INCF 2013 - Uniform Resource Layer
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The document discusses the development and management of a uniform resource layer for neuroscience, facilitated by the Neuroscience Information Framework (NIF) at UC San Diego. It emphasizes the importance of structured metadata for resource cataloging, relationships between biological resources, and methods to keep the registry current. It also highlights a variety of databases and tools related to neuroscience, including the significance of understanding brain region data and community-shared resources.
INCF 2013 - Uniform Resource Layer
- 1. Uniform Resource Layer Anita Bandrowski, Ph. D. Neuroscience Information Framework University of California, San Diego
- 2. Cataloging Biological Resources http://neuinfo.org Databases Tissue banks Software tools Services
- 3. A resource catalog: • Must have a reasonable account of what is out there http://neuinfo.org Image repository Database Atlas NITRC Harvard Nencki Inst.
- 4. How are resources added to the registry? Curators Assign structured metadata to each entry, the metadata is based on a harmonized resource type ontology
- 5. Can we mine relationships between resources? http://neuinfo.org Human annotations give a different graph of relationships Text mining gives a picture of the most used resources PDB
- 6. A shared resource registry http://neuinfo.org NIF
- 7. Social Network of Resources? • 3DVC – 182 • Force11 – 88 • Monarch – 88 • OneMind – 609 • GeneOntology Tools - 140 1 6 1 2 12 6 Which resources are shared by multiple communities? Structured data allows us to answer questions easily http://neurolex.org/
- 8. How do you keep a registry current? http://neuinfo.org
- 9. BUT DATABASES CAN HAVE NEW DATA EVERY DAY
- 10. Each resource implements a different model, which works well for the resource Connectome databases http://neuinfo.org
- 11. Uniform resource layer also means uniform data access http://neuinfo.org Luis Marenco, Rixin Wang; Yale
- 12. >200 data sources >390M data records >1.5M links to Articles
- 13. Data are divided into types http://neuinfo.org
- 15. Data about the subthalamus http://neuinfo.org
- 16. The Brain and its’ data Ontologies provide a semantic framework for understanding data/resource landscape Data sources included in NIF -Complete list: http://disco.neuinfo.org -Services: http://neuinfo.org/developersStriatum Hypothalamus Olfactory bulb Cerebral cortex Brain Brainregion Data source VadimAstakhov, Kepler Workflow Engine
- 17. LET’S PLAY A GAME
- 20. 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. http://neuinfo.org
- 21. Each animal has a set of body regions that it is particularly concerned with http://neuinfo.org
- 22. Is there a data homunculus? If so, how can we know it? http://neuinfo.org
- 23. 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 popular Least popular Brain region popularity http://neuinfo.org
- 24. Which brain regions have most annotations? 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% Level 0: Brain Level 1: Hindbrain Level 2: Medulla Level 3: Amygdalae.g., Sum per LevelSum for Major Brain Region http://neuinfo.org
- 25. 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% ABCD AgingGenesDB AllenInstitute AntibodyRegistry BAMS BioGRID BioNumbers BrainInfo BrainSpan1 BrainSpan3 BREDE CellImageLibrary CerebellarPlatform Chemoreceptors CoriellTissue CTD DrugRelatedGeneDatabase EAM EnsemblHuman EpigenomicsProject Gemma GENSAT Grants.gov HealthData HPOAnnotations IBVD LabforVisualNeuroscience MGITransgenes Monarch NationalMouseMetabolicPhenotyping… Neurodatabase Neurofed NeuronDB NIFIntegratedAnimals NIFIntegratedCellLines NIFIntegratedDisease NIFIntegratedNSC NIFIntegratedSoftware NIFModels NIFBlogs NIFNews ODE OneMind OSB PubMedHealth ResearchCrossroads T3DB Visiome YPED Which data source has any data for brain regions BAMS, BioN ot, BrainInf o, BrainMaps Funded Grants Connectivity OMIM MGI http://neuinfo.org
- 26. Why don’t you have my database of Commissural nucleus of vagusnerve images? • Please register them with NIF – http://neuinfo.org/cindy.htm • E-mail abandrowski@ucsd.edu or info@neuinfo.org • Poster # OP05 or • Demo session D19 http://neuinfo.org