v0.2.22

yh202109 · Sep 6, 2024 · feb9ef8 · feb9ef8
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diff --git a/README.md b/README.md
@@ -27,6 +27,7 @@ Functions are grouped into:
   - WHODrug: 
 - Standard: 
   - CDISC<sup>[*]</sup>: `stdcdisc.lib`
+  - H7/FHIR: 
   - ISO: `stdiso.pdfsummary` 
 
 <sup>[*]</sup> Documents are not executed while building.

diff --git a/docs/example_ectd2.ipynb b/docs/example_ectd2.ipynb
@@ -43,8 +43,7 @@
     "FDA has released guidance on heading hierarchy of eCTD [^3]<sup>,</sup>[^4].\n",
     "The `ectd` module provides functions for listing and searching within the heading hierarchy.\n",
     "\n",
-    "**Disclaimer**: this module is shared for quick searching and preview headings with the intention to be helpful. The author can not guarantee the correctness of the heading. Please notify the author if any typos were found.\n",
-    "\n"
+    "**Disclaimer**: this module is shared for quick searching and preview headings with the intention to be helpful. The author can not guarantee the correctness of the heading. Please notify the author if any typos were found.\n"
    ]
   },
   {

diff --git a/docs/index.md b/docs/index.md
@@ -14,6 +14,7 @@ example_emt.ipynb
 example_emt2.ipynb
 example_emt3.ipynb
 example_emt4.ipynb
+std_hl7fhir_us_pqcmc.ipynb
 std_iso_pdf.ipynb
 std_iso_idmp.ipynb
 std_cdisc.ipynb

diff --git a/docs/std_cdisc.ipynb b/docs/std_cdisc.ipynb
@@ -26,7 +26,7 @@
             "cell_type": "markdown",
             "metadata": {},
             "source": [
-                "# Std/CDISC/Library Resource\n",
+                "# S/CDISC/Library Resource\n",
                 "\n",
                 "CDISC stands for Clinical Data Interchange Standards Consortium. \n",
                 "As the name indicated, the organization engages with clinical data community and creates and maintains data standards for clinical developments, \n",
@@ -131,9 +131,9 @@
                 "### Get CT Packages\n",
                 "\n",
                 "CDISC Controlled Terminology (CT) is maintained and distributed as part of the National Cancer Institute (NCI) Thesaurus [^5].\n",
-                "CT can be downloaded from NCI FTP and multiple file formats are available (Excel, text, odm.xml, pdf, html, and OWL/RDF formats) [^6].\n",
+                "CT can also be downloaded from NCI FTP and multiple file formats are available (Excel, text, odm.xml, pdf, html, and OWL/RDF formats) [^6].\n",
                 "\n",
-                "To get a list of newest CT packages available:\n",
+                "To get a list of newest CT packages available on CDISC Library:\n",
                 "\n",
                 "```python\n",
                 "cl.get_ct_list()\n",

diff --git a/docs/std_hl7fhir_us_pqcmc.ipynb b/docs/std_hl7fhir_us_pqcmc.ipynb
@@ -0,0 +1,65 @@
+{
+    "cells": [
+        {
+            "cell_type": "markdown",
+            "metadata": {},
+            "source": [
+                "# S/HL7/FHIR-R5/US/PQ-CMC\n",
+                "\n",
+                "Health Level Seven International®, or HL7®, is a nonprofit organization developing and maintaining healthcare technology related standards [^1]<sup>,</sup>[^2].\n",
+                "HL7 Fast Healthcare Interoperability Resources, or HL7 FHIR®, is \"a standard for exchanging healthcare information electronically\".\n",
+                "The FHIR includes multiple components arranged in 5 levels to support healthcare data recording, maintaining, and exchanging [^3].\n",
+                "\n",
+                "A \"resource\" in FHIR is defined as a data block with specified representing format and metadata [^4].\n",
+                "By building resource blocks, the standard can combine blocks and be utilized for precise information processing across systems.\n",
+                "There are multiple formats available for FHIR resource definition [^5].\n",
+                "\n",
+                "FDA released draft structured data standard supporting electronic submission of information related to Pharmaceutical Quality/Chemistry, Manufacturing and Controls (PQ/CMC).\n",
+                "The standard is intended for \"concepts that were considered amenable to structuring and would bring value to the quality review process\" [^6]<sup>,</sup>[^7]<sup>,</sup>[^8].\n",
+                "Project level information and structure are available in PQ-CMC IG [^9]<sup>,</sup>[^10]."
+            ]
+        },
+        {
+            "cell_type": "markdown",
+            "metadata": {},
+            "source": [
+                "## Reference\n",
+                "\n",
+                "[^1]: HL7. (year). HL7. ([web page](https://info.hl7.org/learn-more))\n",
+                "[^2]: HL7. (year). HL7 Essentials. ([web page](https://confluence.hl7.org/display/HE/HL7+Essentials))\n",
+                "[^3]: HL7. (year). FHIR. ([web page](https://www.hl7.org/fhir/))\n",
+                "[^4]: HL7. (year). Base Resource Definitions. ([web page](https://www.hl7.org/fhir/resource.html))\n",
+                "[^5]: HL7. (year). Resource Formats. ([web page](https://www.hl7.org/fhir/resource-formats.html))\n",
+                "[^6]: FDA. 2017. Standardization of Pharmaceutical Quality/Chemistry Manufacturing and Control Data Elements and Terminologies; Request for Comments. ([web page](https://www.regulations.gov/docket/FDA-2017-N-2166/document))\n",
+                "[^7]: FDA. 2022. Draft Pharmaceutical Quality/Chemistry Manufacturing and Controls (PQ/CMC) Data Exchange. ([web page](https://www.fda.gov/media/157085/download?attachment))\n",
+                "[^8]: FDA. 2024. Pharmaceutical Quality - Chemistry, Manufacturing & Controls | PQ/CMC. ([web page](https://www.fda.gov/industry/fda-data-standards-advisory-board/pharmaceutical-quality-chemistry-manufacturing-controls-pqcmc))\n",
+                "[^9]: HL7. (2024). Pharmaceutical Quality - Chemistry, Manufacturing and Controls (PQ-CMC) Submissions to FDA IG. ([web page](https://build.fhir.org/ig/HL7/FHIR-us-pq-cmc-fda/))\n",
+                "[^10]: HL7. (2024). Pharmaceutical Quality - Chemistry, Manufacturing and Controls (PQ-CMC) Submissions to FDA IG. ([github](https://github.com/HL7/FHIR-us-pq-cmc-fda/?tab=readme-ov-file))\n",
+                "\n",
+                "\n",
+                "\n"
+            ]
+        }
+    ],
+    "metadata": {
+        "kernelspec": {
+            "display_name": "Python 3",
+            "language": "python",
+            "name": "python3"
+        },
+        "language_info": {
+            "codemirror_mode": {
+                "name": "ipython",
+                "version": 3
+            },
+            "file_extension": ".py",
+            "mimetype": "text/x-python",
+            "name": "python",
+            "nbconvert_exporter": "python",
+            "pygments_lexer": "ipython3",
+            "version": "3.10.13"
+        }
+    },
+    "nbformat": 4,
+    "nbformat_minor": 4
+}
diff --git a/docs/std_iso_idmp.ipynb b/docs/std_iso_idmp.ipynb
@@ -26,17 +26,18 @@
             "cell_type": "markdown",
             "metadata": {},
             "source": [
-                "# Std/ISO/IDMP\n",
+                "# S/ISO/IDMP\n",
                 "\n",
                 "IDMP stands for Identification of Medicinal Products, \n",
                 "which consists five standards related to data elements, formats, and structures \n",
                 "for communicating information related to medicinal products during development, clinical trials, regulatory submission, post approval monitoring, etc. \n",
                 "ISO IDMP standards are maintained by the International Organization for Standardization (ISO)[^1] \n",
-                "and utilized by FDA[^2] and required by EMA  [^3]<sup>,</sup>[^4]. \n",
+                "and utilized by FDA[^2]<sup>,</sup>[^10]<sup>,</sup>[^11] and required by EMA  [^3]<sup>,</sup>[^4]. \n",
                 "\n",
                 "ISO IDMP includes five standards:\n",
                 " \n",
                 "- ISO 11615 and ISO/TS 20443 / Medicinal Product Identification (MPID) \n",
+                "    - this is for human use medicinal product information, including information about packaging, manufacturer, batch, origin, pharmaceutical product, marketing authorization, substance, version control, etc.\n",
                 "- ISO 11616 and ISO/TS 20451 / Pharmaceutical Product Identifier (PhPID)\n",
                 "- ISO 11238 and ISO/TS 19844 / **Substance** Identification (SubID)\n",
                 "- ISO 11239 and ISO/TS 20440 / **Dosage Form and Route** of Administration\n",
@@ -45,7 +46,12 @@
                 "Related ISO standards:\n",
                 "\n",
                 "- ISO Technical Specifications (TS) 16791:2020 (which complements ISO 11615) assists Automatic Identification and Data Capture (AIDC) related to health informatics.\n",
-                "- ISO Technical Requirements (TR) 14872:2019 includes core principles for maintenance of identifiers and terms supporting IDMP\n"
+                "- ISO Technical Requirements (TR) 14872:2019 includes core principles for maintenance of identifiers and terms supporting IDMP\n",
+                "\n",
+                "Related HL7 standards:\n",
+                "\n",
+                "- HL7 Messaging Specifications\n",
+                "    - this is based on HL7 Common Product Model (CPM) using XML"
             ]
         },
         {
@@ -59,7 +65,7 @@
                 "\n",
                 "Related regulation:\n",
                 "\n",
-                "- Implementing Regulation (EU) No 520/2012:\n",
+                "- Commission Implementing Regulation (EU) No 520/2012:\n",
                 "    - Article 25 *Use of internationally agreed terminology*\n",
                 "    - Article 26 *Use of internationally agreed formats and standards* \n",
                 "    - Article 40 *Transitional provisions*\n",
@@ -74,10 +80,22 @@
                 "Submissions are mandated to support the format by Article 81 *EU database* of Clinical Trial Regulation (EU) No 536/2014.\n",
                 "The format of product information will be migrated to IDMP by planned phases.\n",
                 "\n",
-                "### UNICOM project\n",
+                "### UNICOM Project\n",
                 "\n",
                 "UNICOM is a four years project (2019-2023) that generated discussions and resources for implementation of IDMP standards,\n",
                 "testing, regulatory uses of data standards, and harmonizing data formats [^7]. \n",
+                "\n",
+                "### SPOR Data Management Services \n",
+                "\n",
+                "EMA will establish services maintaining four domains of master data include [^4]:\n",
+                "\n",
+                "- The first phase implementation: \n",
+                "    - Organisations Management Services (OMS) [^8];\n",
+                "    - Referentials Management Services (RMS) [^9].\n",
+                "- The subsequent phase implementation: \n",
+                "    - Substance Management Services (SMS);\n",
+                "    - Product Management Services (PMS);\n",
+                "\n",
                 "\n"
             ]
         },
@@ -93,7 +111,11 @@
                 "[^4]: EMA. (2016). Introduction to ISO Identification of Medicinal Products, SPOR programme. ([pdf](https://www.ema.europa.eu/en/documents/other/introduction-iso-identification-medicinal-products-spor-programme_en.pdf))\n",
                 "[^5]: EMA. (year). SPOR. ([web page](https://spor.ema.europa.eu/sporwi/))\n",
                 "[^6]: EMA. (2024). Guidance on the electronic submission of information on investigational medicinal products for human use in the Extended EudraVigilance medicinal product dictionary (XEVMPD). ([pdf](https://www.ema.europa.eu/en/documents/other/guidance-electronic-submission-information-investigational-medicinal-products-human-use-extended-eudravigilance-medicinal-product-dictionary-xevmpd_en.pdf))\n",
-                "[^7]: UNICOM. (2024). About Unicom. ([web page](https://unicom-project.eu/about/))"
+                "[^7]: UNICOM. (2024). About Unicom. ([web page](https://unicom-project.eu/about/))\n",
+                "[^8]: EMA. (year). Organisation Management Service (OMS). ([web page](https://www.ema.europa.eu/en/human-regulatory-overview/research-and-development/data-medicines-iso-idmp-standards-overview/substance-product-organisation-and-referential-spor-master-data/organisation-management-service-oms))\n",
+                "[^9]: EMA. (year). Referentials Management Service (RMS). ([web page](https://www.ema.europa.eu/en/human-regulatory-overview/research-and-development/data-medicines-iso-idmp-standards-overview/substance-product-organisation-and-referential-spor-master-data/referentials-management-service-rms))\n",
+                "[^10]: FDA. (2023). Toward Global IDMP Implementation: A Focus on Global Use Cases. ([web page](https://www.fda.gov/drugs/news-events-human-drugs/toward-global-idmp-implementation-focus-global-use-cases-11282023))\n",
+                "[^11]: FDA. (2023). Guidance: Identification of Medicinal Products — Implementation and Use. ([pdf](https://www.fda.gov/media/166736/download))"
             ]
         }
     ],

diff --git a/docs/std_iso_pdf.ipynb b/docs/std_iso_pdf.ipynb
@@ -30,7 +30,7 @@
                 }
             },
             "source": [
-                "# Std/ISO/PDF \n",
+                "# S/ISO/PDF \n",
                 "\n",
                 "PDF stands for Portable Document Format, which was created by Adobe[^1], \n",
                 "and currently maintained by the International Organization for Standardization (ISO) as an open source international standard [^2]. \n",
@@ -159,7 +159,7 @@
                 }
             },
             "source": [
-                "The `resize()` function above resized the figure before displaying. Use `display(img)` in `Jupyter` if resizing is not required.\n",
+                "The `resize()` function above resized the figure before displaying. Use `display(img)` in Jupyter if resizing is not required.\n",
                 "\n",
                 "To save the 2nd image on the 4th page to a file, add an existing folder path using `outfolder='add_path_here'`:"
             ]
@@ -182,7 +182,7 @@
             "metadata": {},
             "source": [
                 "The function `get_image()` returns a file path instead of the image when the `outfolder` option is not an empty string. \n",
-                "To read and display the saved image file in `Jupyter`:"
+                "To read and display the saved image file in Jupyter:"
             ]
         },
         {