PubChem Upload 1.0f Released

Submitting your data to PubChem is now easier than ever. PubChem Upload: click to see the large image The new PubChem Upload system offers streamlined procedures for data submissions and includes an extensive set of wizards, inline help tips, and templates to assist users.  First released as a beta in April 2013, PubChem Upload is now in final form (1.0f) and replaces the Deposition Gateway as the primary PubChem data submission system.  The PubChem Deposition Gateway, first introduced in April 2005, has been superseded as an interface and will be completely phased out in 2014.

What does it do?

PubChem Upload is a data submission system.  PubChem Upload: click to see the large image It allows contributors to provide substance descriptions (including chemical structures, names, crosslinks, and comments), assay experiment descriptions, and the results of substances being tested in assays.  There is a great deal of flexibility in the information that can be provided to PubChem.  For example, there are no limits (beyond the practical) on the number of assay readouts or the count of substances per assay that can be provided.  An abbreviated list of PubChem Upload features include:

  • PubChem Upload: click to see the large image The means to enter data and descriptive information by web form or by file, based on user preference.
  • Convenient spreadsheet formats (CSV, Excel & OpenOffice) as well as XML-based data specifications accommodate both one-off and frequent data providers.
  • A “Preview” function displays incoming data to show how it will appear in PubChem before being loaded.
  • An automated suite of validation checks help contributors identify potential issues before data is made public.

Why the new release?

Advances in web technologies provided us the opportunity to enhance the user experience by reducing the time and effort required to make substance descriptions and their associated biological activities available and useful for the public. PubChem Upload: click to see the large image The new PubChem Upload interface greets a new contributor who may only be interested in making a quick submission with a simple decision-tree set of wizards to guide them through the process of publishing their data in PubChem.  For the experienced user, the wizards can be avoided, and the enhanced upload and editing capabilities used instead.

There are many improvements over the older Deposition Gateway system. One noteworthy feature is that PubChem Upload offers an expanded ability to edit data directly in the browser.  The spreadsheet editor gives PubChem contributors the ability to upload large spreadsheets with minimal reformatting and to edit those large datasets online.

Potential future directions

PubChem staff places a high importance on continuing to improve the submission process and increasing the usefulness of data to the PubChem end-user.  One such direction is the use of controlled vocabulary annotations, or ontologies, such as BAO, GO, and MeSH, to help streamline the description of provided data.  This may, for example, improve the ability of PubChem end-users to utilize and analyze bioactivity results.

The new PubChem Upload system utilizes a RESTful model of data communication between client and server.  As such, it is now technically possible to document and support the creation of upload utilities that can be incorporated into third-party software such as ELNs and LIMs. Interfacing PubChem Upload directly with a properly configured laboratory data system may dramatically reduce the effort to publish data in PubChem.

Where can I learn more about PubChem Upload?

To get an overview of the PubChem Upload system, please view this presentation.  To get basic information, please read this abbreviated help document.  For a more extensive overview and detailed information about the features, please read the complete help document.

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