[Cod-bugs] Searching in COD

[Andrius Merkys]

Dear Holger,

Let me know whether this works for you.

Best wishes,
Andrius

On 2021-01-18 19:11, Friedrich, Holger wrote:
> Dear Andrius Merkys,
> 
> thank you very much for your quick and assisting answer.
> I will talk to a colleague to test your suggestion.
> I am looking forward to the results.
> 
> Best regards
> 
> Holger
> 
>  
> 
> -----Ursprüngliche Nachricht-----
> Von: Andrius Merkys <andrius.merkys at gmail.com> 
> Gesendet: Montag, 18. Januar 2021 13:24
> An: Friedrich, Holger <holger.friedrich at isc.fraunhofer.de>
> Cc: cod-bugs at ibt.lt
> Betreff: Re: [Cod-bugs] Searching in COD
> 
> Dear Holger Friedrich,
> 
> Thank you for your interest in the COD. Please find my in-line comments below.
> 
> On 2021-01-17 19:47, Friedrich, Holger wrote:
>> I had hoped that by using 1 to 8 elements with the oxygen and the 
>> given cations would give me the result if
>>
>> I specify the number of distinct elements min and max at 2 and 6 
>> respectively. But that did not work out.
> 
> The COD search requires all the elements entered in search boxes to be present in the returned structures. Limiting the number of distinct elements to less than 6 makes the query impossible, as no structure can have all the 8 elements and at the same time have less than 6 elements.
> 
>> If you could give me a suggestion how to proceed and search I would be 
>> very grateful.
> 
> For now I would suggest running a set of queries and collating their results automatically. The COD implements OPTIMADE-compatible [1] search interface, which allows composing more elaborate queries ("OPTIMADE filters").
> 
> As far as I understand, your structures of interest must contain oxygen and 2-5 of elements from this list: Al, Ca, K, Si, Zn. Thus the COD OPTIMADE interface has to be queried with such filters:
> 
> elements HAS "O" AND elements HAS ALL "Al", "Ca" AND elements LENGTH 3 elements HAS "O" AND elements HAS ALL "Al", "K"  AND elements LENGTH 3 ...
> elements HAS "O" AND elements HAS ALL "Al", "Ca", "K", "Si", "Zn" AND elements LENGTH 6
> 
> Here, 'elements HAS "O"' requires structures to contain oxygen, 'elements HAS ALL "Al", "Ca"' requires presence of all enumerated elements and 'elements LENGTH 3' requires the number of elements be equal to 3.
> 
> To query the COD OPTIMADE interface one has to submit queries to https://www.crystallography.net/cod/optimade/v1/structures with filter string URL-encoded and appended with '?filter=' to the URL, for example:
> 
> https://www.crystallography.net/cod/optimade/v1/structures?filter=elements%20HAS%20%22O%22%20AND%20elements%20HAS%20ALL%20%22Al%22,%20%22Ca%22%20AND%20elements%20LENGTH%203
> 
> The output is in JSON:API-compatible [2] JSON output.
> 
>> If this cannot be done, I would like to provide it as a suggestion.
> 
> For now, however, there is no other way to query the COD for these structures. OPTIMADE specification describes 'HAS ONLY' query operator which would considerably reduce the work here, but it is not yet implemented in the COD OPTIMADE interface.
> 
> [1] https://zenodo.org/record/4195051
> [2] https://jsonapi.org
> 
> Hope this helps,
> Andrius Merkys
> 

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