From eric.talevich at gmail.com Mon Feb 3 02:20:22 2014 From: eric.talevich at gmail.com (Eric Talevich) Date: Sun, 2 Feb 2014 23:20:22 -0800 Subject: [BioSQL-l] Google Summer of Code 2014 - Call for project ideas Message-ID: Hi everyone, Google Summer of Code is on again for 2014, and the Open Bioinformatics Foundation (OBF) is once again applying as a mentoring organization. Participating in GSoC as an organization is very competitive, and we will need your help in gathering a good set of ideas and potential mentors for BioSQL's role in GSoC this year. If you have an idea for a Summer of Code project, please post your idea here on the BioSQL mailing list for discussion. We also welcome ideas that fit with OBF's mission but are not part of a single Bio* project, or span multiple projects -- these ideas can be posted on the OBF wiki and discussed on the OBF mailing list: http://www.open-bio.org/wiki/Google_Summer_of_Code#Project_ideas http://lists.open-bio.org/mailman/listinfo/open-bio-l Here's to another fun and productive Summer of Code! Cheers, Eric & Raoul From helton.a at gmail.com Thu Feb 6 16:49:27 2014 From: helton.a at gmail.com (Helton Azevedo) Date: Thu, 6 Feb 2014 19:49:27 -0200 Subject: [BioSQL-l] Loanding data sequence by genre Message-ID: Hello Guys, I am working on a project that integrates data and tools to use the techniques of Multilocus Sequence Analysisfor dealing with the taxonomy of bacteria, and our structure database was assembled using the fantastic scheme BioSQL project. We managed to make the loading of the taxonomy to the bank, but now we need to do the loading sequences of some bacterial genera at first would be only two: Bradyrhizobium and Rhizobium. We are using MySQL Someone already tried to create a script that works that way, collecting sequences by "genre". Could share with us? Thank you very much, Helton -- Helton de Azevedo 43 9997-3605 From helton.a at gmail.com Thu Feb 13 15:48:46 2014 From: helton.a at gmail.com (Helton Azevedo) Date: Thu, 13 Feb 2014 18:48:46 -0200 Subject: [BioSQL-l] Where the "gene" field is imported to into the SQL schema? Message-ID: I've looked through the documentation, but I am unable to determine where the "gene" field is imported to into the SQL schema? There is a table where the gene and stored? -- Helton de Azevedo 43 9997-3605 From p.j.a.cock at googlemail.com Thu Feb 13 16:20:16 2014 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 13 Feb 2014 21:20:16 +0000 Subject: [BioSQL-l] Where the "gene" field is imported to into the SQL schema? In-Reply-To: References: Message-ID: On Thursday, February 13, 2014, Helton Azevedo wrote: > I've looked through the documentation, but I am unable to determine where > the "gene" field is imported to into the SQL schema? > > There is a table where the gene and stored? > > There isn't a single gene field - perhaps an example you help. Are you starting from an EMBL or GenBank file? Peter From helton.a at gmail.com Thu Feb 13 16:48:56 2014 From: helton.a at gmail.com (Helton Azevedo) Date: Thu, 13 Feb 2014 19:48:56 -0200 Subject: [BioSQL-l] Where the "gene" field is imported to into the SQL schema? In-Reply-To: References: Message-ID: Hi Peter, Thanks.. I use GenBank file. On Thu, Feb 13, 2014 at 7:20 PM, Peter Cock wrote: > > > On Thursday, February 13, 2014, Helton Azevedo wrote: > >> I've looked through the documentation, but I am unable to determine where >> the "gene" field is imported to into the SQL schema? >> >> There is a table where the gene and stored? >> >> > There isn't a single gene field - perhaps an example you help. Are you > starting from an EMBL or GenBank file? > > Peter > > -- Helton de Azevedo 43 9997-3605 From p.j.a.cock at googlemail.com Thu Feb 13 16:58:17 2014 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 13 Feb 2014 21:58:17 +0000 Subject: [BioSQL-l] Where the "gene" field is imported to into the SQL schema? In-Reply-To: References: Message-ID: On Thursday, February 13, 2014, Helton Azevedo wrote: > Hi Peter, > Thanks.. > > I use GenBank file. > > OK. Each gene or CDS or tRNA etc is a feature, with a type (e.g. gene or CDS), location, and assorted key:value annotation pairs. Each bit if that goes in a different table or set of tables. Peter From eric.talevich at gmail.com Mon Feb 3 07:20:22 2014 From: eric.talevich at gmail.com (Eric Talevich) Date: Sun, 2 Feb 2014 23:20:22 -0800 Subject: [BioSQL-l] Google Summer of Code 2014 - Call for project ideas Message-ID: Hi everyone, Google Summer of Code is on again for 2014, and the Open Bioinformatics Foundation (OBF) is once again applying as a mentoring organization. Participating in GSoC as an organization is very competitive, and we will need your help in gathering a good set of ideas and potential mentors for BioSQL's role in GSoC this year. If you have an idea for a Summer of Code project, please post your idea here on the BioSQL mailing list for discussion. We also welcome ideas that fit with OBF's mission but are not part of a single Bio* project, or span multiple projects -- these ideas can be posted on the OBF wiki and discussed on the OBF mailing list: http://www.open-bio.org/wiki/Google_Summer_of_Code#Project_ideas http://lists.open-bio.org/mailman/listinfo/open-bio-l Here's to another fun and productive Summer of Code! Cheers, Eric & Raoul From helton.a at gmail.com Thu Feb 6 21:49:27 2014 From: helton.a at gmail.com (Helton Azevedo) Date: Thu, 6 Feb 2014 19:49:27 -0200 Subject: [BioSQL-l] Loanding data sequence by genre Message-ID: Hello Guys, I am working on a project that integrates data and tools to use the techniques of Multilocus Sequence Analysisfor dealing with the taxonomy of bacteria, and our structure database was assembled using the fantastic scheme BioSQL project. We managed to make the loading of the taxonomy to the bank, but now we need to do the loading sequences of some bacterial genera at first would be only two: Bradyrhizobium and Rhizobium. We are using MySQL Someone already tried to create a script that works that way, collecting sequences by "genre". Could share with us? Thank you very much, Helton -- Helton de Azevedo 43 9997-3605 From helton.a at gmail.com Thu Feb 13 20:48:46 2014 From: helton.a at gmail.com (Helton Azevedo) Date: Thu, 13 Feb 2014 18:48:46 -0200 Subject: [BioSQL-l] Where the "gene" field is imported to into the SQL schema? Message-ID: I've looked through the documentation, but I am unable to determine where the "gene" field is imported to into the SQL schema? There is a table where the gene and stored? -- Helton de Azevedo 43 9997-3605 From p.j.a.cock at googlemail.com Thu Feb 13 21:20:16 2014 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 13 Feb 2014 21:20:16 +0000 Subject: [BioSQL-l] Where the "gene" field is imported to into the SQL schema? In-Reply-To: References: Message-ID: On Thursday, February 13, 2014, Helton Azevedo wrote: > I've looked through the documentation, but I am unable to determine where > the "gene" field is imported to into the SQL schema? > > There is a table where the gene and stored? > > There isn't a single gene field - perhaps an example you help. Are you starting from an EMBL or GenBank file? Peter From helton.a at gmail.com Thu Feb 13 21:48:56 2014 From: helton.a at gmail.com (Helton Azevedo) Date: Thu, 13 Feb 2014 19:48:56 -0200 Subject: [BioSQL-l] Where the "gene" field is imported to into the SQL schema? In-Reply-To: References: Message-ID: Hi Peter, Thanks.. I use GenBank file. On Thu, Feb 13, 2014 at 7:20 PM, Peter Cock wrote: > > > On Thursday, February 13, 2014, Helton Azevedo wrote: > >> I've looked through the documentation, but I am unable to determine where >> the "gene" field is imported to into the SQL schema? >> >> There is a table where the gene and stored? >> >> > There isn't a single gene field - perhaps an example you help. Are you > starting from an EMBL or GenBank file? > > Peter > > -- Helton de Azevedo 43 9997-3605 From p.j.a.cock at googlemail.com Thu Feb 13 21:58:17 2014 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 13 Feb 2014 21:58:17 +0000 Subject: [BioSQL-l] Where the "gene" field is imported to into the SQL schema? In-Reply-To: References: Message-ID: On Thursday, February 13, 2014, Helton Azevedo wrote: > Hi Peter, > Thanks.. > > I use GenBank file. > > OK. Each gene or CDS or tRNA etc is a feature, with a type (e.g. gene or CDS), location, and assorted key:value annotation pairs. Each bit if that goes in a different table or set of tables. Peter