ZINC15:Syntax: Difference between revisions

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This is a description of the ZINC 15 api.  
The general form of a ZINC 15 api request is
 
'''http[s]://host:port/reference-table/format:column1,column2,...columnN/query-specification'''
 
We take up each element in turn.
 
- We support both http and https protocols.  
- host name on request
- port number on request


The general form of a ZINC 15 api request is  
= reference-table =
  http://host:port/target/format:variable1,variable2/query_specification
There is one reference table per ZINC api request. Each row in the output corresponds to one row in the reference-table.  Reference tables are always plurals, indicating that the result is always a selection from among the rows in the reference-table. The supported reference-tables are:
 
{| class="wikitable"
|-
! table name !! Description !! Notes/Links
|-
|  substances || substance table || notes about substance table
|-
| ecfp4s || lala || lala
|-
| catalogitems || lala || asdf
|-
| catalogs || asdfasdf || sdfsdfdaf
|-
| protomers || qwer34 || seradsf
|-
| genes || sdfasfd || sadfasdf
|-
| targets || asdfasdf || asdfasdf sa
|-
| activities || sadfasfsd || asdfasfd
|-
| organisms ||asdf asdf || asdfasfd sadf
|}
 
Historical note: In ZINC 12, the reference-table was always substances, and thus the result of any query was always a set of molecules. A few reports such as vendor and target listings were available via the webpages, but were not supported by the API.  This is a substantial change that appeared first in ZINC 15.
 
= Format =
We support the following formats
 
{| class="wikitable"
|-
! format !! Description !! options/links
|-
|  json || substance table || notes about substance table
|-
| txt  || lala || lala
|-
| csv || lala || asdf
|-
| xls || asdfasdf || sdfsdfdaf
|-
| tsv || qwer34 || seradsf
|-
| xml || sdfasfd || sadfasdf
|}
 
 
= Columns =
The result contains the specified columns in the output.  If the column is in the reference-table, it is specified without a table specfification, otherwise, the column specification must be of the form table.item.
 
The following items are supported in each of the tables.
 
 
{| class="wikitable"
|-
! table name !! Description !! Notes/Links
|-
|  substances || substance table || notes about substance table
|-
| ecfp4s  || lala || lala
|-
| catalogitems || lala || asdf
|-
| catalogs || asdfasdf || sdfsdfdaf
|-
| protomers || qwer34 || seradsf
|-
| genes || sdfasfd || sadfasdf
|-
| targets || asdfasdf || asdfasdf sa
|-
| activities || sadfasfsd || asdfasfd
|-
| organisms ||asdf asdf || asdfasfd sadf
|}


= Targets =
There is one target per ZINC api request.  In ZINC 12, all api queries were implicitly substances, thus the result of any query was a set up molecules. A few reports such as vendor and target listings were available via the webpages, but were not supported by the API.  This is a substantial change in ZINC 15.


* substances
* ecfp4s
* catalogitems
* catalogs
* protomers
* genes
* targets
* activities
* organisms


= Query Variables =
Objects from among these may be specified as part of a query_specification.
Objects from among these may be specified as part of a query_specification.
* substance (sub_id, structure, inchikey, up_date, logp, tpsa, hbd, hba)
 
* structure (mwt, logp, tpsa, hba, hbd, num_atoms, num_heavy_atoms, rotatable_bonds, num_hetero_atoms, num_rings, inchi)
 
* protomer (prot_id, sub_id_fk, desolv_apol, desolv_pol, net_charge)
 
* catalog (cat_id, name, short_name, purchasable, free, version, updated, bb, np, drug)
{| class="wikitable"
* catalogitem (sub_id_fk, cat_id_fk, supplier_code, depleted)
|-
* ecfp4 (???)
! table name !! Description !! Notes/Links
* modeltype (???
|-
* gene  (short_name
| substances || sub_id, structure, inchikey, up_date, logp, tpsa, hbd, hba || notes about substance table
* annotation (swissprot, uniprot, target, gene, affinity )
|-
* activity (affinitynM, target, gene, organism)
| structure || mwt, logp, tpsa, hba, hbd, num_atoms, num_heavy_atoms, rotatable_bonds, num_hetero_atoms, num_rings, inchi || lala
* organism (name)
|-
| protomers || prot_id, sub_id_fk, desolv_apol, desolv_pol, net_charge || asdf
|-
| catalogs || cat_id, name, short_name, purchasable, free, version, updated, bb, np, drug || sdfsdfdaf
|-
| catalogitems || sub_id_fk, cat_id_fk, supplier_code, depleted || seradsf
|-
| genes || short_name || sadfasdf
|-
| targets || swissprot, uniprot, target, gene, affinity || asdfasdf sa
|-
| activities || affinitynM, target, gene, organism || asdfasfd
|-
| organisms ||asdf asdf || asdfasfd sadf
|}


= Query operators =  
= Query operators =  
* These may be used : =, > , < ,  >=, <=, !=, @> (contains), <@ (contained in)


* Also: eq, gt, lt, ge, le, ne, contains, containedin, between, like, is, not, startswith, endswith, similarto
 
{| class="wikitable"
|-
! operator !! Description !! synonyms
|-
| @> || lala || contains
|-
| <@ || lala || contained in
|-
| = || equals || eq
|-
| < || less than || lt
|-
| > || greater than || gt
|-
| <= || less than or equal || le
|-
| >= || greater than or equal || ge
|-
| between || sadfasfsd || asdfasfd
|-
| like, is, not , startswith, endswith, similar to ||asdf asdf || asdfasfd sadf
|}


= NP, Drug and BB =  
= NP, Drug and BB =  
* NP = 0=unknown, 1=biogenic, 2=metabolite, 3=endogenous human metabolite
 
* BB; f=not bb, t=bb
 
* Drug: 0 = unknown, 1=in annotated catalog, 2=bioactive,4=bioactive in vitro <= 1uM
{| class="wikitable"
* Drug: 5= bioactive in cells <= 1uM, 6=in man, 8 = world drug, 10=FDA approved drug
|-
! quality !! values !! Notes/Links
|-
| NP || 0=unknown, 1=biogenic, 2=metabolite, 3=endogenous human metabolite || lala
|-
| Drug || 0=unknown, 1=annotated catalog, 2=bioactive, 4=bioactive in vitro < 1uM, 5=bioactive in cells <1uM, 6=in man, 8=world drug, 10=fda approved || lala
|-
| BB  || f=not bb, t=bb || asdf
|}
 


= Similarity and Substructure
= Similarity and Substructure

Revision as of 20:00, 4 November 2014

The general form of a ZINC 15 api request is

http[s]://host:port/reference-table/format:column1,column2,...columnN/query-specification

We take up each element in turn.

- We support both http and https protocols. - host name on request - port number on request

reference-table

There is one reference table per ZINC api request. Each row in the output corresponds to one row in the reference-table. Reference tables are always plurals, indicating that the result is always a selection from among the rows in the reference-table. The supported reference-tables are:

table name Description Notes/Links
substances substance table notes about substance table
ecfp4s lala lala
catalogitems lala asdf
catalogs asdfasdf sdfsdfdaf
protomers qwer34 seradsf
genes sdfasfd sadfasdf
targets asdfasdf asdfasdf sa
activities sadfasfsd asdfasfd
organisms asdf asdf asdfasfd sadf

Historical note: In ZINC 12, the reference-table was always substances, and thus the result of any query was always a set of molecules. A few reports such as vendor and target listings were available via the webpages, but were not supported by the API. This is a substantial change that appeared first in ZINC 15.

Format

We support the following formats

format Description options/links
json substance table notes about substance table
txt lala lala
csv lala asdf
xls asdfasdf sdfsdfdaf
tsv qwer34 seradsf
xml sdfasfd sadfasdf


Columns

The result contains the specified columns in the output. If the column is in the reference-table, it is specified without a table specfification, otherwise, the column specification must be of the form table.item.

The following items are supported in each of the tables.


table name Description Notes/Links
substances substance table notes about substance table
ecfp4s lala lala
catalogitems lala asdf
catalogs asdfasdf sdfsdfdaf
protomers qwer34 seradsf
genes sdfasfd sadfasdf
targets asdfasdf asdfasdf sa
activities sadfasfsd asdfasfd
organisms asdf asdf asdfasfd sadf


Objects from among these may be specified as part of a query_specification.


table name Description Notes/Links
substances sub_id, structure, inchikey, up_date, logp, tpsa, hbd, hba notes about substance table
structure mwt, logp, tpsa, hba, hbd, num_atoms, num_heavy_atoms, rotatable_bonds, num_hetero_atoms, num_rings, inchi lala
protomers prot_id, sub_id_fk, desolv_apol, desolv_pol, net_charge asdf
catalogs cat_id, name, short_name, purchasable, free, version, updated, bb, np, drug sdfsdfdaf
catalogitems sub_id_fk, cat_id_fk, supplier_code, depleted seradsf
genes short_name sadfasdf
targets swissprot, uniprot, target, gene, affinity asdfasdf sa
activities affinitynM, target, gene, organism asdfasfd
organisms asdf asdf asdfasfd sadf

Query operators

operator Description synonyms
@> lala contains
<@ lala contained in
= equals eq
< less than lt
> greater than gt
<= less than or equal le
>= greater than or equal ge
between sadfasfsd asdfasfd
like, is, not , startswith, endswith, similar to asdf asdf asdfasfd sadf

NP, Drug and BB

quality values Notes/Links
NP 0=unknown, 1=biogenic, 2=metabolite, 3=endogenous human metabolite lala
Drug 0=unknown, 1=annotated catalog, 2=bioactive, 4=bioactive in vitro < 1uM, 5=bioactive in cells <1uM, 6=in man, 8=world drug, 10=fda approved lala
BB f=not bb, t=bb asdf


= Similarity and Substructure 

.../substance.structure similarto c1ccccc1CCCOC within .7 using tanimoto

/substance/txt:zinc_id/substance isa metabolite

/substances/txt:zinc_id?sort=substance.structure+near+c1ccccc1CCNC+using+dice


Closest purchasable metabolite 

select s.sub_id, s.smiles, tanimoto_sml(f.data,    bfp_from_binary_text('\x804300004000200080400000800000008220800040000120008002002011000010040081010000002840400009d040048000020200001a404100000002000040')), short_name from fingerprints.ecfp4_data as f join fingerprints.ecfp4_id on ecfp4_id=f.ecfp4_fk join substance as s on s.ecfp4_fk=ecfp4_id join catalog_item on sub_id_fk=s.sub_id join catalog on cat_id_fk=cat_id where f.ecfp4_fk < 1000000 and purchasable > 30 order by bfp_from_binary_text('\x804300004000200080400000800000008220800040000120008002002011000010040081010000002840400009d040048000020200001a404100000002000040') <%> f.data limit 5;
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