Anita comments done

Author: Flythe

main.tex

@@ -48,7 +48,7 @@
 \newcommand{\allard}[1]{\textcolor{magenta}{\textbf{*Allard: }\textit{#1}}}
 \newcommand{\note}[1]{\textcolor{cyan}{\textit{#1}}}
 
-\title{A Data Management System for Obstetric Research}
+\title{A Data Management System for the Dutch Assisted Reproductive Technology Study}
 
 \author{
 	Allard J. van Altena\\

partials/discussion-conclusion/appraisal.tex

@@ -11,9 +11,12 @@ \section{Critical Appraisal}
 Even though the thesis contains a rather extensive research into security, most of the found solutions were not used in the \ivfsystem{} implementation yet.
 Even now, after the first prototype is finished, it would not be advisable to start introducing these to the system.
 First another iteration of function and design development should be ran before it becomes feasible to use intricate security constructs.
-For the purposes of a prototype this is not a big problem, as long as security issues and solutions are kept in mind before starting to use the system in a live environment.
+Also the regulations of the hosting environment should be taken into account. 
+Most likely these regulations will differ between institutions.
+For example, the \AMC{} has a specific set of rules to follow when running a system like the \ivfsystem{}.
+However, for the purposes of a prototype this is not a big problem, as long as security issues and solutions are kept in mind before starting to use the system in a live environment.
 
-While the system's prototype might be lacking user-centred design and functionality, it already illustrates the potential what it could ave after some more development effort.
+While the system's prototype might be lacking user-centred design and functionality, it already illustrates the potential what it could have after some more development effort.
 In the evaluation users noted that the ideas of research workflow management can be used to attract funding because they support so well data reuse.
 Furthermore, big data literature states that the value of an investment into data gathering is increased when sharing and reuse capabilities are added (see chapter \ref{introduction}).
 
@@ -33,14 +36,13 @@ \section{Critical Appraisal}
 This would also mean that a gateway has to be further developed to encompass all the different systems into one interface.
 
 \paragraph{Future research and development considerations}
-Future research mostly refers to further development considerations
+Future research mostly refers to further development considerations.
 The \ivfsystem{} is only a prototype and not ready for real life usage.
 Evaluation of the prototype shows that there is room for much improvement.
 Some are time consuming and are not directly visible, like integrating data provenance.
 Others will take less time and are highly visible, like changing the user interface.
 This study answers the question of what is needed to implement a successful system, but not all solutions could be integrated into the prototype.
 
-%During the brainstorm a lot of functions came up which were not implemented because of time restrictions.
 One of the plus points, the fact that a system like this does not exists yet, is also one of the stumbling points.
 There is no template to follow and, as almost everything is possible, users expect a lot from the system.
 Most notably, better user interfaces for data filtering and selection should be implemented (chapter \ref{evaluation}).

partials/discussion-conclusion/conclusion.tex

@@ -1,6 +1,6 @@
 \section{Conclusion}
 
-The focus of the developed system changed drastically during this study.
+The focus of the developed system changed during this study.
 Initially the system would be supporting researchers in doing research which was the basis for the first research question:
 How do we implement a user-friendly system in a \IVF{}--\PRN{} medical domain which covers problems concerning: data security, data access, data browsing, and data querying?
 The conclusion to this question will be structured through its sub-questions.
@@ -11,9 +11,11 @@ \section{Conclusion}
 Researchers, the data manager, and committee members need to be supported in functions belonging to user, data, request, and publication management.
 Most notable is that the focus of the system now lies on request management and the committee members.
 
-Of course, because the \projectdata{} contains sensitive medical, data security is an important aspect of the system.
+Of course, because the \projectdata{} contains sensitive medical data, security is an important aspect of the system.
 An extensive security review, both in literature as with an interview, lists the possible issues and proposes solutions to them.
-This review can be found in appendix \ref{security-appendix} and an summary is described in section \ref{security}.
+This review can be found in appendix \ref{security-appendix} and a summary is described in section \ref{security}.
+Security solutions are mostly used during the fertility data gathering process, removing most of the privacy sensitive data.
+No solutions were implemented in the system due to time restrictions.
 
 To store the data in the system the data model of an existing system was reused.
 This is the in-house project Rosemary, originally   developed for the neuroscience domain.

partials/discussion-conclusion/overview-implications.tex

@@ -10,10 +10,10 @@ \section{Summary}
 
 In the Netherlands about 5\% to 8\% of all couples remain childless due to infertility or subfertility.
 There are several treatments used to assist in reproduction, for example IUI, IVF, and ICSI.
-While it is known how many treatments result in a pregnancy, it is relatively unknown what the outcomes are for children born out of these pregnancies.
-For this end the \project{} was started: to gather and analyse data from both the fertility clinics as the national birth registry (\ie{} \PRN{}).
+While it is known how many fertility treatments result in a pregnancy, it is relatively unknown what the outcomes are for children born out of these pregnancies.
+For this end a study (\project{}) was started: to gather, link, and analyse data from both the fertility clinics as the national perinatal registry (\ie{} \PRN{}).
 
-Because considerable effort went into data gathering, data management should be supported to get the most gain out of this valuable data set.
+Because considerable effort went into data gathering of the fertility clinics, data management should be supported to get the most gain out of this valuable data set.
 From this vision, the idea for the \ivfsystem{} was formulated.
 Initially no data was available, which made requirement analysis with stakeholders a difficult process.
 A study was performed, resulting in an initial system concept that was then used as input for the brainstorm session with stakeholders.
@@ -38,7 +38,7 @@ \section{Discussion}
 
 In this study the \projectdata{} is considered `fixed' and would be delivered by the \project{} at the start.
 Data gathering should be outside the scope of this study.
-However, data was not available, causing problems with development as described in chapter \ref{requirements}.
+However, fertility datasets were not available, causing problems with development as described in chapter \ref{requirements}.
 It was decided that the gathering would be a joint effort with other participants of the \project{}.
 The experiences and impressions during the data gathering process are described below.
 
@@ -58,8 +58,10 @@ \section{Discussion}
 Furthermore, during the security review (appendix \ref{security-appendix}) the following quote was found in literature: ``They [clinicians] wanted to help achieve these benefits, but also wanted to be sure that patients' rights were protected and that clinicians were not in danger of breaking patient confidentiality and the law''.
 We assume that the same holds in the case of the \project{}.
 This leads to the impression that the real consideration for stakeholders is related to control over their data.
+Most likely the same issues occur at the \PRN{}.
+However, the \PRN{} was not accounted for in this study.
 
-Currently each data request is evaluated by the data owner, which gives them great control over who they deliver data too.
+Currently each data request is evaluated by the data owner, which gives them control over who they deliver data too.
 Furthermore, data has value that can be monetary but also academic (\ie{} scientific value in the form of potential publications).
 Gathering data and putting it in a repository weakens (or removes) ownership of the data and the owner loses the potential profits.
 
@@ -96,7 +98,7 @@ \section{Discussion}
 During the brainstorm session (section \ref{brainstorm}) many hurdles in the current research workflow came to light.
 Normally these might be hidden to spectators as workarounds are used.
 The most critical for the \ivfsystem{} is the need to support data requests for datasets like the \projectdata{}.
-Moreover, the stakeholders representing the researchers said that data analysis was an rather uninteresting feature (\ie{} a `could have').
+Moreover, the stakeholders representing the researchers said that on-line data analysis was an rather uninteresting feature (\ie{} a `could have').
 This in contrary to the vision put forward by big data literature about the benefits of computerised decision making and data mining (see chapter \ref{introduction}).
 
 With the focus on data requests, also a new user of the system was introduced, namely the committee member (section \ref{brainstorm}, figure \ref{fig:brainstorm-after}).
@@ -136,7 +138,7 @@ \section{Discussion}
 \paragraph{Extrapolate to other domains}
 %How can this specific system be used in other settings/knowledge domains?
 
-The previous section argued the benefits of the \ivfsystem{}; however, it is specific to the domain of the \projectdata{}, \ie{} \IVF{} and \PRN{} data.
+The previous section argued the benefits of the \ivfsystem{}; however, it is specific to the domain of the \projectdata{}, \ie{} linked \IVF{} and \PRN{} data.
 Now we will discuss how the system might be used in other domains.
 
 It is a good idea to work towards a modular solution that implements core elements of user, data, request, and publication management.

partials/evaluation/evaluation-transcripts.tex

@@ -2,7 +2,7 @@
 These functions are structured to the research workflow as described in figure \ref{fig:functions-workflow}. 
 This workflow will now be referred to as the `process' of the system.
 
-For the purpose of the evaluation the \ivfprototype{} code was running on the local environment of a laptop.
+For the purpose of the evaluation the \ivfprototype{} code was running on the local environment of an Apple MacBook (laptop).
 No connection to the internet was necessary for testing, therefore performance issues were out of the question.
 The used dataset was randomly generated (strings of letters), because the \projectdata{} was not available yet.
 Screenshots of the running gateway are shown in figures \ref{fig:standard-view-website} and \ref{fig:sunburst-view-zoom-website}.
@@ -64,7 +64,7 @@ \section{User sessions transcripts}
 
 Two of the testers did not notice that the search is instantaneous (like Google search).
 This resulted in pressing 'enter' and clicking the `apply filter' button multiple times before noticing that the data had already changed at the bottom of the screen.
-One of the testers prefers to search the data off-line, \ie{} print the fields and later select the wanted items in the interface.
+One of the testers prefers to search the data both on and off-line, \ie{} print the fields and later select the wanted items in the interface.
 
 Because in the prototype the descriptions are nonsense, it was difficult to find the wanted data headers.
 Therefore, testers were asked to select a couple of random headers.

partials/introduction/frontpage.tex

@@ -4,7 +4,7 @@
 
 \begin{center}
 	\bigskip
-	\huge{A Data Management System for Obstetric Research}
+	\huge{A Data Management System for the Dutch Assisted Reproductive Technology Study}
 \end{center}
 
 %\begin{figure}[H]

partials/introduction/summary-dutch.tex

@@ -1,22 +1,24 @@
+\clearpage
 \phantomsection
 \addcontentsline{toc}{section}{Samenvatting (Dutch summary)}
 
 \section*{Samenvatting}
 
-In Nederland blijven tussen de 5\% en 8\% van alle stellen ongewenst kinderloos door infertiliteit of subfertiliteit.
-Een aantal vruchtbaarheidsbehandelingen worden toegepast.
-Maar het is relatief onbekend wat de uitkomsten zijn voor geboren kinderen.
-Het \project{} is gestart om data te verzamelen en analyseren van fertiliteitsklinieken en het nationale geboorte register.
+In Nederland blijft tussen de 5\% en 8\% van alle stellen ongewenst kinderloos als gevolg van infertiliteit of subfertiliteit.
+Een aantal vruchtbaarheidsbehandelingen kan worden toegepast, maar het is nog relatief onbekend wat de uitkomsten hiervan zijn voor de geboren kinderen.
+Om dit te bestuderen is de studie DARTS! gestart, met als doel om data van fertiliteitsklinieken te verzamelen en te koppelen aan het nationale geboorteregister.
+Deze data is vastgelegd in de \projectdata{}.
 
-Het idee voor de \ivfsystem{} was om data management te ondersteunen, bijvoorbeeld querying en analyse.
-Een requirement studie werd gedaan en een initieel concept werd beschreven.
-Dit concept werd gebruikt als input voor een brainstormsessie met belanghebbende.
-De sessie maakte duidelijk dat er meerdere aspecten zijn aan het systeem, vooral data hergebruik.
+Deze studie beschrijft de ontwikkeling van het \ivfsystem{} en onderzoekt daarnaast de houding ten opzichte van het gebruik van medische (big) data in het algemeen.
+In eerste instatie was het idee voor de \ivfsystem{} om onderzoekers te ondersteunen met datamanagement van de \projectdata{}, bijvoorbeeld querying en analyse.
+Met behulp van een requirement studie werd een initieel concept beschreven, welke werd gebruikt als input voor een brainstormsessie met belanghebbenden.
+De sessie maakte duidelijk dat, naast datamanagement, het \ivfsystem{} meerdere aspecten moest bevatten.
+Waarbij de belangrijkste aspecten zijn: het hergebruik van data en de eigenaren van deze data.
 
-Een intern project werd gekozen als ontwikkel startpunt voor het \ivfsystem{}.
-Met minimale aanpassingen aan het data model was het mogelijk om de \projectdata{} te integreren.
+Een intern project werd gekozen als startpunt voor de ontwikkling van het \ivfsystem{}.
+Met minimale aanpassingen aan het datamodel was het mogelijk om de \projectdata{} te integreren.
 
-Tijdens de evaluatie van het prototype met gebruikers werd het duidelijk dat: de workflow van het systeem (de manier waarop een gebruiker zich door het systeem heen beweegt) verbeterd moet worden en dat een of twee iteraties van user-centred design nodig zijn.
-Verder moeten missende functionaliteit en beveiliging toegevoegd worden aan het systeem.
+Tijdens de evaluatie van het prototype werd duidelijk dat de workflow van het systeem verbeterd moet worden en dat verbetering van de gebruikersomgeving nodig is.
+Verder moet er meer functionaliteit en beveiliging toegevoegd worden aan het systeem.
 
-Bediscussieerd worden: ervaringen en impressies gedurende het data verzameling proces, de focus verandering van het systeem van data management naar data hergebruik en mogelijke extrapolatie naar andere data domeinen.
+In dit artikel worden drie hoofdconcepten bediscussieerd: ervaringen en impressies gedurende het data verzameling proces, de focusverandering van het \ivfsystem{} van datamanagement naar data-hergebruik en mogelijke extrapolatie naar andere datadomeinen.

partials/introduction/summary-english.tex

@@ -4,23 +4,24 @@
 
 \section*{Abstract}
 
-In the Netherlands about 5\% to 8\% of all couples remain childless due to infertility or subfertility.
-Several treatments are used to assist in reproduction.
-However, it is relatively unknown what the outcomes are for the born children.
-The \project{} was started to gather and analyse data from both the fertility clinics as the national birth registry (\ie{} \PRN{}).
+In the Netherlands about 5\% to 8\% of all couples remain childless due to infertility or subfertility. 
+Several treatments may be used to assist in reproduction. 
+However, outcome indicators related to the (born) child are relatively unknown. 
+In order to find out a study (\project{}) was started to gather and link data from both the fertility clinics and the national birth registry. 
+This data is captured in the \projectdata{}.
 
-The idea for the \ivfsystem{} was to support data management, \eg{} querying or analysis.
-First a requirement study was performed. 
-An initial concept was described and used as input for a brainstorm session with stakeholders.
-The session showed that there are many more aspects for the system, mostly concerning data reuse.
+This study describes the development of the \ivfsystem{} and investigates attitudes towards medical (big) data usage. 
+The \ivfsystem{} was initially meant to support researchers with data management of the \projectdata{}, \eg{} querying or analysis. 
+From a requirement study an initial concept was described, which was used as input for a brainstorm session with stakeholders.
+The session showed that apart from data management the \ivfsystem{} should encompass many more aspects, mostly concerning data reuse and aimed at data owners. 
 
-An in-house project was chosen as a development starting point for the \ivfsystem{}.
-With minimal changes to the data model, it was possible to integrate the \projectdata{}.
+An in-house project was chosen as a development starting point for the \ivfsystem{}. 
+With minimal changes to the data model it was possible to integrate the \projectdata{}.
 
-During the evaluation of the prototype with users it became clear that more polishing of the system's workflow (\ie{} the manner in which a user moves through the system) and one or two iterations of user-centred design are needed.
-Furthermore, missing functionality and security should be added to the system.
+During evaluation of the prototype it became clear that more polishing of the system's workflow (i.e., the manner in which a user moves through the system) and several iterations of user-centred design are needed. 
+Furthermore, more functionality and security should be added to the system.
 
-Discussed are the experiences and impressions during the gathering data process, the focus switch of the system from a data management to a data reuse supporting system, and possible extrapolation to other data domains.
+In this article three main concepts are discussed: experiences and impressions during the data gathering process, the focus switch of the \ivfsystem{} from a data management to a data reuse supporting system, and possible extrapolation to other data domains. 
 
 \paragraph{Keywords}
-Software engineering, data reuse, data gathering, request management, medical domain
+Software engineering, data reuse, data gathering, request management, medical domain

partials/introduction/titlepage.tex

@@ -1,7 +1,7 @@
 \thispagestyle{empty}
 
 \begin{center}
-	{\huge{A Data Management System for Obstetric Research}}
+	{\huge{A Data Management System for the Dutch Assisted Reproductive Technology Study}}
 \end{center}
 \bigskip