diff --git a/.nojekyll b/.nojekyll index aa382625..102ffe35 100644 --- a/.nojekyll +++ b/.nojekyll @@ -1 +1 @@ -06bb3302 \ No newline at end of file +a417f2da \ No newline at end of file diff --git a/develop/01_RDM_intro.html b/develop/01_RDM_intro.html index 2307b96a..f2a60d3e 100644 --- a/develop/01_RDM_intro.html +++ b/develop/01_RDM_intro.html @@ -295,7 +295,7 @@

1. Introduction to RDM

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diff --git a/develop/02_DMP.html b/develop/02_DMP.html index 92986f41..97a72663 100644 --- a/develop/02_DMP.html +++ b/develop/02_DMP.html @@ -261,7 +261,7 @@

2. Data Management Plan

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diff --git a/develop/03_DOD.html b/develop/03_DOD.html index a213cacb..d3885aeb 100644 --- a/develop/03_DOD.html +++ b/develop/03_DOD.html @@ -311,7 +311,7 @@

3. Data organization and storage

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Naming conventions

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4. Documentation for biodata

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Sources

  • RMDKit: https://rdmkit.elixir-europe.org/data_brokering#collecting-and-processing-the-metadata-and-data
  • FAIRsharing.org: provide a searchable database of metadata standards for a wide variety of disciplines
  • -

    Other sources: - Johns Hopkins Sheridan libraries, RDM. They provide a list of medical metadata standards resources.
    -- KU Leuven Guidance: https://www.kuleuven.be/rdm/en/guidance/documentation-metadata - Transcriptomics metadata standards and fields - Bionty: Biological ontologies for data scientists. - NIH standardizing data collection - Observational Health Data Sciences and Informatics (OHDSI) OMOP Common Data Model

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    Other sources:

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    Tools and software

    diff --git a/develop/05_VC.html b/develop/05_VC.html index cb1f782c..672ce4dd 100644 --- a/develop/05_VC.html +++ b/develop/05_VC.html @@ -267,7 +267,7 @@

    5. Data Analysis with Version Control

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    6. Processing and analyzing biodata

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    diff --git a/develop/07_repos.html b/develop/07_repos.html index 08bd0abb..1f024e27 100644 --- a/develop/07_repos.html +++ b/develop/07_repos.html @@ -260,7 +260,7 @@

    7. Storing and sharing biodata

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    Practical material

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    diff --git a/develop/examples/NGS_OS_FAIR.html b/develop/examples/NGS_OS_FAIR.html index 5e6ba059..fa706c35 100644 --- a/develop/examples/NGS_OS_FAIR.html +++ b/develop/examples/NGS_OS_FAIR.html @@ -231,7 +231,7 @@

    Applied Open Science and FAIR principles to NGS

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    diff --git a/develop/examples/NGS_management.html b/develop/examples/NGS_management.html index edb18ffa..0e0893d6 100644 --- a/develop/examples/NGS_management.html +++ b/develop/examples/NGS_management.html @@ -259,7 +259,7 @@

    NGS data strategies

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    diff --git a/develop/examples/NGS_metadata.html b/develop/examples/NGS_metadata.html index 61438d88..32735c45 100644 --- a/develop/examples/NGS_metadata.html +++ b/develop/examples/NGS_metadata.html @@ -231,7 +231,7 @@

    NGS Assay and Project metadata

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    Sample metadata fie
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    Project metadata f
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    Assay metadata field
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    Assay metadata field
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    Practical material

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    Suggestions for N
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    Computational Research Data Management

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    diff --git a/practical_workflows.html b/practical_workflows.html index d43e70a3..41c5669d 100644 --- a/practical_workflows.html +++ b/practical_workflows.html @@ -157,7 +157,7 @@

    Computational Research Data Management

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    diff --git a/search.json b/search.json index 00d84638..319328d0 100644 --- a/search.json +++ b/search.json @@ -148,7 +148,7 @@ "href": "develop/04_metadata.html#wrap-up", "title": "4. Documentation for biodata", "section": "Wrap up", - "text": "Wrap up\nIn this lesson, we’ve covered the importance of attaching metadata to your data for future reusability and comprehension. We briefly introduced various controlled vocabularies and provided several sources for inspiration. Implementing ontologies is optional, as their usage complexity varies.\nOptionally, if you’ve gone through the lesson, you’ve learned how to use the metadata YAML files to create a database and a catalog browser using Shiny apps. This makes it easy to manage all assays together.\n\nSources\n\nRMDKit: https://rdmkit.elixir-europe.org/data_brokering#collecting-and-processing-the-metadata-and-data\nFAIRsharing.org: provide a searchable database of metadata standards for a wide variety of disciplines\n\nOther sources: - Johns Hopkins Sheridan libraries, RDM. They provide a list of medical metadata standards resources.\n- KU Leuven Guidance: https://www.kuleuven.be/rdm/en/guidance/documentation-metadata - Transcriptomics metadata standards and fields - Bionty: Biological ontologies for data scientists. - NIH standardizing data collection - Observational Health Data Sciences and Informatics (OHDSI) OMOP Common Data Model\n\n\nTools and software\n\nRightfield: open source tool facilitates the integration of ontology terms into Excel spreadsheet.\nOwlready2: Python package, enables the loading of ontologies as Python objects. This versatile tool allows users to manipulate and store ontology classes, instances, and properties as needed.", + "text": "Wrap up\nIn this lesson, we’ve covered the importance of attaching metadata to your data for future reusability and comprehension. We briefly introduced various controlled vocabularies and provided several sources for inspiration. Implementing ontologies is optional, as their usage complexity varies.\nOptionally, if you’ve gone through the lesson, you’ve learned how to use the metadata YAML files to create a database and a catalog browser using Shiny apps. This makes it easy to manage all assays together.\n\nSources\n\nRMDKit: https://rdmkit.elixir-europe.org/data_brokering#collecting-and-processing-the-metadata-and-data\nFAIRsharing.org: provide a searchable database of metadata standards for a wide variety of disciplines\n\nOther sources:\n\nJohns Hopkins Sheridan libraries, RDM. They provide a list of medical metadata standards resources.\n\nKU Leuven Guidance: https://www.kuleuven.be/rdm/en/guidance/documentation-metadata\nTranscriptomics metadata standards and fields\nBiological ontologies for data scientists,Bionty\nNIH standardizing data collection\nObservational Health Data Sciences and Informatics (OHDSI) OMOP Common Data Model\n\n\n\nTools and software\n\nRightfield: open source tool facilitates the integration of ontology terms into Excel spreadsheet.\nOwlready2: Python package, enables the loading of ontologies as Python objects. This versatile tool allows users to manipulate and store ontology classes, instances, and properties as needed.", "crumbs": [ "Course material", "Key practices", diff --git a/sitemap.xml b/sitemap.xml index f66523ce..83fa03d7 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -2,70 +2,70 @@ https://hds-sandbox.github.io/RDM_NGS_course/develop/03_DOD.html - 2024-04-11T14:04:47.292Z + 2024-04-15T11:59:58.415Z https://hds-sandbox.github.io/RDM_NGS_course/develop/04_metadata.html - 2024-04-11T14:04:47.292Z + 2024-04-15T11:59:58.415Z https://hds-sandbox.github.io/RDM_NGS_course/develop/02_DMP.html - 2024-04-11T14:04:47.292Z + 2024-04-15T11:59:58.415Z https://hds-sandbox.github.io/RDM_NGS_course/develop/contributors.html - 2024-04-11T14:04:47.308Z + 2024-04-15T11:59:58.435Z https://hds-sandbox.github.io/RDM_NGS_course/develop/07_repos.html - 2024-04-11T14:04:47.292Z + 2024-04-15T11:59:58.415Z https://hds-sandbox.github.io/RDM_NGS_course/develop/examples/NGS_metadata.html - 2024-04-11T14:04:47.308Z + 2024-04-15T11:59:58.435Z https://hds-sandbox.github.io/RDM_NGS_course/practical_workflows.html - 2024-04-11T14:04:47.336Z + 2024-04-15T11:59:58.459Z https://hds-sandbox.github.io/RDM_NGS_course/cards/JARomero.html - 2024-04-11T14:04:47.292Z + 2024-04-15T11:59:58.415Z https://hds-sandbox.github.io/RDM_NGS_course/index.html - 2024-04-11T14:04:47.336Z + 2024-04-15T11:59:58.459Z https://hds-sandbox.github.io/RDM_NGS_course/cards/AlbaMartinez.html - 2024-04-11T14:04:47.292Z + 2024-04-15T11:59:58.415Z https://hds-sandbox.github.io/RDM_NGS_course/use_cases.html - 2024-04-11T14:04:47.336Z + 2024-04-15T11:59:58.459Z https://hds-sandbox.github.io/RDM_NGS_course/develop/examples/NGS_OS_FAIR.html - 2024-04-11T14:04:47.308Z + 2024-04-15T11:59:58.435Z https://hds-sandbox.github.io/RDM_NGS_course/develop/examples/NGS_management.html - 2024-04-11T14:04:47.308Z + 2024-04-15T11:59:58.435Z https://hds-sandbox.github.io/RDM_NGS_course/develop/01_RDM_intro.html - 2024-04-11T14:04:47.292Z + 2024-04-15T11:59:58.415Z https://hds-sandbox.github.io/RDM_NGS_course/develop/06_pipelines.html - 2024-04-11T14:04:47.292Z + 2024-04-15T11:59:58.415Z https://hds-sandbox.github.io/RDM_NGS_course/develop/05_VC.html - 2024-04-11T14:04:47.292Z + 2024-04-15T11:59:58.415Z https://hds-sandbox.github.io/RDM_NGS_course/develop/practical_workshop.html - 2024-04-11T14:04:47.336Z + 2024-04-15T11:59:58.459Z diff --git a/use_cases.html b/use_cases.html index cc2382a6..d5b9f3ef 100644 --- a/use_cases.html +++ b/use_cases.html @@ -223,7 +223,7 @@

    RDM use cases

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