From grazulis at ibt.lt Mon Apr 26 18:35:02 2021 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=) Date: Mon, 26 Apr 2021 18:35:02 +0300 Subject: [Cod-bugs] Report issues In-Reply-To: References: Message-ID: <1f2d6221-f463-7bdb-4118-65124f30ff78@ibt.lt> Dear Leon, thank you for the issue! On 2021-04-26 18:06, Li, Qingliang (NIH/NLM/NCBI) [E] wrote: > We got some reports that 'weird' names are observed in the entries > from?Crystallography Open Database > , > which you may want to take a look and improve if allowed.?Thank you!? > > * https://pubchem.ncbi.nlm.nih.gov/substance/385953088 > * https://pubchem.ncbi.nlm.nih.gov/substance/385848982 > * https://pubchem.ncbi.nlm.nih.gov/substance/385942015 > Could you please hint me what was found "weird" in the names? I will double check the compound naming, but I believe the names came from the original papers, we do not generate names ourselves. Sincerely yours, Saulius -- Dr. Saulius Gra?ulis Vilnius University, Life Science Center, Institute of Biotechnology Saul?tekio al. 7, LT-10257 Vilnius, Lietuva (Lithuania) phone (office): (+370-5)-2234353, mobile: (+370-684)-49802, (+370-614)-36366 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: grazulis.vcf Type: text/x-vcard Size: 4 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 228 bytes Desc: OpenPGP digital signature URL: From grazulis at ibt.lt Mon Apr 26 18:47:31 2021 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=) Date: Mon, 26 Apr 2021 18:47:31 +0300 Subject: [Cod-bugs] Report issues In-Reply-To: References: Message-ID: <455ef651-d9ef-4e3b-3f4c-8d5deae5ac25@ibt.lt> On 2021-04-26 18:06, Li, Qingliang (NIH/NLM/NCBI) [E] wrote: > We got some reports that 'weird' names are observed in the entries > from?Crystallography Open Database > , > which you may want to take a look and improve if allowed.?Thank you!? > > * https://pubchem.ncbi.nlm.nih.gov/substance/385953088 > * https://pubchem.ncbi.nlm.nih.gov/substance/385848982 > * https://pubchem.ncbi.nlm.nih.gov/substance/385942015 > > > Best regards, > Leon Update: I see your point. The systematic names are indeed misrepresented in our recors. We'll fix the issue and upload the corrected files. Sincerely, Saulius -- Dr. Saulius Gra?ulis Vilnius University, Life Science Center, Institute of Biotechnology Saul?tekio al. 7, LT-10257 Vilnius, Lietuva (Lithuania) phone (office): (+370-5)-2234353, mobile: (+370-684)-49802, (+370-614)-36366 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: grazulis.vcf Type: text/x-vcard Size: 4 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 228 bytes Desc: OpenPGP digital signature URL: From qingliang.li at nih.gov Mon Apr 26 18:53:20 2021 From: qingliang.li at nih.gov (Li, Qingliang (NIH/NLM/NCBI) [E]) Date: Mon, 26 Apr 2021 15:53:20 +0000 Subject: [Cod-bugs] [Pubchem-deposit-help] Report issues In-Reply-To: <455ef651-d9ef-4e3b-3f4c-8d5deae5ac25@ibt.lt> References: , <455ef651-d9ef-4e3b-3f4c-8d5deae5ac25@ibt.lt> Message-ID: Thanks, Saulius! Great to hear that you will fix the issue and keep the data of high quality! Best, Leon ________________________________ From: Pubchem-deposit-help on behalf of Saulius Gra?ulis Sent: Monday, April 26, 2021 11:47 AM To: Li, Qingliang (NIH/NLM/NCBI) [E] Cc: Shoemaker, Ben (NIH/NLM/NCBI) [E] ; NLM/NCBI List pubchem-deposit-help ; cod-bugs at lists.crystallography.net Subject: Re: [Pubchem-deposit-help] Report issues On 2021-04-26 18:06, Li, Qingliang (NIH/NLM/NCBI) [E] wrote: We got some reports that 'weird' names are observed in the entries from Crystallography Open Database, which you may want to take a look and improve if allowed. Thank you! * https://pubchem.ncbi.nlm.nih.gov/substance/385953088 * https://pubchem.ncbi.nlm.nih.gov/substance/385848982 * https://pubchem.ncbi.nlm.nih.gov/substance/385942015 Best regards, Leon Update: I see your point. The systematic names are indeed misrepresented in our recors. We'll fix the issue and upload the corrected files. Sincerely, Saulius -- Dr. Saulius Gra?ulis Vilnius University, Life Science Center, Institute of Biotechnology Saul?tekio al. 7, LT-10257 Vilnius, Lietuva (Lithuania) phone (office): (+370-5)-2234353, mobile: (+370-684)-49802, (+370-614)-36366 -------------- next part -------------- An HTML attachment was scrubbed... URL: From grazulis at ibt.lt Tue Apr 27 07:30:34 2021 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=) Date: Tue, 27 Apr 2021 07:30:34 +0300 Subject: [Cod-bugs] [Pubchem-deposit-help] Report issues In-Reply-To: References: <455ef651-d9ef-4e3b-3f4c-8d5deae5ac25@ibt.lt> Message-ID: On 2021-04-26 18:53, Li, Qingliang (NIH/NLM/NCBI) [E] wrote: > Great to hear that you will fix the issue and keep the data of high > quality!? We are passionately dedicated to data quality! Will do what is in our capabilities. Actually, I have traced the "weird" names to the original files (so much about the publication quality and data peer review...). But for sure our COD ingestion software missed the issue, which it should have not. Do you know a decent F/LOSS library to check and/or generate IUPAC chemical names? OPSIN is one library which I know, but maybe you have something nice on your site? (Marvin would be another, but that is prorietary so I avoid it). Regards, Saulius -- Dr. Saulius Gra?ulis Vilnius University, Life Science Center, Institute of Biotechnology Saul?tekio al. 7, LT-10257 Vilnius, Lietuva (Lithuania) 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: grazulis.vcf Type: text/x-vcard Size: 4 bytes Desc: not available URL: From andrius.merkys at gmail.com Tue Apr 27 11:46:19 2021 From: andrius.merkys at gmail.com (Andrius Merkys) Date: Tue, 27 Apr 2021 11:46:19 +0300 Subject: [Cod-bugs] possible doublette entry / suggest of consolidation #9013110 and #9016483 In-Reply-To: <20210423172112.4f5fc7fa@carnot2> References: <20210423172112.4f5fc7fa.ref@carnot2> <20210423172112.4f5fc7fa@carnot2> Message-ID: <4b491755-e643-b9f3-74f3-e103bbcf6d16@gmail.com> Dear Norwid, On 2021-04-23 20:21, Norwid Behrnd wrote: > Curious about relevant data in the COD accessed on-line, I noticed > entries #9013110 and #9016483 practically describe the same model: > It is not only by the authors and publication, or about the same > space group, but same about the experimental temperature .and. lattice > constants .and. atomic coordinates. > > Based on these observations and assuming this might be supported on > your database policy, I would like to suggest that either one of the > two entries seen today (2021-04-23) coalesces into the other, e.g. the > ChemSpider based #9013110 into the AMCSD based #9016483, then with a > reference to ChemSpider. Thank you for your report! I have just marked entry 9016483 as duplicate of 9013110. Saulius, Antanas, I have not touched '_cod_related_entry_*' CIF data items though. I suppose both 9013110 and 9016483 should point to the same ChemSpider entry, but not sure what to do with AMCSD link. Best, Andrius -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. From qingliang.li at nih.gov Tue Apr 27 13:17:18 2021 From: qingliang.li at nih.gov (Li, Qingliang (NIH/NLM/NCBI) [E]) Date: Tue, 27 Apr 2021 10:17:18 +0000 Subject: [Cod-bugs] [Pubchem-deposit-help] Report issues In-Reply-To: References: <455ef651-d9ef-4e3b-3f4c-8d5deae5ac25@ibt.lt> , Message-ID: Hi Saulius, Thanks for the updates! Data quality is key. As to the FLOSS library, I don't know more than OPSIN. We have proprietary software, openeye, but which you may also want to avoid as well. Best, Leon ________________________________ From: Saulius Gra?ulis Sent: Tuesday, April 27, 2021 12:30 AM To: Li, Qingliang (NIH/NLM/NCBI) [E] Cc: Shoemaker, Ben (NIH/NLM/NCBI) [E] ; NLM/NCBI List pubchem-deposit-help ; cod-bugs at lists.crystallography.net Subject: Re: [Pubchem-deposit-help] Report issues On 2021-04-26 18:53, Li, Qingliang (NIH/NLM/NCBI) [E] wrote: Great to hear that you will fix the issue and keep the data of high quality! We are passionately dedicated to data quality! Will do what is in our capabilities. Actually, I have traced the "weird" names to the original files (so much about the publication quality and data peer review...). But for sure our COD ingestion software missed the issue, which it should have not. Do you know a decent F/LOSS library to check and/or generate IUPAC chemical names? OPSIN is one library which I know, but maybe you have something nice on your site? (Marvin would be another, but that is prorietary so I avoid it). Regards, Saulius -- Dr. Saulius Gra?ulis Vilnius University, Life Science Center, Institute of Biotechnology Saul?tekio al. 7, LT-10257 Vilnius, Lietuva (Lithuania) 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: From antanas.vaitkus90 at gmail.com Wed Apr 28 14:53:57 2021 From: antanas.vaitkus90 at gmail.com (Antanas Vaitkus) Date: Wed, 28 Apr 2021 14:53:57 +0300 Subject: [Cod-bugs] possible doublette entry / suggest of consolidation #9013110 and #9016483 In-Reply-To: <4b491755-e643-b9f3-74f3-e103bbcf6d16@gmail.com> References: <20210423172112.4f5fc7fa.ref@carnot2> <20210423172112.4f5fc7fa@carnot2> <4b491755-e643-b9f3-74f3-e103bbcf6d16@gmail.com> Message-ID: Dear all, On Tue, 27 Apr 2021 at 11:46, Andrius Merkys wrote: > Dear Norwid, > > On 2021-04-23 20:21, Norwid Behrnd wrote: > > Based on these observations and assuming this might be supported on > > your database policy, I would like to suggest that either one of the > > two entries seen today (2021-04-23) coalesces into the other, e.g. the > > ChemSpider based #9013110 into the AMCSD based #9016483, then with a > > reference to ChemSpider. > Actually, both of these files were retrieved from AMCSD at different times, however, only one of them was later on selected as a linking candidate by ChemSpider. > Saulius, Antanas, I have not touched '_cod_related_entry_*' CIF data > items though. I suppose both 9013110 and 9016483 should point to the > same ChemSpider entry, but not sure what to do with AMCSD link. > I updated the files to have the same information and marked both of the files as being related to the same entries in AMCSD and ChemSpider. I also reported the discrepancies in the original AMCSD entry [1] (incorrect chemical formula, incorrect atoms names) to the maintainers of the AMCSD. Hopefully it gets fixed upstream as well. [1] http://rruff.geo.arizona.edu/AMS/result.php?key=_database_code_amcsd%200014997&viewing=html Sincerely, Antanas -- Antanas Vaitkus, PhD student at Vilnius University Institute of Biotechnology, room V325, Saul?tekio al. 7, LT-10257 Vilnius, Lithuania -- 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: From service at chemicalbook.com Fri Apr 30 12:16:13 2021 From: service at chemicalbook.com (customerservice) Date: Fri, 30 Apr 2021 17:16:13 +0800 Subject: [Cod-bugs] =?utf-8?q?Can_we_link_to_your_website=3F?= Message-ID: Dear friends, We are Chemicalbook, a chemical information display platform for all kinds of chemicals in China. Our website contains millions of chemical products and related substance information. We want to establish a website link with your chemical products. At present, we have established links with some well-known websites such as EMBL-EBI. We rarely ever reach out for this type of arrangement but thought you would be receptive to it. Sincerely, Looking forward to your reply. Best regards Joan ******************************************* Joan Tel: +86-10-86108875 Mobile: 13121529858 Skype: live:info_697287 E-mail: service at chemicalbook.com Web: www.chemicalbook.com -- 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: temp4cj.png Type: application/octet-stream Size: 18256 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: chemicalbook.jpg Type: application/octet-stream Size: 59684 bytes Desc: not available URL: From tomas.moravek at tescan.com Fri Apr 30 15:17:25 2021 From: tomas.moravek at tescan.com (=?iso-8859-2?Q?Tom=E1=B9_Mor=E1vek?=) Date: Fri, 30 Apr 2021 12:17:25 +0000 Subject: [Cod-bugs] COD ID: 3000098 Message-ID: Hi, I would like to report missing CIF file for structure B2BO4 ( COD ID 3000098), see image below. There are 10 entries, but in column CIF there is only "On hold till 2017". Is it possible to provide real CIF file? Best regards Tomas Moravek [cid:image001.png at 01D73DCB.8A360350] Tom?? Mor?vek Application specialist - junior p: +420 530 353 333 a: TESCAN Brno, s.r.o. | Libu?ina t??da 1, 623 00 Brno, Czech Republic w: www.tescan.com | e: tomas.moravek at tescan.com [cid:image002.jpg at 01D73DCB.8A360350] -- 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 18567 bytes Desc: image001.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image002.jpg Type: image/jpeg Size: 2159 bytes Desc: image002.jpg URL: From grazulis at ibt.lt Fri Apr 30 15:21:21 2021 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=) Date: Fri, 30 Apr 2021 15:21:21 +0300 Subject: [Cod-bugs] COD ID: 3000098 In-Reply-To: References: Message-ID: Dear Tom??, thank you for your report, On 2021-04-30 15:17, Tom?? Mor?vek wrote: > I would like to report missing CIF file for structure B2BO4? ( COD ID > 3000098 ), see image > below. There are 10 entries, but in column CIF there is only ?On hold > till 2017?. Is it possible to provide real CIF file? indeed, the structure is on hold for too long... sorry for that. We'll check if the paper is published already and release the data ASAP. Sincerely yours, Saulius -- Dr. Saulius Gra?ulis Vilnius University, Life Science Center, Institute of Biotechnology Saul?tekio al. 7, LT-10257 Vilnius, Lietuva (Lithuania) phone (office): (+370-5)-2234353, mobile: (+370-684)-49802, (+370-614)-36366 -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 228 bytes Desc: OpenPGP digital signature URL: