid, A., Ouzzani, M.: Handson db: managing data dependencies involving human actions. In: IEEE TKDE, no. PrePrints, p. 1 (2013)

  26. Apache hadoop. http://hadoop.apache.org/

  27. Hadoop distributed file system. http://hadoop.apache.org/docs/r2.3.0/hadoop-project-dist/hadoop-hdfs/HdfsUserGuide.html

  28. Apache zookeeper. http://zookeeper.apache.org/

  29. Bernstein, P.A., Goodman, N.: Concurrency control in distributed database systems. ACM Comput. Surv. 13(2), 185–221 (1981)

    Article  MathSciNet  Google Scholar 

  30. Apache hbase coprocessors. https://blogs.apache.org/hbase/entry/coprocessor_introduction

  31. Protocol buffers. https://developers.google.com/protocol-buffers/

  32. Wikimedia Downloads. https://dumps.wikimedia.org/

  33. Wikipedia: Usability. https://en.wikipedia.org/wiki/Usability

  34. Benson, D.A., Cavanaugh, M., Clark, K., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., Sayers, E.W.: GenBank. Nucleic Acids Res. 41(D1), D36–D42 (2012)

    Article  Google Scholar 

Download references

Acknowledgements

This publication was made possible by the support of an NPRP Grant 4-1534-1-247 from the the Qatar National Research Fund (a member of Qatar Foundation) and the National Science Foundation under Grants IIS-1117766 and IIS-0964639. The statements made herein are solely the responsibility of the authors.

Author information

Authors and Affiliations

  1. Arts, Sciences and Technology University in Lebanon, Beirut, Lebanon

    Khaleel Mershad

  2. Qatar University, 2713, Al Hala St, Doha, Qatar

    Qutaibah M. Malluhi

  3. Qatar Computing Research Institute, HBKU, Doha, Qatar

    Mourad Ouzzani

  4. Purdue University, West Lafayette, IN, USA

    Mingjie Tang, Michael Gribskov & Walid G. Aref 

Authors
  1. Khaleel Mershad
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Qutaibah M. Malluhi
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Mourad Ouzzani
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Mingjie Tang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Michael Gribskov
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Walid G. Aref 
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Khaleel Mershad.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Mershad, K., Malluhi, Q.M., Ouzzani, M. et al. AUDIT: approving and tracking updates with dependencies in collaborative databases. Distrib Parallel Databases 36, 81–119 (2018). https://doi.org/10.1007/s10619-017-7208-y

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10619-017-7208-y

Keywords

Search

Navigation