NAME

CDMI_EntityAPI

DESCRIPTION

METHODS

get_entity_AlignmentTree

$return = $obj->get_entity_AlignmentTree($ids, $fields)

Parameter and return types

$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_AlignmentTree
fields_AlignmentTree is a reference to a hash where the following keys are defined:
	id has a value which is a string
	alignment_method has a value which is a string
	alignment_parameters has a value which is a string
	alignment_properties has a value which is a string
	tree_method has a value which is a string
	tree_parameters has a value which is a string
	tree_properties has a value which is a string

Description

An alignment arranges a group of protein sequences so that they match. Each alignment is associated with a phylogenetic tree that describes how the sequences developed and their evolutionary distance. The actual tree and alignment FASTA are stored in separate flat files. The Kbase will maintain a set of alignments and associated trees. The majority of these will be based on protein sequences. We will not have a comprehensive set but we will have tens of thousands of such alignments, and we view them as an imporant resource to support annotation. The alignments/trees will include the tools and parameters used to construct them. Access to the underlying sequences and trees in a form convenient to existing tools will be supported.

It has the following fields:

alignment_method: The name of the program used to produce the alignment.
alignment_parameters: The parameters given to the program when producing the alignment.
alignment_properties: A colon-delimited string of key-value pairs containing additional properties of the alignment.
tree_method: The name of the program used to produce the tree.
tree_parameters: The parameters given to the program when producing the tree.
tree_properties: A colon-delimited string of key-value pairs containing additional properties of the tree.

all_entities_AlignmentTree

$return = $obj->all_entities_AlignmentTree($start, $count, $fields)

Parameter and return types

$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_AlignmentTree
fields_AlignmentTree is a reference to a hash where the following keys are defined:
	id has a value which is a string
	alignment_method has a value which is a string
	alignment_parameters has a value which is a string
	alignment_properties has a value which is a string
	tree_method has a value which is a string
	tree_parameters has a value which is a string
	tree_properties has a value which is a string

Description

get_entity_Annotation

$return = $obj->get_entity_Annotation($ids, $fields)

Parameter and return types

$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_Annotation
fields_Annotation is a reference to a hash where the following keys are defined:
	id has a value which is a string
	annotator has a value which is a string
	comment has a value which is a string
	annotation_time has a value which is a string

Description

An annotation is a comment attached to a feature. Annotations are used to track the history of a feature's functional assignments and any related issues. The key is the feature ID followed by a colon and a complemented ten-digit sequence number.

It has the following fields:

annotator: name of the annotator who made the comment
comment: text of the annotation
annotation_time: date and time at which the annotation was made

all_entities_Annotation

$return = $obj->all_entities_Annotation($start, $count, $fields)

Parameter and return types

$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_Annotation
fields_Annotation is a reference to a hash where the following keys are defined:
	id has a value which is a string
	annotator has a value which is a string
	comment has a value which is a string
	annotation_time has a value which is a string

Description

get_entity_AtomicRegulon

$return = $obj->get_entity_AtomicRegulon($ids, $fields)

Parameter and return types

$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_AtomicRegulon
fields_AtomicRegulon is a reference to a hash where the following keys are defined:
	id has a value which is a string

Description

An atomic regulon is an indivisible group of coregulated features on a single genome. Atomic regulons are constructed so that a given feature can only belong to one. Because of this, the expression levels for atomic regulons represent in some sense the state of a cell. An atomicRegulon is a set of protein-encoding genes that are believed to have identical expression profiles (i.e., they will all be expressed or none will be expressed in the vast majority of conditions). These are sometimes referred to as "atomic regulons". Note that there are more common notions of "coregulated set of genes" based on the notion that a single regulatory mechanism impacts an entire set of genes. Since multiple other mechanisms may impact overlapping sets, the genes impacted by a regulatory mechanism need not all share the same expression profile. We use a distinct notion (CoregulatedSet) to reference sets of genes impacted by a single regulatory mechanism (i.e., by a single transcription regulator).

It has the following fields:

all_entities_AtomicRegulon

$return = $obj->all_entities_AtomicRegulon($start, $count, $fields)

Parameter and return types

$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_AtomicRegulon
fields_AtomicRegulon is a reference to a hash where the following keys are defined:
	id has a value which is a string

Description

get_entity_Attribute

$return = $obj->get_entity_Attribute($ids, $fields)

Parameter and return types

$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_Attribute
fields_Attribute is a reference to a hash where the following keys are defined:
	id has a value which is a string
	description has a value which is a string

Description

An attribute describes a category of condition or characteristic for an experiment. The goals of the experiment can be inferred from its values for all the attributes of interest. It has the following fields:

description: Descriptive text indicating the nature and use of this attribute.

all_entities_Attribute

$return = $obj->all_entities_Attribute($start, $count, $fields)

Parameter and return types

$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_Attribute
fields_Attribute is a reference to a hash where the following keys are defined:
	id has a value which is a string
	description has a value which is a string

Description

get_entity_Biomass

$return = $obj->get_entity_Biomass($ids, $fields)

Parameter and return types

$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_Biomass
fields_Biomass 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 reference to a list where each element is a string

Description

A biomass is a collection of compounds in a specific ratio and in specific compartments that are necessary for a cell to function properly. The prediction of biomasses is key to the functioning of the model. It has the following fields:

mod_date: last modification date of the biomass data
name: descriptive name for this biomass

all_entities_Biomass

$return = $obj->all_entities_Biomass($start, $count, $fields)

Parameter and return types

$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_Biomass
fields_Biomass 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 reference to a list where each element is a string

Description

get_entity_BiomassCompound

$return = $obj->get_entity_BiomassCompound($ids, $fields)

Parameter and return types

$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_BiomassCompound
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

Description

A Biomass Compound represents the occurrence of a particular compound in a biomass. It has the following fields:

coefficient: proportion of the biomass in grams per mole that contains this compound

all_entities_BiomassCompound

$return = $obj->all_entities_BiomassCompound($start, $count, $fields)

Parameter and return types

$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_BiomassCompound
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

Description

get_entity_Compartment

$return = $obj->get_entity_Compartment($ids, $fields)

Parameter and return types

$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_Compartment
fields_Compartment is a reference to a hash where the following keys are defined:
	id has a value which is a string
	abbr has a value which is a string
	mod_date has a value which is a string
	name has a value which is a string
	msid has a value which is a string

Description

A compartment is a section of a single model that represents the environment in which a reaction takes place (e.g. cell wall). It has the following fields:

abbr: short abbreviated name for this compartment (usually a single character)
mod_date: date and time of the last modification to the compartment's definition
name: common name for the compartment
msid: common modeling ID of this compartment

all_entities_Compartment

$return = $obj->all_entities_Compartment($start, $count, $fields)

Parameter and return types

$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_Compartment
fields_Compartment is a reference to a hash where the following keys are defined:
	id has a value which is a string
	abbr has a value which is a string
	mod_date has a value which is a string
	name has a value which is a string
	msid has a value which is a string

Description

get_entity_Complex

$return = $obj->get_entity_Complex($ids, $fields)

Parameter and return types

$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_Complex
fields_Complex 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 reference to a list where each element is a string
	msid has a value which is a string
	mod_date has a value which is a string

Description

A complex is a set of chemical reactions that act in concert to effect a role. It has the following fields:

name: name of this complex. Not all complexes have names.
msid: common modeling ID of this complex.
mod_date: date and time of the last change to this complex's definition

all_entities_Complex

$return = $obj->all_entities_Complex($start, $count, $fields)

Parameter and return types

$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_Complex
fields_Complex 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 reference to a list where each element is a string
	msid has a value which is a string
	mod_date has a value which is a string

Description

get_entity_Compound

$return = $obj->get_entity_Compound($ids, $fields)

Parameter and return types

$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

Description

A compound is a chemical that participates in a reaction. Both ligands and reaction components are treated as compounds. It has the following fields:

label: primary name of the compound, for use in displaying reactions
abbr: shortened abbreviation for the compound name
msid: common modeling ID of this compound
ubiquitous: TRUE if this compound is found in most reactions, else FALSE
mod_date: date and time of the last modification to the compound definition
uncharged_formula: a electrically neutral formula for the compound
formula: a pH-neutral formula for the compound
mass: atomic mass of the compound

all_entities_Compound

$return = $obj->all_entities_Compound($start, $count, $fields)

Parameter and return types

$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

Description

get_entity_Contig

$return = $obj->get_entity_Contig($ids, $fields)

Parameter and return types

$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_Contig
fields_Contig is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source_id has a value which is a string

Description

A contig is thought of as composing a part of the DNA associated with a specific genome. It is represented as an ID (including the genome ID) and a ContigSequence. We do not think of strings of DNA from, say, a metgenomic sample as "contigs", since there is no associated genome (these would be considered ContigSequences). This use of the term "ContigSequence", rather than just "DNA sequence", may turn out to be a bad idea. For now, you should just realize that a Contig has an associated genome, but a ContigSequence does not.

It has the following fields:

source_id: ID of this contig from the core (source) database

all_entities_Contig

$return = $obj->all_entities_Contig($start, $count, $fields)

Parameter and return types

$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_Contig
fields_Contig is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source_id has a value which is a string

Description

get_entity_ContigChunk

$return = $obj->get_entity_ContigChunk($ids, $fields)

Parameter and return types

$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_ContigChunk
fields_ContigChunk is a reference to a hash where the following keys are defined:
	id has a value which is a string
	sequence has a value which is a string

Description

ContigChunks are strings of DNA thought of as being a string in a 4-character alphabet with an associated ID. We allow a broader alphabet that includes U (for RNA) and the standard ambiguity characters. The notion of ContigChunk was introduced to avoid transferring/manipulating huge contigs to access small substrings. A ContigSequence is formed by concatenating a set of one or more ContigChunks. Thus, ContigChunks are the basic units moved from the database to memory. Their existence should be hidden from users in most circumstances (users are expected to request substrings of ContigSequences, and the Kbase software locates the appropriate ContigChunks).

It has the following fields:

sequence: base pairs that make up this sequence

all_entities_ContigChunk

$return = $obj->all_entities_ContigChunk($start, $count, $fields)

Parameter and return types

$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_ContigChunk
fields_ContigChunk is a reference to a hash where the following keys are defined:
	id has a value which is a string
	sequence has a value which is a string

Description

get_entity_ContigSequence

$return = $obj->get_entity_ContigSequence($ids, $fields)

Parameter and return types

$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_ContigSequence
fields_ContigSequence is a reference to a hash where the following keys are defined:
	id has a value which is a string
	length has a value which is an int

Description

ContigSequences are strings of DNA. Contigs have an associated genome, but ContigSequences do not.. We can think of random samples of DNA as a set of ContigSequences. There are no length constraints imposed on ContigSequences -- they can be either very short or very long. The basic unit of data that is moved to/from the database is the ContigChunk, from which ContigSequences are formed. The key of a ContigSequence is the sequence's MD5 identifier.

It has the following fields:

length: number of base pairs in the contig

all_entities_ContigSequence

$return = $obj->all_entities_ContigSequence($start, $count, $fields)

Parameter and return types

$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_ContigSequence
fields_ContigSequence is a reference to a hash where the following keys are defined:
	id has a value which is a string
	length has a value which is an int

Description

get_entity_CoregulatedSet

$return = $obj->get_entity_CoregulatedSet($ids, $fields)

Parameter and return types

$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_CoregulatedSet
fields_CoregulatedSet is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source_id has a value which is a string

Description

We need to represent sets of genes that are coregulated via some regulatory mechanism. In particular, we wish to represent genes that are coregulated using transcription binding sites and corresponding transcription regulatory proteins. We represent a coregulated set (which may, or may not, be considered an atomic regulon) using CoregulatedSet.

It has the following fields:

source_id: original ID of this coregulated set in the source (core) database

all_entities_CoregulatedSet

$return = $obj->all_entities_CoregulatedSet($start, $count, $fields)

Parameter and return types

$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_CoregulatedSet
fields_CoregulatedSet is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source_id has a value which is a string

Description

get_entity_Diagram

$return = $obj->get_entity_Diagram($ids, $fields)

Parameter and return types

$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_Diagram
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

Description

A functional diagram describes a network of chemical reactions, often comprising a single subsystem. It has the following fields:

name: descriptive name of this diagram
content: content of the diagram, in PNG format

all_entities_Diagram

$return = $obj->all_entities_Diagram($start, $count, $fields)

Parameter and return types

$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_Diagram
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

Description

get_entity_EcNumber

$return = $obj->get_entity_EcNumber($ids, $fields)

Parameter and return types

$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_EcNumber
fields_EcNumber is a reference to a hash where the following keys are defined:
	id has a value which is a string
	obsolete has a value which is an int
	replacedby has a value which is a string

Description

EC numbers are assigned by the Enzyme Commission, and consist of four numbers separated by periods, each indicating a successively smaller cateogry of enzymes. It has the following fields:

obsolete: This boolean indicates when an EC number is obsolete.
replacedby: When an obsolete EC number is replaced with another EC number, this string will hold the name of the replacement EC number.

all_entities_EcNumber

$return = $obj->all_entities_EcNumber($start, $count, $fields)

Parameter and return types

$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_EcNumber
fields_EcNumber is a reference to a hash where the following keys are defined:
	id has a value which is a string
	obsolete has a value which is an int
	replacedby has a value which is a string

Description

get_entity_Experiment

$return = $obj->get_entity_Experiment($ids, $fields)

Parameter and return types

$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_Experiment
fields_Experiment is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source has a value which is a string

Description

An experiment is a combination of conditions for which gene expression information is desired. The result of the experiment is a set of expression levels for features under the given conditions. It has the following fields:

source: Publication or lab relevant to this experiment.

all_entities_Experiment

$return = $obj->all_entities_Experiment($start, $count, $fields)

Parameter and return types

$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_Experiment
fields_Experiment is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source has a value which is a string

Description

get_entity_Family

$return = $obj->get_entity_Family($ids, $fields)

Parameter and return types

$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_Family
fields_Family is a reference to a hash where the following keys are defined:
	id has a value which is a string
	type has a value which is a string
	family_function has a value which is a reference to a list where each element is a string

Description

The Kbase will support the maintenance of protein families (as sets of Features with associated translations). We are initially only supporting the notion of a family as composed of a set of isofunctional homologs. That is, the families we initially support should be thought of as containing protein-encoding genes whose associated sequences all implement the same function (we do understand that the notion of "function" is somewhat ambiguous, so let us sweep this under the rug by calling a functional role a "primitive concept"). We currently support families in which the members are translations of features, and we think of Features as having an associated function. Identical protein sequences as products of translating distinct genes may or may not have identical functions, and we allow multiple members of the same Family to share identical protein sequences. This may be justified, since in a very, very, very few cases identical proteins do, in fact, have distinct functions. We would prefer to reach the point where our Families are sets of protein sequence, rather than sets of protein-encoding Features.

It has the following fields:

type: type of protein family (e.g. FIGfam, equivalog)
family_function: optional free-form description of the family. For function-based families, this would be the functional role for the family members.

all_entities_Family

$return = $obj->all_entities_Family($start, $count, $fields)

Parameter and return types

$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_Family
fields_Family is a reference to a hash where the following keys are defined:
	id has a value which is a string
	type has a value which is a string
	family_function has a value which is a reference to a list where each element is a string

Description

get_entity_Feature

$return = $obj->get_entity_Feature($ids, $fields)

Parameter and return types

$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_Feature
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string

Description

A feature (sometimes also called a gene) is a part of a genome that is of special interest. Features may be spread across multiple DNA sequences (contigs) of a genome, but never across more than one genome. Each feature in the database has a unique ID that functions as its ID in this table. Normally a Feature is just a single contigous region on a contig. Features have types, and an appropriate choice of available types allows the support of protein-encoding genes, exons, RNA genes, binding sites, pathogenicity islands, or whatever.

It has the following fields:

feature_type: Code indicating the type of this feature. Among the codes currently supported are "peg" for a protein encoding gene, "bs" for a binding site, "opr" for an operon, and so forth.
source_id: ID for this feature in its original source (core) database
sequence_length: Number of base pairs in this feature.
function: Functional assignment for this feature. This will often indicate the feature's functional role or roles, and may also have comments.

all_entities_Feature

$return = $obj->all_entities_Feature($start, $count, $fields)

Parameter and return types

$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_Feature
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string

Description

get_entity_Genome

$return = $obj->get_entity_Genome($ids, $fields)

Parameter and return types

$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_Genome
fields_Genome is a reference to a hash where the following keys are defined:
	id has a value which is a string
	pegs has a value which is an int
	rnas has a value which is an int
	scientific_name has a value which is a string
	complete has a value which is an int
	prokaryotic has a value which is an int
	dna_size has a value which is an int
	contigs has a value which is an int
	domain has a value which is a string
	genetic_code has a value which is an int
	gc_content has a value which is a float
	phenotype has a value which is a reference to a list where each element is a string
	md5 has a value which is a string
	source_id has a value which is a string

Description

The Kbase houses a large and growing set of genomes. We often have multiple genomes that have identical DNA. These usually have distinct gene calls and annotations, but not always. We consider the Kbase to be a framework for managing hundreds of thousands of genomes and offering the tools needed to support compartive analysis on large sets of genomes, some of which are virtually identical. Each genome has an MD5 value computed from the DNA that is associated with the genome. Hence, it is easy to recognize when you have identical genomes, perhaps annotated by distinct groups.

It has the following fields:

pegs: Number of protein encoding genes for this genome.
rnas: Number of RNA features found for this organism.
scientific_name: Full genus/species/strain name of the genome sequence.
complete: TRUE if the genome sequence is complete, else FALSE
prokaryotic: TRUE if this is a prokaryotic genome sequence, else FALSE
dna_size: Number of base pairs in the genome sequence.
contigs: Number of contigs for this genome sequence.
domain: Domain for this organism (Archaea, Bacteria, Eukaryota, Virus, Plasmid, or Environmental Sample).
genetic_code: Genetic code number used for protein translation on most of this genome sequence's contigs.
gc_content: Percent GC content present in the genome sequence's DNA.
phenotype: zero or more strings describing phenotypic information about this genome sequence
md5: MD5 identifier describing the genome's DNA sequence
source_id: identifier assigned to this genome by the original source

all_entities_Genome

$return = $obj->all_entities_Genome($start, $count, $fields)

Parameter and return types

$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_Genome
fields_Genome is a reference to a hash where the following keys are defined:
	id has a value which is a string
	pegs has a value which is an int
	rnas has a value which is an int
	scientific_name has a value which is a string
	complete has a value which is an int
	prokaryotic has a value which is an int
	dna_size has a value which is an int
	contigs has a value which is an int
	domain has a value which is a string
	genetic_code has a value which is an int
	gc_content has a value which is a float
	phenotype has a value which is a reference to a list where each element is a string
	md5 has a value which is a string
	source_id has a value which is a string

Description

get_entity_Identifier

$return = $obj->get_entity_Identifier($ids, $fields)

Parameter and return types

$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_Identifier
fields_Identifier is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source has a value which is a string
	natural_form has a value which is a string

Description

An identifier is an alternate name for a protein sequence. The identifier is typically stored in a prefixed form that indicates the database it came from. It has the following fields:

source: Specific type of the identifier, such as its source database or category. The type can usually be decoded to convert the identifier to a URL.
natural_form: Natural form of the identifier. This is how the identifier looks without the identifying prefix (if one is present).

all_entities_Identifier

$return = $obj->all_entities_Identifier($start, $count, $fields)

Parameter and return types

$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_Identifier
fields_Identifier is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source has a value which is a string
	natural_form has a value which is a string

Description

get_entity_Media

$return = $obj->get_entity_Media($ids, $fields)

Parameter and return types

$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_Media
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
	type has a value which is a string

Description

A media describes the chemical content of the solution in which cells are grown in an experiment or for the purposes of a model. The key is the common media name. The nature of the media is described by its relationship to its constituent compounds. It has the following fields:

mod_date: date and time of the last modification to the media's definition
name: descriptive name of the media
type: type of the medium (aerobic or anaerobic)

all_entities_Media

$return = $obj->all_entities_Media($start, $count, $fields)

Parameter and return types

$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_Media
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
	type has a value which is a string

Description

get_entity_Model

$return = $obj->get_entity_Model($ids, $fields)

Parameter and return types

$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_Model
fields_Model 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
	version has a value which is an int
	type has a value which is a string
	status has a value which is a string
	reaction_count has a value which is an int
	compound_count has a value which is an int
	annotation_count has a value which is an int

Description

A model specifies a relationship between sets of features and reactions in a cell. It is used to simulate cell growth and gene knockouts to validate annotations. It has the following fields:

mod_date: date and time of the last change to the model data
name: descriptive name of the model
version: revision number of the model
type: ask Chris
status: indicator of whether the model is stable, under construction, or under reconstruction
reaction_count: number of reactions in the model
compound_count: number of compounds in the model
annotation_count: number of annotations used to build the model

all_entities_Model

$return = $obj->all_entities_Model($start, $count, $fields)

Parameter and return types

$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_Model
fields_Model 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
	version has a value which is an int
	type has a value which is a string
	status has a value which is a string
	reaction_count has a value which is an int
	compound_count has a value which is an int
	annotation_count has a value which is an int

Description

get_entity_ModelCompartment

$return = $obj->get_entity_ModelCompartment($ids, $fields)

Parameter and return types

$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_ModelCompartment
fields_ModelCompartment is a reference to a hash where the following keys are defined:
	id has a value which is a string
	compartment_index has a value which is an int
	label has a value which is a reference to a list where each element is a string
	pH has a value which is a float
	potential has a value which is a float

Description

The Model Compartment represents a section of a cell (e.g. cell wall, cytoplasm) as it appears in a specific model. It has the following fields:

compartment_index: number used to distinguish between different instances of the same type of compartment in a single model. Within a model, any two instances of the same compartment must have difference compartment index values.
label: description used to differentiate between instances of the same compartment in a single model
pH: pH used to determine proton balance in this compartment
potential: ask Chris

all_entities_ModelCompartment

$return = $obj->all_entities_ModelCompartment($start, $count, $fields)

Parameter and return types

$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_ModelCompartment
fields_ModelCompartment is a reference to a hash where the following keys are defined:
	id has a value which is a string
	compartment_index has a value which is an int
	label has a value which is a reference to a list where each element is a string
	pH has a value which is a float
	potential has a value which is a float

Description

get_entity_OTU

$return = $obj->get_entity_OTU($ids, $fields)

Parameter and return types

$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_OTU
fields_OTU is a reference to a hash where the following keys are defined:
	id has a value which is a string

Description

An OTU (Organism Taxonomic Unit) is a named group of related genomes. It has the following fields:

all_entities_OTU

$return = $obj->all_entities_OTU($start, $count, $fields)

Parameter and return types

$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_OTU
fields_OTU is a reference to a hash where the following keys are defined:
	id has a value which is a string

Description

get_entity_PairSet

$return = $obj->get_entity_PairSet($ids, $fields)

Parameter and return types

$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_PairSet
fields_PairSet is a reference to a hash where the following keys are defined:
	id has a value which is a string
	score has a value which is an int

Description

A PairSet is a precompute set of pairs or genes. Each pair occurs close to one another of the chromosome. We believe that all of the first members of the pairs correspond to one another (are quite similar), as do all of the second members of the pairs. These pairs (from prokaryotic genomes) offer on of the most powerful clues relating to uncharacterized genes/peroteins.

It has the following fields:

score: Score for this evidence set. The score indicates the number of significantly different genomes represented by the pairings.

all_entities_PairSet

$return = $obj->all_entities_PairSet($start, $count, $fields)

Parameter and return types

$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_PairSet
fields_PairSet is a reference to a hash where the following keys are defined:
	id has a value which is a string
	score has a value which is an int

Description

get_entity_Pairing

$return = $obj->get_entity_Pairing($ids, $fields)

Parameter and return types

$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_Pairing
fields_Pairing is a reference to a hash where the following keys are defined:
	id has a value which is a string

Description

A pairing indicates that two features are found close together in a genome. Not all possible pairings are stored in the database; only those that are considered for some reason to be significant for annotation purposes.The key of the pairing is the concatenation of the feature IDs in alphabetical order with an intervening colon. It has the following fields:

all_entities_Pairing

$return = $obj->all_entities_Pairing($start, $count, $fields)

Parameter and return types

$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_Pairing
fields_Pairing is a reference to a hash where the following keys are defined:
	id has a value which is a string

Description

get_entity_ProbeSet

$return = $obj->get_entity_ProbeSet($ids, $fields)

Parameter and return types

$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_ProbeSet
fields_ProbeSet is a reference to a hash where the following keys are defined:
	id has a value which is a string

Description

A probe set is a device containing multiple probe sequences for use in gene expression experiments. It has the following fields:

all_entities_ProbeSet

$return = $obj->all_entities_ProbeSet($start, $count, $fields)

Parameter and return types

$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_ProbeSet
fields_ProbeSet is a reference to a hash where the following keys are defined:
	id has a value which is a string

Description

get_entity_ProteinSequence

$return = $obj->get_entity_ProteinSequence($ids, $fields)

Parameter and return types

$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_ProteinSequence
fields_ProteinSequence is a reference to a hash where the following keys are defined:
	id has a value which is a string
	sequence has a value which is a string

Description

We use the concept of ProteinSequence as an amino acid string with an associated MD5 value. It is easy to access the set of Features that relate to a ProteinSequence. While function is still associated with Features (and may be for some time), publications are associated with ProteinSequences (and the inferred impact on Features is through the relationship connecting ProteinSequences to Features).

It has the following fields:

sequence: The sequence contains the letters corresponding to the protein's amino acids.

all_entities_ProteinSequence

$return = $obj->all_entities_ProteinSequence($start, $count, $fields)

Parameter and return types

$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_ProteinSequence
fields_ProteinSequence is a reference to a hash where the following keys are defined:
	id has a value which is a string
	sequence has a value which is a string

Description

get_entity_Publication

$return = $obj->get_entity_Publication($ids, $fields)

Parameter and return types

$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_Publication
fields_Publication is a reference to a hash where the following keys are defined:
	id has a value which is a string
	title has a value which is a string
	link has a value which is a string
	pubdate has a value which is a string

Description

Annotators attach publications to ProteinSequences. The criteria we have used to gather such connections is a bit nonstandard. We have sought to attach publications to ProteinSequences when the publication includes an expert asserting a belief or estimate of function. The paper may not be the original characterization. Further, it may not even discuss a sequence protein (much of the literature is very valuable, but reports work on proteins in strains that have not yet been sequenced). On the other hand, reports of sequencing regions of a chromosome (with no specific assertion of a clear function) should not be attached. The attached publications give an ID (usually a Pubmed ID), a URL to the paper (when we have it), and a title (when we have it).

It has the following fields:

title: title of the article, or (unknown) if the title is not known
link: URL of the article
pubdate: publication date of the article

all_entities_Publication

$return = $obj->all_entities_Publication($start, $count, $fields)

Parameter and return types

$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_Publication
fields_Publication is a reference to a hash where the following keys are defined:
	id has a value which is a string
	title has a value which is a string
	link has a value which is a string
	pubdate has a value which is a string

Description

get_entity_Reaction

$return = $obj->get_entity_Reaction($ids, $fields)

Parameter and return types

$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_Reaction
fields_Reaction 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
	msid has a value which is a string
	abbr has a value which is a string
	equation has a value which is a string
	reversibility has a value which is a string

Description

A reaction is a chemical process that converts one set of compounds (substrate) to another set (products). It has the following fields:

mod_date: date and time of the last modification to this reaction's definition
name: descriptive name of this reaction
msid: common modeling ID of this reaction
abbr: abbreviated name of this reaction
equation: displayable formula for the reaction
reversibility: direction of this reaction (> for forward-only, < for backward-only, = for bidirectional)

all_entities_Reaction

$return = $obj->all_entities_Reaction($start, $count, $fields)

Parameter and return types

$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_Reaction
fields_Reaction 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
	msid has a value which is a string
	abbr has a value which is a string
	equation has a value which is a string
	reversibility has a value which is a string

Description

get_entity_ReactionRule

$return = $obj->get_entity_ReactionRule($ids, $fields)

Parameter and return types

$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_ReactionRule
fields_ReactionRule is a reference to a hash where the following keys are defined:
	id has a value which is a string
	direction has a value which is a string
	transproton has a value which is a float

Description

A reaction rule represents the way a reaction takes place within the context of a model. It has the following fields:

direction: reaction directionality (> for forward, < for backward, = for bidirectional) with respect to this complex
transproton: ask Chris

all_entities_ReactionRule

$return = $obj->all_entities_ReactionRule($start, $count, $fields)

Parameter and return types

$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_ReactionRule
fields_ReactionRule is a reference to a hash where the following keys are defined:
	id has a value which is a string
	direction has a value which is a string
	transproton has a value which is a float

Description

get_entity_Reagent

$return = $obj->get_entity_Reagent($ids, $fields)

Parameter and return types

$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_Reagent
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

Description

This entity represents a compound as it is used by a specific reaction. A reaction involves many compounds, and a compound can be involved in many reactions. The reagent describes the use of the compound by a specific reaction. It has the following fields:

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.
cofactor: TRUE if the compound is a cofactor; FALSE if it is a major component of the reaction.
compartment_index: Abstract number that groups this reagent into a compartment. Each group can then be assigned to real compartments when doing comparative analysis.
transport_coefficient: Number of reagents of this type transported. A positive value implies transport into the reactions default compartment; a negative value implies export to the reagent's specified compartment.

all_entities_Reagent

$return = $obj->all_entities_Reagent($start, $count, $fields)

Parameter and return types

$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_Reagent
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

Description

get_entity_Requirement

$return = $obj->get_entity_Requirement($ids, $fields)

Parameter and return types

$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_Requirement
fields_Requirement is a reference to a hash where the following keys are defined:
	id has a value which is a string
	direction has a value which is a string
	transproton has a value which is a float
	proton has a value which is a float

Description

A requirement describes the way a reaction fits into a model. It has the following fields:

direction: reaction directionality (> for forward, < for backward, = for bidirectional) with respect to this model
transproton: ask Chris
proton: ask Chris

all_entities_Requirement

$return = $obj->all_entities_Requirement($start, $count, $fields)

Parameter and return types

$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_Requirement
fields_Requirement is a reference to a hash where the following keys are defined:
	id has a value which is a string
	direction has a value which is a string
	transproton has a value which is a float
	proton has a value which is a float

Description

get_entity_Role

$return = $obj->get_entity_Role($ids, $fields)

Parameter and return types

$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_Role
fields_Role is a reference to a hash where the following keys are defined:
	id has a value which is a string
	hypothetical has a value which is an int

Description

A role describes a biological function that may be fulfilled by a feature. One of the main goals of the database is to assign features to roles. Most roles are effected by the construction of proteins. Some, however, deal with functional regulation and message transmission. It has the following fields:

hypothetical: TRUE if a role is hypothetical, else FALSE

all_entities_Role

$return = $obj->all_entities_Role($start, $count, $fields)

Parameter and return types

$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_Role
fields_Role is a reference to a hash where the following keys are defined:
	id has a value which is a string
	hypothetical has a value which is an int

Description

get_entity_SSCell

$return = $obj->get_entity_SSCell($ids, $fields)

Parameter and return types

$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_SSCell
fields_SSCell is a reference to a hash where the following keys are defined:
	id has a value which is a string

Description

An SSCell (SpreadSheet Cell) represents a role as it occurs in a subsystem spreadsheet row. The key is a colon-delimited triple containing an MD5 hash of the subsystem ID followed by a genome ID (with optional region string) and a role abbreviation. It has the following fields:

all_entities_SSCell

$return = $obj->all_entities_SSCell($start, $count, $fields)

Parameter and return types

$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_SSCell
fields_SSCell is a reference to a hash where the following keys are defined:
	id has a value which is a string

Description

get_entity_SSRow

$return = $obj->get_entity_SSRow($ids, $fields)

Parameter and return types

$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_SSRow
fields_SSRow is a reference to a hash where the following keys are defined:
	id has a value which is a string
	curated has a value which is an int
	region has a value which is a string

Description

An SSRow (that is, a row in a subsystem spreadsheet) represents a collection of functional roles present in the Features of a single Genome. The roles are part of a designated subsystem, and the fids associated with each role are included in the row, That is, a row amounts to an instance of a subsystem as it exists in a specific, designated genome.

It has the following fields:

curated: This flag is TRUE if the assignment of the molecular machine has been curated, and FALSE if it was made by an automated program.
region: Region in the genome for which the machine is relevant. Normally, this is an empty string, indicating that the machine covers the whole genome. If a subsystem has multiple machines for a genome, this contains a location string describing the region occupied by this particular machine.

all_entities_SSRow

$return = $obj->all_entities_SSRow($start, $count, $fields)

Parameter and return types

$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_SSRow
fields_SSRow is a reference to a hash where the following keys are defined:
	id has a value which is a string
	curated has a value which is an int
	region has a value which is a string

Description

get_entity_Scenario

$return = $obj->get_entity_Scenario($ids, $fields)

Parameter and return types

$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_Scenario
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

Description

A scenario is a partial instance of a subsystem with a defined set of reactions. Each scenario converts input compounds to output compounds using reactions. The scenario may use all of the reactions controlled by a subsystem or only some, and may also incorporate additional reactions. Because scenario names are not unique, the actual scenario ID is a number. It has the following fields:

common_name: Common name of the scenario. The name, rather than the ID number, is usually displayed everywhere.

all_entities_Scenario

$return = $obj->all_entities_Scenario($start, $count, $fields)

Parameter and return types

$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_Scenario
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

Description

get_entity_Source

$return = $obj->get_entity_Source($ids, $fields)

Parameter and return types

$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_Source
fields_Source is a reference to a hash where the following keys are defined:
	id has a value which is a string

Description

A source is a user or organization that is permitted to assign its own identifiers or to submit bioinformatic objects to the database. It has the following fields:

all_entities_Source

$return = $obj->all_entities_Source($start, $count, $fields)

Parameter and return types

$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_Source
fields_Source is a reference to a hash where the following keys are defined:
	id has a value which is a string

Description

get_entity_Subsystem

$return = $obj->get_entity_Subsystem($ids, $fields)

Parameter and return types

$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_Subsystem
fields_Subsystem is a reference to a hash where the following keys are defined:
	id has a value which is a string
	version has a value which is an int
	curator has a value which is a string
	notes has a value which is a string
	description has a value which is a string
	usable has a value which is an int
	private has a value which is an int
	cluster_based has a value which is an int
	experimental has a value which is an int

Description

A subsystem is a set of functional roles that have been annotated simultaneously (e.g., the roles present in a specific pathway), with an associated subsystem spreadsheet which encodes the fids in each genome that implement the functional roles in the subsystem.

It has the following fields:

version: version number for the subsystem. This value is incremented each time the subsystem is backed up.
curator: name of the person currently in charge of the subsystem
notes: descriptive notes about the subsystem
description: description of the subsystem's function in the cell
usable: TRUE if this is a usable subsystem, else FALSE. An unusable subsystem is one that is experimental or is of such low quality that it can negatively affect analysis.
private: TRUE if this is a private subsystem, else FALSE. A private subsystem has valid data, but is not considered ready for general distribution.
cluster_based: TRUE if this is a clustering-based subsystem, else FALSE. A clustering-based subsystem is one in which there is functional-coupling evidence that genes belong together, but we do not yet know what they do.
experimental: TRUE if this is an experimental subsystem, else FALSE. An experimental subsystem is designed for investigation and is not yet ready to be used in comparative analysis and annotation.

all_entities_Subsystem

$return = $obj->all_entities_Subsystem($start, $count, $fields)

Parameter and return types

$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_Subsystem
fields_Subsystem is a reference to a hash where the following keys are defined:
	id has a value which is a string
	version has a value which is an int
	curator has a value which is a string
	notes has a value which is a string
	description has a value which is a string
	usable has a value which is an int
	private has a value which is an int
	cluster_based has a value which is an int
	experimental has a value which is an int

Description

get_entity_SubsystemClass

$return = $obj->get_entity_SubsystemClass($ids, $fields)

Parameter and return types

$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_SubsystemClass
fields_SubsystemClass is a reference to a hash where the following keys are defined:
	id has a value which is a string

Description

Subsystem classes impose a hierarchical organization on the subsystems. It has the following fields:

all_entities_SubsystemClass

$return = $obj->all_entities_SubsystemClass($start, $count, $fields)

Parameter and return types

$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_SubsystemClass
fields_SubsystemClass is a reference to a hash where the following keys are defined:
	id has a value which is a string

Description

get_entity_TaxonomicGrouping

$return = $obj->get_entity_TaxonomicGrouping($ids, $fields)

Parameter and return types

$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_TaxonomicGrouping
fields_TaxonomicGrouping is a reference to a hash where the following keys are defined:
	id has a value which is a string
	domain has a value which is an int
	hidden has a value which is an int
	scientific_name has a value which is a string
	alias has a value which is a reference to a list where each element is a string

Description

We associate with most genomes a "taxonomy" based on the NCBI taxonomy. This includes, for each genome, a list of ever larger taxonomic groups.

It has the following fields:

domain: TRUE if this is a domain grouping, else FALSE.
hidden: TRUE if this is a hidden grouping, else FALSE. Hidden groupings are not typically shown in a lineage list.
scientific_name: Primary scientific name for this grouping. This is the name used when displaying a taxonomy.
alias: Alternate name for this grouping. A grouping may have many alternate names. The scientific name should also be in this list.

all_entities_TaxonomicGrouping

$return = $obj->all_entities_TaxonomicGrouping($start, $count, $fields)

Parameter and return types

$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_TaxonomicGrouping
fields_TaxonomicGrouping is a reference to a hash where the following keys are defined:
	id has a value which is a string
	domain has a value which is an int
	hidden has a value which is an int
	scientific_name has a value which is a string
	alias has a value which is a reference to a list where each element is a string

Description

get_entity_Variant

$return = $obj->get_entity_Variant($ids, $fields)

Parameter and return types

$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_Variant
fields_Variant is a reference to a hash where the following keys are defined:
	id has a value which is a string
	role_rule has a value which is a reference to a list where each element is a string
	code has a value which is a string
	type has a value which is a string
	comment has a value which is a string

Description

Each subsystem may include the designation of distinct variants. Thus, there may be three closely-related, but distinguishable forms of histidine degradation. Each form would be called a "variant", with an associated code, and all genomes implementing a specific variant can easily be accessed.

It has the following fields:

role_rule: a space-delimited list of role IDs, in alphabetical order, that represents a possible list of non-auxiliary roles applicable to this variant. The roles are identified by their abbreviations. A variant may have multiple role rules.
code: the variant code all by itself
type: variant type indicating the quality of the subsystem support. A type of "vacant" means that the subsystem does not appear to be implemented by the variant. A type of "incomplete" means that the subsystem appears to be missing many reactions. In all other cases, the type is "normal".
comment: commentary text about the variant

all_entities_Variant

$return = $obj->all_entities_Variant($start, $count, $fields)

Parameter and return types

$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_Variant
fields_Variant is a reference to a hash where the following keys are defined:
	id has a value which is a string
	role_rule has a value which is a reference to a list where each element is a string
	code has a value which is a string
	type has a value which is a string
	comment has a value which is a string

Description

get_entity_Variation

$return = $obj->get_entity_Variation($ids, $fields)

Parameter and return types

$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_Variation
fields_Variation is a reference to a hash where the following keys are defined:
	id has a value which is a string
	notes has a value which is a reference to a list where each element is a string

Description

A variation describes a set of aligned regions in two or more contigs. It has the following fields:

notes: optional text description of what the variation means

all_entities_Variation

$return = $obj->all_entities_Variation($start, $count, $fields)

Parameter and return types

$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_Variation
fields_Variation is a reference to a hash where the following keys are defined:
	id has a value which is a string
	notes has a value which is a reference to a list where each element is a string

Description

get_relationship_AffectsLevelOf

$return = $obj->get_relationship_AffectsLevelOf($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Experiment
	1: a fields_AffectsLevelOf
	2: a fields_AtomicRegulon
fields_Experiment is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source has a value which is a string
fields_AffectsLevelOf is a reference to a hash where the following keys are defined:
	id has a value which is a string
	level has a value which is an int
fields_AtomicRegulon is a reference to a hash where the following keys are defined:
	id has a value which is a string

Description

This relationship indicates the expression level of an atomic regulon for a given experiment. It has the following fields:

level: Indication of whether the feature is expressed (1), not expressed (-1), or unknown (0).

get_relationship_IsAffectedIn

$return = $obj->get_relationship_IsAffectedIn($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_AtomicRegulon
	1: a fields_AffectsLevelOf
	2: a fields_Experiment
fields_AtomicRegulon is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_AffectsLevelOf is a reference to a hash where the following keys are defined:
	id has a value which is a string
	level has a value which is an int
fields_Experiment is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source has a value which is a string

Description

get_relationship_Aligns

$return = $obj->get_relationship_Aligns($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_AlignmentTree
	1: a fields_Aligns
	2: a fields_ProteinSequence
fields_AlignmentTree is a reference to a hash where the following keys are defined:
	id has a value which is a string
	alignment_method has a value which is a string
	alignment_parameters has a value which is a string
	alignment_properties has a value which is a string
	tree_method has a value which is a string
	tree_parameters has a value which is a string
	tree_properties has a value which is a string
fields_Aligns is a reference to a hash where the following keys are defined:
	id has a value which is a string
	begin has a value which is an int
	end has a value which is an int
	len has a value which is an int
	sequence_id has a value which is a string
	properties has a value which is a string
fields_ProteinSequence is a reference to a hash where the following keys are defined:
	id has a value which is a string
	sequence has a value which is a string

Description

This relationship connects each alignment to its constituent protein sequences. Each alignment contains many protein sequences, and a single sequence can be in many alignments. Parts of a single protein can occur in multiple places in an alignment. The sequence-id field is used to keep these unique, and is the string that represents the sequence in the alignment and tree text. It has the following fields:

begin: location within the sequence at which the aligned portion begins
end: location within the sequence at which the aligned portion ends
len: length of the sequence within the alignment
sequence_id: identifier for this sequence in the alignment
properties: additional information about this sequence's participation in the alignment

get_relationship_IsAlignedBy

$return = $obj->get_relationship_IsAlignedBy($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_ProteinSequence
	1: a fields_Aligns
	2: a fields_AlignmentTree
fields_ProteinSequence is a reference to a hash where the following keys are defined:
	id has a value which is a string
	sequence has a value which is a string
fields_Aligns is a reference to a hash where the following keys are defined:
	id has a value which is a string
	begin has a value which is an int
	end has a value which is an int
	len has a value which is an int
	sequence_id has a value which is a string
	properties has a value which is a string
fields_AlignmentTree is a reference to a hash where the following keys are defined:
	id has a value which is a string
	alignment_method has a value which is a string
	alignment_parameters has a value which is a string
	alignment_properties has a value which is a string
	tree_method has a value which is a string
	tree_parameters has a value which is a string
	tree_properties has a value which is a string

Description

get_relationship_Concerns

$return = $obj->get_relationship_Concerns($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Publication
	1: a fields_Concerns
	2: a fields_ProteinSequence
fields_Publication is a reference to a hash where the following keys are defined:
	id has a value which is a string
	title has a value which is a string
	link has a value which is a string
	pubdate has a value which is a string
fields_Concerns is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_ProteinSequence is a reference to a hash where the following keys are defined:
	id has a value which is a string
	sequence has a value which is a string

Description

This relationship connects a publication to the protein sequences it describes. It has the following fields:

get_relationship_IsATopicOf

$return = $obj->get_relationship_IsATopicOf($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_ProteinSequence
	1: a fields_Concerns
	2: a fields_Publication
fields_ProteinSequence is a reference to a hash where the following keys are defined:
	id has a value which is a string
	sequence has a value which is a string
fields_Concerns is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Publication is a reference to a hash where the following keys are defined:
	id has a value which is a string
	title has a value which is a string
	link has a value which is a string
	pubdate has a value which is a string

Description

get_relationship_Contains

$return = $obj->get_relationship_Contains($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_SSCell
	1: a fields_Contains
	2: a fields_Feature
fields_SSCell is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Contains is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string

Description

This relationship connects a subsystem spreadsheet cell to the features that occur in it. A feature may occur in many machine roles and a machine role may contain many features. The subsystem annotation process is essentially the maintenance of this relationship. It has the following fields:

get_relationship_IsContainedIn

$return = $obj->get_relationship_IsContainedIn($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Feature
	1: a fields_Contains
	2: a fields_SSCell
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string
fields_Contains is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_SSCell is a reference to a hash where the following keys are defined:
	id has a value which is a string

Description

get_relationship_Controls

$return = $obj->get_relationship_Controls($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Feature
	1: a fields_Controls
	2: a fields_CoregulatedSet
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string
fields_Controls is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_CoregulatedSet is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source_id has a value which is a string

Description

This relationship connects a coregulated set to the features that are used as its transcription factors. It has the following fields:

get_relationship_IsControlledUsing

$return = $obj->get_relationship_IsControlledUsing($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_CoregulatedSet
	1: a fields_Controls
	2: a fields_Feature
fields_CoregulatedSet is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source_id has a value which is a string
fields_Controls is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string

Description

get_relationship_Describes

$return = $obj->get_relationship_Describes($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Subsystem
	1: a fields_Describes
	2: a fields_Variant
fields_Subsystem is a reference to a hash where the following keys are defined:
	id has a value which is a string
	version has a value which is an int
	curator has a value which is a string
	notes has a value which is a string
	description has a value which is a string
	usable has a value which is an int
	private has a value which is an int
	cluster_based has a value which is an int
	experimental has a value which is an int
fields_Describes is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Variant is a reference to a hash where the following keys are defined:
	id has a value which is a string
	role_rule has a value which is a reference to a list where each element is a string
	code has a value which is a string
	type has a value which is a string
	comment has a value which is a string

Description

This relationship connects a subsystem to the individual variants used to implement it. Each variant contains a slightly different subset of the roles in the parent subsystem. It has the following fields:

get_relationship_IsDescribedBy

$return = $obj->get_relationship_IsDescribedBy($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Variant
	1: a fields_Describes
	2: a fields_Subsystem
fields_Variant is a reference to a hash where the following keys are defined:
	id has a value which is a string
	role_rule has a value which is a reference to a list where each element is a string
	code has a value which is a string
	type has a value which is a string
	comment has a value which is a string
fields_Describes is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Subsystem is a reference to a hash where the following keys are defined:
	id has a value which is a string
	version has a value which is an int
	curator has a value which is a string
	notes has a value which is a string
	description has a value which is a string
	usable has a value which is an int
	private has a value which is an int
	cluster_based has a value which is an int
	experimental has a value which is an int

Description

get_relationship_Displays

$return = $obj->get_relationship_Displays($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Diagram
	1: a fields_Displays
	2: a fields_Reaction
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
fields_Displays 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_Reaction 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
	msid has a value which is a string
	abbr has a value which is a string
	equation has a value which is a string
	reversibility has a value which is a string

Description

This relationship connects a diagram to its reactions. A diagram shows multiple reactions, and a reaction can be on many diagrams. It has the following fields:

location: Location of the reaction's node on the diagram.

get_relationship_IsDisplayedOn

$return = $obj->get_relationship_IsDisplayedOn($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Reaction
	1: a fields_Displays
	2: a fields_Diagram
fields_Reaction 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
	msid has a value which is a string
	abbr has a value which is a string
	equation has a value which is a string
	reversibility has a value which is a string
fields_Displays 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

Description

get_relationship_Encompasses

$return = $obj->get_relationship_Encompasses($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Feature
	1: a fields_Encompasses
	2: a fields_Feature
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string
fields_Encompasses is a reference to a hash where the following keys are defined:
	id has a value which is a string

Description

This relationship connects a feature to a related feature; for example, it would connect a gene to its constituent splice variants, and the splice variants to their exons. It has the following fields:

get_relationship_IsEncompassedIn

$return = $obj->get_relationship_IsEncompassedIn($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Feature
	1: a fields_Encompasses
	2: a fields_Feature
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string
fields_Encompasses is a reference to a hash where the following keys are defined:
	id has a value which is a string

Description

get_relationship_Formulated

$return = $obj->get_relationship_Formulated($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Source
	1: a fields_Formulated
	2: a fields_CoregulatedSet
fields_Source is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Formulated is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_CoregulatedSet is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source_id has a value which is a string

Description

This relationship connects a coregulated set to the source organization that originally computed it. It has the following fields:

get_relationship_WasFormulatedBy

$return = $obj->get_relationship_WasFormulatedBy($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_CoregulatedSet
	1: a fields_Formulated
	2: a fields_Source
fields_CoregulatedSet is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source_id has a value which is a string
fields_Formulated is a reference to a hash where the following keys are defined:
	id 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

Description

get_relationship_GeneratedLevelsFor

$return = $obj->get_relationship_GeneratedLevelsFor($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_ProbeSet
	1: a fields_GeneratedLevelsFor
	2: a fields_AtomicRegulon
fields_ProbeSet is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_GeneratedLevelsFor is a reference to a hash where the following keys are defined:
	id has a value which is a string
	level_vector has a value which is a countVector
countVector is a string
fields_AtomicRegulon is a reference to a hash where the following keys are defined:
	id has a value which is a string

Description

This relationship connects an atomic regulon to a probe set from which experimental data was produced for its features. It contains a vector of the expression levels. It has the following fields:

level_vector: Vector of expression levels (-1, 0, 1) for the experiments, in sequence order.

get_relationship_WasGeneratedFrom

$return = $obj->get_relationship_WasGeneratedFrom($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_AtomicRegulon
	1: a fields_GeneratedLevelsFor
	2: a fields_ProbeSet
fields_AtomicRegulon is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_GeneratedLevelsFor is a reference to a hash where the following keys are defined:
	id has a value which is a string
	level_vector has a value which is a countVector
countVector is a string
fields_ProbeSet is a reference to a hash where the following keys are defined:
	id has a value which is a string

Description

get_relationship_HasAssertionFrom

$return = $obj->get_relationship_HasAssertionFrom($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Identifier
	1: a fields_HasAssertionFrom
	2: a fields_Source
fields_Identifier is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source has a value which is a string
	natural_form has a value which is a string
fields_HasAssertionFrom is a reference to a hash where the following keys are defined:
	id has a value which is a string
	function has a value which is a string
	expert has a value which is an int
fields_Source is a reference to a hash where the following keys are defined:
	id has a value which is a string

Description

Sources (users) can make assertions about identifiers using the annotation clearinghouse. When a user makes a new assertion about an identifier, it erases the old one. It has the following fields:

function: The function is the text of the assertion made about the identifier.
expert: TRUE if this is an expert assertion, else FALSE

get_relationship_Asserts

$return = $obj->get_relationship_Asserts($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Source
	1: a fields_HasAssertionFrom
	2: a fields_Identifier
fields_Source is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_HasAssertionFrom is a reference to a hash where the following keys are defined:
	id has a value which is a string
	function has a value which is a string
	expert has a value which is an int
fields_Identifier is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source has a value which is a string
	natural_form has a value which is a string

Description

get_relationship_HasCompoundAliasFrom

$return = $obj->get_relationship_HasCompoundAliasFrom($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Source
	1: a fields_HasCompoundAliasFrom
	2: a fields_Compound
fields_Source is a reference to a hash where the following keys are defined:
	id has a value which is a string
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

Description

This relationship connects a source (database or organization) with the compounds for which it has assigned names (aliases). The alias itself is stored as intersection data. It has the following fields:

alias: alias for the compound assigned by the source

get_relationship_UsesAliasForCompound

$return = $obj->get_relationship_UsesAliasForCompound($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	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

Description

get_relationship_HasIndicatedSignalFrom

$return = $obj->get_relationship_HasIndicatedSignalFrom($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Feature
	1: a fields_HasIndicatedSignalFrom
	2: a fields_Experiment
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string
fields_HasIndicatedSignalFrom is a reference to a hash where the following keys are defined:
	id has a value which is a string
	rma_value has a value which is a float
	level has a value which is an int
fields_Experiment is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source has a value which is a string

Description

This relationship connects an experiment to a feature. The feature expression levels inferred from the experimental results are stored here. It has the following fields:

rma_value: Normalized expression value for this feature under the experiment's conditions.
level: Indication of whether the feature is expressed (1), not expressed (-1), or unknown (0).

get_relationship_IndicatesSignalFor

$return = $obj->get_relationship_IndicatesSignalFor($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Experiment
	1: a fields_HasIndicatedSignalFrom
	2: a fields_Feature
fields_Experiment is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source has a value which is a string
fields_HasIndicatedSignalFrom is a reference to a hash where the following keys are defined:
	id has a value which is a string
	rma_value has a value which is a float
	level has a value which is an int
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string

Description

get_relationship_HasMember

$return = $obj->get_relationship_HasMember($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Family
	1: a fields_HasMember
	2: a fields_Feature
fields_Family is a reference to a hash where the following keys are defined:
	id has a value which is a string
	type has a value which is a string
	family_function has a value which is a reference to a list where each element is a string
fields_HasMember is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string

Description

This relationship connects each feature family to its constituent features. A family always has many features, and a single feature can be found in many families. It has the following fields:

get_relationship_IsMemberOf

$return = $obj->get_relationship_IsMemberOf($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Feature
	1: a fields_HasMember
	2: a fields_Family
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string
fields_HasMember is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Family is a reference to a hash where the following keys are defined:
	id has a value which is a string
	type has a value which is a string
	family_function has a value which is a reference to a list where each element is a string

Description

get_relationship_HasParticipant

$return = $obj->get_relationship_HasParticipant($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Scenario
	1: a fields_HasParticipant
	2: a fields_Reaction
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
fields_HasParticipant is a reference to a hash where the following keys are defined:
	id has a value which is a string
	type has a value which is an int
fields_Reaction 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
	msid has a value which is a string
	abbr has a value which is a string
	equation has a value which is a string
	reversibility has a value which is a string

Description

A scenario consists of many participant reactions that convert the input compounds to output compounds. A single reaction may participate in many scenarios. It has the following fields:

type: Indicates the type of participaton. If 0, the reaction is in the main pathway of the scenario. If 1, the reaction is necessary to make the model work but is not in the subsystem. If 2, the reaction is part of the subsystem but should not be included in the modelling process.

get_relationship_ParticipatesIn

$return = $obj->get_relationship_ParticipatesIn($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Reaction
	1: a fields_HasParticipant
	2: a fields_Scenario
fields_Reaction 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
	msid has a value which is a string
	abbr has a value which is a string
	equation has a value which is a string
	reversibility has a value which is a string
fields_HasParticipant is a reference to a hash where the following keys are defined:
	id has a value which is a string
	type 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

Description

get_relationship_HasPresenceOf

$return = $obj->get_relationship_HasPresenceOf($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Media
	1: a fields_HasPresenceOf
	2: a fields_Compound
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
	type has a value which is a string
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_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

Description

This relationship connects a media to the compounds that occur in it. The intersection data describes how much of each compound can be found. It has the following fields:

concentration: concentration of the compound in the media
minimum_flux: minimum flux of the compound for this media
maximum_flux: maximum flux of the compound for this media

get_relationship_IsPresentIn

$return = $obj->get_relationship_IsPresentIn($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	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
	type has a value which is a string

Description

get_relationship_HasReactionAliasFrom

$return = $obj->get_relationship_HasReactionAliasFrom($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Source
	1: a fields_HasReactionAliasFrom
	2: a fields_Reaction
fields_Source is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_HasReactionAliasFrom 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_Reaction 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
	msid has a value which is a string
	abbr has a value which is a string
	equation has a value which is a string
	reversibility has a value which is a string

Description

This relationship connects a source (database or organization) with the reactions for which it has assigned names (aliases). The alias itself is stored as intersection data. It has the following fields:

alias: alias for the reaction assigned by the source

get_relationship_UsesAliasForReaction

$return = $obj->get_relationship_UsesAliasForReaction($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Reaction
	1: a fields_HasReactionAliasFrom
	2: a fields_Source
fields_Reaction 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
	msid has a value which is a string
	abbr has a value which is a string
	equation has a value which is a string
	reversibility has a value which is a string
fields_HasReactionAliasFrom 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

Description

get_relationship_HasRepresentativeOf

$return = $obj->get_relationship_HasRepresentativeOf($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Genome
	1: a fields_HasRepresentativeOf
	2: a fields_Family
fields_Genome is a reference to a hash where the following keys are defined:
	id has a value which is a string
	pegs has a value which is an int
	rnas has a value which is an int
	scientific_name has a value which is a string
	complete has a value which is an int
	prokaryotic has a value which is an int
	dna_size has a value which is an int
	contigs has a value which is an int
	domain has a value which is a string
	genetic_code has a value which is an int
	gc_content has a value which is a float
	phenotype has a value which is a reference to a list where each element is a string
	md5 has a value which is a string
	source_id has a value which is a string
fields_HasRepresentativeOf is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Family is a reference to a hash where the following keys are defined:
	id has a value which is a string
	type has a value which is a string
	family_function has a value which is a reference to a list where each element is a string

Description

This relationship connects a genome to the FIGfam protein families for which it has representative proteins. This information can be computed from other relationships, but it is provided explicitly to allow fast access to a genome's FIGfam profile. It has the following fields:

get_relationship_IsRepresentedIn

$return = $obj->get_relationship_IsRepresentedIn($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Family
	1: a fields_HasRepresentativeOf
	2: a fields_Genome
fields_Family is a reference to a hash where the following keys are defined:
	id has a value which is a string
	type has a value which is a string
	family_function has a value which is a reference to a list where each element is a string
fields_HasRepresentativeOf is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Genome is a reference to a hash where the following keys are defined:
	id has a value which is a string
	pegs has a value which is an int
	rnas has a value which is an int
	scientific_name has a value which is a string
	complete has a value which is an int
	prokaryotic has a value which is an int
	dna_size has a value which is an int
	contigs has a value which is an int
	domain has a value which is a string
	genetic_code has a value which is an int
	gc_content has a value which is a float
	phenotype has a value which is a reference to a list where each element is a string
	md5 has a value which is a string
	source_id has a value which is a string

Description

get_relationship_HasResultsIn

$return = $obj->get_relationship_HasResultsIn($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_ProbeSet
	1: a fields_HasResultsIn
	2: a fields_Experiment
fields_ProbeSet is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_HasResultsIn is a reference to a hash where the following keys are defined:
	id has a value which is a string
	sequence has a value which is an int
fields_Experiment is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source has a value which is a string

Description

This relationship connects a probe set to the experiments that were applied to it. It has the following fields:

sequence: Sequence number of this experiment in the various result vectors.

get_relationship_HasResultsFor

$return = $obj->get_relationship_HasResultsFor($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Experiment
	1: a fields_HasResultsIn
	2: a fields_ProbeSet
fields_Experiment is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source has a value which is a string
fields_HasResultsIn is a reference to a hash where the following keys are defined:
	id has a value which is a string
	sequence has a value which is an int
fields_ProbeSet is a reference to a hash where the following keys are defined:
	id has a value which is a string

Description

get_relationship_HasSection

$return = $obj->get_relationship_HasSection($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_ContigSequence
	1: a fields_HasSection
	2: a fields_ContigChunk
fields_ContigSequence is a reference to a hash where the following keys are defined:
	id has a value which is a string
	length has a value which is an int
fields_HasSection is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_ContigChunk is a reference to a hash where the following keys are defined:
	id has a value which is a string
	sequence has a value which is a string

Description

This relationship connects a contig's sequence to its DNA sequences. It has the following fields:

get_relationship_IsSectionOf

$return = $obj->get_relationship_IsSectionOf($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_ContigChunk
	1: a fields_HasSection
	2: a fields_ContigSequence
fields_ContigChunk is a reference to a hash where the following keys are defined:
	id has a value which is a string
	sequence has a value which is a string
fields_HasSection is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_ContigSequence is a reference to a hash where the following keys are defined:
	id has a value which is a string
	length has a value which is an int

Description

get_relationship_HasStep

$return = $obj->get_relationship_HasStep($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Complex
	1: a fields_HasStep
	2: a fields_ReactionRule
fields_Complex 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 reference to a list where each element is a string
	msid has a value which is a string
	mod_date has a value which is a string
fields_HasStep is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_ReactionRule is a reference to a hash where the following keys are defined:
	id has a value which is a string
	direction has a value which is a string
	transproton has a value which is a float

Description

This relationship connects a complex to the reaction rules for the reactions that work together to make the complex happen. It has the following fields:

get_relationship_IsStepOf

$return = $obj->get_relationship_IsStepOf($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_ReactionRule
	1: a fields_HasStep
	2: a fields_Complex
fields_ReactionRule is a reference to a hash where the following keys are defined:
	id has a value which is a string
	direction has a value which is a string
	transproton has a value which is a float
fields_HasStep is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Complex 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 reference to a list where each element is a string
	msid has a value which is a string
	mod_date has a value which is a string

Description

get_relationship_HasUsage

$return = $obj->get_relationship_HasUsage($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	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

Description

This relationship connects a biomass compound specification to the compounds for which it is relevant. It has the following fields:

get_relationship_IsUsageOf

$return = $obj->get_relationship_IsUsageOf($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_BiomassCompound
	1: a fields_HasUsage
	2: a fields_Compound
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
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

Description

get_relationship_HasValueFor

$return = $obj->get_relationship_HasValueFor($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Experiment
	1: a fields_HasValueFor
	2: a fields_Attribute
fields_Experiment is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source has a value which is a string
fields_HasValueFor is a reference to a hash where the following keys are defined:
	id has a value which is a string
	value has a value which is a string
fields_Attribute is a reference to a hash where the following keys are defined:
	id has a value which is a string
	description has a value which is a string

Description

This relationship connects an experiment to its attributes. The attribute values are stored here. It has the following fields:

value: Value of this attribute in the given experiment. This is always encoded as a string, but may in fact be a number.

get_relationship_HasValueIn

$return = $obj->get_relationship_HasValueIn($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Attribute
	1: a fields_HasValueFor
	2: a fields_Experiment
fields_Attribute is a reference to a hash where the following keys are defined:
	id has a value which is a string
	description has a value which is a string
fields_HasValueFor is a reference to a hash where the following keys are defined:
	id has a value which is a string
	value has a value which is a string
fields_Experiment is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source has a value which is a string

Description

get_relationship_Imported

$return = $obj->get_relationship_Imported($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Source
	1: a fields_Imported
	2: a fields_Identifier
fields_Source is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Imported is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Identifier is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source has a value which is a string
	natural_form has a value which is a string

Description

This relationship specifies the import source for identifiers. It is used when reloading identifiers to provide for rapid deletion of the previous load's results. It has the following fields:

get_relationship_WasImportedFrom

$return = $obj->get_relationship_WasImportedFrom($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Identifier
	1: a fields_Imported
	2: a fields_Source
fields_Identifier is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source has a value which is a string
	natural_form has a value which is a string
fields_Imported is a reference to a hash where the following keys are defined:
	id 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

Description

get_relationship_Includes

$return = $obj->get_relationship_Includes($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Subsystem
	1: a fields_Includes
	2: a fields_Role
fields_Subsystem is a reference to a hash where the following keys are defined:
	id has a value which is a string
	version has a value which is an int
	curator has a value which is a string
	notes has a value which is a string
	description has a value which is a string
	usable has a value which is an int
	private has a value which is an int
	cluster_based has a value which is an int
	experimental has a value which is an int
fields_Includes is a reference to a hash where the following keys are defined:
	id has a value which is a string
	sequence has a value which is an int
	abbreviation has a value which is a string
	auxiliary has a value which is an int
fields_Role is a reference to a hash where the following keys are defined:
	id has a value which is a string
	hypothetical has a value which is an int

Description

A subsystem is defined by its roles. The subsystem's variants contain slightly different sets of roles, but all of the roles in a variant must be connected to the parent subsystem by this relationship. A subsystem always has at least one role, and a role always belongs to at least one subsystem. It has the following fields:

sequence: Sequence number of the role within the subsystem. When the roles are formed into a variant, they will generally appear in sequence order.
abbreviation: Abbreviation for this role in this subsystem. The abbreviations are used in columnar displays, and they also appear on diagrams.
auxiliary: TRUE if this is an auxiliary role, or FALSE if this role is a functioning part of the subsystem.

get_relationship_IsIncludedIn

$return = $obj->get_relationship_IsIncludedIn($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Role
	1: a fields_Includes
	2: a fields_Subsystem
fields_Role is a reference to a hash where the following keys are defined:
	id has a value which is a string
	hypothetical has a value which is an int
fields_Includes is a reference to a hash where the following keys are defined:
	id has a value which is a string
	sequence has a value which is an int
	abbreviation has a value which is a string
	auxiliary has a value which is an int
fields_Subsystem is a reference to a hash where the following keys are defined:
	id has a value which is a string
	version has a value which is an int
	curator has a value which is a string
	notes has a value which is a string
	description has a value which is a string
	usable has a value which is an int
	private has a value which is an int
	cluster_based has a value which is an int
	experimental has a value which is an int

Description

get_relationship_IndicatedLevelsFor

$return = $obj->get_relationship_IndicatedLevelsFor($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_ProbeSet
	1: a fields_IndicatedLevelsFor
	2: a fields_Feature
fields_ProbeSet is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_IndicatedLevelsFor is a reference to a hash where the following keys are defined:
	id has a value which is a string
	level_vector has a value which is a countVector
countVector is a string
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string

Description

This relationship connects a feature to a probe set from which experimental data was produced for the feature. It contains a vector of the expression levels. It has the following fields:

level_vector: Vector of expression levels (-1, 0, 1) for the experiments, in sequence order.

get_relationship_HasLevelsFrom

$return = $obj->get_relationship_HasLevelsFrom($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Feature
	1: a fields_IndicatedLevelsFor
	2: a fields_ProbeSet
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string
fields_IndicatedLevelsFor is a reference to a hash where the following keys are defined:
	id has a value which is a string
	level_vector has a value which is a countVector
countVector is a string
fields_ProbeSet is a reference to a hash where the following keys are defined:
	id has a value which is a string

Description

get_relationship_Involves

$return = $obj->get_relationship_Involves($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Reaction
	1: a fields_Involves
	2: a fields_Reagent
fields_Reaction 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
	msid has a value which is a string
	abbr has a value which is a string
	equation has a value which is a string
	reversibility has a value which is a string
fields_Involves 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

Description

This relationship connects a reaction to the reagents representing the compounds that participate in it. It has the following fields:

get_relationship_IsInvolvedIn

$return = $obj->get_relationship_IsInvolvedIn($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Reagent
	1: a fields_Involves
	2: a fields_Reaction
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
fields_Involves is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Reaction 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
	msid has a value which is a string
	abbr has a value which is a string
	equation has a value which is a string
	reversibility has a value which is a string

Description

get_relationship_IsARequirementIn

$return = $obj->get_relationship_IsARequirementIn($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Model
	1: a fields_IsARequirementIn
	2: a fields_Requirement
fields_Model 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
	version has a value which is an int
	type has a value which is a string
	status has a value which is a string
	reaction_count has a value which is an int
	compound_count has a value which is an int
	annotation_count has a value which is an int
fields_IsARequirementIn is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Requirement is a reference to a hash where the following keys are defined:
	id has a value which is a string
	direction has a value which is a string
	transproton has a value which is a float
	proton has a value which is a float

Description

This relationship connects a model to its requirements. A requirement represents the use of a reaction in a single model. It has the following fields:

get_relationship_IsARequirementOf

$return = $obj->get_relationship_IsARequirementOf($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Requirement
	1: a fields_IsARequirementIn
	2: a fields_Model
fields_Requirement is a reference to a hash where the following keys are defined:
	id has a value which is a string
	direction has a value which is a string
	transproton has a value which is a float
	proton has a value which is a float
fields_IsARequirementIn is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Model 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
	version has a value which is an int
	type has a value which is a string
	status has a value which is a string
	reaction_count has a value which is an int
	compound_count has a value which is an int
	annotation_count has a value which is an int

Description

get_relationship_IsAlignedIn

$return = $obj->get_relationship_IsAlignedIn($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Contig
	1: a fields_IsAlignedIn
	2: a fields_Variation
fields_Contig is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source_id has a value which is a string
fields_IsAlignedIn is a reference to a hash where the following keys are defined:
	id has a value which is a string
	start has a value which is an int
	len has a value which is an int
	dir has a value which is a string
fields_Variation is a reference to a hash where the following keys are defined:
	id has a value which is a string
	notes has a value which is a reference to a list where each element is a string

Description

This relationship connects each variation to the contig regions that it aligns. It has the following fields:

start: start location of region
len: length of region
dir: direction of region (+ or -)

get_relationship_IsAlignmentFor

$return = $obj->get_relationship_IsAlignmentFor($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Variation
	1: a fields_IsAlignedIn
	2: a fields_Contig
fields_Variation is a reference to a hash where the following keys are defined:
	id has a value which is a string
	notes has a value which is a reference to a list where each element is a string
fields_IsAlignedIn is a reference to a hash where the following keys are defined:
	id has a value which is a string
	start has a value which is an int
	len has a value which is an int
	dir has a value which is a string
fields_Contig is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source_id has a value which is a string

Description

get_relationship_IsAnnotatedBy

$return = $obj->get_relationship_IsAnnotatedBy($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Feature
	1: a fields_IsAnnotatedBy
	2: a fields_Annotation
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string
fields_IsAnnotatedBy is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Annotation is a reference to a hash where the following keys are defined:
	id has a value which is a string
	annotator has a value which is a string
	comment has a value which is a string
	annotation_time has a value which is a string

Description

This relationship connects a feature to its annotations. A feature may have multiple annotations, but an annotation belongs to only one feature. It has the following fields:

get_relationship_Annotates

$return = $obj->get_relationship_Annotates($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Annotation
	1: a fields_IsAnnotatedBy
	2: a fields_Feature
fields_Annotation is a reference to a hash where the following keys are defined:
	id has a value which is a string
	annotator has a value which is a string
	comment has a value which is a string
	annotation_time has a value which is a string
fields_IsAnnotatedBy is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string

Description

get_relationship_IsBindingSiteFor

$return = $obj->get_relationship_IsBindingSiteFor($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Feature
	1: a fields_IsBindingSiteFor
	2: a fields_CoregulatedSet
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string
fields_IsBindingSiteFor is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_CoregulatedSet is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source_id has a value which is a string

Description

This relationship connects a coregulated set to the binding site to which its feature attaches. It has the following fields:

get_relationship_IsBoundBy

$return = $obj->get_relationship_IsBoundBy($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_CoregulatedSet
	1: a fields_IsBindingSiteFor
	2: a fields_Feature
fields_CoregulatedSet is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source_id has a value which is a string
fields_IsBindingSiteFor is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string

Description

get_relationship_IsClassFor

$return = $obj->get_relationship_IsClassFor($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_SubsystemClass
	1: a fields_IsClassFor
	2: a fields_Subsystem
fields_SubsystemClass is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_IsClassFor is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Subsystem is a reference to a hash where the following keys are defined:
	id has a value which is a string
	version has a value which is an int
	curator has a value which is a string
	notes has a value which is a string
	description has a value which is a string
	usable has a value which is an int
	private has a value which is an int
	cluster_based has a value which is an int
	experimental has a value which is an int

Description

This relationship connects each subsystem class with the subsystems that belong to it. A class can contain many subsystems, but a subsystem is only in one class. Some subsystems are not in any class, but this is usually a temporary condition. It has the following fields:

get_relationship_IsInClass

$return = $obj->get_relationship_IsInClass($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Subsystem
	1: a fields_IsClassFor
	2: a fields_SubsystemClass
fields_Subsystem is a reference to a hash where the following keys are defined:
	id has a value which is a string
	version has a value which is an int
	curator has a value which is a string
	notes has a value which is a string
	description has a value which is a string
	usable has a value which is an int
	private has a value which is an int
	cluster_based has a value which is an int
	experimental has a value which is an int
fields_IsClassFor is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_SubsystemClass is a reference to a hash where the following keys are defined:
	id has a value which is a string

Description

get_relationship_IsCollectionOf

$return = $obj->get_relationship_IsCollectionOf($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_OTU
	1: a fields_IsCollectionOf
	2: a fields_Genome
fields_OTU is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_IsCollectionOf is a reference to a hash where the following keys are defined:
	id has a value which is a string
	representative has a value which is an int
fields_Genome is a reference to a hash where the following keys are defined:
	id has a value which is a string
	pegs has a value which is an int
	rnas has a value which is an int
	scientific_name has a value which is a string
	complete has a value which is an int
	prokaryotic has a value which is an int
	dna_size has a value which is an int
	contigs has a value which is an int
	domain has a value which is a string
	genetic_code has a value which is an int
	gc_content has a value which is a float
	phenotype has a value which is a reference to a list where each element is a string
	md5 has a value which is a string
	source_id has a value which is a string

Description

A genome belongs to only one genome set. For each set, this relationship marks the genome to be used as its representative. It has the following fields:

representative: TRUE for the representative genome of the set, else FALSE.

get_relationship_IsCollectedInto

$return = $obj->get_relationship_IsCollectedInto($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Genome
	1: a fields_IsCollectionOf
	2: a fields_OTU
fields_Genome is a reference to a hash where the following keys are defined:
	id has a value which is a string
	pegs has a value which is an int
	rnas has a value which is an int
	scientific_name has a value which is a string
	complete has a value which is an int
	prokaryotic has a value which is an int
	dna_size has a value which is an int
	contigs has a value which is an int
	domain has a value which is a string
	genetic_code has a value which is an int
	gc_content has a value which is a float
	phenotype has a value which is a reference to a list where each element is a string
	md5 has a value which is a string
	source_id has a value which is a string
fields_IsCollectionOf is a reference to a hash where the following keys are defined:
	id has a value which is a string
	representative has a value which is an int
fields_OTU is a reference to a hash where the following keys are defined:
	id has a value which is a string

Description

get_relationship_IsComposedOf

$return = $obj->get_relationship_IsComposedOf($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Genome
	1: a fields_IsComposedOf
	2: a fields_Contig
fields_Genome is a reference to a hash where the following keys are defined:
	id has a value which is a string
	pegs has a value which is an int
	rnas has a value which is an int
	scientific_name has a value which is a string
	complete has a value which is an int
	prokaryotic has a value which is an int
	dna_size has a value which is an int
	contigs has a value which is an int
	domain has a value which is a string
	genetic_code has a value which is an int
	gc_content has a value which is a float
	phenotype has a value which is a reference to a list where each element is a string
	md5 has a value which is a string
	source_id has a value which is a string
fields_IsComposedOf is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Contig is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source_id has a value which is a string

Description

This relationship connects a genome to its constituent contigs. Unlike contig sequences, a contig belongs to only one genome. It has the following fields:

get_relationship_IsComponentOf

$return = $obj->get_relationship_IsComponentOf($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Contig
	1: a fields_IsComposedOf
	2: a fields_Genome
fields_Contig is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source_id has a value which is a string
fields_IsComposedOf is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Genome is a reference to a hash where the following keys are defined:
	id has a value which is a string
	pegs has a value which is an int
	rnas has a value which is an int
	scientific_name has a value which is a string
	complete has a value which is an int
	prokaryotic has a value which is an int
	dna_size has a value which is an int
	contigs has a value which is an int
	domain has a value which is a string
	genetic_code has a value which is an int
	gc_content has a value which is a float
	phenotype has a value which is a reference to a list where each element is a string
	md5 has a value which is a string
	source_id has a value which is a string

Description

get_relationship_IsComprisedOf

$return = $obj->get_relationship_IsComprisedOf($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Biomass
	1: a fields_IsComprisedOf
	2: a fields_BiomassCompound
fields_Biomass 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 reference to a list where each element is a string
fields_IsComprisedOf 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

Description

This relationship connects a biomass to the compound specifications that define it. It has the following fields:

get_relationship_Comprises

$return = $obj->get_relationship_Comprises($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_BiomassCompound
	1: a fields_IsComprisedOf
	2: a fields_Biomass
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
fields_IsComprisedOf is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Biomass 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 reference to a list where each element is a string

Description

get_relationship_IsConfiguredBy

$return = $obj->get_relationship_IsConfiguredBy($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Genome
	1: a fields_IsConfiguredBy
	2: a fields_AtomicRegulon
fields_Genome is a reference to a hash where the following keys are defined:
	id has a value which is a string
	pegs has a value which is an int
	rnas has a value which is an int
	scientific_name has a value which is a string
	complete has a value which is an int
	prokaryotic has a value which is an int
	dna_size has a value which is an int
	contigs has a value which is an int
	domain has a value which is a string
	genetic_code has a value which is an int
	gc_content has a value which is a float
	phenotype has a value which is a reference to a list where each element is a string
	md5 has a value which is a string
	source_id has a value which is a string
fields_IsConfiguredBy is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_AtomicRegulon is a reference to a hash where the following keys are defined:
	id has a value which is a string

Description

This relationship connects a genome to the atomic regulons that describe its state. It has the following fields:

get_relationship_ReflectsStateOf

$return = $obj->get_relationship_ReflectsStateOf($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_AtomicRegulon
	1: a fields_IsConfiguredBy
	2: a fields_Genome
fields_AtomicRegulon is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_IsConfiguredBy is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Genome is a reference to a hash where the following keys are defined:
	id has a value which is a string
	pegs has a value which is an int
	rnas has a value which is an int
	scientific_name has a value which is a string
	complete has a value which is an int
	prokaryotic has a value which is an int
	dna_size has a value which is an int
	contigs has a value which is an int
	domain has a value which is a string
	genetic_code has a value which is an int
	gc_content has a value which is a float
	phenotype has a value which is a reference to a list where each element is a string
	md5 has a value which is a string
	source_id has a value which is a string

Description

get_relationship_IsConsistentWith

$return = $obj->get_relationship_IsConsistentWith($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_EcNumber
	1: a fields_IsConsistentWith
	2: a fields_Role
fields_EcNumber is a reference to a hash where the following keys are defined:
	id has a value which is a string
	obsolete has a value which is an int
	replacedby has a value which is a string
fields_IsConsistentWith is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Role is a reference to a hash where the following keys are defined:
	id has a value which is a string
	hypothetical has a value which is an int

Description

This relationship connects a functional role to the EC numbers consistent with the chemistry described in the role. It has the following fields:

get_relationship_IsConsistentTo

$return = $obj->get_relationship_IsConsistentTo($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Role
	1: a fields_IsConsistentWith
	2: a fields_EcNumber
fields_Role is a reference to a hash where the following keys are defined:
	id has a value which is a string
	hypothetical has a value which is an int
fields_IsConsistentWith is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_EcNumber is a reference to a hash where the following keys are defined:
	id has a value which is a string
	obsolete has a value which is an int
	replacedby has a value which is a string

Description

get_relationship_IsCoregulatedWith

$return = $obj->get_relationship_IsCoregulatedWith($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Feature
	1: a fields_IsCoregulatedWith
	2: a fields_Feature
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string
fields_IsCoregulatedWith 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

Description

This relationship connects a feature with another feature in the same genome with which it appears to be coregulated as a result of expression data analysis. It has the following fields:

coefficient: Pearson correlation coefficient for this coregulation.

get_relationship_HasCoregulationWith

$return = $obj->get_relationship_HasCoregulationWith($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Feature
	1: a fields_IsCoregulatedWith
	2: a fields_Feature
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string
fields_IsCoregulatedWith 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

Description

get_relationship_IsCoupledTo

$return = $obj->get_relationship_IsCoupledTo($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Family
	1: a fields_IsCoupledTo
	2: a fields_Family
fields_Family is a reference to a hash where the following keys are defined:
	id has a value which is a string
	type has a value which is a string
	family_function has a value which is a reference to a list where each element is a string
fields_IsCoupledTo is a reference to a hash where the following keys are defined:
	id has a value which is a string
	co_occurrence_evidence has a value which is an int
	co_expression_evidence has a value which is an int

Description

This relationship connects two FIGfams that we believe to be related either because their members occur in proximity on chromosomes or because the members are expressed together. Such a relationship is evidence the functions of the FIGfams are themselves related. This relationship is commutative; only the instance in which the first FIGfam has a lower ID than the second is stored. It has the following fields:

co_occurrence_evidence: number of times members of the two FIGfams occur close to each other on chromosomes
co_expression_evidence: number of times members of the two FIGfams are co-expressed in expression data experiments

get_relationship_IsCoupledWith

$return = $obj->get_relationship_IsCoupledWith($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Family
	1: a fields_IsCoupledTo
	2: a fields_Family
fields_Family is a reference to a hash where the following keys are defined:
	id has a value which is a string
	type has a value which is a string
	family_function has a value which is a reference to a list where each element is a string
fields_IsCoupledTo is a reference to a hash where the following keys are defined:
	id has a value which is a string
	co_occurrence_evidence has a value which is an int
	co_expression_evidence has a value which is an int

Description

get_relationship_IsDefaultFor

$return = $obj->get_relationship_IsDefaultFor($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Compartment
	1: a fields_IsDefaultFor
	2: a fields_Reaction
fields_Compartment is a reference to a hash where the following keys are defined:
	id has a value which is a string
	abbr has a value which is a string
	mod_date has a value which is a string
	name has a value which is a string
	msid has a value which is a string
fields_IsDefaultFor is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Reaction 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
	msid has a value which is a string
	abbr has a value which is a string
	equation has a value which is a string
	reversibility has a value which is a string

Description

This relationship connects a reaction to the compartment in which it runs by default. It has the following fields:

get_relationship_RunsByDefaultIn

$return = $obj->get_relationship_RunsByDefaultIn($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Reaction
	1: a fields_IsDefaultFor
	2: a fields_Compartment
fields_Reaction 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
	msid has a value which is a string
	abbr has a value which is a string
	equation has a value which is a string
	reversibility has a value which is a string
fields_IsDefaultFor is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Compartment is a reference to a hash where the following keys are defined:
	id has a value which is a string
	abbr has a value which is a string
	mod_date has a value which is a string
	name has a value which is a string
	msid has a value which is a string

Description

get_relationship_IsDefaultLocationOf

$return = $obj->get_relationship_IsDefaultLocationOf($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Compartment
	1: a fields_IsDefaultLocationOf
	2: a fields_Reagent
fields_Compartment is a reference to a hash where the following keys are defined:
	id has a value which is a string
	abbr has a value which is a string
	mod_date has a value which is a string
	name has a value which is a string
	msid has a value which is a string
fields_IsDefaultLocationOf 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

Description

This relationship connects a reagent to the compartment which is its default location during the reaction. It has the following fields:

get_relationship_HasDefaultLocation

$return = $obj->get_relationship_HasDefaultLocation($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Reagent
	1: a fields_IsDefaultLocationOf
	2: a fields_Compartment
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
fields_IsDefaultLocationOf is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Compartment is a reference to a hash where the following keys are defined:
	id has a value which is a string
	abbr has a value which is a string
	mod_date has a value which is a string
	name has a value which is a string
	msid has a value which is a string

Description

get_relationship_IsDeterminedBy

$return = $obj->get_relationship_IsDeterminedBy($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_PairSet
	1: a fields_IsDeterminedBy
	2: a fields_Pairing
fields_PairSet is a reference to a hash where the following keys are defined:
	id has a value which is a string
	score has a value which is an int
fields_IsDeterminedBy is a reference to a hash where the following keys are defined:
	id has a value which is a string
	inverted has a value which is an int
fields_Pairing is a reference to a hash where the following keys are defined:
	id has a value which is a string

Description

A functional coupling evidence set exists because it has pairings in it, and this relationship connects the evidence set to its constituent pairings. A pairing cam belong to multiple evidence sets. It has the following fields:

inverted: A pairing is an unordered pair of protein sequences, but its similarity to other pairings in a pair set is ordered. Let (A,B) be a pairing and (X,Y) be another pairing in the same set. If this flag is FALSE, then (A =~ X) and (B =~ Y). If this flag is TRUE, then (A =~ Y) and (B =~ X).

get_relationship_Determines

$return = $obj->get_relationship_Determines($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Pairing
	1: a fields_IsDeterminedBy
	2: a fields_PairSet
fields_Pairing is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_IsDeterminedBy is a reference to a hash where the following keys are defined:
	id has a value which is a string
	inverted has a value which is an int
fields_PairSet is a reference to a hash where the following keys are defined:
	id has a value which is a string
	score has a value which is an int

Description

get_relationship_IsDividedInto

$return = $obj->get_relationship_IsDividedInto($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Model
	1: a fields_IsDividedInto
	2: a fields_ModelCompartment
fields_Model 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
	version has a value which is an int
	type has a value which is a string
	status has a value which is a string
	reaction_count has a value which is an int
	compound_count has a value which is an int
	annotation_count has a value which is an int
fields_IsDividedInto is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_ModelCompartment is a reference to a hash where the following keys are defined:
	id has a value which is a string
	compartment_index has a value which is an int
	label has a value which is a reference to a list where each element is a string
	pH has a value which is a float
	potential has a value which is a float

Description

This relationship connects a model to the cell compartments that participate in the model. It has the following fields:

get_relationship_IsDivisionOf

$return = $obj->get_relationship_IsDivisionOf($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_ModelCompartment
	1: a fields_IsDividedInto
	2: a fields_Model
fields_ModelCompartment is a reference to a hash where the following keys are defined:
	id has a value which is a string
	compartment_index has a value which is an int
	label has a value which is a reference to a list where each element is a string
	pH has a value which is a float
	potential has a value which is a float
fields_IsDividedInto is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Model 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
	version has a value which is an int
	type has a value which is a string
	status has a value which is a string
	reaction_count has a value which is an int
	compound_count has a value which is an int
	annotation_count has a value which is an int

Description

get_relationship_IsExemplarOf

$return = $obj->get_relationship_IsExemplarOf($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Feature
	1: a fields_IsExemplarOf
	2: a fields_Role
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string
fields_IsExemplarOf is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Role is a reference to a hash where the following keys are defined:
	id has a value which is a string
	hypothetical has a value which is an int

Description

This relationship links a role to a feature that provides a typical example of how the role is implemented. It has the following fields:

get_relationship_HasAsExemplar

$return = $obj->get_relationship_HasAsExemplar($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Role
	1: a fields_IsExemplarOf
	2: a fields_Feature
fields_Role is a reference to a hash where the following keys are defined:
	id has a value which is a string
	hypothetical has a value which is an int
fields_IsExemplarOf is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string

Description

get_relationship_IsFamilyFor

$return = $obj->get_relationship_IsFamilyFor($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Family
	1: a fields_IsFamilyFor
	2: a fields_Role
fields_Family is a reference to a hash where the following keys are defined:
	id has a value which is a string
	type has a value which is a string
	family_function has a value which is a reference to a list where each element is a string
fields_IsFamilyFor is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Role is a reference to a hash where the following keys are defined:
	id has a value which is a string
	hypothetical has a value which is an int

Description

This relationship connects an isofunctional family to the roles that make up its assigned function. It has the following fields:

get_relationship_DeterminesFunctionOf

$return = $obj->get_relationship_DeterminesFunctionOf($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Role
	1: a fields_IsFamilyFor
	2: a fields_Family
fields_Role is a reference to a hash where the following keys are defined:
	id has a value which is a string
	hypothetical has a value which is an int
fields_IsFamilyFor is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Family is a reference to a hash where the following keys are defined:
	id has a value which is a string
	type has a value which is a string
	family_function has a value which is a reference to a list where each element is a string

Description

get_relationship_IsFormedOf

$return = $obj->get_relationship_IsFormedOf($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_AtomicRegulon
	1: a fields_IsFormedOf
	2: a fields_Feature
fields_AtomicRegulon is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_IsFormedOf is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string

Description

This relationship connects each feature to the atomic regulon to which it belongs. It has the following fields:

get_relationship_IsFormedInto

$return = $obj->get_relationship_IsFormedInto($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Feature
	1: a fields_IsFormedOf
	2: a fields_AtomicRegulon
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string
fields_IsFormedOf is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_AtomicRegulon is a reference to a hash where the following keys are defined:
	id has a value which is a string

Description

get_relationship_IsFunctionalIn

$return = $obj->get_relationship_IsFunctionalIn($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Role
	1: a fields_IsFunctionalIn
	2: a fields_Feature
fields_Role is a reference to a hash where the following keys are defined:
	id has a value which is a string
	hypothetical has a value which is an int
fields_IsFunctionalIn is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string

Description

This relationship connects a role with the features in which it plays a functional part. It has the following fields:

get_relationship_HasFunctional

$return = $obj->get_relationship_HasFunctional($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Feature
	1: a fields_IsFunctionalIn
	2: a fields_Role
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string
fields_IsFunctionalIn is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Role is a reference to a hash where the following keys are defined:
	id has a value which is a string
	hypothetical has a value which is an int

Description

get_relationship_IsGroupFor

$return = $obj->get_relationship_IsGroupFor($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_TaxonomicGrouping
	1: a fields_IsGroupFor
	2: a fields_TaxonomicGrouping
fields_TaxonomicGrouping is a reference to a hash where the following keys are defined:
	id has a value which is a string
	domain has a value which is an int
	hidden has a value which is an int
	scientific_name has a value which is a string
	alias has a value which is a reference to a list where each element is a string
fields_IsGroupFor is a reference to a hash where the following keys are defined:
	id has a value which is a string

Description

The recursive IsGroupFor relationship organizes taxonomic groupings into a hierarchy based on the standard organism taxonomy. It has the following fields:

get_relationship_IsInGroup

$return = $obj->get_relationship_IsInGroup($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_TaxonomicGrouping
	1: a fields_IsGroupFor
	2: a fields_TaxonomicGrouping
fields_TaxonomicGrouping is a reference to a hash where the following keys are defined:
	id has a value which is a string
	domain has a value which is an int
	hidden has a value which is an int
	scientific_name has a value which is a string
	alias has a value which is a reference to a list where each element is a string
fields_IsGroupFor is a reference to a hash where the following keys are defined:
	id has a value which is a string

Description

get_relationship_IsImplementedBy

$return = $obj->get_relationship_IsImplementedBy($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Variant
	1: a fields_IsImplementedBy
	2: a fields_SSRow
fields_Variant is a reference to a hash where the following keys are defined:
	id has a value which is a string
	role_rule has a value which is a reference to a list where each element is a string
	code has a value which is a string
	type has a value which is a string
	comment has a value which is a string
fields_IsImplementedBy is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_SSRow is a reference to a hash where the following keys are defined:
	id has a value which is a string
	curated has a value which is an int
	region has a value which is a string

Description

This relationship connects a variant to the physical machines that implement it in the genomes. A variant is implemented by many machines, but a machine belongs to only one variant. It has the following fields:

get_relationship_Implements

$return = $obj->get_relationship_Implements($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_SSRow
	1: a fields_IsImplementedBy
	2: a fields_Variant
fields_SSRow is a reference to a hash where the following keys are defined:
	id has a value which is a string
	curated has a value which is an int
	region has a value which is a string
fields_IsImplementedBy is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Variant is a reference to a hash where the following keys are defined:
	id has a value which is a string
	role_rule has a value which is a reference to a list where each element is a string
	code has a value which is a string
	type has a value which is a string
	comment has a value which is a string

Description

get_relationship_IsInPair

$return = $obj->get_relationship_IsInPair($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Feature
	1: a fields_IsInPair
	2: a fields_Pairing
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string
fields_IsInPair is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Pairing is a reference to a hash where the following keys are defined:
	id has a value which is a string

Description

A pairing contains exactly two protein sequences. A protein sequence can belong to multiple pairings. When going from a protein sequence to its pairings, they are presented in alphabetical order by sequence key. It has the following fields:

get_relationship_IsPairOf

$return = $obj->get_relationship_IsPairOf($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Pairing
	1: a fields_IsInPair
	2: a fields_Feature
fields_Pairing is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_IsInPair is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string

Description

get_relationship_IsInstantiatedBy

$return = $obj->get_relationship_IsInstantiatedBy($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Compartment
	1: a fields_IsInstantiatedBy
	2: a fields_ModelCompartment
fields_Compartment is a reference to a hash where the following keys are defined:
	id has a value which is a string
	abbr has a value which is a string
	mod_date has a value which is a string
	name has a value which is a string
	msid has a value which is a string
fields_IsInstantiatedBy is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_ModelCompartment is a reference to a hash where the following keys are defined:
	id has a value which is a string
	compartment_index has a value which is an int
	label has a value which is a reference to a list where each element is a string
	pH has a value which is a float
	potential has a value which is a float

Description

This relationship connects a compartment to the instances of that compartment that occur in models. It has the following fields:

get_relationship_IsInstanceOf

$return = $obj->get_relationship_IsInstanceOf($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_ModelCompartment
	1: a fields_IsInstantiatedBy
	2: a fields_Compartment
fields_ModelCompartment is a reference to a hash where the following keys are defined:
	id has a value which is a string
	compartment_index has a value which is an int
	label has a value which is a reference to a list where each element is a string
	pH has a value which is a float
	potential has a value which is a float
fields_IsInstantiatedBy is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Compartment is a reference to a hash where the following keys are defined:
	id has a value which is a string
	abbr has a value which is a string
	mod_date has a value which is a string
	name has a value which is a string
	msid has a value which is a string

Description

get_relationship_IsLocatedIn

$return = $obj->get_relationship_IsLocatedIn($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Feature
	1: a fields_IsLocatedIn
	2: a fields_Contig
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string
fields_IsLocatedIn is a reference to a hash where the following keys are defined:
	id has a value which is a string
	ordinal has a value which is an int
	begin has a value which is an int
	len has a value which is an int
	dir has a value which is a string
fields_Contig is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source_id has a value which is a string

Description

A feature is a set of DNA sequence fragments. Most features are a single contiquous fragment, so they are located in only one DNA sequence; however, fragments have a maximum length, so even a single contiguous feature may participate in this relationship multiple times. A few features belong to multiple DNA sequences. In that case, however, all the DNA sequences belong to the same genome. A DNA sequence itself will frequently have thousands of features connected to it. It has the following fields:

ordinal: Sequence number of this segment, starting from 1 and proceeding sequentially forward from there.
begin: Index (1-based) of the first residue in the contig that belongs to the segment.
len: Length of this segment.
dir: Direction (strand) of the segment: "+" if it is forward and "-" if it is backward.

get_relationship_IsLocusFor

$return = $obj->get_relationship_IsLocusFor($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Contig
	1: a fields_IsLocatedIn
	2: a fields_Feature
fields_Contig is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source_id has a value which is a string
fields_IsLocatedIn is a reference to a hash where the following keys are defined:
	id has a value which is a string
	ordinal has a value which is an int
	begin has a value which is an int
	len has a value which is an int
	dir has a value which is a string
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string

Description

get_relationship_IsModeledBy

$return = $obj->get_relationship_IsModeledBy($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Genome
	1: a fields_IsModeledBy
	2: a fields_Model
fields_Genome is a reference to a hash where the following keys are defined:
	id has a value which is a string
	pegs has a value which is an int
	rnas has a value which is an int
	scientific_name has a value which is a string
	complete has a value which is an int
	prokaryotic has a value which is an int
	dna_size has a value which is an int
	contigs has a value which is an int
	domain has a value which is a string
	genetic_code has a value which is an int
	gc_content has a value which is a float
	phenotype has a value which is a reference to a list where each element is a string
	md5 has a value which is a string
	source_id has a value which is a string
fields_IsModeledBy is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Model 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
	version has a value which is an int
	type has a value which is a string
	status has a value which is a string
	reaction_count has a value which is an int
	compound_count has a value which is an int
	annotation_count has a value which is an int

Description

A genome can be modeled by many different models, but a model belongs to only one genome. It has the following fields:

get_relationship_Models

$return = $obj->get_relationship_Models($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Model
	1: a fields_IsModeledBy
	2: a fields_Genome
fields_Model 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
	version has a value which is an int
	type has a value which is a string
	status has a value which is a string
	reaction_count has a value which is an int
	compound_count has a value which is an int
	annotation_count has a value which is an int
fields_IsModeledBy is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Genome is a reference to a hash where the following keys are defined:
	id has a value which is a string
	pegs has a value which is an int
	rnas has a value which is an int
	scientific_name has a value which is a string
	complete has a value which is an int
	prokaryotic has a value which is an int
	dna_size has a value which is an int
	contigs has a value which is an int
	domain has a value which is a string
	genetic_code has a value which is an int
	gc_content has a value which is a float
	phenotype has a value which is a reference to a list where each element is a string
	md5 has a value which is a string
	source_id has a value which is a string

Description

get_relationship_IsNamedBy

$return = $obj->get_relationship_IsNamedBy($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_ProteinSequence
	1: a fields_IsNamedBy
	2: a fields_Identifier
fields_ProteinSequence is a reference to a hash where the following keys are defined:
	id has a value which is a string
	sequence has a value which is a string
fields_IsNamedBy is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Identifier is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source has a value which is a string
	natural_form has a value which is a string

Description

The normal case is that an identifier names a single protein sequence, while a protein sequence can have many identifiers, but some identifiers name multiple sequences. It has the following fields:

get_relationship_Names

$return = $obj->get_relationship_Names($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Identifier
	1: a fields_IsNamedBy
	2: a fields_ProteinSequence
fields_Identifier is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source has a value which is a string
	natural_form has a value which is a string
fields_IsNamedBy is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_ProteinSequence is a reference to a hash where the following keys are defined:
	id has a value which is a string
	sequence has a value which is a string

Description

get_relationship_IsOwnerOf

$return = $obj->get_relationship_IsOwnerOf($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Genome
	1: a fields_IsOwnerOf
	2: a fields_Feature
fields_Genome is a reference to a hash where the following keys are defined:
	id has a value which is a string
	pegs has a value which is an int
	rnas has a value which is an int
	scientific_name has a value which is a string
	complete has a value which is an int
	prokaryotic has a value which is an int
	dna_size has a value which is an int
	contigs has a value which is an int
	domain has a value which is a string
	genetic_code has a value which is an int
	gc_content has a value which is a float
	phenotype has a value which is a reference to a list where each element is a string
	md5 has a value which is a string
	source_id has a value which is a string
fields_IsOwnerOf is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string

Description

This relationship connects a genome to the features it contains. Though technically redundant (the information is available from the feature's contigs), it simplifies the extremely common process of finding all features for a genome. It has the following fields:

get_relationship_IsOwnedBy

$return = $obj->get_relationship_IsOwnedBy($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Feature
	1: a fields_IsOwnerOf
	2: a fields_Genome
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string
fields_IsOwnerOf is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Genome is a reference to a hash where the following keys are defined:
	id has a value which is a string
	pegs has a value which is an int
	rnas has a value which is an int
	scientific_name has a value which is a string
	complete has a value which is an int
	prokaryotic has a value which is an int
	dna_size has a value which is an int
	contigs has a value which is an int
	domain has a value which is a string
	genetic_code has a value which is an int
	gc_content has a value which is a float
	phenotype has a value which is a reference to a list where each element is a string
	md5 has a value which is a string
	source_id has a value which is a string

Description

get_relationship_IsProposedLocationOf

$return = $obj->get_relationship_IsProposedLocationOf($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Compartment
	1: a fields_IsProposedLocationOf
	2: a fields_ReactionRule
fields_Compartment is a reference to a hash where the following keys are defined:
	id has a value which is a string
	abbr has a value which is a string
	mod_date has a value which is a string
	name has a value which is a string
	msid has a value which is a string
fields_IsProposedLocationOf is a reference to a hash where the following keys are defined:
	id has a value which is a string
	type has a value which is a string
fields_ReactionRule is a reference to a hash where the following keys are defined:
	id has a value which is a string
	direction has a value which is a string
	transproton has a value which is a float

Description

This relationship connects a reaction as it is used in a complex to the compartments in which it usually takes place. Most reactions take place in a single compartment. Transporters take place in two compartments. It has the following fields:

type: role of the compartment in the reaction: 'primary' if it is the sole or starting compartment, 'secondary' if it is the ending compartment in a multi-compartmental reaction

get_relationship_HasProposedLocationIn

$return = $obj->get_relationship_HasProposedLocationIn($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_ReactionRule
	1: a fields_IsProposedLocationOf
	2: a fields_Compartment
fields_ReactionRule is a reference to a hash where the following keys are defined:
	id has a value which is a string
	direction has a value which is a string
	transproton has a value which is a float
fields_IsProposedLocationOf is a reference to a hash where the following keys are defined:
	id has a value which is a string
	type has a value which is a string
fields_Compartment is a reference to a hash where the following keys are defined:
	id has a value which is a string
	abbr has a value which is a string
	mod_date has a value which is a string
	name has a value which is a string
	msid has a value which is a string

Description

get_relationship_IsProteinFor

$return = $obj->get_relationship_IsProteinFor($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_ProteinSequence
	1: a fields_IsProteinFor
	2: a fields_Feature
fields_ProteinSequence is a reference to a hash where the following keys are defined:
	id has a value which is a string
	sequence has a value which is a string
fields_IsProteinFor is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string

Description

This relationship connects a peg feature to the protein sequence it produces (if any). Only peg features participate in this relationship. A single protein sequence will frequently be produced by many features. It has the following fields:

get_relationship_Produces

$return = $obj->get_relationship_Produces($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Feature
	1: a fields_IsProteinFor
	2: a fields_ProteinSequence
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string
fields_IsProteinFor is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_ProteinSequence is a reference to a hash where the following keys are defined:
	id has a value which is a string
	sequence has a value which is a string

Description

get_relationship_IsRealLocationOf

$return = $obj->get_relationship_IsRealLocationOf($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_ModelCompartment
	1: a fields_IsRealLocationOf
	2: a fields_Requirement
fields_ModelCompartment is a reference to a hash where the following keys are defined:
	id has a value which is a string
	compartment_index has a value which is an int
	label has a value which is a reference to a list where each element is a string
	pH has a value which is a float
	potential has a value which is a float
fields_IsRealLocationOf is a reference to a hash where the following keys are defined:
	id has a value which is a string
	type has a value which is a string
fields_Requirement is a reference to a hash where the following keys are defined:
	id has a value which is a string
	direction has a value which is a string
	transproton has a value which is a float
	proton has a value which is a float

Description

This relationship connects a model's instance of a reaction to the compartments in which it takes place. Most instances take place in a single compartment. Transporters use two compartments. It has the following fields:

type: role of the compartment in the reaction: 'primary' if it is the sole or starting compartment, 'secondary' if it is the ending compartment in a multi-compartmental reaction

get_relationship_HasRealLocationIn

$return = $obj->get_relationship_HasRealLocationIn($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Requirement
	1: a fields_IsRealLocationOf
	2: a fields_ModelCompartment
fields_Requirement is a reference to a hash where the following keys are defined:
	id has a value which is a string
	direction has a value which is a string
	transproton has a value which is a float
	proton has a value which is a float
fields_IsRealLocationOf is a reference to a hash where the following keys are defined:
	id has a value which is a string
	type has a value which is a string
fields_ModelCompartment is a reference to a hash where the following keys are defined:
	id has a value which is a string
	compartment_index has a value which is an int
	label has a value which is a reference to a list where each element is a string
	pH has a value which is a float
	potential has a value which is a float

Description

get_relationship_IsRegulatedIn

$return = $obj->get_relationship_IsRegulatedIn($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Feature
	1: a fields_IsRegulatedIn
	2: a fields_CoregulatedSet
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string
fields_IsRegulatedIn is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_CoregulatedSet is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source_id has a value which is a string

Description

This relationship connects a feature to the set of coregulated features. It has the following fields:

get_relationship_IsRegulatedSetOf

$return = $obj->get_relationship_IsRegulatedSetOf($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_CoregulatedSet
	1: a fields_IsRegulatedIn
	2: a fields_Feature
fields_CoregulatedSet is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source_id has a value which is a string
fields_IsRegulatedIn is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Feature is a reference to a hash where the following keys are defined:
	id has a value which is a string
	feature_type has a value which is a string
	source_id has a value which is a string
	sequence_length has a value which is an int
	function has a value which is a string

Description

get_relationship_IsRelevantFor

$return = $obj->get_relationship_IsRelevantFor($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Diagram
	1: a fields_IsRelevantFor
	2: a fields_Subsystem
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
fields_IsRelevantFor is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Subsystem is a reference to a hash where the following keys are defined:
	id has a value which is a string
	version has a value which is an int
	curator has a value which is a string
	notes has a value which is a string
	description has a value which is a string
	usable has a value which is an int
	private has a value which is an int
	cluster_based has a value which is an int
	experimental has a value which is an int

Description

This relationship connects a diagram to the subsystems that are depicted on it. Only diagrams which are useful in curating or annotation the subsystem are specified in this relationship. It has the following fields:

get_relationship_IsRelevantTo

$return = $obj->get_relationship_IsRelevantTo($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Subsystem
	1: a fields_IsRelevantFor
	2: a fields_Diagram
fields_Subsystem is a reference to a hash where the following keys are defined:
	id has a value which is a string
	version has a value which is an int
	curator has a value which is a string
	notes has a value which is a string
	description has a value which is a string
	usable has a value which is an int
	private has a value which is an int
	cluster_based has a value which is an int
	experimental has a value which is an int
fields_IsRelevantFor is a reference to a hash where the following keys are defined:
	id has a value which 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

Description

get_relationship_IsRequiredBy

$return = $obj->get_relationship_IsRequiredBy($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Reaction
	1: a fields_IsRequiredBy
	2: a fields_Requirement
fields_Reaction 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
	msid has a value which is a string
	abbr has a value which is a string
	equation has a value which is a string
	reversibility has a value which is a string
fields_IsRequiredBy is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Requirement is a reference to a hash where the following keys are defined:
	id has a value which is a string
	direction has a value which is a string
	transproton has a value which is a float
	proton has a value which is a float

Description

This relationship links a reaction to the way it is used in a model. It has the following fields:

get_relationship_Requires

$return = $obj->get_relationship_Requires($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Requirement
	1: a fields_IsRequiredBy
	2: a fields_Reaction
fields_Requirement is a reference to a hash where the following keys are defined:
	id has a value which is a string
	direction has a value which is a string
	transproton has a value which is a float
	proton has a value which is a float
fields_IsRequiredBy is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Reaction 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
	msid has a value which is a string
	abbr has a value which is a string
	equation has a value which is a string
	reversibility has a value which is a string

Description

get_relationship_IsRoleOf

$return = $obj->get_relationship_IsRoleOf($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Role
	1: a fields_IsRoleOf
	2: a fields_SSCell
fields_Role is a reference to a hash where the following keys are defined:
	id has a value which is a string
	hypothetical has a value which is an int
fields_IsRoleOf is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_SSCell is a reference to a hash where the following keys are defined:
	id has a value which is a string

Description

This relationship connects a role to the machine roles that represent its appearance in a molecular machine. A machine role has exactly one associated role, but a role may be represented by many machine roles. It has the following fields:

get_relationship_HasRole

$return = $obj->get_relationship_HasRole($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_SSCell
	1: a fields_IsRoleOf
	2: a fields_Role
fields_SSCell is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_IsRoleOf is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Role is a reference to a hash where the following keys are defined:
	id has a value which is a string
	hypothetical has a value which is an int

Description

get_relationship_IsRowOf

$return = $obj->get_relationship_IsRowOf($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_SSRow
	1: a fields_IsRowOf
	2: a fields_SSCell
fields_SSRow is a reference to a hash where the following keys are defined:
	id has a value which is a string
	curated has a value which is an int
	region has a value which is a string
fields_IsRowOf is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_SSCell is a reference to a hash where the following keys are defined:
	id has a value which is a string

Description

This relationship connects a subsystem spreadsheet row to its constituent spreadsheet cells. It has the following fields:

get_relationship_IsRoleFor

$return = $obj->get_relationship_IsRoleFor($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_SSCell
	1: a fields_IsRowOf
	2: a fields_SSRow
fields_SSCell is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_IsRowOf is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_SSRow is a reference to a hash where the following keys are defined:
	id has a value which is a string
	curated has a value which is an int
	region has a value which is a string

Description

get_relationship_IsSequenceOf

$return = $obj->get_relationship_IsSequenceOf($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_ContigSequence
	1: a fields_IsSequenceOf
	2: a fields_Contig
fields_ContigSequence is a reference to a hash where the following keys are defined:
	id has a value which is a string
	length has a value which is an int
fields_IsSequenceOf is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Contig is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source_id has a value which is a string

Description

This relationship connects a Contig as it occurs in a genome to the Contig Sequence that represents the physical DNA base pairs. A contig sequence may represent many contigs, but each contig has only one sequence. It has the following fields:

get_relationship_HasAsSequence

$return = $obj->get_relationship_HasAsSequence($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Contig
	1: a fields_IsSequenceOf
	2: a fields_ContigSequence
fields_Contig is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source_id has a value which is a string
fields_IsSequenceOf is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_ContigSequence is a reference to a hash where the following keys are defined:
	id has a value which is a string
	length has a value which is an int

Description

get_relationship_IsSubInstanceOf

$return = $obj->get_relationship_IsSubInstanceOf($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Subsystem
	1: a fields_IsSubInstanceOf
	2: a fields_Scenario
fields_Subsystem is a reference to a hash where the following keys are defined:
	id has a value which is a string
	version has a value which is an int
	curator has a value which is a string
	notes has a value which is a string
	description has a value which is a string
	usable has a value which is an int
	private has a value which is an int
	cluster_based has a value which is an int
	experimental has a value which is an int
fields_IsSubInstanceOf is a reference to a hash where the following keys are defined:
	id has a value which is a string
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

Description

This relationship connects a scenario to its subsystem it validates. A scenario belongs to exactly one subsystem, but a subsystem may have multiple scenarios. It has the following fields:

get_relationship_Validates

$return = $obj->get_relationship_Validates($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Scenario
	1: a fields_IsSubInstanceOf
	2: a fields_Subsystem
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
fields_IsSubInstanceOf is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Subsystem is a reference to a hash where the following keys are defined:
	id has a value which is a string
	version has a value which is an int
	curator has a value which is a string
	notes has a value which is a string
	description has a value which is a string
	usable has a value which is an int
	private has a value which is an int
	cluster_based has a value which is an int
	experimental has a value which is an int

Description

get_relationship_IsSuperclassOf

$return = $obj->get_relationship_IsSuperclassOf($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_SubsystemClass
	1: a fields_IsSuperclassOf
	2: a fields_SubsystemClass
fields_SubsystemClass is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_IsSuperclassOf is a reference to a hash where the following keys are defined:
	id has a value which is a string

Description

This is a recursive relationship that imposes a hierarchy on the subsystem classes. It has the following fields:

get_relationship_IsSubclassOf

$return = $obj->get_relationship_IsSubclassOf($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_SubsystemClass
	1: a fields_IsSuperclassOf
	2: a fields_SubsystemClass
fields_SubsystemClass is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_IsSuperclassOf is a reference to a hash where the following keys are defined:
	id has a value which is a string

Description

get_relationship_IsTargetOf

$return = $obj->get_relationship_IsTargetOf($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_ModelCompartment
	1: a fields_IsTargetOf
	2: a fields_BiomassCompound
fields_ModelCompartment is a reference to a hash where the following keys are defined:
	id has a value which is a string
	compartment_index has a value which is an int
	label has a value which is a reference to a list where each element is a string
	pH has a value which is a float
	potential has a value which is a float
fields_IsTargetOf 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

Description

This relationship connects a compound in a biomass to the compartment in which it is supposed to appear. It has the following fields:

get_relationship_Targets

$return = $obj->get_relationship_Targets($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_BiomassCompound
	1: a fields_IsTargetOf
	2: a fields_ModelCompartment
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
fields_IsTargetOf is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_ModelCompartment is a reference to a hash where the following keys are defined:
	id has a value which is a string
	compartment_index has a value which is an int
	label has a value which is a reference to a list where each element is a string
	pH has a value which is a float
	potential has a value which is a float

Description

get_relationship_IsTaxonomyOf

$return = $obj->get_relationship_IsTaxonomyOf($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_TaxonomicGrouping
	1: a fields_IsTaxonomyOf
	2: a fields_Genome
fields_TaxonomicGrouping is a reference to a hash where the following keys are defined:
	id has a value which is a string
	domain has a value which is an int
	hidden has a value which is an int
	scientific_name has a value which is a string
	alias has a value which is a reference to a list where each element is a string
fields_IsTaxonomyOf is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Genome is a reference to a hash where the following keys are defined:
	id has a value which is a string
	pegs has a value which is an int
	rnas has a value which is an int
	scientific_name has a value which is a string
	complete has a value which is an int
	prokaryotic has a value which is an int
	dna_size has a value which is an int
	contigs has a value which is an int
	domain has a value which is a string
	genetic_code has a value which is an int
	gc_content has a value which is a float
	phenotype has a value which is a reference to a list where each element is a string
	md5 has a value which is a string
	source_id has a value which is a string

Description

A genome is assigned to a particular point in the taxonomy tree, but not necessarily to a leaf node. In some cases, the exact species and strain is not available when inserting the genome, so it is placed at the lowest node that probably contains the actual genome. It has the following fields:

get_relationship_IsInTaxa

$return = $obj->get_relationship_IsInTaxa($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Genome
	1: a fields_IsTaxonomyOf
	2: a fields_TaxonomicGrouping
fields_Genome is a reference to a hash where the following keys are defined:
	id has a value which is a string
	pegs has a value which is an int
	rnas has a value which is an int
	scientific_name has a value which is a string
	complete has a value which is an int
	prokaryotic has a value which is an int
	dna_size has a value which is an int
	contigs has a value which is an int
	domain has a value which is a string
	genetic_code has a value which is an int
	gc_content has a value which is a float
	phenotype has a value which is a reference to a list where each element is a string
	md5 has a value which is a string
	source_id has a value which is a string
fields_IsTaxonomyOf is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_TaxonomicGrouping is a reference to a hash where the following keys are defined:
	id has a value which is a string
	domain has a value which is an int
	hidden has a value which is an int
	scientific_name has a value which is a string
	alias has a value which is a reference to a list where each element is a string

Description

get_relationship_IsTerminusFor

$return = $obj->get_relationship_IsTerminusFor($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	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

Description

A terminus for a scenario is a compound that acts as its input or output. A compound can be the terminus for many scenarios, and a scenario will have many termini. The relationship attributes indicate whether the compound is an input to the scenario or an output. In some cases, there may be multiple alternative output groups. This is also indicated by the attributes. It has the following fields:

group_number: If zero, then the compound is an input. If one, the compound is an output. If two, the compound is an auxiliary output.

get_relationship_HasAsTerminus

$return = $obj->get_relationship_HasAsTerminus($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Scenario
	1: a fields_IsTerminusFor
	2: a fields_Compound
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
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

Description

get_relationship_IsTriggeredBy

$return = $obj->get_relationship_IsTriggeredBy($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Complex
	1: a fields_IsTriggeredBy
	2: a fields_Role
fields_Complex 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 reference to a list where each element is a string
	msid has a value which is a string
	mod_date has a value which is a string
fields_IsTriggeredBy is a reference to a hash where the following keys are defined:
	id has a value which is a string
	optional has a value which is an int
	type has a value which is a string
fields_Role is a reference to a hash where the following keys are defined:
	id has a value which is a string
	hypothetical has a value which is an int

Description

A complex can be triggered by many roles. A role can trigger many complexes. It has the following fields:

optional: TRUE if the role is not necessarily required to trigger the complex, else FALSE
type: ask Chris

get_relationship_Triggers

$return = $obj->get_relationship_Triggers($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Role
	1: a fields_IsTriggeredBy
	2: a fields_Complex
fields_Role is a reference to a hash where the following keys are defined:
	id has a value which is a string
	hypothetical has a value which is an int
fields_IsTriggeredBy is a reference to a hash where the following keys are defined:
	id has a value which is a string
	optional has a value which is an int
	type has a value which is a string
fields_Complex 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 reference to a list where each element is a string
	msid has a value which is a string
	mod_date has a value which is a string

Description

get_relationship_IsUsedAs

$return = $obj->get_relationship_IsUsedAs($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Reaction
	1: a fields_IsUsedAs
	2: a fields_ReactionRule
fields_Reaction 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
	msid has a value which is a string
	abbr has a value which is a string
	equation has a value which is a string
	reversibility has a value which is a string
fields_IsUsedAs is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_ReactionRule is a reference to a hash where the following keys are defined:
	id has a value which is a string
	direction has a value which is a string
	transproton has a value which is a float

Description

This relationship connects a reaction to its usage in specific complexes. It has the following fields:

get_relationship_IsUseOf

$return = $obj->get_relationship_IsUseOf($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_ReactionRule
	1: a fields_IsUsedAs
	2: a fields_Reaction
fields_ReactionRule is a reference to a hash where the following keys are defined:
	id has a value which is a string
	direction has a value which is a string
	transproton has a value which is a float
fields_IsUsedAs is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Reaction 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
	msid has a value which is a string
	abbr has a value which is a string
	equation has a value which is a string
	reversibility has a value which is a string

Description

get_relationship_Manages

$return = $obj->get_relationship_Manages($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Model
	1: a fields_Manages
	2: a fields_Biomass
fields_Model 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
	version has a value which is an int
	type has a value which is a string
	status has a value which is a string
	reaction_count has a value which is an int
	compound_count has a value which is an int
	annotation_count has a value which is an int
fields_Manages is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Biomass 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 reference to a list where each element is a string

Description

This relationship connects a model to the biomasses that are monitored to determine whether or not the model is effective. It has the following fields:

get_relationship_IsManagedBy

$return = $obj->get_relationship_IsManagedBy($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Biomass
	1: a fields_Manages
	2: a fields_Model
fields_Biomass 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 reference to a list where each element is a string
fields_Manages is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Model 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
	version has a value which is an int
	type has a value which is a string
	status has a value which is a string
	reaction_count has a value which is an int
	compound_count has a value which is an int
	annotation_count has a value which is an int

Description

get_relationship_OperatesIn

$return = $obj->get_relationship_OperatesIn($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Experiment
	1: a fields_OperatesIn
	2: a fields_Media
fields_Experiment is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source has a value which is a string
fields_OperatesIn is a reference to a hash where the following keys are defined:
	id has a value which is a string
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
	type has a value which is a string

Description

This relationship connects an experiment to the media in which the experiment took place. It has the following fields:

get_relationship_IsUtilizedIn

$return = $obj->get_relationship_IsUtilizedIn($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Media
	1: a fields_OperatesIn
	2: a fields_Experiment
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
	type has a value which is a string
fields_OperatesIn is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Experiment is a reference to a hash where the following keys are defined:
	id has a value which is a string
	source has a value which is a string

Description

get_relationship_Overlaps

$return = $obj->get_relationship_Overlaps($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Scenario
	1: a fields_Overlaps
	2: a fields_Diagram
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
fields_Overlaps is a reference to a hash where the following keys are defined:
	id has a value which 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

Description

A Scenario overlaps a diagram when the diagram displays a portion of the reactions that make up the scenario. A scenario may overlap many diagrams, and a diagram may be include portions of many scenarios. It has the following fields:

get_relationship_IncludesPartOf

$return = $obj->get_relationship_IncludesPartOf($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Diagram
	1: a fields_Overlaps
	2: a fields_Scenario
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
fields_Overlaps is a reference to a hash where the following keys are defined:
	id has a value which is a string
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

Description

get_relationship_ParticipatesAs

$return = $obj->get_relationship_ParticipatesAs($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	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

Description

This relationship connects a compound to the reagents that represent its participation in reactions. It has the following fields:

get_relationship_IsParticipationOf

$return = $obj->get_relationship_IsParticipationOf($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Reagent
	1: a fields_ParticipatesAs
	2: a fields_Compound
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
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

Description

get_relationship_ProducedResultsFor

$return = $obj->get_relationship_ProducedResultsFor($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_ProbeSet
	1: a fields_ProducedResultsFor
	2: a fields_Genome
fields_ProbeSet is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_ProducedResultsFor is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Genome is a reference to a hash where the following keys are defined:
	id has a value which is a string
	pegs has a value which is an int
	rnas has a value which is an int
	scientific_name has a value which is a string
	complete has a value which is an int
	prokaryotic has a value which is an int
	dna_size has a value which is an int
	contigs has a value which is an int
	domain has a value which is a string
	genetic_code has a value which is an int
	gc_content has a value which is a float
	phenotype has a value which is a reference to a list where each element is a string
	md5 has a value which is a string
	source_id has a value which is a string

Description

This relationship connects a probe set to a genome for which it was used to produce experimental results. In general, a probe set is used for only one genome and vice versa, but this is not a requirement. It has the following fields:

get_relationship_HadResultsProducedBy

$return = $obj->get_relationship_HadResultsProducedBy($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Genome
	1: a fields_ProducedResultsFor
	2: a fields_ProbeSet
fields_Genome is a reference to a hash where the following keys are defined:
	id has a value which is a string
	pegs has a value which is an int
	rnas has a value which is an int
	scientific_name has a value which is a string
	complete has a value which is an int
	prokaryotic has a value which is an int
	dna_size has a value which is an int
	contigs has a value which is an int
	domain has a value which is a string
	genetic_code has a value which is an int
	gc_content has a value which is a float
	phenotype has a value which is a reference to a list where each element is a string
	md5 has a value which is a string
	source_id has a value which is a string
fields_ProducedResultsFor is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_ProbeSet is a reference to a hash where the following keys are defined:
	id has a value which is a string

Description

get_relationship_ProjectsOnto

$return = $obj->get_relationship_ProjectsOnto($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_ProteinSequence
	1: a fields_ProjectsOnto
	2: a fields_ProteinSequence
fields_ProteinSequence is a reference to a hash where the following keys are defined:
	id has a value which is a string
	sequence has a value which is a string
fields_ProjectsOnto is a reference to a hash where the following keys are defined:
	id has a value which is a string
	gene_context has a value which is an int
	percent_identity has a value which is a float
	score has a value which is a float

Description

This relationship connects two protein sequences for which a clear bidirectional best hit exists in known genomes. The attributes of the relationship describe how good the relationship is between the proteins. The relationship is bidirectional and symmetric, but is only stored in one direction (lower ID to higher ID). It has the following fields:

gene_context: number of homologous genes in the immediate context of the two proteins, up to a maximum of 10
percent_identity: percent match between the two protein sequences
score: score describing the strength of the projection, from 0 to 1, where 1 is the best

get_relationship_IsProjectedOnto

$return = $obj->get_relationship_IsProjectedOnto($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_ProteinSequence
	1: a fields_ProjectsOnto
	2: a fields_ProteinSequence
fields_ProteinSequence is a reference to a hash where the following keys are defined:
	id has a value which is a string
	sequence has a value which is a string
fields_ProjectsOnto is a reference to a hash where the following keys are defined:
	id has a value which is a string
	gene_context has a value which is an int
	percent_identity has a value which is a float
	score has a value which is a float

Description

get_relationship_Provided

$return = $obj->get_relationship_Provided($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Source
	1: a fields_Provided
	2: a fields_Subsystem
fields_Source is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Provided is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Subsystem is a reference to a hash where the following keys are defined:
	id has a value which is a string
	version has a value which is an int
	curator has a value which is a string
	notes has a value which is a string
	description has a value which is a string
	usable has a value which is an int
	private has a value which is an int
	cluster_based has a value which is an int
	experimental has a value which is an int

Description

This relationship connects a source (core) database to the subsystems it submitted to the knowledge base. It has the following fields:

get_relationship_WasProvidedBy

$return = $obj->get_relationship_WasProvidedBy($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Subsystem
	1: a fields_Provided
	2: a fields_Source
fields_Subsystem is a reference to a hash where the following keys are defined:
	id has a value which is a string
	version has a value which is an int
	curator has a value which is a string
	notes has a value which is a string
	description has a value which is a string
	usable has a value which is an int
	private has a value which is an int
	cluster_based has a value which is an int
	experimental has a value which is an int
fields_Provided is a reference to a hash where the following keys are defined:
	id 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

Description

get_relationship_Shows

$return = $obj->get_relationship_Shows($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Diagram
	1: a fields_Shows
	2: a fields_Compound
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
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_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

Description

This relationship indicates that a compound appears on a particular diagram. The same compound can appear on many diagrams, and a diagram always contains many compounds. It has the following fields:

location: Location of the compound's node on the diagram.

get_relationship_IsShownOn

$return = $obj->get_relationship_IsShownOn($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	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

Description

get_relationship_Submitted

$return = $obj->get_relationship_Submitted($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Source
	1: a fields_Submitted
	2: a fields_Genome
fields_Source is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Submitted is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Genome is a reference to a hash where the following keys are defined:
	id has a value which is a string
	pegs has a value which is an int
	rnas has a value which is an int
	scientific_name has a value which is a string
	complete has a value which is an int
	prokaryotic has a value which is an int
	dna_size has a value which is an int
	contigs has a value which is an int
	domain has a value which is a string
	genetic_code has a value which is an int
	gc_content has a value which is a float
	phenotype has a value which is a reference to a list where each element is a string
	md5 has a value which is a string
	source_id has a value which is a string

Description

This relationship connects a genome to the core database from which it was loaded. It has the following fields:

get_relationship_WasSubmittedBy

$return = $obj->get_relationship_WasSubmittedBy($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Genome
	1: a fields_Submitted
	2: a fields_Source
fields_Genome is a reference to a hash where the following keys are defined:
	id has a value which is a string
	pegs has a value which is an int
	rnas has a value which is an int
	scientific_name has a value which is a string
	complete has a value which is an int
	prokaryotic has a value which is an int
	dna_size has a value which is an int
	contigs has a value which is an int
	domain has a value which is a string
	genetic_code has a value which is an int
	gc_content has a value which is a float
	phenotype has a value which is a reference to a list where each element is a string
	md5 has a value which is a string
	source_id has a value which is a string
fields_Submitted is a reference to a hash where the following keys are defined:
	id 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

Description

get_relationship_Uses

$return = $obj->get_relationship_Uses($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_Genome
	1: a fields_Uses
	2: a fields_SSRow
fields_Genome is a reference to a hash where the following keys are defined:
	id has a value which is a string
	pegs has a value which is an int
	rnas has a value which is an int
	scientific_name has a value which is a string
	complete has a value which is an int
	prokaryotic has a value which is an int
	dna_size has a value which is an int
	contigs has a value which is an int
	domain has a value which is a string
	genetic_code has a value which is an int
	gc_content has a value which is a float
	phenotype has a value which is a reference to a list where each element is a string
	md5 has a value which is a string
	source_id has a value which is a string
fields_Uses is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_SSRow is a reference to a hash where the following keys are defined:
	id has a value which is a string
	curated has a value which is an int
	region has a value which is a string

Description

This relationship connects a genome to the machines that form its metabolic pathways. A genome can use many machines, but a machine is used by exactly one genome. It has the following fields:

get_relationship_IsUsedBy

$return = $obj->get_relationship_IsUsedBy($ids, $from_fields, $rel_fields, $to_fields)

Parameter and return types

$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
$rel_fields is a reference to a list where each element is a string
$to_fields is a reference to a list where each element is a string
$return is a reference to a list where each element is a reference to a list containing 3 items:
	0: a fields_SSRow
	1: a fields_Uses
	2: a fields_Genome
fields_SSRow is a reference to a hash where the following keys are defined:
	id has a value which is a string
	curated has a value which is an int
	region has a value which is a string
fields_Uses is a reference to a hash where the following keys are defined:
	id has a value which is a string
fields_Genome is a reference to a hash where the following keys are defined:
	id has a value which is a string
	pegs has a value which is an int
	rnas has a value which is an int
	scientific_name has a value which is a string
	complete has a value which is an int
	prokaryotic has a value which is an int
	dna_size has a value which is an int
	contigs has a value which is an int
	domain has a value which is a string
	genetic_code has a value which is an int
	gc_content has a value which is a float
	phenotype has a value which is a reference to a list where each element is a string
	md5 has a value which is a string
	source_id has a value which is a string

Description

TYPES

annotator

Definition

a string

annotation_time

Definition

an int

comment

Definition

a string

fid

Description

A fid is a "feature id". A feature represents an ordered list of regions from the contigs of a genome. Features all have types. This allows you to speak of not only protein-encoding genes (PEGs) and RNAs, but also binding sites, large regions, etc. The location of a fid is defined as a list of "location of a contiguous DNA string" pieces (see the description of the type "location")

Definition

a string

protein_family

Description

A protein_family is thought of as a set of isofunctional, homologous protein sequences. This is not exactly what other groups have meant by "protein families". There is no hierarchy of super-family, family, sub-family. We plan on loading different collections of protein families, but in many cases there will need to be a transformation into the concept used by Kbase.

Definition

a string

role

Description

The concept of "role" or "functional role" is basically an atomic functional unit. The "function of a protein" is made up of one or more roles. That is, a bifunctional protein with an assigned function of

5-Enolpyruvylshikimate-3-phosphate synthase (EC 2.5.1.19) / Cytidylate kinase (EC 2.7.4.14)

would implement two distinct roles (the "function1 / function2" notation is intended to assert that the initial part of the protein implements function1, and the terminal part of the protein implements function2). It is worth noting that a protein often implements multiple roles due to broad specificity. In this case, we suggest describing the protein function as

function1 @ function2

That is the ' / ' separator is used to represent multiple roles implemented by distinct domains of the protein, while ' @ ' is used to represent multiple roles implemented by distinct domains.

Definition

a string

subsystem

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.

Definition

a string

variant

Definition

a string

variant_of_subsystem

Definition

a reference to a list containing 2 items:
0: a subsystem
1: a variant

variant_subsystem_pairs

Definition

a reference to a list where each element is a variant_of_subsystem

type_of_fid

Definition

a string

types_of_fids

Definition

a reference to a list where each element is a type_of_fid

length

Definition

an int

begin

Definition

an int

strand

Description

In encodings of locations, we often specify strands. We specify the strand as '+' or '-'

Definition

a string

contig

Definition

a string

region_of_dna

Description

A region of DNA is maintained as a tuple of four components:

     the contig
     the beginning position (from 1)
     the strand
     the length

We often speak of "a region".  By "location", we mean a sequence
of regions from the same genome (perhaps from distinct contigs).

Definition

a reference to a list containing 4 items:
0: a contig
1: a begin
2: a strand
3: a length

location

Description

a "location" refers to a sequence of regions

Definition

a reference to a list where each element is a region_of_dna

locations

Definition

a reference to a list where each element is a location

region_of_dna_string

Description

we often need to represent regions or locations as strings. We would use something like

contigA_200+100,contigA_402+188

to represent a location composed of two regions

Definition

a string

region_of_dna_strings

Definition

a reference to a list where each element is a region_of_dna_string

location_string

Definition

a string

dna

Definition

a string

function

Definition

a string

protein

Definition

a string

md5

Definition

a string

genome

Definition

a string

taxonomic_group

Definition

a string

annotation

Description

The Kbase stores annotations relating to features. Each annotation is a 3-tuple:

the text of the annotation (often a record of assertion of function)

the annotator attaching the annotation to the feature

the time (in seconds from the epoch) at which the annotation was attached

Definition

a reference to a list containing 3 items:
0: a comment
1: an annotator
2: an annotation_time

pubref

Description

The Kbase will include a growing body of literature supporting protein functions, asserted phenotypes, etc. References are encoded as 3-tuples:

an id (often a PubMed ID)

a URL to the paper

a title of the paper

The URL and title are often missing (but, can usually be inferred from the pubmed ID).

Definition

a reference to a list containing 3 items:
0: a string
1: a string
2: a string

scored_fid

Definition

a reference to a list containing 2 items:
0: a fid
1: a float

annotations

Definition

a reference to a list where each element is an annotation

pubrefs

Definition

a reference to a list where each element is a pubref

roles

Definition

a reference to a list where each element is a role

optional

Definition

a string

role_with_flag

Definition

a reference to a list containing 2 items:
0: a role
1: an optional

roles_with_flags

Definition

a reference to a list where each element is a role_with_flag

scored_fids

Definition

a reference to a list where each element is a scored_fid

proteins

Definition

a reference to a list where each element is a protein

functions

Definition

a reference to a list where each element is a function

taxonomic_groups

Definition

a reference to a list where each element is a taxonomic_group

subsystems

Definition

a reference to a list where each element is a subsystem

contigs

Definition

a reference to a list where each element is a contig

md5s

Definition

a reference to a list where each element is a md5

genomes

Definition

a reference to a list where each element is a genome

pair_of_fids

Definition

a reference to a list containing 2 items:
0: a fid
1: a fid

pairs_of_fids

Definition

a reference to a list where each element is a pair_of_fids

protein_families

Definition

a reference to a list where each element is a protein_family

score

Definition

a float

evidence

Definition

a reference to a list where each element is a pair_of_fids

fids

Definition

a reference to a list where each element is a fid

row

Definition

a reference to a list containing 2 items:
0: a variant
1: a reference to a hash where the key is a role and the value is a fids

fid_function_pair

Definition

a reference to a list containing 2 items:
0: a fid
1: a function

fid_function_pairs

Definition

a reference to a list where each element is a fid_function_pair

fc_protein_family

Description

A functionally coupled protein family identifies a family, a score, and a function (of the related family)

Definition

a reference to a list containing 3 items:
0: a protein_family
1: a score
2: a function

fc_protein_families

Definition

a reference to a list where each element is a fc_protein_family

aux

Definition

an int

fields

Definition

a reference to a list where each element is a string

complex

Definition

a string

complex_with_flag

Definition

a reference to a list containing 2 items:
0: a complex
1: an optional

complexes_with_flags

Definition

a reference to a list where each element is a complex_with_flag

complexes

Definition

a reference to a list where each element is a complex

name

Definition

a string

reaction

Definition

a string

reactions

Definition

a reference to a list where each element is a reaction

complex_data

Description

Reactions do not connect directly to roles. Rather, the conceptual model is that one or more roles together form a complex. A complex implements one or more reactions. The actual data relating to a complex is spread over two entities: Complex and ReactionComplex. It is convenient to be able to offer access to the complex name, the reactions it implements, and the roles that make it up in a single invocation.

Definition

a reference to a hash where the following keys are defined:
complex_name has a value which is a name
complex_roles has a value which is a roles_with_flags
complex_reactions has a value which is a reactions

genome_data

Definition

a reference to a hash where the following keys are defined:
complete has a value which is an int
contigs has a value which is an int
dna_size has a value which is an int
gc_content has a value which is a float
genetic_code has a value which is an int
pegs has a value which is an int
rnas has a value which is an int
scientific_name has a value which is a string
taxonomy has a value which is a string
genome_md5 has a value which is a string

regulon

Definition

a string

regulons

Definition

a reference to a list where each element is a regulon

regulon_data

Definition

a reference to a hash where the following keys are defined:
regulon_id has a value which is a regulon
regulon_set has a value which is a fids
tfs has a value which is a fids

regulons_data

Definition

a reference to a list where each element is a regulon_data

feature_data

Definition

a reference to a hash where the following keys are defined:
feature_id has a value which is a fid
genome_name has a value which is a string
feature_function has a value which is a string
feature_length has a value which is an int
feature_publications has a value which is a pubrefs
feature_location has a value which is a location

expert

Definition

a string

source

Definition

a string

id

Definition

a string

function_assertion

Definition

a reference to a list containing 4 items:
0: an id
1: a function
2: a source
3: an expert

function_assertions

Definition

a reference to a list where each element is a function_assertion

atomic_regulon

Definition

a string

atomic_regulon_size

Definition

an int

atomic_regulon_size_pair

Definition

a reference to a list containing 2 items:
0: an atomic_regulon
1: an atomic_regulon_size

atomic_regulon_size_pairs

Definition

a reference to a list where each element is an atomic_regulon_size_pair

atomic_regulons

Definition

a reference to a list where each element is an atomic_regulon

protein_sequence

Definition

a string

dna_sequence

Definition

a string

name_parameter

Definition

a string

ss_var_role_tuple

Definition

a reference to a list containing 3 items:
0: a subsystem
1: a variant
2: a role

ss_var_role_tuples

Definition

a reference to a list where each element is a ss_var_role_tuple

genome_name

Definition

a string

entity_name

Definition

a string

weight

Definition

an int

field_name

Definition

a string

search_hit

Definition

a reference to a list containing 2 items:
0: a weight
1: a reference to a hash where the key is a field_name and the value is a string

diamond

Definition

a string

countVector

Definition

a string

rectangle

Definition

a string

fields_AlignmentTree

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
alignment_method has a value which is a string
alignment_parameters has a value which is a string
alignment_properties has a value which is a string
tree_method has a value which is a string
tree_parameters has a value which is a string
tree_properties has a value which is a string

fields_Annotation

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
annotator has a value which is a string
comment has a value which is a string
annotation_time has a value which is a string

fields_AtomicRegulon

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_Attribute

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
description has a value which is a string

fields_Biomass

Definition

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 reference to a list where each element is a string

fields_BiomassCompound

Definition

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

fields_Compartment

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
abbr has a value which is a string
mod_date has a value which is a string
name has a value which is a string
msid has a value which is a string

fields_Complex

Definition

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 reference to a list where each element is a string
msid has a value which is a string
mod_date has a value which is a string

fields_Compound

Definition

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_Contig

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
source_id has a value which is a string

fields_ContigChunk

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
sequence has a value which is a string

fields_ContigSequence

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
length has a value which is an int

fields_CoregulatedSet

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
source_id has a value which is a string

fields_Diagram

Definition

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

fields_EcNumber

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
obsolete has a value which is an int
replacedby has a value which is a string

fields_Experiment

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
source has a value which is a string

fields_Family

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
type has a value which is a string
family_function has a value which is a reference to a list where each element is a string

fields_Feature

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
feature_type has a value which is a string
source_id has a value which is a string
sequence_length has a value which is an int
function has a value which is a string

fields_Genome

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
pegs has a value which is an int
rnas has a value which is an int
scientific_name has a value which is a string
complete has a value which is an int
prokaryotic has a value which is an int
dna_size has a value which is an int
contigs has a value which is an int
domain has a value which is a string
genetic_code has a value which is an int
gc_content has a value which is a float
phenotype has a value which is a reference to a list where each element is a string
md5 has a value which is a string
source_id has a value which is a string

fields_Identifier

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
source has a value which is a string
natural_form has a value which is a string

fields_Media

Definition

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
type has a value which is a string

fields_Model

Definition

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
version has a value which is an int
type has a value which is a string
status has a value which is a string
reaction_count has a value which is an int
compound_count has a value which is an int
annotation_count has a value which is an int

fields_ModelCompartment

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
compartment_index has a value which is an int
label has a value which is a reference to a list where each element is a string
pH has a value which is a float
potential has a value which is a float

fields_OTU

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_PairSet

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
score has a value which is an int

fields_Pairing

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_ProbeSet

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_ProteinSequence

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
sequence has a value which is a string

fields_Publication

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
title has a value which is a string
link has a value which is a string
pubdate has a value which is a string

fields_Reaction

Definition

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
msid has a value which is a string
abbr has a value which is a string
equation has a value which is a string
reversibility has a value which is a string

fields_ReactionRule

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
direction has a value which is a string
transproton has a value which is a float

fields_Reagent

Definition

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

fields_Requirement

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
direction has a value which is a string
transproton has a value which is a float
proton has a value which is a float

fields_Role

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
hypothetical has a value which is an int

fields_SSCell

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_SSRow

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
curated has a value which is an int
region has a value which is a string

fields_Scenario

Definition

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

fields_Source

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_Subsystem

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
version has a value which is an int
curator has a value which is a string
notes has a value which is a string
description has a value which is a string
usable has a value which is an int
private has a value which is an int
cluster_based has a value which is an int
experimental has a value which is an int

fields_SubsystemClass

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_TaxonomicGrouping

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
domain has a value which is an int
hidden has a value which is an int
scientific_name has a value which is a string
alias has a value which is a reference to a list where each element is a string

fields_Variant

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
role_rule has a value which is a reference to a list where each element is a string
code has a value which is a string
type has a value which is a string
comment has a value which is a string

fields_Variation

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
notes has a value which is a reference to a list where each element is a string

fields_AffectsLevelOf

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
level has a value which is an int

fields_Aligns

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
begin has a value which is an int
end has a value which is an int
len has a value which is an int
sequence_id has a value which is a string
properties has a value which is a string

fields_Concerns

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_Contains

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_Controls

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_Describes

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_Displays

Definition

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

fields_Encompasses

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_Formulated

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_GeneratedLevelsFor

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
level_vector has a value which is a countVector

fields_HasAssertionFrom

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
function has a value which is a string
expert has a value which is an int

fields_HasCompoundAliasFrom

Definition

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_HasIndicatedSignalFrom

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
rma_value has a value which is a float
level has a value which is an int

fields_HasMember

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_HasParticipant

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
type has a value which is an int

fields_HasPresenceOf

Definition

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_HasReactionAliasFrom

Definition

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_HasRepresentativeOf

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_HasResultsIn

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
sequence has a value which is an int

fields_HasSection

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_HasStep

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_HasUsage

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_HasValueFor

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
value has a value which is a string

fields_Imported

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_Includes

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
sequence has a value which is an int
abbreviation has a value which is a string
auxiliary has a value which is an int

fields_IndicatedLevelsFor

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
level_vector has a value which is a countVector

fields_Involves

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_IsARequirementIn

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_IsAlignedIn

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
start has a value which is an int
len has a value which is an int
dir has a value which is a string

fields_IsAnnotatedBy

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_IsBindingSiteFor

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_IsClassFor

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_IsCollectionOf

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
representative has a value which is an int

fields_IsComposedOf

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_IsComprisedOf

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_IsConfiguredBy

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_IsConsistentWith

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_IsCoregulatedWith

Definition

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

fields_IsCoupledTo

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
co_occurrence_evidence has a value which is an int
co_expression_evidence has a value which is an int

fields_IsDefaultFor

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_IsDefaultLocationOf

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_IsDeterminedBy

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
inverted has a value which is an int

fields_IsDividedInto

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_IsExemplarOf

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_IsFamilyFor

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_IsFormedOf

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_IsFunctionalIn

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_IsGroupFor

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_IsImplementedBy

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_IsInPair

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_IsInstantiatedBy

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_IsLocatedIn

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
ordinal has a value which is an int
begin has a value which is an int
len has a value which is an int
dir has a value which is a string

fields_IsModeledBy

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_IsNamedBy

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_IsOwnerOf

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_IsProposedLocationOf

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
type has a value which is a string

fields_IsProteinFor

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_IsRealLocationOf

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
type has a value which is a string

fields_IsRegulatedIn

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_IsRelevantFor

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_IsRequiredBy

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_IsRoleOf

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_IsRowOf

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_IsSequenceOf

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_IsSubInstanceOf

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_IsSuperclassOf

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_IsTargetOf

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_IsTaxonomyOf

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_IsTerminusFor

Definition

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_IsTriggeredBy

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
optional has a value which is an int
type has a value which is a string

fields_IsUsedAs

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_Manages

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_OperatesIn

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_Overlaps

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_ParticipatesAs

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_ProducedResultsFor

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_ProjectsOnto

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string
gene_context has a value which is an int
percent_identity has a value which is a float
score has a value which is a float

fields_Provided

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_Shows

Definition

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

fields_Submitted

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

fields_Uses

Definition

a reference to a hash where the following keys are defined:
id has a value which is a string

To install Bio::KBase, copy and paste the appropriate command in to your terminal.

cpanm

cpanm Bio::KBase

CPAN shell

perl -MCPAN -e shell
install Bio::KBase

For more information on module installation, please visit the detailed CPAN module installation guide.

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