Computational Toxicology Research Program
How to Publish a DSSTox Database
Expansion of DSSTox database offerings and growth of this project as a public resource will largely depend on two factors:
community acceptance and adoption of DSSTox database format and standards; and
success at attracting new Sources of public toxicity data to publish databases on the DSSTox website.
Any person or organization, public or private, is invited to submit a toxicity database for publication on the DSSTox website. A variety of resources and file templates are available on this site to aid potential Sources. In addition, we can assist Source collaborators in creating DSSTox SDF files, in reviewing data and documentation files, and with the final website posting of these files. This page provides information to aid persons interested in publishing a database on the DSSTox website.
Benefits of publishing on DSSTox
Who can be a DSSTox database Source?
Source external website
What we ask of potential Sources?
Available resources for aiding DSSTox database construction
What help we can provide?
Databases subject to internal and outside peer review
Some reasons why a potential author or Source should consider publishing a database on DSSTox:
Increased recognition for authorship and expertise relative to a toxicity database;
Increased visibility and use of the database by a wide range of users and scientific disciplines;
Added chemical and structural content;
Ability to merge database with many other toxicity databases in structure-searchable format;
Potential for collaborations and user feedback;
Facilitating development of improved SAR (structure-activity relationship) and predictive toxicology models relative to a database and toxicity endpoint;
Supporting and encouraging the DSSTox standardization effort and public resource.
Ideally, a Source, or main author of DSSTox database, is a person or persons who either generated the data within the database, is a recognized expert on the database, and/or has authored one or more publications reporting the database compilation. A Source could also be a secondary user of the primary data, someone who has some expertise or demonstrated familiarity with the data, and who is willing to act as a Source Main Contact for the DSSTox database in question. Finally, a Source of the primary data could team up with a others willing to aid the database publication effort and would be considered co-Sources or coauthors the DSSTox database publication. Other Source and publishing variations are possible and will be considered if they meet the primary aims of knowledgeable sponsorship of the database in question.
If a Source maintains a separate informational website relative to a published DSSTox database, a link to that site will be provided on the DSSTox main informational, SDF Download Page. Also, once the DSSTox database and documentation files are created, it becomes an easy matter to host this information, or links to this information from any Source website. An advantage of posting a database and documentation files on the DSSTox website is to be able to link easily to the supporting content on this website. In addition, it is recommended the the external Source website provide links to the appropriate DSSTox web pages for accessing the corresponding DSSTox database.
Any person or organization interested in publishing a database on the DSSTox website can use the tools and templates provided on this site to create draft documentation and data files. Alternatively, potential Sources can request DSSTox assistance for whatever aspect of database file creation they are unable to complete. The more assistance that is requested, the lengthier will be the development and time-to-publication.
If a Source wishes to enter into a DSSTox collbaoration, we require at minimum the following:
for the documentation -
- a database summary description
- Main Citation(s)
- Source Contact
- main toxicity data field definitions
for the SDF data file(s), in tab-delimited or spreadsheet format (.xls) -
- chemical names (any type generally accepted)
- CAS numbers
- Tested form of the chemicals (specify any salt or complexes, detailed form, or if unknown, say so)
Not required, but highly desireable:
for the SDF data file(s) -
- chemical structures, printed, or in any transferable electronic form
- chemical structures in mol file or SDF format
- SMILES codes for all structures
What can most facilitate speedy database publication:
Documentation and Data files in as near final form as possible following the templates and standard field guidelines provided on this website.
Potential Sources should consult Templates & Sample Files for samples of documentation files that can be used for constructing DSSTox databases. Documentation files for published databases on this website offer additional examples and details on potential varients of these templates and sample files.
Consult the DSSTox Central Field Definition Table for a full listing of Source-specific toxicity data field names, allowable entries, and definitions for all published DSSTox databases. These can be used to guide the construction of Source-specific data fields for the new database under development.
Consult Technical Procedures for details of the construction of DSSTox data files using particular commercial Chemical Relational Database (CRD) applications.
We have developed internal procedures and tools to facilitate construction of DSSTox SDF files. Hence, we are best prepared to assist in:
extracting existing chemical structure information from DSSTox Master Structure-Index File;
filling of DSSTox Standard Chemical Fields;
creation of the final, clean SDF file(s);
QA review and appropriate formatting and editing of documentation files;
creation of structures.pdf and nostructures.xls data files from the final SDF file(s);
publishing files on DSSTox website.
A major qualification, at present, is that the help that we can offer, and schedule for assistance and completion, will largely depend on the available EPA or community staff resources available to this project at the time of the request.
All documentation and data files considered for DSSTox publication are subject to DSSTox project review, EPA internal review, and in some cases outside peer review. The DSSTox citation for all currently published DSSTox databases, listed on the SDF Download Page for each database, signifies that the set of documents has undergone EPA internal review by at least two scientific reviewers and has been approved for on-line publication. Reviewers are typically listed in the Acknowledgements section on the Source SDF Download Page. In addition, most databases have undergone extensive quality review by DSSTox project staff (some description provided in the Log File for each database), by the Source and their collaborators, and in many cases, by other interested parties. The DSSTox project reserves the right to reject any database for publication on this website based on quality concerns, inadequate documentation, or topic irrelevance (i.e., too distantly related to chemical toxicity).