[MOBY-l] need help in populating a simple DB with biomoby services

[maliha aziz]

Hello Dr Wilkinson :)
 nope noone answered but I figured out the packages and all... I just want to confirm the thought process and the LSID part... All services and all datatypes do have LSIDs right?  I need a unique primary key and LSID is my best shot here :)
One more question the "HAS" and "HASA" relationship types allow me to determine if there are multiple instances of the same datatypes i.e. whether it is a record or a bag... right?

I dont think (at the moment ) that implementing whether a datatype is a record list or a bag etc for biomoby in my project is realistic. I dont know maybe a lot of brain storming is needed for this part... (maybe i need to clear my own concepts on this part first)

Thanks

Maliha 

Mark Wilkinson <markw at illuminae.com> wrote: Did anyone ever answer you?



On Wed, 26 Sep 2007 15:19:07 -0700, maliha aziz   
wrote:

> Hi
> the datatypes in biomoby are either
>
>    records or
>
>    sets (has only one instance of a particular child e.g. geneSNP that  
> is composed of
>
>        aa_pos (HASA) => Integer
>        strain (HASA) => String
>        codon_ref (HASA) => String
>        aa_ref (HASA) => String
>        codon_var (HASA) => String
>        aa_var (HASA) => String
>        aa_change (HASA) => String)     or
>
>    bags ( allows repeat of the same instance within it .g DNA sequence  
> Holder )
> correct?
>
> I have a simple Database that is composed of 5 tables
>
> The first table is called the "Concept class". It will hold the  
> datatypes declared in biomoby and their LSID
> The Second table is called the "Concept structure". It will hold the  
> information about the datatype itself whether it is a record , a set or  
> a bag....
> the third table is the "Concept Components". This table would hold the  
> child information i.e. for geneSNP datatype this table would hold
>    aa_pos (HASA) => Integer
>        strain (HASA) => String
>        codon_ref (HASA) => String
>        aa_ref (HASA) => String
>        codon_var (HASA) => String
>        aa_var (HASA) => String
>        aa_change (HASA) => String)
> LSID of each component would be stored along with other info.
>
> Now this takes care of the datatype. To look at the tool itself
> I have a table "Tools" that hold the information about the webservice  
> registered in biomoby its name the LSID etc
> Another table called the "Tools_io" holds the information about the  
> input and out puts of this particular tool . This is basically a  
> relational entity between the Tools and the Concept compnents.
>
> My first question... Am I on the right track?
> About the concept structure table I would have to find out  
> programmatically myself whether the datatype is a record or a set or a  
> bag by looking at the LSIDz right? (does a simple string have a LSID?)
> Secondly , right now I have just downloaded the webservices in a simple  
> file from biomoby so am not really sure if  this is going to work  
> although the work is pretty simple. It is the biomoby end that is a bit  
> confusing.
> If I download the datatypes and populate the Concept table and then  
> venture towards downloading the tools themselves Can I link the  
> datatypes with the tool IO through the LSID?
> Could someone tell me what packages am I looking at over here while  
> tryin to accomplish this.
>
> There is one thing missing here and that is the declaration of Tools_IO  
> to be collections or enumerated etc at the time of declaring the tool. I  
> still have to figure that out
>
> I would be really grateful if someone could help me out in this... :)
>
> regards
>
> Maliha
>
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-- 
--
Mark Wilkinson
Assistant Professor, Dept. Medical Genetics
University of British Columbia
PI Bioinformatics
iCAPTURE Centre, St. Paul's Hospital
Tel:  604 682 2344 x62129
Fax:  604 806 9274

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