docs: EDC started with subjects plus some minor corrections all around

ddRPB · Sep 27, 2023 · b330c71 · b330c71
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diff --git a/admin/admin.rst b/admin/admin.rst
@@ -1,7 +1,11 @@
 Administration
 ==============
 
-The Administration module is available only to users with ROLE_ADMIN permission.
+.. note::
+	The Administration module is available only to users with ROLE_ADMIN permission.
+
+Concept
+-------
 
 .. image:: /img/administration/admin.png
 

diff --git a/api/api.rst b/api/api.rst
@@ -1,4 +1,8 @@
 Web Services
 ============
 
-The API access it allowed for all users with enabled and valid API-Key.
+.. note::
+	The API access it allowed for all users with enabled and valid API-Key.
+
+Concept
+-------
diff --git a/cms/cms.rst b/cms/cms.rst
@@ -1,4 +1,8 @@
 Content Management
 ==================
 
-The Content Management (CMS) module is available only to users with ROLE_CMS_USER permission.
+.. note::
+	The Content Management (CMS) module is available only to users with ROLE_CMS_USER permission.
+
+Concept
+-------
diff --git a/ctms/ctms.rst b/ctms/ctms.rst
@@ -1,4 +1,8 @@
 Clinical Trial Management
 =========================
 
-The Clinical Trial Management (CTMS) module is available only to users with ROLE_CTMS_USER permission.
+.. note::
+	The Clinical Trial Management (CTMS) module is available only to users with ROLE_CTMS_USER permission.
+
+Concept
+-------
diff --git a/edc/edc.rst b/edc/edc.rst
@@ -57,13 +57,14 @@ allows users to defined access based on these two level hierarchy.
 	EDC module study/sites hierarchy.
 
 .. note::
-	Additional abstract sites such as DELETED and DUMMY are often used to control visibility of patients in the
+	Additional abstract sites such as DROPOUT, DELETED and DUMMY are often used to control visibility of subjects in the
 	project and logically separate the access to the data.
 
 .. toctree::
 	:maxdepth: 1
 	:caption: Tasks:
 
+	partner-site-identifiers
 	view-study-configuration
 	change-study-site
 
@@ -83,6 +84,7 @@ provide and study subjects enrollment overview, :numref:`img-edc-subjects`.
 	:maxdepth: 1
 	:caption: Tasks:
 
+	subject-ids
 	enroll-subjects
 	reidentify-subject
 

diff --git a/edc/enroll-subjects.rst b/edc/enroll-subjects.rst
@@ -1,5 +1,9 @@
 Enroll New Study Subjects
 =========================
 
+.. note::
+	ROLE_PID_NEW ROLE_EDC_SUBMIT
+
+Before the new subject can be enrolled to the study, it is usually necessary to generate PID for this subject (When PID generator aka patient identity management system is used), see Fig. 8. The user is asked to fill some basic identity data. The optional identity data (like place or residence, ZIP code and birthname) are recommended if they are available for data entry personnel in order to guarantee uniqueness of generated PID. After data is provided the click on button Generate will trigger the process. The algorithm is trying to figure out if the patient with provided identity data is already in registered in the system (return his PID) or if it is new patient (generate new PID). After PID is provided the second Submit button is responsible for triggering the enrolment of the subject to the study.
 
 
diff --git a/edc/partner-site-identifiers.rst b/edc/partner-site-identifiers.rst
@@ -0,0 +1,148 @@
+Explaining Partner Site Identifiers
+===================================
+
+Each partner site registered in RPB is assigned a unique capitalised identifier. These global identifiers are supposed
+to be used also across multiple RPB platform instances. They are among other things utilised as prefix e.g.
+while defining study site protocol codes or patient pseudonyms in muli centre trials.
+
+.. note::
+	Additional abstract partners sites such as DROPOUT, DELETED and DUMMY used to control visibility of subjects in the
+	project also have their own reserved identifier DRO, DEL and DUM.
+
+The following table represents the curent global list of *partner site identifiers* governed by RPB maintainers:
+
++------------+---------------------------------------------------+
+| Identifier | Partner Site Name                                 |
++============+===================================================+
+| AUH        | Aarhus University Hospital                        |
++------------+---------------------------------------------------+
+| AVL        | Antoni van Leeuwenhoek Hospital                   |
++------------+---------------------------------------------------+
+| B          | Charité Berlin                                    |
++------------+---------------------------------------------------+
+| BFS        | Bundesamt für Strahlenschutz                      |
++------------+---------------------------------------------------+
+| CAU        | Christian-Albrechts-Universität zu Kiel           |
++------------+---------------------------------------------------+
+| CHM        | Christie Hospital, Manchester                     |
++------------+---------------------------------------------------+
+| CUH        | Copenhagen University Hospital Herlev             |
++------------+---------------------------------------------------+
+| CZE        | Catharina Ziekenhuis Eindhoven                    |
++------------+---------------------------------------------------+
+| D          | Universitätsklinikum Düsseldorf                   |
++------------+---------------------------------------------------+
+| DD         | Universitätsklinikum Dresden                      |
++------------+---------------------------------------------------+
+| DEL        | DELETED                                           |
++------------+---------------------------------------------------+
+| DKFZ       | Deutsches Krebsforschungszentrum                  |
++------------+---------------------------------------------------+
+| DKTK       | German Cancer Consortium                          |
++------------+---------------------------------------------------+
+| DRO        | DROPOUT                                           |
++------------+---------------------------------------------------+
+| DUM        | DUMMY                                             |
++------------+---------------------------------------------------+
+| HZDR       | Helmholtz-Zentrum Dresden-Rossendorf              |
++------------+---------------------------------------------------+
+| ICR        | Institut Claudius Regaud                          |
++------------+---------------------------------------------------+
+| IGR        | Institut Gustave Roussy                           |
++------------+---------------------------------------------------+
+| KSSG       | Kantonsspital St.Gallen                           |
++------------+---------------------------------------------------+
+| KMH        | Kliniken Maria Hilf                               |
++------------+---------------------------------------------------+
+| SKC        | Klinikum Chemnitz                                 |
++------------+---------------------------------------------------+
+| KGR        | Klinikum Görlitz                                  |
++------------+---------------------------------------------------+
+| KHDF       | Krankenhaus Dresden-Friedrichstadt                |
++------------+---------------------------------------------------+
+| LKHI       | Landeskrankenhaus Innsbruck                       |
++------------+---------------------------------------------------+
+| LKHS       | Landeskrankenhaus Salzburg                        |
++------------+---------------------------------------------------+
+| MRO        | Maastro                                           |
++------------+---------------------------------------------------+
+| MHS        | Marienhospital Stuttgart                          |
++------------+---------------------------------------------------+
+| MHH        | Medizinische Hochschule Hannover                  |
++------------+---------------------------------------------------+
+| MVZUKT     | MVZ Stuttgart                                     |
++------------+---------------------------------------------------+
+| MHU        | München LMU                                       |
++------------+---------------------------------------------------+
+| MTU        | München TUM                                       |
++------------+---------------------------------------------------+
+| NO         | Olsztyn                                           |
++------------+---------------------------------------------------+
+| PZ         | Poznan                                            |
++------------+---------------------------------------------------+
+| RUMC       | Radboud University Medical Center                 |
++------------+---------------------------------------------------+
+| RMH        | Royal Marsden                                     |
++------------+---------------------------------------------------+
+| STRHAR     | Strahlentherapie Harburg                          |
++------------+---------------------------------------------------+
+| UZGENT     | University Hospital Ghent                         |
++------------+---------------------------------------------------+
+| USZ        | University Hospital Zürich                        |
++------------+---------------------------------------------------+
+| UZL        | University Hospitals Leuven                       |
++------------+---------------------------------------------------+
+| UMCG       | University Medical Centre Groningen               |
++------------+---------------------------------------------------+
+| UL         | Universität zu Lübeck                             |
++------------+---------------------------------------------------+
+| UKB        | Universitätsklinikum Bonn                         |
++------------+---------------------------------------------------+
+| UKS        | Universitätsklinikum des Saarlandes               |
++------------+---------------------------------------------------+
+| DD         | Universitätsklinikum Dresden                      |
++------------+---------------------------------------------------+
+| D          | Universitätsklinikum Düsseldorf                   |
++------------+---------------------------------------------------+
+| ER         | Universitätsklinikum Erlangen                     |
++------------+---------------------------------------------------+
+| E          | Universitätsklinikum Essen                        |
++------------+---------------------------------------------------+
+| F          | Universitätsklinikum Frankfurt Goethe-Universität |
++------------+---------------------------------------------------+
+| FR         | Universitätsklinikum Freiburg                     |
++------------+---------------------------------------------------+
+| UKH        | Universitätsklinikum Halle (Saale)                |
++------------+---------------------------------------------------+
+| UKE        | Universitätsklinikum Hamburg-Eppendorf            |
++------------+---------------------------------------------------+
+| HD         | Universitätsklinikum Heidelberg                   |
++------------+---------------------------------------------------+
+| UKJ        | Universitätsklinikum Jena                         |
++------------+---------------------------------------------------+
+| UKK        | Universitätsklinikum Köln                         |
++------------+---------------------------------------------------+
+| UKL        | Universitätsklinikum Leipzig                      |
++------------+---------------------------------------------------+
+| OVGU       | Universitätsklinikum Magdeburg                    |
++------------+---------------------------------------------------+
+| UKM        | Universitätsklinikum Münster                      |
++------------+---------------------------------------------------+
+| UKR        | Universitätsklinikum Regensburg                   |
++------------+---------------------------------------------------+
+| UKSH       | Universitätsklinikum Schleswig-Holstein           |
++------------+---------------------------------------------------+
+| TUE        | Universitätsklinikum Tübingen                     |
++------------+---------------------------------------------------+
+| UMG        | Universitätsmedizin Göttingen                     |
++------------+---------------------------------------------------+
+| UMMZ       | Universitätsmedizin Mainz                         |
++------------+---------------------------------------------------+
+| UMM        | Universitätsmedizin Mannheim                      |
++------------+---------------------------------------------------+
+| HRO        | Universitätsmedizin Rostock                       |
++------------+---------------------------------------------------+
+| UCL        | Université catholique de Louvain                  |
++------------+---------------------------------------------------+
+| HUVR       | Virgen del Rocío University Hospital              |
++------------+---------------------------------------------------+
diff --git a/edc/reidentify-subject.rst b/edc/reidentify-subject.rst
@@ -1,5 +1,10 @@
 Re-identify Study Subject
 =========================
 
+.. note::
+	ROLE_REIDENTIFY permission is needed to allow subject re-identification.
+
 if RPB PID generator was used to pseudonymise the participating subject it is possible to re-identify the subject
 given the user has the necessary rights.
+
+Once the patient is successfully registered and enrolled into the study it is easy to get get back his identity details when necessary (according to PID), see Fig. 8. The identity information stored in patient identity management system is retrieved when the user click on Reidentify button.
diff --git a/edc/subject-ids.rst b/edc/subject-ids.rst
@@ -0,0 +1,19 @@
+Explaining Subject ID Types
+===========================
+
+At this place it is important to explain that there are three main types of subject identifiers which are used in RPB.
+Each of the type has its own purpose and one should understand what is the meaning of it:
+
+* 	*Study Subject ID*: is identifying subject within one study. It can be automatically generated or manually specified
+	(depending on EDC study configuration). One patient taking part in multiple studies will have
+	different Study Subject ID in each study. This ID has nothing to do with patient identity and cannot be use to obtain
+	first or last name of patient.
+
+* 	*PID - pseudonym*: is a unique identifier of the patient in RPB platform. One patient taking part in multiple studies
+	will have the same PID in each one of them. It is generated from patient identity data (first name, last name, etc.)
+	by patient identity management system in RPB. It is possible to not to use identity management system and manually
+	provide PID, but in this case one has to guarantee the uniqueness of PID per patient and store the identity association
+	somewhere outside of RPB. PID is also used in case of DICOM Patient ID tag when DICOM imaging data are de-identified.
+
+* 	*Secondary ID*: sometimes it is useful to store patient ID from different systems and associate this ID to our study
+	subject. And for this case we have a possibility to use this Secondary ID field.
diff --git a/epro/epro.rst b/epro/epro.rst
@@ -0,0 +1,12 @@
+Mobile Forms
+============
+
+.. note::
+	The Mobile Forms (Mobile) module is available only to users with ROLE_EDC_PARTICIPATE permission. The accessible
+	studies need to be configured to use ePRO component.
+
+Concept
+-------
+
+Open Mobile
+-----------
diff --git a/introduction.rst b/introduction.rst
@@ -1,13 +1,15 @@
 Platform Introduction
 =====================
 
+.. warning:: RPB platform is not a turn-key system that is operational out-of-the-box. It rather requires intensive
+	configuration and continuous operative data management activities.
+
 The platform design was motivated by a need of linkage of research data that would have been otherwise managed
-separately within dedicated databases (e.g.: clinical, imaging, laboratory). This linkage is possible if defined
+individually within dedicated databases (e.g.: clinical, imaging, laboratory). This linkage is possible if defined
 naming and configuration conventions (data management strategy) are followed when setting up research projects.
 RPB platform, see :numref:`img-rpb-building-blocks`, is therefore in no means a fully generic configurable solution,
 but it rather provides opinionated selection of software system components and data integration use cases which have
-been found useful in academic clinical research field. This platform is not a turn-key system that is operational
-out-of-the-box. The following is the overall high level view on the platform infrastructure:
+been found useful in the scope of academic clinical studies. The following is the overall high level view on the platform infrastructure:
 
 .. figure:: /img/rpb-building-blocks.png
 	:name: img-rpb-building-blocks
@@ -18,23 +20,23 @@ out-of-the-box. The following is the overall high level view on the platform inf
 Standard Components
 -------------------
 
-* standalone web interfaces and components API endpoints
-* implement project specific data models
-* persist project research data
-* Open/LibreClinica, Conquest, LabKey, Mainzelliste
+* standalone web applications and API endpoints
+* implement project specific data models (per study)
+* persist project research data (per subject)
+* Open/LibreClinica, Conquest, LabKey
 
 Integration Core
 ----------------
 
 * defines radiotherapy research data model
 * contains domains that give modality based access to linked data
 * persists infrastructure model of integrated software components
-* persists the core research project management data
+* persists the core project management/ administrative data
 
 Custom Applications
 -------------------
 
 * web portal for accessing the platform
-* mobile webapp for tablet friendly data collection
-* tool for de-identification and upload of DICOM data
+* mobile webapp for mobile friendly data collection
+* tools for de-identification and upload of DICOM data
 * platform exposed API endpoints
diff --git a/lab/lab.rst b/lab/lab.rst
@@ -1,4 +1,8 @@
 Data Tables
 ===========
 
-The Data Tables (LAB) module is available only to users with ROLE_LAB_USER permission.
+.. note::
+	The Data Tables (LAB) module is available only to users with ROLE_LAB_USER permission.
+
+Concept
+-------
diff --git a/pacs/pacs.rst b/pacs/pacs.rst
@@ -1,4 +1,7 @@
 Medical Imaging
 ===============
 
-The Medical Imaging (PACS) module is available only to users with ROLE_PACS_USER permission.
+.. note:: The Medical Imaging (PACS) module is available only to users with ROLE_PACS_USER permission.
+
+Concept
+-------
diff --git a/pid/pid.rst b/pid/pid.rst
@@ -1,4 +1,8 @@
 Patient Identity
 ================
 
-The Patient Identity (PID) module is available only to users with ROLE_PID_USER permission.
+.. note::
+	The Patient Identity (PID) module is available only to users with ROLE_PID_USER permission.
+
+Concept
+-------
diff --git a/user.rst b/user.rst
@@ -10,6 +10,7 @@ Information about general system usage of all RPB platform components.
 	overview/overview
 	ctms/ctms
 	edc/edc
+	epro/epro
 	pacs/pacs
 	lab/lab
 	pid/pid