INCF 2013 - Uniform Resource Layer


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Anita Bandrowski explains how the uniform resource layer of the Neuroscience Information Framework allows several interesting questions about the state of scientific research to be answered.

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INCF 2013 - Uniform Resource Layer

  1. 1. Uniform Resource Layer Anita Bandrowski, Ph. D. Neuroscience Information Framework University of California, San Diego
  2. 2. Cataloging Biological Resources Databases Tissue banks Software tools Services
  3. 3. A resource catalog: • Must have a reasonable account of what is out there Image repository Database Atlas NITRC Harvard Nencki Inst.
  4. 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. 5. 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
  6. 6. A shared resource registry NIF
  7. 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
  8. 8. How do you keep a registry current?
  10. 10. Each resource implements a different model, which works well for the resource Connectome databases
  11. 11. Uniform resource layer also means uniform data access Luis Marenco, Rixin Wang; Yale
  12. 12. >200 data sources >390M data records >1.5M links to Articles
  13. 13. Data are divided into types
  14. 14. Uniform search
  15. 15. Data about the subthalamus
  16. 16. The Brain and its’ data Ontologies provide a semantic framework for understanding data/resource landscape Data sources included in NIF -Complete list: -Services: Hypothalamus Olfactory bulb Cerebral cortex Brain Brainregion Data source VadimAstakhov, Kepler Workflow Engine
  17. 17. LET’S PLAY A GAME
  18. 18. What is this?
  19. 19. Homunculus
  20. 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.
  21. 21. Each animal has a set of body regions that it is particularly concerned with
  22. 22. Is there a data homunculus? If so, how can we know it?
  23. 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
  24. 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
  25. 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 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
  26. 26. Why don’t you have my database of Commissural nucleus of vagusnerve images? • Please register them with NIF – • E-mail or • Poster # OP05 or • Demo session D19
  27. 27. Maryann Martone, PI