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 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 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
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

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
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 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.

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 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
	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

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
	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
	reason 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:

reason

Description of how this coregulated set was derived.

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
	reason 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 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 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 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 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 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 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 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 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
	citation 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 lietarture 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:

citation

Hyperlink of the article. The text is the article title.

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
	citation 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
	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

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
	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 has a value which is a string
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

description

descriptive text for this role

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 has a value which is a string
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
	name 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:

name

name of this subsystem

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
	name 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 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 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 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 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 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 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
	citation 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
	citation 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_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
	name 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 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 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
	name 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 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
	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
	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 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_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
	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
	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 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 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
	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
	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
	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
	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
	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
	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 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 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 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 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 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 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
	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
	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_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
	name 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 has a value which is a string
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
	description has a value which is a string
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
	name 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
	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
	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 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 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
	reason 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
	reason 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
	name 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
	name 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 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 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 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 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 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 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 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 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 has a value which is a string
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
	description 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_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_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_IsControlledUsing
	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
	reason has a value which is a string
fields_IsControlledUsing is a reference to a hash where the following keys are defined:
	id has a value which is a string
	effector 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

This relationship connects a coregulated set to the protein that is used as its transcription factor. It has the following fields:

effector

TRUE if this transcription factor is an effector (up-regulates), FALSE if it is a suppressor (down-regulates)

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_IsControlledUsing
	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_IsControlledUsing is a reference to a hash where the following keys are defined:
	id has a value which is a string
	effector has a value which is an int
fields_CoregulatedSet is a reference to a hash where the following keys are defined:
	id has a value which is a string
	reason 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 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 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
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
	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
	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
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
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
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 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 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 has a value which is a string
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
	description 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_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 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 has a value which is a string
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
	description has a value which 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_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 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
	description 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_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 has a value which is a string
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 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 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 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 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
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 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 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
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 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 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 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 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
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
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 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 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
	reason 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
	reason 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 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
	name 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
	name 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 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
	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
	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
	description 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_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 has a value which is a string
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
	name 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
	name 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 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 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 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 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 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 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
	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
	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 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 has a value which is a string
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
	description 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_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 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
	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
	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 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 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 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 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
	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
	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 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 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
	name 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
	name 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 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
	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
	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 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 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 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 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 string
	md5 has a value which is a string
	source_id has a value which is a string
Description


TYPES

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 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

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 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
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
reason 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 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 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 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 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
citation 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
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
description has a value which is a string

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
name 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 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 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 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_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_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_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_IsControlledUsing

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

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