aboutPagesContent.yaml

--- 
-  
  page: /purpose
  title: Purpose
  primaryContentImage: 'https://raw.githubusercontent.com/CBIIT/datacommons-assets/main/icdc/aboutPages/Photo-About_Purpose.jpeg'
  content: 
    - 
      paragraph: "NCI's Division of Cancer Treatment and Diagnosis (DCTD) tasked the Frederick National Laboratory for Cancer Research (FNLCR) with building the Integrated Canine Data Commons (ICDC), a cloud-based repository of spontaneously-arising canine cancer data. ICDC was established to further research on human cancers by enabling comparative analysis with canine cancer. The data in the ICDC is sourced from multiple different programs and projects; all focused on canine subjects. The data is harmonized into an integrated data model and then made available to the research community. The ICDC is part of the $$[Cancer Research Data Commons (CRDC)](https://datacommons.cancer.gov/)$$, an initiative from NCI’s Center for Biomedical Informatics and Information Technology (CBIIT). Bioinformatic analysis of the ICDC data is accomplished using the CRDC’s $$[Cloud Resources](target:_self url:/#/crdc type:0)$$."
    - 
      paragraph: "The FNLCR Bioinformatics and Computational Science (BACS) Directorate has a focus on software engineering and data science and is responsible for devlopment of the ICDC web application and overall management of the project and The Applied and Developmental Research Directorate (ADRD) has a focus on clinical and biological monitoring and assay development and manages the ICDC Steering Committee and provides one of the data sources for the ICDC. The ICDC Steering Committee is comprised of external members, FNLCR and NCI staff that provide guidance to DCTD on the ICDC."
- 
  page: /steeringCommittee
  title: "Steering Committee"
  primaryContentImage: 'https://raw.githubusercontent.com/CBIIT/datacommons-assets/main/icdc/aboutPages/Photo-About_SteeringCommittee.jpeg'
  content: 
    - 
      paragraph: "The Integrated Canine Data Commons (ICDC) is community-driven and built with input and collaboration from many groups to foster a diversity of ideas and to ensure needs are identified across the broad research community. To achieve this collaboration, the ICDC Steering Committee was formed to advise the NCI and FNLCR on the ICDC. The Steering Committee is composed of members from the non-NIH research community, NCI, NHGRI, and NCATS. There is also ex-officio members who are FNLCR staff. All chairpersons are from the non-NIH research community."
    - 
      paragraph: "The Steering Committee has two sub-committees: the $$[Data Governance Advisory Board](target:_self url:/#/dgab type:0)$$ (DGAB) and the $$[Best Practices Sub-Committee](target:_self url:/#/bpsc type:0)$$ (BPSC)."
    - 
      table: 
        - 
          head: 
            - name
            - institution
            - affliation
            - subcommitee
        - 
          body: 
            - 
              row: 
                - $$[Anne Avery](target:_blank url:https://vetmedbiosci.colostate.edu/directory/member/?id=anne-avery-3106)$$
                - "Colorado State University"
                - External
                - "-"
            -
              row:
                - $$[Erika Berger](target:_blank url:https://www.linkedin.com/in/erika-berger-b051836a/)$$
                - FNLCR
                - FNL
                - "-"
            -
              row: 
                - $$[Matthew Breen](target:_blank url:https://cvm.ncsu.edu/directory/breen-matthew/)$$
                - "North Carolina State University"
                - External
                - DGAB
            - 
              row: 
                - $$[M. Renee Chambers](target:_blank url:https://www.medicalwesthospital.org/doctor.php?cn=498)$$
                - "University of Alabama at Birmingham"
                - External
                - BPSC
            - 
              row: 
                - $$[James Dattilo](target:_blank url:https://www.precinctnetwork.org/)$$
                - "University of Pennslyvania"
                - External
                - BPSC
            - 
              row: 
                - $$[Dawn Duval](target:_blank url:https://vetmedbiosci.colostate.edu/directory/member/?id=dawn-duval-1011)$$
                - "Colorado State University"
                - External
                - BPSC
            - 
              row: 
                - $$[Toby Hecht](target:_blank url:https://trp.cancer.gov/about_trp/bios/hecht_toby.htm)$$
                - DCTD/NCI
                - NIH
                - BPSC
            - 
              row: 
                - $$[William Hendricks](target:_blank url:https://www.tgen.org/faculty-profiles/will-hendricks/)$$
                - "Translational Genomics Research Institute (TGen)"
                - External
                - DGAB
            - 
              row: 
                - $$[Paula Jacobs](target:_blank url:https://www.researchgate.net/profile/Paula_Jacobs)$$
                - CIP/DCTD/NCI
                - NIH
                - BPSC
            - 
              row: 
                - $$[Warren Kibbe](target:_blank url:https://scholars.duke.edu/person/warren.kibbe)$$
                - "Duke University"
                - External
                - DGAB
            - 
              row: 
                - $$[Erika Kim](target:_blank url:https://datascience.cancer.gov/about/staff-directory/erika-kwon)$$
                - CBIIT/NCI
                - NIH
                - "DGAB, BPSC"
            - 
              row: 
                - $$[Deborah Knapp](target:_blank url:https://vet.purdue.edu/directory/person.php?id=28)$$
                - "Purdue University"
                - External
                - BPSC
            - 
              row: 
                - $$[Gina Kuffel](target:_blank url:https://orcid.org/0000-0003-4061-0092)$$
                - FNLCR
                - FNL
                - "DGAB, BPSC"
            -
              row: 
                - $$[Amy LeBlanc](target:_blank url:https://ccr.cancer.gov/molecular-imaging-program/amy-k-leblanc)$$
                - COP/CCR/NCI
                - NIH
                - DGAB
            - 
              row: 
                - $$[Cheryl London](target:_blank url:https://vetprofiles.tufts.edu/profile/cheryl-london/)$$
                - "Tufts University"
                - External
                - BPSC
            - 
              row: 
                - $$[Christina Mazcko](target:_blank url:https://ccr.cancer.gov/comparative-oncology-program/contact-us)$$
                - COP/CCR/NCI
                - NIH
                - "-"
            - 
              row: 
                - $$[Philip Musk](target:_blank url:https://www.linkedin.com/in/philipmusk/)$$
                - FNLCR
                - FNL
                - DGAB
            - 
              row: 
                - $$[Elaine Ostrander](target:_blank url:https://irp.nih.gov/pi/elaine-ostrander)$$
                - CGCGB/NHGRI
                - NIH
                - BPSC
            - 
              row: 
                - $$[John Otridge](target:_blank url:https://frederick.cancer.gov/about/people/john-otridge)$$
                - FNLCR
                - FNL
                - "-"
            - 
              row: 
                - $$[Ralph Parchment](target:_blank url:https://frederick.cancer.gov/about/people/ralph-parchment)$$
                - FNLCR
                - FNL
                - "-"
            - 
              row: 
                - $$[Adam Resnick](target:_blank url:https://www.research.chop.edu/people/adam-c-resnick)$$
                - Children's Hospital of Philadelphia
                - External
                - "-"
            - 
              row: 
                - $$[Connie Sommers](target:_blank url:https://dtp.cancer.gov/organization/iob/staff_profiles.htm)$$
                - IOB/DTP/DCTD/NCI
                - NIH
                - "DGAB, BPSC"
            - 
              row: 
                - $$[Greg Tawa](target:_blank url:https://ncats.nih.gov/staff/tawagj)$$
                - TRNDP/NCATS
                - NIH
                - DGAB
            - 
              row: 
                - $$[Jeff Trent](target:_blank url:https://www.tgen.org/faculty-profiles/jeffrey-trent/)$$
                - "Translational Genomics Research Institute (TGen)"
                - External
                - BPSC
            - 
              row: 
                - $$[Roel Verhaak](target:_blank url:https://medicine.yale.edu/profile/roel-verhaak/)$$
                - "Yale School of Medicine"
                - External
                - DGAB
            - 
              row: 
                - $$[Shaying Zhao](target:_blank url:https://www.bmb.uga.edu/directory/people/shaying-zhao)$$
                - "University of Georgia"
                - External
                - BPSC 
- 
  page: /DGAB
  title: Data Governance Advisory Board 
  primaryContentImage: 'https://raw.githubusercontent.com/CBIIT/datacommons-assets/main/icdc/aboutPages/Photo-About_DGAB.jpeg'
  content: 
    - 
      paragraph: "The Integrated Canine Data Commons (ICDC) was established to further research on human cancers by enabling comparative analysis with canine malignancies. Researchers willing to contribute and share relevant data to this mission via the ICDC are encouraged to make a data submission request through the $${title: Data Submission Request Process [PDF],link:https://github.com/CBIIT/icdc-codebase/raw/master/src/main/frontend/src/content/files/ICDC_DGAB_Guidelines_v1.3.pdf}$$, and per our $$[Data Submission Guidelines](target:_self url:/#/submit)$$. The request will be processed by ICDC’s Data Governance Advisory Board (DGAB) which consists of 4 external members (all members of the ICDC Steering Committee, with one of the four acting as the DGAB Chair), 2 NIH members, and supported by FNLCR staff. The DGAB meets regularly to prioritize data submission requests and to advise the NCI on the suitability of each proposed data submission for its inclusion in the ICDC. The individual members of the DGAB are identified below."
    - 
      paragraph: ~
    - 
      table: 
        - 
          head: 
            - name
            - position
            - affiliation
        - 
          body: 
            - 
              row: 
                - "Warren Kibbe"
                - Chair
                - "Duke University"
            - 
              row: 
                - "Matthew Breen"
                - Member
                - "North Carolina State University"
            - 
              row: 
                - "William Hendricks"
                - Member
                - "Translational Genomics Research Institute (TGen)"
            - 
              row: 
                - "Erika Kim"
                - Member
                - NIH/NCI/CBIIT
            - 
              row: 
                - "Gina Kuffel"
                - Member
                - FNLCR
            - 
              row: 
                - "Philip Musk"
                - Member
                - FNLCR
            -
              row: 
                - "Greg Tawa"
                - Member
                - NIH/TRNDP/NCATS
            - 
              row: 
                - "Roel Verhaak"
                - Member
                - "Yale School of Medicine"   
    - 
      paragraph: ~
    - 
      paragraph: ~
    - 
      paragraph: "Based upon recommendations from the DGAB, the NCI Senior Advisory Committee (SAC) subsequently makes all final decisions as to the approval and prioritization of incoming studies, including any re-prioritization that may become necessary. The individual members of the SAC are identified below."
    - 
      table: 
        - 
          head: 
            - name
            - position
            - affiliation
        - 
          body: 
            - 
              row: 
                - "Connie Sommers"
                - Chair
                - NIH/NCI/DCTD
            - 
              row: 
                - "Javed Kahn"
                - Member
                - NIH/NCI/CCR/CGB
            - 
              row: 
                - "Amy LeBlanc"
                - Member
                - NIH/NCI/CCR/COP
-
  page: /BPSC
  title: Best Practices Subcommittee 
  primaryContentImage: 'https://raw.githubusercontent.com/CBIIT/datacommons-assets/main/icdc/aboutPages/BPSC-publication.png'
  content: 
    - 
      paragraph: "The Best Practices Subcommittee (BPSC) is responsible for examining completed and planned studies to identify and recommend best practices that the Integrated Canine Data Commons (ICDC) will implement to streamline and harmonize data collection, standardize data formats and platforms, and manage and annotate data (especially clinical data). Moreover, these recommendations will help the broader community in study design and data collection to enhance research to better enable human and canine data comparison. The BPSC is composed of 8 external members, 5 NCI staff, 1 NHGRI staff, and is supported by FNLCR staff."
    -
      paragraph: "A manuscript from the ICDC BPSC was published by the Journal of Veterinary and Comparative Oncology on October 1, 2023, titled $$[Leading the pack, Best practices in comparative canine cancer genomics to inform human oncology.](target:_blank url:https://doi.org/10.1111/vco.12935)$$"
    - 
      table: 
        - 
          head: 
            - name
            - position
            - affiliation
        - 
          body: 
            - 
              row: 
                - "M. Renee Chambers"
                - Member
                - "University of Alabama at Birmingham"
            - 
              row: 
                - "Dawn Duval"
                - Member
                - "Colorado State University"
            - 
              row: 
                - "Heather Gardner"
                - Member
                - "Translational Genomics Research Institute (TGen)"
            - 
              row: 
                - "Paula Jacobs"
                - Member
                - NIH/NCI/DCTD
            -
              row:
                - "Debbie Knapp"
                - Member
                - "Purdue University"
            - 
              row: 
                - "Gina Kuffel"
                - Member
                - FNLCR
            - 
              row: 
                - "Amy LeBlanc"
                - Member
                - NIH/NCI/CCR/COP
            - 
              row: 
                - "Cheryl London"
                - Member
                - "Tufts University"

            - 
              row: 
                - "Elaine Ostrander"
                - Member
                - NIH/NHGRI/CGCGB
            - 
              row: 
                - "Connie Sommers"
                - Member
                - NIH/NCI/DCTD/DTP/IOB
            -
              row:
                - "Jeff Trent"
                - BPSC Chair
                - Translational Genomics Research Institue (TGen)
            - 
              row: 
                - "Shaying Zhao"
                - Member
                - "University of Georgia"
-
  page: /Working Groups
  title: Working Groups 
  primaryContentImage: 'https://raw.githubusercontent.com/CBIIT/datacommons-assets/main/icdc/aboutPages/Photo-About_BPSC.jpeg'
  
  content:    
    - 
      paragraph: "The ICDC encompasses many data types and is currently focused into three working groups; Imaging, Genomics, and Longitudinal Data Use and Acquistion." 
    - 
      paragraph: "$$#Working Group Goals#$$"
    - 
      paragraph: "$$*Imaging Working Group*$$ To provide the comparative cancer research community with guidelines and best practices for the collection, formatting and reporting of imaging data collected from canine companion animals with naturally-occurring cancers into the Integrated Canine Data Commons (ICDC). Accomplishing this goal will facilitate the utilization and analysis of such data by stakeholders in the cancer research community and advance dog-to-human translational research in the comparative oncology space."
    # - 
    #   paragraph: "$$*Clinical/Pathology*$$: To provide a standard set of clinical and pathological information to be collected when conducting canine clinical trials. By defining these data points for the community, and including an appropriate list of values, we hope to be able to more easily compare subjects and their data across studies."
    - 
      paragraph: "$$*Genomics Working Group*$$ To provide an overview of next generation sequencing (NGS) study design, assays and analysis approaches (focusing on genomics and transcriptomics) used by diverse canine cancer research teams alongside annotation of validation studies, canine-specific tooling and parameters, identify common data elements across published analyses, establish general principles in canine cancer genomics best practices modeled on human cancer genomics best practice principles; identify gaps in canine cancer genomics best practices and propose solutions."
    # - 
    #   paragraph: "$$*Immunology*$$: To provide a standard and expandable set of immunologic measurements to contextualize the changes that occur during treatment of spontaneously arising cancer in canines. Basic measurements will be compared across studies, while specialized study measurements will be used to understand specific outcomes. We hope this will lead to a better understanding of response to immunologic treatment and potentially to providing potential lines of investigation for treatment in humans."
    -
      paragraph: "$$*Longitudinal Data Use & Acquistion Working Group (LDAUWG)*$$ To survey the landscape of available longitudinal datasets and identify potential collaborators. Scientific questions and use cases will motivate the efforts to acquire this data for ingestion into the ICDC."
    - 
      table: 
        - 
          head: 
            - name
            - position
            - affiliation
            - "Working Group"
        - 
          body: 
            - 
              row: 
                - "Erika Berger"
                - Member
                - FNLCR
                - "Longitudinal Data Use & Acquistion"
            - 
              row: 
                - "Matthew Breen"
                - "LDAUWG Chair"
                - "North Carolina State University"
                - Longitudinal Data Use & Acquistion
            - 
              row: 
                - "M. Renee Chambers"
                - Member
                # - "Chair, Clin/Path WG"
                - "University of Alabama at Birmingham"
                # - Clinical/Pathology
                - Longitudinal Data Use & Acquistion
            - 
              row: 
                - "James Dattilo"
                - Member
                - University of Pennslyvania
                - "Longitudinal Data Use & Acquistion"
            - 
              row: 
                - "Dawn Duval"
                - Member
                - "Colorado State University"
                - Genomics, Longitudinal Data Use & Acquistion
            - 
              row: 
                - "Heather Gardner"
                - Member
                - "Translational Genomics Research Institute (TGen)"
                - Genomics, Longitudinal Data Use & Acquistion
            - 
              row: 
                - "Toby Hecht"
                - Member
                - NIH/NCI/DCTD
                # - Immunology
                - Longitudinal Data Use & Acquistion
            - 
              row: 
                - "Paula Jacobs"
                - "Imaging WG Co-Chair"
                - NIH/NCI/DCTD
                - Imaging, Longitudinal Data Use & Acquistion
            - 
              row: 
                - "Warren Kibbe"
                - Member
                - Duke University
                - "Longitudinal Data Use & Acquistion"
            - 
              row: 
                - "Gina Kuffel"
                - Member
                - FNLCR
                - "Longitudinal Data Use & Acquistion"
            - 
              row: 
                - "Amy LeBlanc"
                - "Imaging WG Co-Chair"
                - NIH/NCI/CCR/COP
                - Imaging, Longitudinal Data Use & Acquistion
            # - 
            #   row: 
            #     - "Deborah Knapp"
            #     - "Co-Chair, Immunology WG"
            #     - "Purdue University"
            #     - "Clinical/Pathology, Immunology"
            # - 
            #   row: 
            #     - "Cheryl London"
            #     - "Co-Chair, Clin/Path WG, Co-Chair, Immunology WG"
            #     - "Tufts University"
            #     - "Clincal/Pathology, Immunology"
            - 
              row: 
                - "Elaine Ostrander"
                - Member
                - NIH/NHGRI/CGCGB
                - Genomics, Longitudinal Data Use & Acquistion
            - 
              row: 
                - "Connie Sommers"
                - Member
                - NIH/NCI/DCTD/DTP/IOB
                # - Immunology
                - Longitudinal Data Use & Acquistion
            - 
              row: 
                - "Gregory Tawa"
                - Member
                - TRNDP/NCATS
                - "Longitudinal Data Use & Acquistion"
            - 
              row: 
                - "Roel Verhaak"
                - Member
                - Yale School of Medicine
                - "Longitudinal Data Use & Acquistion"
            - 
              row: 
                - "Shaying Zhao"
                - "Genomics WG Co-Chair"
                - "University of Georgia"
                # - "Genomics, Immunology"
                - "Genomics, Longitudinal Data Use & Acquistion"
-
  page: /crdc
  title: "Cancer Research Data Commons (CRDC) and Analysis"
  primaryContentImage: 'https://raw.githubusercontent.com/CBIIT/datacommons-assets/main/icdc/aboutPages/Photo-About_CRDC.jpeg'
  content: 
    - 
      paragraph: "$$#The CRDC#$$"
    - 
      paragraph: "$$[The Cancer Research Data Commons (CRDC)](https://datacommons.cancer.gov/)$$ is an initiative from NCI’s Center for Biomedical Informatics & Information Technology ($$[CBIIT](https://datascience.cancer.gov/)$$). CBIIT’s vision for the project consists of a virtual, expandable infrastructure that provides secure access to many different data types across scientific domains, allowing users to analyze, share, and store results, leveraging the storage, elastic compute, and scalability of the cloud. The ability to combine diverse data types and perform cross-domain analysis of large data sets can lead to new discoveries in cancer prevention, treatment and diagnosis, and supports the goals of precision medicine and the Cancer Moonshot℠."
    - 
      paragraph: "$$#The CRDC Cloud Resources#$$"
    - 
      paragraph: "The CRDC has three Cloud Resources ($$[Seven Bridges Cancer Genomics Cloud powered by Velsera ](http://www.cancergenomicscloud.org/)$$,$$[ISB Cancer Genomics Cloud ](https://isb-cgc.appspot.com/)$$, $$[Broad Firecloud ](https://firecloud.terra.bio/)$$), each providing analysis platforms for the community to use when working with data from the CRDC ecosystem."
    - 
      paragraph: "These cloud-based platforms eliminate the need for researchers to download and store extremely large files by bringing datasets and powerful analysis tools together within the cloud. The Cloud Resources also provide access to on-demand computational capacity for conducting analysis using publicly available best practice tools and pipelines or building new tools and workflows."
    - 
      paragraph: "All three Cloud Resources provide support for data access through a web-based user interface in addition to programmatic access to analytic tools and workflows, and the capability of sharing results with collaborators. Each Cloud Resource is continually developing new functionality to improve the user experience and add new tools for researchers."
    - 
      paragraph: "$$*The Seven Bridges Cancer Genomics Cloud (CGC)*$$ is powered by Velsera and hosted on Amazon Web Services (AWS). The CGC has a rich user interface that allows researchers to find data of interest and combine it with their own private data. Data can be analyzed using more than 900 preinstalled, curated bioinformatics tools and workflows. Researchers can also extend the functionality of the platform by adding their own data and tools via an intuitive software development kit (SDK)."
    - 
      paragraph: "$$*Institute for Systems Biology Cancer Genomics Cloud (ISB-CGC)*$$ leverages many aspects of the Google Cloud Platform (GCP) and allows scientists to interactively define and compare cohorts, examine underlying molecular data for specific genes and pathways, and share insights with collaborators. For computational users, application program interfaces (APIs) and GCP resources such as BigQuery and Google Pipeline service allow complex queries from R or Python scripts or Dockerized workflows to run on data available in Google Cloud Storage."
    - 
      paragraph: "$$*Broad Institute Firecloud*$$ is an open, standards-based platform powered by Terra for performing production-scale data analysis in the cloud. Built on the Google Cloud Platform (GCP), Firecloud empowers analysts, tool developers, and production managers to run large-scale analysis and to share results with collaborators. Users can upload their own analysis methods and data to workspaces or run the Broad’s best practice tools and pipelines."
    - 
      paragraph: "$$*From the ICDC to the Cloud Resources*$$"
    - 
      paragraph: "Currently the ICDC supports analysis via the Seven Bridges Cancer Genomics Cloud powered by Velsera."
    - 
      paragraph: "One of the primary goals of the ICDC data portal is to make data findable, accessible, interoperable, and reusable (FAIR) to lower the barriers for researchers to go from cohort discovery to a meaningful analysis. Researchers can find cases and build cohorts in the ICDC and then send the associated files required for analysis to the My Files Cart page where the list of files is compiled into a File Manifest. The File Manifest is simply a csv file consisting of rich metadata and Data Repository Service (DRS) Unique Resource Identifiers (URIs) for every file object listed. Using the new Export to the CGC button enables the simple and immediate transfer of a File Manifest to the CGC with only a single click. The CGC uses information in the File Manifest to fetch the file from a DRS server and storage buckets located in the cloud. Alternatively, users can download the File Manifest locally and then subsequently upload the File Manifest directly into the CGC to load files into a CGC project."  
    - 
      paragraph: "This Cloud Resource analysis model eliminates the need for researchers to download and store extremely large data sets by allowing them to bring analysis tools to the data in the cloud, instead of the traditional process of bringing the data to the tools on local hardware. The Cloud Resources also provide access to on-demand computational capacity to analyze these data, allow users to run best practice tools and pipelines already implemented, and upload their own data or analysis methods to workspaces."
    - 
      paragraph: "All three Cloud Resources provide support for data access through a web-based user interface in addition to programmatic access to analytic tools and workflows, and the capability of sharing results with collaborators. Each Cloud Resource is continually developing new functionality to improve the user experience and add new tools for researchers."
-

#   page: /icdc-data-model
#   title: "ICDC Data and Model"
#   primaryContentImage: 'https://raw.githubusercontent.com/CBIIT/datacommons-assets/main/icdc/aboutPages/Photo-About_ICDC_model.jpeg'
#   secondaryZoomImageTitle: "The ICDC Data Model" 
#   secondaryZoomImage: 'https://cbiit.github.io/icdc-model-tool/model-desc/icdc-model.svg'
#   content: 
#     - 
#       paragraph: "$$#HARMONIZATION/INTEGRATION:#$$"
#     - 
#       paragraph: "The ICDC functions best for the research community when the data is integrated. Once a project is accepted into the ICDC, the ICDC data team will work with the submitter to review the data looking at data structure, data values, data quality as well as identifying any standards that were utilized. Based on that review, a plan for how to submit the data will be agreed upon between ICDC and the submitter."
#     - 
#       paragraph: "$$#FAIR AND CITING:#$$"
#     - 
#       paragraph: "The ICDC will adhere to $$[FAIR](https://www.go-fair.org/fair-principles/)$$ principles of data stewardship: Findable, Accessible, Interoperable, and Reusable. Please credit the ICDC in your manuscript. When citing individual projects, please refer to the attribution policies of the project when available."
#     - 
#       paragraph: "$$#LICENSE#$$"
#     - 
#       paragraph: "Data made available through the ICDC is for research purposes only. The ICDC provides researchers with access to data from canine cancer studies to enable exploratory analysis that cannot be considered definitive for outcomes. All data is publicly available."
#     - 
#       paragraph: "$$#DATA MODEL:#$$"
#     - 
#       paragraph: "The ICDC data model is a representation of how all the constituent data are arranged relative to each other. Given the number of studies, the range of study types and the multiple data types that the ICDC needs to support, the data model will need to adapt to the needs of the science. The data model is not static and is expected to change as new needs are identified."
#     - 
#       paragraph: "The SVG graphic below represents the current ICDC data model consisting of data nodes, node properties, and relationships (edges). It provides a comprehensive mapping of the system data, part of which may be viewed in the application interface and UI. In other words, additional nodes and properties are available for inspection and querying beyond those presented on the front-end."
#     - 
#       paragraph: "Additionally, the ICDC Data Model serves as a template for similar initiatives and data structures, including graph-based database schemas. The model will continue to evolve as data needs are further discerned."
#     - 
#       paragraph: "The tool used to generate this visual may be sourced on Github at: $$[https://github.com/CBIIT/icdc-model-tool](https://github.com/CBIIT/icdc-model-tool)$$."
#     - 
#       paragraph: "The model and associated files may be viewed here: $$[https://cbiit.github.io/icdc-model-tool/](https://cbiit.github.io/icdc-model-tool/)$$."
  
# - 
  page: /developers
  title: Developers
  primaryContentImage: 'https://raw.githubusercontent.com/CBIIT/datacommons-assets/main/icdc/aboutPages/Photo-About_Developer.jpeg'
  content: 
    - 
      paragraph: "The ICDC has a graph database featuring a read-only GraphQL API based in Java that is available for public consumption and a frontend built from the JavaScript based React library. Each tier in the application stack is designed to be modular and adaptable for a variety of use cases. Users do not require authentication to the system and all data are public."
    -
      paragraph: $$[https://caninecommons.cancer.gov/v1/graphql/](https://caninecommons.cancer.gov/v1/graphql/)$$
    - 

      paragraph: "These APIs are provided “as is”; there are no warranties or conditions arising out of usage of these services."
    - 
      paragraph: "$$#GitHub#$$"
    - 
      paragraph: "As a resource for the public and cancer research, the following repos are available for research, usage, forking, and pull requests. The codebase is intended for sharing and building frameworks for related initiatives and projects. The ICDC GitHub repositories have documentation about how to access the system, including endpoints and recommendations for tools and example queries. Both the project and documentation are currently maintained and updated."
    -
      paragraph: $$[bento-icdc-frontend](https://github.com/CBIIT/bento-icdc-frontend)$$
    - 
      paragraph: $$[bento-icdc-backend](https://github.com/CBIIT/bento-icdc-backend)$$
    - 
      paragraph: $$[bento-icdc-interoperation](https://github.com/CBIIT/bento-icdc-interoperation)$$
    - 
      paragraph: $$[icdc-model-tools](https://github.com/CBIIT/icdc-model-tool)$$
    - 
      paragraph: $$[icdc-bioinformatics](https://github.com/CBIIT/icdc-bioinformatics)$$
      

- 
  page: /support
  title: Support
  primaryContentImage: 'https://raw.githubusercontent.com/CBIIT/datacommons-assets/main/icdc/aboutPages/About_Support.jpeg'
  content: 
    - 
      paragraph: "Please direct questions, comments, or concerns to $$@ICDCHelpDesk@mail.nih.gov@$$."
- 
  page: /submit
  title: "Submitting Data"
  primaryContentImage: 'https://raw.githubusercontent.com/CBIIT/datacommons-assets/main/icdc/aboutPages/Photo-About_SubmittingData.jpeg'
  content: 
    - 
      paragraph: "$$#Data Submission Requests and Approvals#$$"
    -
      paragraph: "The Integrated Canine Data Commons (ICDC) was established to further research on human cancers by enabling comparative analysis with canine malignancies. Researchers who have data that will contribute to this mission and who are willing to share that data via the ICDC are encouraged to make a data submission request through the $${title:Submission Request Process [PDF],link:https://github.com/CBIIT/icdc-codebase/raw/master/src/main/frontend/src/content/files/ICDC_DGAB_Guidelines_v1.3.pdf}$$. Please email $$@ICDCHelpDesk@mail.nih.gov@$$ for specific instructions. All proposed data submissions are reviewed by the Data Governance Advisory Board $$[(DGAB)](target:_self url:/#/DGAB)$$ to assess their scientific value and suitability for inclusion. Once any given study has been fully on-boarded, all data submitted will become publicly available."
    -  
      paragraph: "To initiate a Data Submission Request, please use this $${title:Template,link:https://github.com/CBIIT/icdc-codebase/raw/master/src/main/frontend/src/content/files/ICDC_Data_Submission_Request_Template.docx}$$"
    - 
      paragraph: "Importantly, studies need not be complete to start a submission request. Indeed, working with the ICDC development team before defining your data collection processes can be beneficial, since we can advise on best practices and existing precedent to make the data submission process more efficient and thereby speed up the on-boarding of each new study. For studies that have already been completed, the ICDC Data Team will nonetheless provide appropriate guidance on data alignment."
    - 
      paragraph: "$$#The Data Model Navigator and Data Preparation#$$"
    -
      paragraph: "In support of data submissions, the ICDC application now includes a sophisticated and intuitive $$[Data Model Navigator](target:_self url:/#/icdc-data-model)$$ which provides end users in general, and data submitters in particular, with access to a wealth of information regarding the graph-based data model upon which the ICDC is based."
    -
      paragraph: "The Data Model Navigator’s Graph View provides an interactive, graphical rendering of the data model, which can be filtered in order to identify the nodes (equivalent to tables in traditional relational databases) and therefore properties (equivalent to fields) of most relevance to any given study. The associated Table View function displays detailed tabular views of each node which fully-define the properties within them, inclusive of the applicable controlled vocabularies of acceptable terms, and identify which properties are required versus preferred or optional."
    -  
      paragraph: "Comprehensive documentation of the data model’s nodes and property requirements can be downloaded in PDF format, alongside node-specific data loading templates into which data submitters can insert the relevant data values and thereby create loading-ready data files. In addition, machine-readable versions of any given controlled vocabulary of interest can be downloaded, in support of data submitters validating their templated data prior to its submission. All potential data submitters are therefore strongly encouraged to use the Data Model Navigator to familiarize themselves with the ICDC data model prior to initiating the data submission process."
    -
      paragraph: "$$#The Data Onboarding Process#$$"
    -
      paragraph: "Once a study submission has been reviewed by the DGAB and accepted for inclusion, the ICDC Data Team will work directly with the data submitter(s) to review the data in terms of its structure, the data values in use versus ICDC’s preferred terminology, and overall data quality and consistency. This collaborative review process will, in turn, lead to the development of a data submission plan and a timeline over which the study on-boarding work is anticipated to be conducted."
    -
      paragraph: "In developing the submission plan, a primary consideration is that consumers of the data will not be as familiar with the data as the data owners. For example, a diagnosis of “Lymphoma” may be implicit for a study that examines only that type of malignancy, but a value for diagnosis would still need to be explicitly stated for the benefit of the research community as a whole. In line with this policy, the ICDC also favors the use of relatively broad terminology in some places (e.g. diagnosis and primary disease site), versus very specific terminology (e.g. sample pathology and sample site)."
    -
      paragraph: "As more and more studies have been incorporated into the ICDC, and in the interests of data consistency, clear expectations have now been established around the level of case and sample annotations and the appropriate sets of acceptable values. Common data quality issues include inconsistent terminology (e.g. Transitional Cell Carcinoma vs. Urothelial Bladder Cancer), inconsistent spelling (e.g. Tumour vs. Tumor), inconsistent formatting (e.g. Male vs. male), concatenated values which should be separated (e.g. “Spayed female”, which should instead be provided as values for two separate properties of Sex and Neutered Status), and gaps in data (e.g. missing data vs. situations where data values should be quoted as “Not Applicable” vs. data values deliberately not collected, i.e. “Not Determined”). The ICDC Data Team will work with the submitter to identify and resolve any such issues, and in situations where the existing controlled vocabularies need to be extended by the addition of new terms, the data model will be updated accordingly. All data is fully validated against the requirements specified by the data model during data loading to ensure correct data alignment and preserve data consistency. "    
- 
  page: /guideline
  title: "Data Use"
  primaryContentImage: 'https://raw.githubusercontent.com/CBIIT/datacommons-assets/main/icdc/aboutPages/Photo-About_SubmittingData.jpeg'
  content: 
    - 
      paragraph: "$$#License#$$"
    - 
      paragraph: "Data made available through the ICDC is for research purposes only. The ICDC provides researchers with access to data from canine cancer studies to enable exploratory analysis that cannot be considered definitive for outcomes. All data is publicly available. ICDC Data received by the requestor is considered Licensed Material as defined below. ICDC data submission and data use is governed by $$[Creative Commons CC-BY 4.0.](https://creativecommons.org/licenses/by/4.0/)$$ licensing terms."
    - 
      paragraph: "By exercising the Licensed Rights, You accept and agree to be bound by the terms and conditions of this Creative Commons Attribution 4.0 International Public License (“Public License“). To the extent this Public License may be interpreted as a contract, You are granted the Licensed Rights in consideration of Your acceptance of these terms and conditions, and the Licensor grants You such rights in consideration of benefits the Licensor receives from making the Licensed Material available under these terms and conditions."
    - 
      paragraph: "$$#Intellectual Property Policy Statement#$$"
    - 
      paragraph: "The ICDC discourages use of the data to acquire ownership interest in pre-competitive technologies necessary for the development of the field (“research tools”).  The ICDC places no restrictions on the use of data to develop downstream technologies that may lead to discoveries that address public needs, especially therapeutics.  For further information about the ICDC Intellectual Property policy, please contact us at $$@ICDCHelpDesk@mail.nih.gov@$$"
    - 
      paragraph: "$$#FAIR Data#$$"
    - 
      paragraph: "The ICDC will adhere to $$[FAIR](https://www.go-fair.org/fair-principles/)$$ principles of data stewardship: Findable, Accessible, Interoperable, and Reusable."
    - 
      paragraph: "$$#Harmonization and Integration#$$"
    - 
      paragraph: "The ICDC functions best for the research community when the data is integrated. Once a project is accepted into the ICDC, the ICDC data team will work with the submitter to review the data looking at data structure, data values, data quality as well as identifying any standards that were utilized. Based on that review, a plan for how to submit the data will be agreed upon between ICDC and the submitter."
    -
      paragraph: "$$#Citing the ICDC in Publications#$$"
    - 
      paragraph: "To cite the ICDC as a resource, reference the data as being available via the NCI’s Integrated Canine Data Commons (ICDC) at $$[https://caninecommons.cancer.gov ](https://caninecommons.cancer.gov )$$ "
    - 
      paragraph: "$$#Citing Individual Studies#$$"
    - 
      paragraph: "ICDC uses human readable identifiers for representing studies referred to as accession IDs."
    - 
      paragraph: "To cite an individual study, cite the native ICDC accession ID as displayed within the User Interface, prefixed by “icdc:” to create a compact identifier that can be resolved via $$[identifiers.org](https://identifiers.org/)$$ (e.g., icdc:000003), and/or cite the URL to the study (e.g., $$[https://caninecommons.cancer.gov/#/study/000003](https://caninecommons.cancer.gov/#/study/000003)$$), where the URL ends with the native ICDC accession ID."

    - 
      paragraph: "$$#Embargo Period for Datasets#$$"
    - 
      paragraph: "Certain datasets made available in the ICDC will have an embargo period during which an associated publication is in the process of being accepted and or published.  An embargo is the release of limited metadata on the ICDC portal until an approval is obtained from the respective data submitter. There are several visual icons intended to flag studies that have an active embargo to inform users that the data will be released to ICDC in the near future."