From antanas.vaitkus90 at gmail.com  Wed Jun  3 16:12:18 2020
From: antanas.vaitkus90 at gmail.com (Antanas Vaitkus)
Date: Wed, 3 Jun 2020 16:12:18 +0300
Subject: [Cod-bugs] Feature suggest COD search with sketcher
In-Reply-To: <20200603050348.3e76c17f@carnot2>
References: <20200603050348.3e76c17f.ref@carnot2>
 <20200603050348.3e76c17f@carnot2>
Message-ID: <CALHYoX4n22qE84O9p7Dz4uHCG10hH=ztuND=y7S10TYLeDuHQg@mail.gmail.com>

Dear Norwid,

thank you for the bug reports. The COD team is quite swamped at the moment
so it may take us some time to
implement the fixes, but the suggested usability improvements indeed seem
useful.

As a side note, I do not mind you writing directly to this e-mail, but in
the future it would be better to send any bug
reports or feature requests to the COD support e-mail (cod-bugs at ibt.lt).
This way it becomes visible to the entire
COD team and is slightly easier for us to track. In this spirit, I will
also forward my reply to the support e-mail.

Sincerely,
Antanas


On Wed, 3 Jun 2020 at 12:04, Norwid Behrnd <nbehrnd at yahoo.com> wrote:

> Dear Antanas,
>
> based on a previous helpful exchange with you as one of the curators of
> the COD, I would like to suggest an addition of the features the data
> base offers when searching with the sketcher by Ertl et al.
>
>
> Point #1:
> A lecture about alkylated polythiophenes / polythiophene polymers (e.g.,
> slide #4 of the reprinted .pdf attached) lead me to check if the COD would
> contain similar models -- maybe not polymers, but tri- or tetramers fitting
> better into the scope of the database's criterion of ?small molecules?.
> One of the structure motifs for example was translated on the ?search
> results? page into the SMILES string of 'CCc3csc(c2sc(c1sccc1CC)cc2CC)c3',
> with two model data indexed.
>
> I notice that the bottom of the page listing COD entries offers a link
> to return to the search form to refine the query.  In my case, however, the
> SMILES string was not retained; in other words, I _speculated_ the search
> mask's second field ?OpenBabel FastSearch? would contain this string to
> continue further.  This however, was not (yet) the case and I would like to
> suggest that this piece of information is transferred to the text-based
> search automatically.
>
>
> Point #2:
> In this case, retrieving the two models was iterative.  With a dimer at
> hand, for example ('CCc2csc(c1sccc1CC)c2' as motif), there already are
> three
> indexed models.  Not knowing (enough / at all) about the technical
> background
> of the COD to bring a solution to the table, I would like to suggest to
> add a second function to the list of results:  If a query was based on a
> structure formula, to offer a return to the page with sketcher where this
> query structure is ?still alive? for an adjustment / refinement.
>
> E.g., if you would like to query the COD of halonitrostilbenes; here, I'm
> not aware if the sketcher allows the definition of a ?placeholder? then
> covering the set of (F .or. Cl .or. Br .or. I) as in CCDC's conquest GUI.
> So far -- if not simply querying the database with nitrostilbene as
> substructure -- this requires to draw the molecular structure again from
> the beginning.  And again if one of the arenes were substituted by pyridine
> or an other heterocycle where conquest permits to define a arene atom to be
> either (C .or. N); this would not be a simple sub-structure search possibly
> addressed by one query.
>
> With best regards,
>
> Norwid
>


-- 
Antanas Vaitkus,
PhD student at Vilnius University Institute of Biotechnology,
room V325, Saul?tekio al. 7,
LT-10257 Vilnius, Lithuania

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From violaine.rebouillat.auditeur at lecnam.net  Thu Jun  4 11:46:43 2020
From: violaine.rebouillat.auditeur at lecnam.net (REBOUILLAT Violaine)
Date: Thu, 4 Jun 2020 08:46:43 +0000
Subject: [Cod-bugs] Crystallography Open Database - Study on the Audience of
 Scientific Databases and Data Repositories
Message-ID: <PR2P264MB001310C5C043C7008A9F21B5A0890@PR2P264MB0013.FRAP264.PROD.OUTLOOK.COM>

Dear Ms/Mr,

I am taking the liberty of contacting you in the course of my research in information science. I am a researcher at the Cnam in Paris and I am interested in open science and the sharing of research data.

I am currently conducting a study on the consultation of data available in online data repositories and databases. The aim of this study is to understand what role repositories play in the reuse of data and how users have appropriated them.

My approach is to collect repositories audience data from their administrators.

That's why I am turning to you. The Crystallography Open Database is one of the 200 databases recommended by the FAIRsharing<https://fairsharing.org/> directory.

So my question is: would you agree to have Crystallography Open Database included in this study? If so, could you provide me with its audience data for the period 2015-2020?

I would need, as far as possible, the most accurate records you have.
The information I would ideally like to know is as follows:

- The number of hits and (if any) downloads of each available dataset;

- The evolution of this number (hits and/or downloads) over months or even years between 2015 and 2020.
However, if you cannot or do not wish to provide me with detailed information for each dataset, I am also interested in more aggregated data.

In addition, could you summarize in a few words the method you use to measure the data repository audience?

The data you will provide will remain confidential and will only be used for the purposes of this study. The published results will be in the form of aggregate statistical data. They will be the subject of a paper to be presented at the 7th <https://docsoc2020.sciencesconf.org/> Document num?rique & Soci?t?<https://docsoc2020.sciencesconf.org/> conference<https://docsoc2020.sciencesconf.org/> next September. A summary of these results will be sent to you during the summer.

If the files you want to send me are too numerous or too large to be sent by email, I can suggest you the open source solution Framadrop (the submission procedure is attached).

If you don't currently have a device to measure the database audience, could you let me know that as well? I would be interested to have that information and the reason why.

I thank you in advance and remain at your disposal for any further information.

Kind regards,


Violaine Rebouillat

Doctor in Information Science

Dicen-IDF laboratory (Cnam, Paris)

https://www.dicen-idf.org/membre/rebouillat-violaine/

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From awalseng at sparceurope.org  Fri Jun  5 10:14:19 2020
From: awalseng at sparceurope.org (=?utf-8?Q?Angela=20Walseng?=)
Date: Fri,  5 Jun 2020 07:14:19 +0000
Subject: [Cod-bugs] =?utf-8?q?=7BDisarmed=7D_Survey_deadline_extended_by_?=
 =?utf-8?q?one_week?=
Message-ID: <ca023fcd073a276f9a0a200b6.95dcb06b7d.20200605071415.60c5eff9a8.f2d28605@mail182.sea22.mcdlv.net>

Survey seeking essential insights into Europe's Open infra landscape extended to June 12

View this email in your browser (https://mailchi.mp/a4ae3035a23e/latest-news-from-sparc-europe-726720?e=95dcb06b7d)
5 June 2020

One more week: OA & OS Infrastructure survey deadline extended

Your help is needed to see that we capture feedback from as many respondents as possible.

============================================================

Colleagues,

We?re reaching out to let you know that we have extended the deadline for our survey of digital OA and OS infrastructure providers to Friday, 12 June 2020. While we are encouraged by and very much appreciate all of the responses we have received to date, there are many services we would still like to hear from; and multiple countries underrepresented so far.

A reminder of why we are doing this work: In recent years, a rich field of Open Access, Open Science/Scholarship resources and infrastructure, many essential, has organically developed in Europe. Many of these resources, as you may well know, are not necessarily sustainable ? even though they underpin our evolving Open Access and Open Science landscape.

Hence, our survey targets digital OA and OS infrastructure providers with a regional, national or international scope in Europe. We are appealing to you for help in getting this 30-minute survey into the hands of as many OA and OS infrastructure service providers as possible.

Their feedback is necessary if we are to gain a comprehensive understanding of existing resources; and this knowledge will be important to efforts aimed at garnering funding support these services and resources might need in future.

Using information gained through this survey, we hope to bring greater visibility and a deeper understanding of the many European-based scholarly communications resources on offer. This should help funders ? governments, funding organisations and agencies, institutions, libraries, service providers and others ? conceive effective strategies for financing essential Open infrastructure.

Again, we ask that you take a moment to consider any services that you think should be involved in this survey, particularly those resources that we might not know about from your country, and share it with them.

Below, please find an email we have drafted that you are free to use when reaching out to potential survey participants. It includes a link to the survey itself.

** The survey (https://www.surveymonkey.com/r/V8Q7R2X)
, which is being conducted for** Invest in Open Infrastructure (https://investinopen.org/)
, should take approximately 30 minutes to complete. It will remain open until 12 June 2020,  and no additional extension will be offered. Once closed, we will use the following two months to review and compile the results, which will be shared during the late summer/early autumn 2020.

Thank you very much for your support.
** Take the survey here (https://www.surveymonkey.com/r/V8Q7R2X)
, or ** download the survey PDF (https://sparceurope.org/download/8627/)
first to know what to expect.

If you have any questions, please reach out to
** survey at sparceurope.org (mailto:survey at sparceurope.org)
.

Best regards,
Vanessa Proudman
Director, SPARC Europe
Please feel free to copy and paste the following text into a new email and share with any services you know of that should participate in the survey. The same text is available to copy and paste in ** this Google document (https://docs.google.com/document/d/1vE0wWbwJhhN3iLzlXjtjmgEVgB_nOGyxxmXnuL8A9aA/edit?usp=sharing)
.

Hello,

I am sharing the below email with you as I believe that it would be important for you to fill in this survey, which is looking to map Open Access / Open Science infrastructure in Europe. The survey is a first of its kind aiming to establish a more comprehensive understanding of existing resources so that services like yours may have a greater chance of garnering the funding support they may need in future.

Thank you,

[Your name]

Hello,

If you?re reading this, you are most likely based in Europe and a part of the rich field of Open Access, Open Science/Scholarship resources and infrastructure, many essential, that has organically developed in Europe in recent years. Many of these resources, as you may well know, are not sustainable ? even though they underpin our evolving Open Access and Open Science landscape.

With your help, though, we are working to change this.
** By taking part in this survey (https://www.surveymonkey.com/r/V8Q7R2X)
, you can help us bring greater visibility and a deeper understanding of the rich offering of scholarly communication resources based in the European region; and ultimately, help attract more funding. Based on what we learn, we also plan to showcase some of you as leading open infrastructure champions.

Your feedback is critical. The information you share will ultimately help funders ? governments, funding organisations and agencies, institutions, libraries, service providers and others ? conceive effective strategies for financing essential Open infrastructure.

** The survey (https://www.surveymonkey.com/r/V8Q7R2X)
, which is being conducted for** Invest in Open Infrastructure (https://investinopen.org/)
, should take you approximately 30 minutes to complete and will be open until 5 June 2020.

If you are based in Europe and are running a service or infrastructure that supports OA or OS anywhere in the research cycle, we?d like to hear from you. In the event that you are responsible for more than one, please submit entries for each. Once closed, we will use the following two months to review and compile the survey results which will be shared during late summer/early autumn 2020.

Thank you very much for your support. If you have any questions, please reach out to
** survey at sparceurope.org (mailto:survey at sparceurope.org)
.

** TAKE ME TO THE SURVEY (https://www.surveymonkey.com/r/V8Q7R2X)

Best regards,
Vanessa Proudman
Director, SPARC Europe

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