Data Life Cycle Patterns in the Life Sciences

The UK Research Information Network (RIN) and the British Library (BL) have produced an amazing report looking at the patterns of flow of data in its production and tranformation in the research process of life scientists.
Patterns of information use and exchange: case studies of researchers in the life sciences. A report by the Research Information Network and the British Library November 2009.
They have seven case studies that look at the data lifecycles of data for researchers in the following life science disciplines:
  • Animal genetics and animal diseases
  • Transgenesis in the chick and development of the chick embryo
  • Epidemiology of zoonotic diseases
  • Neuroscience
  • Systems biology
  • Regenerative medicine
They have extended Chuck Humphrey's data lifecycle model, and use this extended model to illustrate how the data lifecycles are expressed in these different disciplines:



The diagrams (below) for the different disciplines are very revealing, and show the great deal of diversity in and between these disciplines, as well as the complexity within many of these areas.

In doing this analysis, the researchers found that an effective representation of this information involved the following two axes:
  • "the volume of data being handled"
  • "the complexity or heterogeneity of that data"
The researchers plotted the seven disciplines into this space, shown in the following diagram:

Discipline data lifecycle diagrams:
  • Animal genetics and animal diseases


  • Transgenesis in the chick and development of the chick embryo

  • Epidemiology of zoonotic diseases

  • Neuroscience
  • Systems biology (Computing-bases and Lab-based)



  • Regenerative medicine


  • Regenerative medicine

Note: All of these diagrams presented here are from the publication, which has the following license: Creative Commons Attribution-Non-Commercial-Share-Alike 2.0 UK: England and Wales License.


Other discussions of this document:

Comments

Post a Comment

Popular posts from this blog

Java, MySql increased performance with Huge Pages

[Resources updates: 2010.07.07 , 2009.11.03 , 2009.05.27 ] Long running, large memory, high performant applications often have special needs with respect to their memory management. On Linux, Solaris and other modern OSes, the translation look-aside buffer ( TLB ) - whose page size of 4k for many CPUs/OSes - becomes a scalability issue in these extreme conditions. In order to get around TLB scalability issues, huge page sizes are used to reduce the impact on performance. This can be of use to installations with large scale Java, MySql and other large memory applications. 300% improvement : " Well, in my case, I was able to achieve an over 3x improvement in my EJB 3 application, of which fully 60 to 70% of that was due to using large page memory with a 3.5GB heap. Now, a 3.5GB heap without the large memory pages didn't provide any benefit over smaller heaps without large pages. Besides the throughput improvements, I also noticed that GC frequency was cut down by two-third
Read more

Canadian Science Policy Conference

The Canadian Science Policy Conference is to held in Toronto, October 28-30, 2009. While the five themes , sub-panels and speakers looking both interesting and relevant, I am disappointed and perhaps a little alarmed that there appears to be no (explicit) mention of research data issues, research data management or research data archiving, despite the series of Canadian consultations examining these issues ( National Consultation on Access to Scientific Research Data (NCASRD) , 2004; National Data Archive Consultation Building Infrastructure for Access to and Preservation of Research Data , 2002; Data Access in Canada: Issues for Global Change Research” (Royal Society of Canada), 1996 ) and indicating the pressing need for 1) A research data archiving strategy and policy; 2) A research data archive. I think this is an issue that has too long been neglected (although there are some positive signs, like International Polar Year ), impacting Canadian science and innovation, especiall
Read more

Project Torngat: Building Large-Scale Semantic 'Maps of Science' with LuSql, Lucene, Semantic Vectors, R and Processing from Full-Text

Image
Project Torngat is a research project here at NRC - CISTI   [ Note that I am no longer at CISTI and that I am now continuing this work at Carleton University - GN 2010 04 07 ] that looks to use the full-text of journal articles to construct semantic journal maps for use in -- among other things -- projecting article search results onto the map to visualize the results and support interactive exploration and discovery of related articles, term and journals. Starting with 5.7 million full-text articles from 2200+ journals (mostly science, technology and medical (STM)), and using LuSql , Lucene , Semantic Vectors , R , and processing , a two dimensional mapping of a 512 dimension semantic space was created which revealed an excellent correspondence with the 23 human-created journal categories: Semantic Journal Space of 2231 Journals Scaled to Two Dimensions This initial work was initiated to find a technique that would scale, and follow-up work is looking at integrating t
Read more