TFBS::DB::JASPAR4(3pm)

NAME

TFBS::DB::JASPAR4 - interface to MySQL relational database of pattern
matrices

SYNOPSIS

o   creating a database object by connecting to the existing
    JASPAR2-type database

        my $db = TFBS::DB::JASPAR4->connect("dbi:mysql:JASPAR4:myhost",
                                            "myusername",
                                            "mypassword");

o   retrieving a TFBS::Matrix::* object from the database

        # retrieving a PFM by ID
        my $pfm = $db->get_Matrix_by_ID('M0079','PFM');

        #retrieving a PWM by name
        my $pwm = $db->get_Matrix_by_name('NF-kappaB', 'PWM');

o   retrieving a set of matrices as a TFBS::MatrixSet object according
    to various criteria

        # retrieving a set of PWMs from a list of IDs:
        my @IDlist = ('M0019', 'M0045', 'M0073', 'M0101');
        my $matrixset = $db->get_MatrixSet(-IDs => \@IDlist,
                                           -matrixtype => "PWM");

        # retrieving a set of ICMs from a list of names:
        my @namelist = ('p50', 'p53', 'HNF-1'. 'GATA-1', 'GATA-2', 'GATA-3');
        my $matrixset = $db->get_MatrixSet(-names => \@namelist,
                                           -matrixtype => "ICM");

        # retrieving a set of all PFMs in the database
        # derived from human genes:
        my $matrixset = $db->get_MatrixSet(-species => ['Homo sapiens'],
                                           -matrixtype => "PFM");

o   creating a new JASPAR4-type database named MYJASPAR4:

        my $db = TFBS::DB::JASPAR4->create("dbi:mysql:MYJASPAR4:myhost",
                                           "myusername",
                                           "mypassword");

o   storing a matrix in the database (currently only PFMs):

        #let $pfm is a TFBS::Matrix::PFM object
        $db->store_Matrix($pfm);

DESCRIPTION

TFBS::DB::JASPAR4 is a read/write database interface module that
retrieves and stores TFBS::Matrix::* and TFBS::MatrixSet objects in a
relational database. The interface is nearly identical to the
JASPAR2interface, while the underlying data model is different

JASPAR2 DATA MODEL

JASPAR4 is working name for a relational database model used for
storing transcriptional factor pattern matrices in a MySQL database.
It was initially designed (JASPAR2) to store matrices for the JASPAR
database of high quality eukaryotic transcription factor specificity
profiles by Albin Sandelin and Wyeth W. Wasserman. Besides the profile matrix itself, this data model stores profile ID (unique), name,
structural class, basic taxonomic and bibliographic information as well as some additional opseqdbtional tags.

Tags that are commonly used in the actual JASPAR database include: 'medline' # PubMed ID
'species' # Species name
'superclass' #Species supergroup, eg 'vertebrate', 'plant' etc
'total_ic' # total information content - redundant, present
# for historical; 'type' #experimental nethod
'acc' #accession number for TF protein sequence
'seqdb' #corresponding database name
but any tag is storable and searchable.
----------------------- ADVANCED ---------------------------------
For the developers and the curious, here is the JASPAR4 data model:
It is our best intention to hide the details of this data model, which we are using on a daily basis in our work, from most TFBS users. Most users should only know the methods to store the data and which tags are supported.
-------------------------------------------------------------------------

FEEDBACK

Please send bug reports and other comments to the author.

AUTHOR - Boris Lenhard

Boris Lenhard <Boris.Lenhard@cgb.ki.se>

APPENDIX

The rest of the documentation details each of the object methods.
Internal methods are preceded with an underscore.
new: Title : new
Usage : DEPRECATED - for backward compatibility only
Use connect() or create() instead
connect: Title : connect
Usage : my $db =
TFBS::DB::JASPAR4->connect("dbi:mysql:DATABASENAME:HOSTNAME",
"USERNAME",
"PASSWORD");

Function: connects to the existing JASPAR4-type database and

returns a database object that interfaces the database

Returns : a TFBS::DB::JASPAR4 object
Args : a standard database connection triplet

("dbi:mysql:DATABASENAME:HOSTNAME", "USERNAME", "PASSWORD") In place of DATABASENAME, HOSTNAME, USERNAME and PASSWORD,
use the actual values. PASSWORD and USERNAME might be
optional, depending on the user's acces permissions for
the database server.
dbh: Title : dbh
Usage : my $dbh = $db->dbh();
$dbh->do("UPDATE matrix_data SET name='ADD1' WHERE NAME='SREBP2'");; Function: returns the DBI database handle of the MySQL database
interfaced by $db; THIS IS USED FOR WRITING NEW METHODS
FOR DIRECT RELATIONAL DATABASE MANIPULATION - if you
have write access AND do not know what you are doing,
you can severely corrupt the data
For documentation about database handle methods, see L<DBI>; Returns : the database (DBI) handle of the MySQL JASPAR2-type
relational database associated with the TFBS::DB::JASPAR2
object; Args : none
store_Matrix: Title : store_Matrix
Usage : $db->store_Matrix($matrixobject);
Function: Stores the contents of a TFBS::Matrix::DB object in the database Returns : 0 on success; $@ contents on failure
(this is too C-like and may change in future versions); Args : (PFM_object)
A TFBS::Matrix::PFM, FBS::Matrix::PWM or FBS::Matrix::ICM object. PFM object are recommended to use, as they are eaily converted to other formats; Comment : this is an experimental method that is not 100% bulletproof;
use at your own risk
get_Matrix_by_ID: Title : get_Matrix_by_ID
Usage : my $pfm = $db->get_Matrix_by_ID('M00034', 'PFM');
Function: fetches matrix data under the given ID from the
database and returns a TFBS::Matrix::* object; Returns : a TFBS::Matrix::* object; the exact type of the
object depending on what form the matrix is stored
in the database (PFM is default); Args : (Matrix_ID)
Matrix_ID is a string;
get_Matrix_by_name: Title : get_Matrix_by_name
Usage : my $pfm = $db->get_Matrix_by_name('HNF-1');
Function: fetches matrix data under the given name from the
database and returns a TFBS::Matrix::* object; Returns : a TFBS::Matrix::* object; the exact type of the object
depending on what form the matrix object was stored in
the database (default PFM)); Args : (Matrix_name); Warning : According to the current JASPAR4 data model, name is
not necessarily a unique identifier. In the case where
there are several matrices with the same name in the
database, the function fetches the first one and prints
a warning on STDERR. You've been warned.
get_MatrixSet: Title : get_MatrixSet
Usage : my $matrixset = $db->get_MatrixSet(%args);
Function: fetches matrix data under for all matrices in the database
matching criteria defined by the named arguments
and returns a TFBS::MatrixSet object; Returns : a TFBS::MatrixSet object
Args : This method accepts named arguments, corresponding to arbitrary tags.
Note that this is different from JASPAR2. As any tag is supported for database storage, any tag can be used for information retrieval. Additionally, arguments as 'name' and 'class' can be used (even though they are not tags.
As with get_Matrix methods, it is important to realize taht any matrix format can be stored in the database: the TFBS::MatrixSet might therefore consist of PFMs, ICMs and PWMS, depending on how matrices are stored,

Examples include
-ID # a reference to an array of IDs (strings)
-name # a reference to an array of
# transcription factor names (string)

-class # a reference to an array of

# structural class names (strings)

-species # a reference to an array of

# Latin species names (strings)

-sysgroup # a reference to an array of

# higher taxonomic categories (strings)
-min_ic # float, minimum total information content: # of the matrix. IMPORTANT:if retrieved matrices are in PWM format there is no way to measureinformation content.
-matrixtype #string describing type of matrix to retrieve. If left out, the format: will revert to the database format. Note that this option only works
if the database format is pfm
The arguments that expect list references are used in database query formulation: elements within lists are combined with 'OR' operators, and the lists of different types with 'AND'. For example,: my $matrixset = $db->(-class => ['TRP_CLUSTER', 'FORKHEAD'],
-species => ['Homo sapiens', 'Mus musculus'], );
gives a set of TFBS::Matrix::PFM objects (given that the matrix models are stored as such): whose (structural clas is 'TRP_CLUSTER' OR'FORKHEAD') AND (the species
they are derived: from is 'Homo sapiens'OR 'Mus musculus').
The -min_ic filter is applied after the query in the sense that the matrices profiles with total infromation content less than specified are not included in the set.
delete_Matrix_having_ID: Title : delete_Matrix_having_ID
Usage : $db->delete_Matrix_with_ID('M00045');
Function: Deletes the matrix having the given ID from the database
Returns : 0 on success; $@ contents on failure
(this is too C-like and may change in future versions); Args : (ID)
A string; Comment : Yeah, yeah, 'delete_Matrix_having_ID' is a stupid name
for a method, but at least it should be obviuos what it does.

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