From hlapp at gnf.org Tue Feb 1 12:52:13 2005 From: hlapp at gnf.org (Hilmar Lapp) Date: Tue Feb 1 12:48:06 2005 Subject: [BioSQL-l] questions In-Reply-To: <41F95C58.3080700@mayo.edu> Message-ID: <011F1964-747A-11D9-B82F-000A959EB4C4@gnf.org> On Thursday, January 27, 2005, at 01:25 PM, Tamas Hegedus wrote: > ----------------------------- > 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? I summarized the most popular use cases at BOSC03. You may want to check out http://www.open-bio.org/bosc2003/slides/Persistent_Bioperl_BOSC03.pdf > => 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... There is an adaptor that bridges biosql to be used by gbrowse, there's just been a thread on this on the gbrowse mailing list. There's possibly some wrinkles though that need to be worked out so that Gbrowse finds the features it is supposed to find. Check out the last week in the gbrowse mailing list archive. > => 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)? Bioperl-db provides you with an interface (object-relational mapper) that lets you interact with the database through bioperl and query objects, not SQL. When you run a search ($adaptor->find_by_XXX) you'll get bioperl objects returned. Note though that ultimately SQL is always going to be so much more powerful. > ---- > 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. > ---- Have you checked out the doc directory in the repository? There is a schema overview and an ERD. Those two will still leave many questions open, like 'rank', but it could be a start nonetheless. > 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. Unfortunately, almost all developers have the same enthusiasm for creating web-pages as you have. Volunteering web-page authors is what the OBF needs most desperately. I have no doubt that informative, well-organized, and most importantly regularly updated web pages would help the biosql project, but this is also the area where people could volunteer most easily. Biosql like all other OBF (and generally open-source) projects is a project built by people who volunteer their time ... > > ----------------------------- > 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. This is how it worked initially. When the schema evolved it became a pain for two reasons. First, the schema translator wasn't capable of the full SQL standard and bringing it up to requirements was more work than maintaining multiple versions of the schema, and second, the MySQL version used to be used as the reference, which is bad because in MySQL you can express only a small subset of the DDL capabilities that you have in other RDBMSs. Note that biosql is meant to be a very stable schema. There may be changes in the future, but not at a rapid pace. It's not been a big time sink to maintain 3 versions since the Singapore changes. This is not a programming library - it's a schema. > [...] > > ------------------------------ > 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). You may want to talk to the guys on the biopython list on how they stored sequences in biosql. -hilmar -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From Hegedus.Tamas at mayo.edu Fri Feb 4 11:55:07 2005 From: Hegedus.Tamas at mayo.edu (Tamas Hegedus) Date: Fri Feb 4 11:49:50 2005 Subject: [BioSQL-l] questions In-Reply-To: <011F1964-747A-11D9-B82F-000A959EB4C4@gnf.org> References: <011F1964-747A-11D9-B82F-000A959EB4C4@gnf.org> Message-ID: <4203A8EB.5020405@mayo.edu> Hilmar Lapp wrote: > On Thursday, January 27, 2005, at 01:25 PM, Tamas Hegedus wrote: >> ----------------------------- >> 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? > I summarized the most popular use cases at BOSC03. You may want to check > out > http://www.open-bio.org/bosc2003/slides/Persistent_Bioperl_BOSC03.pdf Thanks. But my problem was that it is pretty difficult to find on the web. If somebody is looking for solutions on the web, he will not stop at your site, will not strugle to find out if BioSQL is OK for him or not. >> => 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... > There is an adaptor that bridges biosql to be used by gbrowse, there's > just been a thread on this on the gbrowse mailing list. There's possibly > some wrinkles though that need to be worked out so that Gbrowse finds > the features it is supposed to find. Check out the last week in the > gbrowse mailing list archive. Sorry. I was very theoretical in my posting. I do not need gbrowse. I just wanted to picture that it would be great for visitors to see what type of 'client'/ready-to-use program package (like gbrowse) can be used with BioSQL. >> => 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)? > Bioperl-db provides you with an interface (object-relational mapper) > that lets you interact with the database through bioperl and query > objects, not SQL. When you run a search ($adaptor->find_by_XXX) you'll > get bioperl objects returned. > Note though that ultimately SQL is always going to be so much more > powerful. This means that only/mainly programmers with SQL and perl (java) experience are able to use the features of this RDBMS system. I may be impatient: I would like to have everything now, although the BioSQL project is not at the final stage of development. >> 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. > Have you checked out the doc directory in the repository? There is a > schema overview and an ERD. Those two will still leave many questions > open, like 'rank', but it could be a start nonetheless. I checked. But it is so frustrating for me, that I always stop and start again after 2 months. But this could be because of my stupidity :-( >> 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. > Unfortunately, almost all developers have the same enthusiasm for > creating web-pages as you have. Volunteering web-page authors is what > the OBF needs most desperately. I have no doubt that informative, > well-organized, and most importantly regularly updated web pages would > help the biosql project, but this is also the area where people could > volunteer most easily. > Biosql like all other OBF (and generally open-source) projects is a > project built by people who volunteer their time ... I know. I really appreciate. And thanks for all answers, 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 barry.moore at genetics.utah.edu Tue Feb 15 01:39:24 2005 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Tue Feb 15 01:34:42 2005 Subject: [BioSQL-l] ERD Creation In-Reply-To: <4203A8EB.5020405@mayo.edu> References: <011F1964-747A-11D9-B82F-000A959EB4C4@gnf.org> <4203A8EB.5020405@mayo.edu> Message-ID: <4211991C.2010903@genetics.utah.edu> Hi Hilmar- What software did you use to create that ERD for BioSQL? Barry -- Barry Moore Dept. of Human Genetics University of Utah Salt Lake City, UT From hlapp at gnf.org Tue Feb 15 11:24:36 2005 From: hlapp at gnf.org (Hilmar Lapp) Date: Tue Feb 15 11:20:28 2005 Subject: [BioSQL-l] Re: ERD Creation In-Reply-To: <4211991C.2010903@genetics.utah.edu> Message-ID: <1561BF84-7F6E-11D9-96C2-000A959EB4C4@gnf.org> ERWin (from CA). Does a good job but very expensive. -hilmar On Monday, February 14, 2005, at 10:39 PM, Barry Moore wrote: > Hi Hilmar- > > What software did you use to create that ERD for BioSQL? > > Barry > > -- > Barry Moore > Dept. of Human Genetics > University of Utah > Salt Lake City, UT > > > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From barry.moore at genetics.utah.edu Tue Feb 15 14:12:46 2005 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Tue Feb 15 14:09:00 2005 Subject: [BioSQL-l] Re: ERD Creation In-Reply-To: <1561BF84-7F6E-11D9-96C2-000A959EB4C4@gnf.org> References: <1561BF84-7F6E-11D9-96C2-000A959EB4C4@gnf.org> Message-ID: <421249AE.1000704@genetics.utah.edu> $4K! Ouch. Have you used any open source or less expensive alternatives that you found worthwhile? Barry Hilmar Lapp wrote: > ERWin (from CA). Does a good job but very expensive. -hilmar > > On Monday, February 14, 2005, at 10:39 PM, Barry Moore wrote: > >> Hi Hilmar- >> >> What software did you use to create that ERD for BioSQL? >> >> Barry >> >> -- >> Barry Moore >> Dept. of Human Genetics >> University of Utah >> Salt Lake City, UT >> >> >> >> -- Barry Moore Dept. of Human Genetics University of Utah Salt Lake City, UT From hlapp at gnf.org Tue Feb 15 15:05:20 2005 From: hlapp at gnf.org (Hilmar Lapp) Date: Tue Feb 15 15:00:49 2005 Subject: [BioSQL-l] Re: ERD Creation In-Reply-To: <421249AE.1000704@genetics.utah.edu> References: <1561BF84-7F6E-11D9-96C2-000A959EB4C4@gnf.org> <421249AE.1000704@genetics.utah.edu> Message-ID: None of them was even close, sadly. There was three requirements though that I had that you may not care about. First, I needed the tool to read in an existing model in DDL (data definition language, i.e., CREATE blah, ALTER blah, etc) SQL and then allow me to modify it. Second, I needed the tool to be able to generate DDL from the modified model. Third, I needed the tool to support Oracle with its generated DDL. ERWin distinguishes between a logical model and a physical model. It applies rules that you can configure when translating (or sync'ing) between logical and physical model. For instance, my logical BioSQL model follows the table naming convention known from the mysql/Pg schemas and uses only standard SQL92 types, whereas the physical model is for Oracle, applies prefixes to all table names to avoid name clashes, and uses better-suited Oracle SQL types where applicable. The physical model also defines indexes, whereas the logical model only defines primary key column(s), foreign key relationships, and alternative key column(s). I found that feature very helpful while the schema was actively undergoing changes; now it's so stable it's not that important anymore. So, depending on what you're trying to do an open-source tool may be sufficient. Just the last thing I wanted to do was to draw it up in e.g. Dia, b/c that just gives you a lot of grief without much benefit except the diagram. -hilmar On Feb 15, 2005, at 11:12 AM, Barry Moore wrote: > $4K! Ouch. Have you used any open source or less expensive > alternatives that you found worthwhile? > > Barry > > Hilmar Lapp wrote: > >> ERWin (from CA). Does a good job but very expensive. -hilmar >> >> On Monday, February 14, 2005, at 10:39 PM, Barry Moore wrote: >> >>> Hi Hilmar- >>> >>> What software did you use to create that ERD for BioSQL? >>> >>> Barry >>> >>> -- >>> Barry Moore >>> Dept. of Human Genetics >>> University of Utah >>> Salt Lake City, UT >>> >>> >>> >>> > > -- > Barry Moore > Dept. of Human Genetics > University of Utah > Salt Lake City, UT > > > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From barry.moore at genetics.utah.edu Tue Feb 15 19:29:46 2005 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Tue Feb 15 19:25:10 2005 Subject: [BioSQL-l] Re: ERD Creation In-Reply-To: References: <1561BF84-7F6E-11D9-96C2-000A959EB4C4@gnf.org> <421249AE.1000704@genetics.utah.edu> Message-ID: <421293FA.90500@genetics.utah.edu> That looks like it will work great Jason. Thanks. Hilmar, this program will allow me to import ERWIN 4.1 XML model. Would it be possible to get and ERWIN XML dump of the bio-sql model from you (that I could then import into DBDesigner to add my local tables)? Barry Jason Stajich wrote: > DBDesigner isn't too bad for mysql schemas. > http://www.fabforce.net/dbdesigner4/ > > -- > Jason Stajich > jason.stajich at duke.edu > http://www.duke.edu/~jes12/ > > On Feb 16, 2005, at 7:05 AM, Hilmar Lapp wrote: > >> None of them was even close, sadly. >> >> There was three requirements though that I had that you may not care >> about. First, I needed the tool to read in an existing model in DDL >> (data definition language, i.e., CREATE blah, ALTER blah, etc) SQL >> and then allow me to modify it. Second, I needed the tool to be able >> to generate DDL from the modified model. Third, I needed the tool to >> support Oracle with its generated DDL. >> >> ERWin distinguishes between a logical model and a physical model. It >> applies rules that you can configure when translating (or sync'ing) >> between logical and physical model. For instance, my logical BioSQL >> model follows the table naming convention known from the mysql/Pg >> schemas and uses only standard SQL92 types, whereas the physical >> model is for Oracle, applies prefixes to all table names to avoid >> name clashes, and uses better-suited Oracle SQL types where >> applicable. The physical model also defines indexes, whereas the >> logical model only defines primary key column(s), foreign key >> relationships, and alternative key column(s). >> >> I found that feature very helpful while the schema was actively >> undergoing changes; now it's so stable it's not that important anymore. >> >> So, depending on what you're trying to do an open-source tool may be >> sufficient. Just the last thing I wanted to do was to draw it up in >> e.g. Dia, b/c that just gives you a lot of grief without much benefit >> except the diagram. >> >> -hilmar >> >> On Feb 15, 2005, at 11:12 AM, Barry Moore wrote: >> >>> $4K! Ouch. Have you used any open source or less expensive >>> alternatives that you found worthwhile? >>> >>> Barry >>> >>> Hilmar Lapp wrote: >>> >>>> ERWin (from CA). Does a good job but very expensive. -hilmar >>>> >>>> On Monday, February 14, 2005, at 10:39 PM, Barry Moore wrote: >>>> >>>>> Hi Hilmar- >>>>> >>>>> What software did you use to create that ERD for BioSQL? >>>>> >>>>> Barry >>>>> >>>>> -- >>>>> Barry Moore >>>>> Dept. of Human Genetics >>>>> University of Utah >>>>> Salt Lake City, UT >>>>> >>>>> >>>>> >>>>> >>> >>> -- >>> Barry Moore >>> Dept. of Human Genetics >>> University of Utah >>> Salt Lake City, UT >>> >>> >>> >>> >> -- >> ------------------------------------------------------------- >> 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 >> -- Barry Moore Dept. of Human Genetics University of Utah Salt Lake City, UT From hlapp at gnf.org Tue Feb 15 20:35:32 2005 From: hlapp at gnf.org (Hilmar Lapp) Date: Tue Feb 15 20:31:03 2005 Subject: [BioSQL-l] Re: ERD Creation Message-ID: I'll have to check whether I have v4.1. It looks though like it can also reverse-engineer from DDL SQL. -hilmar -----Original Message----- From: Barry Moore [mailto:barry.moore@genetics.utah.edu] Sent: Tue 2/15/2005 4:29 PM To: Jason Stajich Cc: Hilmar Lapp; biosql-l@open-bio.org Subject: Re: [BioSQL-l] Re: ERD Creation That looks like it will work great Jason. Thanks. Hilmar, this program will allow me to import ERWIN 4.1 XML model. Would it be possible to get and ERWIN XML dump of the bio-sql model from you (that I could then import into DBDesigner to add my local tables)? Barry Jason Stajich wrote: > DBDesigner isn't too bad for mysql schemas. > http://www.fabforce.net/dbdesigner4/ > > -- > Jason Stajich > jason.stajich at duke.edu > http://www.duke.edu/~jes12/ > > On Feb 16, 2005, at 7:05 AM, Hilmar Lapp wrote: > >> None of them was even close, sadly. >> >> There was three requirements though that I had that you may not care >> about. First, I needed the tool to read in an existing model in DDL >> (data definition language, i.e., CREATE blah, ALTER blah, etc) SQL >> and then allow me to modify it. Second, I needed the tool to be able >> to generate DDL from the modified model. Third, I needed the tool to >> support Oracle with its generated DDL. >> >> ERWin distinguishes between a logical model and a physical model. It >> applies rules that you can configure when translating (or sync'ing) >> between logical and physical model. For instance, my logical BioSQL >> model follows the table naming convention known from the mysql/Pg >> schemas and uses only standard SQL92 types, whereas the physical >> model is for Oracle, applies prefixes to all table names to avoid >> name clashes, and uses better-suited Oracle SQL types where >> applicable. The physical model also defines indexes, whereas the >> logical model only defines primary key column(s), foreign key >> relationships, and alternative key column(s). >> >> I found that feature very helpful while the schema was actively >> undergoing changes; now it's so stable it's not that important anymore. >> >> So, depending on what you're trying to do an open-source tool may be >> sufficient. Just the last thing I wanted to do was to draw it up in >> e.g. Dia, b/c that just gives you a lot of grief without much benefit >> except the diagram. >> >> -hilmar >> >> On Feb 15, 2005, at 11:12 AM, Barry Moore wrote: >> >>> $4K! Ouch. Have you used any open source or less expensive >>> alternatives that you found worthwhile? >>> >>> Barry >>> >>> Hilmar Lapp wrote: >>> >>>> ERWin (from CA). Does a good job but very expensive. -hilmar >>>> >>>> On Monday, February 14, 2005, at 10:39 PM, Barry Moore wrote: >>>> >>>>> Hi Hilmar- >>>>> >>>>> What software did you use to create that ERD for BioSQL? >>>>> >>>>> Barry >>>>> >>>>> -- >>>>> Barry Moore >>>>> Dept. of Human Genetics >>>>> University of Utah >>>>> Salt Lake City, UT >>>>> >>>>> >>>>> >>>>> >>> >>> -- >>> Barry Moore >>> Dept. of Human Genetics >>> University of Utah >>> Salt Lake City, UT >>> >>> >>> >>> >> -- >> ------------------------------------------------------------- >> 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 >> -- Barry Moore Dept. of Human Genetics University of Utah Salt Lake City, UT From b.juergensmeyer at sbcglobal.net Thu Feb 17 10:15:37 2005 From: b.juergensmeyer at sbcglobal.net (Brian L. Juergensmeyer) Date: Thu Feb 17 10:13:03 2005 Subject: [BioSQL-l] ERD applications Message-ID: <4214B519.1050709@sbcglobal.net> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi, All, I've been watching the discussions about ERD applications going back and forth the last couple of days. You may want to look at CASE Studio 2. It looks like it would have most of what I need, and the price is FAR more reasonable than ERWin's price ($369 vs. $4K). It also has a demo mode that will let you try it out. I've not purchased it myself (my company doesn't want to buy it, and I'm having a hard time with the concept of paying $370 for a non-reimbursed work expense for something I think they should buy). I just suggest it as an alternative. HTH, Brian - -- "The trouble with fighting for human freedom is that one spends most of one's time defending scoundrels. For it is against scoundrels that oppressive laws are first aimed, and oppression must be stopped at the beginning if it is to be stopped at all." - H. L. Mencken -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.4 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://enigmail.mozdev.org iD8DBQFCFLUZHhd3K9r81FMRAnjrAKCsKMJxTStBbg8cclT2NAcKFR7DCQCglFMG CyVY7hRTByBanxb8k49cSsY= =Fdr+ -----END PGP SIGNATURE----- From Wolfgang.Strasser at fh-hagenberg.at Thu Feb 17 11:03:36 2005 From: Wolfgang.Strasser at fh-hagenberg.at (Wolfgang Strasser) Date: Thu Feb 17 10:58:50 2005 Subject: [BioSQL-l] Reference for BioSQL Message-ID: <532D7AB7D5A2A34EAD3A39A7B650E877194E3C@postfux.fhs-hagenberg.ac.at> Hi everybody! We are currently in the process of writing a paper about our research project and therefore we would need a reference cite BioSQL. Could you please give me some hints where to find such a reference? Thanks in advance, Wolfgang -- DI (FH) Wolfgang Stra?er FH O? F&E GmbH Hauptstra?e 117 4232 Hagenberg BIOMIS - Insilico Proteomics System http://biomis.fh-hagenberg.at From hlapp at gnf.org Thu Feb 17 12:49:03 2005 From: hlapp at gnf.org (Hilmar Lapp) Date: Thu Feb 17 12:44:21 2005 Subject: [BioSQL-l] Reference for BioSQL In-Reply-To: <532D7AB7D5A2A34EAD3A39A7B650E877194E3C@postfux.fhs-hagenberg.ac.at> References: <532D7AB7D5A2A34EAD3A39A7B650E877194E3C@postfux.fhs-hagenberg.ac.at> Message-ID: <3650DD36-810C-11D9-BBC0-000A95AE92B0@gnf.org> The paper is in preparation. I suggest you cite the website obda.open-bio.org, and Lapp H, Mackey AJ, Stupka E, and Birney E. as authors. -hilmar On Feb 17, 2005, at 8:03 AM, Wolfgang Strasser wrote: > Hi everybody! > > > > We are currently in the process of writing a paper about our research > project and therefore we would need a reference cite BioSQL. Could you > please give me some hints where to find such a reference? > > > > Thanks in advance, > > Wolfgang > > > > > > -- > > DI (FH) Wolfgang Stra?er > > FH O? F&E GmbH > > Hauptstra?e 117 > > 4232 Hagenberg > > > > BIOMIS - Insilico Proteomics System > > http://biomis.fh-hagenberg.at > > > > > _______________________________________________ > 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.stajich at duke.edu Tue Feb 15 18:09:10 2005 From: jason.stajich at duke.edu (Jason Stajich) Date: Fri Feb 18 07:18:28 2005 Subject: [BioSQL-l] Re: ERD Creation In-Reply-To: References: <1561BF84-7F6E-11D9-96C2-000A959EB4C4@gnf.org> <421249AE.1000704@genetics.utah.edu> Message-ID: DBDesigner isn't too bad for mysql schemas. http://www.fabforce.net/dbdesigner4/ -- Jason Stajich jason.stajich at duke.edu http://www.duke.edu/~jes12/ On Feb 16, 2005, at 7:05 AM, Hilmar Lapp wrote: > None of them was even close, sadly. > > There was three requirements though that I had that you may not care > about. First, I needed the tool to read in an existing model in DDL > (data definition language, i.e., CREATE blah, ALTER blah, etc) SQL and > then allow me to modify it. Second, I needed the tool to be able to > generate DDL from the modified model. Third, I needed the tool to > support Oracle with its generated DDL. > > ERWin distinguishes between a logical model and a physical model. It > applies rules that you can configure when translating (or sync'ing) > between logical and physical model. For instance, my logical BioSQL > model follows the table naming convention known from the mysql/Pg > schemas and uses only standard SQL92 types, whereas the physical model > is for Oracle, applies prefixes to all table names to avoid name > clashes, and uses better-suited Oracle SQL types where applicable. The > physical model also defines indexes, whereas the logical model only > defines primary key column(s), foreign key relationships, and > alternative key column(s). > > I found that feature very helpful while the schema was actively > undergoing changes; now it's so stable it's not that important > anymore. > > So, depending on what you're trying to do an open-source tool may be > sufficient. Just the last thing I wanted to do was to draw it up in > e.g. Dia, b/c that just gives you a lot of grief without much benefit > except the diagram. > > -hilmar > > On Feb 15, 2005, at 11:12 AM, Barry Moore wrote: > >> $4K! Ouch. Have you used any open source or less expensive >> alternatives that you found worthwhile? >> >> Barry >> >> Hilmar Lapp wrote: >> >>> ERWin (from CA). Does a good job but very expensive. -hilmar >>> >>> On Monday, February 14, 2005, at 10:39 PM, Barry Moore wrote: >>> >>>> Hi Hilmar- >>>> >>>> What software did you use to create that ERD for BioSQL? >>>> >>>> Barry >>>> >>>> -- >>>> Barry Moore >>>> Dept. of Human Genetics >>>> University of Utah >>>> Salt Lake City, UT >>>> >>>> >>>> >>>> >> >> -- >> Barry Moore >> Dept. of Human Genetics >> University of Utah >> Salt Lake City, UT >> >> >> >> > -- > ------------------------------------------------------------- > 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 > -------------- next part -------------- A non-text attachment was scrubbed... Name: PGP.sig Type: application/pgp-signature Size: 186 bytes Desc: This is a digitally signed message part Url : http://open-bio.org/pipermail/biosql-l/attachments/20050216/9a81c05a/PGP-0001.bin From luca at cs.ualberta.ca Fri Feb 18 11:25:31 2005 From: luca at cs.ualberta.ca (Luca Pireddu) Date: Fri Feb 18 11:23:06 2005 Subject: [BioSQL-l] Re: ERD Creation In-Reply-To: References: <1561BF84-7F6E-11D9-96C2-000A959EB4C4@gnf.org> Message-ID: <200502180925.31267.luca@cs.ualberta.ca> On February 15, 2005 16:09, Jason Stajich wrote: > DBDesigner isn't too bad for mysql schemas. > http://www.fabforce.net/dbdesigner4/ > > -- > Jason Stajich > jason.stajich at duke.edu > http://www.duke.edu/~jes12/ > > > > On Feb 15, 2005, at 11:12 AM, Barry Moore wrote: > > > >> $4K! Ouch. Have you used any open source or less expensive > >> alternatives that you found worthwhile? > >> > >> Barry > >> > >> Hilmar Lapp wrote: > >> > >>> ERWin (from CA). Does a good job but very expensive. -hilmar > >>> > >>> On Monday, February 14, 2005, at 10:39 PM, Barry Moore wrote: > >>> > >>>> Hi Hilmar- > >>>> > >>>> What software did you use to create that ERD for BioSQL? > >>>> > >>>> Barry > >>>> For relatively cheap you can also get "Data Architect" by theKompany (60 USD). Look here: http://www.thekompany.com/products/dataarchitect/ It runs on Linux, Mac OSX, and Windows. It supports ODBC, MySQL, PostgreSQL, DB2. Luca