MuteinDB: the mutein database linking substrates, products and enzymatic reactions directly with genetic variants of enzymes by Andreas Braun, Bettina Halwachs, Martina Geier, Katrin Weinhandl, Michael Guggemos, Jan Marienhagen, Anna J. Ruff, Ulrich Schwaneberg, Vincent Rabin, Daniel E. Torres Pazmiño, Gerhard G. Thallinger, and Anton Glieder.
Mutational events as well as the selection of the optimal variant are essential steps in the evolution of living organisms. The same principle is used in laboratory to extend the natural biodiversity to obtain better catalysts for applications in biomanufacturing or for improved biopharmaceuticals. Furthermore, single mutation in genes of drug-metabolizing enzymes can also result in dramatic changes in pharmacokinetics. These changes are a major cause of patient-specific drug responses and are, therefore, the molecular basis for personalized medicine. MuteinDB systematically links laboratory-generated enzyme variants (muteins) and natural isoforms with their biochemical properties including kinetic data of catalyzed reactions. Detailed information about kinetic characteristics of muteins is available in a systematic way and searchable for known mutations and catalyzed reactions as well as their substrates and known products. MuteinDB is broadly applicable to any known protein and their variants and makes mutagenesis and biochemical data searchable and comparable in a simple and easy-to-use manner. For the import of new mutein data, a simple, standardized, spreadsheet-based data format has been defined. To demonstrate the broad applicability of the MuteinDB, first data sets have been incorporated for selected cytochrome P450 enzymes as well as for nitrilases and peroxidases.
Database URL: http://www.muteindb.org/
Why is this relevant to topic maps or semantic diversity you ask?
I will let the author’s answer:
Information about specific proteins and their muteins are widely spread in the literature. Many studies only describe single mutation and its effects without comparison to already known muteins. Possible additive effects of single amino acid changes are scarcely described or used. Even after a thorough and time-consuming literature search, researchers face the problem of assembling and presenting the data in an easy understandable and comprehensive way. Essential information may be lost such as details about potentially cooperative mutations or reactions one would not expect in certain protein families. Therefore, a web-accessible database combining available knowledge about a specific enzyme and its muteins in a single place are highly desirable. Such a database would allow researchers to access relevant information about their protein of interest in a fast and easy way and accelerate the engineering of new and improved variants. (Third paragraph of the introduction)
I would have never dreamed that gene data would be spread to Hell and back.
The article will give you insight into how gene data is collected, searched, organized, etc. All of which will be valuable to you whether you are designing or using information systems in this area.
I was a bit let down when I read about data formats:
Most of them are XML based, which can be difficult to create and manipulate. Therefore, simpler, spreadsheet-based formats have been introduced which are more accessible for the individual researcher.
I’ve never had any difficulties with XML based formats but will admit that may not be a universal experience. Sounds to me like the XML community should concentrate a bit less on making people write angle-bang syntax and more on long term useful results. (Which I think XML can deliver.)