FAQ

  • If you were genotyped by 23andMe, deCODEme, or FamilyTreeDNA, you can upload the raw genotype data downloaded from your DTC test provider. The data will then be openly available for the world to see and download. We also parse these SNPs and annotate them.

    For annotation, we include the manually curated SNPedia and find open-access primary publications appearing in the journals of The Public Library of Science (PLoS), an open-access publishing group. Additionally, we screen Mendeley, a crowd-sourced repository of scientific publications.

    You can also publish some of your phenotypes so, someday, it might be possible to associate some SNPs with phenotypes (because of this we really would like to encourage you to do so; helping science generates this warm, fuzzy feeling inside of you).

    And, of course, you can also share your knowledge about SNPs and phenotypes with other users and can socialize.

  • The site is hosted and was coded by Bastian, Helge and Philipp. We are not working full time on this project, this is more of a hobby. Please give us some time to answer your questions, fix bugs and stuff like this as we are doing this in our free time besides our studies and day jobs. You can find some more details on our About Us page.

  • openSNP is a non-profit, open-source project that is about sharing genetic and phenotypic information. The idea for this project came to Bastian after he was genotyped by 23andMe in May 2011 and started playing around with his data. During his research he became frustrated, because it was not that easy to find more data. He started working on openSNP to fix this. To be clear: This project is not about making money, selling data or to quote Google: “We don’t wanna be evil”. We are just interested in making science more open and accessible.

  • We take the "open" in openSNP seriously, so everything is free of charge.

  • 23andMe customers can download the data here. deCODEme customers can find the data here. If you were genotyped by FamilytreeDNA you can find your files here.

  • This heavily depends on how many other users are in the queue, waiting for their data to be parsed. Right now openSNP runs on a small scale server so it may take 2-3 days until all your variations can be found on the site. But you can start using openSNP right away and others can download your raw-data right from the start. The parsing only affects the "other users sharing this SNP" and the "my genotype"-views.

  • 23andMe has a limited exome sequencing offer. If you've have had your exome sequenced through 23andMe you can now upload the VCF (Variant Call Format, see the filetypes-FAQ) version of your exome as well. But there are some limitations: While users will be able to download your complete VCF-file we currently don't have the computing power to parse all of your variation. So currently we will only parse the already known SNPs out of your file. For the same reasons we currently can't offer uploads of the raw sequence data.

    The feature is still in an early beta stage, so please notify us if something goes wrong.

  • We are always interested in adding more data. If your company is missing up to now it is because we did not have an example-file to optimize our parser on it. But if you contact us at parsing@opensnp.org and send us your file we can fix this, so that all customers of the DTC company of your choice can participate.

  • Completely open: Everyone can see everything you enter or upload (except your private messages and your password, of course). We warn every user twice about this: Once during the user-creation and once before the genotyping-file-upload. You can find more information about the risks of publishing the data by reading the disclaimer

  • You can easily add this phenotype as long as you are logged in. Just visit the page for phenotype creation and enter a name and a description that enables other users to understand what you are interested in.

  • 1.You should read the description on the phenotype you are about to enter. Often the description gives further details on which kind of answers people are interested in. You can also take a look on the answers which are given so far by other users. This should also give you a feeling about what kind of information is wanted for this phenotype.
    2. As soon as you start to enter your own variation we will try to auto-complete your writing to avoid duplicate entries into the openSNP-database. Having multiple entries for the same thing, like "blue-green" plus "green-blue" in case of eye-colour makes it harder for (citizen) scientists to use the data for their studies.
    3. The thing you are about to enter doesn't get auto-completed? Great. You are about to enter a variation which has not been reported so far, have fun entering your data!

  • 1. Use a reasonable name for your characteristic. Don't make it too long, but at the same time make sure that people get the general idea of what you want to know.
    2. You should also make sure that the same phenotype is not already available in the openSNP-database. As soon as you start writing your characteristics name openSNP will try to auto-complete what you are writing. This should reduce duplicate phenotypes, so if you are about to enter "eye-colour" you will get a suggestions for the already available "eye-color" (Sorry, we can't solve the AE / BE issue here).
    3. Write a description about the characteristic you are interested in. Give users some words why this is interesting. Maybe add what research has been done so far on this phenotype. Links to further web-resources and/or Wikipedia might also be a good idea. If you already have suggestions which different answers might apply to this phenotype: List them in the description.
    4. Enter your own variation: The last field, "variation" is meant to carry your own variation for this phenotype. Don't enter all possible answers (You can list those in the description). Other users can easily add their own variation and take your suggestions from the description or - if you forgot to list a possible answer - give completely new answers.

  • Fitbit is a wearable gadget which allows you to track your activities (How many steps have you taken? How many floors have you climbed?) and your sleep (How long did you sleep? How often have you awoken at night?). The tracker displays this information on the Fitbit website and calculates how efficient you sleep and many calories you have burned. Their website also allows you to track your body-development (i.e. your weight/BMI) and how much food you have eaten.

  • If you connect your Fitbit account with openSNP we will save data for up to three different categories: Activities, Body and Sleep. In the activity category we will save your step-count and the number of floors you've climbed for each day. For the body category we will save your Body Mass Index and your weight for each day. In the sleep category we will save how many minutes you have slept, how many minutes you were awake while you tried to sleep, how long it took you to fall asleep and the number of times you awoke for each night.

    If you connect your Fitbit account we will also save as much data of past days as it's possible to get through the API of Fitbit. This data is as public as are the genotyping datasets or all standard phenotypes which are entered into openSNP. So please be sure you want the world to be able to see this data.

  • Yes, you can choose which for which categories we should save the data. For example you can share our activity-data, so people can see the number of steps you have taken for each day, along with the floors you have climbed, but keep your body and sleep data on FitBit.Two things you should keep in mind: You can (de)activate the saving of data for different categories at any time.

    1. If you deactivate a category we will delete all of your data of this category from openSNP (but of course not on Fitbit).
    2. If activate a category we will try to save as many data from the past as possible. So if there is past data you don't want to share you probably should not activate it (or delete the data from Fitbit).

  • No, if you connect your Fitbit account with openSNP we only have read-access. The read-access gives us access to all data you have in your Fitbit account, but we will only read and save the data for which you have given us permission. We're sorry that you have to trust us in this point but the Fitbit API currently doesn't allow for a more granular setting.

  • Yes, once your Fitbit account is connected and set up we will get an notification from Fitbit each time you enter or change any data in their system. So each time your tracker uploads new data to Fitbit we will get those changes as well. This also works for past records. So if you change or delete entries on the Fitbit website those changes will be reflected on openSNP as well.

Not sure what kind of file you've got? Take a look at our example-files

  •                 		# More Comments up here
                    		# More information on reference human assembly build 36:
                    		# http://www.ncbi.nlm.nih.gov/projects/mapview/map_search.cgi?taxid=9606&build=36
                    		#
                    		# rsid	chromosome	position	genotype
                    		rs4477212	  1	        72017	    AA
                    		rs3094315	  1	        742429	  AA
                    		rs3131972	  1	        742584	  GG
                    		rs12124819	1	        766409	  AG
                    		rs11240777	1	        788822	  AG
                    		rs6681049	  1	        789870	  CC
                    		rs4970383	  1	        828418	  CC
                    		rs4475691	  1	        836671	  CC
                    		rs7537756	  1	        844113	  AA
    	                

  •                     Name,Variation,Chromosome,Position,Strand,YourCode
                        rs4477212,A/G,1,72017,+,AA
                        rs2185539,C/T,1,556738,+,CC
                        rs6681105,C/T,1,581938,+,TT
                        rs11240767,C/T,1,718814,+,CC
                        rs3094315,C/T,1,742429,-,TT
                        rs3131972,C/T,1,742584,-,CC
                        rs3131969,C/T,1,744045,-,CC
                        rs1048488,C/T,1,750775,+,TT
                        rs2905046,A/G,1,752518,-,GG
                      

  •                 		RSID,CHROMOSOME,POSITION,RESULT
                    		"rs3094315","1","742429","AG"
                    		"rs3131972","1","742584","AG"
                    		"rs12562034","1","758311","GG"
                    		"rs12124819","1","766409","AA"
                    		"rs11240777","1","788822","GG"
                    		"rs6681049","1","789870","CC"
                    		"rs4970383","1","828418","CC"
                    		"rs4475691","1","836671","CC"
                    		"rs7537756","1","844113","AA"
                  		

  •                   ##fileformat=VCFv4.1
                      ##CombineVariants=[...]
                      ##FILTER= 200.0">
                      [...]
                      ##FORMAT=
                      [...]
                      ##INFO=
                      [...]
                      ##contig=
                      ##contig=
                      [...]
                      #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  USERID
                      1       14907   rs79585140      A       G       317.34  MQFilter40 AB=0.604;AC=1;AF=0.50; [...]     GT:AD:DP:GQ:PL  0/1:32,21:54:99:347,0,514
                      1       14930   rs75454623      A       G       351.37  MQFilter40  AB=0.61;AC=1;AF=0.50; [...]     GT:AD:DP:GQ:PL  0/1:36,23:59:99:381,0,680
                    
  • We are always interested in adding more data. If your company is missing up to now it is, because we did not have an example-file to optimize our parser on it. But if you contact us at parsing@opensnp.org and send us your file we can fix this, so that all customers of the DTC company of your choice can participate.

  • We provide some methods to make it easier to get data back from openSNP. Currently we are implementing some JavaScript Object Notation (short: JSON) methods that will make it easier to code some awesome openSNP-utilizing stuff. As you can see on the Wikipedia-page there are many JSON-parsers around for all major programming languages and it is fairly human readable as well. Plus: It is one of the de facto webstandards for APIs. The full overview of the openSNP JSON API is on GitHub at this link.
  • There are many ways in which this problem can be fixed. First of all: If you are able to code some Rails and have got some basic understanding of JSON feel invited to help us with the development of openSNP. The source code is freely available at GitHub and we are always looking for some motivated people who want to join us. Just start coding the stuff you are interested in and make a pull request. Or what about joining the openSNP development mailinglist/Google group and you can get to know us a bit better?
    But don't worry if you don't feel like spending that much time with us (letting alone having that much time left): We are working on implementing more of this stuff, so if you've got a great idea that we should absolutely include just let us know: Write us at info@opensnp.org or drop Philipp or Basti a note. And the same is true if you need some more support with those methods already in place.

  • We've implemented some basic commands of the Distributed Annotation System (DAS). Those are for example used for the genome browsers on the SNP-pages in openSNP.

  • If you want to learn more about the use at openSNP you can watch this video which explains a bit about it. You can also read the specifications or read about example commands at the DASRegistry.

  • To find all DAS-sources you can point your browser to http://opensnp.org/das/sources. You should get back some XML which roughly looks like this:

                        <SOURCES>
                          <SOURCE uri="6" title="6" description="6">
                            <MAINTAINER email="admin@opensnp.org"/>
                            <VERSION created="29.09.2011 15:43" uri="6">
                            <COORDINATES uri="http://www.dasregistry.org/dasregistry/coordsys/CS_DS311" taxid="9606" source="Chromosome" authority="GRCh" test_range="" version="37">GRCh_37,Chromosome,Homo sapiens</COORDINATES>
                            <CAPABILITY query_uri="http://opensnp.org/das/6/features" type="das1:features"/>
                            <CAPABILITY type="das1:unknown-segment"/>
                            </VERSION>
                          </SOURCE>
                            <SOURCE uri="10" title="10" description="10">
                            <MAINTAINER email="admin@opensnp.org"/>
                            <VERSION created="29.09.2011 20:54" uri="10">
                            <COORDINATES uri="http://www.dasregistry.org/dasregistry/coordsys/CS_DS311" taxid="9606" source="Chromosome" authority="GRCh" test_range="" version="37">GRCh_37,Chromosome,Homo sapiens</COORDINATES>
                            <CAPABILITY query_uri="http://opensnp.org/das/10/features" type="das1:features"/>
                            <CAPABILITY type="das1:unknown-segment"/>
                            </VERSION>
                          </SOURCE>
                        </SOURCES>
                      
    The title of each source corresponds to a single openSNP-user. Even if users have provided more than one file you can query all the data available for this user through a single DAS-source.

  • To query a DAS-source you can use the features-command and provide the chromosome and slice you are interested in. For example http://opensnp.org/das/1/features?segment=1:1,1000000 will provide you with all SNPs which are located between base 1 and 1000000 for the user with the ID #1. It will produce a similar XML-output like shown below:
                      <DASGFF>
                        <GFF version="1.0" href="http://opensnp.org/das/1/features?segment=1:1,1000000">
                        <SEGMENT id="1" version="1.0" start="1" stop="1000000">
                        <FEATURE id="rs6681049">
                          <TYPE id="CC"/>
                          <METHOD id=""/>
                          <START>789870</START>
                          <END>789870</END>
                          <LINK href="http://opensnp.org/snps/rs6681049">http://opensnp.org/snps/rs6681049</LINK>
                        </FEATURE>
                        <FEATURE id="rs6657048">
                          <TYPE id="CC"/>
                          <METHOD id=""/>
                          <START>947503</START>
                          <END>947503</END>
                          <LINK href="http://opensnp.org/snps/rs6657048">http://opensnp.org/snps/rs6657048</LINK>
                        </FEATURE>
                        <FEATURE id="rs28415373">
                          <TYPE id="CC"/>
                          <METHOD id=""/>
                          <START>883844</START>
                          <END>883844</END>
                          <LINK href="http://opensnp.org/snps/rs28415373">http://opensnp.org/snps/rs28415373</LINK>
                        </FEATURE>
                      </DASGFF>
                    
    The general URL-schema for DAS-feature-requests is http://opensnp.org/das/$USER_ID/features?segment=$CHROMOSOME:$START_BASE,$STOP_BASE.