Date post: | 17-Jan-2016 |
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The Uniform Resource Layer
http://neuinfo.org
Anita [email protected]
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
*not a paper*
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)
Database (2200)Software tool
(900)Biobanks (550)Services (100)
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
What is data?
How do you search for data?
Ever heard of metadata?
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
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
http://neuinfo.org
Description of the database
Anatomical Structure
Aligned to 7 options
Aligned to NLM Taxonomy names
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
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
Diseases of nervous system
Neuro
deg
enera
tive
Seizu
re d
isord
ers
Neopla
stic dise
ase
of n
erv
ous
syste
m
NIH Reporter
NIF
data
federa
ted
sou
rces
http://neuinfo.org
My brain scan