bioCADDIE Webinar: The NIDDK Information Network (dkNET) - A Community Research Resource, Information, and Data Discovery Portal
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dkNET provides a single portal for discovering over 3,500 biomedical research resources and datasets. It aims to make these resources findable, accessible, interoperable, and reusable in accordance with the FAIR principles. The portal contains three main sections for browsing community resources, additional resources, and literature. It utilizes faceted searching and provides analytics and notifications to help users track changes to resources over time.
bioCADDIE Webinar: The NIDDK Information Network (dkNET) - A Community Research Resource, Information, and Data Discovery Portal
- 1. dkNET: Capabilities and the FAIR Principles Dr. Jeffrey Grethe & Dr. Maryann Martone June 16, 2016 The NIDDK Information Network (dkNET) - A Community Research Resource, Information, and Data Discovery Portal Jeffrey S. Grethe, Ph.D. September 8, 2016 bioCADDIE Webinar
- 2. Community Data and Information Resources • Over 3500 resources have been identified – Researchers can’t visit them all – Most content from these resources not easily found through standard search engines – Even more structured content on the web • Resources provide domain specific views of data – Must provide a snapshot of information in a simple to understand form that can be further explored in the native database – Must provide a biomedical science based semantic framework for resource description and search
- 3. Building a Community Resource, Information, and Data Index • It is quite difficult to access, collate, and filter the incredible array of information and data in the public domain. • dkNET was established in recognition of the need to interconnect research communities, both basic and clinical, by providing seamless access to large pools of resources, information, and data relevant to the mission of the Neuroscience Blueprint. •dkNET provides a single point-of-entry for discovering this information to allow researchers to make good decisions in the research process, thereby increasing both the speed and efficiency of the process.
- 4. The FAIR Principles and dkNET Findable: A core aspect of dkNET’s mission - facilitate access to a collection of diverse research resources Accessible: Assist users by directing them to available resources Interoperable: Provide unified views of certain data and information across resources Reusable: Supports community standards and develops standard representations for resources Attribution and Recognition: Leading initiative to unambiguously cite resources via Research Resource Identifiers Applies to data, resources, knowledge, and information
- 5. dkNET: A “Resource” Discovery Index
- 6. Datab ase Software Application Data Analysis Service Topical Portal Core Facility Ontol ogy Software Resource Year s: dkNET Offers… • A search portal to find community- vetted research resources: materials, data and tools for your research • Access to hundreds of databases across biomedicine with one easy search • Personalized search and display of results • Information hub for community news and social networking • Support for resource providers
- 7. dkNET Investigator's RetreatJune16, 2014 Shared Resources dkNET is built on the SciCrunch platform Resource Identification Portal Neuroscience dkNET Drug Design • Pull from and push to a common pool of data • Customize according to communities • Common interface elements across platforms
- 8. National Institute of Diabetes and Digestive and Kidney Diseases Information Network Neuroscience Information Framework Open Data Commons For Spinal Cord Injury Shared Infrastructure… Drug Design Data Resource Resource Identification Initiative Shared Costs… Community Specific Views
- 9. Shared Infrastructure: dkNET and SciCrunch • Community “Apps”: Portal features driven by individual communities can be re-used by other communities • Community Resource Curation: All communities have access to shared data platform Can utilize portal infrastructure for challenges being developed by another SciCrunch project
- 10. Resource IDs from aggregated databases RRIDs: a single portal for authors • >25 authoritative databases • One search interface • Simple directions • Prominent “Cite This” button Specialized Portals
- 11. Overview of the dkNET Portal
- 12. Results are returned in specific tabs. Community resources are presented first if they are available. But all searches can be executed across all resources. Community More resources Literature Specialized NIDDK-relevant resources 200+ database and information resources across biomedicine Literature dkNET’s Three Primary Resource Views
- 13. Community resources NURSA BCBC DiaComp GUDMAP T1DB MMPC NIDDK Central Repository dkNET Community Funding AddGene: Plasmids Clinical trials.gov: Clinical trials and data Antibody Registry: 2M+ antibodies Integrated animals: Model organism databases SciCrunch Resource Registry: 13K+ tools Grants.gov NIDDK-funded resources and centers Additional relevant databases vis SciCrunch
- 14. dkNET connects resources Social media Research resource analytics Other SciCrunch communities More resources LiteratureCommunity RRID’s
- 15. Each index is organized slightly differently Community More resources Literature Navigation differs across indices Resource categories Sources Data and/or resource type System level Individual records Source Functions and filters Results display Functions and filters Results display Collections and Analytics Analytics Facets Articles Functions and filters Results display
- 16. Structure of dkNET Resources ● 3 main sections ○ Community resources ○ More resources ○ Literature ● Faceted search to drill down into a single source ● Deep search into information and data resources
- 21. Community Resource Curation and Maintenance Pilot and Feasibility Program Database
- 22. Information Backstop for Retired Resources
- 23. User Notifications: Save Searches Provide user regular updates associated with user’s saved search via webpage alert and e-mail.
- 24. A core community resource: SciCrunch Registry
- 25. • Automated text mining is used to look for “web page last updated” or copyright dates Identified for 570 resources 373 were not updated within the last 2 years (65%) • Manual review of ~200 resources 38 not updated within the past 2 years (~20%) 8 migrated to new addresses or institutions 7 are no longer in service (~3%) 3 were deemed no longer appropriate Tracking digital resources since 2008
- 26. Text Mining for Resources
- 27. User Notifications: Resource Subscriptions 1. Users can track their resources 2. Provides updated information on citations of their resources 3. Resource mentions are retrieved from external data source, text mining, and user submission Subscribe
- 28. User Notifications: Resource Subscriptions
- 30. Facilitating broad use of biomedical digital assets Aggregation and Discovery platforms like dkNETcan help mediate this complex world, much as the journals do for publishing articles
- 31. RRIDs An easy, practical method for improving reproducibility and transparency
- 32. Unique ID’s for all! Resource Identification Initiative • It is currently impossible to query the biomedical literature to find out what research resources have been used to produce the results of a study • authors don’t provide enough information to unambiguously identify key research resources • Impossible to find all studies that used a resource • Critical for reproducibility and data mining • Critical for trouble-shooting Faulty Antibodies Continue to Enter US and European Markets, Warns Top Clinical Chemistry Researcher- Genome Web Daily, October 11, 2013
- 33. Digital objects are a new beast RRID: Provides foundation for establishing an alerting service for research resources Trust: Not just who produced it but what produced it
- 35. But the author knows what was used! This author got back to us within 2 hours with the stock number of this mouse Hypothes.is annotation overlay allows anyone to leave notes like this stock number from JAX
- 36. Authors supply database accession numbers for key research resources used in research
- 37. Paper published in participating journal
- 38. Materials automatically detected by SciBot(s) Made openly available
- 39. Increased identifiability of resources after the Resource Identification Initiative Pilot Bandrowski et al, 2015
- 40. New Authentication of Key Biological Resources Guidelines are already affecting most NIH applications (May 2016 deadline)
- 41. Which Journals now ask for RRIDs? ~25 Elsevier Journals – typesetting + App BMC – checklist, typesetting* Frontiers – moving to typesetting* Cell Press – author nagging, typesetting Wiley – author nagging, typesetting Working with Endocrine Society for incorporation of RRIDs
- 43. Application Programming Interfaces (APIs) 1. API specification, infrastructure and initial services for push and pull of data 2. Service documentation using Swagger.io 3. Portal dashboard for requesting API keys (e.g. Project based keys) 4. Future: Additional services for resources 5. Future: Applets using the published APIs that can be embedded on external sites
- 45. dkNET and the NIH BD2K Data Discovery Index (bioCADDIE) A Focus on the Community
- 46. e.g. NIH Commons
- 47. Interactions with Community Aggregators Global Data Set Index Community Aggregation Best Practices Community Resources $ Funding Protocols
- 48. Thank You...