[Bioperl-l] Phenotype interface and OMIMentry

[Chris Zmasek]

Hello:

Thanks to all who gave useful input regarding my question about an OMIM parser.

I intend to implement it as follows.

1. The parser will be stream based. I.e. it has a "next" method which returns "OMIMentry" objects.

2. The class "OMIMentry" will be a member of the Bio::Organism::Phenotype namespace.

3. Bio::Organism::Phenotype::OMIMentry will implement a yet to be defined Bio::Organism::Phenotype interface ("PhenotypeI ").

Unfortunatly, I am not clear what a Phenotype interface should contain (or, to be more precise -- what the community's preferences are for such an interface).

My suggestion is as follows:

* a phenotype interface has to be very generic: 

* it should force its implemetors to provide access to at least the following fields:

- a name
- a code/symbol
- a description
- a "location": maybe a reference to a genotype, a gene, and/or a mutation
- a Species
- a list of references
- a comment

What are your suggestions/comments regarding such an Phenotype interface?

OMIMentry would add a lot more specific fields to PhenotypeI: such as MIM number, clinical symptoms, creator, editors, ...

Thank you,

Christian [czmasek@gnf.org]