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#https://www.mkdocs.org/user-guide/configuration/#
site_name: HEAL Data Packaging
site_url: https://norc-heal.github.io/heal-data-pkg-guide
repo_url: https://github.com/norc-heal/heal-data-pkg-guide
nav:
- What is a data package:
- intro/index.md
- Study files: intro/study-file.md
- Standard data package metadata: intro/sdpmd.md
- Shareable data package: intro/shareable.md
#- The Resource Tracker: overview/resource.md
- Create your data package:
- fit/index.md
- Best fit questions: fit/best-fit-questions.md
- Best fit annotation recs:
- fit/best-fit-recs/index.md
- Early, results-support, standard resources: fit/best-fit-recs/early-res-stand.md
- Early, results-support, low resources: fit/best-fit-recs/early-res-low.md
- Early, dataset-sharing, standard resources: fit/best-fit-recs/early-data-stand.md
- Early, dataset-sharing, low resources: fit/best-fit-recs/early-data-low.md
- Late, results-support, standard resources: fit/best-fit-recs/late-res-stand.md
- Late, results-support, low resources: fit/best-fit-recs/late-res-low.md
- Late, dataset-sharing, standard resources: fit/best-fit-recs/late-data-stand.md
- Late, dataset-sharing, low resources: fit/best-fit-recs/late-data-low.md
#- Your data sharing orientation: fit/data-sharing-orientation.md
#- Your study stage: fit/study-stage.md
#- Early in study: fit/guidance-1.md
#- Late in study: fit/late.md
- Prepare your data package for submission:
- submit/index.md
- Create an open-access now shareable data package: submit/open-access-now.md
- Create an open-access by date shareable data package: submit/open-access-date.md
- Create a managed-access now shareable data package: submit/managed-access-now.md
- Create a managed-access by date shareable data package: submit/managed-access-date.md
#- Annotation:
# - Annotation Approaches: annot/index.md
# - Wholistic vs. Minimal: annot/introholmin.md
# - As you go vs. Top-down: annot/introaddtop.md
- More information about data packaging:
- overview/index.md
- What is a data package?: overview/what.md
- Who should create a data package?: overview/who.md
- Why should you create a data package?: overview/why.md
- Where should you create a data package?: overview/where.md
- When should you start thinking about creating a data package?: overview/when.md
- How should you create your data package?: overview/how.md
- Guidance & Resources:
- g-and-r/index.md
- Guidance:
- guidance/index.md
- File org and naming:
- file-o-and-n/index.md
- File organization: guidance/file-org.md
- File naming: guidance/file-name.md
- Deidentification:
- g-and-r/deid/index.md
- Deidentification of non-genomic data: g-and-r/deid/deid.md
- Deidentification of genomic data: g-and-r/deid/deidgenome.md
- Repositories:
- g-and-r/repo/index.md
- Repository selection: g-and-r/repo/repo.md
- Repository submission:
- g-and-r/repo/submit/index.md
- Use case - SRA submission: g-and-r/repo/submit/srasubmit.md
- Research community-specific metadata standards: g-and-r/rescommet.md
- Resources:
- resources/index.md
- Metadata schemas:
- schemas/index.md
- Study Overview: schemas/md_study_overview.md
- Experiment Tracker: schemas/md_experiment_tracker.md
- Resource Tracker: schemas/md_resource_tracker.md
- Results Tracker: schemas/md_results_tracker.md
- Data Dictionary: schemas/md_data_dictionary.md
- Terms & Concepts:
- terms/index.md
#- File Types: terms/files.md
#- Holistic vs. Minimal Annotation: terms/holmin.md
#- Add-as-you-go vs. Top-down Annotation: terms/addtop.md
#- File org and naming:
# - File organization: terms/name.md
# - File naming: terms/name.md
#- Data sharing orientations: terms/sharing.md
#- Metadata schemas:
# - Experiment Tracker: schemas/md_experiment_tracker.md
# - Resource Tracker: schemas/md_resource_tracker.md
# - Results Tracker: schemas/md_results_tracker.md
# - Metadata templates:
# - Overview: terms/standard-data-pkg-metadata.md
#- Study-level Metadata:
# - Resource Tracker: terms/studylevel/resource.md
# - Experiment Tracker: terms/studylevel/exp.md
#- File-level Metadata: terms/filelevel.md
#- Documenting dependencies: terms/depend.md
theme:
name: material
palette:
scheme: heal_platform
font:
text: Montserrat
logo: assets/HEAL_Initiative_White-cropped.svg
features:
- navigation.indexes
# Disable for now, as it causes problems with links to sections in Safari
# https://github.com/squidfunk/mkdocs-material/issues/3797
# - navigation.instant
- navigation.indexes
#- navigation.tabs
#- navigation.tabs.sticky
- navigation.tracking
#- navigation.sections
#- toc.integrate
favicon: assets/heal_logo.png
extra_css:
- stylesheets/extra.css
extra:
homepage: https://github.com/norc-heal
use_directory_urls: true
markdown_extensions:
- admonition
- attr_list
- md_in_html
- mdx_truly_sane_lists
- toc:
permalink: True
baselevel: 1
- pymdownx.superfences
- pymdownx.extra
- pymdownx.tabbed:
alternate_style: true
- pymdownx.details
- pymdownx.snippets:
# url_download: True
check_paths: true
base_path: docs
plugins:
- search
- mkdocs-video:
is_video: True
- external-markdown
- drawio_file
#- exclude:
# glob:
# - snippets/*
# - snippets
# TODO: add footer (this may be included in the custom jinja template?)
# [](https://ctds.uchicago.edu/gen3)[](https://ctds.uchicago.edu/)
# [](anchor link)
# function readMore() { var dots = document.getElementById("dots"); var moreText = document.getElementById("more"); var btnText = document.getElementById("read-more-btn"); var btnText = document.getElementById("read-more-explorer"); if (dots.style.display === "none") { dots.style.display = "inline"; btnText.innerHTML = "Read more"; moreText.style.display = "none"; } else { dots.style.display = "none"; btnText.innerHTML = "Read less"; moreText.style.display = "inline"; } }