Issue 3691: The spec mentions IUPAC-IUB single letter codes (biomolecular-ftf) Source: (Mr. Philip Lijnzaad, p.lijnzaad@med.uu.nl) Nature: Uncategorized Issue Severity: Summary: The spec mentions IUPAC-IUB single letter codes, I think this has been renamed to IUPAC-IUBMB Joint Commission on Biochemical Nomenclature (JCBN); the best web site for this is http://www.chem.qmw.ac.uk/iupac/AminoAcid/ (amino acids) http://www.chem.qmw.ac.uk/iubmb/misc/naseq.html (nucleic acids) http://www.chem.qmw.ac.uk/iubmb/nomenclature/ (all biostandards) Might be useful to include in the references. IUB allows termination characters in amino acids; I think we should not allow them. Also, it might be good to explicitly state that gap characters ('-' or so) are not supposed to be in sequences (this is fairly implicit in IUPAC, so I think had doesn't hurt to be clear about this). Resolution: accepted Revised Text: Change the IUPAC references in Appendix A to http://www.chem.qmw.ac.uk/iupac/AminoAcid/ (amino acids) http://www.chem.qmw.ac.uk/iubmb/misc/naseq.html (nucleic acids) http://www.chem.qmw.ac.uk/iubmb/nomenclature/ (all biostandards) Change IUPAC-IUB to IUPAC-IUBMB Joint Commission on Biochemical Nomenclature (JCBN). Add a single sentence to the seq return value box in section 2.1.9. The string will not contain any termination characters, e.g., '*' or gap characters, e.g., '-'. Actions taken: June 9, 2000: received issue May 24, 2001: closed issue Discussion: End of Annotations:===== Date: Fri, 9 Jun 2000 15:39:29 +0100 (BST) Message-Id: <200006091439.e59EdTA17797@o2-3.ebi.ac.uk> X-Authentication-Warning: o2-3.ebi.ac.uk: lijnzaad set sender to lijnzaad@ebi.ac.uk using -f From: Philip Lijnzaad To: biomolecular-ftf@emerald.omg.org cc: muilu@ebi.ac.uk Subject: some issues ... Reply-to: lijnzaad@ebi.ac.uk Content-Type: text X-UIDL: [C#!! Organization: NetGenics, Inc. X-Mailer: Mozilla 4.73 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: BSA FTF Subject: [OMG-BSA] proposed resolutions for some issues Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii X-UIDL: W9!e9QLE!!'Okd9>SPe9 In accordance with the consensus at last week's FTF meeting, here are the proposed resolutions for the issues that were considered straightforward. Note that as some multi-issue issues are split apart, some of those may also fall into this category. I'm not reproducing the entire text of the individual issues. You can find that at http://cgi.omg.org/issues/biomolecular-ftf.html. Issues can be reported online at http://www.omg.org/technology/issuesform.htm. This message is *not* a vote. I just want to make sure these particular issues are as straightforward as some of us thought last week. Please let me know if you disagree. Actually it would be nice to know if you agree, too. :) If there's been no response by early next week (Philip is out until then), I'll send out a message kicking off a vote. If there are responses, hopefully we'll get the resolutions resolved and still vote on these issues next week. Scott Issue 3691: The spec mentions IUPAC-IUB single letter codes Resolution: Change the IUPAC references in Appendix A to http://www.chem.qmw.ac.uk/iupac/AminoAcid/ (amino acids) http://www.chem.qmw.ac.uk/iubmb/misc/naseq.html (nucleic acids) http://www.chem.qmw.ac.uk/iubmb/nomenclature/ (all biostandards) Change IUPAC-IUB to IUPAC-IUBMB Joint Commission on Biochemical Nomenclature (JCBN). Add a single sentence to the seq return value box in section 2.1.9. The string will not contain any termination characters, e.g., '*' or gap characters, e.g., '-'. The EBI would like to withdraw the terminator sub-issue of issue 3691, and resolve the gap sub-issue with Scott's suggestion to add "Gap characters are not permitted." after "Any internal stop ... by '*'." in the Return value slot for both translate_seq() and translate_seq_region() (section 2.1.10, page 2-29). (with many thanks to Scott for the wording :-) Philip Date: Tue, 26 Sep 2000 10:54:25 -0700 From: Scott Markel Organization: NetGenics, Inc. X-Mailer: Mozilla 4.73 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: lijnzaad@ebi.ac.uk CC: biomolecular-ftf@omg.org, juergen@omg.org, senger@ebi.ac.uk, muilu@ebi.ac.uk Subject: Re: issue: no gaps allowed References: <200009191107.e8JB7ix43099@o2-3.ebi.ac.uk> <39C7BDDC.C5930A94@netgenics.com> <200009251213.e8PCDRK44948@o2-3.ebi.ac.uk> <39CF9750.D1261830@netgenics.com> <200009261105.e8QB54G46993@o2-3.ebi.ac.uk> Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii X-UIDL: N5V!!\nOe92H\d9~;'!! Philip, Philip Lijnzaad wrote: > > The EBI would like to withdraw the terminator sub-issue of issue 3691, and > resolve the gap sub-issue with Scott's suggestion to add > > "Gap characters are not permitted." after "Any internal stop ... by '*'." > > in the Return value slot for both translate_seq() and translate_seq_region() > (section 2.1.10, page 2-29). > > (with many thanks to Scott for the wording :-) Once we've got new issue numbers, I'll send around some of the proposed resolutions we've been accumulating. Scott -- Scott Markel, Ph.D. NetGenics, Inc. smarkel@netgenics.com 4350 Executive Drive Tel: 858 455 5223 Suite 260 FAX: 858 455 1388 San Diego, CA 92121