Return more reaction metadata to populate reaction data page

[jonrkarr]

Return more metadata from this endpoint: https://api.datanator.info/reactions/kinlaw_by_name/?substrates=Glucose&products=Glucose&_from=0&size=1000&bound=tight

Metadata we could potentially integrate

• Name
• Alternative name
• Systematic name
• Cofactors
• Pathways
• Comments (Appears to typically be redundant with cofactors)

Potential places to get metadata for each EC number. We only need to use one source. In order of decreasing amount of metadata:

• KEGG: also has pathway information
• https://www.enzyme-database.org/downloads.php
• https://enzyme.expasy.org/, ftp://ftp.expasy.org/databases/enzyme (but doesn't have "systematic name")

[lzy7071]

reaction documents now contain a field called ec_meta If an EC number has cofactor information, there will be a field called cofactor contained in the ec_meta object.

[lzy7071]

reaction document now may contain a field named kegg_meta (depending on if an enzyme subunit has corresponding kegg info or not).

[yosefdroth]

Thanks! Does it currently return pathway information? If not, can we include that?

[lzy7071]

Thanks! Does it currently return pathway information? If not, can we include that?

it's in kegg_meta

[yosefdroth]

Hi! Do you have any examples of reactions with cofactors? I was not able to find any

[lzy7071]

Hi! Do you have any examples of reactions with cofactors? I was not able to find any

Reaction with kinlaw_id 44

[yosefdroth]

The way frontend is queried is by searching based on the substrates and products (as opposed by by kinlaw_id). I searched with the substrates and products from that reaction id, but nothing came up. Any idea why?

Here is the link: https://api.datanator.info/reactions/kinlaw_by_name/?substrates=S-Adenosyl-L-methionine,8-Amino-7-oxononanoate&products=7,8-Diaminononanoate,S-Adenosyl-4-methylthio-2-oxobutanoatehttps://api.datanator.info/reactions/kinlaw_by_name/?substrates=8-Amino-7-oxononanoate,S-Adenosylmethioninamine&products=S-Adenosyl-3-methylthiopropanal,7,8-Diaminononanoate&_from=0&size=10&bound=tight

[lzy7071]

The way frontend is queried is by searching based on the substrates and products (as opposed by by kinlaw_id). I searched with the substrates and products from that reaction id, but nothing came up. Any idea why?

Here is the link: https://api.datanator.info/reactions/kinlaw_by_name/?substrates=S-Adenosyl-L-methionine,8-Amino-7-oxononanoate&products=7,8-Diaminononanoate,S-Adenosyl-4-methylthio-2-oxobutanoatehttps://api.datanator.info/reactions/kinlaw_by_name/?substrates=8-Amino-7-oxononanoate,S-Adenosylmethioninamine&products=S-Adenosyl-3-methylthiopropanal,7,8-Diaminononanoate&_from=0&size=10&bound=tight

Yeah, you were searching for the names contained within ec_meta, which was parsed from ExPASy. The endpoint /kinlaw_by_name queries names given by sabio-rk

[yosefdroth]

Do you know of any examples of cofactors that can be searched with substrate and product names? I would like to add cofactors to the webpage, but I cant find an example I can test it on.

It's in the last reply. Click the endpoint hyperlink.

[yosefdroth]

thanks! this works