Re: [Savannah-hackers] submission of BioDB - savannah.nongnu.org

[Dan Bolser]

Thanks very much for this email -  I will get on to the authors of
Mandarax and Prova about this point. Both of these packages are available
at source forge for you to review...

http://sourceforge.net/project/showfiles.php?group_id=50817
http://sourceforge.net/project/showfiles.php?group_id=50817&package_id=126814

The source code for one of our applications (building the SCOP relational
database) can be found under the examples section of the prova
distribution...

(The length of the code is a feature of prova...)

:- eval(consult("utils.prova")).

:- eval(parse(scop,des,"/prova/des.txt")).
:- eval(parse(scop,cla,"/prova/cla.txt")).

% Database locations
location(database,scop,"jdbc:mysql://localhost","username","password").

% SCOP: Populate
parse(DBName,Type,File) :-
        dbopen(DBName,DB),
        fopen(File,Reader),
        read_enum(Reader,Line),
        db_import(DB,DBName,Type,Line).
db_import(DB,scop,des,Line) :-
        tokenize_list(Line,"\t",[T|Ts]),
        %println([T|Ts]," "),
        sql_insert(DB,des,[id,type,sccs,sid,description],[T|Ts]).
db_import(DB,scop,cla,Line) :-
        tokenize_list(Line,"\t",[Sid,Pid,DDefs,Sccs,PX,Trace]),
        tokenize_enum(DDefs,",",DDef),
        parse_list(DDef,"(?:(\w*):|)(-?\d*\w?)-?(\d*)",[T|Ts]),
        sql_insert(DB,subchain,[px,chain_id,begin,end],[PX,T|Ts]).
db_import(DB,scop,cla,Line) :-
        tokenize_list(Line,"\t",[Sid,Pid,DDefs,Sccs,PX,Trace]),
        parse_nv(Trace,"(?:(\w+)=(\w+),?)",[N|Ns],[V|Vs]),
        sql_insert(DB,cla,[sid,pdb_id,sccs,N|Ns],[Sid,Pid,Sccs,V|Vs]).


I will let you know,
Dan.

On Tue, 19 Oct 2004, Michael McTails wrote:

>I'm evaluating the project you submitted for approval in Savannah.
>
>You must determine whether your project and it's dependencies
>can run on a Free Software Java suite (see 
>http://www.gnu.org/software/java/
>for more information).
>
>We recommend you to test your project using GCJ and GNU Classpath, and
>ensure that your Java code runs on this Free Software Java suite.
>
>GCJ is the GNU Compiler for Java, part of the GCC (GNU Compiler
>Collection).  The Classpath project aims to develop a free and portable
>implementation of the Java API (the classes in the 'java' package).
>
>More information is available at http://gcc.gnu.org/ and
>http://www.gnu.org/software/classpath/,
>
>Furthermore, please include an (perhaps temporary)
>URL pointing to the source code. We wish to review your source code,
>even if it is not functional, to catch potential legal issues early.
>The description you gave whenregistering will not be read by the 
>general public.
>If you are still concerned with privacy, however, you can forward the 
>code to me by email
>address@hidden
>
>Please provide us with more information about this point.
>
>> A package was submitted to savannah.nongnu.org
>> This mail was sent to address@hidden, 
>> address@hidden
>>
>>
>> Dan Bolser <address@hidden> described the package as 
>> follows:
>> License: gpl
>> Other License:
>> Package: BioDB
>> System name: biodb
>> Type: non-GNU
>>
>> Description:
>> This project aims to produce very simple software to produce and 
>> maintain a set
>> of biological databases in relational form. The software will download 
>> text
>> versions of various databases, and produce a 'standardized' relational 
>> version
>> of that database in tab delimited form, suitable for loading into any
>> relational database system (such as mysql).
>>
>> The standard versions of these databases can then form components of 
>> other
>> projects.
>>
>> First, the SCOP databases will be 'processed'
>> (http://scop.mrc-lmb.cam.ac.uk/scop/) which is open access.
>>
>> We will then consider looking at ENZYME 
>> (http://www.expasy.org/enzyme/),
>> SwissProt (http://us.expasy.org/sprot/) and GO 
>> (http://www.geneontology.org/),
>> based on the evaluation of the licence.
>>
>> Initally Perl will be used.
>>
>> This rather simple project may form a test bed for the new experimental
>> software language, Prova.
>> http://osdn.dl.sourceforge.net/sourceforge/mandarax/prova_all_1.7.1.zip
>>
>>
>>
>> Other Software Required:
>> Mandarax (http://mandarax.sourceforge.net/)
>> Prova (http://comas.soi.city.ac.uk/prova/)
>>
>> Other Comments:
>> I previously submitted this project some time last year. SCOP is freely
>> available and open source (the old licence has elapsed). Prova is 
>> LPGL. The
>> code is trivial.