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The Uniform Resource Layer

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Anita Bandrowski …

Anita Bandrowski
CMB 2013

Published in: Technology, Design
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  • 1. The Uniform Resource Layer http://neuinfo.org Anita Bandrowski abandrowski@ucsd.edu Neuroscience Information Framework
  • 2. Resource? http://neuinfo.org …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. How Can We Find Resources?  “I would like funding to create an RNAi database because one does not exist.” – biomedical researcher  But… http://neuinfo.org There must be a place where researchers can go to find resources before they create them again!
  • 4. How Can We Find Resources? http://neuinfo.org Database (2200) Software tool (900) Biobanks (550) Services (100) Database (2200) Software tool (900) Biobanks (550) Services (100)
  • 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. What is data?
  • 7. How do you search for data?
  • 8. Ever heard of metadata?
  • 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. Each resource implements a different model; systems are complex and difficult to learn, in many cases Access to Biomedical Resources Must Be Uniform! http://neuinfo.org
  • 11. http://neuinfo.org Description of the database Anatomical Structure Aligned to 7 options Aligned to NLM Taxonomy names
  • 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...” http://neuinfo.org
  • 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  http://neuinfo.org/cindy.php  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 http://neuinfo.org
  • 14. Diseases of nervous system Neurodegenerative Seizuredisorders Neoplasticdiseaseofnervous system NIH Reporter NIFdatafederatedsources http://neuinfo.org
  • 15. My brain scan

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