Commit b2fb0578 authored by taco@waag.org's avatar taco@waag.org
Browse files

capitalization

parent fd7b1e00
......@@ -25,7 +25,7 @@ To illustrate the complexity of what we were trying to tackle, the following fiv
<img src="eye_melanoma_2.png" alt="drawing" width="500" style="display:block;margin-left: auto;margin-right:auto;"/>
2\. The donor sends a bio sample (genetic material) to the Researcher and fills out a form with phenotypical information (things like gender, age, lifestyle, etc.) that are needed to conduct the research. The researcher is responsible for secure storage of this sensitive data.
2\. The donor sends a bio sample (genetic material) to the researcher and fills out a form with phenotypical information (things like gender, age, lifestyle, etc.) that are needed to conduct the research. The researcher is responsible for secure storage of this sensitive data.
<img src="eye_melanoma_3.png" alt="drawing" width="500" style="display:block;margin-left: auto;margin-right:auto;"/>
......@@ -40,7 +40,7 @@ The third party lab stores the bio sample in a bio vault (think refrigerator). I
<img src="eye_melanoma_4.png" alt="drawing" width="500" style="display:block;margin-left: auto;margin-right:auto;"/>
4\. The researcher performs analysis on the Array data with software in a "Research Cloud" service, specifically the [Copy Number Variation](https://www.genome.gov/genetics-glossary/Copy-Number-Variation) a statistical analysis that counts the number of variations of a specific segment of DNA. The result is again saved as a binary file and a human readable report based on the statistical analysis and the phenotypical data. Both files are saved in a data vault. This can be a secure database or filesystem with protections. If the researcher wants to make this data available for future research, some form of research meta data is extracted and saved in a catalog. For any additional kinds of research, this process is repeated (e.g. for Biomarker analysis):
4\. The researcher performs analysis on the array data with software in a "Research Cloud" service, specifically the [Copy Number Variation](https://www.genome.gov/genetics-glossary/Copy-Number-Variation) a statistical analysis that counts the number of variations of a specific segment of DNA. The result is again saved as a binary file and a human readable report based on the statistical analysis and the phenotypical data. Both files are saved in a data vault. This can be a secure database or filesystem with protections. If the researcher wants to make this data available for future research, some form of research meta data is extracted and saved in a catalog. For any additional kinds of research, this process is repeated (e.g. for Biomarker analysis):
> Biological measurements that can be used to predict risk of disease, to enable early detection of disease, to improve treatment selection and to monitor the outcome of therapeutic interventions
[source](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3377087/)
......@@ -49,7 +49,7 @@ The third party lab stores the bio sample in a bio vault (think refrigerator). I
5\. The researcher sends the outcome of the research as a report to the donor either by normal mail, email or other digital channels.
Now, generally speaking, the donor is focused on the end result and will be happy with the process if they finally receive a report from the researcher. But there are many questions that can be asked for each step described above. What exactly happens with sensitive data during the steps? Is the agreement itself personal data? (1) How does the researcher store contact information? Is the Bio sample tagged with the name of the donor? How is the phenotype information stored? (2) Does the bio sample get destroyed after processing? Does the third-party lab keep a copy of the array data? If so what are they going to use it for? (3) On what servers is the research cloud hosted? How is the array data transferred to the research cloud? Is the array data removed from the research cloud after the analysis? What meta data is extracted for the catalog? How is this information aggregated? What happens to the copies of the CNV file and the report? How are they transferred? Who will be able to do predictions based on the donor's biomarkers in the future? (4) And finally, what happens with the contact information of the donor when the research is concluded? (5)
Now, generally speaking, the donor is focused on the end result and will be happy with the process if they finally receive a report from the researcher. But there are many questions that can be asked for each step described above. What exactly happens with sensitive data during the steps? Is the agreement itself personal data? (1) How does the researcher store contact information? Is the bio sample tagged with the name of the donor? How is the phenotype information stored? (2) Does the bio sample get destroyed after processing? Does the third-party lab keep a copy of the array data? If so what are they going to use it for? (3) On what servers is the research cloud hosted? How is the array data transferred to the research cloud? Is the array data removed from the research cloud after the analysis? What meta data is extracted for the catalog? How is this information aggregated? What happens to the copies of the CNV file and the report? How are they transferred? Who will be able to do predictions based on the donor's biomarkers in the future? (4) And finally, what happens with the contact information of the donor when the research is concluded? (5)
## Genetic data and ownership
......@@ -148,7 +148,7 @@ The **researcher** defines a research 'request' and creates invitation codes tha
<img src="Screenshot2022-04-08at113319.png" alt="drawing" width="500" style="display:block;margin-left: auto;margin-right:auto;"/>
Each research request is signed by the researcher with a cryptographic function. For this we used [Dyne's](https://dyne.org) [zenroom](https://zenroom.org) execution environment. Zenroom uses a special language called Zencode, "a non Turing-complete, English-like DSL" (Domain Specific Language). The intended use of this language is to program 'smart contracts', using code that is fairly readable even if you have no or little experience as a coder. Zenroom enables donors (and other readers of the invitation) to verify the origin of the request. In our case, the zenroom environment is hosted in a wallet web extension that also contains the private key of the researcher. The following code is what we used to sign the Request:
Each research request is signed by the researcher with a cryptographic function. For this we used [Dyne's](https://dyne.org) [zenroom](https://zenroom.org) execution environment. Zenroom uses a special language called Zencode, "a non Turing-complete, English-like DSL" (Domain Specific Language). The intended use of this language is to program 'smart contracts', using code that is fairly readable even if you have no or little experience as a coder. Zenroom enables donors (and other readers of the invitation) to verify the origin of the request. In our case, the zenroom environment is hosted in a wallet web extension that also contains the private key of the researcher. The following code is what we used to sign the request:
```
rule check version 1.0.0
......
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