Towards the First Data Acquisition Standard in Synthetic Biology

One of key drivers for the transformation of synthetic biology into a fully-pledged engineering discipline, will be the explosion of data captured and analyzed— thanks in no small part to the availability of new imaging modalities (generating ever larger files) and the development of high throughput platforms. At present there is no established standard supporting data acquisition. Developing such a standard is therefore of the utmost importance for the field.

We present here DICOM-SB, an extension to the Digital Imaging and Communications in Medicine (DICOM) standard and de facto standard in biomedicine. Developing such an extension of DICOM is advantageous, as DICOM has properties that would benefit any data acquisition standard, namely: 

1. It is built on a modular, extensible data model for the experimental process.
2. Its binary representation optimizes data storage.
3. It provides services oriented to automate the exchange of information between modalities and repositories.

Also, it has long term success and proven industry orientation. Therefore any extension can be expected to enjoy swift adoption by hardware manufacturers and the engineering community.

Originally developed at Imperial College to support its multistage characterisation pipeline of biological parts (called SynBIS) and work by partners such as NTU Singapore, DICOM-SB has now matured to the point a formal submission to the DICOM committee is in process. The main achievements regarding DICOM-SB are as follows.

1 – Data model. The DICOM-SB Hierarchical Information Model was constructed by modifying DICOM’s model and adding synthetic biology-specific Information Entities, including Tranformation (of a host by a set of components/bioparts), Experiments ( performing the procedures required to analyze the change of behavior that the integrated components produce in the host), Compartments (wells), Stimuli , Equipment and Series.

2 – Supporting new modalities. A new Synthetic Biology module (called the SBRD) has been constructed to model some of the modalities used in synthetic biology, but not already present in DICOM – specifically plate reader data and flow cytometry.  The SBRD was constructed both by reusing the Waveform Information Module of DICOM, and defining new objects for the metadata.

3- Supporting communication. DICOM offers services to allow the communication of data objects between different Application Entities. In a data acquisition context, there is a need for a service that stores the acquired object into a data repository - we have developed a web service that implements a DICOM Message Service Element (DIMSE): the Store service.

It is important to note that far from competing with other synthetic biology standards, DICOM-SB actually actively complements them.  This coexistence is demonstrated within our SynBIS platform where SBOL, protocol, SBML and DICOM-SB files are bound by our datasheet model.

Medical imaging has benefited from this automation for over the last decade thanks to DICOM being embedded in most of their commercial modalities. We believe the adoption of a similar standard by the synthetic biology modality suppliers would be a key milestone for synthetic biology — particularly in relation to interoperability and industrial translation.