Pistoia represents biomolecular data better

Efforts to improve the way that biomolecules are represented got a boost this week when the Pistoia Alliance announced that it had selected quattro research GmbH to implement the HELM 2.0 project (Ambiguous HELM).

The announcement comes shortly after the appointment of Dr Steve Arlington as the Pistoia Alliance’s new president, and after five companies were announced as finalists in the Alliance’s ‘Start-up Challenge 2015’.

HELM is an open standard to enable the representation complex macromolecules including nucleotides, proteins, antibodies, and drug-antibody conjugates. The Pistoia Alliance’s initiative will enable HELM to represent biomolecules in which some aspects of the structural composition or assembly are not fully determined.

Scientists have struggled to represent non-standard biomolecules in their systems leading to ‘pick and mix’ approach of multiple nomenclatures and textual descriptions.

The HELM notation was created by a team at Pfizer, and the Pistoia Alliance formalised it as an open standard in early 2013 and publicly released software tools to the Open Source community. Since its release, HELM has benefited from a growing range of global adopters and contributors, which includes ACD Labs, Arxspan, Biomax, Biovia, BMS, ChemAxon, EMBL-EBI, eMolecules, GSK, Lundbeck, Merck, NextMove, Novartis, Pfizer, quattro research, Roche, and Scilligence.

While the existing HELM approach solves the problem of representing unnatural complex biomolecules, it still assumes that the scientist knows everything about the structure. In biology this is rarely the case, with the outcome of experiments subject to a number of uncertainties. Currently scientists have a difficult choice: either imply they have all the information and guess at a structure, or record a textual description and put no structural information in their corporate databases. Ambiguous HELM allows the structural information that is available to be captured in a useful way, while also identifying what is not known.

The Pistoia Alliance is a global, not-for-profit alliance of life science companies, vendors, publishers, and academic groups that work together to lower barriers to innovation in R&D through pre-competitive collaboration. Members collaborate as equals on open projects that generate significant value for the worldwide life sciences community.

Its new president, Dr Steve Arlington, joins the Alliance from PwC, where he was the Global Lead Partner, Pharmaceuticals and Life Sciences consulting. He began his career in research at Smith Kline, and has held senior roles at Unipath, PA Consulting and IBM.

In one of his first acts as president, Arlington announced the shortlist of finalists for the Pistoia Alliance President’s Start-up Challenge 2015, showcasing a range of start-up companies with exciting new ideas from across Europe and the USA.

The five entries selected as finalists are: BSSN Software GmbH (Germany) for developing software to improve access to scientific data through an integrated approach; Informatics Unlimited (UK) for its services and novel informatics solutions for Life Science R&D organisations; Novaseek Research (USA) which has produced a platform that enables access to real-world real-time clinical data and human biospecimens to accelerate R&D; Ontoforce (Belgium) for its pioneering technology for information flow and management; and Repositive Limited (UK) which offers efficient access to genomic data through a novel platform.

The finalists will each receive three months’ mentorship from a Pistoia Alliance member company and a small cash prize of US$5,000 to help them develop their business plans further. Final judging will take place in January with the overall winners announced at an awards ceremony in London, UK, in February 2016. The overall winners will each receive an additional cash prize of US$15,000 and a further six months of expert mentorship.

Mentors in the Start-up Challenge are senior industry figures drawn from the Pistoia Alliance membership, offering valuable industry insight to the Finalists and Winners and a chance for them to validate their ideas against real industry needs.

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