[Bioperl-l] Description of PhenotypeI and OMIMentry

[Chris Zmasek]

Recently, I submitted a number of classes: 

Bio::Phenotype::PhenotypeI
Bio::Phenotype::Measure
Bio::Phenotype::Correlate
Bio::Phenotype::OMIM::OMIMentry
Bio::Phenotype::OMIM::MiniMIMentry
Bio::Phenotype::OMIM::OMIMentryAllelicVariant
Bio::Phenotype::OMIM::OMIMparser
Bio::Tools::ECnumber


In the following, classes Bio::Phenotype::PhenotypeI
and Bio::Phenotype::OMIM::OMIMentry are described.

Descriptions of the other classes will follow shortly.



Bio::Phenotype::PhenotypeI
--------------------------

This class is a basic interface for phenotypes.

It provides the following methods for accessing its
data members:

-- name        set/get for the name or id of this phenotype [scalar]

-- description set/get for the description of this phenotype [scalar]

-- species     set/get for the species of this phenotype [Bio::Species]

-- comment     set/get for a comment about this phenotype [scalar]


[array of [scalar]] gene symbols like "fgl1"
-- each_gene_symbol
-- add_gene_symbols
-- remove_gene_symbols 

[array of [Bio::Variation::VariantI]]: the mutations causing this phenotype
-- each_Variant
-- add_Variants
-- remove_Variants

[array of [Bio::Annotation::Reference]]: references describing this phenotype
-- each_Reference 
-- add_References 
-- remove_References  

[array of [Bio::Map::CytoPosition]]: chromosomal positions associated with this phenotype
-- each_CytoPosition 
-- add_CytoPositions
-- remove_CytoPositions

Correlates are correlating phenotypes in different species;
inspired by mouse correlates of human phenotypes in the OMIM
database:
[array of [Bio::Phenotype::Correlate]]
-- each_Correlate
-- add_Correlates
-- remove_Correlates

Bio::Phenotype::Measure is for biochemically defined phenotypes
or any other types of measures.
[array of [Bio::Phenotype::Measure]]
-- each_Measure
-- add_Measures
-- remove_Measures

[array of [scalar]]
-- each_keyword
-- add_keywords
-- remove_keywords

[array of [Bio::Annotation::DBLink]]
-- each_DBLink
-- add_DBLink
-- remove_DBLinks

A list of "genotypes" associated with this phenotype.
The "genotypes" data member and its methods certainly needs
to be improved -- currently there is no specific class for genotypes, 
hence any scalar can be used at the moment:
-- each_Genotype 
-- add_Genotypes
-- remove_Genotypes



Bio::Phenotype::OMIM::OMIMentry
-------------------------------

OMIMentry - represents OMIM (Online Mendelian Inheritance in Man) database entries and implements Bio::Phenotype::PhenotypeI.


It adds the following methods:

-- new
-- init (sets all data to "" or [])
-- to_string


-- MIM_number  set/get for the MIM number of this OMIM entry

-- title       alias for name

-- alternative_titles_and_symbols 
           set/get for the "alternative titles and symbols" of this
           OMIM entry.
           Currently, everything after the first line of title (TI)
           field is
           considered "alternative titles and symbols".

-- more_than_two_genes 
           this is true if this phenotype can be caused
           by mutation in any of two or more genes.
           In OMIM, this is indicated by a number symbol (#)
           before an entry number (e.g. #114480 -- BREAST CANCER).


-- is_separate
           this is true if the phenotype determined by the gene at
           the given locus is separate from those represented by
           other entries where "is_separate" is true and if the mode
           of inheritance of the phenotype has been proved
           (in the judgment of the authors and editors).
           In OMIM, this is indicated by a asterisk  (*)
           before an entry number (e.g. *113705 BREAST CANCER,
           TYPE 1; BRCA1).



-- mapping_method set/get for the mapping method of this OMIM entry
                  e.g. "PCR of somatic cell hybrid DNA" 



-- gene_status 
              C = confirmed - observed in at least two laboratories or
                  in several families.
              P = provisional - based on evidence from one laboratory
                  or one family.
              I = inconsistent - results of different laboratories
                  disagree.
              L = limbo - evidence not as strong as that provisional,
                  but included for heuristic reasons. (Same as 
                  `tentative'.)


-- clinical_symptoms set/get for the clinical symptoms of this OMIM entry

-- created       Name(s) and date(s) [scalar - free form].
-- contributors  Name(s) and date(s) [scalar - free form].
-- edited        Name(s) and date(s) [scalar - free form].

-- additional_references   Set/get for the additional references of this OMIM antry
                           (SA: see also)


-- miniMIM   set/get for the Mini MIM associated with this OMIM antry

[array of [Bio::Phenotype::OMIM::OMIMentryAllelicVariant]]:
-- each_AllelicVariant
-- add_AllelicVariants
-- remove_AllelicVariants



Thanks,

Christian Zmasek [czmasek@gnf.org]











> -----Original Message-----
> From: Ewan Birney [mailto:birney@ebi.ac.uk]
> Sent: Wednesday, September 11, 2002 11:38 PM
> To: bioperl-l@bioperl.org
> Subject: [Bioperl-l] Re: [Bioperl-guts-l] bioperl commit
> 
> 
> 
> 
> Chris Z - great looking commits - at some point, can you give the list
> an overview of the functionality you have checked in? I would be
> interested in a quick tutorial ;)
> 
> 
> 
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