The Uniform Resource Layer

http://neuinfo.org

Anita Bandrowskiabandrowski@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

*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

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http://neuinfo.org

My brain scan