lzy7071
commented
4 years ago To start advertising Datantor, I submitted it to a few registries of biology resources. One of these is the Identifiers.org database of namespaces. They accepted our metabolite and gene namespaces. To accept our reaction namespace, we need to disallow spaces.
Two alternative to
{comma-separated-list-of-substrates-names}-->{comma-separated-list-of-product-names}:
{comma-separated-list-of-substrate-inchikeys}-->{comma-separated-list-of-product-inchikeys}- Assign a unique id to each reaction
This is not critical. Although our reaction namespace wasn't accepted, Datanator will be findable through Identifiers.org.
I think the first bullet point is a good idea and can be easily implemented.
-
The documents in
sabio_reaction_entriesindex / collection already have inchikey information for both products and substrates inproductsandsubstratesfields, correspondingly. So generating the URL for reaction-specific page will just be a matter of changing field names. -
For the reaction-specific page, one just needs to change the endpoint used from
/reactions/kinlaw_by_name/to/reactions/kinlaw_by_rxn/.
The second bullet point can help avoid a long URL.
-
For each unique reaction, in terms of the same products and substrates,
rxn_idinsabio_reaction_entriesindex / collection is the unique id attached. -
For the reaction-specific page, one just needs to change the endpoint used from
/reactions/kinlaw_by_name/to/reactions/kinlaw_entry/(this endpoint needs some editing as it doesn't contain kegg_meta at the moment). -
One fallout is that all future reactions will have to be assigned a
rxn_idmanually.
jonrkarr
To start advertising Datantor, I submitted it to a few registries of biology resources. One of these is the Identifiers.org database of namespaces. They accepted our metabolite and gene namespaces. To accept our reaction namespace, we need to disallow spaces.
Two alternative to
{comma-separated-list-of-substrates-names}-->{comma-separated-list-of-product-names}:{comma-separated-list-of-substrate-inchikeys}-->{comma-separated-list-of-product-inchikeys}This is not critical. Although our reaction namespace wasn't accepted, Datanator will be findable through Identifiers.org.