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Knowledge-Graph-Hub / kg-microbe

https://knowledge-graph-hub.github.io/kg-microbe/index.html
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ingest the EC hierarchy #114

Open realmarcin opened 7 months ago

realmarcin commented 7 months ago

A bare minimum would be to ingest this file: https://ftp.expasy.org/databases/enzyme/enzclass.txt

This has more useful info including a synonymous enzyme names, description, and reaction strings (but without chemical or reaction ids): https://ftp.expasy.org/databases/enzyme/enzyme.dat

There is also an RDF file: https://ftp.expasy.org/databases/enzyme/enzyme.rdf

realmarcin commented 7 months ago

@hrshdhgd take a look when you have a moment and let's discuss next time

hrshdhgd commented 7 months ago

I downloaded the pdf and processed it via oak, this is what I see:

http://purl.uniprot.org/enzyme/2.4.2.1#SIP002CE5576A208B63> ! adenosine + phosphate = adenine + alpha-D-ribose 1-phosphate.
<http://purl.uniprot.org/enzyme/2.4.2.1#SIP27AFE350A04FF7E3> ! 2'-deoxyadenosine + phosphate = 2-deoxy-alpha-D-ribose 1-phosphate + adenine.
<http://purl.uniprot.org/enzyme/2.4.2.1#SIP2FC1C04FB20803A8> ! a purine D-ribonucleoside + phosphate = a purine nucleobase + alpha-D-ribose 1-phosphate.
<http://purl.uniprot.org/enzyme/2.4.2.1#SIP3600FB5EE9B9F6FE> ! guanosine + phosphate = alpha-D-ribose 1-phosphate + guanine.
<http://purl.uniprot.org/enzyme/2.4.2.1#SIP7488AAF6E740541B> ! 2'-deoxyguanosine + phosphate = 2-deoxy-alpha-D-ribose 1-phosphate + guanine.
<http://purl.uniprot.org/enzyme/2.4.2.1#SIP9A2AF843478805E2> ! inosine + phosphate = alpha-D-ribose 1-phosphate + hypoxanthine.
<http://purl.uniprot.org/enzyme/2.4.2.1#SIPB3542FD8DD9D80EE> ! phosphate + xanthosine = alpha-D-ribose 1-phosphate + xanthine.
<http://purl.uniprot.org/enzyme/2.4.2.1#SIPBC18CBFB06AAFE9B> ! 2'-deoxyinosine + phosphate = 2-deoxy-alpha-D-ribose 1-phosphate + hypoxanthine.
<http://purl.uniprot.org/enzyme/2.4.2.1#SIPC7C20EEF56E99DA3> ! a purine 2'-deoxy-D-ribonucleoside + phosphate = 2-deoxy-alpha-D-ribose 1-phosphate + a purine nucleobase.
<http://purl.uniprot.org/enzyme/2.4.2.10#SIPD4087459D3CB30D0> ! diphosphate + orotidine 5'-phosphate = 5-phospho-alpha-D-ribose 1-diphosphate + orotate.
<http://purl.uniprot.org/enzyme/2.4.2.10> ! None
<http://purl.uniprot.org/enzyme/2.4.2.11> ! None
<http://purl.uniprot.org/enzyme/2.4.2.12#SIPB9BF7B63034270A0> ! beta-nicotinamide D-ribonucleotide + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + H(+) + nicotinamide.
<http://purl.uniprot.org/enzyme/2.4.2.12> ! None
<http://purl.uniprot.org/enzyme/2.4.2.13> ! None
<http://purl.uniprot.org/enzyme/2.4.2.14#SIP152ACBE3C4614AD0> ! 5-phospho-beta-D-ribosylamine + diphosphate + L-glutamate = 5-phospho-alpha-D-ribose 1-diphosphate + H2O + L-glutamine.
<http://purl.uniprot.org/enzyme/2.4.2.14> ! None
<http://purl.uniprot.org/enzyme/2.4.2.15#SIP3600FB5EE9B9F6FE> ! guanosine + phosphate = alpha-D-ribose 1-phosphate + guanine.
<http://purl.uniprot.org/enzyme/2.4.2.15> ! None
<http://purl.uniprot.org/enzyme/2.4.2.16#SIP6B188645EC6747BF> ! phosphate + urate D-ribonucleoside = alpha-D-ribose 1-phosphate + urate.
<http://purl.uniprot.org/enzyme/2.4.2.16> ! None
<http://purl.uniprot.org/enzyme/2.4.2.17#SIPF1413620EE85D209> ! 1-(5-phospho-beta-D-ribosyl)-ATP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + ATP.
<http://purl.uniprot.org/enzyme/2.4.2.17> ! None
<http://purl.uniprot.org/enzyme/2.4.2.18#SIP7165B4B1E7C35ED3> ! diphosphate + N-(5-phospho-beta-D-ribosyl)anthranilate = 5-phospho-alpha-D-ribose 1-diphosphate + anthranilate.
<http://purl.uniprot.org/enzyme/2.4.2.18> ! None
<http://purl.uniprot.org/enzyme/2.4.2.19#SIPB4210697AF1BDA40> ! CO2 + diphosphate + nicotinate beta-D-ribonucleotide = 5-phospho-alpha-D-ribose 1-diphosphate + 2 H(+) + quinolinate.
<http://purl.uniprot.org/enzyme/2.4.2.19> ! None
<http://purl.uniprot.org/enzyme/2.4.2.1> ! None
<http://purl.uniprot.org/enzyme/2.4.2.2#SIP116D5629599CA3B5> ! cytidine + phosphate = alpha-D-ribose 1-phosphate + cytosine.
<http://purl.uniprot.org/enzyme/2.4.2.2#SIP62F073966B56F77A> ! 2'-deoxyuridine + phosphate = 2-deoxy-alpha-D-ribose 1-phosphate + uracil.
<http://purl.uniprot.org/enzyme/2.4.2.2#SIPB6DAA0B77834E339> ! phosphate + uridine = alpha-D-ribose 1-phosphate + uracil.
<http://purl.uniprot.org/enzyme/2.4.2.2#SIPE6C02E2AFB1054B6> ! phosphate + thymidine = 2-deoxy-alpha-D-ribose 1-phosphate + thymine.
<http://purl.uniprot.org/enzyme/2.4.2.20#SIPD4EE3301A6366327> ! 5,6-dihydrouridine 5'-monophosphate + diphosphate = 5,6-dihydrouracil + 5-phospho-alpha-D-ribose 1-diphosphate.

and

<http://purl.uniprot.org/pubmed/16953575> ! None
<http://purl.uniprot.org/pubmed/16956885> ! None
<http://purl.uniprot.org/pubmed/16957230> ! None
<http://purl.uniprot.org/pubmed/1695830> ! None
<http://purl.uniprot.org/pubmed/16960392> ! None
<http://purl.uniprot.org/pubmed/16962103> ! None
<http://purl.uniprot.org/pubmed/16963083> ! None
<http://purl.uniprot.org/pubmed/16963086> ! None
<http://purl.uniprot.org/pubmed/16963440> ! None
<http://purl.uniprot.org/pubmed/16963551> ! None
<http://purl.uniprot.org/pubmed/16964241> ! None
<http://purl.uniprot.org/pubmed/16964976> ! None
<http://purl.uniprot.org/pubmed/1696553> ! None
<http://purl.uniprot.org/pubmed/16967980> ! None
<http://purl.uniprot.org/pubmed/16968710> ! None
<http://purl.uniprot.org/pubmed/16970904> ! None
<http://purl.uniprot.org/pubmed/16971463> ! None
<http://purl.uniprot.org/pubmed/1697166> ! None
<http://purl.uniprot.org/pubmed/16980461> ! None
<http://purl.uniprot.org/pubmed/16980563> ! None
<http://purl.uniprot.org/pubmed/16981709> ! None
<http://purl.uniprot.org/pubmed/16982622> ! None
<http://purl.uniprot.org/pubmed/16983083> ! None
<http://purl.uniprot.org/pubmed/16989822> ! None
<http://purl.uniprot.org/pubmed/16990135> ! None
<http://purl.uniprot.org/pubmed/16990279> ! None
<http://purl.uniprot.org/pubmed/16995898> ! None

Do any of these seem likeEC terms?

hrshdhgd commented 7 months ago

I tried this: <http://purl.uniprot.org/enzyme/2.4.2.2#SIP116D5629599CA3B5> ! cytidine + phosphate = alpha-D-ribose 1-phosphate + cytosine.

assumed this was EC:2.4.2.2. Looked this up and give me https://www.genome.jp/dbget-bin/www_bget?ec:2.4.2.2 which may be a match? I don't know.