Category Archives: General

Now included: FitBit-data (plus minor design changes)

Hi there,

Basti has been hard at work linking the Fitbit-API to openSNP – if you’re a customer of Fitbit, you can now connect your Fitbit-data with your openSNP-profile to give researchers around the world an even better picture of how your genes interact with your health.

The new Fitbit-phenotype-overview – still kind of empty!

Why this data?

There are several SNPs associated with an increased risk of developing obesity, SNPedia has a very good overview here. For example, some variations are involved in how early your body starts to store fat, or how strong your appetite is.

Carrying these variants, however, does not mean that there’s nothing you can do about your weight – there are some studies showing that regular exercise helps alleviate these effects (see here, for example). This is where the Fitbit-data comes in – it gives researchers a detailed overview of your movement-patterns, the status of your body-weight and your sleep patterns. Using this data scientists can then perform association-studies by comparing weight and activity-data to known and unknown SNPs linked to obesity. You can also link your sleep-data (if you are tracking it) – this enables research into the genetics behind some sleep disorders.

Another reason why it’s great to collect data through a technical device instead through surveys it that all data which comes through the Fitbit-API is normalized into standardized units. This makes it much easier to compare the data, as you don’t have to convert between units (metric & imperial system) or have to work around spelling mistakes etc., while it also allows to circumvent the cognitive biases we all have while answering questions about ourselves. And of course it’s also is more convenient for you, because you don’t have to update your BMI and activity-pages manually, as we automatically will get your latest Fitbit-data. This means there is one profile less you have to worry about!

As a bonus, the level of detail in this data is a level researchers usually can’t reach due to time and financial constraints.

Basti’s page

How to link your data

Linking a Fitbit-account to openSNP is a matter of just a few clicks – once you’re logged in, click on My Account, then on Settings and under the Fitbit-tab you’ll be able to go through the procedure. Alternatively, here’s the direct link to the page. Of course, you can specify which data is going to be shared with openSNP – we don’t automatically take all of it, because that wouldn’t be very nice of us. After you’ve approved that you want to link Fitbit and openSNP you will get redirected to a page where you can choose which categories should be shared and mirrored on openSNP. And yes, you have to submit the form which selects which categories you want to share, until you’ve done so we will not grab any data.

Note that: a) the data at openSNP is automatically updated with new data from Fitbit along with all the data you have put into Fitbit so far and b) you can always unlink your Fitbit account from openSNP, this also deletes your Fitbit-data on our end, in the settings.

This is where we hid the bodies the link

For researchers

If you’re interested in this data, it’s from now on available in all data-dumps in CSV-format for easy parsing (available on the genotypes-page, or directly here). Please note that the CSV lists 0 (that is zero) for missing data-points.

Slight re-design

We’ve also slightly updated the design of openSNP to the newest Bootstrap-version. You shouldn’t have been affected by that (except in the way that things now look a bit nicer. For example take a look at the SNP-pages which now show pie charts for the allele & genotype-frequencies) , but if you find anything wrong, please tell us in the comments or at info@opensnp.org!

Thanks for reading and have a wonderful weekend,

the openSNP-team

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New API methods & Vagrant images

Additions to the API

We can announce some minor additions to our API:

  1. You can now grab annotations for a SNP by using http://opensnp.org/snps/json/annotation/$SNP_NAME.json. For example http://opensnp.org/snps/json/annotation/rs7903146.json returns all Mendeley-, PLOS- and SNPedia-annotations we have for Rs7903146.
  2. You can now get additional information for phenotypes. You can get a list of all phenotypes by visiting http://opensnp.org/phenotypes.json. You can use this call to find out the IDs of the phenotypes you are interested in. 
  3. And you can get all phenotypic variation and the description for a given phenotype by visiting http://opensnp.org/phenotypes/json/variations/$PHENOTYPE_ID.json. For example http://opensnp.org/phenotypes/json/variations/12.json gives you the variation for each user at the phenotype with the ID 12.

We also added some more extensive documentation of the API to our Wiki at GitHub. The wiki also lists the attributes each call will return.

Vagrant Image

We compiled two Vagrant-images which should make running the openSNP source and development much easier. Installing Ruby, Redis, PostgreSQL, Java, and all the right versions of the Ruby gems can be painful and often takes a significant amount of time – so we created the Vagrant-Image, which is the whole server-runtime with all gems pre-installed inside a virtual environment for easy development.  This Railscast gives you a nice idea of how to install and use Vagrant.

Our Vagrant-images (downloadable as 32 bit version and 64 bit version) are based on Lucid64 and Lucid32 and come with the Ruby version manager rbenv, Ruby 1.9.2 including bundler, Sun’s Java and Postgres 8.4 (the development-tables are already migrated) pre-installed. Getting the development-server running should now be really easy:

  1. Install the image using vagrant box add opensnp http://opensnp.org/opensnp32.box
  2. Initialize the image inside your openSNP-folder using vagrant init opensnp
  3. Run vagrant up to start your image and afterwards connect to it using vagrant ssh
  4. Go to the mounted directory using cd /vagrant
  5. Run bundle to see if all gems are working as expected and try bundle exec rails s to start the web-server

You can watch this Railscast to learn more about how you can put Vagrant to use and download our Vagrant-image as 32bit version or 64bit version. One caveat: You need to delete the .rvmrc file if you want to run vagrant from inside the directory which has your copy of the openSNP-source code. The file can be found in the root-folder of the openSNP-source code. If you keep the file your copy of RVM might lead to some problems with vagrant. Let us know if you encounter any problems or need help.

Recent Talks – re:publica & SIGINT

In the last post Philipp already told you that we’ve been giving talks on Personal Genetics and a possible future of Biomedicine over the last months. In May Fabian and I visited the re:publica in Berlin and the SIGINT in Cologne. Now the recordings of those conferences are available. So if you couldn’t make it to Berlin and/or Cologne you can watch it those talks.

Unfortunately the talk on The Future of Genetics which we gave on the re:publica wasn’t recorded, but you can at read and download our slides of the talk. And on the same conference I was also part of a (German, sorry rest of the world!) panel discussion called “Die totale Selbstkontrolle als Wunsch und nicht Bedrohung” (total self-control as wish instead as thread) which mainly focussed on the Quantified Self-movement, but also covered a bit of personal genetics.

On the SIGINT we talked about Power to the Patient and how modern technology along with the web, think of personal health records, could be put to use to change how medicine is done. You can again download the slides or as this talk was also recorded watch the video.

Thanks to all of you who joined the conferences, listened to our talks and – most importantly – took their time to discuss the topics with us.

Milestone reached: 200 genotypings!

We’re happy to announce that openSNP has reached the magnificent number of 200 open genotypings! It’s great that you guys support open science so much, we didn’t think to reach this number so fast. openSNP has been growing constantly, here are some interesting stats:

Here’s the amount of data downloaded from openSNP.org every day over the last 6 months, with the days on the x-axis and the traffic in megabytes on the y-axis:

Image

As you can see, the amount of data jumps around wildly – that’s because the data-dump with all genotypings is fairly large, and there are lots of days in there where no-one downloaded any genotypings, and some days where a lot of people download data – nothing much in between!

And for fun, here’s the amount of daily attacks on the server (usually automated scripts that look for open administrator-interfaces)

Image
What happened there in May? Two articles were released on openSNP and Basti and Fabian held two talks (at the SIGINT and at the re:publica), so that increased positive and negative attention.

Some things that are coming soon:

- picture-uploads for phenotypes

It would be great if users could upload pictures of their phenotypes and variations, for example, the shape of their heads or the form and color of their eyes. We’re currently working on this, might take a while longer.

- more secure backend

In light of the recent attacks on linkedin, last.fm and others we’ve switched the password-storing system from salted SHA512 to salted bcrypt-hashes. If you’re interested in how that works, check out this article, Keeping passwords safe by staying up to date.
We’re currently testing how well the implementation works but it’s looking good, coming very soon. You’ll probably not notice any changes.

- a couple more talks

We’ve submitted some more applications to talk at different conferences but haven’t heard back from any. If we go and hold a talk somewhere, we’ll link to the videos!

Thank you for your interest & help and time, we couldn’t have done it without you!

The openSNP-team

A petition on Open Access

We are strong supporters of the open-science movement and are happy to see that there is a new petition aimed at the Obama administration. The goal of this new petition is to make Open Access mandatory for all publications funded by tax-money.

While one of the aims of openSNP is to provide an Open Data platform it would be impossible to provide this service without the great benefits of Open Access, of which we make extensive use when we link to external information and papers. Would all research still be hidden behind paywalls we could not provide you with information on any SNPs. If Open Access would be mandatory we could provide you with even more information and literature!

This is the full text of the petition:

WE PETITION THE OBAMA ADMINISTRATION TO:

Require free, timely access over the Internet to journal articles arising from taxpayer-funded research.

We believe in the power of the Internet to foster innovation, research, and education. Requiring the published results of taxpayer-funded research to be posted on the Internet in human and machine readable form would provide access to patients and caregivers, students and their teachers, researchers, entrepreneurs, and other taxpayers who paid for the research. Expanding access would speed the research process and increase the return on our investment in scientific research.

The highly successful Public Access Policy of the National Institutes of Health proves that this can be done without disrupting the research process, and we urge President Obama to act now to implement open access policies for all federal agencies that fund scientific research.

The best thing is that you don’t have to be a US citizen to sign the petition. Just register on the petition platform and give your signature. In total 25,000 signatures are required before June 19 2012. If this limit is reached the petition will be placed in the Executive Office of the President for review.

The campaign behind it, access2research, is driven by many open access advocates, including Michael Carroll, Heather Joseph, Mike Rossner, and John Wilbanks.

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Some progress on the API: JSON endpoints

Some weeks ago we stated that we are working on implementing the Distributed Annotation System into openSNP. And I’m sorry that I’ll have to announce that we are not finished with this yet. We just underestimated the amount of time it would take to finish this. But to make up for this we just released some JSON (JavaScript Object Notation) endpoints which you can use to get data out of openSNP. JSON can be easily parsed using software and is already widely used, especially in web applications. For a start we added JSON support for the user-index, for genotypes at single SNPs and for all phenotypes of a given user and I’ll briefly discuss how you can access the different JSON endpoints.

Let’s start with the user-index, which can easily be accessed at http://opensnp.org/users.json. This includes the complete list of all openSNP-users and their names, their unique user-IDs and all the genotyping-files (with the unique genotype-IDs and the download-links). We hope that this makes an ideal entry-point if you are looking for genotyping-files and the user-IDs to further query the openSNP-database.

If you want to get genotypes of single or multiple users for a given SNP you can use the JSON endpoint at http://opensnp.org/snps/json/$snpname/$userid.json. Just replace $snpname by the Rs-ID you are interested in and $userid by the unique ID of the user you are interested in. For example: http://opensnp.org/snps/json/rs9939609/1.json gives you my genotype at Rs9939609. If you are interested in the genotypes of multiple users you can concatenate this into a single query by either using commas to provide multiple User-IDs (for example http://opensnp.org/snps/json/rs9939609/1,6,8.json) or by giving a range of user-IDs (for example http://opensnp.org/snps/json/rs9939609/1-8.json).

Similarly you can access all phenotypic information of a given user by using http://opensnp.org/phenotypes/json/$userid.json. Again: Just replace $userid by the unique ID of the user you are interested in. For example http://opensnp.org/phenotypes/json/1.json gives you all the phenotypic information I have entered about myself so far. Concatenating multiple users into one query works just as for the SNP/User-combinations by using commas (http://opensnp.org/phenotypes/json/1,6,8.json) or ranges (http://opensnp.org/phenotypes/json/1-8.json). In any case: If you request data of users or user/SNP-combinations that don’t exist the JSON-hash you will get back includes the key “error”, just like this.

This are all the options you can supply by using our JSON-endpoints right now. There are no API-keys and no rate limits. We will just see how it turns out and if any limiting of the access will be necessary in the future. We hope that this will allow more easily reusing the openSNP-data and you maybe have already some nice ideas for remixes/browser plugins/younameit. If you have any requests, which kind of JSON-endpoints you need or would like us to add, just let us know. We are currently experimenting with this JSON-stuff and are open for any critique, comments, ideas etc. If you want to help us to implement further features into openSNP: Please do so, we are open for everybody who wants to participate and want to invite you to do so. The source code is freely available and there is a Google Group/mailinglist where we discuss bug-fixing, new features etc. So you might want to join us there.

Happy Holidays

We have some last news before we leave for our holidays. Let’s start with the biggest news: We were able to secure a little funding through the WissensWert-contest of the german Wikimedia Foundation (sorry, the posting is in German as well). This means that we will have up to 5000 Euros that we can spent to get some more people, who are in love with sharing as we are, genotyped. We will release more details on this as soon as possible.

Additionally Philipp and I will be in Berlin between 12/27 and 12/31. As we have mentioned before we will give a talk on openSNP and crowd-sourced genome-wide association studies at the 28th Chaos Communication Congress. The talk will be on 12/28 at 11 pm. This talk will be in english and there should be day passes, so if you are in town you can pay us a visit. If you are If you’re able to speak or understand German you can also pay a visit to the 0th Spackeriade which takes place on 12/29. We will talk about the implications of the post-genomics-era on privacy.

Thanks again for all your support, for voting for openSNP in the different contests we have entered, for sharing your data with us, for finding bugs, for spreading the word. Have some nice holidays and maybe we’ll see some of you for a beer in Berlin.

Results of the Binary Battle

We are happy to announce that we won the Mendeley / PLoS Binary Battle. This comes unexpected, although we worked hard to achieve this. As we see openSNP as a community-driven project: We really want to thank all of you: For voting for openSNP in the final round of the Battle. For sharing your data. For finding bugs. For your critique. For your ideas and feature suggestions. For all of your support. This is a great source of motivation, especially if I think of implementing all the upcoming feature-ideas we have.

We also want to send our congratulations to PaperCritic, which came in second, and rOpenSci which is the second runner up. Both are definitely worth a look (as are all the other entries of the binary battle as well). It is really great to see what creative minds can build with open data and open APIs.

As Philipp is currently writing his master thesis (and I’m also working for the last exam of this year) there hasn’t been much new in terms of features in the last weeks. But this should end in a week or two and we already have some plans. And we are also applying for some small funding via the german Wikimedia Foundation and their WissensWert-contest, which funds projects that support open knowledge. We are trying to get the funding in order to get data of more people who are into sharing their data genotyped (and may lack the financial resources to get it done). This could lead to some more data sets on openSNP.

Thanks a lot ! And if you have any questions: Just contact us, we are really looking forward to get in touch with you.

You can vote for us

The Mendeley/PLoS Binary Battle now also features a public vote where you can vote for the Top 10+1 submissions. The result of the public vote will count as one point to be added to the expert judges votes.

If you want to help us, give us your vote and spread the word. Thanks a lot!

First Results of the Survey on Sharing Genetic Information

General Information

We have finally taken the time to analyze some of the results of the survey on sharing genetic information we did before we started working on openSNP.

Some general information: Overall 229 people participated in this survey. About 25% of participants gave their chromosomal sex as XX, 74% as XY and there are no differences in terms of usage of DTC-companies between those groups. The mean age of the participants is ~33, the youngest being 15, the oldest being 70. Over 80% of participants gave their ethnicity as caucasian.

Nearly 40% of all participants have already used a DTC-company to get themselves genotyped, further 30% plan to do so while 30% don’t plan to get genotyped. This high amount of participants that got themselves genotyped seems to be the result of the ways we spread the survey: We posted it at the 23andMe-community, sent it to the DIYBio-mailing list and some bloggers out of the fields of genetics/personal genomics also wrote posts on the survey (again: Thanks a lot for your support). We also spread the survey using Twitter, Facebook and Google+. We chose this approach as our goal was not to survey a representative sample, but to assess the demand for a service like openSNP.

68% of all participants said they would agree to share data with their DTC-company, no matter if it shared the data with others, 26% would agree to share, given that the company didn’t distribute the data to others and about 7% were not willing to share at all. No real surprise here: Those who have already been genotyped or are planning to get genotyped are more willing to share than those who don’t plan to. It would be interesting to know if people don’t want to get genotyped because they don’t want to share their data with a company (e.g. Don’t trust DTC-companies).

General reasons (not) to share

My girlfriend says I'm not allowed to display the mean of scaled answers, but then again, she also objects to the bars having shadows, so I wouldn't listen to her.

We also asked a few questions on why people would or wouldn’t share their data with others. Each question could be answered by making a selection on a five point scale, ranging from 1 (strongly disagree) to 5 (strongly agree). There are quite large differences in reasons why people would like to share. The most agreed upon answer is to help scientists with their work (mean = 4.53, median = 5), followed by personal benefits (mean = 3.64, median = 4) and curiosity (mean = 3.5, median = 4). Over half of all people strongly disagree with personalized advertising as a motivation for sharing data (mean = 1,72, median = 1).

There is less diversity in reasons not to publish the results, although the median of “fear of discrimination” and targeted advertising show that over half of all participants at least agree on those questions (medians = 4), while the medians of the questions about consequences for closely related and privacy breaches are in general more neutral (medians = 3).

Differences between customers/non-customers?

We also used an ANOVA and Tukey’s range test to see if there are any differences in agreeing/disagreeing on those questions between survey participants who have already gotten genotyped, those who plan to get genotyped and those who don’t plan to get genotyped. On the topics why people would share their data we found significant differences for the questions regarding helping scientists, having personal benefits and curiosity. Participants who have already gotten genotyped do agree more on those questions, compared to those who don’t plan to get genotyped. For out of curiosity and to help scientists this is even true for comparing the don’t plan to-group to the plan to-group, with the latter one agreeing more.

Regarding reasons not to share genetical information we find similar results: Those who don’t plan to get genotyped agree significantly more on all four questions, compared to those who have gotten themselves genotyped.

Summary (tl;dr)

Although there are no big surprises in those statistics, it is great to get some results regarding our own guesses:

  • People who are already customers of Direct-To-Consumer testing companies (or at least plan on becoming a customer) are more likely to share their data with the company, even if the company allows others to use the data.
  • Customers of DTC testing companies do agree more on questions regarding reasons to share genetical information than those participants who don’t plan to become customers.
  • Those who don’t plan to get genotyped do agree more on topics regarding reasons not to share their data than those who are already genotyped.

It seems that participants who (plan to) get genotyped are feeling more optimistic about the benefits of sharing their data with the DTC company as well as the public and see less problems in possible reasons not to share their data with others, compared to those who don’t plan to get themselves genotyped. And the same seems true vice versa, of course: those who do not plan to get themselves genotyped will agree more to questions concerning the risks of sharing, while scoring lower on questions concerning the possible benefits of doing so.

It’s too bad that we can’t find out (given the current survey) if this is more than correlation. Do people feel more optimistic and lose some of their fears about sharing their data, after they’ve gotten genotyped? Or do they get themselves genotyped because they feel more optimistic about it in the first place (which seems more likely to me)?

We will explore the data set a bit more in the future. Do you have ideas what things we should take a look at?

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