Adding NPA database?

[typewritermonkey]

Hi, not really an issue but a request, would you be able to add the Natural Products Atlas database to the searchable database list in the next update? Its useful for people doing microbial metabolomics.

[marcus-ludwig]

Hi, thanks for the suggestion.
Yes, we have not added some of the smaller, specific databases such as NPAtlas. I believe we can never provide all databases users are interested in.
But with the latest version, SIRIUS 6, we added LOTUS which may give you similar information (I think it uses NPAtlas as one of many sources): https://lotus.naturalproducts.net/

Please feel free to re-open the issue and comment if you think NPAtlas provides specific information that you can't obtain using LOTUS.

[typewritermonkey]

Ok yeah I can understand not wanting to add every smaller db it's just if you know you are looking for microbial compounds specifically it's helpful to have a microbes only database. Is there a way I can convert it myself and add it as a custom library to Sirius? I can download it as an excel or tsv file with Smiles and Inchis Get Outlook for iOS<https://aka.ms/o0ukef>

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________________________________ From: marcus-ludwig ***@***.***> Sent: Wednesday, June 19, 2024 8:09:35 PM To: sirius-ms/sirius ***@***.***> Cc: typewritermonkey ***@***.***>; Author ***@***.***> Subject: Re: [sirius-ms/sirius] Adding NPA database? (Issue #169) Hi, thanks for the suggestion. Yes, we have not added some of the smaller, specific databases such as NPAtlas. I believe we can never provide all databases users are interested in. But with the latest version, SIRIUS 6, we added LOTUS which may give you similar information (I think it uses NPAtlas as one of many sources): https://lotus.naturalproducts.net/ Please feel free to re-open the issue and comment if you think NPAtlas provides specific information that you can't obtain using LOTUS. — Reply to this email directly, view it on GitHub<#169 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A5WH2GH4IOX73ACVYNKY433ZIE4D7AVCNFSM6AAAAABJPFZJFWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNZYGAZTQNBZGY>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[marcus-ludwig]

Yes, you can import custom databases: https://v6.docs.sirius-ms.io/gui/#import-of-custom-structure-and-spectra-databases.

Currently, a limitation of custom databases is that you cannot automatically link to the database website. You still need to search it manually.

To import the data either use a .tsv file of smiles (and optionally id and name in the 2nd and 3rd column, no header) or use a .sdf.