Bio-KBase
21 results

 view release on metacpan or  search on metacpan

er_scripts/all_entities_Compound  view on Meta::CPAN 

=item label

=item abbr

=item msid

=item ubiquitous

=item mod_date

=item uncharged_formula

=item formula

=item mass

=back    
   
=back

=head2 Output Format

The standard output is a tab-delimited file. It consists of the input
file with an extra column added for each requested field.  Input lines that cannot
be extended are written to stderr.  

=cut

use Bio::KBase::CDMI::CDMIClient;
use Getopt::Long;

#Default fields

my @all_fields = ( 'label', 'abbr', 'msid', 'ubiquitous', 'mod_date', 'uncharged_formula', 'formula', 'mass' );
my %all_fields = map { $_ => 1 } @all_fields;

my $usage = "usage: all_entities_Compound [-show-fields] [-a | -f field list] > entity.data";

my $a;
my $f;
my @fields;
my $show_fields;
my $geO = Bio::KBase::CDMI::CDMIClient->new_get_entity_for_script("a" 		=> \$a,
								  "show-fields" => \$show_fields,

er_scripts/get_entity_Compound  view on Meta::CPAN 

=item label

=item abbr

=item msid

=item ubiquitous

=item mod_date

=item uncharged_formula

=item formula

=item mass

=back    

=back

=head2 Output Format

The standard output is a tab-delimited file. It consists of the input
file with an extra column added for each requested field.  Input lines that cannot
be extended are written to stderr.  

=cut

use Bio::KBase::CDMI::CDMIClient;
use Getopt::Long;

#Default fields

my @all_fields = ( 'label', 'abbr', 'msid', 'ubiquitous', 'mod_date', 'uncharged_formula', 'formula', 'mass' );
my %all_fields = map { $_ => 1 } @all_fields;

my $usage = "usage: get_entity_Compound [-h] [-c column] [-a | -f field list] < ids > extended.by.a.column(s)";

my $column;
my $a;
my $f;
my $i = "-";
my @fields;
my $show_fields;

er_scripts/get_relationship_HasAsTerminus  view on Meta::CPAN 

=item label

=item abbr

=item msid

=item ubiquitous

=item mod_date

=item uncharged_formula

=item formula

=item mass

=back    

=item -rel field-list

Choose a set of fields from the relationship to return. Field-list is a comma-separated list of 
strings. The following fields are available:

er_scripts/get_relationship_HasAsTerminus  view on Meta::CPAN 


=cut
use Bio::KBase::Utilities::ScriptThing;
use Bio::KBase::CDMI::CDMIClient;
use Getopt::Long;

#Default fields
 
my @all_from_fields = ( 'id', 'common_name' );
my @all_rel_fields = ( 'from_link', 'to_link', 'group_number' );
my @all_to_fields = ( 'id', 'label', 'abbr', 'msid', 'ubiquitous', 'mod_date', 'uncharged_formula', 'formula', 'mass' );

my %all_from_fields = map { $_ => 1 } @all_from_fields;
my %all_rel_fields = map { $_ => 1 } @all_rel_fields;
my %all_to_fields = map { $_ => 1 } @all_to_fields;

my @default_fields = ('from-link', 'to-link');

my @from_fields;
my @rel_fields;
my @to_fields;

er_scripts/get_relationship_HasCompoundAliasFrom  view on Meta::CPAN 

=item label

=item abbr

=item msid

=item ubiquitous

=item mod_date

=item uncharged_formula

=item formula

=item mass

=back    

=back

=head2 Output Format

The standard output is a tab-delimited file. It consists of the input

er_scripts/get_relationship_HasCompoundAliasFrom  view on Meta::CPAN 


=cut
use Bio::KBase::Utilities::ScriptThing;
use Bio::KBase::CDMI::CDMIClient;
use Getopt::Long;

#Default fields
 
my @all_from_fields = ( 'id',  );
my @all_rel_fields = ( 'from_link', 'to_link', 'alias' );
my @all_to_fields = ( 'id', 'label', 'abbr', 'msid', 'ubiquitous', 'mod_date', 'uncharged_formula', 'formula', 'mass' );

my %all_from_fields = map { $_ => 1 } @all_from_fields;
my %all_rel_fields = map { $_ => 1 } @all_rel_fields;
my %all_to_fields = map { $_ => 1 } @all_to_fields;

my @default_fields = ('from-link', 'to-link');

my @from_fields;
my @rel_fields;
my @to_fields;

er_scripts/get_relationship_HasPresenceOf  view on Meta::CPAN 

=item label

=item abbr

=item msid

=item ubiquitous

=item mod_date

=item uncharged_formula

=item formula

=item mass

=back    

=back

=head2 Output Format

The standard output is a tab-delimited file. It consists of the input

er_scripts/get_relationship_HasPresenceOf  view on Meta::CPAN 


=cut
use Bio::KBase::Utilities::ScriptThing;
use Bio::KBase::CDMI::CDMIClient;
use Getopt::Long;

#Default fields
 
my @all_from_fields = ( 'id', 'mod_date', 'name', 'type' );
my @all_rel_fields = ( 'from_link', 'to_link', 'concentration', 'minimum_flux', 'maximum_flux' );
my @all_to_fields = ( 'id', 'label', 'abbr', 'msid', 'ubiquitous', 'mod_date', 'uncharged_formula', 'formula', 'mass' );

my %all_from_fields = map { $_ => 1 } @all_from_fields;
my %all_rel_fields = map { $_ => 1 } @all_rel_fields;
my %all_to_fields = map { $_ => 1 } @all_to_fields;

my @default_fields = ('from-link', 'to-link');

my @from_fields;
my @rel_fields;
my @to_fields;

er_scripts/get_relationship_HasUsage  view on Meta::CPAN 

=item label

=item abbr

=item msid

=item ubiquitous

=item mod_date

=item uncharged_formula

=item formula

=item mass

=back    

=item -rel field-list

Choose a set of fields from the relationship to return. Field-list is a comma-separated list of 
strings. The following fields are available:

er_scripts/get_relationship_HasUsage  view on Meta::CPAN 

file with an extra column added for each requested field.  Input lines that cannot
be extended are written to stderr.  

=cut
use Bio::KBase::Utilities::ScriptThing;
use Bio::KBase::CDMI::CDMIClient;
use Getopt::Long;

#Default fields
 
my @all_from_fields = ( 'id', 'label', 'abbr', 'msid', 'ubiquitous', 'mod_date', 'uncharged_formula', 'formula', 'mass' );
my @all_rel_fields = ( 'from_link', 'to_link',  );
my @all_to_fields = ( 'id', 'coefficient' );

my %all_from_fields = map { $_ => 1 } @all_from_fields;
my %all_rel_fields = map { $_ => 1 } @all_rel_fields;
my %all_to_fields = map { $_ => 1 } @all_to_fields;

my @default_fields = ('from-link', 'to-link');

my @from_fields;

er_scripts/get_relationship_IsParticipationOf  view on Meta::CPAN 

=item label

=item abbr

=item msid

=item ubiquitous

=item mod_date

=item uncharged_formula

=item formula

=item mass

=back    

=item -rel field-list

Choose a set of fields from the relationship to return. Field-list is a comma-separated list of 
strings. The following fields are available:

er_scripts/get_relationship_IsParticipationOf  view on Meta::CPAN 


=cut
use Bio::KBase::Utilities::ScriptThing;
use Bio::KBase::CDMI::CDMIClient;
use Getopt::Long;

#Default fields
 
my @all_from_fields = ( 'id', 'stoichiometry', 'cofactor', 'compartment_index', 'transport_coefficient' );
my @all_rel_fields = ( 'from_link', 'to_link',  );
my @all_to_fields = ( 'id', 'label', 'abbr', 'msid', 'ubiquitous', 'mod_date', 'uncharged_formula', 'formula', 'mass' );

my %all_from_fields = map { $_ => 1 } @all_from_fields;
my %all_rel_fields = map { $_ => 1 } @all_rel_fields;
my %all_to_fields = map { $_ => 1 } @all_to_fields;

my @default_fields = ('from-link', 'to-link');

my @from_fields;
my @rel_fields;
my @to_fields;

er_scripts/get_relationship_IsPresentIn  view on Meta::CPAN 

=item label

=item abbr

=item msid

=item ubiquitous

=item mod_date

=item uncharged_formula

=item formula

=item mass

=back    

=back

=head2 Output Format

The standard output is a tab-delimited file. It consists of the input
file with an extra column added for each requested field.  Input lines that cannot
be extended are written to stderr.  

=cut
use Bio::KBase::Utilities::ScriptThing;
use Bio::KBase::CDMI::CDMIClient;
use Getopt::Long;

#Default fields
 
my @all_from_fields = ( 'id', 'label', 'abbr', 'msid', 'ubiquitous', 'mod_date', 'uncharged_formula', 'formula', 'mass' );
my @all_rel_fields = ( 'from_link', 'to_link', 'concentration', 'minimum_flux', 'maximum_flux' );
my @all_to_fields = ( 'id', 'mod_date', 'name', 'type' );

my %all_from_fields = map { $_ => 1 } @all_from_fields;
my %all_rel_fields = map { $_ => 1 } @all_rel_fields;
my %all_to_fields = map { $_ => 1 } @all_to_fields;

my @default_fields = ('from-link', 'to-link');

my @from_fields;

er_scripts/get_relationship_IsShownOn  view on Meta::CPAN 

=item label

=item abbr

=item msid

=item ubiquitous

=item mod_date

=item uncharged_formula

=item formula

=item mass

=back    

=back

=head2 Output Format

The standard output is a tab-delimited file. It consists of the input
file with an extra column added for each requested field.  Input lines that cannot
be extended are written to stderr.  

=cut
use Bio::KBase::Utilities::ScriptThing;
use Bio::KBase::CDMI::CDMIClient;
use Getopt::Long;

#Default fields
 
my @all_from_fields = ( 'id', 'label', 'abbr', 'msid', 'ubiquitous', 'mod_date', 'uncharged_formula', 'formula', 'mass' );
my @all_rel_fields = ( 'from_link', 'to_link', 'location' );
my @all_to_fields = ( 'id', 'name', 'content' );

my %all_from_fields = map { $_ => 1 } @all_from_fields;
my %all_rel_fields = map { $_ => 1 } @all_rel_fields;
my %all_to_fields = map { $_ => 1 } @all_to_fields;

my @default_fields = ('from-link', 'to-link');

my @from_fields;

er_scripts/get_relationship_IsTerminusFor  view on Meta::CPAN 

=item label

=item abbr

=item msid

=item ubiquitous

=item mod_date

=item uncharged_formula

=item formula

=item mass

=back    

=item -rel field-list

Choose a set of fields from the relationship to return. Field-list is a comma-separated list of 
strings. The following fields are available:

er_scripts/get_relationship_IsTerminusFor  view on Meta::CPAN 

file with an extra column added for each requested field.  Input lines that cannot
be extended are written to stderr.  

=cut
use Bio::KBase::Utilities::ScriptThing;
use Bio::KBase::CDMI::CDMIClient;
use Getopt::Long;

#Default fields
 
my @all_from_fields = ( 'id', 'label', 'abbr', 'msid', 'ubiquitous', 'mod_date', 'uncharged_formula', 'formula', 'mass' );
my @all_rel_fields = ( 'from_link', 'to_link', 'group_number' );
my @all_to_fields = ( 'id', 'common_name' );

my %all_from_fields = map { $_ => 1 } @all_from_fields;
my %all_rel_fields = map { $_ => 1 } @all_rel_fields;
my %all_to_fields = map { $_ => 1 } @all_to_fields;

my @default_fields = ('from-link', 'to-link');

my @from_fields;

er_scripts/get_relationship_IsUsageOf  view on Meta::CPAN 

=item label

=item abbr

=item msid

=item ubiquitous

=item mod_date

=item uncharged_formula

=item formula

=item mass

=back    

=item -rel field-list

Choose a set of fields from the relationship to return. Field-list is a comma-separated list of 
strings. The following fields are available:

er_scripts/get_relationship_IsUsageOf  view on Meta::CPAN 


=cut
use Bio::KBase::Utilities::ScriptThing;
use Bio::KBase::CDMI::CDMIClient;
use Getopt::Long;

#Default fields
 
my @all_from_fields = ( 'id', 'coefficient' );
my @all_rel_fields = ( 'from_link', 'to_link',  );
my @all_to_fields = ( 'id', 'label', 'abbr', 'msid', 'ubiquitous', 'mod_date', 'uncharged_formula', 'formula', 'mass' );

my %all_from_fields = map { $_ => 1 } @all_from_fields;
my %all_rel_fields = map { $_ => 1 } @all_rel_fields;
my %all_to_fields = map { $_ => 1 } @all_to_fields;

my @default_fields = ('from-link', 'to-link');

my @from_fields;
my @rel_fields;
my @to_fields;

er_scripts/get_relationship_ParticipatesAs  view on Meta::CPAN 

=item label

=item abbr

=item msid

=item ubiquitous

=item mod_date

=item uncharged_formula

=item formula

=item mass

=back    

=item -rel field-list

Choose a set of fields from the relationship to return. Field-list is a comma-separated list of 
strings. The following fields are available:

er_scripts/get_relationship_ParticipatesAs  view on Meta::CPAN 

file with an extra column added for each requested field.  Input lines that cannot
be extended are written to stderr.  

=cut
use Bio::KBase::Utilities::ScriptThing;
use Bio::KBase::CDMI::CDMIClient;
use Getopt::Long;

#Default fields
 
my @all_from_fields = ( 'id', 'label', 'abbr', 'msid', 'ubiquitous', 'mod_date', 'uncharged_formula', 'formula', 'mass' );
my @all_rel_fields = ( 'from_link', 'to_link',  );
my @all_to_fields = ( 'id', 'stoichiometry', 'cofactor', 'compartment_index', 'transport_coefficient' );

my %all_from_fields = map { $_ => 1 } @all_from_fields;
my %all_rel_fields = map { $_ => 1 } @all_rel_fields;
my %all_to_fields = map { $_ => 1 } @all_to_fields;

my @default_fields = ('from-link', 'to-link');

my @from_fields;

er_scripts/get_relationship_Shows  view on Meta::CPAN 

=item label

=item abbr

=item msid

=item ubiquitous

=item mod_date

=item uncharged_formula

=item formula

=item mass

=back    

=back

=head2 Output Format

The standard output is a tab-delimited file. It consists of the input

er_scripts/get_relationship_Shows  view on Meta::CPAN 


=cut
use Bio::KBase::Utilities::ScriptThing;
use Bio::KBase::CDMI::CDMIClient;
use Getopt::Long;

#Default fields
 
my @all_from_fields = ( 'id', 'name', 'content' );
my @all_rel_fields = ( 'from_link', 'to_link', 'location' );
my @all_to_fields = ( 'id', 'label', 'abbr', 'msid', 'ubiquitous', 'mod_date', 'uncharged_formula', 'formula', 'mass' );

my %all_from_fields = map { $_ => 1 } @all_from_fields;
my %all_rel_fields = map { $_ => 1 } @all_rel_fields;
my %all_to_fields = map { $_ => 1 } @all_to_fields;

my @default_fields = ('from-link', 'to-link');

my @from_fields;
my @rel_fields;
my @to_fields;

er_scripts/get_relationship_UsesAliasForCompound  view on Meta::CPAN 

=item label

=item abbr

=item msid

=item ubiquitous

=item mod_date

=item uncharged_formula

=item formula

=item mass

=back    

=back

=head2 Output Format

The standard output is a tab-delimited file. It consists of the input
file with an extra column added for each requested field.  Input lines that cannot
be extended are written to stderr.  

=cut
use Bio::KBase::Utilities::ScriptThing;
use Bio::KBase::CDMI::CDMIClient;
use Getopt::Long;

#Default fields
 
my @all_from_fields = ( 'id', 'label', 'abbr', 'msid', 'ubiquitous', 'mod_date', 'uncharged_formula', 'formula', 'mass' );
my @all_rel_fields = ( 'from_link', 'to_link', 'alias' );
my @all_to_fields = ( 'id',  );

my %all_from_fields = map { $_ => 1 } @all_from_fields;
my %all_rel_fields = map { $_ => 1 } @all_rel_fields;
my %all_to_fields = map { $_ => 1 } @all_to_fields;

my @default_fields = ('from-link', 'to-link');

my @from_fields;

er_scripts/query_entity_Compound  view on Meta::CPAN 

=item label

=item abbr

=item msid

=item ubiquitous

=item mod_date

=item uncharged_formula

=item formula

=item mass

=back    
   
=back

=head2 Output Format

The standard output is a tab-delimited file containing a column
for each requested field.

=cut

use Bio::KBase::CDMI::CDMIClient;
use Getopt::Long;

#Default fields

my @all_fields = ( 'label', 'abbr', 'msid', 'ubiquitous', 'mod_date', 'uncharged_formula', 'formula', 'mass' );
my %all_fields = map { $_ => 1 } @all_fields, 'id';

my $usage = "usage: query_entity_Compound [-is field,value] [-like field,value] [-op operator,field,value] [-show-fields] [-a | -f field list] > entity.data";

my $a;
my $f;
my @fields;
my $show_fields;
my @query_is;
my @query_like;

lib/Bio/KBase/CDMI/CDMI_APIImpl.pm  view on Meta::CPAN 


=end text



=item Description

Since we accumulate data relating to the co-occurrence (i.e., chromosomal
clustering) of genes in prokaryotic genomes,  we can note which pairs of genes tend to co-occur.
From this data, one can compute the protein families that tend to co-occur (i.e., tend to
cluster on the chromosome).  This allows one to formulate conjectures for unclustered pairs, based
on clustered pairs from the same protein_families.

=back

=cut

sub protein_families_to_co_occurring_families
{
    my $self = shift;
    my($protein_families) = @_;

lib/Bio/KBase/CDMI/CDMI_APIImpl.pm  view on Meta::CPAN 


=over 4



=item Description

A substem is composed of two components: a set of roles that are gathered to be annotated
simultaneously and a spreadsheet depicting the proteins within each genome that implement
the roles.  The set of roles may correspond to a pathway, a complex, an inventory (say, "transporters")
or whatever other principle an annotator used to formulate the subsystem.

The subsystem spreadsheet is a list of "rows", each representing the subsytem in a specific genome.
Each row includes a variant code (indicating what version of the molecular machine exists in the
genome) and cells.  Each cell is a 2-tuple:

     [role,protein-encoding genes that implement the role in the genome]

Annotators construct subsystems, and in the process impose a controlled vocabulary
for roles and functions.

lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm  view on Meta::CPAN 

		    'mod_date' => 1,
	
    },
    'Compound' => {
	id => 1,
		    'label' => 1,
		    'abbr' => 1,
		    'msid' => 1,
		    'ubiquitous' => 1,
		    'mod_date' => 1,
		    'uncharged_formula' => 1,
		    'formula' => 1,
		    'mass' => 1,
	
    },
    'Contig' => {
	id => 1,
		    'source_id' => 1,
	
    },
    'ContigChunk' => {
	id => 1,

lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm  view on Meta::CPAN 

$ids is a reference to a list where each element is a string
$fields is a reference to a list where each element is a string
$return is a reference to a hash where the key is a string and the value is a fields_Compound
fields_Compound is a reference to a hash where the following keys are defined:
	id has a value which is a string
	label has a value which is a string
	abbr has a value which is a string
	msid has a value which is a string
	ubiquitous has a value which is an int
	mod_date has a value which is a string
	uncharged_formula has a value which is a string
	formula has a value which is a string
	mass has a value which is a float

</pre>

=end html

=begin text

$ids is a reference to a list where each element is a string
$fields is a reference to a list where each element is a string
$return is a reference to a hash where the key is a string and the value is a fields_Compound
fields_Compound is a reference to a hash where the following keys are defined:
	id has a value which is a string
	label has a value which is a string
	abbr has a value which is a string
	msid has a value which is a string
	ubiquitous has a value which is an int
	mod_date has a value which is a string
	uncharged_formula has a value which is a string
	formula has a value which is a string
	mass has a value which is a float


=end text



=item Description

A compound is a chemical that participates in a reaction. Both

lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm  view on Meta::CPAN 


TRUE if this compound is found in most reactions, else FALSE


=item mod_date

date and time of the last modification to the
compound definition


=item uncharged_formula

a electrically neutral formula for the compound


=item formula

a pH-neutral formula for the compound


=item mass

atomic mass of the compound



=back

lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm  view on Meta::CPAN 

	2: a string
$fields is a reference to a list where each element is a string
$return is a reference to a hash where the key is a string and the value is a fields_Compound
fields_Compound is a reference to a hash where the following keys are defined:
	id has a value which is a string
	label has a value which is a string
	abbr has a value which is a string
	msid has a value which is a string
	ubiquitous has a value which is an int
	mod_date has a value which is a string
	uncharged_formula has a value which is a string
	formula has a value which is a string
	mass has a value which is a float

</pre>

=end html

=begin text

$qry is a reference to a list where each element is a reference to a list containing 3 items:
	0: a string

lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm  view on Meta::CPAN 

	2: a string
$fields is a reference to a list where each element is a string
$return is a reference to a hash where the key is a string and the value is a fields_Compound
fields_Compound is a reference to a hash where the following keys are defined:
	id has a value which is a string
	label has a value which is a string
	abbr has a value which is a string
	msid has a value which is a string
	ubiquitous has a value which is an int
	mod_date has a value which is a string
	uncharged_formula has a value which is a string
	formula has a value which is a string
	mass has a value which is a float


=end text



=item Description

lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm  view on Meta::CPAN 

$count is an int
$fields is a reference to a list where each element is a string
$return is a reference to a hash where the key is a string and the value is a fields_Compound
fields_Compound is a reference to a hash where the following keys are defined:
	id has a value which is a string
	label has a value which is a string
	abbr has a value which is a string
	msid has a value which is a string
	ubiquitous has a value which is an int
	mod_date has a value which is a string
	uncharged_formula has a value which is a string
	formula has a value which is a string
	mass has a value which is a float

</pre>

=end html

=begin text

$start is an int
$count is an int
$fields is a reference to a list where each element is a string
$return is a reference to a hash where the key is a string and the value is a fields_Compound
fields_Compound is a reference to a hash where the following keys are defined:
	id has a value which is a string
	label has a value which is a string
	abbr has a value which is a string
	msid has a value which is a string
	ubiquitous has a value which is an int
	mod_date has a value which is a string
	uncharged_formula has a value which is a string
	formula has a value which is a string
	mass has a value which is a float


=end text



=item Description

lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm  view on Meta::CPAN 

common modeling ID of this reaction


=item abbr

abbreviated name of this reaction


=item equation

displayable formula for the reaction


=item reversibility

direction of this reaction (> for forward-only,
< for backward-only, = for bidirectional)



=back

lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm  view on Meta::CPAN 

=over 4


=item stoichiometry

Number of molecules of the compound that participate
in a single instance of the reaction. For example, if a
reaction produces two water molecules, the stoichiometry of
water for the reaction would be two. When a reaction is
written on paper in chemical notation, the stoichiometry is
the number next to the chemical formula of the
compound. The value is negative for substrates and positive
for products.


=item cofactor

TRUE if the compound is a cofactor; FALSE if it is a major
component of the reaction.

lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm  view on Meta::CPAN 

fields_HasCompoundAliasFrom is a reference to a hash where the following keys are defined:
	id has a value which is a string
	alias has a value which is a string
fields_Compound is a reference to a hash where the following keys are defined:
	id has a value which is a string
	label has a value which is a string
	abbr has a value which is a string
	msid has a value which is a string
	ubiquitous has a value which is an int
	mod_date has a value which is a string
	uncharged_formula has a value which is a string
	formula has a value which is a string
	mass has a value which is a float

</pre>

=end html

=begin text

$ids is a reference to a list where each element is a string
$from_fields is a reference to a list where each element is a string

lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm  view on Meta::CPAN 

fields_HasCompoundAliasFrom is a reference to a hash where the following keys are defined:
	id has a value which is a string
	alias has a value which is a string
fields_Compound is a reference to a hash where the following keys are defined:
	id has a value which is a string
	label has a value which is a string
	abbr has a value which is a string
	msid has a value which is a string
	ubiquitous has a value which is an int
	mod_date has a value which is a string
	uncharged_formula has a value which is a string
	formula has a value which is a string
	mass has a value which is a float


=end text



=item Description

This relationship connects a source (database or organization)

lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm  view on Meta::CPAN 

	0: a fields_Compound
	1: a fields_HasCompoundAliasFrom
	2: a fields_Source
fields_Compound is a reference to a hash where the following keys are defined:
	id has a value which is a string
	label has a value which is a string
	abbr has a value which is a string
	msid has a value which is a string
	ubiquitous has a value which is an int
	mod_date has a value which is a string
	uncharged_formula has a value which is a string
	formula has a value which is a string
	mass has a value which is a float
fields_HasCompoundAliasFrom is a reference to a hash where the following keys are defined:
	id has a value which is a string
	alias has a value which is a string
fields_Source is a reference to a hash where the following keys are defined:
	id has a value which is a string

</pre>

=end html

lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm  view on Meta::CPAN 

	0: a fields_Compound
	1: a fields_HasCompoundAliasFrom
	2: a fields_Source
fields_Compound is a reference to a hash where the following keys are defined:
	id has a value which is a string
	label has a value which is a string
	abbr has a value which is a string
	msid has a value which is a string
	ubiquitous has a value which is an int
	mod_date has a value which is a string
	uncharged_formula has a value which is a string
	formula has a value which is a string
	mass has a value which is a float
fields_HasCompoundAliasFrom is a reference to a hash where the following keys are defined:
	id has a value which is a string
	alias has a value which is a string
fields_Source is a reference to a hash where the following keys are defined:
	id has a value which is a string


=end text

lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm  view on Meta::CPAN 

	concentration has a value which is a float
	minimum_flux has a value which is a float
	maximum_flux has a value which is a float
fields_Compound is a reference to a hash where the following keys are defined:
	id has a value which is a string
	label has a value which is a string
	abbr has a value which is a string
	msid has a value which is a string
	ubiquitous has a value which is an int
	mod_date has a value which is a string
	uncharged_formula has a value which is a string
	formula has a value which is a string
	mass has a value which is a float

</pre>

=end html

=begin text

$ids is a reference to a list where each element is a string
$from_fields is a reference to a list where each element is a string

lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm  view on Meta::CPAN 

	concentration has a value which is a float
	minimum_flux has a value which is a float
	maximum_flux has a value which is a float
fields_Compound is a reference to a hash where the following keys are defined:
	id has a value which is a string
	label has a value which is a string
	abbr has a value which is a string
	msid has a value which is a string
	ubiquitous has a value which is an int
	mod_date has a value which is a string
	uncharged_formula has a value which is a string
	formula has a value which is a string
	mass has a value which is a float


=end text



=item Description

This relationship connects a media to the compounds that

lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm  view on Meta::CPAN 

	0: a fields_Compound
	1: a fields_HasPresenceOf
	2: a fields_Media
fields_Compound is a reference to a hash where the following keys are defined:
	id has a value which is a string
	label has a value which is a string
	abbr has a value which is a string
	msid has a value which is a string
	ubiquitous has a value which is an int
	mod_date has a value which is a string
	uncharged_formula has a value which is a string
	formula has a value which is a string
	mass has a value which is a float
fields_HasPresenceOf is a reference to a hash where the following keys are defined:
	id has a value which is a string
	concentration has a value which is a float
	minimum_flux has a value which is a float
	maximum_flux has a value which is a float
fields_Media is a reference to a hash where the following keys are defined:
	id has a value which is a string
	mod_date has a value which is a string
	name has a value which is a string

lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm  view on Meta::CPAN 

	0: a fields_Compound
	1: a fields_HasPresenceOf
	2: a fields_Media
fields_Compound is a reference to a hash where the following keys are defined:
	id has a value which is a string
	label has a value which is a string
	abbr has a value which is a string
	msid has a value which is a string
	ubiquitous has a value which is an int
	mod_date has a value which is a string
	uncharged_formula has a value which is a string
	formula has a value which is a string
	mass has a value which is a float
fields_HasPresenceOf is a reference to a hash where the following keys are defined:
	id has a value which is a string
	concentration has a value which is a float
	minimum_flux has a value which is a float
	maximum_flux has a value which is a float
fields_Media is a reference to a hash where the following keys are defined:
	id has a value which is a string
	mod_date has a value which is a string
	name has a value which is a string

lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm  view on Meta::CPAN 

	0: a fields_Compound
	1: a fields_HasUsage
	2: a fields_BiomassCompound
fields_Compound is a reference to a hash where the following keys are defined:
	id has a value which is a string
	label has a value which is a string
	abbr has a value which is a string
	msid has a value which is a string
	ubiquitous has a value which is an int
	mod_date has a value which is a string
	uncharged_formula has a value which is a string
	formula has a value which is a string
	mass has a value which is a float
fields_HasUsage is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_BiomassCompound is a reference to a hash where the following keys are defined:
	id has a value which is a string
	coefficient has a value which is a float

</pre>

=end html

lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm  view on Meta::CPAN 

	0: a fields_Compound
	1: a fields_HasUsage
	2: a fields_BiomassCompound
fields_Compound is a reference to a hash where the following keys are defined:
	id has a value which is a string
	label has a value which is a string
	abbr has a value which is a string
	msid has a value which is a string
	ubiquitous has a value which is an int
	mod_date has a value which is a string
	uncharged_formula has a value which is a string
	formula has a value which is a string
	mass has a value which is a float
fields_HasUsage is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_BiomassCompound is a reference to a hash where the following keys are defined:
	id has a value which is a string
	coefficient has a value which is a float


=end text

lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm  view on Meta::CPAN 

	coefficient has a value which is a float
fields_HasUsage is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Compound is a reference to a hash where the following keys are defined:
	id has a value which is a string
	label has a value which is a string
	abbr has a value which is a string
	msid has a value which is a string
	ubiquitous has a value which is an int
	mod_date has a value which is a string
	uncharged_formula has a value which is a string
	formula has a value which is a string
	mass has a value which is a float

</pre>

=end html

=begin text

$ids is a reference to a list where each element is a string
$from_fields is a reference to a list where each element is a string

lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm  view on Meta::CPAN 

	coefficient has a value which is a float
fields_HasUsage is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Compound is a reference to a hash where the following keys are defined:
	id has a value which is a string
	label has a value which is a string
	abbr has a value which is a string
	msid has a value which is a string
	ubiquitous has a value which is an int
	mod_date has a value which is a string
	uncharged_formula has a value which is a string
	formula has a value which is a string
	mass has a value which is a float


=end text



=item Description

lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm  view on Meta::CPAN 

	0: a fields_Compound
	1: a fields_IsTerminusFor
	2: a fields_Scenario
fields_Compound is a reference to a hash where the following keys are defined:
	id has a value which is a string
	label has a value which is a string
	abbr has a value which is a string
	msid has a value which is a string
	ubiquitous has a value which is an int
	mod_date has a value which is a string
	uncharged_formula has a value which is a string
	formula has a value which is a string
	mass has a value which is a float
fields_IsTerminusFor is a reference to a hash where the following keys are defined:
	id has a value which is a string
	group_number has a value which is an int
fields_Scenario is a reference to a hash where the following keys are defined:
	id has a value which is a string
	common_name has a value which is a string

</pre>

lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm  view on Meta::CPAN 

	0: a fields_Compound
	1: a fields_IsTerminusFor
	2: a fields_Scenario
fields_Compound is a reference to a hash where the following keys are defined:
	id has a value which is a string
	label has a value which is a string
	abbr has a value which is a string
	msid has a value which is a string
	ubiquitous has a value which is an int
	mod_date has a value which is a string
	uncharged_formula has a value which is a string
	formula has a value which is a string
	mass has a value which is a float
fields_IsTerminusFor is a reference to a hash where the following keys are defined:
	id has a value which is a string
	group_number has a value which is an int
fields_Scenario is a reference to a hash where the following keys are defined:
	id has a value which is a string
	common_name has a value which is a string


=end text

lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm  view on Meta::CPAN 

fields_IsTerminusFor is a reference to a hash where the following keys are defined:
	id has a value which is a string
	group_number has a value which is an int
fields_Compound is a reference to a hash where the following keys are defined:
	id has a value which is a string
	label has a value which is a string
	abbr has a value which is a string
	msid has a value which is a string
	ubiquitous has a value which is an int
	mod_date has a value which is a string
	uncharged_formula has a value which is a string
	formula has a value which is a string
	mass has a value which is a float

</pre>

=end html

=begin text

$ids is a reference to a list where each element is a string
$from_fields is a reference to a list where each element is a string

lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm  view on Meta::CPAN 

fields_IsTerminusFor is a reference to a hash where the following keys are defined:
	id has a value which is a string
	group_number has a value which is an int
fields_Compound is a reference to a hash where the following keys are defined:
	id has a value which is a string
	label has a value which is a string
	abbr has a value which is a string
	msid has a value which is a string
	ubiquitous has a value which is an int
	mod_date has a value which is a string
	uncharged_formula has a value which is a string
	formula has a value which is a string
	mass has a value which is a float


=end text



=item Description

lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm  view on Meta::CPAN 

	0: a fields_Compound
	1: a fields_ParticipatesAs
	2: a fields_Reagent
fields_Compound is a reference to a hash where the following keys are defined:
	id has a value which is a string
	label has a value which is a string
	abbr has a value which is a string
	msid has a value which is a string
	ubiquitous has a value which is an int
	mod_date has a value which is a string
	uncharged_formula has a value which is a string
	formula has a value which is a string
	mass has a value which is a float
fields_ParticipatesAs is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Reagent is a reference to a hash where the following keys are defined:
	id has a value which is a string
	stoichiometry has a value which is a float
	cofactor has a value which is an int
	compartment_index has a value which is an int
	transport_coefficient has a value which is a float

lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm  view on Meta::CPAN 

	0: a fields_Compound
	1: a fields_ParticipatesAs
	2: a fields_Reagent
fields_Compound is a reference to a hash where the following keys are defined:
	id has a value which is a string
	label has a value which is a string
	abbr has a value which is a string
	msid has a value which is a string
	ubiquitous has a value which is an int
	mod_date has a value which is a string
	uncharged_formula has a value which is a string
	formula has a value which is a string
	mass has a value which is a float
fields_ParticipatesAs is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Reagent is a reference to a hash where the following keys are defined:
	id has a value which is a string
	stoichiometry has a value which is a float
	cofactor has a value which is an int
	compartment_index has a value which is an int
	transport_coefficient has a value which is a float

lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm  view on Meta::CPAN 

	transport_coefficient has a value which is a float
fields_ParticipatesAs is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Compound is a reference to a hash where the following keys are defined:
	id has a value which is a string
	label has a value which is a string
	abbr has a value which is a string
	msid has a value which is a string
	ubiquitous has a value which is an int
	mod_date has a value which is a string
	uncharged_formula has a value which is a string
	formula has a value which is a string
	mass has a value which is a float

</pre>

=end html

=begin text

$ids is a reference to a list where each element is a string
$from_fields is a reference to a list where each element is a string

lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm  view on Meta::CPAN 

	transport_coefficient has a value which is a float
fields_ParticipatesAs is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Compound is a reference to a hash where the following keys are defined:
	id has a value which is a string
	label has a value which is a string
	abbr has a value which is a string
	msid has a value which is a string
	ubiquitous has a value which is an int
	mod_date has a value which is a string
	uncharged_formula has a value which is a string
	formula has a value which is a string
	mass has a value which is a float


=end text



=item Description

lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm  view on Meta::CPAN 

	id has a value which is a string
	location has a value which is a rectangle
rectangle is a string
fields_Compound is a reference to a hash where the following keys are defined:
	id has a value which is a string
	label has a value which is a string
	abbr has a value which is a string
	msid has a value which is a string
	ubiquitous has a value which is an int
	mod_date has a value which is a string
	uncharged_formula has a value which is a string
	formula has a value which is a string
	mass has a value which is a float

</pre>

=end html

=begin text

$ids is a reference to a list where each element is a string
$from_fields is a reference to a list where each element is a string

lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm  view on Meta::CPAN 

	id has a value which is a string
	location has a value which is a rectangle
rectangle is a string
fields_Compound is a reference to a hash where the following keys are defined:
	id has a value which is a string
	label has a value which is a string
	abbr has a value which is a string
	msid has a value which is a string
	ubiquitous has a value which is an int
	mod_date has a value which is a string
	uncharged_formula has a value which is a string
	formula has a value which is a string
	mass has a value which is a float


=end text



=item Description

This relationship indicates that a compound appears on a

lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm  view on Meta::CPAN 

	0: a fields_Compound
	1: a fields_Shows
	2: a fields_Diagram
fields_Compound is a reference to a hash where the following keys are defined:
	id has a value which is a string
	label has a value which is a string
	abbr has a value which is a string
	msid has a value which is a string
	ubiquitous has a value which is an int
	mod_date has a value which is a string
	uncharged_formula has a value which is a string
	formula has a value which is a string
	mass has a value which is a float
fields_Shows is a reference to a hash where the following keys are defined:
	id has a value which is a string
	location has a value which is a rectangle
rectangle is a string
fields_Diagram is a reference to a hash where the following keys are defined:
	id has a value which is a string
	name has a value which is a string
	content has a value which is a reference to a list where each element is a string

lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm  view on Meta::CPAN 

	0: a fields_Compound
	1: a fields_Shows
	2: a fields_Diagram
fields_Compound is a reference to a hash where the following keys are defined:
	id has a value which is a string
	label has a value which is a string
	abbr has a value which is a string
	msid has a value which is a string
	ubiquitous has a value which is an int
	mod_date has a value which is a string
	uncharged_formula has a value which is a string
	formula has a value which is a string
	mass has a value which is a float
fields_Shows is a reference to a hash where the following keys are defined:
	id has a value which is a string
	location has a value which is a rectangle
rectangle is a string
fields_Diagram is a reference to a hash where the following keys are defined:
	id has a value which is a string
	name has a value which is a string
	content has a value which is a reference to a list where each element is a string

lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm  view on Meta::CPAN 


=over 4



=item Description

A substem is composed of two components: a set of roles that are gathered to be annotated
simultaneously and a spreadsheet depicting the proteins within each genome that implement
the roles.  The set of roles may correspond to a pathway, a complex, an inventory (say, "transporters")
or whatever other principle an annotator used to formulate the subsystem.

The subsystem spreadsheet is a list of "rows", each representing the subsytem in a specific genome.
Each row includes a variant code (indicating what version of the molecular machine exists in the
genome) and cells.  Each cell is a 2-tuple:

     [role,protein-encoding genes that implement the role in the genome]

Annotators construct subsystems, and in the process impose a controlled vocabulary
for roles and functions.

lib/Bio/KBase/CDMI/CDMI_EntityAPIImpl.pm  view on Meta::CPAN 

=begin html

<pre>
a reference to a hash where the following keys are defined:
id has a value which is a string
label has a value which is a string
abbr has a value which is a string
msid has a value which is a string
ubiquitous has a value which is an int
mod_date has a value which is a string
uncharged_formula has a value which is a string
formula has a value which is a string
mass has a value which is a float

</pre>

=end html

=begin text

a reference to a hash where the following keys are defined:
id has a value which is a string
label has a value which is a string
abbr has a value which is a string
msid has a value which is a string
ubiquitous has a value which is an int
mod_date has a value which is a string
uncharged_formula has a value which is a string
formula has a value which is a string
mass has a value which is a float


=end text

=back



=head2 fields_Contig

lib/Bio/KBase/CDMI/Client.pm  view on Meta::CPAN 

    }
}



=head2 $result = protein_families_to_co_occurring_families(protein_families)

Since we accumulate data relating to the co-occurrence (i.e., chromosomal
clustering) of genes in prokaryotic genomes,  we can note which pairs of genes tend to co-occur.
From this data, one can compute the protein families that tend to co-occur (i.e., tend to
cluster on the chromosome).  This allows one to formulate conjectures for unclustered pairs, based
on clustered pairs from the same protein_families.

=cut

sub protein_families_to_co_occurring_families
{
    my($self, @args) = @_;

    if ((my $n = @args) != 1)
    {

lib/Bio/KBase/CDMI/Client.pm  view on Meta::CPAN 


TRUE if this compound is found in most reactions, else FALSE


=item mod_date

date and time of the last modification to the
compound definition


=item uncharged_formula

a electrically neutral formula for the compound


=item formula

a pH-neutral formula for the compound


=item mass

atomic mass of the compound



=back

lib/Bio/KBase/CDMI/Client.pm  view on Meta::CPAN 

common modeling ID of this reaction


=item abbr

abbreviated name of this reaction


=item equation

displayable formula for the reaction


=item reversibility

direction of this reaction (> for forward-only,
< for backward-only, = for bidirectional)



=back

lib/Bio/KBase/CDMI/Client.pm  view on Meta::CPAN 

=over 4


=item stoichiometry

Number of molecules of the compound that participate
in a single instance of the reaction. For example, if a
reaction produces two water molecules, the stoichiometry of
water for the reaction would be two. When a reaction is
written on paper in chemical notation, the stoichiometry is
the number next to the chemical formula of the
compound. The value is negative for substrates and positive
for products.


=item cofactor

TRUE if the compound is a cofactor; FALSE if it is a major
component of the reaction.

lib/Bio/KBase/CDMI/EntityImpl.pm  view on Meta::CPAN 

		    'mod_date' => 1,
	
    },
    'Compound' => {
	id => 1,
		    'label' => 1,
		    'abbr' => 1,
		    'msid' => 1,
		    'ubiquitous' => 1,
		    'mod_date' => 1,
		    'uncharged_formula' => 1,
		    'formula' => 1,
		    'mass' => 1,
	
    },
    'Contig' => {
	id => 1,
		    'source_id' => 1,
	
    },
    'ContigChunk' => {
	id => 1,

lib/Bio/KBase/InvocationService/ValidCommands.pm  view on Meta::CPAN 

our @command_groups = (
   { name => 'modeling_scripts', title => 'Modeling scripts', items => [
	{ cmd => 'exchangeFormat_to_gapfillingFormulation', link => '' },
	{ cmd => 'exchangeformat_to_fbamodel', link => '' },
	{ cmd => 'fbamodel_to_exchangeformat', link => '' },
	{ cmd => 'fbamodel_to_html', link => '' },
	{ cmd => 'fbamodel_to_sbml', link => '' },
	{ cmd => 'gapfill_fbamodel', link => '' },
	{ cmd => 'gapfillingFormulation_to_exchangeFormat', link => '' },
	{ cmd => 'genome_to_fbamodel', link => '' },
	{ cmd => 'get_gapfilling_formulation', link => '' },
	{ cmd => 'runfba', link => '' },
   ]},
   { name => 'scripts', title => 'CDMI Scripts', items => [
	{ cmd => 'all_roles_used_in_models', link => '' },
	{ cmd => 'all_roles_used_in_models_and_subsystems', link => '' },
	{ cmd => 'alleles_to_bp_locs', link => '' },
	{ cmd => 'alleles_to_traits', link => '' },
	{ cmd => 'atomic_regulons_to_fids', link => '' },
	{ cmd => 'close_genomes', link => '' },
	{ cmd => 'co_occurrence_evidence', link => '' },

scripts/protein_families_to_co_occurring_families  view on Meta::CPAN 

#
# This is a SAS Component
#

=head1 protein_families_to_co_occurring_families


Since we accumulate data relating to the co-occurrence (i.e., chromosomal
clustering) of genes in prokaryotic genomes,  we can note which pairs of genes tend to co-occur.
From this data, one can compute the protein families that tend to co-occur (i.e., tend to
cluster on the chromosome).  This allows one to formulate conjectures for unclustered pairs, based
on clustered pairs from the same protein_families.


Example:

    protein_families_to_co_occurring_families [arguments] < input > output

The standard input should be a tab-separated table (i.e., each line
is a tab-separated set of fields).  Normally, the last field in each
line would contain the identifer. If another column contains the identifier



( run in 1.328 second using v1.01-cache-2.11-cpan-3cd7ad12f66 )