From rodrigo.garcia at tervalis.com  Tue Oct 15 14:01:36 2024
From: rodrigo.garcia at tervalis.com (Rodrigo Garcia)
Date: Tue, 15 Oct 2024 13:01:36 +0200
Subject: [Cod-bugs] Posible error.
Message-ID: <CAE-Ztk0W+TSsqviW6QS0jXOfx3zhXBWx+LBS-au1yPvR_ry6rQ@mail.gmail.com>

Excuse my ignorance, but is the common name for this phase correct?:

https://www.crystallography.net/cod/7202572.html


I thought apatite corresponds to several calcium phosphates, not to the one
covered by entry 7202572.

Best regards,

Rodrigo Garc?a Cantera
Spain

-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.crystallography.net/pipermail/cod-bugs/attachments/20241015/c692fe20/attachment.htm>

From grazulis at ibt.lt  Tue Oct 15 14:15:53 2024
From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=C5=BEulis?=)
Date: Tue, 15 Oct 2024 14:15:53 +0300
Subject: [Cod-bugs] Posible error.
In-Reply-To: <CAE-Ztk0W+TSsqviW6QS0jXOfx3zhXBWx+LBS-au1yPvR_ry6rQ@mail.gmail.com>
References: <CAE-Ztk0W+TSsqviW6QS0jXOfx3zhXBWx+LBS-au1yPvR_ry6rQ@mail.gmail.com>
Message-ID: <d368b9a6-8c4b-4541-8ba6-dc104c21bc0a@ibt.lt>

Dear Rodrigo,

On 2024-10-15 14:01, Rodrigo Garcia wrote:
> Excuse my ignorance, but is the common name for this phase correct?:
>
>     https://www.crystallography.net/cod/7202572.html
>
>
> I thought apatite corresponds to several calcium phosphates, not to 
> the one covered by entry 7202572.
>
I also though that 'apatite' refers to phosphates, not silicates.

The paper, however, claims in the title: "Oxide ion conduction in Ba, Ca 
and Sr doped apatite-type lanthanum silicates", i.e. these are silicates 
that apparently have an apatite-like structure (although I am also not 
an expert in the field). Also, in the source CIFs that are provided as 
supplementary materials and which were the source of the COD data, 
another structure from this paper is called "_chemical_name_common? 'Ba 
doped apatite'".

Apparently the authors think that it is appropriate to call their 
investigated materials 'apatite'.

In this case, COD leaves the authors' opinion in the entry. Also, we do 
not regularise '_chemical_name_common' and will probably never do that, 
since this is, eh, a common name which can be different in different 
communities.

In the searches it is better to rely on formula (especially the 
calculated one), systematic names (these might be regularised in the 
future) and crystallographic parameters.

I hope that clarifies the situation and serves you data search needs...

Regards,
Saulius

-- 
Dr. Saulius Gra?ulis
Vilnius University Institute of Biotechnology, Saul?tekio al. 7
LT-10257 Vilnius, Lietuva (Lithuania)
mobile: (+370-684)-49802, (+370-614)-36366

-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.crystallography.net/pipermail/cod-bugs/attachments/20241015/0f6452c9/attachment.htm>

From rodrigo.garcia at tervalis.com  Tue Oct 15 14:25:07 2024
From: rodrigo.garcia at tervalis.com (Rodrigo Garcia)
Date: Tue, 15 Oct 2024 13:25:07 +0200
Subject: [Cod-bugs] Posible error.
In-Reply-To: <d368b9a6-8c4b-4541-8ba6-dc104c21bc0a@ibt.lt>
References: <CAE-Ztk0W+TSsqviW6QS0jXOfx3zhXBWx+LBS-au1yPvR_ry6rQ@mail.gmail.com>
 <d368b9a6-8c4b-4541-8ba6-dc104c21bc0a@ibt.lt>
Message-ID: <CAE-Ztk1BzrY7SUT=0FXx1JjL=WPCPft=iB0bVXkAq0XhBD_xPA@mail.gmail.com>

Dear Saulius,

Thank you very much for your quick and complete answer.
And thanks a lot for maintaining such a helpful public service as COD.

Best regards,

Rodrigo

El mar, 15 oct 2024 a las 13:15, Saulius Gra?ulis (<grazulis at ibt.lt>)
escribi?:

> Dear Rodrigo,
>
> On 2024-10-15 14:01, Rodrigo Garcia wrote:
>
> Excuse my ignorance, but is the common name for this phase correct?:
>
> https://www.crystallography.net/cod/7202572.html
>
>
> I thought apatite corresponds to several calcium phosphates, not to the
> one covered by entry 7202572.
>
> I also though that 'apatite' refers to phosphates, not silicates.
>
> The paper, however, claims in the title: "Oxide ion conduction in Ba, Ca
> and Sr doped apatite-type lanthanum silicates", i.e. these are silicates
> that apparently have an apatite-like structure (although I am also not an
> expert in the field). Also, in the source CIFs that are provided as
> supplementary materials and which were the source of the COD data, another
> structure from this paper is called "_chemical_name_common  'Ba doped
> apatite'".
>
> Apparently the authors think that it is appropriate to call their
> investigated materials 'apatite'.
>
> In this case, COD leaves the authors' opinion in the entry. Also, we do
> not regularise '_chemical_name_common' and will probably never do that,
> since this is, eh, a common name which can be different in different
> communities.
>
> In the searches it is better to rely on formula (especially the calculated
> one), systematic names (these might be regularised in the future) and
> crystallographic parameters.
>
> I hope that clarifies the situation and serves you data search needs...
>
> Regards,
> Saulius
>
> --
> Dr. Saulius Gra?ulis
> Vilnius University Institute of Biotechnology, Saul?tekio al. 7
> LT-10257 Vilnius, Lietuva (Lithuania)
> mobile: (+370-684)-49802, (+370-614)-36366
>
>
> --
> This message has been scanned for viruses and
> dangerous content by *MailScanner* <http://www.mailscanner.info/>, and is
> believed to be clean.
>

-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.crystallography.net/pipermail/cod-bugs/attachments/20241015/0670225f/attachment.htm>

From pdomin at chem.uw.edu.pl  Thu Oct 17 16:04:48 2024
From: pdomin at chem.uw.edu.pl (Paulina Dominiak)
Date: Thu, 17 Oct 2024 15:04:48 +0200
Subject: [Cod-bugs] crystal structure deposition
Message-ID: <b7acaaa4-80bd-4e8c-a904-bfb3b5e06978@chem.uw.edu.pl>

Dear COD team,

I've just deposited two structures to the COD (1572876-1572877). I've 
discovered, however, that there is nowhere possible to add information 
about the research project from which these structures resulted from. My 
funding agency is requiring this kind of information to be associated 
with the data. How I can do this?

With regards,

Paulina


-- 
Prof. dr hab. Paulina M. Dominiak
Group Leader
Electron Density Modelling Group
Laboratory for Structural and Biochemical Research (LBSBio)
Biological and Chemical Research Centre
Department of Chemistry
University of Warsaw
ul. Zwirki i Wigury 101
02-089 Warszawa, Poland
Room: 3.125
E-mail: pdomin at chem.uw.edu.pl
Phone: (48) 22 55 26 714
WWW: http://4xeden.uw.edu.pl


-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.



From saulius.grazulis at bti.vu.lt  Thu Oct 17 21:13:18 2024
From: saulius.grazulis at bti.vu.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=)
Date: Thu, 17 Oct 2024 21:13:18 +0300
Subject: [Cod-bugs] crystal structure deposition
In-Reply-To: <b7acaaa4-80bd-4e8c-a904-bfb3b5e06978@chem.uw.edu.pl>
References: <b7acaaa4-80bd-4e8c-a904-bfb3b5e06978@chem.uw.edu.pl>
Message-ID: <38b9528f-6368-0740-8f47-cf7109337293@bti.vu.lt>

On 2024-10-17 16:04, Paulina Dominiak wrote:
> I've just deposited two structures to the COD (1572876-1572877). I've 
> discovered, however, that there is nowhere possible to add information 
> about the research project from which these structures resulted from. 
> My funding agency is requiring this kind of information to be 
> associated with the data. How I can do this?

We can create a dedicated CIF data item for that purpose, if such item 
does not yet exist.

We'll have a look at the CIF dictionaries for such data item and I'll 
come back to you with the exact instructions.

Regards,
Saulius

-- 
Dr. Saulius Gra?ulis
Vilnius University Institute of Biotechnology, Saul?tekio al. 7
LT-10257 Vilnius, Lietuva (Lithuania)
fax: (+370-5)-2234367 / phone (office): (+370-5)-2234353
mobile: (+370-684)-49802, (+370-614)-36366


-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.



From pdomin at chem.uw.edu.pl  Fri Oct 18 07:33:20 2024
From: pdomin at chem.uw.edu.pl (Paulina Dominiak)
Date: Fri, 18 Oct 2024 06:33:20 +0200
Subject: [Cod-bugs] crystal structure deposition
In-Reply-To: <38b9528f-6368-0740-8f47-cf7109337293@bti.vu.lt>
References: <b7acaaa4-80bd-4e8c-a904-bfb3b5e06978@chem.uw.edu.pl>
 <38b9528f-6368-0740-8f47-cf7109337293@bti.vu.lt>
Message-ID: <62b9b5ef-8633-405a-8f55-1151140290d0@chem.uw.edu.pl>

Hello Saulius,
Thank you for the replay!
I am happy that something can be done. I would be very grateful for the 
information how much time you need to investigate this issue. Is it 
about couple of days or longer?
Best,
Paulina

W dniu 17.10.2024 o?20:13, Saulius Gra?ulis pisze:
> On 2024-10-17 16:04, Paulina Dominiak wrote:
>> I've just deposited two structures to the COD (1572876-1572877). I've 
>> discovered, however, that there is nowhere possible to add 
>> information about the research project from which these structures 
>> resulted from. My funding agency is requiring this kind of 
>> information to be associated with the data. How I can do this?
>
> We can create a dedicated CIF data item for that purpose, if such item 
> does not yet exist.
>
> We'll have a look at the CIF dictionaries for such data item and I'll 
> come back to you with the exact instructions.
>
> Regards,
> Saulius
>
-- 
Prof. dr hab. Paulina M. Dominiak
Group Leader
Electron Density Modelling Group
Laboratory for Structural and Biochemical Research (LBSBio)
Biological and Chemical Research Centre
Department of Chemistry
University of Warsaw
ul. Zwirki i Wigury 101
02-089 Warszawa, Poland
Room: 3.125
E-mail: pdomin at chem.uw.edu.pl
Phone: (48) 22 55 26 714
WWW: http://4xeden.uw.edu.pl


-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.



From grazulis at ibt.lt  Fri Oct 18 09:09:15 2024
From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=C5=BEulis?=)
Date: Fri, 18 Oct 2024 09:09:15 +0300
Subject: [Cod-bugs] crystal structure deposition
In-Reply-To: <62b9b5ef-8633-405a-8f55-1151140290d0@chem.uw.edu.pl>
References: <b7acaaa4-80bd-4e8c-a904-bfb3b5e06978@chem.uw.edu.pl>
 <38b9528f-6368-0740-8f47-cf7109337293@bti.vu.lt>
 <62b9b5ef-8633-405a-8f55-1151140290d0@chem.uw.edu.pl>
Message-ID: <1703cfab-6aad-4135-9c8b-90946c1948d8@ibt.lt>

On 2024-10-18 07:33, Paulina Dominiak wrote:
> Hello Saulius,
> Thank you for the replay!
> I am happy that something can be done. I would be very grateful for 
> the information how much time you need to investigate this issue. Is 
> it about couple of days or longer?
> Best,
> Paulina
>
> W dniu 17.10.2024 o?20:13, Saulius Gra?ulis pisze:
>> On 2024-10-17 16:04, Paulina Dominiak wrote:
>>> I've just deposited two structures to the COD (1572876-1572877). 
>>> I've discovered, however, that there is nowhere possible to add 
>>> information about the research project from which these structures 
>>> resulted from. My funding agency is requiring this kind of 
>>> information to be associated with the data. How I can do this?
>>
>> We can create a dedicated CIF data item for that purpose, if such 
>> item does not yet exist.
>>
>> We'll have a look at the CIF dictionaries for such data item and I'll 
>> come back to you with the exact instructions.
>>
>> Regards,
>> Saulius
>>

-- 
Dr. Saulius Gra?ulis
Vilnius University Institute of Biotechnology, Saul?tekio al. 7
LT-10257 Vilnius, Lietuva (Lithuania)
mobile: (+370-684)-49802, (+370-614)-36366


-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.



From grazulis at ibt.lt  Fri Oct 18 09:15:07 2024
From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=C5=BEulis?=)
Date: Fri, 18 Oct 2024 09:15:07 +0300
Subject: [Cod-bugs] crystal structure deposition
In-Reply-To: <62b9b5ef-8633-405a-8f55-1151140290d0@chem.uw.edu.pl>
References: <b7acaaa4-80bd-4e8c-a904-bfb3b5e06978@chem.uw.edu.pl>
 <38b9528f-6368-0740-8f47-cf7109337293@bti.vu.lt>
 <62b9b5ef-8633-405a-8f55-1151140290d0@chem.uw.edu.pl>
Message-ID: <8d01ec07-c90d-4148-9a6c-ad97c95c9c4d@ibt.lt>

Hi, Paulina,

actually, Antanas already looked in the issue yesterday, and he reported 
that there are already standard data items in the COF CORE dictionary, 
albeit only in the new DDLm dictionary:

> ??? loop_
> ??? _audit_support.id
> ??? _audit_support.funding_organization
> ??? _audit_support.funding_organization_doi
> ??? _audit_support.award_type
> ??? _audit_support.award_number
> ??? _audit_support.award_recipient
>
> ??? 1 'Engineering and Physical Sciences Research Council'
> ??? 'https://doi.org/10.13039/501100000266'
> ??? studentship 'EP-M506515-1' 'E. T. Broadhurst'

Sine the matter, as I understand, is urgent, I suggest using these data 
items, which I am 99% sure are the right way to convey the funding 
information.

I suggest that you insert this information into all entries that you 
have deposited and that need the acknowledgement. You can of course use 
only part of the data names (e.g. if the _....funding_organization_doi 
is not known you can skip it or use '?' as a value, and if it is not 
available doe you organisation you can use a lone dot '.' as a value 
(both values should be used without the quotes)).

You can either edit your deposition yourself using the Web interface, or 
send us (me) the info and the COD IDs that need to be updated, and we 
insert the information for you.

We can also make this information prominent on the HTML "card" 
representation of your COD entry, but this requires some coding so will 
take form several weeks to a couple of months. Is this needed/urgent for 
you?

Sincerely yours,
Saulius

On 2024-10-18 07:33, Paulina Dominiak wrote:
> Hello Saulius,
> Thank you for the replay!
> I am happy that something can be done. I would be very grateful for 
> the information how much time you need to investigate this issue. Is 
> it about couple of days or longer?
> Best,
> Paulina
>
> W dniu 17.10.2024 o?20:13, Saulius Gra?ulis pisze:
>> On 2024-10-17 16:04, Paulina Dominiak wrote:
>>> I've just deposited two structures to the COD (1572876-1572877). 
>>> I've discovered, however, that there is nowhere possible to add 
>>> information about the research project from which these structures 
>>> resulted from. My funding agency is requiring this kind of 
>>> information to be associated with the data. How I can do this?
>>
>> We can create a dedicated CIF data item for that purpose, if such 
>> item does not yet exist.
>>
>> We'll have a look at the CIF dictionaries for such data item and I'll 
>> come back to you with the exact instructions.
>>
>> Regards,
>> Saulius
>>

-- 
Dr. Saulius Gra?ulis
Vilnius University Institute of Biotechnology, Saul?tekio al. 7
LT-10257 Vilnius, Lietuva (Lithuania)
mobile: (+370-684)-49802, (+370-614)-36366


-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.



From saulius.grazulis at bti.vu.lt  Fri Oct 18 10:51:09 2024
From: saulius.grazulis at bti.vu.lt (=?UTF-8?Q?Saulius_Gra=C5=BEulis?=)
Date: Fri, 18 Oct 2024 10:51:09 +0300
Subject: [Cod-bugs] crystal structure deposition
In-Reply-To: <41873363-8c04-4b85-87bb-7afae7715079@chem.uw.edu.pl>
References: <b7acaaa4-80bd-4e8c-a904-bfb3b5e06978@chem.uw.edu.pl>
 <38b9528f-6368-0740-8f47-cf7109337293@bti.vu.lt>
 <62b9b5ef-8633-405a-8f55-1151140290d0@chem.uw.edu.pl>
 <1703cfab-6aad-4135-9c8b-90946c1948d8@ibt.lt>
 <d0e20e21-07d0-4c17-9312-5f768d44ff5b@bti.vu.lt>
 <41873363-8c04-4b85-87bb-7afae7715079@chem.uw.edu.pl>
Message-ID: <3f51b94e-f84c-4fae-9b3f-f8f80ac20c82@bti.vu.lt>

On 2024-10-18 10:46, Paulina Dominiak wrote:
> Thank yo? for quick response.? Yes, you understood me very well, it is 
> urgent ? . I will contact the agency if extra information in the .cif 
> file only would be enough for time being.
Great, we'll assist you in high priority with this data deposition 
update; we'll
> But this will be in general very good solution for Polish 
> crystallographers to have the funding information exposed on the web 
> page of a given structure. We have now policy to deposit the data 
> under CC0 or CC BY license, which is not fulfilled by CCDC (along with 
> unique identifier, funding info, and scientific article if existing). 
> I will have soon many more such structures to deposit. 
This sounds like a good policy to promote Open science :)
> Of course I could deposit my cif to any generic data base (including 
> the one our university is providing), but then it is waste of the 
> information - no one will search there for crystal structures.....

Deposition to the COD does not exclude deposition to other databases; in 
fact we could even forward the data to your University on your behalf if 
the University would so desire.

But of course COD is a central, long lasting resource (20+ years :) 
where structures will for sure be found now and in the future :)

Sincerely yours,
Saulius

-- 
Dr. Saulius Gra?ulis
Vilnius University Institute of Biotechnology, Saul?tekio al. 7
LT-10257 Vilnius, Lietuva (Lithuania)
mobile: (+370-684)-49802, (+370-614)-36366



From pdomin at chem.uw.edu.pl  Fri Oct 18 15:31:25 2024
From: pdomin at chem.uw.edu.pl (Paulina Dominiak)
Date: Fri, 18 Oct 2024 14:31:25 +0200
Subject: [Cod-bugs] crystal structure deposition
In-Reply-To: <3f51b94e-f84c-4fae-9b3f-f8f80ac20c82@bti.vu.lt>
References: <b7acaaa4-80bd-4e8c-a904-bfb3b5e06978@chem.uw.edu.pl>
 <38b9528f-6368-0740-8f47-cf7109337293@bti.vu.lt>
 <62b9b5ef-8633-405a-8f55-1151140290d0@chem.uw.edu.pl>
 <1703cfab-6aad-4135-9c8b-90946c1948d8@ibt.lt>
 <d0e20e21-07d0-4c17-9312-5f768d44ff5b@bti.vu.lt>
 <41873363-8c04-4b85-87bb-7afae7715079@chem.uw.edu.pl>
 <3f51b94e-f84c-4fae-9b3f-f8f80ac20c82@bti.vu.lt>
Message-ID: <4fc1802e-6e22-4b20-8606-da82e5c95c18@chem.uw.edu.pl>

Dear Saulius,

I have updated my entries myself. I've added to the .cif the following:

loop_
_audit_support.id
_audit_support.funding_organization
_audit_support.funding_organization_doi
_audit_support.award_type
_audit_support.award_number
_audit_support.award_recipient
1 'Narodowe Centrum Nauki' 'https://ror.org/03ha2q922' OPUS 
'2020/39/I/ST4/02904' 'P. M. Dominiak'

Seems to be sufficient for my funding agency.

Thank you for you help!

I agree, this should bring you more depositions and in general make 
scientific data more open, at least the one generated within the NCN 
projects. The only problem is that now all scientific institutions have 
their own scientific data bases, where everything is deposited - so it 
is no so easy to do more sophisticated queries on them.... So it is one 
I preferred to use your COD for .cif deposition.

All the best,

Paulina


W dniu 18.10.2024 o?09:51, Saulius Gra?ulis pisze:
> On 2024-10-18 10:46, Paulina Dominiak wrote:
>> Thank yo? for quick response.? Yes, you understood me very well, it 
>> is urgent ? . I will contact the agency if extra information in the 
>> .cif file only would be enough for time being.
> Great, we'll assist you in high priority with this data deposition 
> update; we'll
>> But this will be in general very good solution for Polish 
>> crystallographers to have the funding information exposed on the web 
>> page of a given structure. We have now policy to deposit the data 
>> under CC0 or CC BY license, which is not fulfilled by CCDC (along 
>> with unique identifier, funding info, and scientific article if 
>> existing). I will have soon many more such structures to deposit. 
> This sounds like a good policy to promote Open science :)
>> Of course I could deposit my cif to any generic data base (including 
>> the one our university is providing), but then it is waste of the 
>> information - no one will search there for crystal structures.....
>
> Deposition to the COD does not exclude deposition to other databases; 
> in fact we could even forward the data to your University on your 
> behalf if the University would so desire.
>
> But of course COD is a central, long lasting resource (20+ years :) 
> where structures will for sure be found now and in the future :)
>
> Sincerely yours,
> Saulius
>
-- 
Prof. dr hab. Paulina M. Dominiak
Group Leader
Electron Density Modelling Group
Laboratory for Structural and Biochemical Research (LBSBio)
Biological and Chemical Research Centre
Department of Chemistry
University of Warsaw
ul. Zwirki i Wigury 101
02-089 Warszawa, Poland
Room: 3.125
E-mail: pdomin at chem.uw.edu.pl
Phone: (48) 22 55 26 714
WWW: http://4xeden.uw.edu.pl



From antanas.vaitkus90 at gmail.com  Fri Oct 18 15:54:20 2024
From: antanas.vaitkus90 at gmail.com (Antanas Vaitkus)
Date: Fri, 18 Oct 2024 15:54:20 +0300
Subject: [Cod-bugs] crystal structure deposition
In-Reply-To: <4fc1802e-6e22-4b20-8606-da82e5c95c18@chem.uw.edu.pl>
References: <b7acaaa4-80bd-4e8c-a904-bfb3b5e06978@chem.uw.edu.pl>
 <38b9528f-6368-0740-8f47-cf7109337293@bti.vu.lt>
 <62b9b5ef-8633-405a-8f55-1151140290d0@chem.uw.edu.pl>
 <1703cfab-6aad-4135-9c8b-90946c1948d8@ibt.lt>
 <d0e20e21-07d0-4c17-9312-5f768d44ff5b@bti.vu.lt>
 <41873363-8c04-4b85-87bb-7afae7715079@chem.uw.edu.pl>
 <3f51b94e-f84c-4fae-9b3f-f8f80ac20c82@bti.vu.lt>
 <4fc1802e-6e22-4b20-8606-da82e5c95c18@chem.uw.edu.pl>
Message-ID: <CALHYoX5VqAok87qWj5jBuCiBh6S=Jgx9sGjaXQe=S4+z89tuBg@mail.gmail.com>

Dear Paulina,
Dear Saulius,

The AUDIT_SUPPORT loop looks great, but I have two minor comments:

1. The _audit_support.award_type cannot be specified as OPUS and must
instead be one
    of the 'gift', 'grant', 'contract', 'studentship', 'contract' or
'other' predefined values  as
    defined in [1]. I assume that in this case it is a 'grant'?
2. The _audit_support.funding_organization_doi should be a DOI and not an
URL if possible.
    In case of your organisation (Narodowe Centrum Nauki), the DOI should be
    https://doi.org/10.13039/501100004281.

[1]
https://github.com/COMCIFS/cif_core/blob/d99d2c8c65d9856511e3e34e5486535e950386b9/cif_core.dic#L15679

Hope this helps.

Sincerely,
Antanas

On Fri, 18 Oct 2024 at 15:36, Paulina Dominiak <pdomin at chem.uw.edu.pl>
wrote:

> Dear Saulius,
>
> I have updated my entries myself. I've added to the .cif the following:
>
> loop_
> _audit_support.id
> _audit_support.funding_organization
> _audit_support.funding_organization_doi
> _audit_support.award_type
> _audit_support.award_number
> _audit_support.award_recipient
> 1 'Narodowe Centrum Nauki' 'https://ror.org/03ha2q922' OPUS
> '2020/39/I/ST4/02904' 'P. M. Dominiak'
>
> Seems to be sufficient for my funding agency.
>
> Thank you for you help!
>
> I agree, this should bring you more depositions and in general make
> scientific data more open, at least the one generated within the NCN
> projects. The only problem is that now all scientific institutions have
> their own scientific data bases, where everything is deposited - so it
> is no so easy to do more sophisticated queries on them.... So it is one
> I preferred to use your COD for .cif deposition.
>
> All the best,
>
> Paulina
>
>
> W dniu 18.10.2024 o 09:51, Saulius Gra?ulis pisze:
> > On 2024-10-18 10:46, Paulina Dominiak wrote:
> >> Thank yo  for quick response.  Yes, you understood me very well, it
> >> is urgent ? . I will contact the agency if extra information in the
> >> .cif file only would be enough for time being.
> > Great, we'll assist you in high priority with this data deposition
> > update; we'll
> >> But this will be in general very good solution for Polish
> >> crystallographers to have the funding information exposed on the web
> >> page of a given structure. We have now policy to deposit the data
> >> under CC0 or CC BY license, which is not fulfilled by CCDC (along
> >> with unique identifier, funding info, and scientific article if
> >> existing). I will have soon many more such structures to deposit.
> > This sounds like a good policy to promote Open science :)
> >> Of course I could deposit my cif to any generic data base (including
> >> the one our university is providing), but then it is waste of the
> >> information - no one will search there for crystal structures.....
> >
> > Deposition to the COD does not exclude deposition to other databases;
> > in fact we could even forward the data to your University on your
> > behalf if the University would so desire.
> >
> > But of course COD is a central, long lasting resource (20+ years :)
> > where structures will for sure be found now and in the future :)
> >
> > Sincerely yours,
> > Saulius
> >
> --
> Prof. dr hab. Paulina M. Dominiak
> Group Leader
> Electron Density Modelling Group
> Laboratory for Structural and Biochemical Research (LBSBio)
> Biological and Chemical Research Centre
> Department of Chemistry
> University of Warsaw
> ul. Zwirki i Wigury 101
> 02-089 Warszawa, Poland
> Room: 3.125
> E-mail: pdomin at chem.uw.edu.pl
> Phone: (48) 22 55 26 714
> WWW: http://4xeden.uw.edu.pl
>
> _______________________________________________
> Cod-bugs mailing list
> Cod-bugs at lists.crystallography.net
> http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs
>


-- 
Antanas Vaitkus,
Vilnius University,
Life Sciences Center,
Institute of Biotechnology,
room C521, Saul?tekio al. 7,
LT-10257 Vilnius, Lithuania
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.crystallography.net/pipermail/cod-bugs/attachments/20241018/16fd2cf2/attachment.htm>

From pdomin at chem.uw.edu.pl  Fri Oct 18 17:49:16 2024
From: pdomin at chem.uw.edu.pl (Paulina Dominiak)
Date: Fri, 18 Oct 2024 16:49:16 +0200
Subject: [Cod-bugs] crystal structure deposition
In-Reply-To: <CALHYoX5VqAok87qWj5jBuCiBh6S=Jgx9sGjaXQe=S4+z89tuBg@mail.gmail.com>
References: <b7acaaa4-80bd-4e8c-a904-bfb3b5e06978@chem.uw.edu.pl>
 <38b9528f-6368-0740-8f47-cf7109337293@bti.vu.lt>
 <62b9b5ef-8633-405a-8f55-1151140290d0@chem.uw.edu.pl>
 <1703cfab-6aad-4135-9c8b-90946c1948d8@ibt.lt>
 <d0e20e21-07d0-4c17-9312-5f768d44ff5b@bti.vu.lt>
 <41873363-8c04-4b85-87bb-7afae7715079@chem.uw.edu.pl>
 <3f51b94e-f84c-4fae-9b3f-f8f80ac20c82@bti.vu.lt>
 <4fc1802e-6e22-4b20-8606-da82e5c95c18@chem.uw.edu.pl>
 <CALHYoX5VqAok87qWj5jBuCiBh6S=Jgx9sGjaXQe=S4+z89tuBg@mail.gmail.com>
Message-ID: <8c1458d9-70ec-4400-98f3-2e6e6b77ae23@chem.uw.edu.pl>

Thank you for the corrections!
I've updated my entries.
Paulina


W dniu 18.10.2024 o?14:54, Antanas Vaitkus pisze:
> Dear Paulina,
> Dear Saulius,
>
> The AUDIT_SUPPORT loop looks great, but I have two minor comments:
>
> 1. The _audit_support.award_type cannot be specified as OPUS and must 
> instead be one
> ??? of the 'gift', 'grant', 'contract', 'studentship', 'contract' or 
> 'other' predefined values? as
> ??? defined in [1]. I assume that in this case it is a 'grant'?
> 2. The _audit_support.funding_organization_doi should be a DOI and not 
> an URL if possible.
> ??? In case of your organisation (Narodowe Centrum Nauki), the DOI 
> should be
> https://doi.org/10.13039/501100004281.
>
> [1] 
> https://github.com/COMCIFS/cif_core/blob/d99d2c8c65d9856511e3e34e5486535e950386b9/cif_core.dic#L15679
>
> Hope this helps.
>
> Sincerely,
> Antanas
>
> On Fri, 18 Oct 2024 at 15:36, Paulina Dominiak <pdomin at chem.uw.edu.pl> 
> wrote:
>
>     Dear Saulius,
>
>     I have updated my entries myself. I've added to the .cif the
>     following:
>
>     loop_
>     _audit_support.id <http://audit_support.id>
>     _audit_support.funding_organization
>     _audit_support.funding_organization_doi
>     _audit_support.award_type
>     _audit_support.award_number
>     _audit_support.award_recipient
>     1 'Narodowe Centrum Nauki' 'https://ror.org/03ha2q922' OPUS
>     '2020/39/I/ST4/02904' 'P. M. Dominiak'
>
>     Seems to be sufficient for my funding agency.
>
>     Thank you for you help!
>
>     I agree, this should bring you more depositions and in general make
>     scientific data more open, at least the one generated within the NCN
>     projects. The only problem is that now all scientific institutions
>     have
>     their own scientific data bases, where everything is deposited -
>     so it
>     is no so easy to do more sophisticated queries on them.... So it
>     is one
>     I preferred to use your COD for .cif deposition.
>
>     All the best,
>
>     Paulina
>
>
>     W dniu 18.10.2024 o?09:51, Saulius Gra?ulis pisze:
>     > On 2024-10-18 10:46, Paulina Dominiak wrote:
>     >> Thank yo? for quick response.? Yes, you understood me very
>     well, it
>     >> is urgent ? . I will contact the agency if extra information
>     in the
>     >> .cif file only would be enough for time being.
>     > Great, we'll assist you in high priority with this data deposition
>     > update; we'll
>     >> But this will be in general very good solution for Polish
>     >> crystallographers to have the funding information exposed on
>     the web
>     >> page of a given structure. We have now policy to deposit the data
>     >> under CC0 or CC BY license, which is not fulfilled by CCDC (along
>     >> with unique identifier, funding info, and scientific article if
>     >> existing). I will have soon many more such structures to deposit.
>     > This sounds like a good policy to promote Open science :)
>     >> Of course I could deposit my cif to any generic data base
>     (including
>     >> the one our university is providing), but then it is waste of the
>     >> information - no one will search there for crystal structures.....
>     >
>     > Deposition to the COD does not exclude deposition to other
>     databases;
>     > in fact we could even forward the data to your University on your
>     > behalf if the University would so desire.
>     >
>     > But of course COD is a central, long lasting resource (20+ years :)
>     > where structures will for sure be found now and in the future :)
>     >
>     > Sincerely yours,
>     > Saulius
>     >
>     -- 
>     Prof. dr hab. Paulina M. Dominiak
>     Group Leader
>     Electron Density Modelling Group
>     Laboratory for Structural and Biochemical Research (LBSBio)
>     Biological and Chemical Research Centre
>     Department of Chemistry
>     University of Warsaw
>     ul. Zwirki i Wigury 101
>     02-089 Warszawa, Poland
>     Room: 3.125
>     E-mail: pdomin at chem.uw.edu.pl
>     Phone: (48) 22 55 26 714
>     WWW: http://4xeden.uw.edu.pl
>
>     _______________________________________________
>     Cod-bugs mailing list
>     Cod-bugs at lists.crystallography.net
>     http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs
>
>
>
> -- 
> Antanas Vaitkus,
> Vilnius University,
> Life Sciences Center,
> Institute of Biotechnology,
> room C521, Saul?tekio al. 7,
> LT-10257 Vilnius, Lithuania
>
>
-- 
Prof. dr hab. Paulina M. Dominiak
Group Leader
Electron Density Modelling Group
Laboratory for Structural and Biochemical Research (LBSBio)
Biological and Chemical Research Centre
Department of Chemistry
University of Warsaw
ul. Zwirki i Wigury 101
02-089 Warszawa, Poland
Room: 3.125
E-mail:pdomin at chem.uw.edu.pl
Phone: (48) 22 55 26 714
WWW:http://4xeden.uw.edu.pl
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.crystallography.net/pipermail/cod-bugs/attachments/20241018/47a55a82/attachment.htm>

From antanas.vaitkus90 at gmail.com  Fri Oct 18 18:00:51 2024
From: antanas.vaitkus90 at gmail.com (Antanas Vaitkus)
Date: Fri, 18 Oct 2024 18:00:51 +0300
Subject: [Cod-bugs] crystal structure deposition
In-Reply-To: <8c1458d9-70ec-4400-98f3-2e6e6b77ae23@chem.uw.edu.pl>
References: <b7acaaa4-80bd-4e8c-a904-bfb3b5e06978@chem.uw.edu.pl>
 <38b9528f-6368-0740-8f47-cf7109337293@bti.vu.lt>
 <62b9b5ef-8633-405a-8f55-1151140290d0@chem.uw.edu.pl>
 <1703cfab-6aad-4135-9c8b-90946c1948d8@ibt.lt>
 <d0e20e21-07d0-4c17-9312-5f768d44ff5b@bti.vu.lt>
 <41873363-8c04-4b85-87bb-7afae7715079@chem.uw.edu.pl>
 <3f51b94e-f84c-4fae-9b3f-f8f80ac20c82@bti.vu.lt>
 <4fc1802e-6e22-4b20-8606-da82e5c95c18@chem.uw.edu.pl>
 <CALHYoX5VqAok87qWj5jBuCiBh6S=Jgx9sGjaXQe=S4+z89tuBg@mail.gmail.com>
 <8c1458d9-70ec-4400-98f3-2e6e6b77ae23@chem.uw.edu.pl>
Message-ID: <c782202a-ce97-4e1e-afbe-b76d322edf82@gmail.com>

Dear Paulina,

thank you for a quick response, the changes look great. There is nothing
more you need to do, the rest of the email is of informational nature.

We discussed a bit more with Saulius and decided that it would be worthwhile
to also retain the organisation URL that you originally provided (the 
website is
much more human-readable. However, since currently there are no appropriate
tags for this purpose, I have temporarily placed the URL under the
_[local]_audit_support.funding_organization_url tag. It will be upgraded 
to a proper
tag once the IUCr accepts this tag as official.

Thank you for using the COD!

Sincerely,
Antanas

On 10/18/24 17:49, Paulina Dominiak wrote:
> Thank you for the corrections!
> I've updated my entries.
> Paulina
>
>
> W dniu 18.10.2024 o?14:54, Antanas Vaitkus pisze:
>> Dear Paulina,
>> Dear Saulius,
>>
>> The AUDIT_SUPPORT loop looks great, but I have two minor comments:
>>
>> 1. The _audit_support.award_type cannot be specified as OPUS and must 
>> instead be one
>> ??? of the 'gift', 'grant', 'contract', 'studentship', 'contract' or 
>> 'other' predefined values? as
>> ??? defined in [1]. I assume that in this case it is a 'grant'?
>> 2. The _audit_support.funding_organization_doi should be a DOI and 
>> not an URL if possible.
>> ??? In case of your organisation (Narodowe Centrum Nauki), the DOI 
>> should be
>> https://doi.org/10.13039/501100004281.
>>
>> [1] 
>> https://github.com/COMCIFS/cif_core/blob/d99d2c8c65d9856511e3e34e5486535e950386b9/cif_core.dic#L15679
>>
>> Hope this helps.
>>
>> Sincerely,
>> Antanas
>>
>> On Fri, 18 Oct 2024 at 15:36, Paulina Dominiak 
>> <pdomin at chem.uw.edu.pl> wrote:
>>
>>     Dear Saulius,
>>
>>     I have updated my entries myself. I've added to the .cif the
>>     following:
>>
>>     loop_
>>     _audit_support.id <http://audit_support.id>
>>     _audit_support.funding_organization
>>     _audit_support.funding_organization_doi
>>     _audit_support.award_type
>>     _audit_support.award_number
>>     _audit_support.award_recipient
>>     1 'Narodowe Centrum Nauki' 'https://ror.org/03ha2q922' OPUS
>>     '2020/39/I/ST4/02904' 'P. M. Dominiak'
>>
>>     Seems to be sufficient for my funding agency.
>>
>>     Thank you for you help!
>>
>>     I agree, this should bring you more depositions and in general make
>>     scientific data more open, at least the one generated within the NCN
>>     projects. The only problem is that now all scientific
>>     institutions have
>>     their own scientific data bases, where everything is deposited -
>>     so it
>>     is no so easy to do more sophisticated queries on them.... So it
>>     is one
>>     I preferred to use your COD for .cif deposition.
>>
>>     All the best,
>>
>>     Paulina
>>
>>
>>     W dniu 18.10.2024 o?09:51, Saulius Gra?ulis pisze:
>>     > On 2024-10-18 10:46, Paulina Dominiak wrote:
>>     >> Thank yo? for quick response.? Yes, you understood me very
>>     well, it
>>     >> is urgent ? . I will contact the agency if extra information
>>     in the
>>     >> .cif file only would be enough for time being.
>>     > Great, we'll assist you in high priority with this data deposition
>>     > update; we'll
>>     >> But this will be in general very good solution for Polish
>>     >> crystallographers to have the funding information exposed on
>>     the web
>>     >> page of a given structure. We have now policy to deposit the data
>>     >> under CC0 or CC BY license, which is not fulfilled by CCDC (along
>>     >> with unique identifier, funding info, and scientific article if
>>     >> existing). I will have soon many more such structures to deposit.
>>     > This sounds like a good policy to promote Open science :)
>>     >> Of course I could deposit my cif to any generic data base
>>     (including
>>     >> the one our university is providing), but then it is waste of the
>>     >> information - no one will search there for crystal structures.....
>>     >
>>     > Deposition to the COD does not exclude deposition to other
>>     databases;
>>     > in fact we could even forward the data to your University on your
>>     > behalf if the University would so desire.
>>     >
>>     > But of course COD is a central, long lasting resource (20+
>>     years :)
>>     > where structures will for sure be found now and in the future :)
>>     >
>>     > Sincerely yours,
>>     > Saulius
>>     >
>>     -- 
>>     Prof. dr hab. Paulina M. Dominiak
>>     Group Leader
>>     Electron Density Modelling Group
>>     Laboratory for Structural and Biochemical Research (LBSBio)
>>     Biological and Chemical Research Centre
>>     Department of Chemistry
>>     University of Warsaw
>>     ul. Zwirki i Wigury 101
>>     02-089 Warszawa, Poland
>>     Room: 3.125
>>     E-mail: pdomin at chem.uw.edu.pl
>>     Phone: (48) 22 55 26 714
>>     WWW: http://4xeden.uw.edu.pl
>>
>>     _______________________________________________
>>     Cod-bugs mailing list
>>     Cod-bugs at lists.crystallography.net
>>     http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs
>>
>>
>>
>> -- 
>> Antanas Vaitkus,
>> Vilnius University,
>> Life Sciences Center,
>> Institute of Biotechnology,
>> room C521, Saul?tekio al. 7,
>> LT-10257 Vilnius, Lithuania
>>
>>
> -- 
> Prof. dr hab. Paulina M. Dominiak
> Group Leader
> Electron Density Modelling Group
> Laboratory for Structural and Biochemical Research (LBSBio)
> Biological and Chemical Research Centre
> Department of Chemistry
> University of Warsaw
> ul. Zwirki i Wigury 101
> 02-089 Warszawa, Poland
> Room: 3.125
> E-mail:pdomin at chem.uw.edu.pl
> Phone: (48) 22 55 26 714
> WWW:http://4xeden.uw.edu.pl

-- 
Antanas Vaitkus,
Vilnius University,
Life Sciences Center,
Institute of Biotechnology,
room C521, Saul?tekio al. 7,
LT-10257 Vilnius, Lithuania
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.crystallography.net/pipermail/cod-bugs/attachments/20241018/c00a9722/attachment.htm>

From fx.coudert at chimieparistech.psl.eu  Fri Oct 18 21:38:12 2024
From: fx.coudert at chimieparistech.psl.eu (Fx COUDERT)
Date: Fri, 18 Oct 2024 18:38:12 +0000
Subject: [Cod-bugs] Filtering structures with/without disorder
Message-ID: <956DDB2A-5D5A-4CD4-906C-DD3C79AD691A@chimieparistech.psl.eu>

Hi,

In my research, I am currently working on identifying bonding characteristics and topology of inorganic materials, through a topology identification code developed in my group (https://progs.coudert.name/topology). I would like to apply this to the COD database, or rather, to begin with, to a well-defined subset which would be:

- inorganic structures
- with no disorder

I have been wondering: in the COD display page for individual structures, you have a flag for ?is the structure disordered?. So presumably, you store this information somewhere. However, I cannot find a way to query for that, either through the API or even the web interface.

Would you be able to help me with this? Do you know how this could be achieved? I am available to discuss this project more if you are interested, of course.


Best regards,

-- 
Dr. Fran?ois-Xavier Coudert
Senior Researcher / Directeur de Recherche CNRS at Chimie ParisTech
Professeur attach? ENS / PSL University
Webpage: https://www.coudert.name/


-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.