the uniform resource layer anita bandrowski abandrowski@ucsd.edu neuroscience information framework

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

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