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The Uniform
Resource
Layer
http://neuinfo.org
Anita Bandrowski
abandrowski@ucsd.edu
Neuroscience Information
Framework
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
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!
How Can We Find Resources?
http://neuinfo.org
Database (2200)
Software tool (900)
Biobanks (550)
Services (100)
Access to Biomedical Resources
Must Be Uniform!
http://neuinfo.org
Each resource implements
a different, though related
model; systems are
complex and difficult to
learn, in many cases
Access to Biomedical Resources
Must Be Uniform!
http://neuinfo.org
Need a Common Platform for
Access to Biological Data
http://neuinfo.org
Need a Common Platform for
Access to Biological Data
 Not just RDF!
 Not just XML!
 Nosql! –no
 Data, to a biologist is something that can be
understood.
 “…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
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 have 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
Diseases of nervous system
Neurodegenerative
Seizuredisorders
Neoplasticdiseaseofnervous
system
NIH
Reporter
NIFdatafederatedsources
http://neuinfo.org

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NIF: A vision for a uniform resource layer

  • 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
  • 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)
  • 5. Access to Biomedical Resources Must Be Uniform! http://neuinfo.org
  • 6. Each resource implements a different, though related model; systems are complex and difficult to learn, in many cases Access to Biomedical Resources Must Be Uniform! http://neuinfo.org
  • 7. Need a Common Platform for Access to Biological Data http://neuinfo.org
  • 8. Need a Common Platform for Access to Biological Data  Not just RDF!  Not just XML!  Nosql! –no  Data, to a biologist is something that can be understood.  “…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
  • 9. 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 have 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
  • 10. Diseases of nervous system Neurodegenerative Seizuredisorders Neoplasticdiseaseofnervous system NIH Reporter NIFdatafederatedsources http://neuinfo.org