From hurwitz at cshl.edu Tue Jan 4 12:01:36 2005 From: hurwitz at cshl.edu (Bonnie Hurwitz) Date: Fri Jan 7 09:37:30 2005 Subject: [BioSQL-l] FPC maps in the marker database Message-ID: <4B3607B6-5E72-11D9-8C81-000D9344D428@cshl.edu> Hi, I was just wondering if anyone is using the markerdb portion of BioSQL to store FPC maps? If so, are there any useful load scripts available? I also noticed that BioPerl 1.5 will have parsers for FPC data, is this going to be connected in with BioSQL and the marker database? Thanks, Bonnie From hlapp at gnf.org Fri Jan 7 13:07:00 2005 From: hlapp at gnf.org (Hilmar Lapp) Date: Fri Jan 7 13:04:10 2005 Subject: [BioSQL-l] FPC maps in the marker database In-Reply-To: <4B3607B6-5E72-11D9-8C81-000D9344D428@cshl.edu> References: <4B3607B6-5E72-11D9-8C81-000D9344D428@cshl.edu> Message-ID: The markerdb part of biosql was retired 2 years ago ... I don't know whether Jason (the author of that part) has had any other plans in this direction. -hilmar On Jan 4, 2005, at 9:01 AM, Bonnie Hurwitz wrote: > Hi, > > I was just wondering if anyone is using the markerdb portion of BioSQL > to store FPC maps? If so, are there any useful load scripts > available? I also noticed that BioPerl 1.5 will have parsers for FPC > data, is this going to be connected in with BioSQL and the marker > database? > > Thanks, > Bonnie > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From mark.schreiber at group.novartis.com Fri Jan 14 04:10:32 2005 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Fri Jan 14 04:08:38 2005 Subject: [BioSQL-l] Consistency between bio* projects Message-ID: Hello all - I've begun using BioSQL for a project we have here and have noticed a consistency problem with the way that BioJava and BioPerl persist objects. Basically I want to know if there is some contract for how certain common formats should be stored in the DB? If not then there really needs to be for the reasons outlined below. For example I'm developing an object that keeps my DB in sync with a small subset of GenBank (Dengue Virus sequences). To do this the object gets GenBank GI's for dengue virus and compares them with the DB to see if any new ones need adding. Unfortunately, Bioperl stores identifiers as follows: Bioentry.bioentry_id is the unique internal reference number Bioentry.name is the GI number Bioentry.accession is the accession Bioentry.biodatabase_id refers to Biodatabase, from which (if you set this correctly whilst loading the sequence) you can check to see which database the sequence came from (eg. GenBank), so that you know it really is a GI number. BioJava is the same except that Bioentry.name is the Accession as is Bioentry.accession, BioJava (oddly) stores GIs as Annotations. Arguably BioPerl's system is better but it's all meaningless if the two don't agree. What if I use bioperl to load some sequences and later change to biojava. Suddenly my first set of records has GIs in different places from my second. >From memory the basic idea of BioSQL was to define a schema that bio* projects could both read and write from in a language independant manner. For reasons best left to the designers (mostly I think cause MySQL couldn't handle stored proceedures) the level of interaction is right down at the schema level. Unfortunaltey this means that the way data is stored needs to be very consistent between projects if any API's that use BioSQL can be portable. My biojava API cannot be applied to a DB previously setup with bioperl which was the original idea behind BioSQL in the first place. Help!! Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 From hlapp at gnf.org Fri Jan 14 12:58:15 2005 From: hlapp at gnf.org (Hilmar Lapp) Date: Fri Jan 14 12:54:53 2005 Subject: [BioSQL-l] Consistency between bio* projects In-Reply-To: Message-ID: On Friday, January 14, 2005, at 01:10 AM, mark.schreiber@group.novartis.com wrote: > Unfortunately, Bioperl stores identifiers as > follows: > > Bioentry.bioentry_id is the unique internal reference number > Bioentry.name is the GI number The GI number goes to Bioentry.Identifier, which is was designated the purpose of storing the identifier within an external database. Bioentry.name should hold the locus name, which for contigs and many other entries etc will be identical to the accession (but not the GI number!). If you find it in Bioentry.name then I suspect you weren't loading from genbank or embl formatted input? From memory the basic idea of BioSQL was to define a schema that bio* > projects could both read and write from in a language independant > manner. > For reasons best left to the designers (mostly I think cause MySQL > couldn't handle stored proceedures) the level of interaction is right > down > at the schema level. Right. Also, not all database drivers in all languages support stored procedure calls equally well. In e.g. PostgreSQL and Oracle you can always get around this by writing a view and putting an INSTEAD OF INSERT (or UPDATE) trigger on it that will then call the procedure, but this is clearly not even close to an option in MySQL. It's maybe worth considering whether opening a dichotomy here between MySQL and the rest to provide people who need it with a SQL-level API that both perl and java will use. People who are interested in this by definition will not be interested in MySQL anyway. > Unfortunaltey this means that the way data is stored > needs to be very consistent between projects if any API's that use > BioSQL > can be portable. My biojava API cannot be applied to a DB previously > setup > with bioperl which was the original idea behind BioSQL in the first > place. > > Help!! I think you're raising a great point. Indeed, such a contract hasn't really been written. We're probably one of few who use both perl and java to access a biosql database (and I'm not using biojava as the object model on the java side, which is why I'm not running into this problem). (Note as an aside that you could also write adaptors that transform between the SymGene and the Biojava model when storing or retrieving objects from/to the database.) It'd be great if you were willing to take the lead for getting this all spelled out and laid down in a document? -hilmar -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From jason at cgt.duhs.duke.edu Thu Jan 13 22:01:05 2005 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Sat Jan 15 10:16:22 2005 Subject: [BioSQL-l] FPC maps in the marker database In-Reply-To: References: <4B3607B6-5E72-11D9-8C81-000D9344D428@cshl.edu> Message-ID: <87F1959C-65D8-11D9-A1F6-000393C44276@cgt.duhs.duke.edu> I don't think there is much one way or another anymore. I stopped work on those modules quite a long time ago. I had some hope that Ken's CMAP stuff would be able to generally handle lots of different map types but it would need someone to dedicate a fair amount of time to get the FPC stuff working. You also might have more luck talking to the FPC module authors about their ideas as they probably store stuff in DBs there. If there is a logical mapping of the FPC stuff into the BioSQL system I'm all for it, but as of now the map stuff it is pretty much just remnants. I also expect the chado guys to integrate some sort of map stuff into their models as well since there is a lot of genetic map data in most of the model system dbs but I don't know anything about their plans. Maybe would be good if you can talk a little more about the type of functionality you really wanted with the DB and that might stir up some more memories of what it would take to get it in the system. -jason On Jan 7, 2005, at 1:07 PM, Hilmar Lapp wrote: > The markerdb part of biosql was retired 2 years ago ... I don't know > whether Jason (the author of that part) has had any other plans in > this direction. > > -hilmar > > On Jan 4, 2005, at 9:01 AM, Bonnie Hurwitz wrote: > >> Hi, >> >> I was just wondering if anyone is using the markerdb portion of >> BioSQL to store FPC maps? If so, are there any useful load scripts >> available? I also noticed that BioPerl 1.5 will have parsers for FPC >> data, is this going to be connected in with BioSQL and the marker >> database? >> >> Thanks, >> Bonnie >> >> _______________________________________________ >> BioSQL-l mailing list >> BioSQL-l@open-bio.org >> http://open-bio.org/mailman/listinfo/biosql-l >> > -- > ------------------------------------------------------------- > Hilmar Lapp email: lapp at gnf.org > GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 > ------------------------------------------------------------- > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > > -- Jason Stajich Duke University jason at cgt.duhs.duke.edu From mark.schreiber at group.novartis.com Sun Jan 16 21:41:15 2005 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Sun Jan 16 21:37:38 2005 Subject: [BioSQL-l] Consistency between bio* projects Message-ID: It would seem that what is needed is a mapping of each field from a file format to a field in a BioSQL table. I think initially this would only need to be done for EMBL, SwissProt and GenBank. In many ways I prefer the idea of developing a SQL API which would be more robust and would serve to define what is expected of each proceedure call. However I think it should be achievable for the schema. In fact there is no reason why both cannot co-exist. For any API there should be a possbile implementation so naturally the schema could be used to generate an API. People could then happilly make other schemata that fit the API which may be optimised for their needs. Does anyone have a recent UML or similar diagram for the schema? I can then use this to suggest mappings from GenBank fields to the API. I think it may be easier in many cases to follow bioperl's lead. BioJava seems to follow the 'store everything that isn't a feature as a bioentry_qualifier' approach so I just need to add some special cases. Hilmar, would you be prepared to do any work on the BioPerl side for synchronization of the two? - Mark Hilmar Lapp 01/15/2005 01:58 AM To: Mark Schreiber/GP/Novartis@PH cc: biosql-l@open-bio.org Subject: Re: [BioSQL-l] Consistency between bio* projects On Friday, January 14, 2005, at 01:10 AM, mark.schreiber@group.novartis.com wrote: > Unfortunately, Bioperl stores identifiers as > follows: > > Bioentry.bioentry_id is the unique internal reference number > Bioentry.name is the GI number The GI number goes to Bioentry.Identifier, which is was designated the purpose of storing the identifier within an external database. Bioentry.name should hold the locus name, which for contigs and many other entries etc will be identical to the accession (but not the GI number!). If you find it in Bioentry.name then I suspect you weren't loading from genbank or embl formatted input? From memory the basic idea of BioSQL was to define a schema that bio* > projects could both read and write from in a language independant > manner. > For reasons best left to the designers (mostly I think cause MySQL > couldn't handle stored proceedures) the level of interaction is right > down > at the schema level. Right. Also, not all database drivers in all languages support stored procedure calls equally well. In e.g. PostgreSQL and Oracle you can always get around this by writing a view and putting an INSTEAD OF INSERT (or UPDATE) trigger on it that will then call the procedure, but this is clearly not even close to an option in MySQL. It's maybe worth considering whether opening a dichotomy here between MySQL and the rest to provide people who need it with a SQL-level API that both perl and java will use. People who are interested in this by definition will not be interested in MySQL anyway. > Unfortunaltey this means that the way data is stored > needs to be very consistent between projects if any API's that use > BioSQL > can be portable. My biojava API cannot be applied to a DB previously > setup > with bioperl which was the original idea behind BioSQL in the first > place. > > Help!! I think you're raising a great point. Indeed, such a contract hasn't really been written. We're probably one of few who use both perl and java to access a biosql database (and I'm not using biojava as the object model on the java side, which is why I'm not running into this problem). (Note as an aside that you could also write adaptors that transform between the SymGene and the Biojava model when storing or retrieving objects from/to the database.) It'd be great if you were willing to take the lead for getting this all spelled out and laid down in a document? -hilmar -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From hlapp at gnf.org Mon Jan 17 15:00:22 2005 From: hlapp at gnf.org (Hilmar Lapp) Date: Mon Jan 17 14:56:47 2005 Subject: [BioSQL-l] Consistency between bio* projects In-Reply-To: References: Message-ID: <6BE9F628-68C2-11D9-860A-000A95AE92B0@gnf.org> On Jan 16, 2005, at 6:41 PM, mark.schreiber@group.novartis.com wrote: > It would seem that what is needed is a mapping of each field from a > file > format to a field in a BioSQL table. I think initially this would only > need to be done for EMBL, SwissProt and GenBank. Note that this has at least been started for bioperl in the extent that the destination in the bioperl object model is documented. (Jason, Brian, anything you wanted to comment?) Once you know where it is in the bioperl object model, it is relatively straight forward to predict where it ends up in the schema; still it's not written down in plain text anywhere I think. > In many ways I prefer the idea of developing a SQL API which would be > more > robust and would serve to define what is expected of each proceedure > call. > However I think it should be achievable for the schema. In fact there > is > no reason why both cannot co-exist. For any API there should be a > possbile > implementation so naturally the schema could be used to generate an > API. > People could then happilly make other schemata that fit the API which > may > be optimised for their needs. Right - I guess so far my idea was that the object model is the API, and the OR mapper implements the bridge to your chosen schema. Clearly, the problem with this level of API is that it's not cross-bio* by definition since we don't use the exact same object model. > > Does anyone have a recent UML or similar diagram for the schema? There is a ERD in the doc directory. Other than that, there is no UML model. > I can then use this to suggest mappings from GenBank fields to the > API. I think > it may be easier in many cases to follow bioperl's lead. BioJava seems > to > follow the 'store everything that isn't a feature as a > bioentry_qualifier' > approach so I just need to add some special cases. > > Hilmar, would you be prepared to do any work on the BioPerl side for > synchronization of the two? Certainly, if it is really needed. Generally speaking, I would not want to introduce object model and genbank-to-object model mapping changes to bioperl if they openly break backward compatibility unless everybody agrees to go forward. It's also not necessarily needed; the OR mapping code (bioperl-db) may be the better place, depending on scope and what's involved. -hilmar > > - Mark > > > > > > Hilmar Lapp > 01/15/2005 01:58 AM > > > To: Mark Schreiber/GP/Novartis@PH > cc: biosql-l@open-bio.org > Subject: Re: [BioSQL-l] Consistency between bio* > projects > > > > On Friday, January 14, 2005, at 01:10 AM, > mark.schreiber@group.novartis.com wrote: >> Unfortunately, Bioperl stores identifiers as >> follows: >> >> Bioentry.bioentry_id is the unique internal reference number >> Bioentry.name is the GI number > > The GI number goes to Bioentry.Identifier, which is was designated the > purpose of storing the identifier within an external database. > > Bioentry.name should hold the locus name, which for contigs and many > other entries etc will be identical to the accession (but not the GI > number!). > > If you find it in Bioentry.name then I suspect you weren't loading from > genbank or embl formatted input? > > From memory the basic idea of BioSQL was to define a schema that bio* >> projects could both read and write from in a language independant >> manner. >> For reasons best left to the designers (mostly I think cause MySQL >> couldn't handle stored proceedures) the level of interaction is right >> down >> at the schema level. > > Right. Also, not all database drivers in all languages support stored > procedure calls equally well. In e.g. PostgreSQL and Oracle you can > always get around this by writing a view and putting an INSTEAD OF > INSERT (or UPDATE) trigger on it that will then call the procedure, but > this is clearly not even close to an option in MySQL. > > It's maybe worth considering whether opening a dichotomy here between > MySQL and the rest to provide people who need it with a SQL-level API > that both perl and java will use. People who are interested in this by > definition will not be interested in MySQL anyway. > >> Unfortunaltey this means that the way data is stored >> needs to be very consistent between projects if any API's that use >> BioSQL >> can be portable. My biojava API cannot be applied to a DB previously >> setup >> with bioperl which was the original idea behind BioSQL in the first >> place. >> >> Help!! > > I think you're raising a great point. Indeed, such a contract hasn't > really been written. We're probably one of few who use both perl and > java to access a biosql database (and I'm not using biojava as the > object model on the java side, which is why I'm not running into this > problem). (Note as an aside that you could also write adaptors that > transform between the SymGene and the Biojava model when storing or > retrieving objects from/to the database.) > > It'd be great if you were willing to take the lead for getting this all > spelled out and laid down in a document? > > -hilmar > -- > ------------------------------------------------------------- > Hilmar Lapp email: lapp at gnf.org > GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 > ------------------------------------------------------------- > > > > > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From awagner at nimblegen.com Tue Jan 18 11:55:58 2005 From: awagner at nimblegen.com (Andrew Wagner) Date: Tue Jan 18 11:56:56 2005 Subject: [BioSQL-l] Copy of script for simplified biosql Oracle Message-ID: <41ED3F9E.7050302@nimblegen.com> Skipped content of type multipart/alternative-------------- next part -------------- A non-text attachment was scrubbed... Name: awagner.vcf Type: text/x-vcard Size: 173 bytes Desc: not available Url : http://open-bio.org/pipermail/biosql-l/attachments/20050118/4d467296/awagner.vcf From hlapp at gnf.org Tue Jan 18 13:10:02 2005 From: hlapp at gnf.org (Hilmar Lapp) Date: Tue Jan 18 13:07:32 2005 Subject: [BioSQL-l] Copy of script for simplified biosql Oracle In-Reply-To: <41ED3F9E.7050302@nimblegen.com> References: <41ED3F9E.7050302@nimblegen.com> Message-ID: <2C7CD45E-697C-11D9-A4D3-000A95AE92B0@gnf.org> If there is anything special about this script then I believe it should be in the repository. I'm not exactly sure what 'simplified' encompasses here; the biosql schema and API does sit entirely in a single user account by default. The biosql standard names are not exported as public synonyms by default, but first, if you're going to access the database through the schema owner, this doesn't concern you anyway, and second, there's a script that generates a script with which to establish the synonyms for any user, and third, it is trivial to modify this script such that the created synonyms are public instead of private. Did you hit a specific error or problem? -hilmar On Jan 18, 2005, at 8:55 AM, Andrew Wagner wrote: > > I am looking for a copy of the script for simplified biosql in oracle. > > Thanks, > > Andrew > > *Simplifed*: by Len Trigg, this version is simplified in structure and > sits entirely inside a single user account, requiring no sysdba access > to install. You'll have to ask for a copy of the script from the > biosql-l mailing > lists. > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From hlapp at gnf.org Tue Jan 18 14:44:00 2005 From: hlapp at gnf.org (Hilmar Lapp) Date: Tue Jan 18 14:40:11 2005 Subject: [BioSQL-l] Copy of script for simplified biosql Oracle In-Reply-To: <41ED5625.6030707@nimblegen.com> Message-ID: <4CE746EE-6989-11D9-966A-000A959EB4C4@gnf.org> Whether or not you need sysdba access depends largely on whether you have a DBA that would do those things you can't normally do yourself, or grant you permissions that by default Oracle doesn't give to every user. Take a look at the BS-create-all.sql script, and make sure only those steps are commented in that you really want to be executed. E.g., if you don't care to create users or your DBA does that then leave out that step. Similarly for roles. There is also a part that creates public synonyms for views and by default Oracle doesn't grant this permission to a user, so if you want that you'll either need sysdba access or a DBA who grants the permission to you ('you' standing for the schema owner). However, if all you intend to use this for is Biojava then the views published as public synonyms (SG_%) aren't even going to be used and so you can do without that step. You can easily add that later if at some point you decide to access the schema through other levels as well. This holds as well for the PL/SQL API; Biojava will neither need nor use it. In other words, for Biojava or Bioperl alone basically what you need is BS-DDL.sql and then decide on one of the two Biosql APIs. Biojava needs the view-based API, Bioperl needs (at this point) the synonym-based. Let me know if you hit a problem or if you're unsure how to proceed. Your endeavor is a good test for the release. -hilmar On Tuesday, January 18, 2005, at 10:32 AM, Andrew Wagner wrote: > No error or problems... I did not attempt the Original script.... just > reading > http://www.biojava.org/docs/bj_in_anger/bj_and_bsql_oracle_howto.htm > > "You'll need the latest version of BioJava to take advantage of the > full functionality of BioSQL. This can be downloaded from biojava.org. > You'll also need the latest Oracle BioSQL schema. Here you have a > choice of two options: > > ? Original: by Hilmar Lapp, the original BioSQL schema takes full > advantage of Oracle's security mechanisms and produces a complex but > high quality schema. You'll need sysdba access to your database to > install it. Go to cvs.open-bio.org, select the biosql project, and > navigate to and download the entire biosql-schema/sql/biosql-ora > folder. > ? Simplifed: by Len Trigg, this version is simplified in structure > and sits entirely inside a single user account, requiring no sysdba > access to install. You'll have to ask for a copy of the script from > the biosql-l mailing lists." > > I thought Simplified was the place to start but I cna easily start > with the Original if that's what you reccomend. > > Andrew > > > > Hilmar Lapp wrote: > > If there is anything special about this script then I believe it > should be in the repository. I'm not exactly sure what 'simplified' > encompasses here; the biosql schema and API does sit entirely in a > single user account by default. The biosql standard names are not > exported as public synonyms by default, but first, if you're going to > access the database through the schema owner, this doesn't concern you > anyway, and second, there's a script that generates a script with > which to establish the synonyms for any user, and third, it is trivial > to modify this script such that the created synonyms are public > instead of private. > > Did you hit a specific error or problem? > > ????-hilmar > > On Jan 18, 2005, at 8:55 AM, Andrew Wagner wrote: > > > I? am looking for a copy of the script for simplified biosql in oracle. > > Thanks, > > Andrew > > *Simplifed*: by Len Trigg, this version is simplified in structure and > sits entirely inside a single user account, requiring no sysdba access > to install. You'll have to ask for a copy of the script from the > biosql-l mailing > lists. > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From hlapp at gnf.org Tue Jan 18 18:14:59 2005 From: hlapp at gnf.org (Hilmar Lapp) Date: Tue Jan 18 18:12:01 2005 Subject: [BioSQL-l] Re: BIoJava ffor Mysql In-Reply-To: <41ED966B.4040801@nimblegen.com> References: <4CE746EE-6989-11D9-966A-000A959EB4C4@gnf.org> <41ED966B.4040801@nimblegen.com> Message-ID: I'm afraid the schema is not too old but too new ... hard to tell what was expected but not found if the original (root cause) exception with the SQL exception and the statement that caused it is not shown. Mark/Mat/Thomas, any idea what this may be caused by? -hilmar (Andrew, please do copy the mailing list - possibly also biojava-l - for such questions; that way it reaches way more people who can provide clues and look at the problem.) On Jan 18, 2005, at 3:06 PM, Andrew Wagner wrote: > A related question if you would be so kind to answer it.... > > Using version 1.40 of biosqldb-mysql.sql I created a MySql Database > > -- $Id: biosqldb-mysql.sql,v 1.40 2004/11/04 01:49:41 lapp Exp $ > > -- conventions: > -- _id is primary internal id (usually autogenerated) > > -- Authors: Ewan Birney, Elia Stupka, Hilmar Lapp, Aaron Mackey > -- > -- Copyright Ewan Birney. You may use, modify, and distribute this > code under > -- the same terms as Perl. See the Perl Artistic License. > -- > -- comments to biosql - biosql-l@open-bio.org > -- > -- Migration of the MySQL schema to InnoDB by Hilmar Lapp gmx.net> > -- Post-Cape Town changes by Hilmar Lapp. > -- Singapore changes by Hilmar Lapp and Aaron Mackey. > -- post-Singapore changes by Hilmar Lapp. > -- > > > I then attempted to access it with biojava-1.3.1 and even though > the comments in version 1.40 of biosqldb-mysql.sql say it is Post-Cape > Town, > I get the following exception calling: > BioSQLSequenceDB db1 = new BioSQLSequenceDB(dbURL, > dbUser, > dbPass, > biodatabase, > createIfMissing); > > org.biojava.bio.BioException: This database appears to be an old > (pre-Cape-Town) BioSQL. If you need to access it, try an older > BioJava snapshot > at > org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.(BioSQLSequenceDB. > java:100) > at TreeFrame.main(TreeFrame.java:87) > Exception in thread "main" > > > Thanks, > > Andrew > > > Hilmar Lapp wrote: > > Whether or not you need sysdba access depends largely on whether you > have a DBA that would do those things you can't normally do yourself, > or grant you permissions that by default Oracle doesn't give to every > user. > > Take a look at the BS-create-all.sql script, and make sure only those > steps are commented in that you really want to be executed. E.g., if > you don't care to create users or your DBA does that then leave out > that step. Similarly for roles. There is also a part that creates > public synonyms for views and by default Oracle doesn't grant this > permission to a user, so if you want that you'll either need sysdba > access or a DBA who grants the permission to you ('you' standing for > the schema owner). However, if all you intend to use this for is > Biojava then the views published as public synonyms (SG_%) aren't even > going to be used and so you can do without that step. You can easily > add that later if at some point you decide to access the schema > through other levels as well. This holds as well for the PL/SQL API; > Biojava will neither need nor use it. > > In other words, for Biojava or Bioperl alone basically what you need > is BS-DDL.sql and then decide on one of the two Biosql APIs. Biojava > needs the view-based API, Bioperl needs (at this point) the > synonym-based. > > Let me know if you hit a problem or if you're unsure how to proceed. > Your endeavor is a good test for the release. > > ????-hilmar > > On Tuesday, January 18, 2005, at 10:32? AM, Andrew Wagner wrote: > > > No error or problems... I did not attempt the Original script.... > just reading > http://www.biojava.org/docs/bj_in_anger/bj_and_bsql_oracle_howto.htm > > "You'll need the latest version of BioJava to take advantage of the > full functionality of BioSQL. This can be downloaded from biojava.org. > You'll also need the latest Oracle BioSQL schema. Here you have a > choice of two options: > > ????? Original: by Hilmar Lapp, the original BioSQL schema takes full > advantage of Oracle's security mechanisms and produces a complex but > high quality schema. You'll need sysdba access to your database to > install it. Go to cvs.open-bio.org, select the biosql project, and > navigate to and download the entire biosql-schema/sql/biosql-ora > folder. > ????? Simplifed: by Len Trigg, this version is simplified in > structure and sits entirely inside a single user account, requiring no > sysdba access to install. You'll have to ask for a copy of the script > from the biosql-l mailing lists." > > I thought Simplified was the place to start but I cna easily start > with the Original if that's what you reccomend. > > Andrew > > > > Hilmar Lapp wrote: > > If there is anything special about this script then I believe it > should be in the repository. I'm not exactly sure what 'simplified' > encompasses here; the biosql schema and API does sit entirely in a > single user account by default. The biosql standard names are not > exported as public synonyms by default, but first, if you're going to > access the database through the schema owner, this doesn't concern you > anyway, and second, there's a script that generates a script with > which to establish the synonyms for any user, and third, it is trivial > to modify this script such that the created synonyms are public > instead of private. > > Did you hit a specific error or problem? > > ????-hilmar > > On Jan 18, 2005, at 8:55 AM, Andrew Wagner wrote: > > > I? am looking for a copy of the script for simplified biosql in > oracle. > > Thanks, > > Andrew > > *Simplifed*: by Len Trigg, this version is simplified in structure > and sits entirely inside a single user account, requiring no sysdba > access to install. You'll have to ask for a copy of the script from > the biosql-l > mailing lists. > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > > > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From mark.schreiber at group.novartis.com Tue Jan 18 19:36:02 2005 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Tue Jan 18 19:32:20 2005 Subject: [BioSQL-l] Copy of script for simplified biosql Oracle Message-ID: Hi - The main difference is that the 'official' version has lots of different users with different privileges and views that make the oracle schema look like the BioSQL schema, it's pretty much a by-the-book how-you-should-do-it implementation. The 'simplified' version has only one user and I think has no views. It is much easier for Oracle or DB novices to understand but may not be well suited to a production or mutli-user environment. In some limited testing it can be a little faster but that probably has more to do with your computer and how Oracle has been set up. I'll feret around to get it and post it to the list. Richard, do you have a copy? - Mark Hilmar Lapp Sent by: biosql-l-bounces@portal.open-bio.org 01/19/2005 03:44 AM To: Andrew Wagner cc: Biosql , (bcc: Mark Schreiber/GP/Novartis) Subject: Re: [BioSQL-l] Copy of script for simplified biosql Oracle Whether or not you need sysdba access depends largely on whether you have a DBA that would do those things you can't normally do yourself, or grant you permissions that by default Oracle doesn't give to every user. Take a look at the BS-create-all.sql script, and make sure only those steps are commented in that you really want to be executed. E.g., if you don't care to create users or your DBA does that then leave out that step. Similarly for roles. There is also a part that creates public synonyms for views and by default Oracle doesn't grant this permission to a user, so if you want that you'll either need sysdba access or a DBA who grants the permission to you ('you' standing for the schema owner). However, if all you intend to use this for is Biojava then the views published as public synonyms (SG_%) aren't even going to be used and so you can do without that step. You can easily add that later if at some point you decide to access the schema through other levels as well. This holds as well for the PL/SQL API; Biojava will neither need nor use it. In other words, for Biojava or Bioperl alone basically what you need is BS-DDL.sql and then decide on one of the two Biosql APIs. Biojava needs the view-based API, Bioperl needs (at this point) the synonym-based. Let me know if you hit a problem or if you're unsure how to proceed. Your endeavor is a good test for the release. -hilmar On Tuesday, January 18, 2005, at 10:32 AM, Andrew Wagner wrote: > No error or problems... I did not attempt the Original script.... just > reading > http://www.biojava.org/docs/bj_in_anger/bj_and_bsql_oracle_howto.htm > > "You'll need the latest version of BioJava to take advantage of the > full functionality of BioSQL. This can be downloaded from biojava.org. > You'll also need the latest Oracle BioSQL schema. Here you have a > choice of two options: > > ? Original: by Hilmar Lapp, the original BioSQL schema takes full > advantage of Oracle's security mechanisms and produces a complex but > high quality schema. You'll need sysdba access to your database to > install it. Go to cvs.open-bio.org, select the biosql project, and > navigate to and download the entire biosql-schema/sql/biosql-ora > folder. > ? Simplifed: by Len Trigg, this version is simplified in structure > and sits entirely inside a single user account, requiring no sysdba > access to install. You'll have to ask for a copy of the script from > the biosql-l mailing lists." > > I thought Simplified was the place to start but I cna easily start > with the Original if that's what you reccomend. > > Andrew > > > > Hilmar Lapp wrote: > > If there is anything special about this script then I believe it > should be in the repository. I'm not exactly sure what 'simplified' > encompasses here; the biosql schema and API does sit entirely in a > single user account by default. The biosql standard names are not > exported as public synonyms by default, but first, if you're going to > access the database through the schema owner, this doesn't concern you > anyway, and second, there's a script that generates a script with > which to establish the synonyms for any user, and third, it is trivial > to modify this script such that the created synonyms are public > instead of private. > > Did you hit a specific error or problem? > > ????-hilmar > > On Jan 18, 2005, at 8:55 AM, Andrew Wagner wrote: > > > I? am looking for a copy of the script for simplified biosql in oracle. > > Thanks, > > Andrew > > *Simplifed*: by Len Trigg, this version is simplified in structure and > sits entirely inside a single user account, requiring no sysdba access > to install. You'll have to ask for a copy of the script from the > biosql-l mailing > lists. > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- _______________________________________________ BioSQL-l mailing list BioSQL-l@open-bio.org http://open-bio.org/mailman/listinfo/biosql-l From mark.schreiber at group.novartis.com Tue Jan 18 19:44:09 2005 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Tue Jan 18 19:40:26 2005 Subject: [BioSQL-l] Re: BIoJava ffor Mysql Message-ID: My immediate thinking is that your version of BioJava is too old. The BioSQL stuff is still a work in progress. Take heart that there are actually some people actively working on it know. I think it lay dormant for about a year but is now getting some stress testing. I would suggest getting a very recent version of BioJava. Preferably from CVS as there have been a few bug fixes in the last few months. Unfotunately I'm not working with MySQL so I may not be able to help with specific errors caused by the MySQL helpers. Hope this helps. - Mark Hilmar Lapp 01/19/2005 07:14 AM To: Andrew Wagner cc: Len Trigg , Mark Schreiber/GP/Novartis@PH, Matthew Pocock , Biosql , Thomas Down Subject: Re: BIoJava ffor Mysql I'm afraid the schema is not too old but too new ... hard to tell what was expected but not found if the original (root cause) exception with the SQL exception and the statement that caused it is not shown. Mark/Mat/Thomas, any idea what this may be caused by? -hilmar (Andrew, please do copy the mailing list - possibly also biojava-l - for such questions; that way it reaches way more people who can provide clues and look at the problem.) On Jan 18, 2005, at 3:06 PM, Andrew Wagner wrote: > A related question if you would be so kind to answer it.... > > Using version 1.40 of biosqldb-mysql.sql I created a MySql Database > > -- $Id: biosqldb-mysql.sql,v 1.40 2004/11/04 01:49:41 lapp Exp $ > > -- conventions: > -- _id is primary internal id (usually autogenerated) > > -- Authors: Ewan Birney, Elia Stupka, Hilmar Lapp, Aaron Mackey > -- > -- Copyright Ewan Birney. You may use, modify, and distribute this > code under > -- the same terms as Perl. See the Perl Artistic License. > -- > -- comments to biosql - biosql-l@open-bio.org > -- > -- Migration of the MySQL schema to InnoDB by Hilmar Lapp gmx.net> > -- Post-Cape Town changes by Hilmar Lapp. > -- Singapore changes by Hilmar Lapp and Aaron Mackey. > -- post-Singapore changes by Hilmar Lapp. > -- > > > I then attempted to access it with biojava-1.3.1 and even though > the comments in version 1.40 of biosqldb-mysql.sql say it is Post-Cape > Town, > I get the following exception calling: > BioSQLSequenceDB db1 = new BioSQLSequenceDB(dbURL, > dbUser, > dbPass, > biodatabase, > createIfMissing); > > org.biojava.bio.BioException: This database appears to be an old > (pre-Cape-Town) BioSQL. If you need to access it, try an older > BioJava snapshot > at > org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.(BioSQLSequenceDB. > java:100) > at TreeFrame.main(TreeFrame.java:87) > Exception in thread "main" > > > Thanks, > > Andrew > > > Hilmar Lapp wrote: > > Whether or not you need sysdba access depends largely on whether you > have a DBA that would do those things you can't normally do yourself, > or grant you permissions that by default Oracle doesn't give to every > user. > > Take a look at the BS-create-all.sql script, and make sure only those > steps are commented in that you really want to be executed. E.g., if > you don't care to create users or your DBA does that then leave out > that step. Similarly for roles. There is also a part that creates > public synonyms for views and by default Oracle doesn't grant this > permission to a user, so if you want that you'll either need sysdba > access or a DBA who grants the permission to you ('you' standing for > the schema owner). However, if all you intend to use this for is > Biojava then the views published as public synonyms (SG_%) aren't even > going to be used and so you can do without that step. You can easily > add that later if at some point you decide to access the schema > through other levels as well. This holds as well for the PL/SQL API; > Biojava will neither need nor use it. > > In other words, for Biojava or Bioperl alone basically what you need > is BS-DDL.sql and then decide on one of the two Biosql APIs. Biojava > needs the view-based API, Bioperl needs (at this point) the > synonym-based. > > Let me know if you hit a problem or if you're unsure how to proceed. > Your endeavor is a good test for the release. > > ????-hilmar > > On Tuesday, January 18, 2005, at 10:32? AM, Andrew Wagner wrote: > > > No error or problems... I did not attempt the Original script.... > just reading > http://www.biojava.org/docs/bj_in_anger/bj_and_bsql_oracle_howto.htm > > "You'll need the latest version of BioJava to take advantage of the > full functionality of BioSQL. This can be downloaded from biojava.org. > You'll also need the latest Oracle BioSQL schema. Here you have a > choice of two options: > > ????? Original: by Hilmar Lapp, the original BioSQL schema takes full > advantage of Oracle's security mechanisms and produces a complex but > high quality schema. You'll need sysdba access to your database to > install it. Go to cvs.open-bio.org, select the biosql project, and > navigate to and download the entire biosql-schema/sql/biosql-ora > folder. > ????? Simplifed: by Len Trigg, this version is simplified in > structure and sits entirely inside a single user account, requiring no > sysdba access to install. You'll have to ask for a copy of the script > from the biosql-l mailing lists." > > I thought Simplified was the place to start but I cna easily start > with the Original if that's what you reccomend. > > Andrew > > > > Hilmar Lapp wrote: > > If there is anything special about this script then I believe it > should be in the repository. I'm not exactly sure what 'simplified' > encompasses here; the biosql schema and API does sit entirely in a > single user account by default. The biosql standard names are not > exported as public synonyms by default, but first, if you're going to > access the database through the schema owner, this doesn't concern you > anyway, and second, there's a script that generates a script with > which to establish the synonyms for any user, and third, it is trivial > to modify this script such that the created synonyms are public > instead of private. > > Did you hit a specific error or problem? > > ????-hilmar > > On Jan 18, 2005, at 8:55 AM, Andrew Wagner wrote: > > > I? am looking for a copy of the script for simplified biosql in > oracle. > > Thanks, > > Andrew > > *Simplifed*: by Len Trigg, this version is simplified in structure > and sits entirely inside a single user account, requiring no sysdba > access to install. You'll have to ask for a copy of the script from > the biosql-l > mailing lists. > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > > > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From hollandr at gis.a-star.edu.sg Tue Jan 18 20:09:30 2005 From: hollandr at gis.a-star.edu.sg (Richard HOLLAND) Date: Tue Jan 18 20:09:05 2005 Subject: [BioSQL-l] Copy of script for simplified biosql Oracle Message-ID: <6D9E9B9DF347EF4385F6271C64FB8D560140F171@BIONIC.biopolis.one-north.com> Mark's right about the differences between the versions. You should only use the single-user script if you are going to be keeping your dataset fairly small and really don't have DBA access to be able to set up the full version. The single-user script written by Len Trigg is not in the BioSQL repository. Hilmar, where should I put it? The copy I have here works just fine, but I had to make one or two changes to the original version. Andrew I will email the script directly to you as you can't send attachments to this mailing list. cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 --------------------------------------------- This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its content to any other person. Thank you. --------------------------------------------- > -----Original Message----- > From: mark.schreiber@group.novartis.com > [mailto:mark.schreiber@group.novartis.com] > Sent: Wednesday, January 19, 2005 8:36 AM > To: Hilmar Lapp > Cc: Andrew Wagner; Biosql; > biosql-l-bounces@portal.open-bio.org; Richard HOLLAND > Subject: Re: [BioSQL-l] Copy of script for simplified biosql Oracle > > > Hi - > > The main difference is that the 'official' version has lots > of different > users with different privileges and views that make the > oracle schema look > like the BioSQL schema, it's pretty much a by-the-book > how-you-should-do-it implementation. The 'simplified' version > has only one > user and I think has no views. It is much easier for Oracle > or DB novices > to understand but may not be well suited to a production or > mutli-user > environment. In some limited testing it can be a little > faster but that > probably has more to do with your computer and how Oracle has > been set up. > > I'll feret around to get it and post it to the list. Richard, > do you have > a copy? > > - Mark > > > > > > Hilmar Lapp > Sent by: biosql-l-bounces@portal.open-bio.org > 01/19/2005 03:44 AM > > > To: Andrew Wagner > cc: Biosql , (bcc: Mark > Schreiber/GP/Novartis) > Subject: Re: [BioSQL-l] Copy of script for > simplified biosql Oracle > > > Whether or not you need sysdba access depends largely on whether you > have a DBA that would do those things you can't normally do yourself, > or grant you permissions that by default Oracle doesn't give to every > user. > > Take a look at the BS-create-all.sql script, and make sure only those > steps are commented in that you really want to be executed. E.g., if > you don't care to create users or your DBA does that then leave out > that step. Similarly for roles. There is also a part that creates > public synonyms for views and by default Oracle doesn't grant this > permission to a user, so if you want that you'll either need sysdba > access or a DBA who grants the permission to you ('you' standing for > the schema owner). However, if all you intend to use this for is > Biojava then the views published as public synonyms (SG_%) > aren't even > going to be used and so you can do without that step. You can easily > add that later if at some point you decide to access the > schema through > other levels as well. This holds as well for the PL/SQL API; Biojava > will neither need nor use it. > > In other words, for Biojava or Bioperl alone basically what > you need is > BS-DDL.sql and then decide on one of the two Biosql APIs. > Biojava needs > the view-based API, Bioperl needs (at this point) the synonym-based. > > Let me know if you hit a problem or if you're unsure how to proceed. > Your endeavor is a good test for the release. > > -hilmar > > On Tuesday, January 18, 2005, at 10:32 AM, Andrew Wagner wrote: > > > No error or problems... I did not attempt the Original > script.... just > > reading > > http://www.biojava.org/docs/bj_in_anger/bj_and_bsql_oracle_howto.htm > > > > "You'll need the latest version of BioJava to take advantage of the > > full functionality of BioSQL. This can be downloaded from > biojava.org. > > You'll also need the latest Oracle BioSQL schema. Here you have a > > choice of two options: > > > > ? Original: by Hilmar Lapp, the original BioSQL schema > takes full > > advantage of Oracle's security mechanisms and produces a > complex but > > high quality schema. You'll need sysdba access to your database to > > install it. Go to cvs.open-bio.org, select the biosql project, and > > navigate to and download the entire biosql-schema/sql/biosql-ora > > folder. > > ? Simplifed: by Len Trigg, this version is > simplified in > structure > > and sits entirely inside a single user account, requiring no sysdba > > access to install. You'll have to ask for a copy of the script from > > the biosql-l mailing lists." > > > > I thought Simplified was the place to start but I cna easily start > > with the Original if that's what you reccomend. > > > > Andrew > > > > > > > > Hilmar Lapp wrote: > > > > If there is anything special about this script then I believe it > > should be in the repository. I'm not exactly sure what 'simplified' > > encompasses here; the biosql schema and API does sit entirely in a > > single user account by default. The biosql standard names are not > > exported as public synonyms by default, but first, if > you're going to > > access the database through the schema owner, this doesn't > concern you > > anyway, and second, there's a script that generates a script with > > which to establish the synonyms for any user, and third, it > is trivial > > to modify this script such that the created synonyms are public > > instead of private. > > > > Did you hit a specific error or problem? > > > > ????-hilmar > > > > On Jan 18, 2005, at 8:55 AM, Andrew Wagner wrote: > > > > > > I? am looking for a copy of the script for simplified > biosql in oracle. > > > > Thanks, > > > > Andrew > > > > *Simplifed*: by Len Trigg, this version is simplified in > structure and > > sits entirely inside a single user account, requiring no > sysdba access > > to install. You'll have to ask for a copy of the script from the > > biosql-l > mailing > > lists. > > > > _______________________________________________ > > BioSQL-l mailing list > > BioSQL-l@open-bio.org > > http://open-bio.org/mailman/listinfo/biosql-l > > > > > -- > ------------------------------------------------------------- > Hilmar Lapp email: lapp at gnf.org > GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 > ------------------------------------------------------------- > > > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > > > > From mark.schreiber at group.novartis.com Tue Jan 18 20:44:05 2005 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Tue Jan 18 20:40:23 2005 Subject: [BioSQL-l] namespace Message-ID: Hello - I'm doing some work on a package to manage a BioSQL db in Java called (for want of a better name, charm). The default implementation that i'm writing is backed by BioJava but the interfaces are generic enough that it doesn't need to be. Anyhow, all of this needs a namespace. I see that www.biosql.org doesn't have a website. Is this namespace reserved by open-bio?? Would I be better to use org.open-bio.obda.charm.* for my development? Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 From hlapp at gnf.org Tue Jan 18 23:34:08 2005 From: hlapp at gnf.org (Hilmar Lapp) Date: Tue Jan 18 23:30:45 2005 Subject: [BioSQL-l] namespace Message-ID: biosql.org slipped (in fact was missed to register by us) a few years ago ... very sad but true, now it's taken (squatted on). Are you talking about a domain name or a java package name? Your suggestion resembles more the latter, hence my confusion. -hilmar -----Original Message----- From: biosql-l-bounces@portal.open-bio.org on behalf of mark.schreiber@group.novartis.com Sent: Tue 1/18/2005 5:44 PM To: biosql-l@open-bio.org Cc: Subject: [BioSQL-l] namespace Hello - I'm doing some work on a package to manage a BioSQL db in Java called (for want of a better name, charm). The default implementation that i'm writing is backed by BioJava but the interfaces are generic enough that it doesn't need to be. Anyhow, all of this needs a namespace. I see that www.biosql.org doesn't have a website. Is this namespace reserved by open-bio?? Would I be better to use org.open-bio.obda.charm.* for my development? Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 _______________________________________________ BioSQL-l mailing list BioSQL-l@open-bio.org http://open-bio.org/mailman/listinfo/biosql-l From mark.schreiber at group.novartis.com Wed Jan 19 00:01:59 2005 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Tue Jan 18 23:58:10 2005 Subject: [BioSQL-l] namespace Message-ID: java package name. By convention to prevent namespace collisions it's best to name a package with a namespace that you have some control over. I'm guessing that org.open-bio.obda might be the way to go. - Mark "Hilmar Lapp" 01/19/2005 12:34 PM To: Mark Schreiber/GP/Novartis@PH, cc: Subject: RE: [BioSQL-l] namespace biosql.org slipped (in fact was missed to register by us) a few years ago ... very sad but true, now it's taken (squatted on). Are you talking about a domain name or a java package name? Your suggestion resembles more the latter, hence my confusion. -hilmar -----Original Message----- From: biosql-l-bounces@portal.open-bio.org on behalf of mark.schreiber@group.novartis.com Sent: Tue 1/18/2005 5:44 PM To: biosql-l@open-bio.org Cc: Subject: [BioSQL-l] namespace Hello - I'm doing some work on a package to manage a BioSQL db in Java called (for want of a better name, charm). The default implementation that i'm writing is backed by BioJava but the interfaces are generic enough that it doesn't need to be. Anyhow, all of this needs a namespace. I see that www.biosql.org doesn't have a website. Is this namespace reserved by open-bio?? Would I be better to use org.open-bio.obda.charm.* for my development? Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 _______________________________________________ BioSQL-l mailing list BioSQL-l@open-bio.org http://open-bio.org/mailman/listinfo/biosql-l From hlapp at gnf.org Wed Jan 19 11:35:01 2005 From: hlapp at gnf.org (Hilmar Lapp) Date: Wed Jan 19 11:31:04 2005 Subject: [BioSQL-l] namespace In-Reply-To: Message-ID: <10C53405-6A38-11D9-848A-000A959EB4C4@gnf.org> If it's tied to biosql, why not org.open-bio.biosql? Other than that, sounds good :-) On Tuesday, January 18, 2005, at 09:01 PM, mark.schreiber@group.novartis.com wrote: > java package name. By convention to prevent namespace collisions it's > best > to name a package with a namespace that you have some control over. I'm > guessing that org.open-bio.obda might be the way to go. > > - Mark > > > > > > "Hilmar Lapp" > 01/19/2005 12:34 PM > > > To: Mark Schreiber/GP/Novartis@PH, > cc: > Subject: RE: [BioSQL-l] namespace > > > biosql.org slipped (in fact was missed to register by us) a few years > ago > ... very sad but true, now it's taken (squatted on). > > Are you talking about a domain name or a java package name? Your > suggestion resembles more the latter, hence my confusion. > > -hilmar > > -----Original Message----- > From: biosql-l-bounces@portal.open-bio.org on behalf > of > mark.schreiber@group.novartis.com > Sent: Tue 1/18/2005 5:44 PM > To: biosql-l@open-bio.org > Cc: > Subject: [BioSQL-l] namespace > > > > Hello - > > I'm doing some work on a package to manage a BioSQL > db in > Java called (for > want of a better name, charm). The default > implementation > that i'm writing > is backed by BioJava but the interfaces are generic > enough that it doesn't > need to be. Anyhow, all of this needs a namespace. I > see > that > www.biosql.org doesn't have a website. Is this > namespace > reserved by > open-bio?? Would I be better to use > org.open-bio.obda.charm.* for my > development? > > Mark Schreiber > Principal Scientist (Bioinformatics) > > Novartis Institute for Tropical Diseases (NITD) > 10 Biopolis Road > #05-01 Chromos > Singapore 138670 > www.nitd.novartis.com > > phone +65 6722 2973 > fax +65 6722 2910 > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > > > > > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From jason at cgt.duhs.duke.edu Wed Jan 19 16:35:18 2005 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Wed Jan 19 16:36:38 2005 Subject: [BioSQL-l] Consistency between bio* projects In-Reply-To: <6BE9F628-68C2-11D9-860A-000A95AE92B0@gnf.org> References: <6BE9F628-68C2-11D9-860A-000A95AE92B0@gnf.org> Message-ID: <03D9674E-6A62-11D9-88CC-000393C44276@cgt.duhs.duke.edu> Most of the specifics of what fields the annotations are stored in the BioPerl Annotation model is documented in the Bio::SeqIO::genbank and Bio::SeqIO::embl POD. Some of the info is in the Bio::Seq::RichSeq (and its interface) documentation. Brian has written down a lot of the nuances in his HOWTOs as well see (http://bioperl.org/HOWTOs/). The object model is different for different projects - Bioperl differentiates between Features (things with a defined location in sequence) and Annotations (things attached to an entire record). Some proposals for a next-generation (NG) object model will probably not distinguish these types as much remove the dependancy on things being sequence-centric. (Our parsers were written first to be able to roundtrip the formats where most of the data was stored - the sequence repositories so genbank,embl,swissprot). A NG model will probably be more feature-centric - in the DAS-flavor of things probably. I'm not sure what will really happen, requires people to roll up their sleeves and get some prototypes out there for us to really play with. -jason On Jan 17, 2005, at 3:00 PM, Hilmar Lapp wrote: > > On Jan 16, 2005, at 6:41 PM, mark.schreiber@group.novartis.com wrote: > >> It would seem that what is needed is a mapping of each field from a >> file >> format to a field in a BioSQL table. I think initially this would only >> need to be done for EMBL, SwissProt and GenBank. > > Note that this has at least been started for bioperl in the extent > that the destination in the bioperl object model is documented. > (Jason, Brian, anything you wanted to comment?) > > Once you know where it is in the bioperl object model, it is > relatively straight forward to predict where it ends up in the schema; > still it's not written down in plain text anywhere I think. > >> In many ways I prefer the idea of developing a SQL API which would be >> more >> robust and would serve to define what is expected of each proceedure >> call. >> However I think it should be achievable for the schema. In fact there >> is >> no reason why both cannot co-exist. For any API there should be a >> possbile >> implementation so naturally the schema could be used to generate an >> API. >> People could then happilly make other schemata that fit the API which >> may >> be optimised for their needs. > > Right - I guess so far my idea was that the object model is the API, > and the OR mapper implements the bridge to your chosen schema. > > Clearly, the problem with this level of API is that it's not > cross-bio* by definition since we don't use the exact same object > model. > >> >> Does anyone have a recent UML or similar diagram for the schema? > > There is a ERD in the doc directory. Other than that, there is no UML > model. > >> I can then use this to suggest mappings from GenBank fields to the >> API. I think >> it may be easier in many cases to follow bioperl's lead. BioJava >> seems to >> follow the 'store everything that isn't a feature as a >> bioentry_qualifier' >> approach so I just need to add some special cases. >> >> Hilmar, would you be prepared to do any work on the BioPerl side for >> synchronization of the two? > > Certainly, if it is really needed. Generally speaking, I would not > want to introduce object model and genbank-to-object model mapping > changes to bioperl if they openly break backward compatibility unless > everybody agrees to go forward. It's also not necessarily needed; the > OR mapping code (bioperl-db) may be the better place, depending on > scope and what's involved. > > -hilmar > > >> >> - Mark >> >> >> >> >> >> Hilmar Lapp >> 01/15/2005 01:58 AM >> >> >> To: Mark Schreiber/GP/Novartis@PH >> cc: biosql-l@open-bio.org >> Subject: Re: [BioSQL-l] Consistency between bio* >> projects >> >> >> >> On Friday, January 14, 2005, at 01:10 AM, >> mark.schreiber@group.novartis.com wrote: >>> Unfortunately, Bioperl stores identifiers as >>> follows: >>> >>> Bioentry.bioentry_id is the unique internal reference number >>> Bioentry.name is the GI number >> >> The GI number goes to Bioentry.Identifier, which is was designated the >> purpose of storing the identifier within an external database. >> >> Bioentry.name should hold the locus name, which for contigs and many >> other entries etc will be identical to the accession (but not the GI >> number!). >> >> If you find it in Bioentry.name then I suspect you weren't loading >> from >> genbank or embl formatted input? >> >> From memory the basic idea of BioSQL was to define a schema that bio* >>> projects could both read and write from in a language independant >>> manner. >>> For reasons best left to the designers (mostly I think cause MySQL >>> couldn't handle stored proceedures) the level of interaction is right >>> down >>> at the schema level. >> >> Right. Also, not all database drivers in all languages support stored >> procedure calls equally well. In e.g. PostgreSQL and Oracle you can >> always get around this by writing a view and putting an INSTEAD OF >> INSERT (or UPDATE) trigger on it that will then call the procedure, >> but >> this is clearly not even close to an option in MySQL. >> >> It's maybe worth considering whether opening a dichotomy here between >> MySQL and the rest to provide people who need it with a SQL-level API >> that both perl and java will use. People who are interested in this by >> definition will not be interested in MySQL anyway. >> >>> Unfortunaltey this means that the way data is stored >>> needs to be very consistent between projects if any API's that use >>> BioSQL >>> can be portable. My biojava API cannot be applied to a DB previously >>> setup >>> with bioperl which was the original idea behind BioSQL in the first >>> place. >>> >>> Help!! >> >> I think you're raising a great point. Indeed, such a contract hasn't >> really been written. We're probably one of few who use both perl and >> java to access a biosql database (and I'm not using biojava as the >> object model on the java side, which is why I'm not running into this >> problem). (Note as an aside that you could also write adaptors that >> transform between the SymGene and the Biojava model when storing or >> retrieving objects from/to the database.) >> >> It'd be great if you were willing to take the lead for getting this >> all >> spelled out and laid down in a document? >> >> -hilmar >> -- >> ------------------------------------------------------------- >> Hilmar Lapp email: lapp at gnf.org >> GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 >> ------------------------------------------------------------- >> >> >> >> >> >> > -- > ------------------------------------------------------------- > Hilmar Lapp email: lapp at gnf.org > GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 > ------------------------------------------------------------- > > -- Jason Stajich Duke University jason at cgt.duhs.duke.edu From dlondon at ebi.ac.uk Thu Jan 20 12:58:59 2005 From: dlondon at ebi.ac.uk (Darin London) Date: Thu Jan 20 13:01:54 2005 Subject: [BioSQL-l] BOSC 2005 Message-ID: <20050120175859.GA7254@parrot.ebi.ac.uk> {Please pass the word!} MEETING ANNOUNCEMENT & CALL FOR SPEAKERS The 6th annual Bioinformatics Open Source Conference (BOSC'2005) is organized by the not-for-profit Open Bioinformatics Foundation. The meeting will take place June 23-24, 2005 in Detroit, Michigan, USA, and is one of several Special Interest Group (SIG) meetings occurring in conjunction with the 13th International Conference on Intelligent Systems for Molecular Biology. see http://www.iscb.org/ismb2005 for more information. Because of the power of many Open Source bioinformatics packages in use by the Research Community today, it is not too presumptuous to say that the work of the Open Source Bioinformatics Community represents the cutting edge of Bioinformatics in general. This has been repeatedly demonstrated by the quality of presentations at previous BOSC conferences. This year, at BOSC 2006, we want to continue this tradition of excellence, while presenting this message to a wider part of the Research Community. Please, pass this message on to anyone you know that is interested in Bioinformatics software. BOSC PROGRAM & CONTACT INFO * Web: http://www.open-bio.org/bosc2005/ * Email: bosc@open-bio.org FEES TO BE ANNOUNCED. Watch the bosc website for more information. SPEAKERS & ABSTRACTS WANTED The program committee is currently seeking abstracts for talks at BOSC 2005. BOSC is a great opportunity for you to tell the community about your use, development, or philosophy of open source software development in bioinformatics. The committee will select several submitted abstracts for 25-minute talks and others for shorter "lightning" talks. Accepted abstracts will be published on the BOSC web site. If you are interested in speaking at BOSC 2005, please send us before April 26, 2005: * an abstract (no more than a few paragraphs) * a URL for the project page, if applicable * information about the open source license used for your software or your release plans. Abstracts will be accepted for submission until April 26, 2005. Abstracts chosen for presentation will be announced May 12, 2005 (before the ISMB Early Registration Deadline). LIGHTNING-TALK SPEAKERS WANTED! The program committee is currently seeking speakers for the lightning talks at BOSC 2005. Lightning talks are quick - only five minutes long - and a great opportunity for you to give people a quick summary of your open source project, code, idea, or vision of the future. If you are interested in giving a lightning talk at BOSC 2005, please send us: * a brief title and summary (one or two lines) * a URL for the project page, if applicable * information about the open source license used for your software or your release plans. We will accept entries on-line until BOSC starts, but space for demos and lightning talks is limited.
SOFTWARE DEMONSTRATIONS WANTED! If you are involved in the development of Open Source Bioinformatics Software, you are invited to provide a short demonstration to attendees of BOSC 2005. If you are interested in giving a software demonstration at BOSC 2005, please send us: * a brief title and summary (one or two lines) * a URL for the project page, if applicable * Internet connectivity requirements (e.g. website Application served on the world wide web, or web based client application). We will accept entries on-line until the BOSC starts, but space for demos and lightning talks is limited. ** Because the mission of the OBF is to promote Open Source software, we will favor submissions for projects that apply a recognized Open Source License, or adhere to the general Open Source Philosophy. See the following websites for further details: href="http://www.opensource.org/licenses/ href="http://www.opensource.org/docs/definition.php SESSION CHAIRS WANTED If you would like to be involved BOSC 2005, we invite you to chair a session. This will not require much of your time. You will be given a schedule of presenters during your session. You simply introduce each speaker, and manage the time of their presentation (25 minutes for full presentations, 5-10 minutes for lightning talks/demos, depending on the number of entries). If you are interested in chairing a session, please send us your name and affiliation (if applicable). -- cheers, Darin London dlondon@ebi.ac.uk European Bioinformatics Institute, +44 (0)1223 49 2566 Wellcome Trust Genome Campus, Hinxton +44 (0)1223 49 4468 (fax) Cambridgeshire CB10 1SD, UK -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 189 bytes Desc: not available Url : http://open-bio.org/pipermail/biosql-l/attachments/20050120/9bb1da79/attachment.bin From Hegedus.Tamas at mayo.edu Thu Jan 20 14:45:33 2005 From: Hegedus.Tamas at mayo.edu (Tamas Hegedus) Date: Thu Jan 20 14:43:05 2005 Subject: [BioSQL-l] object-mapping Message-ID: <41F00A5D.2000608@mayo.edu> Hi, I also would like to understand the mapping between different 'flat file databases' (like SwissPrt, InterPro.xml) and the BioSQL schema. I think I tried most of the docs: => Bio::SeqIO::genbank and Bio::SeqIO::embl POD; Bio::Seq::RichSeq; => BioPerl, SeqIO howto and others; => I also tried to understand the 'loading'.pl scripts to find the mapping, but I lost in the code. It would be great help for me if you could point a piece of code, or give a reference to read about the 'general concept' behind the BioSQL structure (e.g. in order to find out, how to map other, not implemented databases into the BioSQL). Thanks, Tamas -- Tamas Hegedus, Research Fellow | phone: (1) 480-301-6041 Mayo Clinic Scottsdale | fax: (1) 480-301-7017 13000 E. Shea Blvd | mailto:hegedus@mayo.edu Scottsdale, AZ, 85259 | http://hegedus.brumart.org From hlapp at gnf.org Thu Jan 20 14:54:44 2005 From: hlapp at gnf.org (Hilmar Lapp) Date: Thu Jan 20 14:50:42 2005 Subject: [BioSQL-l] object-mapping In-Reply-To: <41F00A5D.2000608@mayo.edu> Message-ID: <21BBFD84-6B1D-11D9-928A-000A959EB4C4@gnf.org> I'll write this up. I need it anyway for the paper. It'll take a week or two though. -hilmar On Thursday, January 20, 2005, at 11:45 AM, Tamas Hegedus wrote: > Hi, > > I also would like to understand the mapping between different 'flat > file databases' (like SwissPrt, InterPro.xml) and the BioSQL schema. > > I think I tried most of the docs: > => Bio::SeqIO::genbank and Bio::SeqIO::embl POD; Bio::Seq::RichSeq; > => BioPerl, SeqIO howto and others; > => I also tried to understand the 'loading'.pl scripts to find the > mapping, but I lost in the code. > > It would be great help for me if you could point a piece of code, or > give a reference to read about the 'general concept' behind the BioSQL > structure (e.g. in order to find out, how to map other, not > implemented databases into the BioSQL). > > Thanks, > Tamas > > -- > Tamas Hegedus, Research Fellow | phone: (1) 480-301-6041 > Mayo Clinic Scottsdale | fax: (1) 480-301-7017 > 13000 E. Shea Blvd | mailto:hegedus@mayo.edu > Scottsdale, AZ, 85259 | http://hegedus.brumart.org > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From gad14 at cornell.edu Fri Jan 21 14:06:53 2005 From: gad14 at cornell.edu (Genevieve Ann DeClerck) Date: Fri Jan 21 14:03:11 2005 Subject: [BioSQL-l] (no subject) Message-ID: <54252.128.84.180.146.1106334413.squirrel@128.84.180.146> Hi, I've recently installed biosql v.1.7 and bioperl-db v.1.2 (w/ mysql, on OS X) and successfully loaded some sample data (parkin.fasta, parkin.gb). I'm now trying to get this biosql database to work with gbrowse (1.62), but have not been successfully as of yet. From what I've gathered from scanning the BioSQL-l archives and from various google searches, it may not be possible to view a biosql database with gbrowse yet. Is this true? Thanks, Genevieve From hlapp at gnf.org Fri Jan 21 14:27:35 2005 From: hlapp at gnf.org (Hilmar Lapp) Date: Fri Jan 21 14:23:58 2005 Subject: [BioSQL-l] Re: gbrowse on top of biosql In-Reply-To: <54252.128.84.180.146.1106334413.squirrel@128.84.180.146> Message-ID: <81345703-6BE2-11D9-951A-000A959EB4C4@gnf.org> It is possible. There were even benchmarks run for gbrowse against dbgff, chado, and biosql. Gbrowse will need a special adaptor that was written and tested by Simon at CSHL last year. I'm not sure whether this was included in the last gbrowse release, but the folks at the gbrowse mailing list can probably help you out. -hilmar On Friday, January 21, 2005, at 11:06 AM, Genevieve Ann DeClerck wrote: > Hi, > > I've recently installed biosql v.1.7 and bioperl-db v.1.2 (w/ mysql, > on OS > X) and successfully loaded some sample data (parkin.fasta, parkin.gb). > I'm > now trying to get this biosql database to work with gbrowse (1.62), but > have not been successfully as of yet. From what I've gathered from > scanning the BioSQL-l archives and from various google searches, it may > not be possible to view a biosql database with gbrowse yet. Is this > true? > > Thanks, > Genevieve > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From Marc.Logghe at devgen.com Fri Jan 21 16:12:34 2005 From: Marc.Logghe at devgen.com (Marc Logghe) Date: Fri Jan 21 16:10:05 2005 Subject: [BioSQL-l] Re: gbrowse on top of biosql Message-ID: > It is possible. There were even benchmarks run for gbrowse against > dbgff, chado, and biosql. Gbrowse will need a special adaptor > that was > written and tested by Simon at CSHL last year. I'm not sure whether > this was included in the last gbrowse release, but the folks at the > gbrowse mailing list can probably help you out I can confirm this. Don't know what is the situation now, but it _used_ to work with version 1.61. > > have not been successfully as of yet. Genevieve, could you elaborate on that ? Do you see error messages ? Is there a problem of configuration ? Marc From gad14 at cornell.edu Mon Jan 24 12:44:29 2005 From: gad14 at cornell.edu (Genevieve DeClerck) Date: Mon Jan 24 12:40:17 2005 Subject: [BioSQL-l] Re: gbrowse on top of biosql Message-ID: <41F533FD.9070105@cornell.edu> Thanks for the responses Hilmar, Marc and Lincoln. Since biosql and gbrowse 1.62 should be working together, I suspect my problem might be config related. I can get the front GBrowse page to display in web browser, but when I enter a Landmark or Region in the search box (e.g. AB019558) and Search, a GBrowse error message in bold red font at the top of the page: "The landmark named AB019558 is not recognized. See the help pages for suggestions." AB019558 is the accession number of the feature I loaded into this test database (from bioperl-db/t/data/parkin.gb) so it should be found. Here's what the httpd error log has (many lines of this repeated. One for each of my Search attempts on biosql gbrowse page): Use of uninitialized value in concatenation (.) or string at /Library/Perl/5.8.1/darwin-thread-multi-2level/Bio/DB/Das/BioSQL/BioDatabaseAdaptor.pm line 116. Line 116 is inside of sub fetch_Seq_by_accession. It looks like a BioQuery object cannot be made because an argument is missing? I've tried many combinations of likely "Region" or "Location" names and coordinates using data loaded into the db in seqfeature and location tables... but always get the "not recognized" error. The conf file I have is basically a copy of 06.biosql.conf.. except for the first, [GENERAL], stanza where I put in my info. The 'pass' field could be a problem - i have '', while, 06.biosql.conf has a string (xyzzy) -- but I was under the impression that you don't set a password in mysql for user 'nobody.' This is setup I have for the other non-biosql gbrowse-mysql databases I'm running. Besides, I experimented with this by setting a password for 'nobody' in mysql and entered the password in my biosql.conf file in the 'pass' field in [General]. All it did was break my other gbrowse-mysql db's which don't use passwords for nobody - it had no effect on the gbrowse-biosql db - still getting "not recognized" error when Searching... I figure this might be a good time to post the contents of my biosql.conf file.. see below. I thought of providing a dump of my biosql database (which was simply loaded with test data from biopero-db/t/data/parkin.gb) but I'm not sure how helpful that would be.. Thanks for all your help, Genevieve #*********************************************** # originated from 06.biosql.conf (http://darwin.biochem.okstate.edu/gbrowse/contrib/conf_files/06.biosql.conf) [GENERAL] description = BioSQL db_adaptor = Bio::DB::Das::BioSQL db_args = driver mysql dbname biosql biodbname genbank host localhost user nobody pass "" plugins = SequenceDumper FastaDumper RestrictionAnnotator # Web site configuration info stylesheet = /gbrowse/gbrowse.css buttons = /gbrowse/images/buttons tmpimages = /gbrowse/tmp # where to link to when user clicks in detaild view link = http://localhost/gbrowse?ref=$ref;start=$start;stop=$end # what image widths to offer image widths = 450 640 800 1024 # default width of detailed view (pixels) default width = 800 default features = CDS repeat_region # max and default segment sizes for detailed view max segment = 500000 default segment = 50000 # zoom levels zoom levels = 100 200 1000 2000 5000 10000 20000 40000 100000 200000 500000 1000000 low res = 200000 # colors of the overview, detailed map and key overview bgcolor = wheat detailed bgcolor = white key bgcolor = beige footer =
For the source code for this browser, see the Generic Model Organism Database Project. For other questions, send mail to lstein@cshl.org. 
$Id: 06.biosql.conf,v 1.7 2003/06/26 12:32:23 lstein dead $
# examples to show in the introduction examples = AB019558 # "automatic" classes to try when an unqualified identifier is given automatic classes = Accession [TRACK DEFAULTS] glyph = generic height = 8 bgcolor = cyan fgcolor = cyan fontcolor = black font2color = blue label density = 25 bump density = 100 ################################################################################ # the remainder of the sections configure particular features to sho ################################################################################ [CDS] feature = CDS glyph = transcript2 #glyph = generic bgcolor = turquoise fgcolor = black height = 10 connector = solid label = sub { my $feature = shift; warn "feature = $feature"; my @tags = $feature->each_tag_value('cds_id'); $tags[0]; } description = sub { my $feature = shift; warn "feature = $feature"; my @tags = $feature->each_tag_value('gene_id'); warn "tag = $tags[0]"; $tags[0]; } # key = Predicted transcripts [REPEAT] feature = repeat_region glyph = generic bgcolor = red height = 10 description = 1 key = Repeat regionss [TranslationF] glyph = translation global feature = 1 frame0 = cadetblue frame1 = blue frame2 = darkblue height = 20 fgcolor = purple strand = +1 translation = 3frame key = 3-frame translation (forward) [DNA/GC Content] glyph = dna global feature = 1 height = 40 do_gc = 1 fgcolor = red axis_color = blue [TranslationR] glyph = translation global feature = 1 frame0 = darkred frame1 = red frame2 = crimson height = 20 fgcolor = blue strand = -1 translation = 3frame key = 3-frame translation (reverse) #*********************************************** -- >> The adaptor you want is Bio::DB::Das::BioSQL. Once you install >> GBrowse, do "perldoc Bio::DB::Das::BioSQL" and it will describe the >> parameters you need to pass in the conf file. Also see >> contrib/conf/06.biosql.conf for an example. >> >> There is also a BIOSQL HOWTO in the pod documentation. It seems to be >> unecessarily pessimistic, saying that "the biosql adaptor is not >> known to work." >> >> One thing I just noticed, is that there is a typo in the example conf >> file. It says the adaptor is Bio::DB::BioSQL, but it should be >> Bio::DB::Das::BioSQL. >> >> Lincoln Marc Logghe wrote: >>It is possible. There were even benchmarks run for gbrowse against >>dbgff, chado, and biosql. Gbrowse will need a special adaptor >>that was >>written and tested by Simon at CSHL last year. I'm not sure whether >>this was included in the last gbrowse release, but the folks at the >>gbrowse mailing list can probably help you out > > > I can confirm this. Don't know what is the situation now, but it _used_ to work with version 1.61. > > >>>have not been successfully as of yet. > > > Genevieve, could you elaborate on that ? Do you see error messages ? Is there a problem of configuration ? > > Marc > > > > It is possible. There were even benchmarks run for gbrowse against dbgff, chado, and biosql. Gbrowse will need a special adaptor that was written and tested by Simon at CSHL last year. I'm not sure whether this was included in the last gbrowse release, but the folks at the gbrowse mailing list can probably help you out. > > -hilmar > > On Friday, January 21, 2005, at 11:06 AM, Genevieve Ann DeClerck wrote: > >> Hi, >> >> I've recently installed biosql v.1.7 and bioperl-db v.1.2 (w/ mysql, on OS >> X) and successfully loaded some sample data (parkin.fasta, parkin.gb). I'm >> now trying to get this biosql database to work with gbrowse (1.62), but >> have not been successfully as of yet. From what I've gathered from >> scanning the BioSQL-l archives and from various google searches, it may >> not be possible to view a biosql database with gbrowse yet. Is this true? >> >> Thanks, >> Genevieve >> >> _______________________________________________ >> BioSQL-l mailing list >> BioSQL-l@open-bio.org >> http://open-bio.org/mailman/listinfo/biosql-l >> > -- > ------------------------------------------------------------- > Hilmar Lapp email: lapp at gnf.org > GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 > ------------------------------------------------------------- > > From Marc.Logghe at devgen.com Mon Jan 24 17:19:58 2005 From: Marc.Logghe at devgen.com (Marc Logghe) Date: Mon Jan 24 17:19:20 2005 Subject: [BioSQL-l] RE: [Gmod-gbrowse] Re: gbrowse on top of biosql Message-ID: Hi Genevieve, the error you mention is the one you get when the namespace is not set in the conf. It should read: db_args = driver mysql dbname biosql biodbname genbank host localhost user nobody pass "" namespace A bioentry search in BioSQL needs a namespace. When you did not provide it explicitely while populating biosql it is probably the default 'bioperl'. HTH, Marc -----Oorspronkelijk bericht----- Van: gmod-gbrowse-admin@lists.sourceforge.net namens Genevieve DeClerck Verzonden: ma 24-1-2005 18:44 Aan: biosql-l@open-bio.org; hlapp@gnf.org; gmod-gbrowse@lists.sourceforge.net; lstein@cshl.edu Onderwerp: [Gmod-gbrowse] Re: gbrowse on top of biosql Thanks for the responses Hilmar, Marc and Lincoln. Since biosql and gbrowse 1.62 should be working together, I suspect my problem might be config related. I can get the front GBrowse page to display in web browser, but when I enter a Landmark or Region in the search box (e.g. AB019558) and Search, a GBrowse error message in bold red font at the top of the page: "The landmark named AB019558 is not recognized. See the help pages for suggestions." AB019558 is the accession number of the feature I loaded into this test database (from bioperl-db/t/data/parkin.gb) so it should be found. Here's what the httpd error log has (many lines of this repeated. One for each of my Search attempts on biosql gbrowse page): Use of uninitialized value in concatenation (.) or string at /Library/Perl/5.8.1/darwin-thread-multi-2level/Bio/DB/Das/BioSQL/BioDatabaseAdaptor.pm line 116. Line 116 is inside of sub fetch_Seq_by_accession. It looks like a BioQuery object cannot be made because an argument is missing? I've tried many combinations of likely "Region" or "Location" names and coordinates using data loaded into the db in seqfeature and location tables... but always get the "not recognized" error. The conf file I have is basically a copy of 06.biosql.conf.. except for the first, [GENERAL], stanza where I put in my info. The 'pass' field could be a problem - i have '', while, 06.biosql.conf has a string (xyzzy) -- but I was under the impression that you don't set a password in mysql for user 'nobody.' This is setup I have for the other non-biosql gbrowse-mysql databases I'm running. Besides, I experimented with this by setting a password for 'nobody' in mysql and entered the password in my biosql.conf file in the 'pass' field in [General]. All it did was break my other gbrowse-mysql db's which don't use passwords for nobody - it had no effect on the gbrowse-biosql db - still getting "not recognized" error when Searching... I figure this might be a good time to post the contents of my biosql.conf file.. see below. I thought of providing a dump of my biosql database (which was simply loaded with test data from biopero-db/t/data/parkin.gb) but I'm not sure how helpful that would be.. Thanks for all your help, Genevieve #*********************************************** # originated from 06.biosql.conf (http://darwin.biochem.okstate.edu/gbrowse/contrib/conf_files/06.biosql.conf) [GENERAL] description = BioSQL db_adaptor = Bio::DB::Das::BioSQL db_args = driver mysql dbname biosql biodbname genbank host localhost user nobody pass "" plugins = SequenceDumper FastaDumper RestrictionAnnotator # Web site configuration info stylesheet = /gbrowse/gbrowse.css buttons = /gbrowse/images/buttons tmpimages = /gbrowse/tmp # where to link to when user clicks in detaild view link = http://localhost/gbrowse?ref=$ref;start=$start;stop=$end # what image widths to offer image widths = 450 640 800 1024 # default width of detailed view (pixels) default width = 800 default features = CDS repeat_region # max and default segment sizes for detailed view max segment = 500000 default segment = 50000 # zoom levels zoom levels = 100 200 1000 2000 5000 10000 20000 40000 100000 200000 500000 1000000 low res = 200000 # colors of the overview, detailed map and key overview bgcolor = wheat detailed bgcolor = white key bgcolor = beige footer =
For the source code for this browser, see the Generic Model Organism Database Project. For other questions, send mail to lstein@cshl.org. 
$Id: 06.biosql.conf,v 1.7 2003/06/26 12:32:23 lstein dead $
# examples to show in the introduction examples = AB019558 # "automatic" classes to try when an unqualified identifier is given automatic classes = Accession [TRACK DEFAULTS] glyph = generic height = 8 bgcolor = cyan fgcolor = cyan fontcolor = black font2color = blue label density = 25 bump density = 100 ################################################################################ # the remainder of the sections configure particular features to sho ################################################################################ [CDS] feature = CDS glyph = transcript2 #glyph = generic bgcolor = turquoise fgcolor = black height = 10 connector = solid label = sub { my $feature = shift; warn "feature = $feature"; my @tags = $feature->each_tag_value('cds_id'); $tags[0]; } description = sub { my $feature = shift; warn "feature = $feature"; my @tags = $feature->each_tag_value('gene_id'); warn "tag = $tags[0]"; $tags[0]; } # key = Predicted transcripts [REPEAT] feature = repeat_region glyph = generic bgcolor = red height = 10 description = 1 key = Repeat regionss [TranslationF] glyph = translation global feature = 1 frame0 = cadetblue frame1 = blue frame2 = darkblue height = 20 fgcolor = purple strand = +1 translation = 3frame key = 3-frame translation (forward) [DNA/GC Content] glyph = dna global feature = 1 height = 40 do_gc = 1 fgcolor = red axis_color = blue [TranslationR] glyph = translation global feature = 1 frame0 = darkred frame1 = red frame2 = crimson height = 20 fgcolor = blue strand = -1 translation = 3frame key = 3-frame translation (reverse) #*********************************************** -- >> The adaptor you want is Bio::DB::Das::BioSQL. Once you install >> GBrowse, do "perldoc Bio::DB::Das::BioSQL" and it will describe the >> parameters you need to pass in the conf file. Also see >> contrib/conf/06.biosql.conf for an example. >> >> There is also a BIOSQL HOWTO in the pod documentation. It seems to be >> unecessarily pessimistic, saying that "the biosql adaptor is not >> known to work." >> >> One thing I just noticed, is that there is a typo in the example conf >> file. It says the adaptor is Bio::DB::BioSQL, but it should be >> Bio::DB::Das::BioSQL. >> >> Lincoln Marc Logghe wrote: >>It is possible. There were even benchmarks run for gbrowse against >>dbgff, chado, and biosql. Gbrowse will need a special adaptor >>that was >>written and tested by Simon at CSHL last year. I'm not sure whether >>this was included in the last gbrowse release, but the folks at the >>gbrowse mailing list can probably help you out > > > I can confirm this. Don't know what is the situation now, but it _used_ to work with version 1.61. > > >>>have not been successfully as of yet. > > > Genevieve, could you elaborate on that ? Do you see error messages ? Is there a problem of configuration ? > > Marc > > > > It is possible. There were even benchmarks run for gbrowse against dbgff, chado, and biosql. Gbrowse will need a special adaptor that was written and tested by Simon at CSHL last year. I'm not sure whether this was included in the last gbrowse release, but the folks at the gbrowse mailing list can probably help you out. > > -hilmar > > On Friday, January 21, 2005, at 11:06 AM, Genevieve Ann DeClerck wrote: > >> Hi, >> >> I've recently installed biosql v.1.7 and bioperl-db v.1.2 (w/ mysql, on OS >> X) and successfully loaded some sample data (parkin.fasta, parkin.gb). I'm >> now trying to get this biosql database to work with gbrowse (1.62), but >> have not been successfully as of yet. From what I've gathered from >> scanning the BioSQL-l archives and from various google searches, it may >> not be possible to view a biosql database with gbrowse yet. Is this true? >> >> Thanks, >> Genevieve >> >> _______________________________________________ >> BioSQL-l mailing list >> BioSQL-l@open-bio.org >> http://open-bio.org/mailman/listinfo/biosql-l >> > -- > ------------------------------------------------------------- > Hilmar Lapp email: lapp at gnf.org > GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 > ------------------------------------------------------------- > > ------------------------------------------------------- This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting Tool for open source databases. Create drag-&-drop reports. Save time by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc. Download a FREE copy at http://www.intelliview.com/go/osdn_nl _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse From gad14 at cornell.edu Tue Jan 25 10:05:55 2005 From: gad14 at cornell.edu (Genevieve DeClerck) Date: Tue Jan 25 10:02:47 2005 Subject: [BioSQL-l] Re: [Gmod-gbrowse] Re: gbrowse on top of biosql In-Reply-To: References: Message-ID: <41F66053.3090800@cornell.edu> Marc, When I loaded the sample parkin data here are the commands i used: bioperl-db/scripts/biosql/load_seqdatabase.pl -dbuser gad14 -dbname biosql -dbpass XXXXXX -namespace genbank -format fasta ~/downloads/bioperl-db/t/data/parkin.fasta bioperl-db/scripts/biosql/load_seqdatabase.pl -dbuser gad14 -dbname biosql -dbpass XXXXXX -namespace genbank -format genbank ~/downloads/bioperl-db/t/data/parkin.gb I added 'namespace genbank' to the db_args definition in my conf file and retried gbrowse. This time when I Search for AB019558 I get an "Internal Server Error" (default white html page). Here's what my http error file has: Can't locate object method "class" via package "Bio::DB::Das::BioSQL::Segment" at /Library/Perl/5.8.1/darwin-thread-multi-2level/Bio/Graphics/Browser.pm line 1682. [Tue Jan 25 10:00:29 2005] [error] [client 132.XX.XX.XX] Premature end of script headers: /Library/WebServer/CGI-Executables/gbrowse I tried, for the heck of it, setting namespace to 'bioperl' too - with this the gbrowse ref font "is not recognized" error returns. -Genevieve Marc Logghe wrote: > Hi Genevieve, > the error you mention is the one you get when the namespace is not set in the conf. > It should read: > db_args = driver mysql > dbname biosql > biodbname genbank > host localhost > user nobody > pass "" > namespace > > A bioentry search in BioSQL needs a namespace. When you did not provide it explicitely while populating biosql it is probably the default 'bioperl'. > HTH, > Marc > > > > -----Oorspronkelijk bericht----- > Van: gmod-gbrowse-admin@lists.sourceforge.net namens Genevieve DeClerck > Verzonden: ma 24-1-2005 18:44 > Aan: biosql-l@open-bio.org; hlapp@gnf.org; gmod-gbrowse@lists.sourceforge.net; lstein@cshl.edu > Onderwerp: [Gmod-gbrowse] Re: gbrowse on top of biosql > > Thanks for the responses Hilmar, Marc and Lincoln. > Since biosql and gbrowse 1.62 should be working together, I > suspect my problem might be config related. I can get the front GBrowse > page to display in web browser, but when I enter a Landmark or Region in > the search box (e.g. AB019558) and Search, a GBrowse error message in > bold red font at the top of the page: "The landmark named AB019558 is > not recognized. See the help pages for suggestions." AB019558 is the > accession number of the feature I loaded into this test database (from > bioperl-db/t/data/parkin.gb) so it should be found. > > Here's what the httpd error log has (many lines of this repeated. One for > each of my Search attempts on biosql gbrowse page): > > Use of uninitialized value in concatenation (.) or string at > /Library/Perl/5.8.1/darwin-thread-multi-2level/Bio/DB/Das/BioSQL/BioDatabaseAdaptor.pm > line 116. > > Line 116 is inside of sub fetch_Seq_by_accession. It looks like a > BioQuery object cannot be made because an argument is missing? > > I've tried many combinations of likely "Region" or "Location" names and > coordinates using data loaded into the db in seqfeature and location > tables... but always get the "not recognized" error. > > The conf file I have is basically a copy of 06.biosql.conf.. except for > the first, [GENERAL], stanza where I put in my info. The 'pass' field > could be a problem - i have '', while, 06.biosql.conf has a string > (xyzzy) -- but I was under the impression that you don't set a password > in mysql for user 'nobody.' This is setup I have for the other > non-biosql gbrowse-mysql databases I'm running. Besides, I experimented > with this by setting a password for 'nobody' in mysql and entered the > password in my biosql.conf file in the 'pass' field in [General]. All it > did was break my other gbrowse-mysql db's which don't use passwords for > nobody - it had no effect on the gbrowse-biosql db - still getting "not > recognized" error when Searching... > > I figure this might be a good time to post the contents of my > biosql.conf file.. see below. I thought of providing a dump of my biosql > database (which was simply loaded with test data from > biopero-db/t/data/parkin.gb) but I'm not sure how helpful that would be.. > > Thanks for all your help, > Genevieve > > #*********************************************** > # originated from 06.biosql.conf > (http://darwin.biochem.okstate.edu/gbrowse/contrib/conf_files/06.biosql.conf) > [GENERAL] > description = BioSQL > db_adaptor = Bio::DB::Das::BioSQL > db_args = driver mysql > dbname biosql > biodbname genbank > host localhost > user nobody > pass "" > > plugins = SequenceDumper FastaDumper RestrictionAnnotator > > # Web site configuration info > stylesheet = /gbrowse/gbrowse.css > buttons = /gbrowse/images/buttons > tmpimages = /gbrowse/tmp > > # where to link to when user clicks in detaild view > link = http://localhost/gbrowse?ref=$ref;start=$start;stop=$end > > # what image widths to offer > image widths = 450 640 800 1024 > > # default width of detailed view (pixels) > default width = 800 > default features = CDS > repeat_region > > # max and default segment sizes for detailed view > max segment = 500000 > default segment = 50000 > > # zoom levels > zoom levels = 100 200 1000 2000 5000 10000 20000 40000 100000 200000 > 500000 1000000 > low res = 200000 > > # colors of the overview, detailed map and key > overview bgcolor = wheat > detailed bgcolor = white > key bgcolor = beige > > footer =
> > > > >
> For the source code for this browser, see the href="http://www.gmod.org"> > Generic Model Organism Database Project. For other questions, send > mail to lstein@cshl.org. >
>
> 
$Id: 06.biosql.conf,v 1.7 2003/06/26 12:32:23 lstein dead $
> > # examples to show in the introduction > examples = AB019558 > > # "automatic" classes to try when an unqualified identifier is given > automatic classes = Accession > > [TRACK DEFAULTS] > glyph = generic > height = 8 > bgcolor = cyan > fgcolor = cyan > fontcolor = black > font2color = blue > label density = 25 > bump density = 100 > > ################################################################################ > # the remainder of the sections configure particular features to sho > ################################################################################ > > [CDS] > feature = CDS > glyph = transcript2 > #glyph = generic > bgcolor = turquoise > fgcolor = black > height = 10 > connector = solid > label = sub { > my $feature = shift; > warn "feature = $feature"; > my @tags = $feature->each_tag_value('cds_id'); > $tags[0]; > } > description = sub { > my $feature = shift; > warn "feature = $feature"; > my @tags = $feature->each_tag_value('gene_id'); > warn "tag = $tags[0]"; > $tags[0]; > } > # key = Predicted transcripts > > [REPEAT] > feature = repeat_region > glyph = generic > bgcolor = red > height = 10 > description = 1 > key = Repeat regionss > > [TranslationF] > glyph = translation > global feature = 1 > frame0 = cadetblue > frame1 = blue > frame2 = darkblue > height = 20 > fgcolor = purple > strand = +1 > translation = 3frame > key = 3-frame translation (forward) > > [DNA/GC Content] > glyph = dna > global feature = 1 > height = 40 > do_gc = 1 > fgcolor = red > axis_color = blue > > [TranslationR] > glyph = translation > global feature = 1 > frame0 = darkred > frame1 = red > frame2 = crimson > height = 20 > fgcolor = blue > strand = -1 > translation = 3frame > key = 3-frame translation (reverse) > > #*********************************************** > > -- > > >> The adaptor you want is Bio::DB::Das::BioSQL. Once you install > >> GBrowse, do "perldoc Bio::DB::Das::BioSQL" and it will describe the > >> parameters you need to pass in the conf file. Also see > >> contrib/conf/06.biosql.conf for an example. > >> > >> There is also a BIOSQL HOWTO in the pod documentation. It seems to be > >> unecessarily pessimistic, saying that "the biosql adaptor is not > >> known to work." > >> > >> One thing I just noticed, is that there is a typo in the example conf > >> file. It says the adaptor is Bio::DB::BioSQL, but it should be > >> Bio::DB::Das::BioSQL. > >> > >> Lincoln > > > > Marc Logghe wrote: > >>It is possible. There were even benchmarks run for gbrowse against > >>dbgff, chado, and biosql. Gbrowse will need a special adaptor > >>that was > >>written and tested by Simon at CSHL last year. I'm not sure whether > >>this was included in the last gbrowse release, but the folks at the > >>gbrowse mailing list can probably help you out > > > > > > I can confirm this. Don't know what is the situation now, but it > _used_ to work with version 1.61. > > > > > >>>have not been successfully as of yet. > > > > > > Genevieve, could you elaborate on that ? Do you see error messages ? > Is there a problem of configuration ? > > > > Marc > > > > > > > > It is possible. There were even benchmarks run for gbrowse against > dbgff, chado, and biosql. Gbrowse will need a special adaptor that was > written and tested by Simon at CSHL last year. I'm not sure whether this > was included in the last gbrowse release, but the folks at the gbrowse > mailing list can probably help you out. > > > > -hilmar > > > > On Friday, January 21, 2005, at 11:06 AM, Genevieve Ann DeClerck wrote: > > > >> Hi, > >> > >> I've recently installed biosql v.1.7 and bioperl-db v.1.2 (w/ mysql, > on OS > >> X) and successfully loaded some sample data (parkin.fasta, > parkin.gb). I'm > >> now trying to get this biosql database to work with gbrowse (1.62), but > >> have not been successfully as of yet. From what I've gathered from > >> scanning the BioSQL-l archives and from various google searches, it may > >> not be possible to view a biosql database with gbrowse yet. Is this > true? > >> > >> Thanks, > >> Genevieve > >> > >> _______________________________________________ > >> BioSQL-l mailing list > >> BioSQL-l@open-bio.org > >> http://open-bio.org/mailman/listinfo/biosql-l > >> > > -- > > ------------------------------------------------------------- > > Hilmar Lapp email: lapp at gnf.org > > GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 > > ------------------------------------------------------------- > > > > > > > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting > Tool for open source databases. Create drag-&-drop reports. Save time > by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc. > Download a FREE copy at http://www.intelliview.com/go/osdn_nl > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > > From hlapp at gnf.org Tue Jan 25 12:36:12 2005 From: hlapp at gnf.org (Hilmar Lapp) Date: Tue Jan 25 12:32:16 2005 Subject: [BioSQL-l] Re: [Gmod-gbrowse] Re: gbrowse on top of biosql In-Reply-To: <41F66053.3090800@cornell.edu> References: <41F66053.3090800@cornell.edu> Message-ID: <9AFC1CBA-6EF7-11D9-BF48-000A95AE92B0@gnf.org> This is a weird error. Just wanted to say thanks to everybody who chipped in and helped out, and special thanks to Marc for following this through. -hilmar On Jan 25, 2005, at 7:05 AM, Genevieve DeClerck wrote: > Marc, > When I loaded the sample parkin data here are the commands i used: > > bioperl-db/scripts/biosql/load_seqdatabase.pl -dbuser gad14 -dbname > biosql -dbpass XXXXXX -namespace genbank -format fasta > ~/downloads/bioperl-db/t/data/parkin.fasta > bioperl-db/scripts/biosql/load_seqdatabase.pl -dbuser gad14 -dbname > biosql -dbpass XXXXXX -namespace genbank -format genbank > ~/downloads/bioperl-db/t/data/parkin.gb > > I added 'namespace genbank' to the db_args definition in my conf file > and retried gbrowse. This time when I Search for AB019558 I get an > "Internal Server Error" (default white html page). Here's what my http > error file has: > > Can't locate object method "class" via package > "Bio::DB::Das::BioSQL::Segment" at > /Library/Perl/5.8.1/darwin-thread-multi-2level/Bio/Graphics/Browser.pm > line 1682. > [Tue Jan 25 10:00:29 2005] [error] [client 132.XX.XX.XX] Premature end > of script headers: /Library/WebServer/CGI-Executables/gbrowse > > I tried, for the heck of it, setting namespace to 'bioperl' too - with > this the gbrowse ref font "is not recognized" error returns. > > -Genevieve > > > Marc Logghe wrote: >> Hi Genevieve, >> the error you mention is the one you get when the namespace is not >> set in the conf. >> It should read: >> db_args = driver mysql >> dbname biosql >> biodbname genbank >> host localhost >> user nobody >> pass "" >> namespace >> A bioentry search in BioSQL needs a namespace. When you did not >> provide it explicitely while populating biosql it is probably the >> default 'bioperl'. >> HTH, >> Marc >> -----Oorspronkelijk bericht----- >> Van: gmod-gbrowse-admin@lists.sourceforge.net namens Genevieve >> DeClerck >> Verzonden: ma 24-1-2005 18:44 >> Aan: biosql-l@open-bio.org; hlapp@gnf.org; >> gmod-gbrowse@lists.sourceforge.net; lstein@cshl.edu >> Onderwerp: [Gmod-gbrowse] Re: gbrowse on top of biosql >> Thanks for the responses Hilmar, Marc and Lincoln. >> Since biosql and gbrowse 1.62 should be working together, I >> suspect my problem might be config related. I can get the front >> GBrowse >> page to display in web browser, but when I enter a Landmark or Region >> in >> the search box (e.g. AB019558) and Search, a GBrowse error message in >> bold red font at the top of the page: "The landmark named AB019558 is >> not recognized. See the help pages for suggestions." AB019558 is the >> accession number of the feature I loaded into this test database (from >> bioperl-db/t/data/parkin.gb) so it should be found. >> Here's what the httpd error log has (many lines of this repeated. One >> for >> each of my Search attempts on biosql gbrowse page): >> Use of uninitialized value in concatenation (.) or string at >> /Library/Perl/5.8.1/darwin-thread-multi-2level/Bio/DB/Das/BioSQL/ >> BioDatabaseAdaptor.pm >> line 116. >> Line 116 is inside of sub fetch_Seq_by_accession. It looks like a >> BioQuery object cannot be made because an argument is missing? >> I've tried many combinations of likely "Region" or "Location" names >> and >> coordinates using data loaded into the db in seqfeature and location >> tables... but always get the "not recognized" error. >> The conf file I have is basically a copy of 06.biosql.conf.. except >> for the first, [GENERAL], stanza where I put in my info. The 'pass' >> field could be a problem - i have '', while, 06.biosql.conf has a >> string (xyzzy) -- but I was under the impression that you don't set a >> password in mysql for user 'nobody.' This is setup I have for the >> other non-biosql gbrowse-mysql databases I'm running. Besides, I >> experimented with this by setting a password for 'nobody' in mysql >> and entered the password in my biosql.conf file in the 'pass' field >> in [General]. All it did was break my other gbrowse-mysql db's which >> don't use passwords for nobody - it had no effect on the >> gbrowse-biosql db - still getting "not recognized" error when >> Searching... >> I figure this might be a good time to post the contents of my >> biosql.conf file.. see below. I thought of providing a dump of my >> biosql >> database (which was simply loaded with test data from >> biopero-db/t/data/parkin.gb) but I'm not sure how helpful that would >> be.. >> Thanks for all your help, >> Genevieve >> #*********************************************** >> # originated from 06.biosql.conf >> (http://darwin.biochem.okstate.edu/gbrowse/contrib/conf_files/ >> 06.biosql.conf) >> [GENERAL] >> description = BioSQL >> db_adaptor = Bio::DB::Das::BioSQL >> db_args = driver mysql >> dbname biosql >> biodbname genbank >> host localhost >> user nobody >> pass "" >> plugins = SequenceDumper FastaDumper RestrictionAnnotator >> # Web site configuration info >> stylesheet = /gbrowse/gbrowse.css >> buttons = /gbrowse/images/buttons >> tmpimages = /gbrowse/tmp >> # where to link to when user clicks in detaild view >> link = >> http://localhost/gbrowse?ref=$ref;start=$start;stop=$end >> # what image widths to offer >> image widths = 450 640 800 1024 >> # default width of detailed view (pixels) >> default width = 800 >> default features = CDS >> repeat_region >> # max and default segment sizes for detailed view >> max segment = 500000 >> default segment = 50000 >> # zoom levels >> zoom levels = 100 200 1000 2000 5000 10000 20000 40000 100000 >> 200000 >> 500000 1000000 >> low res = 200000 >> # colors of the overview, detailed map and key >> overview bgcolor = wheat >> detailed bgcolor = white >> key bgcolor = beige >> footer =
>> >> >> >> >>
>> For the source code for this browser, see the > href="http://www.gmod.org"> >> Generic Model Organism Database Project. For other questions, >> send >> mail to lstein@cshl.org. >>
>>
>> 
$Id: 06.biosql.conf,v 1.7 2003/06/26 12:32:23 lstein dead  
>> $
>> # examples to show in the introduction >> examples = AB019558 >> # "automatic" classes to try when an unqualified identifier is given >> automatic classes = Accession >> [TRACK DEFAULTS] >> glyph = generic >> height = 8 >> bgcolor = cyan >> fgcolor = cyan >> fontcolor = black >> font2color = blue >> label density = 25 >> bump density = 100 >> ###################################################################### >> ########## >> # the remainder of the sections configure particular features to sho >> ###################################################################### >> ########## >> [CDS] >> feature = CDS >> glyph = transcript2 >> #glyph = generic >> bgcolor = turquoise >> fgcolor = black >> height = 10 >> connector = solid >> label = sub { >> my $feature = shift; >> warn "feature = $feature"; >> my @tags = $feature->each_tag_value('cds_id'); >> $tags[0]; >> } >> description = sub { >> my $feature = shift; >> warn "feature = $feature"; >> my @tags = $feature->each_tag_value('gene_id'); >> warn "tag = $tags[0]"; >> $tags[0]; >> } >> # key = Predicted transcripts >> [REPEAT] >> feature = repeat_region >> glyph = generic >> bgcolor = red >> height = 10 >> description = 1 >> key = Repeat regionss >> [TranslationF] >> glyph = translation >> global feature = 1 >> frame0 = cadetblue >> frame1 = blue >> frame2 = darkblue >> height = 20 >> fgcolor = purple >> strand = +1 >> translation = 3frame >> key = 3-frame translation (forward) >> [DNA/GC Content] >> glyph = dna >> global feature = 1 >> height = 40 >> do_gc = 1 >> fgcolor = red >> axis_color = blue >> [TranslationR] >> glyph = translation >> global feature = 1 >> frame0 = darkred >> frame1 = red >> frame2 = crimson >> height = 20 >> fgcolor = blue >> strand = -1 >> translation = 3frame >> key = 3-frame translation (reverse) >> #*********************************************** >> -- >> >> The adaptor you want is Bio::DB::Das::BioSQL. Once you install >> >> GBrowse, do "perldoc Bio::DB::Das::BioSQL" and it will describe >> the >> >> parameters you need to pass in the conf file. Also see >> >> contrib/conf/06.biosql.conf for an example. >> >> >> >> There is also a BIOSQL HOWTO in the pod documentation. It seems >> to be >> >> unecessarily pessimistic, saying that "the biosql adaptor is not >> >> known to work." >> >> >> >> One thing I just noticed, is that there is a typo in the example >> conf >> >> file. It says the adaptor is Bio::DB::BioSQL, but it should be >> >> Bio::DB::Das::BioSQL. >> >> >> >> Lincoln >> Marc Logghe wrote: >> >>It is possible. There were even benchmarks run for gbrowse against >> >>dbgff, chado, and biosql. Gbrowse will need a special adaptor >> >>that was >> >>written and tested by Simon at CSHL last year. I'm not sure >> whether >> >>this was included in the last gbrowse release, but the folks at >> the >> >>gbrowse mailing list can probably help you out >> > >> > >> > I can confirm this. Don't know what is the situation now, but it >> _used_ to work with version 1.61. >> > >> > >> >>>have not been successfully as of yet. >> > >> > >> > Genevieve, could you elaborate on that ? Do you see error >> messages ? >> Is there a problem of configuration ? >> > >> > Marc >> > >> > >> > >> > It is possible. There were even benchmarks run for gbrowse against >> dbgff, chado, and biosql. Gbrowse will need a special adaptor that was >> written and tested by Simon at CSHL last year. I'm not sure whether >> this >> was included in the last gbrowse release, but the folks at the gbrowse >> mailing list can probably help you out. >> > >> > -hilmar >> > >> > On Friday, January 21, 2005, at 11:06 AM, Genevieve Ann DeClerck >> wrote: >> > >> >> Hi, >> >> >> >> I've recently installed biosql v.1.7 and bioperl-db v.1.2 (w/ >> mysql, >> on OS >> >> X) and successfully loaded some sample data (parkin.fasta, >> parkin.gb). I'm >> >> now trying to get this biosql database to work with gbrowse >> (1.62), but >> >> have not been successfully as of yet. From what I've gathered >> from >> >> scanning the BioSQL-l archives and from various google searches, >> it may >> >> not be possible to view a biosql database with gbrowse yet. Is >> this >> true? >> >> >> >> Thanks, >> >> Genevieve >> >> >> >> _______________________________________________ >> >> BioSQL-l mailing list >> >> BioSQL-l@open-bio.org >> >> http://open-bio.org/mailman/listinfo/biosql-l >> >> >> > -- >> > ------------------------------------------------------------- >> > Hilmar Lapp email: lapp at gnf.org >> > GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 >> > ------------------------------------------------------------- >> > >> > >> ------------------------------------------------------- >> This SF.Net email is sponsored by: IntelliVIEW -- Interactive >> Reporting >> Tool for open source databases. Create drag-&-drop reports. Save time >> by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc. >> Download a FREE copy at http://www.intelliview.com/go/osdn_nl >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From gad14 at cornell.edu Tue Jan 25 17:08:08 2005 From: gad14 at cornell.edu (Genevieve DeClerck) Date: Tue Jan 25 17:04:34 2005 Subject: [BioSQL-l] Re: [Gmod-gbrowse] Re: gbrowse on top of biosql In-Reply-To: References: Message-ID: <41F6C348.3010303@cornell.edu> Thanks a lot for all the help everyone - especially Marc Logghe for #2,3. Summary of what I changed in my conf file and modules to get gbrowse working with biosql: 1) changed 'biodbname' tag in db_args definition in .conf file to 'namespace' 2) replaced line 1682 in Bio/Graphics/Browser.pm with: my $n = $_->display_name.$_->abs_ref.(eval{$_->version}||'').(eval{$_->class}||''); 3) entirely replaced sub 'asString' in Bio/DB/Das/BioSQL/Segment.pm with: sub asString { my $self = shift; my $label = $self->display_name; my $start = $self->start || ''; my $stop = $self->stop || ''; return "$label:$start,$stop"; } -Genevieve From hlapp at gnf.org Tue Jan 25 17:16:55 2005 From: hlapp at gnf.org (Hilmar Lapp) Date: Tue Jan 25 17:13:05 2005 Subject: [BioSQL-l] Re: [Gmod-gbrowse] Re: gbrowse on top of biosql In-Reply-To: <41F6C348.3010303@cornell.edu> References: <41F6C348.3010303@cornell.edu> Message-ID: This is great to hear that you got it working! Thanks so much Marc and everybody else. -hilmar On Jan 25, 2005, at 2:08 PM, Genevieve DeClerck wrote: > Thanks a lot for all the help everyone - especially Marc Logghe for > #2,3. Summary of what I changed in my conf file and modules to get > gbrowse working with biosql: > > 1) changed 'biodbname' tag in db_args definition in .conf file to > 'namespace' > > 2) replaced line 1682 in Bio/Graphics/Browser.pm with: > > my $n = > $_->display_name.$_->abs_ref.(eval{$_->version}||'').(eval{$_- > >class}||''); > > 3) entirely replaced sub 'asString' in Bio/DB/Das/BioSQL/Segment.pm > with: > > sub asString { > my $self = shift; > my $label = $self->display_name; > my $start = $self->start || ''; > my $stop = $self->stop || ''; > return "$label:$start,$stop"; > } > > -Genevieve > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From mark.schreiber at group.novartis.com Wed Jan 26 04:42:42 2005 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Wed Jan 26 04:38:54 2005 Subject: [BioSQL-l] Rank terms Message-ID: Several tables have 'rank' columns which in some cases are not nullable. What are they for? - Mark Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 From Marc.Logghe at devgen.com Wed Jan 26 04:53:00 2005 From: Marc.Logghe at devgen.com (Marc Logghe) Date: Wed Jan 26 04:49:08 2005 Subject: [BioSQL-l] Rank terms Message-ID: > Several tables have 'rank' columns which in some cases are > not nullable. > What are they for? > That is because biosql would be able to return the exact same entry as was put in the database originally. Meaning, it has to preserve the order of e.g. features in the (genbank) record. This information is stored in the rank fields. HTH, Marc From hollandr at gis.a-star.edu.sg Wed Jan 26 04:55:25 2005 From: hollandr at gis.a-star.edu.sg (Richard HOLLAND) Date: Wed Jan 26 04:52:15 2005 Subject: [BioSQL-l] Rank terms Message-ID: <6D9E9B9DF347EF4385F6271C64FB8D56015B2E4A@BIONIC.biopolis.one-north.com> It's to maintain comments/references/annotations etc. in a particular order so that they always appear in the same order when extracting information from the database. Theoretically, anyway. However the only script in bioperl-db which refers to it is scripts/merge-unique-ann.pl, and nothing else in bioperl-db or biojava-live currently refer to it which suggests it is usually entirely ignored. cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 --------------------------------------------- This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its content to any other person. Thank you. --------------------------------------------- > -----Original Message----- > From: biosql-l-bounces@portal.open-bio.org > [mailto:biosql-l-bounces@portal.open-bio.org] On Behalf Of > mark.schreiber@group.novartis.com > Sent: Wednesday, January 26, 2005 5:43 PM > To: biosql-l@open-bio.org > Subject: [BioSQL-l] Rank terms > > > Several tables have 'rank' columns which in some cases are > not nullable. > What are they for? > > - Mark > > Mark Schreiber > Principal Scientist (Bioinformatics) > > Novartis Institute for Tropical Diseases (NITD) > 10 Biopolis Road > #05-01 Chromos > Singapore 138670 > www.nitd.novartis.com > > phone +65 6722 2973 > fax +65 6722 2910 > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > From Marc.Logghe at devgen.com Wed Jan 26 06:40:29 2005 From: Marc.Logghe at devgen.com (Marc Logghe) Date: Wed Jan 26 06:36:36 2005 Subject: [BioSQL-l] Rank terms Message-ID: > biojava-live currently refer to it which suggests it is > usually entirely > ignored. I don't think this is the case. All this is handled _implicitely_ by the different Adaptor modules. I don't really know the inners, but I only can notice that when you fetch an entry using bioentry2flat.pl, the genbank record comes out, in the exact way as you have loaded it into biosql. Features, annotations, references come out in the exact same order. And the most important line in bioentry2flat.pl is only $seq = $seqadaptor->find_by_unique_key($seq); So the rank must be used somewhere, sometime. my 0.02 $ Cheers, Marc From nedwards at umiacs.umd.edu Wed Jan 26 12:12:34 2005 From: nedwards at umiacs.umd.edu (Nathan Edwards) Date: Wed Jan 26 12:10:04 2005 Subject: [BioSQL-l] Loading SwissProt to BioSQL? Message-ID: <41F7CF82.4000003@umiacs.umd.edu> What is the current recommended solution for those wanting to load SwissProt database files (uniprot_sprot.dat) to BioSQL via BioPython? As far as I can tell, the situtation is this: * The SwissProt .dat file parsers under Bio.SwissProt.SProt don't produce SeqRecord objects required by BioSeqDatabase.load. * The SwissProt .dat file parsers under FormatIO can't parse SwissProt .dat files, period. Does *anyone* have a working SwissProt .dat file to BioSQL solution working in Python? The most recent solution I see suggested: http://biopython.org/pipermail/biopython/2004-May/002088.html doesn't work as advertised: SProt.SequenceParser produces SeqRecord objects with only minimal instantiation of SeqRecord fields (sequence and accession) and BioSeqDatabase dies because it expects a field that SequenceParser never instantiates; and FormatIO.readFile doesn't recognize the uniprot_sprot.dat as any format it recognizes, and if forced, with format='swissprot/38' or format='swissprot/40' it dies while parsing. Note: My entire BioPython, BioSQL, etc installation is new, pristine, the latest update from CVS. Thanks, nathan -- Nathan Edwards, Ph.D. Center for Bioinformatics and Computational Biology 3119 Agriculture/Life Sciences Surge Building #296 University of Maryland, College Park, MD 20742-3360 Phone: +1 301-405-9901 Email: nedwards@umiacs.umd.edu WWWeb: http://www.umiacs.umd.edu/~nedwards From hlapp at gnf.org Wed Jan 26 13:51:57 2005 From: hlapp at gnf.org (Hilmar Lapp) Date: Wed Jan 26 13:48:05 2005 Subject: [BioSQL-l] Rank terms In-Reply-To: References: Message-ID: <5AC074A8-6FCB-11D9-9E4D-000A95AE92B0@gnf.org> Basically counters, e.g. index in an array, or any other number introducing an ordering. They were originally nullable, but we made all rank columns NOT NULL that take part in a unique key constraint in order to get correct and consistent behaviour from all supported RDBMS platforms (MySQL was giving problems due to its deviant treatment of null columns in compound keys). -hilmar On Jan 26, 2005, at 1:42 AM, mark.schreiber@group.novartis.com wrote: > Several tables have 'rank' columns which in some cases are not > nullable. > What are they for? > > - Mark > > Mark Schreiber > Principal Scientist (Bioinformatics) > > Novartis Institute for Tropical Diseases (NITD) > 10 Biopolis Road > #05-01 Chromos > Singapore 138670 > www.nitd.novartis.com > > phone +65 6722 2973 > fax +65 6722 2910 > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From hlapp at gnf.org Wed Jan 26 14:01:25 2005 From: hlapp at gnf.org (Hilmar Lapp) Date: Wed Jan 26 13:57:27 2005 Subject: [BioSQL-l] Loading SwissProt to BioSQL? In-Reply-To: <41F7CF82.4000003@umiacs.umd.edu> References: <41F7CF82.4000003@umiacs.umd.edu> Message-ID: I can't comment on the biopython side. Just one thought, if perl isn't too scary for you and if you think you can manage to install the requirement (or if you have a sysadmin you can bug with this), loading the database through bioperl-db's load_seqdatabase.pl may get you set up to then retrieve the content through biophyton. It is in this case also untested though whether the storage of annotation and feature annotation is compatible with how biopython wants to find it. We just came upon a similar problem between bioperl and biojava. -hilmar On Jan 26, 2005, at 9:12 AM, Nathan Edwards wrote: > > What is the current recommended solution for those wanting to load > SwissProt database files (uniprot_sprot.dat) to BioSQL via BioPython? > > As far as I can tell, the situtation is this: > > * The SwissProt .dat file parsers under Bio.SwissProt.SProt don't > produce SeqRecord objects required by BioSeqDatabase.load. > > * The SwissProt .dat file parsers under FormatIO can't parse SwissProt > .dat files, period. > > Does *anyone* have a working SwissProt .dat file to BioSQL solution > working in Python? > > The most recent solution I see suggested: > > http://biopython.org/pipermail/biopython/2004-May/002088.html > > doesn't work as advertised: SProt.SequenceParser produces SeqRecord > objects with only minimal instantiation of SeqRecord fields (sequence > and accession) and BioSeqDatabase dies because it expects a field that > SequenceParser never instantiates; and FormatIO.readFile doesn't > recognize the uniprot_sprot.dat as any format it recognizes, and if > forced, with format='swissprot/38' or format='swissprot/40' it dies > while parsing. > > Note: My entire BioPython, BioSQL, etc installation is new, pristine, > the latest update from CVS. > > Thanks, > > nathan > > -- > Nathan Edwards, Ph.D. > Center for Bioinformatics and Computational Biology > 3119 Agriculture/Life Sciences Surge Building #296 > University of Maryland, College Park, MD 20742-3360 > Phone: +1 301-405-9901 > Email: nedwards@umiacs.umd.edu > WWWeb: http://www.umiacs.umd.edu/~nedwards > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From hlapp at gnf.org Wed Jan 26 14:42:32 2005 From: hlapp at gnf.org (Hilmar Lapp) Date: Wed Jan 26 14:38:31 2005 Subject: [BioSQL-l] Rank terms In-Reply-To: References: Message-ID: <6B7C673E-6FD2-11D9-9E4D-000A95AE92B0@gnf.org> Bioperl-db carries through the rank on persistent objects, including generating it corresponding to array index if it isn't set yet. It therefore also pulls it out of the database. I was trying to find the code though that would *order* retrieved associations by rank, and as I recalled there isn't any, unless I'm maybe overlooking something. The reason you're getting the annotation or features back in the same order as loaded is most likely due to the fact that in the absence of joins and explicit ORDER BYs you get the rows either in the same order they were inserted into the DB, or in the order imposed by the unique key constraint or other index that supported the search. It depends on the RDBMS; I have seen that MySQL will at least most of the time do the former, whereas Oracle will do the latter. Either way, you'll get your annotation and feature arrays in the right order. It would certainly be good to make the ordering explicit, but I recall that that's one of those things I've always wanted to add and never found the time to. Volunteers of course greatly welcome :-) -hilmar On Jan 26, 2005, at 3:40 AM, Marc Logghe wrote: > >> biojava-live currently refer to it which suggests it is >> usually entirely >> ignored. > I don't think this is the case. All this is handled _implicitely_ by > the different Adaptor modules. > I don't really know the inners, but I only can notice that when you > fetch an entry using bioentry2flat.pl, the genbank record comes out, > in the exact way as you have loaded it into biosql. Features, > annotations, references come out in the exact same order. And the most > important line in bioentry2flat.pl is only > $seq = $seqadaptor->find_by_unique_key($seq); > So the rank must be used somewhere, sometime. > my 0.02 $ > > Cheers, > Marc > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From mark.schreiber at group.novartis.com Thu Jan 27 00:49:22 2005 From: mark.schreiber at group.novartis.com (mark.schreiber@group.novartis.com) Date: Thu Jan 27 00:45:23 2005 Subject: [BioSQL-l] Loading SwissProt to BioSQL? Message-ID: Richard Holland and I are trying to compile a document stating where things should go to make the projects more compatible. Initially we are finding out where things currently go for bioperl and biojava and then we can argue about where they should go. If anyone can do something similar for biopython and bioruby that would be cool. - Mark Hilmar Lapp Sent by: biosql-l-bounces@portal.open-bio.org 01/27/2005 03:01 AM To: Nathan Edwards cc: biopython@biopython.org, biosql-l@open-bio.org, (bcc: Mark Schreiber/GP/Novartis) Subject: Re: [BioSQL-l] Loading SwissProt to BioSQL? I can't comment on the biopython side. Just one thought, if perl isn't too scary for you and if you think you can manage to install the requirement (or if you have a sysadmin you can bug with this), loading the database through bioperl-db's load_seqdatabase.pl may get you set up to then retrieve the content through biophyton. It is in this case also untested though whether the storage of annotation and feature annotation is compatible with how biopython wants to find it. We just came upon a similar problem between bioperl and biojava. -hilmar On Jan 26, 2005, at 9:12 AM, Nathan Edwards wrote: > > What is the current recommended solution for those wanting to load > SwissProt database files (uniprot_sprot.dat) to BioSQL via BioPython? > > As far as I can tell, the situtation is this: > > * The SwissProt .dat file parsers under Bio.SwissProt.SProt don't > produce SeqRecord objects required by BioSeqDatabase.load. > > * The SwissProt .dat file parsers under FormatIO can't parse SwissProt > .dat files, period. > > Does *anyone* have a working SwissProt .dat file to BioSQL solution > working in Python? > > The most recent solution I see suggested: > > http://biopython.org/pipermail/biopython/2004-May/002088.html > > doesn't work as advertised: SProt.SequenceParser produces SeqRecord > objects with only minimal instantiation of SeqRecord fields (sequence > and accession) and BioSeqDatabase dies because it expects a field that > SequenceParser never instantiates; and FormatIO.readFile doesn't > recognize the uniprot_sprot.dat as any format it recognizes, and if > forced, with format='swissprot/38' or format='swissprot/40' it dies > while parsing. > > Note: My entire BioPython, BioSQL, etc installation is new, pristine, > the latest update from CVS. > > Thanks, > > nathan > > -- > Nathan Edwards, Ph.D. > Center for Bioinformatics and Computational Biology > 3119 Agriculture/Life Sciences Surge Building #296 > University of Maryland, College Park, MD 20742-3360 > Phone: +1 301-405-9901 > Email: nedwards@umiacs.umd.edu > WWWeb: http://www.umiacs.umd.edu/~nedwards > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- _______________________________________________ BioSQL-l mailing list BioSQL-l@open-bio.org http://open-bio.org/mailman/listinfo/biosql-l From Hegedus.Tamas at mayo.edu Thu Jan 27 16:25:44 2005 From: Hegedus.Tamas at mayo.edu (Tamas Hegedus) Date: Thu Jan 27 16:22:43 2005 Subject: [BioSQL-l] questions In-Reply-To: <21BBFD84-6B1D-11D9-928A-000A959EB4C4@gnf.org> References: <21BBFD84-6B1D-11D9-928A-000A959EB4C4@gnf.org> Message-ID: <41F95C58.3080700@mayo.edu> Hi all, Hilmar Lapp wrote: > I'll write this up. I need it anyway for the paper. => I am also preparing a paper, reading and thinking more. => I see higher activity on the list. ==>> So I think this is a good time to ask a few questions. Please note, I am wet biologist, but I like the programming. In the last 2-3 years I was playing a little bit with RDBMS that does not mean I know everything about them: the steepness of my learning curve is pretty low (e.g. after a year I start to find the BioSQL schema very interesting :-)). But I would like to understand more things. ----------------------------- DOCUMENTATION; WHYs; packing ----------------------------- However, I know that BioSQL is under development, but it is not a 'theoretical' projects, intend to be used by users. More users, more feedback, more development, happier programmer. But at this moment very difficult to recognize its advantages: => Why is BioSQL (RDBMS) better than other solution (e.g. flat files); why should I use it for my project? => What to download, from where to download? (In my opinion CVS is definitely for programmers not for biologist.) => What programs can I use to access the data? Only scripting? No! I can use it e.g. with GBrowse, exactly what I need... => Is there any convinient way to query the database? I do not really want to learn SQL. How to perform and link queries/returned entries to 'conventional' analysis tools (like pattern search)? ---- For developers: if you work on BioSQL constantly (from the beginning), you will know what column is for what (like 'Rank'), what are the role in a specific relation; but you can find out these things, if you populate the database, and dig into it: so much energy needed that the developer find out an easier way to solve his problem. ---- I know that it is a huge work to create (and keep uptodate) a website. Personally I really do not like (hate) creating web-pages. But I think a web-site for BioSQL would greatly accelerate the BioSQL project. ----------------------------- SCHEMA; RDBMSs ----------------------------- I may rise the next question, since I do not see the deepness of BioSQL, I know only PgSQL and MySQL. Why do you have different schema for different database servers (PgSQL, hsqldb, Oracle)? I guess why for MySQL... Would not be possible to manage only one schema? It could free energies/time for other things. E.g. generating the schema through an intelligent script (pseudo code): db = create_biosql_conn( 'postgresql', db, user, pwd) biodatabase_table = generate_table( name='Biodatabase', col_def=[('biodatabase_id', 'int', 'PK'), ( 'name', 'varchar( 128)'),..]) db.create_table( biodatabase_table); I do not know how to formulate this: having an intermediate layer before the database drivers to translate a standard SQL/table creation for the appropriate RDBMS. Table creation is a simple example, e.g. implementing of sequences is not so simple (especially if you count with MySQL). (The ODBC may be intend to do this? I do not know; but I do not think so after half an hour reading.) ------------------------------ PYTHON ------------------------------ I prefer python over perl (e.g. because of this I had extra struggles to install BioSQL with SwissProt). If I would know the object-mapping I think I could write a python script to load the the SwissProt into the BioSQL (it should be easy and straightforward). ============================================ Best regards, Tamas -- Tamas Hegedus, Research Fellow | phone: (1) 480-301-6041 Mayo Clinic Scottsdale | fax: (1) 480-301-7017 13000 E. Shea Blvd | mailto:hegedus@mayo.edu Scottsdale, AZ, 85259 | http://hegedus.brumart.org From lstein at cshl.edu Fri Jan 21 17:22:59 2005 From: lstein at cshl.edu (Lincoln Stein) Date: Fri Jan 28 09:15:03 2005 Subject: [BioSQL-l] Re: [Gmod-gbrowse] Re: gbrowse on top of biosql In-Reply-To: <81345703-6BE2-11D9-951A-000A959EB4C4@gnf.org> References: <81345703-6BE2-11D9-951A-000A959EB4C4@gnf.org> Message-ID: <200501211723.00178.lstein@cshl.edu> The adaptor you want is Bio::DB::Das::BioSQL. Once you install GBrowse, do "perldoc Bio::DB::Das::BioSQL" and it will describe the parameters you need to pass in the conf file. Also see contrib/conf/06.biosql.conf for an example. There is also a BIOSQL HOWTO in the pod documentation. It seems to be unecessarily pessimistic, saying that "the biosql adaptor is not known to work." One thing I just noticed, is that there is a typo in the example conf file. It says the adaptor is Bio::DB::BioSQL, but it should be Bio::DB::Das::BioSQL. Lincoln On Friday 21 January 2005 02:27 pm, Hilmar Lapp wrote: > It is possible. There were even benchmarks run for gbrowse against > dbgff, chado, and biosql. Gbrowse will need a special adaptor that > was written and tested by Simon at CSHL last year. I'm not sure > whether this was included in the last gbrowse release, but the > folks at the gbrowse mailing list can probably help you out. > > -hilmar > > On Friday, January 21, 2005, at 11:06 AM, Genevieve Ann DeClerck wrote: > > Hi, > > > > I've recently installed biosql v.1.7 and bioperl-db v.1.2 (w/ > > mysql, on OS > > X) and successfully loaded some sample data (parkin.fasta, > > parkin.gb). I'm > > now trying to get this biosql database to work with gbrowse > > (1.62), but have not been successfully as of yet. From what I've > > gathered from scanning the BioSQL-l archives and from various > > google searches, it may not be possible to view a biosql database > > with gbrowse yet. Is this true? > > > > Thanks, > > Genevieve > > > > _______________________________________________ > > BioSQL-l mailing list > > BioSQL-l@open-bio.org > > http://open-bio.org/mailman/listinfo/biosql-l -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 NOTE: Please copy Sandra Michelsen on all emails regarding scheduling and other time-critical topics. -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 189 bytes Desc: not available Url : http://open-bio.org/pipermail/biosql-l/attachments/20050121/90fb00eb/attachment.bin