Anita Bandrowski CMB 2013

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