dkNET Introduction for Librarians
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DKNET is a research resource portal funded by the NIH, aimed at connecting biomedical researchers to valuable resources and tools across various biomedical domains. It offers resource reports, authentication services, fair data assistance, and a discovery portal to facilitate research rigor, reproducibility, and hypothesis generation. Researchers can utilize DKNET to navigate a comprehensive database of research resources and funding opportunities effectively.
dkNET Introduction for Librarians
- 1. An NIDDK Resource dknet.org The NIDDK Information Network
- 2. An NIDDK Resource dknet.org About dkNET • Research resource information portal for biomedical researchers • Information network to connect DK researchers and NIH-funded centers • Funded by National Institute of Health (NIH) - National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) • Developed and maintained by the FAIR Data Informatics Laboratory (fdilab.org) at UCSD (Supports major informatics projects in neuroscience and biomedicine)
- 3. An NIDDK Resource dknet.org • Basic and clinical researchers in diabetes, digestive, obesity, endocrine, metabolic, kidney, urologic, nutrition, bone and blood diseases. • Tools and services are relevant across all biomedical domains Image credits: NIDDK, NLM Diabetes Digestive System Endocrine System Urinary System WhWHO IS dkNET’S TARGET AUDIENCE?
- 4. An NIDDK Resource dknet.org 5 AREAS IN THE PORTAL ● dkNET provides: ○ Resource Reports: helps researchers find and evaluate resources ○ Authentication Reports: assists researchers in preparing NIH authentication plans ○ FAIR Data Services: assists researchers in finding data repositories and standards for preparing data management plans ○ Discovery Portal: connects researchers to more than 200 biomedical databases ○ Hypothesis Center: powerful tools for data mining and hypothesis generation of FAIR ‘omics data
- 5. dknet.orgAn NIDDK Resource How Can dkNET Help Researchers? Construct a hypothesis Ask a question Do background research Plan experiments Collect and analyze data Publish results Discovery Portal Hypothesis Center Resource Reports Authentication Reports Information Material Data Tools Funded grant and funding opportunities Literature Tutorials Resource Reports Hypothesis Center FAIR Data Resources Data Management Data Repositories Resource Reports Cite RRID Track Resources Resource Identification Authentication plansNIH Mandates on Rigor and Reproducibility for grant submission
- 6. dknet.orgAn NIDDK Resource dkNET Portal https://dknet.org
- 7. An NIDDK Resource dknet.org Resource Reports Find and evaluate key research resources: Antibodies, organisms, cell lines, tools and services, plasmids, biosamples I’m planning my experiments, and would like to find and evaluate key resources. I’m publishing a paper, and would like to find RRIDs for citing key resources. Construct a hypothesis Ask a question Do background research Plan experiments Collect and analyze data Publish results
- 8. dknet.orgAn NIDDK Resource Resource Reports Report includes: ● Citations of usage and mentions ● Who is using them? ● Do they have issues? ● How do they compare? ● Is anyone near me familiar with them?
- 9. dknet.orgAn NIDDK Resource The resource information network Alerts RRID Sources and metadata Literature Collaborators Validation & Ratings Assembled a unique data set that aggregates information about key research resources for biomedical research using Research Resource Identifiers (RRIDs)
- 10. dknet.orgAn NIDDK Resource RRID:AB_1855196 Fothergill LJ et al. Cell and Tissue Research. 375 (2) 359-69, 2019. WHAT ARE RRIDS? ● A persistent identifier for research resources ● FDILabs was instrumental in the development and adoption of RRIDs ● Supplied by authors to identify resources in the materials and methods section ● Designed to answer two simple questions: ○ What resources were used in a study ○ Who else has published with this resource?
- 11. dknet.orgAn NIDDK Resource Growth of RRIDs ● RRIDs in use across major publishers: ○ Cell Press ○ Elsevier ○ Wiley ○ Nature ● 2019: Part of JATS standard (Journal Article Tag Suite) ● Over 205,700 resources have been identified +1,000 Distinct Journals
- 12. dknet.orgAn NIDDK Resource Resources Rating and Alerts RRIDs provide us with an opportunity to alert researchers to issues with a particular resource at time of publication dkNET aggregates information from multiple sources about known issues with these resources
- 13. The Resource Information Network is inserted into the Publication Process ● RRIDs stand between authors and publications ● Authors go to a single portal, the Resource Information Portal, to obtain RRIDs, which are issued by over 25 distinct authorities for different types of resources ● Powered by dkNET
- 14. dknet.orgAn NIDDK Resource Impact of RRIDs: Use of RRIDs associated with a lower reported use of problematic cell lines Babic Z, et al. eLIFE 2019; 8:e41676 DOI: 10.7554/eLife.41676 8.66% 3.33% 16.11% 5.36% 61.55% decrease 66.73% decrease
- 15. dknet.orgAn NIDDK Resource Authentication Reports 1. Alert researchers of any issues with cell lines and antibodies before the study is performed 2. Compliance with the NIH requirements for grant applications I’m writing a proposal, and would like to know how to prepare “authentication of key biological resources” section. I’m planning my experiments and would like to know how to identify and validate resources. Construct a hypothesis Ask a question Do background research Plan experiments Collect and analyze data Publish results
- 16. dknet.orgAn NIDDK Resource NIH Rigor & Reproducibility Guidelines https://grants.nih.gov/reproducibility/documents/grant-guideline.pdf dkNET provides help to researchers: ● Comply with new mandates for research rigor and reproducibility ● Make it easier for identifying resources and preparing authentication plans ● Manage and share FAIR research data
- 17. dknet.orgAn NIDDK Resource Custom Authentication Report - Cell lines and Antibodies • NIH requires that you create an authentication plan for key research resources in your grant application • dkNET can help! • Tool for evaluating how your resources perform and best practices for designing an authentication plan
- 18. dknet.orgAn NIDDK Resource FAIR data resources for biomedicine FDILabs: Co-authors of the FAIR data principles I’m writing a proposal, and would like to know how to prepare data management plan. Construct a hypothesis Ask a question Do background research Plan experiments Collect and analyze data Publish results I’m publishing a paper, and would like to find a data repository to share my data.
- 19. dknet.orgAn NIDDK Resource FAIR Data Resources We are assisting with the interpretation of FAIR for DK domains and providing tools to help with ● Research data management to support FAIR ● Sharing data: Suggested data repositories and the standards they use
- 20. dknet.orgAn NIDDK Resource FAIR data principles High level principles to make data: • Findable • Accessible • Interoperable • Re-usable Mark D. Wilkinson et al. The FAIR Guiding Principles for scientific data management and stewardship, Scientific Data (2016). DOI: 10.1038/sdata.2016.18 …for humans and machines
- 21. Findable ● F1. (meta)data are assigned a globally unique and persistent identifier ● F2. data are described with rich metadata ● F3. metadata clearly and explicitly include the identifier of the data it describes ● F4. (meta)data are registered or indexed in a searchable resource Accessible ● A1. (meta)data are retrievable by their identifier using a standardized communications protocol ● A1.1 the protocol is open, free, and universally implementable ● A1.2 the protocol allows for an authentication and authorization procedure, where necessary ● A2. metadata are accessible, even when the data are no longer available 15 attributes of FAIR ● I1. (meta)data use a formal, accessible, shared, and broadly applicable language for knowledge representation. ● I2. (meta)data use vocabularies that follow FAIR principles ● I3. (meta)data include qualified references to other (meta)data Re-usable ● R1. meta(data) are richly described with a plurality of accurate and relevant attributes ● R1.1. (meta)data are released with a clear and accessible data usage license ● R1.2. (meta)data are associated with detailed provenance ● R1.3. (meta)data meet domain-relevant community standards Interoperable
- 22. FAIR Partnership Researchers Repositories and Registries Indexers Aggregators • Good data management • Good documentation • Rich metadata • Prepare to share • Submit to repository • Persistent identifier • Machine based access • Clear license • Open, domain specific standards • Machine readable metadata • Persistent metadata • Bidirectional links • Data citation • Index • Effective Search • Persistent metadata Community Organizations
- 23. dknet.orgAn NIDDK Resource Research Data Management Overview Provide information about: • What is research data management? • Provide links to resource, such as California Digital Library data management planning tool • Provide specificity for DK applications
- 24. dknet.orgAn NIDDK Resource Where Can I Deposit My Data? • List of DK specific repositories, recommended by NLM and various journals • Created in conjunction with NIDDK
- 25. dknet.orgAn NIDDK Resource dkNET Summer of Data Student Internship Program Project Duration: 6 weeks starting June 22 to July 31, 2020 Application Due Date: April 17, 2020 Goal: • Provide students an opportunity to use the dkNET tools and resources for their research projects • Enable students to provide feedback on their experience to the dkNET team • Students will learn best practices to enhance rigor and reproducibility • Students will learn the basics of good data management by following the FAIR data principles Award: $1000 awards to a limited number of students who are working in a lab during summer 2020 https://dknet.org/about/Summer-Internship
- 26. dknet.orgAn NIDDK Resource Discovery Portal I would like to know what research resources such as information, data or materials are available. I’m looking for funding opportunities or funded grant information. Construct a hypothesis Ask a question Do background research Plan experiments Collect and analyze data Publish results
- 27. dknet.orgAn NIDDK Resource Discovery Portal • 200+ biomedical databases • Literature • Centralized search • DK specific content • Funding opportunities - original databases
- 28. dknet.orgAn NIDDK Resource Discovery Portal - dkNET Resources Cell Lines Software Antibodies Organisms Pilot funding Opportunities Plasmids
- 29. dknet.orgAn NIDDK Resource Hypothesis Center I would like to find top genes that are relevant to a signaling pathway. Construct a hypothesis Ask a question Do background research Plan experiments Collect and analyze data Publish results I have a gene or a list of genes and would like to find relevant signaling pathways.
- 30. dknet.orgAn NIDDK Resource Hypothesis Center - Signaling Pathways Project SPP simplifies data mining of ‘omics data, connects bench researchers to FAIR data to allow them to easily interrogate the data to generate hypotheses ● Find genes with important roles in receptors, enzymes, organs and tissues ● Define signaling pathways relevant to a single gene or a regulation
- 31. dknet.orgAn NIDDK Resource Summary How can dkNET help researchers?
- 32. dknet.orgAn NIDDK Resource Summary - How Can dkNET Help Researchers? • Resource Reports • help researchers find resources for their research • Keeps researchers updated on resources with warnings, ratings and validation information • Find RRIDs and register resources • Find who else used the resources • Rigor and Reproducibility Support • Authentication Reports: assists in creating authentication plans • FAIR Data Services: assists in developing DMP by finding appropriate data repositories • Discovery Portal connects researchers to the broader biomedical community (+200 databases) • Hypothesis Center enables researchers to harness the power of FAIR big data • Analyze omics data to develop research hypotheses
- 33. dknet.orgAn NIDDK Resource Get involved in the dkNET Community dkNET Homepage: dkNET.org Sign up Newsletter Join Webinar Join Summer Program Follow us @dknet_info Check Out or Post News and Funding Opportunities Blog, Calendar
- 34. dknet.orgAn NIDDK Resource Links to Available Resources General Information • dkNET Information https://dknet.org/about/product_info • Research Resource Identifier (RRID) Information https://dknet.org/about/rrid • What is Resource Reports? https://dknet.org/about/resource_reports_info • NIH Mandates on Rigor and Transparency https://dknet.org/about/NIH-Policy-Rigor-Reproducibility Services • Resource Reports https://dknet.org/rin/rrids • Authentication Reports https://dknet.org/rin/rrid-report • Discovery portal https://dknet.org/data/search#all • Hypothesis Center https://dknet.org/about/hypothesis_center • Pilot funding databases https://dknet.org/about/funding Data management • FAIR data/research data management https://dknet.org/rin/research-data-management • Suggested data repositories https://dknet.org/about/Suggested-data-repositories-niddk Newsletter (Funding opportunity, events, news, new tools...etc.) • https://dknet.org/about/maillist Webinar • Upcoming webinar https://dknet.org/about/webinar • dkNET recorded webinar https://www.youtube.com/channel/UCwukSrB8L61Fhwjv3x20lOQ Summer of Data Student Internship • https://dknet.org//about/Summer-Internship • Download Flyer
- 35. dknet.orgAn NIDDK Resource Thank You Questions & Demos?