Approval for lineage

Hello, I’m Andrew Riha, and I’m posting a review request for lineage, which is applying for project approval on Open Humans.

This project adds a data source to Open Humans (OH). Specifically, for an OH user, it will merge their files from 23andMe Upload, AncestryDNA Upload, and FamilyTreeDNA integration, and return the merged file back to the user’s OH account (lineage_GRCh37.csv). Additionally, any SNPs tested differently at each company will also be returned (lineage_discrepant_snps.csv). Finally, the project will return the SNPs remapped to Build 36 (lineage_NCBI36.csv) and Build 38 (lineage_GRCh38.csv).

(If the user only has one data source used by lineage, the project will return lineage_GRCh37.csv, lineage_NCBI36.csv, and lineage_GRCh38.csv to the user’s OH account. If the user has no data sources used by lineage, the project will not return any files to the user’s OH account.)

Once an Open Humans user has created an account with lineage, they will be able to upload files from 23andMe, AncestryDNA, and Family Tree DNA for other individuals for which they have permission / rights to do so. Then, the user will be able to compare individuals within the web app to determine shared DNA, shared genes, and discordant SNPs. However, data generated from these analyses will not be returned to Open Humans.

Should this project be visible and available for all Open Humans members to join?

Please vote Approve or Deny, and/or comment.

Quick Links

Project Info

  • Title: lineage
  • Managed by: Andrew Riha, Scedastic Software, LLC
  • Description: lineage provides a framework for analyzing genotype (raw data) files from direct-to-consumer DNA testing companies (e.g., 23andMe, Family Tree DNA, and Ancestry), primarily for the purposes of genetic genealogy. Specifically, users can merge raw data files from different DNA testing companies (identifying discrepant SNPs in the process), compute centiMorgans (cMs) of shared DNA between individuals using the HapMap Phase II genetic map, plot shared DNA between individuals, determine genes shared between individuals (i.e., genes transcribed from shared DNA segments), find discordant SNPs between child and parent(s), and remap SNPs between assemblies / builds (e.g., convert SNPs from build 36 to build 37, etc.).
  • Project website:
  • Connections: 3 members
  • Requested sources: 23andMe Upload, AncestryDNA Upload, and FamilyTreeDNA integration
  • Data added: lineage_NCBI36.csv, lineage_GRCh37.csv, lineage_GRCh38.csv, and lineage_discrepant_snps.csv

Code looks great from a security point of view, only suggestion I have is to upgrade to Django 2.1.5 for the security fix it contains.

I’m :+1: to approve.

1 Like

Thanks for the review, Beau! Django has been upgraded to 2.1.5.

1 Like

This was fun to use! I’m excited to see it shared :smiley:

I’ve reviewed and have some small stuff below. I think it’s probably fine as is despite these though, so I’m already :+1: to approve.

  1. Information about the project - this looks pretty good, but I think I have some small suggestions…

    • :question: who manages it? I see Scedastic Software in the footer, but it’s a bit unclear what/who it refers to – maybe a brief mention explaining who that is could go into the “About” page?
    • :white_check_mark: what will it do? The about page has a nice explanation of different things the tool does. :+1:
    • :question: what is in the data it has access to? arguably redundant with permissions in Open Humans, but maybe nice to have a brief statement like “will request access to your genetic data in Open Humans (e.g. 23andMe)”
    • :white_check_mark: security, privacy, and data management? the site has terms of use and data use policies :+1:
  2. Maybe remove the language about “coming January” now that it’s (nearly) complete?

Thanks for the review, Mad! All suggestions have been addressed.

Thanks @apriha ! This looks good to me.

And thanks to @beau for reviewing as well :smiley:

I don’t see any further feedback, so I’m going to mark this project as approved. :+1: