UniChem: a unified chemical structure cross-referencing and identifier tracking system by Jon Chambers, Mark Davies, Anna Gaulton, Anne Hersey, Sameer Velankar, Robert Petryszak, Janna Hastings, Louisa Bellis, Shaun McGlinchey and John P Overington. (Journal of Cheminformatics 2013, 5:3 doi:10.1186/1758-2946-5-3)
Abstract:
UniChem is a freely available compound identifier mapping service on the internet, designed to optimize the efficiency with which structure-based hyperlinks may be built and maintained between chemistry-based resources. In the past, the creation and maintenance of such links at EMBL-EBI, where several chemistry-based resources exist, has required independent efforts by each of the separate teams. These efforts were complicated by the different data models, release schedules, and differing business rules for compound normalization and identifier nomenclature that exist across the organization. UniChem, a large-scale, non-redundant database of Standard InChIs with pointers between these structures and chemical identifiers from all the separate chemistry resources, was developed as a means of efficiently sharing the maintenance overhead of creating these links. Thus, for each source represented in UniChem, all links to and from all other sources are automatically calculated and immediately available for all to use. Updated mappings are immediately available upon loading of new data releases from the sources. Web services in UniChem provide users with a single simple automatable mechanism for maintaining all links from their resource to all other sources represented in UniChem. In addition, functionality to track changes in identifier usage allows users to monitor which identifiers are current, and which are obsolete. Lastly, UniChem has been deliberately designed to allow additional resources to be included with minimal effort. Indeed, the recent inclusion of data sources external to EMBL-EBI has provided a simple means of providing users with an even wider selection of resources with which to link to, all at no extra cost, while at the same time providing a simple mechanism for external resources to link to all EMBL-EBI chemistry resources.
From the background section:
Since these resources are continually developing in response to largely distinct active user communities, a full integration solution, or even the imposition of a requirement to adopt a common unifying chemical identifier, was considered unnecessarily complex, and would inhibit the freedom of each of the resources to successfully evolve in future. In addition, it was recognized that in the future more small molecule-containing databases might reside at EMBL-EBI, either because existing databases may begin to annotate their data with chemical information, or because entirely new resources are developed or adopted. This would make a full integration solution even more difficult to sustain. A need was therefore identified for a flexible integration solution, which would create, maintain and manage links between the resources, with minimal maintenance costs to the participant resources, whilst easily allowing the inclusion of additional sources in the future. Also, since the solution should allow different resources to maintain their own identifier systems, it was recognized as important for the system to have some simple means of tracking identifier usage, at least in the sense of being able to archive obsolete identifiers and assignments, and indicate when obsolete assignments were last in use.
The UniChem project highlights an important aspect of mapping identifiers: How much mapping can you afford?
Or perhaps even better: What is the cost/benefit ratio for a complete mapping?
The mapping in question isn’t a academic exercise in elegance and completeness.
It’s users have immediate need for the mapping data and it is it not quite right, human users are in the best position to correct it and suggest corrections.
Not to mention that new identifiers are likely to arrive before the old ones are completely mapped.
Suggestive that evolving mappings may be an appropriate paradigm for topic maps.
