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Summer of Data Program

Description of dkNET Tools and Services


dkNET.org provides tools and services covering a variety of areas. The primary mission of dkNET is to make it easier for researchers to find and use research resources like antibodies, organisms, software tools and data.


Resource Reports

Resource reports are based on a unique integrated data set and analytics platform that combines Research Resource Identifiers (RRIDs), text mining and data aggregation to provide:

  • A detailed overview of each resource.
  • Citation metrics on published papers that have used a particular resource.
  • Information about what resources have been used together.

    • Examples of how Resource Reports can help you:

  • Before planning to use cell lines in an experiment, a researcher could check Resource Reports to see if there are reported problems with the cell lines, e.g., contamination, what studies have already been published using this cell line, and who could be potential collaborators.
  • Before choosing antibodies for a particular experimental application, a researcher could check Resource Reports to see if there is validation information available for these antibodies.


    • Rigor/Reproducibility

    dkNET gives researchers the tools and services to help them comply with funding and publishing mandates in support of robust and reproducible science.

  • Comply with NIH mandates on resource identification and authentication.
  • Manage and share FAIR research data.
  • Generate a resource reproducibility report when you submit a proposal or publication.

    • Find information fore best practices in managing research data and community approved repositories.

    Examples include:

  • Before planning an experiment or submitting a proposal, a researcher can generate a Reproducibility Report to make authentication plans for cell lines and antibodies, as required by the new NIH guidelines.
  • A researcher is planning to produce or has produced several datasets in a research project and does not know how best to comply with data sharing mandates. A researcher can use dkNET FAIR Data resources to find appropriate data repositories and learn how to comply with the FAIR principles.


    • Data Science

    dkNET offers a gateway to data science resources and computational tools, provides quick access to grant information, high-value datasets, bioinformatics core facilities, and training materials to advance biomedical research. dkNET’s bioinformatics learning hub (Hypothesis Center) brings together a collection of online tools that will allow researchers to explore different datasets and utilize analytics and visualization tools. Additionally, the new Computational Core (dkNET-AI.org) provides AI/ML-driven tools powered by Texera, supporting collaborative, scalable, and reproducible research.


    Signaling Pathways Project

    The Signaling Pathways Project (SPP) knowledgebase is a new component of dkNET designed to assist cell signaling researchers in generating research hypotheses using the large volume of public archived transcriptomic and ChIP-Seq datasets. A cornerstone of the SPP is consensome analysis, which uses transcriptomic and ChIP-Seq datasets to rank genomic targets on the basis of their regulatory relationships with signaling pathway nodes (receptor, enzymes and transcription factors). To learn more about generating hypotheses using SSP, contact [email protected].


    Ochsner, S et al. (2018) The Signaling Pathways Project: an integrated 'omics knowledgebase for mammalian cellular signaling pathways. BioRxiv.
    https://doi.org/10.1101/401729


    Example project use cases include:

  • The SPP adipose tissue consensome assigns a high ranking to a target about which little is known in the literature, implying a previously uncharacterized role in adipose biology. A researcher designs experiments to validate its potential role in a facet of adipose tissue biology under study in their laboratory.
  • A researcher has a list of genes with known roles in inflammatory bowel disease (IBD). They query this gene list against SPP and finds that these genes are frequently targeted by a transcription factor. The researcher designs experiments to explore the role of this transcription factor in driving IBD.

    • About

    The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.

    Recent News Entries

    Join the Whole Person Physiome 1st Data Jamboree on August 24-25

    Join Dr. Chen Li for a Knowledge Portal Network Webinar on the dkNET Computational Core on August 6

    Join NIH ODSS Data Sharing and Reuse Seminar "PanKbase: An Open, FAIR Knowledge Base of the Human Pancreas to Accelerate Diabetes Research"

    Contact Us

    Email: info_at_ dknet.org

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