The PubChem Deposition Gateway

The PubChem databases were created to incorporate chemical structure
data and biological assay data into Entrez to be searchable and
cross-linked to the other biological databases.  With the start of the
NIH roadmap screening initiative and considerable interest in the
biological and chemical communities for open access to such data, many
researchers are interested in depositing their data.  There are,
however, many variations, redundancies and errors associated with
chemical structure data and even more so with biological assay data.
We have developed a deposition system, the PubChem Deposition Gateway,
to handle the automated acquisition of data with syntactic validation
and structure standardization.  A web interface is available for
guiding depositors through the process and an ftp site handles
automated institutional updates and additions.  A balance is made
between requiring strict format requirements for data files and
allowing flexibility in data, particularly the inherently free-form
biological assays.  The system reports all errors and warnings to
users requiring the most serious to be fixed before upload to PubChem
is allowed.  Through this process we encourage depositors to
standardize their data so that structures can be more easily found via
associations with neighbors and related terms; and so that assays can
be searched and graphed via numerical quantities such as activity.