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