Common Questions

About Polbase

Where does the information in Polbase come from?

Polbase is populated with references found in PubMed and structures from the RCSB PDB. Information from references is manually extracted and added as Polbase results. Polymerase entries are linked with UniProt. Host organisms are linked with the NCBI Taxonomy tree.

What kind of information is included in Polbase?

Polbase includes detailed information reported about wild-type, mutant and engineered polymerases in peer-reviewed, primary sources. It also includes bibliographic information for review articles. If present, unpublished results are clearly distinguishable from published results and are associated with the investigator reporting those results.

Who is responsible for Polbase?

Polbase is developed at New England Biolabs in collaboration with numerous contributors from around the world.

How is Polbase populated with information?

Polbase uses a combination of automated tools to identify and extract information from relevant polymerase papers, but we depend on the participation of experts to fully represent a paper. Polymerase authors help us maintain Polbase as a current and accurate resource by contributing and certifying the information related to their publications. By using this collaborative model, we can spread the effort of maintaining Polbase across many people and keep the effort required of any one person to a minimum.

How do I contribute to Polbase?

You can sign up for a user account to begin entering relevant information. If you wish to submit a reference library please contact us.

Is Polbase complete?

Certainly not! Polbase is intended to be a dynamic resource that responds to the changing landscape of Polymerase knowledge and community needs. Polbase has many useful features right now, and will continue to be improved as more data is contributed and more features are added.

How is Polbase kept up-to-date?

Polbase has an "incoming" queue section that is automatically populated with new information from PubMed and the RCSB PDB regularly. These entries are manually checked for relevance and imported.

How is Polbase funded?

Polbase is funded by a grant from the National Institutes of Health and supported by New England Biolabs

Can I contribute data I don't plan to publish?

Yes, simply add a reference of type "unpublished" to contain it. This data will appear in Polbase with a mark to indicate that it has not been through a peer-review process.

Polbase Features

How can I search Polbase?

Polbase has 3 distinct search tools:

1. Instantaneous searching/filtering of the information in tables

   Simply start typing into any "Search this table" field to pull out rows that contain your search term.

2. Simple site-wide searching

   Polbase includes a simple but powerful search feature. It can be accessed by typing into the search field at the top right corner of the page or by following on the "Search" link in the navigation menu on the left.

3. Advanced searching

   An advanced search tool allows a user to find all polymerases or references containing information about a specific topic, or all those from a specified organism, or in a polymerase family ...

How can I sort through all the data contained in Polbase?

Polbase provides many views of the data it contains. You can list polymerases, references, structures, and results by property by reference or by polymerase (with the Results link at the bottom of these pages) You can also view summary results at the polymerase properties page.

How can I be sure the data I'm seeing is accurate? (Validation)

Polbase has a feature that allows authors and other users to "Validate" the correctness of Polbase's representation of results extracted from a reference. Since Polbase does not take an editorial position on the data, these validations refer only to the quality of reference's representation in Polbase. All results are linked with their source reference so you can easily find more detailed information (see I found an error, how can I report it? ).

How does Polbase address conflicting data?

Polbase does not take an editorial position on scientific data. Instead all results are presented with their experimental context to allow the user to assess which value is most relevant.

Can I use/consume this information programmatically?

Yes, most Polbase pages are presented as XML and/or JSON data if you append ".xml" or ".json" to the end of the URL e.g. /polymerases/T4.xml

Troubleshooting

What is the best browser to use with Polbase?

Polbase is designed to work with any web browser, however some pages may be slower to load in Internet Explorer. If you must use Internet Explorer we recommend installing the Chrome frame plugin, (no administrator access required)

Why can't I find reference X?

Did you try visiting the reference index page and typing in an author name? You could also search for a term from the title, abstract, or author list with the search tools. If you know the PubMed ID, you can go directly to the reference by typing it into your web browser's address bar (e.g. /references/PMID1608969).

Polbase may not have indexed your reference yet. Polbase has avoided an automated reference discovery process to decrease the number of irrelevant papers in the database.

If you know the PubMed ID and are willing to become a contributor, you can add a reference quickly by creating a new reference and entering the PubMed ID in the first field on the form. If you are willing to contribute polymerase-centric reference collection please contact us to become a contributor.

I found an error, how can I report it?

Error types

1. Incorrect/conflicting scientific data

   Polbase presents all data from the scientific literature without taking an editorial position. If you are aware of of a paper with more relevant results, please contact us or become a contributor and add the the results (see Why can't I find reference X?).

2. Polbase incorrectly represents a paper's results

   If you find an error in Polbase's representation of a result, please contact us to report the error.

How can I suggest a new feature?

If you have a suggestion for a new feature, please use the feedback link found on the left side of every page.

How can I verify that the data from my own papers is represented accurately in Polbase?

Sign up for an account. You can then easily complete/correct and validate the results displayed for your work. If you find something wrong please contact us.