BIN-Databases

Bioinformatics Databases

(Database principles for bioinformatics)

 

Abstract:

Large, scalable, multi-user database systems require a fair amount of technology underneath the hood. In particular, they need to fulfill the ACID requirements that ensure database integrity. This unit introduces the principles, and then moves onto an overview of current bioinformatics databases, and Web services.

---

Objectives: This unit will ... ... describes construction principles for database systems; ... mentions some general aspects of dtabase use in bioinformatics; ... explores the current NAR database and Web service issues.

Outcomes: After working through this unit you ... ... can define the four ACID requirements for tranactional integrity of databases; ... are familar with a spectrum of database and Web service offerings in bioinformatics.

---

Deliverables:

Time management: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.

Journal: Document your progress in your Course Journal. Some tasks may ask you to include specific items in your journal. Don't overlook these.

Insights: If you find something particularly noteworthy about this unit, make a note in your insights! page.

---

Prerequisites:
This unit builds on material covered in the following prerequisite units:

• BIN-Storing_data (Storing Data)

 

This page is tagged for revision; expect changes and proceed with caution.

 

 

Contents

In this unit we develop the technical context of bioinformatics databases and get a perspective on the multitude of data offerings in the field. Data and service offerings have no clearly defined boundaries, and many sites offer a mix of both. Thus we explore current Web services as well to define the landscape.

Task:

• Read the introductory notes on construction principles for large, multi-user, scalable database systems.
• Visit the current Database Issue of NAR and browse the titles.
• Read the editorial article in this issue:

Galperin et al. (2017) The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. Nucleic Acids Res 45:D1-D11. (pmid: 28053160)

[ PubMed ] [ DOI ] This year's Database Issue of Nucleic Acids Research contains 152 papers that include descriptions of 54 new databases and update papers on 98 databases, of which 16 have not been previously featured in NAR As always, these databases cover a broad range of molecular biology subjects, including genome structure, gene expression and its regulation, proteins, protein domains, and protein-protein interactions. Following the recent trend, an increasing number of new and established databases deal with the issues of human health, from cancer-causing mutations to drugs and drug targets. In accordance with this trend, three recently compiled databases that have been selected by NAR reviewers and editors as 'breakthrough' contributions, denovo-db, the Monarch Initiative, and Open Targets, cover human de novo gene variants, disease-related phenotypes in model organisms, and a bioinformatics platform for therapeutic target identification and validation, respectively. We expect these databases to attract the attention of numerous researchers working in various areas of genetics and genomics. Looking back at the past 12 years, we present here the 'golden set' of databases that have consistently served as authoritative, comprehensive, and convenient data resources widely used by the entire community and offer some lessons on what makes a successful database. The Database Issue is freely available online at the https://academic.oup.com/nar web site. An updated version of the NAR Molecular Biology Database Collection is available at http://www.oxfordjournals.org/nar/database/a/.

• Visit the current Web Service Issue of NAR and browse the titles.
• Read the editorial article on this issue.

Self-evaluation

Notes

Further reading, links and resources

 

---

 

If in doubt, ask! If anything about this learning unit is not clear to you, do not proceed blindly but ask for clarification. Post your question on the course mailing list: others are likely to have similar problems. Or send an email to your instructor.

---

 

About ...
 
Author:

Boris Steipe <boris.steipe@utoronto.ca>

Created:

2017-08-05

Modified:

2017-10-01

Version:

1.0

Version history:

• 1.0 First live version.
• 0.1 First stub

---

This copyrighted material is licensed under a Creative Commons Attribution 4.0 International License. Follow the link to learn more.