Uniform Resource Layer Anita Bandrowski, Ph. D. Neuroscience Information Framework University of California, San Diego

Cataloging Biological Resources Databases Tissue banks Software tools Services

A resource catalog: Must have a reasonable account of what is out there Image repository Database Atlas NITRC Harvard Nencki Inst.

How are resources added to the registry? Curators Assign structured metadata to each entry, the metadata is based on a harmonized resource type ontology

Can we mine relationships between resources? Human annotations give a different graph of relationships Text mining gives a picture of the most used resources PDB

A shared resource registry NIF

Social Network of Resources? 3DVC – 182 Force11 – 88 Monarch – 88 OneMind – 609 GeneOntology Tools Which resources are shared by multiple communities? Structured data allows us to answer questions easily

How do you keep a registry current?

BUT DATABASES CAN HAVE NEW DATA EVERY DAY

Each resource implements a different model, which works well for the resource Connectome databases

Uniform resource layer also means uniform data access Luis Marenco, Rixin Wang; Yale

>200 data sources >390M data records >1.5M links to Articles >200 data sources >390M data records >1.5M links to Articles

Data are divided into types

Uniform search

Data about the subthalamus

The Brain and its’ data Ontologies provide a semantic framework for understanding data/resource landscape Data sources included in NIF -Complete list: -Services: Striatum Hypothalamus Olfactory bulb Cerebral cortex Brain Brain region Data source Vadim Astakhov, Kepler Workflow Engine

LET’S PLAY A GAME

What is this?

Homunculus

Homunculus *Careful mapping of the entire somatosensory cortex yields a representation of the amount of area devoted to sensing each body region. *From the homunculus we learn that humans pay attention to the lips, hands and genitals.

Each animal has a set of body regions that it is particularly concerned with

Is there a data homunculus? If so, how can we know it?

Medial lemniscus of midbrain Habenulo-interpeduncular tract of midbrain Commissural nucleus of vagus nerve Medullary raphe nuclear complex Dorsal longitudinal fasciculus of medulla Trochlear nerve root Spinothalamic tract of midbrain Superior cerebellar peduncle of midbrain Medial longitudinal fasciculus of midbrain Central tegmental tract of midbrain Dorsal longitudinal fasciculus of midbrain Vagus nerve root Accessory nerve root White matter of the cerebellar cortex Oculomotor nerve root Brain Striatum Amygdala Thalamus Cerebellar cortex Cerebellum Hypothalamus Forebrain Midbrain Substantia nigra Third ventricle Ventral tegmental area Pons Medulla oblongata Cochlear nuclear complex Most popularLeast popular Brain region popularity

Which brain regions have most annotations? Sum per Level Sum for Major Brain Region

Which data source has any data for brain regions BAMS, BioNot, BrainInfo, BrainMaps BAMS, BioNot, BrainInfo, BrainMaps Funded Grants Connectivity OMIM MGI

Why don’t you have my database of Commissural nucleus of vagus nerve images? Please register them with NIF – or Poster # OP05 or Demo session D19

Maryann Martone, PI