Polbase is a collaborative, open database focused exclusively on DNA polymerases. It is intended to provide a unified information resource for both polymerase experts and those just entering the field. Polbase does not attempt to replace existing protein and genetic information resources. Instead, Polbase compiles the information available in external resources, extending it with results extracted from the primary literature and polymerase-specific features. Since authors are in the best position to enter the important results from their publications quickly and accurately, we ask them to perform this critical function. Polbase was begun with the contribution of references and curation efforts from a small number of founding collaborators. More recently the larger polymerase community has been engaged to finish the work of cataloging the wealth of information in this mature field. By spreading the effort of maintaining Polbase throughout the polymerase community, minimal effort is required of any single research group.
New polymerase references are discovered and added to Polbase via automated tools or manual submission. As new papers are added, the corresponding author is contacted by email and asked to complete and validate the Polbase representation of their work.
Each reference follows a linear path as it is imported into Polbase. After a reference is created, its topics are specified by picking from a short list of polymerase relevant topics. Polymerases are then added to the reference's entry. If a new polymerase is encountered, a place-holder polymerase entry is created. After all polymerases and mutants are listed, the paper's primary results and the relevant experimental conditions are added by the contributor and indexed for searching. When all the results from a paper have been entered, an author ‘validates’ Polbase's representation of their work. Users may track the status of each reference in a queue on their personal account page. Polbase captures increasing amounts of information as the paper progresses through this pathway.
Topic and polymerase specifications allow Polbase to expand PubMed's author, abstract and title searching to include not only reference searches by polymerase (including aliases), polymerase family and host organism, but also by polymerase-specific topics. Topics such as ‘Nucleotide Substitution’ and ‘Kinetic Parameters’ improve searches for references and primary data () and simplify results entry. Polbase also extracts polymerase features from the RCSB Protein Data Bank (PDB) (9
) allowing users to find structures by polymerase, family and presence or absence of DNA in the protein structure.
Advantages of polymerase-specific search features
Relevant experimental details from each paper are stored and displayed with results to allow users to assess information in context. Available contextual information varies by result type, and includes details such as salt concentration, presence of accessory factors, reactants, experimental technique used, etc. This system can be readily extended to accommodate new contexts as they arise or increase in importance to the user community. All results are also linked to their source publication so they can be easily found in their original context.
Polbase avoids editorial positions on the quality of any given result and does not present averaged values. Instead, summarized results are presented as ranges and link to individual results, which are presented with their context allowing the user to assess which are most relevant. Authenticated users and authors of primary data are encouraged to mark references as completely and/or correctly represented in Polbase to facilitate such assessment.
References are not limited to journal articles; negative results and other data not suitable for traditional publication can be made publicly available in Polbase with appropriate indications about the source of this information.
Polbase is built on a carefully designed table structure in a proven relational database system (10
) so that the compiled information will be available to future applications in addition to its current web interface.