COMBINE 2016 Day 3: From Grassroots community standards to ISO Standards

COMBINE 2016

Martin Golebiewski

You need standards at every stage of the systems biology life cycle. These standards need to work together, be interoperable. From modelling to simulation, to experimental data and back again – there are standards for each step. There are a large number of community standards for the life sciences, in many different subdomains (he references biosharing.org here.)

This presence of many standards for different domains creates quite a lot of overlap, which can cause issues. Even within a single domain, it is normal to see different standards for different purposes, e.g. for the model description and the simulation of the model, and the results of the simulation etc. The way in which the synbio and sysbio standards interrelate is complex.

In COMBINE, there are the official standards, the associated standardization efforts, and the related standardization efforts. The tasks in COMBINE for the board and the whole community are to: organize concerted meetings (COMBINE and HARMONY), training events for the application of the standards, coordinate standards development, develop common procedures and tools (such as the COMBINE archive) and provide a recognized voice.

A similar approach, but with a broader focus, is the European CHARME network, which has been created to harmonize standardization strategies to increase efficiency and competitiveness of European life-science research. This funds networking action for five years from March 2016. See http://www.cost-charme.eu.  There are 5 working groups within CHARME. WG2 involves innovation transfer, to have more involvement with industry.

NormSys is intended to bring together standards developers, research initiatives, publishers, industry, journals, funders, and standardization bodies. How should standards be published and distributed? How do we convince communities to apply standards, and how do we certify the implementation of standards? There is a nice matrix of the standards they are dealing with at http://normsys.h-its.org/biological/application/matrix.

NormSys is meant to be a bridge builder between research communities, industry and standardization bodies. There are actually a very large number of standardization bodies worldwide. ISO is the world’s largest developer of voluntary international standards. Anything that comes from ISO has to come out of a consensus of 164 national standards bodies, therefore finding such a consensus within ISO can be tricky. Most of the experts involved in the ISO standards are doing it voluntarily, or through dedicated non-ISO projects which fund it.

Within ISO, there are technical committees. These TCs might have further subgroups or working groups. There can also be national groups which have mirror committees, and then delegates from these committees are sent to the international committee meetings. The timeline for the full 6 stages of standard development with ISO can be around 36 months. However, this doesn’t include any of the preliminary work that needs to happen before the official stages begin.

There are three main ISO document types: IS (International standard), TS (Technical specification) and TR (Technical Report). Most relevant for us here is the ISO TC 276 for Biotechnology. Its scope is the standardization in the field of biotechnology processes that include the following: terms and definitions, biobanks and bioresources, analytical methods, bioprocessing, data processing including annotation, analysis, validation, comparability and integration, and finally meterology.

There are 5 WG for this TC: yerminology, biobanks, analytical methods, bioprocessing, and finally data processing and integration (WG5). ISO/IEC JTC 1/SC 29 involves the coding of audio, picture, multimedia and hypermedia information (this includes genome compression). ISO TC 276 WG5 was established in April 2015, and there are 60 experts from 13 countries. He says the next meeting is in Dublin, and there is still scope for people to join and help in this effort.

They’ve been working on standards for data collection, structuring and handling during deposition, preservation and distribution of microbes, recommended MI data set for data publication. One of the most important tasks of WG5 is the standardization of genome compression. This was identified as a need from the MPEG consortium.

The biggest deal for COMBINE is the focus on developing an ISO standard for applying and connecting community modelling standards. “Downstream data processing and integration workflows – minimal requirements for downstream data processing and integration workflows for interfacing and linking heterogeneous data, models and corresponding metadata.”

Please note that this post is merely my notes on the presentation. I may have made mistakes: these notes are not guaranteed to be correct. Unless explicitly stated, they represent neither my opinions nor the opinions of my employers. Any errors you can assume to be mine and not the speaker’s. I’m happy to correct any errors you may spot – just let me know!

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