From 25573ece1cfeb99d90939cf4c0c290f58a21bb53 Mon Sep 17 00:00:00 2001 From: Joel Laxamana Date: Wed, 4 Sep 2024 23:10:18 +0000 Subject: [PATCH] updated github link on home page --- _quarto.yml | 3 + docs/index.html | 3 +- .../osdocumeta_proposal_fda_qtrly.html | 1333 ++++++++--------- docs/search.json | 15 +- index.qmd | 2 + 5 files changed, 609 insertions(+), 747 deletions(-) diff --git a/_quarto.yml b/_quarto.yml index 6f43c1e..aee23f1 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -16,5 +16,8 @@ format: theme: cosmo css: styles.css toc: true + other-links: + - text: Github + href: https://github.com/phuse-org/OSDocuMeta editor: visual \ No newline at end of file diff --git a/docs/index.html b/docs/index.html index d7b748d..459542f 100644 --- a/docs/index.html +++ b/docs/index.html @@ -123,7 +123,7 @@

On this page

    • - +

    Other Links

    @@ -141,6 +141,7 @@

    Background

    Mission

    This project aims to develop a new template, or enhance an existing one such as the Study Data Standardization Plan (SDSP) or Analysis Data Reviewer’s Guide (ADRG), to ensure that metadata pertaining to the versions of statistical packages and procedures is consistently documented in alignment with health authority expectations. This standardized template will streamline the submission of clinical study metadata to health authorities as part of the regulatory review process.

    +

    Github

    diff --git a/docs/references/osdocumeta_proposal_fda_qtrly.html b/docs/references/osdocumeta_proposal_fda_qtrly.html index 118edf4..c457a98 100644 --- a/docs/references/osdocumeta_proposal_fda_qtrly.html +++ b/docs/references/osdocumeta_proposal_fda_qtrly.html @@ -1,361 +1,191 @@ - - - - - - - - - - + - - PHUSE WG : Open-Source Metadata Documentation (OSDocuMeta) – ADRG Template Update Proposal : An Open-Source Edition - - - - - - - - - - - - - .callout .callout-body-container { - flex-grow: 1; - } - - .callout.callout-style-simple .callout-body { - font-size: 1rem; - font-weight: 400; - } - - .callout.callout-style-default .callout-body { - font-size: 0.9rem; - font-weight: 400; - } - - .callout.callout-titled.callout-style-simple .callout-body { - margin-top: 0.2em; - } - - .callout:not(.callout-titled) .callout-body { - display: flex; - } - .callout:not(.no-icon).callout-titled.callout-style-simple .callout-content { - padding-left: 1.6em; - } - - .callout.callout-titled .callout-header { - padding-top: 0.2em; - margin-bottom: -0.2em; - } - - .callout.callout-titled .callout-title p { - margin-top: 0.5em; - margin-bottom: 0.5em; - } - - .callout.callout-titled.callout-style-simple .callout-content p { - margin-top: 0; - } + + + + + + + + + + + + + + + + + + + + + - .callout.callout-titled.callout-style-default .callout-content p { - margin-top: 0.7em; - } + - .callout.callout-style-simple div.callout-title { - border-bottom: none; - font-size: .9rem; - font-weight: 600; - opacity: 75%; - } +
    +
    + +
    + +
    + + + + +
    - .callout.callout-style-default div.callout-title { - border-bottom: none; - font-weight: 600; - opacity: 85%; - font-size: 0.9rem; - padding-left: 0.5em; - padding-right: 0.5em; - } +
    +
    +

    ADRG Template Update Proposal : An Open-Source Edition

    +
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    +
    Author
    +
    +

    OSDocuMeta Working Group

    +
    +
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- } - - div.callout-caution.callout-style-default .callout-title { - background-color: #ffe5d0 - } + + +
    + - - - - -
    -
    -
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    ADRG Template Update Proposal : An Open-Source Edition

    +
    -
    -
    -
    -OSDocuMeta Working Group -
    -
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    -
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    +

    About the WG

    - -
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    Add background and mission statement - see Home page of website.

    +
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    Add background and mission statement - see Home page of website.

    • Background
    • Mission
    -
    -
    -
    -

    About Us

    -
    -
    -

    Pics of us and 2 sentences about each of us

    +
    +
    +

    About Us

    +
    +

    Pics of us and 2 sentences about each of us

    • Lovemore Gavaka (Co-Lead)

    • Joel Laxamana (Co-Lead)

      • @@ -364,458 +194,477 @@

      Pics of us and 2 sentences about each of us

    • … add others

    • Chris Price (Sponsor)

    -
    -
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    -

    Where we are

    -
    -
    -

    Share the current ADRG template we have now and how we want to update the template to include open-source metadata - Lovemore

    +
    +
    +

    Where we are

    +
    +

    Share the current ADRG template we have now and how we want to update the template to include open-source metadata - Lovemore

    • Current ADRG Template
    • How we want to update the template
    -
    -

    Current ADRG from Pinnacle 21 vs an ADRG where Open-source submission was used,

    +
    +

    Current ADRG from Pinnacle 21 vs an ADRG where Open-source submission was used,

    -
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    list out the differences and note these differecnes as the updates we want to make to the current ADRG template to be Open-Source friendly.

    -
    -
    -
    -

    Where we’re going

    - +
    +

    list out the differences and note these differecnes as the updates we want to make to the current ADRG template to be Open-Source friendly.

    -
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    List out all of the tables in this ADRG, here, that we can automate and generate sourcing available metadata

    +
    +
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    Where we’re going

    +
    +

    List out all of the tables in this ADRG, here, that we can automate and generate sourcing available metadata

    • 1.2 Study Data Standards and Dictionary Inventory (Can this come from the TS SDTM domain?)

    • 3.1 Core Variables (come from the define.xml specificaions) -4.2 Data Dependencies (may need to some code scraping to read through each ADaM program and identify any other ADaMs being sourced in to create the ADaM) -5.2 Analysis Datasets (read in all of the .xpts in the submission package to extract the metadata for each ADaM to fill in this table) -6.2 Issues Summary (extract report from P21) -7.2 ADaM Programs (read in all of the .xpts in the submission package to extract the list of ADaMs and it’s label for each ADaM to fill in this table) -7.3 Analysis Output Programs (this one may be tricky as there are many study specific Selection Criteria to include) -7.4 Proprietary R Packages (Joel has some code for this, in R, essentially using SessionInfo() and {renv}) eCTD structure.

    • With these listed updates we want to make, we can utilize metadata to help fill in this information in the ADRG

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    Challenge the file format delivered to the FDA, not only .pdf, but can we additionally submit .qmd files (or other file formats) as well so that the ADRG can be reproduced on the Agency side to help better click on code from the ADRG to help execute. Note : eCTD specifications say we can submit .qmd for analysis, but can we also submit it as a form of ADRG documentation.

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    A new tool to automate ADRG generation

    - +
    +

    Challenge the file format delivered to the FDA, not only .pdf, but can we additionally submit .qmd files (or other file formats) as well so that the ADRG can be reproduced on the Agency side to help better click on code from the ADRG to help execute. Note : eCTD specifications say we can submit .qmd for analysis, but can we also submit it as a form of ADRG documentation.

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    Do we want to bring up the possibility of creating an open-source package for this to help automate the use of metadata in the ADRG documentation.

    +
    +
    +

    A new tool to automate ADRG generation

    +
    +

    Do we want to bring up the possibility of creating an open-source package for this to help automate the use of metadata in the ADRG documentation.

    • {osdocumeta}
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    -
    +
    +
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    The End. Questions?

    -
    -
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    - - - - - - - - - - - - - - - - - - - - - - + const findCites = (el) => { + const parentEl = el.parentElement; + if (parentEl) { + const cites = parentEl.dataset.cites; + if (cites) { + return { + el, + cites: cites.split(' ') + }; + } else { + return findCites(el.parentElement) + } + } else { + return undefined; + } + }; + var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]'); + for (var i=0; i + + + + \ No newline at end of file diff --git a/docs/search.json b/docs/search.json index ead1a29..716526f 100644 --- a/docs/search.json +++ b/docs/search.json @@ -4,7 +4,7 @@ "href": "index.html", "title": "Welcome to the PHUSE Open-Source Metadata Documentation Working Group Site", "section": "", - "text": "Link to PHUSE Working Group Proposal, here.\n\n\nHistorically, the use of proprietary statistical programming languages entailed the inclusion of general statements within the Statistical Analysis Plan (SAP) regarding the software and version employed for generating analyses. However, with the increasing adoption of open-source statistical programming languages, there is a necessity to provide detailed metadata for each package used, as a general statement is no longer adequate.\n\n\n\nThis project aims to develop a new template, or enhance an existing one such as the Study Data Standardization Plan (SDSP) or Analysis Data Reviewer’s Guide (ADRG), to ensure that metadata pertaining to the versions of statistical packages and procedures is consistently documented in alignment with health authority expectations. This standardized template will streamline the submission of clinical study metadata to health authorities as part of the regulatory review process." + "text": "Link to PHUSE Working Group Proposal, here.\n\n\nHistorically, the use of proprietary statistical programming languages entailed the inclusion of general statements within the Statistical Analysis Plan (SAP) regarding the software and version employed for generating analyses. However, with the increasing adoption of open-source statistical programming languages, there is a necessity to provide detailed metadata for each package used, as a general statement is no longer adequate.\n\n\n\nThis project aims to develop a new template, or enhance an existing one such as the Study Data Standardization Plan (SDSP) or Analysis Data Reviewer’s Guide (ADRG), to ensure that metadata pertaining to the versions of statistical packages and procedures is consistently documented in alignment with health authority expectations. This standardized template will streamline the submission of clinical study metadata to health authorities as part of the regulatory review process.\nGithub" }, { "objectID": "index.html#background", @@ -18,7 +18,7 @@ "href": "index.html#mission", "title": "Welcome to the PHUSE Open-Source Metadata Documentation Working Group Site", "section": "", - "text": "This project aims to develop a new template, or enhance an existing one such as the Study Data Standardization Plan (SDSP) or Analysis Data Reviewer’s Guide (ADRG), to ensure that metadata pertaining to the versions of statistical packages and procedures is consistently documented in alignment with health authority expectations. This standardized template will streamline the submission of clinical study metadata to health authorities as part of the regulatory review process." + "text": "This project aims to develop a new template, or enhance an existing one such as the Study Data Standardization Plan (SDSP) or Analysis Data Reviewer’s Guide (ADRG), to ensure that metadata pertaining to the versions of statistical packages and procedures is consistently documented in alignment with health authority expectations. This standardized template will streamline the submission of clinical study metadata to health authorities as part of the regulatory review process.\nGithub" }, { "objectID": "minutes.html", @@ -101,8 +101,8 @@ "objectID": "references/osdocumeta_proposal_fda_qtrly.html#add-background-and-mission-statement---see-home-page-of-website.", "href": "references/osdocumeta_proposal_fda_qtrly.html#add-background-and-mission-statement---see-home-page-of-website.", "title": "ADRG Template Update Proposal : An Open-Source Edition", - "section": "Add background and mission statement - see Home page of website.", - "text": "Add background and mission statement - see Home page of website.\n\nBackground\nMission" + "section": "", + "text": "Background\nMission" }, { "objectID": "references/osdocumeta_proposal_fda_qtrly.html#pics-of-us-and-2-sentences-about-each-of-us", @@ -152,5 +152,12 @@ "title": "ADRG Template Update Proposal : An Open-Source Edition", "section": "Do we want to bring up the possibility of creating an open-source package for this to help automate the use of metadata in the ADRG documentation.", "text": "Do we want to bring up the possibility of creating an open-source package for this to help automate the use of metadata in the ADRG documentation.\n\n{osdocumeta}" + }, + { + "objectID": "references/osdocumeta_proposal_fda_qtrly.html", + "href": "references/osdocumeta_proposal_fda_qtrly.html", + "title": "ADRG Template Update Proposal : An Open-Source Edition", + "section": "", + "text": "Background\nMission" } ] \ No newline at end of file diff --git a/index.qmd b/index.qmd index ae852e1..099451c 100644 --- a/index.qmd +++ b/index.qmd @@ -14,4 +14,6 @@ Historically, the use of proprietary statistical programming languages entailed This project aims to develop a new template, or enhance an existing one such as the Study Data Standardization Plan (SDSP) or Analysis Data Reviewer’s Guide (ADRG), to ensure that metadata pertaining to the versions of statistical packages and procedures is consistently documented in alignment with health authority expectations. This standardized template will streamline the submission of clinical study metadata to health authorities as part of the regulatory review process. +[Github](https://phuse-org.github.io/OSDocuMeta/) + ##