Help Overview
Thank you for using STRENDA DB, the electronic data submission system for functional enzyme data.
In order to enable first-time users to successfully enter their functional enzyme data in the data acquisition forms and to support experienced users with detailed information, here, the STRENDA DB User Documentation is provided which includes step-by-step data entry instructions.
This help file can be downloaded in PDF format: Download
Please feel free to inform you if you find in this document any errors, misleading statements or to make suggestions for improvement and additions.
Features in Version 1.3
- adaptation of the units table to EnzymeML (SBML) standards
- replacement of the font in the PDF to allow additional special characters
- change from legacy API to RESTFul API of UniProt
- synonyms and MeSH heading are now pulled from PubChem with the MeSH being handled prior to synonyms in the hit list
Features in Version 1.2
- ORCID in the user profile
- DOIs and PMIDs of the reference paper linked to the corresponding site
- extension of unit table
- extension of the query table
- bug fixes
Features (not yet) implemented
This first version of STRENDA DB cannot fulfil all demands and requirements that might be desirable – there are still some limitations that should be known by the users before entering data and giving up frustrated. The missing features are subject of subsequent versions of STRENDA DB.
The open issues are:
- simple database interface to query data; data retrieval will be made possible by providing a “Google”-like search mask which allows the user to query for SRN, proteins, author names, organisms but not for numerical data such as KM values between x and y mM.
- simple user or manuscript administration; the focus is set on the enzyme data input;
- special cases of data types can not be handled such as unknown protein or protein name, protein without UniProtKB entry, or only the reaction is known (e.g. crude extracts);
- multi-component enzymes cannot be entered; data for the catalytic active subunits can be entered;
- missing cross check of post-translational modifications against original protein sequence (e.g. validation whether phosphorylation at the correct amino acid residue);
- restricted user support for macromolecules; automatic search in PubChem only. Further databases can be selected in subsequent versions.
- Kinetics data for macromolecules cannot be entered, yet.
- entry of cell lines (different from cell types) along with the definition of the organ;
- validation of names of organisms (at NCBI Taxonomy) with TaxonID in particular if one of each entry is changed.
- Validation and use of standardized termes of e.g. tissues (using BTO).
- bi-substrate reactions; Vmax and KM values of a specific depends on the concentration;
- grid datasets with the concentration of both/all substrates changed;
- progress curves or time-course data