Queries can be submitted in a tab-separated format, where each line contains the compound ID (optional) followed by the compound's structural representation. To submit SMILES or InChI strings, select the 'Chemical' query type. To submit IUPAC names as input, select the 'IUPAC Name' query type. For illustrative purposes, click on the respective example buttons (STRUCTURE or IUPAC NAME) on the home page.

Small molecules can also be imported/drawn via the Marvin JS application. The resulting structure will then be processed and classified.

A third option for submitting input structures is through upload of a TSV or SDF file. Please make sure that each file contains less than 3 MB of data, to ensure that the resources are shared properly with other users.

Sequences of polypeptides and nucleic acids can be submitted for classification using the FASTA format. Here, a minimum length of 2 residues is required for oligo-/polypeptides and oligo-/polynucleotides. In this case, the user must select the 'Protein/DNA/RNA' query type. For illustrative purposes, click on the respective example button (FASTA) on the home page. Sofar, upoad of FASTA sequences is not supported.

Classification results can be displayed as JSON, SDF, or CSV files, beside the classic HTML format. This applied for single molecules (entities or sequences) as well as queries (composed of one or more molecules).

Entities are accessible through their inchikey. For instance, Aspirin (InChIKey=BSYNRYMUTXBXSQ-UHFFFAOYSA-N) is accesible at the following URL: classyfire.wishartlab.com/entities/BSYNRYMUTXBXSQ-UHFFFAOYSA-N. The JSON, SDF, or CSV can be accessed by adding the ending (.json, .sdf, or .csv) to the URL.

Sequences are accessible through their fingerprint. For instance, a sequence with fingerprint a5f9a934bb335291c1c8eddd72a24b53 is accesible at the following URL: http://classyfire.wishartlab.com/sequences/a0452532fb71718ad277e1960804bba5. The JSON, or CSV can be accessed by adding the ending (.json, or .csv) to the URL.

Queries here are accessible through they id. For instance, the query with ID = 1 is displayed as a JSON file at the following address: http://classyfire.wishartlab.com/queries/1. Moreover, the JSON, SDF (only for queries of the STRUCTURE type), or CSV can be accessed by adding the ending (.json, .sdf, or .csv) to the URL.

When retrieving classification results for a query, CSV or SDF files are now automatically returned for download. Because of their size, JSON files are now paginated (10 compounds/page). To retrieve the first 10 classification results (page 1) of query 2018 for instance, use the following for instance, use the following URL
classyfire.wishartlab.com/queries/2018.json?page=1.

Each page must be downloaded separately. To find the number of pages, select the attribute "number_of_pages". To find the number of entities/sequences that were classified for this query, select the attribute "number_of_elements"

Queries can be submitted or retrieved using a REST API. While Queries can be submitted in JSON format, they can be retrieved in JSON or SDF format. Users can also use this API to retrieve classifications for single entities, in JSON or SDF format.

A REST API written in Ruby is accessible here.

Please limit your POST requests to 12 per minute.