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API

GNPS2

TODO

ChemicalStructureWebService

Web Server for Chemical Structure pictures as well as other chemical structure things

Web API Endpoints

Full resolution of all structural information conversion

https://structure.gnps2.org/convert?smiles=CCO

InChI Conversion

https://structure.gnps2.org/inchi?smiles=CN1C=NC2=C1C(=O)N(C(=O)N2C)C

InChIKey Conversion

https://structure.gnps2.org/inchikey?smiles=CN1C=NC2=C1C(=O)N(C(=O)N2C)C

Smiles Conversion

https://structure.gnps2.org/inchikey?smiles=InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3

Mol Conversion

https://structure.gnps2.org/mol?smiles=InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3

ClassyFire

https://structure.gnps2.org/classyfire?inchi=InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3

Formula

https://structure.gnps2.org/formula?inchi=InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3

Structure Mass

https://structure.gnps2.org/structuremass?inchi=InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3

https://structure.gnps2.org/structuremass?formula=C8H10N4O2

Adduct Masses

https://structure.gnps2.org/adductcalc?inchi=InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3

Structure Fingerprint

https://structure.gnps2.org/structurefingerprint?inchi=InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3

Structure Drawing

https://structure.gnps2.org/structureimg?inchi=InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3

Structure Similarity

https://structure.gnps2.org/structuresimilarity?inchi1=InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3&smiles2=CN1C=NC2=C1C(=O)N(C(=O)N2C)C

Structure Natural Product Classifier (NP Classifier)

If you have Smiles

https://npclassifier.gnps2.org/classify?smiles=<smiles string>

Example

Example JSON Output 
{
    class_results: [
        "Purine alkaloids"
    ],
    superclass_results: [
        "Pseudoalkaloids"
    ],
    pathway_results: [
        "Alkaloids"
    ],
    isglycoside: false,
    fp1: [
        0,
        0
        ...
    ],
    fp2: [
        0,
        0,
        ...
    ]
}

NPClassifier

NPClassifier is A Deep Neural Network-Based Structural Classification Tool for Natural Products - check it out here. For citation: Kim, Hyun Woo, Mingxun Wang, Christopher A. Leber, Louis-Félix Nothias, Raphael Reher, Kyo Bin Kang, Justin JJ van der Hooft, Pieter C. Dorrestein, William H. Gerwick, and Garrison W. Cottrell. "NPClassifier: A deep neural network-based structural classification tool for natural products." Journal of Natural Products (2020). https://doi.org/10.1021/acs.jnatprod.1c00399. Checkout the tool index for a large scale workflow for batch classification.

ReDU Metadata

Getting files for a given metadata category 

https://redu.gnps2.org/attribute/<attribute>/attributeterm/<term>/files?filters=%5B%5D

Getting all terms per attribute 

https://redu.gnps2.org/attribute/<attribute>/attributeterms?filters=%5B%5D

Rapidly search pre-made libraries GNPS and MassIVE spectral data.

Search by peaks in json format using query_spectrum:

https://fasst.gnps2.org/search?usi=None&precursor_mz=981.54&charge=1&library=gnpslibrary&query_spectrum={%22n_peaks%22:15,%22peaks%22:[[165.06979370117188,0.38009798526763916],[167.072998046875,1.7413330078125],[179.07260131835938,0.2999509871006012],[180.08079528808594,100.0],[181.08859252929688,2.8455820083618164],[182.09649658203125,23.914995193481445],[192.08079528808594,0.6896359920501709],[193.0886993408203,0.2419929951429367],[208.07569885253906,3.9236950874328613],[210.09129333496094,51.83255386352539],[236.0706024169922,4.025279998779297],[253.09719848632812,21.652437210083008],[254.08120727539062,46.069068908691406],[255.0872039794922,0.3038550019264221],[271.1077880859375,0.7285820245742798]],%22precursor_charge%22:0,%22precursor_mz%22:271.1077}

Search by USI:

https://fasst.gnps2.org/search?library=gnpslibrary&usi=mzspec:GNPS:GNPS-LIBRARY:accession:CCMSLIB00000001547

Parameters: * usi (mutually exclusive with query spectrum) * library: The pre-built library index, options are listed on the Fast Search GUI * analog: [Yes/No], Defaults to "No" * cache: [Yes/No], Defaults to "No" * lower_delta: defaults to 130 * upper_delta: defaults to 200 * pm_tolerance (Da): The tolerance for precursor mass matching in daltons, defaults to 0.05 * fragment_tolerance (Da): The tolerance for matching individual peaks in daltons, defaults to 0.05 * cosine_threshold: The minimum cosine threshold to be included in the results, defaults to 0.7 * query_spectrum (mututally exclusive with USI): A json formatted peak list

Public Dataset Files

Access spectral data by USI or SpectrumID Getting all files per dataset

https://explorer.gnps2.org/api/datasets/{accession}/files

Getting file path per USI

https://dashboard.gnps2.org/downloadlink?usi={file usi}

Getting spectrum data from Spectrum ID

https://external.gnps2.org/gnpsspectrum?SpectrumID={Spectrum ID}

JSON Peak List from USI 

https://fasst.gnps2.org/search?library=gnpslibrary&usi={file usi}
JSON Peak List from USI (Example): 
https://fasst.gnps2.org/search?library=gnpslibrary&usi=mzspec:GNPS:GNPS-LIBRARY:accession:CCMSLIB00000001547

ModiFinder

Some functions of the ModiFinder visualizer module are accessible via APIs. For details on the parameters you can pass to these functions, refer to the GitHub repository or the documentation.

Draw Molecule

https://modifinder.gnps2.org/api/visualizer/draw_molecule?{function argument1}={argument1}&{function argument2}={value2}...{function argumentn}={argumentn}.{type}
More details on the function arguments and the argument type are available on the documentation page. The type can be png or svg.

Exampes: * https://modifinder.gnps2.org/api/visualizer/draw_molecule?mol=CCO.svg * https://modifinder.gnps2.org/api/visualizer/draw_molecule?mol=CCMSLIB00010102097&size=400,400&highlightAtoms=0,1,5.png

Draw Modification

You can also draw the modification between two molecules 

https://modifinder.gnps2.org/api/visualizer/draw_modifications?{function argument1}={argument1}&{function argument2}={value2}...{function argumentn}={argumentn}.{type}

Example: * https://modifinder.gnps2.org/api/visualizer/draw_modifications?mol1=CCMSLIB00010101989&mol2=CCMSLIB00010102097.png

Draw Spectrum

https://modifinder.gnps2.org/api/visualizer/draw_spectrum?{function argument1}={argument1}&{function argument2}={value2}...{function argumentn}={argumentn}.{type}
Example: * https://modifinder.gnps2.org/api/visualizer/draw_spectrum?spectrum=CCMSLIB00010102097&bar_width=1.png

Draw Alignment

https://modifinder.gnps2.org/api/visualizer/draw_alignment?{function argument1}={argument1}&{function argument2}={value2}...{function argumentn}={argumentn}.{type}

Example: