The Uniform Resource Layer


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Anita Bandrowski
CMB 2013

Published in: Technology, Design
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The Uniform Resource Layer

  1. 1. The Uniform Resource Layer Anita Bandrowski Neuroscience Information Framework
  2. 2. Resource? …websites that have significant value to the greater neuroscience community, including biomedical resources. For the most part, these are limited to not-for-profit. It shall be considered an individual resource if it is maintained by a single entity, and has the properties of one or more individual web pages that are related by a theme and HTML links. Most often the individual pages share portions of the URL, however, unrelated URLs may be incorporated into a single web resource. In the event that a subgroup of pages represents a sufficient shift in theme, it should be classified as an independent resource. For example, the department of neuroscience of a university (resource 1) may have a lab led by a researcher (resource 2). Website/web tool produced by or useful to, a biomedical researcher *not a paper*
  3. 3. How Can We Find Resources?  “I would like funding to create an RNAi database because one does not exist.” – biomedical researcher  But… There must be a place where researchers can go to find resources before they create them again!
  4. 4. How Can We Find Resources? Database (2200) Software tool (900) Biobanks (550) Services (100) Database (2200) Software tool (900) Biobanks (550) Services (100)
  5. 5. What is a database?  an organized collection of data. The data are typically organized to model relevant aspects of reality in a way that supports processes requiring this information. • -Wikipedia
  6. 6. What is data?
  7. 7. How do you search for data?
  8. 8. Ever heard of metadata?
  9. 9. Try this in your favorite search engine  pinky and the brain  bicycle  CA1 connectivity  YFG expression in cortex  estradiol levels in mouse  Binding affinity (Ki) of Acetylcholine to nicotinic receptors
  10. 10. Each resource implements a different model; systems are complex and difficult to learn, in many cases Access to Biomedical Resources Must Be Uniform!
  11. 11. Description of the database Anatomical Structure Aligned to 7 options Aligned to NLM Taxonomy names
  12. 12. Need a Common Platform for Access to Biological Data  Data, to a biologist is something that can be understood, not just computed.  “…according to Bonda (2000) the Amygdaloid nucleus is connected to Field CA1 in the young adult monkey, subjected to the following conditions...”
  13. 13. Are We There Yet?  Of 2200 databases that NIF has in the Registry, we have only deeply registered 200  Of the 800 software tools, <100 have deep metadata and user communities  Not yet, but some things can help  If you know of a tool / data please register at   If you have a choice, use open formats  If you have a choice, use common vocabularies  If you can, in papers and databases, use identifiers
  14. 14. Diseases of nervous system Neurodegenerative Seizuredisorders Neoplasticdiseaseofnervous system NIH Reporter NIFdatafederatedsources
  15. 15. My brain scan