Team:UC Davis/Database

From 2013.igem.org

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From the registry, to the wikis, iGEM is founded upon the idea of sharing. Having an open culture allows scientific communities to validate successes and understand failures, while supporting future researchers downstream. To participate in this open culture, our team wanted to share our RiboTALs' multivariate characterization data in the most useful way possible. While the current use of registry pages serve many part types and iGEM teams well, the complexity and volume of data we collected made this method of sharing feel less appropriate, and less accessible. We also noticed in our research of sharing data that teams focused on sharing conclusions and calculations of their data, but rarely found the time to share their raw numbers.
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Our team wanted to share our work in the clearest and most useful way possible, given the multivariance of RiboTals. We did so in the prescribed way of sharing part characterizations through the iGEM registry's experience pages, but excel charts and text summaries left us feeling like we could do more to communicate our work. An imminent solution was to upload our raw, RiboTal data in an intuitive, easy-to-follow form; we implemented such a solution in what we call The Depot, which we expanded to include characterization data for all part types.
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With continued research, it was clear that our dilemma with RiboTALs was not unique. Sharing data for <b>any</b> part type in a way that is useful to everyone is an extremely difficult objective, but we wanted to take a step towards making it easier. Now we are pleased to introduce our step towards that solution, The Depot, an open BioBrick characterization database to further promote sharing in iGEM.
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In addition to being a useful way for iGEM-ers to share their data, The Depot can be a platform for iGEM-ers to think about the human elements of synthetic biology. In participating in The Depot, iGEM-ers would encounter issues of sharing raw data such as, <br>  
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-How would others want to use my work? <br>
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-Who is my work relevant to, and how should I account for that? <br>
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-What can be standardized to make shared data comparable, and therefore more useful for everyone? <br><br>
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We are very excited to present The Depot as an intuitive way to share data, as well as a platform to iGEM-ers to think about the human elements of sharing their work.  
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<h1 class="title">Approaches to Data Standardization: The Past and The Depot</h1>
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<h1 class="title">Approaches to Data Standardization: </h1>
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Past approaches to designing a BioBrick characterization database dealt with difficult questions<a href="#external_links"><sup>5</sup></a>, which entailed two main topics: what are reasonable standards that a database can enforce, and how to make characterizations across labs or experiments comparable. To answer these questions, one would have to make many, many decisions. Decisions like choosing between the use of different characterization protocols, lab equipment, machine settings, data format, and the list goes on and on for each part type.  Additionally, these decisions are posed for a global scale, where accessibility and timetables are major concerns. Moreover, since synthetic biology is a relatively young field, many facets of part characterizations are likely to change over time. The complexity of decisions and synthetic biology's youth make shelving the idea of a completely standardized database very appealing.  
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An online database needs its standards; unfortunately, Biobrick-raw-data (BRD), standardization has been and still is a difficult problem to address because it requires answering many interconnected questions of comparability and enforceability<a href="#external_links"><sup>5</sup></a>. Additionally, BRD standardization is even harder to address because the needs of the community, in both and wet and dry lab, are not strictly defined in an young, changing field like synthetic biology.
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We agreed, at least in some senses. An enforced, strictly standardized database for all part types is not the approach we took for the Depot. In our approach, we instead created a flexible data format standard that many different characterizations could easily conform to. Additionally, we standardized sections of the protocol to promoters, a part type with a history<a href="#external_links"><sup>6</sup></a> of data standardization, more comparable across experiments.  
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Our approach, The Depot, is not an attempt to answer all BRD standardization questions at once. We instead focused two matters, data <b>format</b> standards and openness of raw data, while keeping the aforementioned issues of comparability and enforceability in mind.
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Revision as of 01:55, 29 October 2013

Sharing is what makes us human, but as synthetic biologists, how can we improve the ways we share with each other? Originally proposed as a way for our team to share the multivariate characterization data for our RiboTALs, The Depot was expanded to promote sharing in iGEM for any BioBrick type.

Links

Motivation: Sharing

Our team wanted to share our work in the clearest and most useful way possible, given the multivariance of RiboTals. We did so in the prescribed way of sharing part characterizations through the iGEM registry's experience pages, but excel charts and text summaries left us feeling like we could do more to communicate our work. An imminent solution was to upload our raw, RiboTal data in an intuitive, easy-to-follow form; we implemented such a solution in what we call The Depot, which we expanded to include characterization data for all part types.

In addition to being a useful way for iGEM-ers to share their data, The Depot can be a platform for iGEM-ers to think about the human elements of synthetic biology. In participating in The Depot, iGEM-ers would encounter issues of sharing raw data such as,
-How would others want to use my work?
-Who is my work relevant to, and how should I account for that?
-What can be standardized to make shared data comparable, and therefore more useful for everyone?

We are very excited to present The Depot as an intuitive way to share data, as well as a platform to iGEM-ers to think about the human elements of sharing their work.

Approaches to Data Standardization:

An online database needs its standards; unfortunately, Biobrick-raw-data (BRD), standardization has been and still is a difficult problem to address because it requires answering many interconnected questions of comparability and enforceability5. Additionally, BRD standardization is even harder to address because the needs of the community, in both and wet and dry lab, are not strictly defined in an young, changing field like synthetic biology.

Our approach, The Depot, is not an attempt to answer all BRD standardization questions at once. We instead focused two matters, data format standards and openness of raw data, while keeping the aforementioned issues of comparability and enforceability in mind.

Uploading to the Depot^back to top

The process is straightforward. Users register, then upload their four files that adhere to Depot standards, as well as other information relevant to their experiment. A prototype page that shows the basic functional elements is shown here.

Searching The Depot

Search functionality is currently geared towards location of user-specified data values for BioBrick parts. This demonstrates a very simple, yet illustrative example of leveraging a database. The results of your searches are downloadable.

A prototype page that shows the basic functional elements of search is shown here: A prototype example search is shown here:

Which results in the downloadable table partially shown here:

Visit the Depot

Data Standards

See the Depot's standards and data requirements so you can share your data as well.

Initial Population

See how we initially populated the Depot.

About the Depot

Check out the motivations behind the Depot.

External Links

1 https://2011.igem.org/Jamborees
2 https://2012.igem.org/Jamborees
3 http://www.ncbi.nlm.nih.gov/genbank
4 http://www.pdb.org/pdb/home/home.do
5 http://openwetware.org/wiki/Parts_characterization#Discussion_Topics
6 http://www.jbioleng.org/content/3/1/4

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