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Development of NeuronBank v2.0

Development of NeuronBank v2.0. Akshaye Dhawan B&B Fellow Department of Computer Science In collaboration with the Neuroscience Institute. Understanding the brain requires understanding its circuitry. http://www.cajal.csic.es/V.

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Development of NeuronBank v2.0

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  1. Development of NeuronBank v2.0 Akshaye Dhawan B&B Fellow Department of Computer Science In collaboration with the Neuroscience Institute

  2. Understanding the brain requires understanding its circuitry http://www.cajal.csic.es/V

  3. Problem: We are using publications as a method to catalog neurons and neural circuits • Information is distributed and fragmented. • No means to efficiently search this knowledge. • No means to publish incremental knowledge without a functional story.

  4. Neuromics • Genomics is the study of the Genome, where the Genome consists of all of the genes in an organism • Neuromics is the study of the Neurome,where the Neurome consists of all of the neurons in an organism

  5. The Neurome is harder to represent than the Genome. • Neurons are identified based on their properties. • Idiosyncratic • Species-specific • Constantly evolving

  6. The Neurome is harder to represent than the Genome. • No standards for representing our knowledge of neural circuits. • No means to database this knowledge

  7. Our Approach • Traditional databases are not a good fit - Changes in representation would cause the database schema to change • Ontology: A formal representation of a set of concepts within a domain and the relationships between those concepts – A Vocabulary • We created a core ontology that applies to all nervous systems • We also support extensible species-specific ontologies.

  8. NeuronBank is to neurons what GenBank is to genes. A place to publish knowledge about neurons and neural connectivity Tools to represent, search, analyze, and share knowledge of neurons and neural circuitry. Collection of ontologies and tools to access them NeuronBank.org: A Neuromics Tool

  9. NeuronBank.org: A Neuromics Tool

  10. NeuronBank.org: A Neuromics Tool

  11. NeuronBank.org: A Neuromics Tool DSI

  12. NeuronBank.org: A Neuromics Tool DSI

  13. NeuronBank.org: A Neuromics Tool

  14. So what else have we been up to? • Stable version out on www.neuronbank.org • Efforts underway to: • Make our data useful to a larger community • Expand NeuronBank to other species • Summer 2008, Leech Ontology Meeting, Woods Hole, Ma

  15. Lesson 0: (Obvious) Cross-Disciplinary Challenges • Different disciplines • Different cultures/languages • Reward: The satisfaction of working on real problems • Key: Realistic expectations.

  16. Lesson 1:Defining Requirements • Requirements describe in detail what a software system is supposed to do • Easier said than done • The Myth of Stable Requirements • Specially true in a research project such as this • Give and take of size/scope through the funding process

  17. Example: NeuroViz • Moved from a 3D program to a 2D web browser based applet • That:

  18. Became this

  19. NeuronBank v2.0 • NeuronBank 1.0 achieved its objectives. • First system to: • Support a varying data model for Species specific representation • While still allowing searches across species • At the time of commencing work on v1.0 no clear standards existed for storing data as per our requirements

  20. Problems with v1.0 • Since v1.0 a lot of research has gone towards realizing the Semantic Web • Extension to the WWW where the semantics of the information is defined • We used a combination of technologies to build v1.0 • This works… But: • Standards have now emerged for the Semantic Web (OWL) and Biological Ontologies (OBO). We need to conform to these. • Development Challenges. • Interface problems.

  21. Project updates • Aim to bring the data in NeuronBank into the Open Biomedical Ontologies (OBO)project. • OBO’s goal is to create interoperable ontologies in the biological domain. • Enables access to our data by other tools that are a part of the OBO Foundry

  22. Lesson 2: Design for Change • Need to design for change • It’s the only thing that’s a given • Projects should have the ability to evolve, discard and replace individual components with minimal impact on other pieces • Going from a stand alone 3-D Viz Tool to a browser based tool meant several changes for the branch • Moving to a Semantic Web version

  23. Lesson 3: Community Building is hard • A lot of excitement every time we pitch this to a group of researchers working on some species. • But who will enter the data? 80/20 rule • The system is only as good as what’s in it. • Some sort of an incentive is needed to get new species started • Using NeuronBank wiki in classes • Then moving this data into NeuronBank

  24. Lesson 4: Managing Humans • Who owns this? • Code • Project/Sub-project • Academic Attrition • Publication potential to keep students interested • Ideally enough research for this to be the thesis/dissertation topic for a student

  25. .org • Neuroscience Institute • Paul Katz • Computer Science • Sushil Prasad, Ph.D. • Ying Zhu, Ph.D. • Raj Sunderraman, Ph.D. • Students: • Chad Frederick • Weiling Li • Rasanjalee Dissanayaka Mudiyanselage • Shuman Gao • Akshaye Dhawan Past Members Bob Calin-Jageman, (now at Dominican University) Jason Pamplin Hao Tian Hong Yang Hsui Wang Janaka Balasooriya Xiuyun Shen Wenjun Ma Piyaphol Phoungphol Naveen Hiremath Monika Patel Suzy Gentner

  26. Thank You for your time and attention Questions?

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