search

NCATS-Tangerine / translator-knowledge-beacon

NCATS Translator Knowledge Beacon Application Programming Interface plus Sample code
MIT License
7 stars 2 forks source link

KEGG beacon? #63

Open lhannest opened 6 years ago

lhannest commented 6 years ago

Has biothings explorer ingested enough of KEGG? If not, then should we create a KEGG beacon?

RichardBruskiewich commented 6 years ago

I don't really know. Who is asking for KEGG?

@cmungall is, I believe, thinking that Rhea will sufficient cover the domain.

mellybelly commented 6 years ago

Kegg has restrictive licensing. Be careful. Use reactome?

cmungall commented 6 years ago

For reactions yes. KEGG also has pathways

On 25 Oct 2018, at 10:17, Richard Bruskiewich wrote:

I don't really know. Who is asking for KEGG?

@cmungall is, I believe, thinking that Rhea will sufficient cover the domain.

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/NCATS-Tangerine/translator-knowledge-beacon/issues/63#issuecomment-433114468

RichardBruskiewich commented 6 years ago

Melissa suggests that Reactome would adequately suit our needs. Do we wrap Reactome as a beacon or is it adequately covered elsewhere?

srensi commented 6 years ago

Looking at the licensing terms for KEGG, it seems like our use case is covered. On the other hand they charge $5,000 for organizational subscription.

"Licensor grants [...] license to [...] provide a web-based service using KEGG FTP Data. [...] Your Product or Service must not allow Your users to obtain KEGG FTP Data, except in small quantities."

https://www.bioinformatics.jp/docs/subscription_organizational.pdf

RichardBruskiewich commented 6 years ago

Stefano, will the Reactome suffice? Or is KEGG essential? Reactome IP is apparently less onerous ... we could wrap their API (https://reactome.org/dev/content-service)... Oops, @mellybelly, KEGG has their tentacles in that:

Finally, KEGG gene and pathway annotations, used to construct the Reactome Functional Interaction (FI) Network, are provided under license to OICR by Pathway Solutions, Inc. The Reactome FI Network data set is intended for use only by the original recipient. The recipient may not distribute the Reactome Functional interaction data files to other users without a license from Pathway Solutions, Inc.

If KEGG is a critical data resource, NIH would have to negotiate something. That is not a bad thing, perhaps, since it fosters international collaboration and buy-in. Just don't know how far NIH will go on this project to support that spirit... how much engagement with the Japanese.