HELM (Hierarchical Editing Language for Macromolecules) enables the representation of a wide range of biomolecules (e.g. proteins, nucleotides, antibody drug conjugates) whose size and complexity render existing small-molecule and sequence-based informatics methodologies impractical or unusable. HELM solves this problem through a hierarchical notation that represents complex macromolecules as polymeric structures with support for unnatural components (e.g. unnatural amino acids) and chemical modifications. (http://http://www.pistoiaalliance.o…biologics/)
In essence, the information and data management systems in the Biopharmaceutical industry and academic institutions do not have a standard 'language' or representation for these larger molecules that capture the level of detail needed to unambiguously identify and describe them. These molecules are generally made up of a series of monomers, or building blocks, that combine to form the larger (or 'macro') molecules, which could also be thought of as 'polymers', and are significantly larger than classic 'drug' sized molecules. (These macromolecules also generally fold into specific 3-dimensional structures, but that aspect, or dimension, is not part of HELM). Nucleic acids (RNA, DNA) and proteins (proteins, peptides, antibodies) have their own sets of building blocks, and sometimes the macromolecules can be attached to one another, or to a drug sized molecule. The HELM notation standardizes the detailed description of the building blocks, and the macromolecules they comprise.
The deliverables of the project include establishing HELM (first developed at Pfizer) as "The" standard for describing these molecules (including a governance model and repository), as well as the open sourcing of software tools that were written to read, write, edit, and display the standard representations. The Pistoia Alliance (see below) has provided the organization to raise awareness for the standard, and nurture and attract funding for the project. The potential impact is very broad across the pharmaceutical industry and the vendor community that provides software to the industry. This exciting project has moved very rapidly, and is approaching the first release of the standard and source code.
About the Pistoia Alliance (http://http://www.pistoiaalliance.org/)
The Pistoia Alliance is a global, not-for-profit, precompetitive alliance of life science companies, vendors, publishers, and academic groups that aims to lower barriers to innovation by improving the interoperability of R&D business processes. We differ from standards groups because we bring together the key constituents to identify the root causes that lead to R&D inefficiencies and develop best practices and technology pilots to overcome common obstacles.
The logo will be used in the efforts to promote and socialize the standard, and potentially on user interface components. The target audience is fairly technical, comprised of scientists and software or IT experts, so will likely find designs that convey or reflect the scientific basis most appealing, while keeping graphic elements simple enough to be recognizable as an icon. The community uses social media, open source tools, pre-competitive collaborations to significant degree.
Example images of the types of molecules that HELM will be used for are attached. Searching Google images for examples of the following could also be instructive: