In recent years, ChEBI has become increasingly utilised by the systems biology community as a repository of persistent, unambiguous identifiers with which to semantically annotate models.
are tagged with unambiguous identifiers from publicly available, third party databases.
This knowledge is captured within a so-called "ontology", i.e., an extensive and detailed network of "concepts", terms that are unambiguous identifiers of a scientific domain such as "gene chip" in the field of genetic high-throughput screening, or "humane endpoints" in the field of the 3Rs.
We therefore believe there is a need for a standardized and consistent method to uniquely identify an alternatively spliced isoform using a short and unambiguous identifier, whose purpose is to describe its structure, in terms of the exact succession of exons and introns that characterizes it, in a simple and concise way.
In general, this procedure involves generating an unambiguous identifier of a compound independent of the tautomeric form that was used as the input.
For the calculation of unhashed Morgan fingerprints [45], each compound substructure in the dataset, with a maximal diameter of four bonds, was assigned to an unambiguous identifier.
Once the molecules are loaded into a python list, the method extract_substructure_information from the class bioalerts.LoadMolecules.GetDataSetInfo permits the generation of a dictionary of substructures, whose keys correspond to substructure unambiguous integer identifiers, and the values to the molecule indices within the molecule list.
For their computation, each substructure in a molecule, with a maximal user-defined bond radius, is assigned an unambiguous integer identifier.
Instead of current lax approach, I would suggest the use of unambiguous strain identifier, such as a hypertext tag pointing to the vendor's description web page (if the strain is commercial), or to the "digital object identifier" (d.o.i). of the original publication, if the strain was obtained by other means.
Despite the emergence of author identifier systems such as Researcher ID from Thomson Reuters [ 5] and Scopus Author ID from Elsevier [ 6], Open Researcher and Contributor ID (ORCID) [ 7] and many others, universal, unique and unambiguous author identifier for author disambiguation remains elusive [ 18].
Essentially, it amounts to the use of unambiguous strain identifier, such as a hypertext tag pointing to the vendor's description web page (if the strain is commercial), or to the "digital object identifier" (doi) of the original publication, if the strain was obtained by other means.
