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sirius-ms / sirius

SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)
GNU Affero General Public License v3.0
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Adding NPA database? #169

Closed typewritermonkey closed 2 months ago

typewritermonkey commented 5 months ago

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 commented 5 months ago

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 commented 5 months ago

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

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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.

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marcus-ludwig commented 5 months ago

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.

Sclllllll commented 4 months ago

SIRIUS5 8 6-databse I want to import the SMILES of my own compounds into SIRIUS to create a database, but I can't click the creat button below. What is the correct format for importing data?

mfleisch commented 3 months ago

SIRIUS5 8 6-databse I want to import the SMILES of my own compounds into SIRIUS to create a database, but I can't click the creat button below. What is the correct format for importing data?

@marcus-ludwig suggestions referred to SIRIUS 6, where the custom database feature has been much improved. Please upgrade to SIRIUS 6.0.4 or later if possible.

mfleisch commented 2 months ago

Closed since issue seems to be stale and there is nothing to do from development side. Please join our new sirius-ms gitter channel for further discussion and questions. https://matrix.to/#/#sirius-ms:gitter.im