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NMPDR Database Documentation

The NMPDR database design is based on conceptualizing the data as an entity-relationship model, describing the metadata as an XML document, and then generating the detailed relational schema directly from the metadata. This document describes the entities and the relationships that make up the basic design. It includes descriptions of the relations that implement each entity and relationship. We maintain this as a working document for our developers.

• Entities
  1. Annotation
  2. CDD
  3. Compound
  4. CompoundCAS
  5. CompoundName
  6. Contig
  7. Diagram
  8. ExternalAliasFunc
  9. ExternalAliasOrg
  10. Family
  11. Feature
  12. FeatureAlias
  13. Genome
  14. GenomeSubset
  15. Ligand
  16. PDB
  17. Property
  18. Reaction
  19. Role
  20. RoleEC
  21. RoleSubset
  22. SSCell
  23. Sequence
  24. Source
  25. SproutUser
  26. Subsystem
  27. SynonymGroup
• Relationships
  1. Role Catalyzes Reaction (many-to-many)
  2. Genome ComesFrom Source (many-to-many)
  3. GenomeSubset ConsistsOfGenomes Genome (many-to-many)
  4. RoleSubset ConsistsOfRoles Role (many-to-many)
  5. SSCell ContainsFeature Feature (many-to-many)
  6. PDB DocksWith Ligand (many-to-many)
  7. Compound HasCompoundName CompoundName (many-to-many)
  8. Genome HasContig Contig (one-to-many)
  9. Genome HasFeature Feature (one-to-many)
  10. Subsystem HasGenomeSubset GenomeSubset (one-to-many)
  11. Feature HasProperty Property (many-to-many)
  12. Feature HasRoleInSubsystem Subsystem (many-to-many)
  13. Subsystem HasRoleSubset RoleSubset (one-to-many)
  14. Subsystem HasSSCell SSCell (one-to-many)
  15. Compound IsAComponentOf Reaction (many-to-many)
  16. FeatureAlias IsAliasOf Feature (many-to-many)
  17. Family IsFamilyForFeature Feature (many-to-many)
  18. Genome IsGenomeOf SSCell (one-to-many)
  19. Compound IsIdentifiedByCAS CompoundCAS (many-to-many)
  20. Role IsIdentifiedByEC RoleEC (many-to-many)
  21. Feature IsLocatedIn Contig (many-to-many)
  22. Contig IsMadeUpOf Sequence (one-to-many)
  23. CDD IsPresentOnProteinOf Feature (many-to-many)
  24. PDB IsProteinForFeature Feature (many-to-many)
  25. Role IsRoleOf SSCell (one-to-many)
  26. SynonymGroup IsSynonymGroupFor Feature (many-to-many)
  27. Feature IsTargetOfAnnotation Annotation (one-to-many)
  28. SproutUser IsTrustedBy SproutUser (many-to-many)
  29. SproutUser MadeAnnotation Annotation (one-to-many)
  30. Role OccursInSubsystem Subsystem (many-to-many)
  31. Genome ParticipatesIn Subsystem (many-to-many)
  32. Role RoleOccursIn Diagram (many-to-many)
• Join Table

Entities

Annotation

An annotation contains supplementary information about a feature. Annotations are currently the only objects that may be inserted directly into the database. All other information is loaded from data exported by the SEED.

Relationships for Annotation

• Feature IsTargetOfAnnotation Annotation (one-to-many)
• SproutUser MadeAnnotation Annotation (one-to-many)

Relations for Annotation

Annotation
Field	Type	Description
id	name-string	Unique identifier for this Annotation.
time	date	Date and time of the annotation.
annotation	text	Text of the annotation.

• Index idx0
  • This index allows the user to find recent annotations.
  • time DESC
• Index idx1 (unique)
  • Primary index for Annotation.
  • id

CDD

A CDD is a protein domain designator. It represents the shape of a molecular unit on a feature's protein. The ID is six-digit string assigned by the public Conserved Domain Database. A CDD can occur on multiple features and a feature generally has multiple CDDs.

Relationships for CDD

• CDD IsPresentOnProteinOf Feature (many-to-many)

Relations for CDD

CDD
Field	Type	Description
id	key-string	Unique identifier for this CDD.

• Index idx0 (unique)
  • Primary index for CDD.
  • id

Compound

A compound is a chemical that participates in a reaction. All compounds have a unique ID and may also have one or more names.

Relationships for Compound

• Compound HasCompoundName CompoundName (many-to-many)
• Compound IsAComponentOf Reaction (many-to-many)
• Compound IsIdentifiedByCAS CompoundCAS (many-to-many)

Relations for Compound

Compound
Field	Type	Description
id	name-string	Unique identifier for this Compound.
label	string	Name used in reaction display strings. It is the same as the name possessing a priority of 1, but it is placed here to speed up the query used to create the display strings.

• Index idx0 (unique)
  • Primary index for Compound.
  • id

CompoundCAS

This entity represents the Chemical Abstract Service ID for a compound. Each Compound has at most one CAS ID.

Relationships for CompoundCAS

• Compound IsIdentifiedByCAS CompoundCAS (many-to-many)

Relations for CompoundCAS

CompoundCAS
Field	Type	Description
id	name-string	Unique identifier for this CompoundCAS.

• Index idx0 (unique)
  • Primary index for CompoundCAS.
  • id

CompoundName

A compound name is a common name for the chemical represented by a compound.

Relationships for CompoundName

• Compound HasCompoundName CompoundName (many-to-many)

Relations for CompoundName

CompoundName
Field	Type	Description
id	string	Unique identifier for this CompoundName.

• Index idx0 (unique)
  • Primary index for CompoundName.
  • id

Contig

A contig is a contiguous run of residues. The contig's ID consists of the genome ID followed by a name that identifies which contig this is for the parent genome. As is the case with all keys in this database, the individual components are separated by a period.

A contig can contain over a million residues. For performance reasons, therefore, the contig is split into multiple pieces called sequences. The sequences contain the characters that represent the residues as well as data on the quality of the residue identification.

Relationships for Contig

• Genome HasContig Contig (one-to-many)
• Feature IsLocatedIn Contig (many-to-many)
• Contig IsMadeUpOf Sequence (one-to-many)

Relations for Contig

Contig
Field	Type	Description
id	name-string	Unique identifier for this Contig.

• Index idx0 (unique)
  • Primary index for Contig.
  • id

Diagram

A functional diagram describes the chemical reactions, often comprising a single subsystem. A diagram is identified by a short name and contains a longer descriptive name. The actual diagram shows which functional roles guide the reactions along with the inputs and outputs; the database, however, only indicate which roles belong to a particular map.

Relationships for Diagram

• Role RoleOccursIn Diagram (many-to-many)

Relations for Diagram

Diagram
Field	Type	Description
id	name-string	Unique identifier for this Diagram.
name	text	Descriptive name of this diagram.

• Index idx0 (unique)
  • Primary index for Diagram.
  • id

ExternalAliasFunc

An external alias is a feature name for a functional assignment that is not a FIG ID. Functional assignments for external aliases are kept in a separate section of the database. This table contains the functional role for the external alias functional assignment.

Relationships for ExternalAliasFunc

Relations for ExternalAliasFunc

ExternalAliasFunc
Field	Type	Description
id	name-string	Unique identifier for this ExternalAliasFunc.
func	text	Functional role for this external alias.

• Index idx0 (unique)
  • Primary index for ExternalAliasFunc.
  • id

ExternalAliasOrg

An external alias is a feature name for a functional assignment that is not a FIG ID. Functional assignments for external aliases are kept in a separate section of the database. This table contains a description of the relevant organism for an external alias functional assignment.

Relationships for ExternalAliasOrg

Relations for ExternalAliasOrg

ExternalAliasOrg
Field	Type	Description
id	name-string	Unique identifier for this ExternalAliasOrg.
org	text	Descriptive name of the target organism for this external alias.

• Index idx0 (unique)
  • Primary index for ExternalAliasOrg.
  • id

Family

A family is a group of homologous PEGs believed to have the same function. Protein families provide a mechanism for verifying the accuracy of functional assignments and are also used in determining phylogenetic trees.

Relationships for Family

• Family IsFamilyForFeature Feature (many-to-many)

Relations for Family

Family
Field	Type	Description
id	id-string	Unique identifier for this Family.
size	int	The number of proteins in this family. This may be larger than the number of PEGs included in the family, since the family may also contain external IDs.
function	text	The functional assignment expected for all PEGs in this family.

• Index idx0 (unique)
  • Primary index for Family.
  • id

Feature

A feature is a part of a genome that is of special interest. Features may be spread across multiple contigs of a genome, but never across more than one genome. Features can be assigned to roles via spreadsheet cells, and are the targets of annotation.

Relationships for Feature

• SSCell ContainsFeature Feature (many-to-many)
• Genome HasFeature Feature (one-to-many)
• Feature HasProperty Property (many-to-many)
• Feature HasRoleInSubsystem Subsystem (many-to-many)
• FeatureAlias IsAliasOf Feature (many-to-many)
• Family IsFamilyForFeature Feature (many-to-many)
• Feature IsLocatedIn Contig (many-to-many)
• CDD IsPresentOnProteinOf Feature (many-to-many)
• PDB IsProteinForFeature Feature (many-to-many)
• SynonymGroup IsSynonymGroupFor Feature (many-to-many)
• Feature IsTargetOfAnnotation Annotation (one-to-many)

Relations for Feature

Feature
Field	Type	Description
id	id-string	Unique identifier for this Feature.
active	boolean	TRUE if this feature is still considered valid, FALSE if it has been logically deleted.
assignment-maker	name-string	name of the user who made the functional assignment
assignment-quality	char	quality of the functional assignment, usually a space, but may be W (indicating weak) or X (indicating experimental)
cello	name-string	The cello value specifies the expected location of the protein: cytoplasm, cell wall, inner membrane, and so forth.
feature-type	id-string	Code indicating the type of this feature.
assignment	text	Default functional assignment for this feature.
keywords	text	This is a list of search keywords for the feature. It includes the functional assignment, subsystem roles, and special properties.
location-string	text	Location of the feature, expressed as a comma-delimited list of Sprout location strings. This gives us a fast mechanism for extracting the feature location. Otherwise, we have to painstakingly paste together the IsLocatedIn records, which are themselves designed to help look for genes in a particular region rather than to find the location of a gene.

• Index idx0
  • This index allows us to locate a feature by its CELLO value.
  • cello
• Index idx1 (unique)
  • Primary index for Feature.
  • id

FeatureConservation
Field	Type	Description
id	id-string	Unique identifier for this Feature.
conservation	float	A number between 0 and 1 that indicates the degree to which this feature's DNA is conserved in related genomes. A value of 1 indicates perfect conservation. A value less than 1 is a reflection of the degree to which gap characters interfere in the alignment between the feature and its close relatives.

• Index idx0
  • id

FeatureEssential
Field	Type	Description
id	id-string	Unique identifier for this Feature.
essential	text	A value indicating the essentiality of the feature, coded as HTML. In most cases, this will be a word describing whether the essentiality is confirmed (essential) or potential (potential-essential), hyperlinked to the document from which the essentiality was curated. If a feature is not essential, this field will have no values; otherwise, it may have multiple values.

• Index idx0
  • id

FeatureIEDB
Field	Type	Description
id	id-string	Unique identifier for this Feature.
iedb	text	A value indicating whether or not the feature can be found in the Immune Epitope Database. If the feature has not been matched to that database, this field will have no values. Otherwise, it will have an epitope name and/or sequence, hyperlinked to the database.

• Index idx0
  • id

FeatureLink
Field	Type	Description
id	id-string	Unique identifier for this Feature.
link	text	Web hyperlink for this feature. A feature have no hyperlinks or it can have many. The links are to other websites that have useful about the gene that the feature represents, and are coded as raw HTML, using <a href="link">text</a> notation.

• Index idx0
  • id

FeatureTranslation
Field	Type	Description
id	id-string	Unique identifier for this Feature.
translation	text	(optional) A translation of this feature's residues into character codes, formed by concatenating the pieces of the feature together. For a protein encoding group, this is the protein characters. For other types it is the DNA characters.

• Index idx0
  • id

FeatureUpstream
Field	Type	Description
id	id-string	Unique identifier for this Feature.
upstream-sequence	text	Upstream sequence the feature. This includes residues preceding the feature as well as some of the feature's initial residues.

• Index idx0
  • id

FeatureVirulent
Field	Type	Description
id	id-string	Unique identifier for this Feature.
virulent	text	A value indicating the virulence of the feature, coded as HTML. In most cases, this will be a phrase or SA number hyperlinked to the document from which the virulence information was curated. If the feature is not virulent, this field will have no values; otherwise, it may have multiple values.

• Index idx0
  • id

FeatureAlias

Alternative names for features. A feature can have many aliases. In general, each alias corresponds to only one feature, but there are exceptionsis is not strictly enforced.

Relationships for FeatureAlias

• FeatureAlias IsAliasOf Feature (many-to-many)

Relations for FeatureAlias

FeatureAlias
Field	Type	Description
id	medium-string	Unique identifier for this FeatureAlias.

• Index idx0 (unique)
  • Primary index for FeatureAlias.
  • id

Genome

A genome contains the sequence data for a particular individual organism.

Relationships for Genome

• Genome ComesFrom Source (many-to-many)
• GenomeSubset ConsistsOfGenomes Genome (many-to-many)
• Genome HasContig Contig (one-to-many)
• Genome HasFeature Feature (one-to-many)
• Genome IsGenomeOf SSCell (one-to-many)
• Genome ParticipatesIn Subsystem (many-to-many)

Relations for Genome

Genome
Field	Type	Description
id	name-string	Unique identifier for this Genome.
access-code	key-string	The access code determines which users can look at the data relating to this genome. Each user is associated with a set of access codes. In order to view a genome, one of the user's access codes must match this value.
complete	boolean	TRUE if the genome is complete, else FALSE
dna-size	counter	number of base pairs in the genome
genus	name-string	Genus of the relevant organism.
primary-group	name-string	The primary NMPDR group for this organism. There is always exactly one NMPDR group (either based on the organism name or the default value "Supporting"), whereas there can be multiple named groups or even none.
species	name-string	Species of the relevant organism.
unique-characterization	medium-string	The unique characterization identifies the particular organism instance from which the genome is taken. It is possible to have in the database more than one genome for a particular species, and every individual organism has variations in its DNA.
version	name-string	version string for this genome, generally consisting of the genome ID followed by a period and a string of digits.
taxonomy	text	The taxonomy string contains the full taxonomy of the organism, while individual elements separated by semi-colons (and optional white space), starting with the domain and ending with the disambiguated genus and species (which is the organism's scientific name plus an identifying string).

• Index idx0
  • This index allows the applications to find all genomes associated with a specific access code, so that a complete list of the genomes users can view may be generated.
  • access-code, genus, species, unique-characterization
• Index idx1
  • This index allows the applications to find all genomes associated with a specific primary (NMPDR) group.
  • primary-group, genus, species, unique-characterization
• Index idx2
  • This index allows the applications to find all genomes for a particular species.
  • genus, species, unique-characterization
• Index idx3 (unique)
  • Primary index for Genome.
  • id

GenomeSubset

A genome subset is a named collection of genomes that participate in a particular subsystem. The subset names are generally very short, non-unique strings. The ID of the parent subsystem is prefixed to the subset ID in order to make it unique.

Relationships for GenomeSubset

• GenomeSubset ConsistsOfGenomes Genome (many-to-many)
• Subsystem HasGenomeSubset GenomeSubset (one-to-many)

Relations for GenomeSubset

GenomeSubset
Field	Type	Description
id	string	Unique identifier for this GenomeSubset.

• Index idx0 (unique)
  • Primary index for GenomeSubset.
  • id

Ligand

A Ligand is a chemical of interest in computing docking energies against a PDB. The ID of the ligand is an 8-digit ZINC ID number.

Relationships for Ligand

• PDB DocksWith Ligand (many-to-many)

Relations for Ligand

Ligand
Field	Type	Description
id	id-string	Unique identifier for this Ligand.
name	long-string	Chemical name of this ligand.

• Index idx0 (unique)
  • Primary index for Ligand.
  • id

PDB

A PDB is a protein database containing information that can be used to determine the shape of the protein and the energies required to dock with it. The ID is the four-character name used on the PDB web site.

Relationships for PDB

• PDB DocksWith Ligand (many-to-many)
• PDB IsProteinForFeature Feature (many-to-many)

Relations for PDB

PDB
Field	Type	Description
id	id-string	Unique identifier for this PDB.
docking-count	int	The number of ligands that have been docked against this PDB.

• Index idx0
  • docking-count DESC, id
• Index idx1 (unique)
  • Primary index for PDB.
  • id

Property

A property is a type of assertion that could be made about the properties of a particular feature. Each property instance is a key/value pair and can be associated with many different features. Conversely, a feature can be associated with many key/value pairs, even some that notionally contradict each other. For example, there can be evidence that a feature is essential to the organism's survival and evidence that it is superfluous.

Relationships for Property

• Feature HasProperty Property (many-to-many)

Relations for Property

Property
Field	Type	Description
id	int	Unique identifier for this Property.
property-name	name-string	Name of this property.
property-value	string	Value associated with this property. For each property name, there must by a property record for all of its possible values.

• Index idx0
  • This index enables the application to find all values for a specified property name, or any given name/value pair.
  • property-name, property-value
• Index idx1 (unique)
  • Primary index for Property.
  • id

Reaction

A reaction is a chemical process catalyzed by a protein. The reaction ID is generally a small number preceded by a letter.

Relationships for Reaction

• Role Catalyzes Reaction (many-to-many)
• Compound IsAComponentOf Reaction (many-to-many)

Relations for Reaction

Reaction
Field	Type	Description
id	key-string	Unique identifier for this Reaction.
rev	boolean	TRUE if this reaction is reversible, else FALSE

• Index idx0 (unique)
  • Primary index for Reaction.
  • id

ReactionURL
Field	Type	Description
id	key-string	Unique identifier for this Reaction.
url	string	HTML string containing a link to a web location that describes the reaction. This field is optional.

• Index idx0
  • id

Role

A role describes a biological function that may be fulfilled by a feature. One of the main goals of the database is to record the roles of the various features.

Relationships for Role

• Role Catalyzes Reaction (many-to-many)
• RoleSubset ConsistsOfRoles Role (many-to-many)
• Role IsIdentifiedByEC RoleEC (many-to-many)
• Role IsRoleOf SSCell (one-to-many)
• Role OccursInSubsystem Subsystem (many-to-many)
• Role RoleOccursIn Diagram (many-to-many)

Relations for Role

Role
Field	Type	Description
id	string	Unique identifier for this Role.

• Index idx0 (unique)
  • Primary index for Role.
  • id

RoleEC

EC code for a role.

Relationships for RoleEC

• Role IsIdentifiedByEC RoleEC (many-to-many)

Relations for RoleEC

RoleEC
Field	Type	Description
id	string	Unique identifier for this RoleEC.

• Index idx0 (unique)
  • Primary index for RoleEC.
  • id

RoleSubset

A role subset is a named collection of roles in a particular subsystem. The subset names are generally very short, non-unique strings. The ID of the parent subsystem is prefixed to the subset ID in order to make it unique.

Relationships for RoleSubset

• RoleSubset ConsistsOfRoles Role (many-to-many)
• Subsystem HasRoleSubset RoleSubset (one-to-many)

Relations for RoleSubset

RoleSubset
Field	Type	Description
id	string	Unique identifier for this RoleSubset.

• Index idx0 (unique)
  • Primary index for RoleSubset.
  • id

SSCell

Part of the process of locating and assigning features is creating a spreadsheet of genomes and roles to which features are assigned. A spreadsheet cell represents one of the positions on the spreadsheet.

Relationships for SSCell

• SSCell ContainsFeature Feature (many-to-many)
• Subsystem HasSSCell SSCell (one-to-many)
• Genome IsGenomeOf SSCell (one-to-many)
• Role IsRoleOf SSCell (one-to-many)

Relations for SSCell

SSCell
Field	Type	Description
id	hash-string	Unique identifier for this SSCell.

• Index idx0 (unique)
  • Primary index for SSCell.
  • id

Sequence

A sequence is a continuous piece of a contig. Contigs are split into sequences so that we don't have to have the entire contig in memory when we are manipulating it. The key of the sequence is the contig ID followed by the index of the begin point.

Relationships for Sequence

• Contig IsMadeUpOf Sequence (one-to-many)

Relations for Sequence

Sequence
Field	Type	Description
id	name-string	Unique identifier for this Sequence.
quality-vector	text	String describing the quality data for each base pair. Individual values will be separated by periods. The value represents negative exponent of the probability of error. Thus, for example, a quality of 30 indicates the probability of error is 10^-30. A higher quality number a better chance of a correct match. It is possible that the quality data is not known for a sequence. If that is the case, the quality vector will contain the unknown.
sequence	text	String consisting of the residues. Each residue is described by a single character in the string.

• Index idx0 (unique)
  • Primary index for Sequence.
  • id

Source

A source describes a place from which genome data was taken. This can be an organization or a paper citation.

Relationships for Source

• Genome ComesFrom Source (many-to-many)

Relations for Source

Source
Field	Type	Description
id	medium-string	Unique identifier for this Source.
description	text	Description the source. The description can be a street address or a citation.

• Index idx0 (unique)
  • Primary index for Source.
  • id

SourceURL
Field	Type	Description
id	medium-string	Unique identifier for this Source.
URL	string	URL the paper cited or of the organization's web site. This field optional.

• Index idx0
  • id

SproutUser

A user is a person who can make annotations and view data in the database. The user object is keyed on the user's login name.

Relationships for SproutUser

• SproutUser IsTrustedBy SproutUser (many-to-many)
• SproutUser MadeAnnotation Annotation (one-to-many)

Relations for SproutUser

SproutUser
Field	Type	Description
id	name-string	Unique identifier for this SproutUser.
description	string	Full name or description of this user.

• Index idx0 (unique)
  • Primary index for SproutUser.
  • id

UserAccess
Field	Type	Description
id	name-string	Unique identifier for this SproutUser.
access-code	key-string	Access code possessed by this user. A user can have many access codes; a genome is accessible to the user if its access code matches any one of the user's access codes.

• Index idx0
  • id

Subsystem

A subsystem is a collection of roles that work together in a cell. Identification of subsystems is an important tool for recognizing parallel genetic features in different organisms.

Relationships for Subsystem

• Subsystem HasGenomeSubset GenomeSubset (one-to-many)
• Feature HasRoleInSubsystem Subsystem (many-to-many)
• Subsystem HasRoleSubset RoleSubset (one-to-many)
• Subsystem HasSSCell SSCell (one-to-many)
• Role OccursInSubsystem Subsystem (many-to-many)
• Genome ParticipatesIn Subsystem (many-to-many)

Relations for Subsystem

Subsystem
Field	Type	Description
id	string	Unique identifier for this Subsystem.
curator	string	Name of the person currently in charge of the subsystem.
notes	text	Descriptive notes about the subsystem.

• Index idx0 (unique)
  • Primary index for Subsystem.
  • id

SubsystemClass
Field	Type	Description
id	string	Unique identifier for this Subsystem.
classification	string	Classification string, colon-delimited. This string organizes the subsystems into a hierarchy.

• Index idx0
  • id

SynonymGroup

A synonym group represents a group of features. Substantially identical features are mapped to the same synonym group, and this information is used to expand similarities.

Relationships for SynonymGroup

• SynonymGroup IsSynonymGroupFor Feature (many-to-many)

Relations for SynonymGroup

SynonymGroup
Field	Type	Description
id	id-string	Unique identifier for this SynonymGroup.

• Index idx0 (unique)
  • Primary index for SynonymGroup.
  • id

Relationships

Role Catalyzes Reaction

Each Role relates to multiple Reactions. Each Reaction relates to multiple Roles.

This relationship connects a role to the reactions it catalyzes. The purpose of a role is to create proteins that trigger certain chemical reactions. A single reaction can be triggered by many roles, and a role can trigger many reactions.

Catalyzes
Field	Type	Description
from-link	string	id of the source Role.
to-link	key-string	id of the target Reaction.

• Index idxFrom
  • from-link
• Index idxTo
  • to-link

Genome ComesFrom Source

Each Genome relates to multiple Sources. Each Source relates to multiple Genomes.

This relationship connects a genome to the sources that mapped it. A genome can come from a single source or from a cooperation among multiple sources.

ComesFrom
Field	Type	Description
from-link	name-string	id of the source Genome.
to-link	medium-string	id of the target Source.

• Index idxFrom
  • from-link
• Index idxTo
  • to-link

GenomeSubset ConsistsOfGenomes Genome

Each GenomeSubset relates to multiple Genomes. Each Genome relates to multiple GenomeSubsets.

This relationship connects a subset to the genomes that it covers. A subset is, essentially, a named group of genomes participating in a specific subsystem, and this relationship effects that. Note that while a genome may belong to many subsystems, a subset belongs to only one subsystem, and all genomes in the subset must have that subsystem in common.

ConsistsOfGenomes
Field	Type	Description
from-link	string	id of the source GenomeSubset.
to-link	name-string	id of the target Genome.

• Index idxFrom
  • from-link
• Index idxTo
  • to-link

RoleSubset ConsistsOfRoles Role

Each RoleSubset relates to multiple Roles. Each Role relates to multiple RoleSubsets.

This relationship connects a role subset to the roles that it covers. A subset is, essentially, a named group of roles belonging to a specific subsystem, and this relationship effects that. Note that will a role may belong to many subsystems, a subset belongs to only one subsystem, and all roles in the subset must have that subsystem in common.

ConsistsOfRoles
Field	Type	Description
from-link	string	id of the source RoleSubset.
to-link	string	id of the target Role.

• Index idxFrom
  • from-link
• Index idxTo
  • to-link

SSCell ContainsFeature Feature

Each SSCell relates to multiple Features. Each Feature relates to multiple SSCells.

This relationship connects a subsystem's spreadsheet cell to the features assigned to it.

ContainsFeature
Field	Type	Description
from-link	hash-string	id of the source SSCell.
to-link	id-string	id of the target Feature.
cluster-number	int	ID of this feature's cluster. Clusters represent families of related proteins participating in a subsystem.

• Index idxFrom
  • from-link
• Index idxTo
  • to-link

PDB DocksWith Ligand

Each PDB relates to multiple Ligands. Each Ligand relates to multiple PDBs.

Indicates that a docking result exists between a PDB and a ligand. The docking result describes the energy required for the ligand to dock with the protein described by the PDB. A lower energy indicates the ligand has a good chance of disabling the protein. At the current time, only the best docking results are kept.

DocksWith
Field	Type	Description
from-link	id-string	id of the source PDB.
to-link	id-string	id of the target Ligand.
electrostatic-energy	float	Docking energy in kcal/mol that results from the movement of electrons (electrostatic force) between the PDB and the ligan.
reason	id-string	Indication of the reason for determining the docking result. A value of Random indicates the docking was attempted as a part of a random survey used to determine the docking characteristics of the PDB. A value of Rich indicates the docking was attempted because a low-energy docking result was predicted for the ligand with respect to the PDB.
tool	id-string	Name of the tool used to produce the docking result.
total-energy	float	Total energy required for the ligand to dock with the PDB protein, in kcal/mol. A negative value means energy is released.
vanderwalls-energy	float	Docking energy in kcal/mol that results from the geometric fit (Van der Waals force) between the PDB and the ligand.

• Index idxFrom
  • This index enables the application to view a PDB's docking results from the lowest energy (best docking) to highest energy (worst docking).
  • from-link, total-energy
• Index idxTo
  • This index enables the application to view a ligand's docking results from the lowest energy (best docking) to highest energy (worst docking). Note that since we only keep the best docking results for a PDB, this index is not likely to provide useful results.
  • to-link

Compound HasCompoundName CompoundName

Each Compound relates to multiple CompoundNames. Each CompoundName relates to multiple Compounds.

Connects a compound to its names. A compound generally has several names

HasCompoundName
Field	Type	Description
from-link	name-string	id of the source Compound.
to-link	string	id of the target CompoundName.
priority	int	Priority of this name, with 1 being the highest priority, 2 the next highest, and so forth.

• Index idxFrom
  • This index enables the application to view the names of a compound in priority order.
  • from-link, priority
• Index idxTo
  • to-link

Genome HasContig Contig

Each Genome relates to multiple Contigs.

This relationship connects a genome to the contigs that contain the actual genetic information.

HasContig
Field	Type	Description
from-link	name-string	id of the source Genome.
to-link	name-string	id of the target Contig.

• Index idxFrom
  • from-link
• Index idxTo (unique)
  • to-link

Genome HasFeature Feature

Each Genome relates to multiple Features.

This relationship connects a genome to all of its features. This relationship is redundant in a sense, because the genome ID is part of the feature ID; however, it makes the creation of certain queries more convenient because you can drag in filtering information for a feature's genome.

HasFeature
Field	Type	Description
from-link	name-string	id of the source Genome.
to-link	id-string	id of the target Feature.
type	key-string	Feature type (eg. peg, rna)

• Index idxFrom
  • This index enables the application to view the features of a Genome sorted by type.
  • from-link, type
• Index idxTo (unique)
  • to-link

Subsystem HasGenomeSubset GenomeSubset

Each Subsystem relates to multiple GenomeSubsets.

This relationship connects a subsystem to its constituent genome subsets. Note that some genomes in a subsystem may not belong to a subset, so the relationship between genomes and subsystems cannot be derived from the relationships going through the subset.

HasGenomeSubset
Field	Type	Description
from-link	string	id of the source Subsystem.
to-link	string	id of the target GenomeSubset.

• Index idxFrom
  • from-link
• Index idxTo (unique)
  • to-link

Feature HasProperty Property

Each Feature relates to multiple Propertys. Each Property relates to multiple Features.

This relationship connects a feature to its known property values. The relationship contains text data that indicates the paper or organization that discovered evidence that the feature possesses the property. So, for example, if two papers presented evidence that a feature is essential, there would be an instance of this relationship for both.

HasProperty
Field	Type	Description
from-link	id-string	id of the source Feature.
to-link	int	id of the target Property.
evidence	text	URL or citation of the paper or institution that reported evidence of the relevant feature possessing the specified property value.

• Index idxFrom
  • from-link
• Index idxTo
  • to-link

Feature HasRoleInSubsystem Subsystem

Each Feature relates to multiple Subsystems. Each Subsystem relates to multiple Features.

This relationship connects a feature to the subsystems in which it participates. This is technically redundant information, but it is used so often that it deserves its own table.

HasRoleInSubsystem
Field	Type	Description
from-link	id-string	id of the source Feature.
to-link	string	id of the target Subsystem.
genome	name-string	ID of the genome containing the feature
type	key-string	Feature type (eg. peg, rna)

• Index idxFrom
  • from-link
• Index idxTo
  • This index enables the application to view the features of a subsystem sorted by genome and feature type.
  • to-link, genome, type

Subsystem HasRoleSubset RoleSubset

Each Subsystem relates to multiple RoleSubsets.

This relationship connects a subsystem to its constituent role subsets. Note that some roles in a subsystem may not belong to a subset, so the relationship between roles and subsystems cannot be derived from the relationships going through the subset.

HasRoleSubset
Field	Type	Description
from-link	string	id of the source Subsystem.
to-link	string	id of the target RoleSubset.

• Index idxFrom
  • from-link
• Index idxTo (unique)
  • to-link

Subsystem HasSSCell SSCell

Each Subsystem relates to multiple SSCells.

This relationship connects a subsystem to the spreadsheet cells used to analyze and display it. The cells themselves can be thought of as a grid with Roles on one axis and Genomes on the other. The various features of the subsystem are then assigned to the cells.

HasSSCell
Field	Type	Description
from-link	string	id of the source Subsystem.
to-link	hash-string	id of the target SSCell.

• Index idxFrom
  • from-link
• Index idxTo (unique)
  • to-link

Compound IsAComponentOf Reaction

Each Compound relates to multiple Reactions. Each Reaction relates to multiple Compounds.

This relationship connects a reaction to the compounds that participate in it.

IsAComponentOf
Field	Type	Description
from-link	name-string	id of the source Compound.
to-link	key-string	id of the target Reaction.
discriminator	int	A unique ID for this record. The discriminator does not provide any useful data, but it prevents identical records from being collapsed by the SELECT DISTINCT command used by ERDB to retrieve data.
loc	key-string	An optional character string that indicates the relative position of this compound in the reaction's chemical formula. The location affects the way the compounds present as we cross the relationship from the reaction side. The product/substrate flag comes first, then the value of this field, then the main flag. The default value is an empty string; however, the empty string sorts first, so if this field is used, it should probably be used for every compound in the reaction.
main	boolean	TRUE if this compound is one of the main participants in the reaction, else FALSE. It is permissible for none of the compounds in the reaction to be considered main, in which case this value would be FALSE for all of the relevant compounds.
product	boolean	TRUE if the compound is a product of the reaction, FALSE if it is a substrate. When a reaction is written on paper in chemical notation, the substrates are left of the arrow and the products are to the right. Sorting on this field will cause the substrates to appear first, followed by the products. If the reaction is reversible, then the notion of substrates and products is not at intuitive; however, a value here of FALSE still puts the compound left of the arrow and a value of TRUE still puts it to the right.
stoichiometry	key-string	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.

• Index idxFrom
  • from-link
• Index idxTo
  • This index presents the compounds in the reaction in the order they should be displayed when writing it in chemical notation. All the substrates appear before all the products, and within that ordering, the main compounds appear first.
  • to-link, product, loc, main DESC

FeatureAlias IsAliasOf Feature

Each FeatureAlias relates to multiple Features. Each Feature relates to multiple FeatureAliass.

Connects an alias to the feature it represents. Every alias connects to at least 1 feature, and a feature connects to many aliases.

IsAliasOf
Field	Type	Description
from-link	medium-string	id of the source FeatureAlias.
to-link	id-string	id of the target Feature.

• Index idxFrom
  • from-link
• Index idxTo
  • to-link

Family IsFamilyForFeature Feature

Each Family relates to multiple Features. Each Feature relates to multiple Familys.

This relationship connects a protein family to all of its PEGs and connects each PEG to all of its protein families.

IsFamilyForFeature
Field	Type	Description
from-link	id-string	id of the source Family.
to-link	id-string	id of the target Feature.

• Index idxFrom
  • from-link
• Index idxTo
  • to-link

Genome IsGenomeOf SSCell

Each Genome relates to multiple SSCells.

This relationship connects a subsystem's spreadsheet cell to the genome for the spreadsheet column.

IsGenomeOf
Field	Type	Description
from-link	name-string	id of the source Genome.
to-link	hash-string	id of the target SSCell.

• Index idxFrom
  • from-link
• Index idxTo (unique)
  • to-link

Compound IsIdentifiedByCAS CompoundCAS

Each Compound relates to multiple CompoundCASs. Each CompoundCAS relates to multiple Compounds.

Relates a compound's CAS ID to the compound itself. Every CAS ID is associated with a compound, and some are associated with two compounds, but not all compounds have CAS IDs.

IsIdentifiedByCAS
Field	Type	Description
from-link	name-string	id of the source Compound.
to-link	name-string	id of the target CompoundCAS.

• Index idxFrom
  • from-link
• Index idxTo
  • to-link

Role IsIdentifiedByEC RoleEC

Each Role relates to multiple RoleECs. Each RoleEC relates to multiple Roles.

Relates a role to its EC number. Every EC number is associated with a role, but not all roles have EC numbers.

IsIdentifiedByEC
Field	Type	Description
from-link	string	id of the source Role.
to-link	string	id of the target RoleEC.

• Index idxFrom
  • from-link
• Index idxTo
  • to-link

Feature IsLocatedIn Contig

Each Feature relates to multiple Contigs. Each Contig relates to multiple Features.

This relationship connects a feature to the contig segments that work together to effect it. The segments are numbered sequentially starting from 1. The database is required to place an upper limit on the length of each segment. If a segment is longer than the maximum, it can be broken into smaller bits.

The upper limit enables applications to locate all features that contain a specific residue. For example, if the upper limit is 100 and we are looking for a feature that contains residue 234 of contig ABC, we can look for features with a begin point between 135 and 333. The results can then be filtered by direction and length of the segment.

IsLocatedIn
Field	Type	Description
from-link	id-string	id of the source Feature.
to-link	name-string	id of the target Contig.
beg	int	Index (1-based) of the first residue in the contig that belongs to the segment.
dir	char	Direction of the segment: + if it is forward and - if it is backward.
len	int	Number of residues in the segment. A length of 0 identifies a specific point between residues. This is the point before the residue if the direction is forward and the point after the residue if the direction is backward.
locN	int	Sequence number of this segment.

• Index idxFrom
  • This index allows the application to find all the segments of a feature in the proper order.
  • from-link, locN
• Index idxTo
  • This index is the one used by applications to find all the feature segments that contain a specific residue.
  • to-link, beg

Contig IsMadeUpOf Sequence

Each Contig relates to multiple Sequences.

A contig is stored in the database as an ordered set of sequences. By splitting the contig into sequences, we get a performance boost from only needing to keep small portions of a contig in memory at any one time. This relationship connects the contig to its constituent sequences.

IsMadeUpOf
Field	Type	Description
from-link	name-string	id of the source Contig.
to-link	name-string	id of the target Sequence.
len	int	Length of the sequence.
start-position	int	Index (1-based) of the point in the contig where this sequence starts.

• Index idxFrom
  • This index enables the application to find all of the sequences in a contig in order, and makes it easier to find a particular residue section.
  • from-link, start-position, len
• Index idxTo (unique)
  • to-link

CDD IsPresentOnProteinOf Feature

Each CDD relates to multiple Features. Each Feature relates to multiple CDDs.

This relationship connects a feature to its CDD protein domains. The match score is included as intersection data.

IsPresentOnProteinOf
Field	Type	Description
from-link	key-string	id of the source CDD.
to-link	id-string	id of the target Feature.
score	float	This is the match score between the feature and the CDD. A lower score is a better match.

• Index idxFrom
  • from-link, score
• Index idxTo
  • to-link

PDB IsProteinForFeature Feature

Each PDB relates to multiple Features. Each Feature relates to multiple PDBs.

Relates a PDB to features that produce highly similar proteins.

IsProteinForFeature
Field	Type	Description
from-link	id-string	id of the source PDB.
to-link	id-string	id of the target Feature.
end-location	int	Ending location within the feature of the matching region.
score	float	Similarity score for the comparison between the feature and the PDB protein. A lower score indicates a better match.
start-location	int	Starting location within the feature of the matching region.

• Index idxFrom
  • This index enables the application to view the features of a PDB in order from the closest match to the furthest.
  • from-link, score
• Index idxTo
  • This index enables the application to view the PDBs of a feature in order from the closest match to the furthest.
  • to-link, score

Role IsRoleOf SSCell

Each Role relates to multiple SSCells.

This relationship connects a subsystem's spreadsheet cell to the role for the spreadsheet row.

IsRoleOf
Field	Type	Description
from-link	string	id of the source Role.
to-link	hash-string	id of the target SSCell.

• Index idxFrom
  • from-link
• Index idxTo (unique)
  • to-link

SynonymGroup IsSynonymGroupFor Feature

Each SynonymGroup relates to multiple Features. Each Feature relates to multiple SynonymGroups.

This relation connects a synonym group to the features that make it up.

IsSynonymGroupFor
Field	Type	Description
from-link	id-string	id of the source SynonymGroup.
to-link	id-string	id of the target Feature.

• Index idxFrom
  • from-link
• Index idxTo
  • to-link

Feature IsTargetOfAnnotation Annotation

Each Feature relates to multiple Annotations.

This relationship connects a feature to its annotations.

IsTargetOfAnnotation
Field	Type	Description
from-link	id-string	id of the source Feature.
to-link	name-string	id of the target Annotation.

• Index idxFrom
  • from-link
• Index idxTo (unique)
  • to-link

SproutUser IsTrustedBy SproutUser

Each SproutUser relates to multiple SproutUsers.

This relationship identifies the users trusted by each particular user. When viewing functional assignments, the assignment displayed is the most recent one by a user trusted by the current user. The current user implicitly trusts himself. If no trusted users are specified in the database, the user also implicitly trusts the user FIG.

IsTrustedBy
Field	Type	Description
from-link	name-string	id of the source SproutUser.
to-link	name-string	id of the target SproutUser.

• Index idxFrom
  • from-link
• Index idxTo
  • to-link

SproutUser MadeAnnotation Annotation

Each SproutUser relates to multiple Annotations.

This relationship connects an annotation to the user who made it.

MadeAnnotation
Field	Type	Description
from-link	name-string	id of the source SproutUser.
to-link	name-string	id of the target Annotation.

• Index idxFrom
  • from-link
• Index idxTo (unique)
  • to-link

Role OccursInSubsystem Subsystem

Each Role relates to multiple Subsystems. Each Subsystem relates to multiple Roles.

This relationship connects roles to the subsystems that implement them.

OccursInSubsystem
Field	Type	Description
from-link	string	id of the source Role.
to-link	string	id of the target Subsystem.
abbr	name-string	Abbreviated name for the role, generally non-unique, but useful in column headings for HTML tables.
column-number	int	Column number for this role in the specified subsystem's spreadsheet.

• Index idxFrom
  • from-link
• Index idxTo
  • This index enables the application to see the subsystem roles in column order. The ordering of the roles is usually significant, so it is important to preserve it.
  • to-link, column-number

Genome ParticipatesIn Subsystem

Each Genome relates to multiple Subsystems. Each Subsystem relates to multiple Genomes.

This relationship connects subsystems to the genomes that use it. If the subsystem has been curated for the genome, then the subsystem's roles will also be connected to the genome features through the SSCell object.

ParticipatesIn
Field	Type	Description
from-link	name-string	id of the source Genome.
to-link	string	id of the target Subsystem.
variant-code	key-string	Code indicating the subsystem variant to which this genome belongs. Each subsystem can have multiple variants. A variant code of -1 indicates that the genome does not have a functional variant of the subsystem. A variant code of 0 indicates that the genome's participation is considered iffy.

• Index idxFrom
  • from-link
• Index idxTo
  • This index enables the application to find all of the genomes using a subsystem in order by variant code, which is how we wish to display them in the spreadsheets.
  • to-link, variant-code

Role RoleOccursIn Diagram

Each Role relates to multiple Diagrams. Each Diagram relates to multiple Roles.

This relationship connects a role to the diagrams on which it appears. A role frequently identifies an enzyme, and can appear in many diagrams. A diagram generally contains many different roles.

RoleOccursIn
Field	Type	Description
from-link	string	id of the source Role.
to-link	name-string	id of the target Diagram.

• Index idxFrom
  • from-link
• Index idxTo
  • to-link

Join Table

Join Table
Source	Target	Join Condition
Annotation	Feature IsTargetOfAnnotation Annotation (one-to-many)	Annotation.id = IsTargetOfAnnotation.to_link
Annotation	SproutUser MadeAnnotation Annotation (one-to-many)	Annotation.id = MadeAnnotation.to_link
CDD	CDD IsPresentOnProteinOf Feature (many-to-many)	CDD.id = IsPresentOnProteinOf.from_link
Role Catalyzes Reaction (many-to-many)	RoleSubset ConsistsOfRoles Role (many-to-many)	Catalyzes.from_link = ConsistsOfRoles.to_link
Role Catalyzes Reaction (many-to-many)	Compound IsAComponentOf Reaction (many-to-many)	Catalyzes.to_link = IsAComponentOf.to_link
Role Catalyzes Reaction (many-to-many)	Role IsIdentifiedByEC RoleEC (many-to-many)	Catalyzes.from_link = IsIdentifiedByEC.from_link
Role Catalyzes Reaction (many-to-many)	Role IsRoleOf SSCell (one-to-many)	Catalyzes.from_link = IsRoleOf.from_link
Role Catalyzes Reaction (many-to-many)	Role OccursInSubsystem Subsystem (many-to-many)	Catalyzes.from_link = OccursInSubsystem.from_link
Role Catalyzes Reaction (many-to-many)	Reaction	Reaction.id = Catalyzes.to_link
Role Catalyzes Reaction (many-to-many)	Role	Role.id = Catalyzes.from_link
Role Catalyzes Reaction (many-to-many)	Role RoleOccursIn Diagram (many-to-many)	Catalyzes.from_link = RoleOccursIn.from_link
Genome ComesFrom Source (many-to-many)	GenomeSubset ConsistsOfGenomes Genome (many-to-many)	ComesFrom.from_link = ConsistsOfGenomes.to_link
Genome ComesFrom Source (many-to-many)	Genome	Genome.id = ComesFrom.from_link
Genome ComesFrom Source (many-to-many)	Genome HasContig Contig (one-to-many)	ComesFrom.from_link = HasContig.from_link
Genome ComesFrom Source (many-to-many)	Genome HasFeature Feature (one-to-many)	ComesFrom.from_link = HasFeature.from_link
Genome ComesFrom Source (many-to-many)	Genome IsGenomeOf SSCell (one-to-many)	ComesFrom.from_link = IsGenomeOf.from_link
Genome ComesFrom Source (many-to-many)	Genome ParticipatesIn Subsystem (many-to-many)	ComesFrom.from_link = ParticipatesIn.from_link
Genome ComesFrom Source (many-to-many)	Source	Source.id = ComesFrom.to_link
Compound	Compound HasCompoundName CompoundName (many-to-many)	Compound.id = HasCompoundName.from_link
Compound	Compound IsAComponentOf Reaction (many-to-many)	Compound.id = IsAComponentOf.from_link
Compound	Compound IsIdentifiedByCAS CompoundCAS (many-to-many)	Compound.id = IsIdentifiedByCAS.from_link
CompoundCAS	Compound IsIdentifiedByCAS CompoundCAS (many-to-many)	CompoundCAS.id = IsIdentifiedByCAS.to_link
CompoundName	Compound HasCompoundName CompoundName (many-to-many)	CompoundName.id = HasCompoundName.to_link
GenomeSubset ConsistsOfGenomes Genome (many-to-many)	Genome ComesFrom Source (many-to-many)	ConsistsOfGenomes.to_link = ComesFrom.from_link
GenomeSubset ConsistsOfGenomes Genome (many-to-many)	Genome	Genome.id = ConsistsOfGenomes.to_link
GenomeSubset ConsistsOfGenomes Genome (many-to-many)	GenomeSubset	GenomeSubset.id = ConsistsOfGenomes.from_link
GenomeSubset ConsistsOfGenomes Genome (many-to-many)	Genome HasContig Contig (one-to-many)	ConsistsOfGenomes.to_link = HasContig.from_link
GenomeSubset ConsistsOfGenomes Genome (many-to-many)	Genome HasFeature Feature (one-to-many)	ConsistsOfGenomes.to_link = HasFeature.from_link
GenomeSubset ConsistsOfGenomes Genome (many-to-many)	Subsystem HasGenomeSubset GenomeSubset (one-to-many)	ConsistsOfGenomes.from_link = HasGenomeSubset.to_link
GenomeSubset ConsistsOfGenomes Genome (many-to-many)	Genome IsGenomeOf SSCell (one-to-many)	ConsistsOfGenomes.to_link = IsGenomeOf.from_link
GenomeSubset ConsistsOfGenomes Genome (many-to-many)	Genome ParticipatesIn Subsystem (many-to-many)	ConsistsOfGenomes.to_link = ParticipatesIn.from_link
RoleSubset ConsistsOfRoles Role (many-to-many)	Role Catalyzes Reaction (many-to-many)	ConsistsOfRoles.to_link = Catalyzes.from_link
RoleSubset ConsistsOfRoles Role (many-to-many)	Subsystem HasRoleSubset RoleSubset (one-to-many)	ConsistsOfRoles.from_link = HasRoleSubset.to_link
RoleSubset ConsistsOfRoles Role (many-to-many)	Role IsIdentifiedByEC RoleEC (many-to-many)	ConsistsOfRoles.to_link = IsIdentifiedByEC.from_link
RoleSubset ConsistsOfRoles Role (many-to-many)	Role IsRoleOf SSCell (one-to-many)	ConsistsOfRoles.to_link = IsRoleOf.from_link
RoleSubset ConsistsOfRoles Role (many-to-many)	Role OccursInSubsystem Subsystem (many-to-many)	ConsistsOfRoles.to_link = OccursInSubsystem.from_link
RoleSubset ConsistsOfRoles Role (many-to-many)	Role	Role.id = ConsistsOfRoles.to_link
RoleSubset ConsistsOfRoles Role (many-to-many)	Role RoleOccursIn Diagram (many-to-many)	ConsistsOfRoles.to_link = RoleOccursIn.from_link
RoleSubset ConsistsOfRoles Role (many-to-many)	RoleSubset	RoleSubset.id = ConsistsOfRoles.from_link
SSCell ContainsFeature Feature (many-to-many)	Feature	Feature.id = ContainsFeature.to_link
SSCell ContainsFeature Feature (many-to-many)	Genome HasFeature Feature (one-to-many)	ContainsFeature.to_link = HasFeature.to_link
SSCell ContainsFeature Feature (many-to-many)	Feature HasProperty Property (many-to-many)	ContainsFeature.to_link = HasProperty.from_link
SSCell ContainsFeature Feature (many-to-many)	Feature HasRoleInSubsystem Subsystem (many-to-many)	ContainsFeature.to_link = HasRoleInSubsystem.from_link
SSCell ContainsFeature Feature (many-to-many)	Subsystem HasSSCell SSCell (one-to-many)	ContainsFeature.from_link = HasSSCell.to_link
SSCell ContainsFeature Feature (many-to-many)	FeatureAlias IsAliasOf Feature (many-to-many)	ContainsFeature.to_link = IsAliasOf.to_link
SSCell ContainsFeature Feature (many-to-many)	Family IsFamilyForFeature Feature (many-to-many)	ContainsFeature.to_link = IsFamilyForFeature.to_link
SSCell ContainsFeature Feature (many-to-many)	Genome IsGenomeOf SSCell (one-to-many)	ContainsFeature.from_link = IsGenomeOf.to_link
SSCell ContainsFeature Feature (many-to-many)	Feature IsLocatedIn Contig (many-to-many)	ContainsFeature.to_link = IsLocatedIn.from_link
SSCell ContainsFeature Feature (many-to-many)	CDD IsPresentOnProteinOf Feature (many-to-many)	ContainsFeature.to_link = IsPresentOnProteinOf.to_link
SSCell ContainsFeature Feature (many-to-many)	PDB IsProteinForFeature Feature (many-to-many)	ContainsFeature.to_link = IsProteinForFeature.to_link
SSCell ContainsFeature Feature (many-to-many)	Role IsRoleOf SSCell (one-to-many)	ContainsFeature.from_link = IsRoleOf.to_link
SSCell ContainsFeature Feature (many-to-many)	SynonymGroup IsSynonymGroupFor Feature (many-to-many)	ContainsFeature.to_link = IsSynonymGroupFor.to_link
SSCell ContainsFeature Feature (many-to-many)	Feature IsTargetOfAnnotation Annotation (one-to-many)	ContainsFeature.to_link = IsTargetOfAnnotation.from_link
SSCell ContainsFeature Feature (many-to-many)	SSCell	SSCell.id = ContainsFeature.from_link
Contig	Genome HasContig Contig (one-to-many)	Contig.id = HasContig.to_link
Contig	Feature IsLocatedIn Contig (many-to-many)	Contig.id = IsLocatedIn.to_link
Contig	Contig IsMadeUpOf Sequence (one-to-many)	Contig.id = IsMadeUpOf.from_link
Diagram	Role RoleOccursIn Diagram (many-to-many)	Diagram.id = RoleOccursIn.to_link
PDB DocksWith Ligand (many-to-many)	PDB IsProteinForFeature Feature (many-to-many)	DocksWith.from_link = IsProteinForFeature.from_link
PDB DocksWith Ligand (many-to-many)	Ligand	Ligand.id = DocksWith.to_link
PDB DocksWith Ligand (many-to-many)	PDB	PDB.id = DocksWith.from_link
Family	Family IsFamilyForFeature Feature (many-to-many)	Family.id = IsFamilyForFeature.from_link
Feature	SSCell ContainsFeature Feature (many-to-many)	Feature.id = ContainsFeature.to_link
Feature	Genome HasFeature Feature (one-to-many)	Feature.id = HasFeature.to_link
Feature	Feature HasProperty Property (many-to-many)	Feature.id = HasProperty.from_link
Feature	Feature HasRoleInSubsystem Subsystem (many-to-many)	Feature.id = HasRoleInSubsystem.from_link
Feature	FeatureAlias IsAliasOf Feature (many-to-many)	Feature.id = IsAliasOf.to_link
Feature	Family IsFamilyForFeature Feature (many-to-many)	Feature.id = IsFamilyForFeature.to_link
Feature	Feature IsLocatedIn Contig (many-to-many)	Feature.id = IsLocatedIn.from_link
Feature	CDD IsPresentOnProteinOf Feature (many-to-many)	Feature.id = IsPresentOnProteinOf.to_link
Feature	PDB IsProteinForFeature Feature (many-to-many)	Feature.id = IsProteinForFeature.to_link
Feature	SynonymGroup IsSynonymGroupFor Feature (many-to-many)	Feature.id = IsSynonymGroupFor.to_link
Feature	Feature IsTargetOfAnnotation Annotation (one-to-many)	Feature.id = IsTargetOfAnnotation.from_link
FeatureAlias	FeatureAlias IsAliasOf Feature (many-to-many)	FeatureAlias.id = IsAliasOf.from_link
Genome	Genome ComesFrom Source (many-to-many)	Genome.id = ComesFrom.from_link
Genome	GenomeSubset ConsistsOfGenomes Genome (many-to-many)	Genome.id = ConsistsOfGenomes.to_link
Genome	Genome HasContig Contig (one-to-many)	Genome.id = HasContig.from_link
Genome	Genome HasFeature Feature (one-to-many)	Genome.id = HasFeature.from_link
Genome	Genome IsGenomeOf SSCell (one-to-many)	Genome.id = IsGenomeOf.from_link
Genome	Genome ParticipatesIn Subsystem (many-to-many)	Genome.id = ParticipatesIn.from_link
GenomeSubset	GenomeSubset ConsistsOfGenomes Genome (many-to-many)	GenomeSubset.id = ConsistsOfGenomes.from_link
GenomeSubset	Subsystem HasGenomeSubset GenomeSubset (one-to-many)	GenomeSubset.id = HasGenomeSubset.to_link
Compound HasCompoundName CompoundName (many-to-many)	Compound	Compound.id = HasCompoundName.from_link
Compound HasCompoundName CompoundName (many-to-many)	CompoundName	CompoundName.id = HasCompoundName.to_link
Compound HasCompoundName CompoundName (many-to-many)	Compound IsAComponentOf Reaction (many-to-many)	HasCompoundName.from_link = IsAComponentOf.from_link
Compound HasCompoundName CompoundName (many-to-many)	Compound IsIdentifiedByCAS CompoundCAS (many-to-many)	HasCompoundName.from_link = IsIdentifiedByCAS.from_link
Genome HasContig Contig (one-to-many)	Genome ComesFrom Source (many-to-many)	HasContig.from_link = ComesFrom.from_link
Genome HasContig Contig (one-to-many)	GenomeSubset ConsistsOfGenomes Genome (many-to-many)	HasContig.from_link = ConsistsOfGenomes.to_link
Genome HasContig Contig (one-to-many)	Contig	Contig.id = HasContig.to_link
Genome HasContig Contig (one-to-many)	Genome	Genome.id = HasContig.from_link
Genome HasContig Contig (one-to-many)	Genome HasFeature Feature (one-to-many)	HasContig.from_link = HasFeature.from_link
Genome HasContig Contig (one-to-many)	Genome IsGenomeOf SSCell (one-to-many)	HasContig.from_link = IsGenomeOf.from_link
Genome HasContig Contig (one-to-many)	Feature IsLocatedIn Contig (many-to-many)	HasContig.to_link = IsLocatedIn.to_link
Genome HasContig Contig (one-to-many)	Contig IsMadeUpOf Sequence (one-to-many)	HasContig.to_link = IsMadeUpOf.from_link
Genome HasContig Contig (one-to-many)	Genome ParticipatesIn Subsystem (many-to-many)	HasContig.from_link = ParticipatesIn.from_link
Genome HasFeature Feature (one-to-many)	Genome ComesFrom Source (many-to-many)	HasFeature.from_link = ComesFrom.from_link
Genome HasFeature Feature (one-to-many)	GenomeSubset ConsistsOfGenomes Genome (many-to-many)	HasFeature.from_link = ConsistsOfGenomes.to_link
Genome HasFeature Feature (one-to-many)	SSCell ContainsFeature Feature (many-to-many)	HasFeature.to_link = ContainsFeature.to_link
Genome HasFeature Feature (one-to-many)	Feature	Feature.id = HasFeature.to_link
Genome HasFeature Feature (one-to-many)	Genome	Genome.id = HasFeature.from_link
Genome HasFeature Feature (one-to-many)	Genome HasContig Contig (one-to-many)	HasFeature.from_link = HasContig.from_link
Genome HasFeature Feature (one-to-many)	Feature HasProperty Property (many-to-many)	HasFeature.to_link = HasProperty.from_link
Genome HasFeature Feature (one-to-many)	Feature HasRoleInSubsystem Subsystem (many-to-many)	HasFeature.to_link = HasRoleInSubsystem.from_link
Genome HasFeature Feature (one-to-many)	FeatureAlias IsAliasOf Feature (many-to-many)	HasFeature.to_link = IsAliasOf.to_link
Genome HasFeature Feature (one-to-many)	Family IsFamilyForFeature Feature (many-to-many)	HasFeature.to_link = IsFamilyForFeature.to_link
Genome HasFeature Feature (one-to-many)	Genome IsGenomeOf SSCell (one-to-many)	HasFeature.from_link = IsGenomeOf.from_link
Genome HasFeature Feature (one-to-many)	Feature IsLocatedIn Contig (many-to-many)	HasFeature.to_link = IsLocatedIn.from_link
Genome HasFeature Feature (one-to-many)	CDD IsPresentOnProteinOf Feature (many-to-many)	HasFeature.to_link = IsPresentOnProteinOf.to_link
Genome HasFeature Feature (one-to-many)	PDB IsProteinForFeature Feature (many-to-many)	HasFeature.to_link = IsProteinForFeature.to_link
Genome HasFeature Feature (one-to-many)	SynonymGroup IsSynonymGroupFor Feature (many-to-many)	HasFeature.to_link = IsSynonymGroupFor.to_link
Genome HasFeature Feature (one-to-many)	Feature IsTargetOfAnnotation Annotation (one-to-many)	HasFeature.to_link = IsTargetOfAnnotation.from_link
Genome HasFeature Feature (one-to-many)	Genome ParticipatesIn Subsystem (many-to-many)	HasFeature.from_link = ParticipatesIn.from_link
Subsystem HasGenomeSubset GenomeSubset (one-to-many)	GenomeSubset ConsistsOfGenomes Genome (many-to-many)	HasGenomeSubset.to_link = ConsistsOfGenomes.from_link
Subsystem HasGenomeSubset GenomeSubset (one-to-many)	GenomeSubset	GenomeSubset.id = HasGenomeSubset.to_link
Subsystem HasGenomeSubset GenomeSubset (one-to-many)	Feature HasRoleInSubsystem Subsystem (many-to-many)	HasGenomeSubset.from_link = HasRoleInSubsystem.to_link
Subsystem HasGenomeSubset GenomeSubset (one-to-many)	Subsystem HasRoleSubset RoleSubset (one-to-many)	HasGenomeSubset.from_link = HasRoleSubset.from_link
Subsystem HasGenomeSubset GenomeSubset (one-to-many)	Subsystem HasSSCell SSCell (one-to-many)	HasGenomeSubset.from_link = HasSSCell.from_link
Subsystem HasGenomeSubset GenomeSubset (one-to-many)	Role OccursInSubsystem Subsystem (many-to-many)	HasGenomeSubset.from_link = OccursInSubsystem.to_link
Subsystem HasGenomeSubset GenomeSubset (one-to-many)	Genome ParticipatesIn Subsystem (many-to-many)	HasGenomeSubset.from_link = ParticipatesIn.to_link
Subsystem HasGenomeSubset GenomeSubset (one-to-many)	Subsystem	Subsystem.id = HasGenomeSubset.from_link
Feature HasProperty Property (many-to-many)	SSCell ContainsFeature Feature (many-to-many)	HasProperty.from_link = ContainsFeature.to_link
Feature HasProperty Property (many-to-many)	Feature	Feature.id = HasProperty.from_link
Feature HasProperty Property (many-to-many)	Genome HasFeature Feature (one-to-many)	HasProperty.from_link = HasFeature.to_link
Feature HasProperty Property (many-to-many)	Feature HasRoleInSubsystem Subsystem (many-to-many)	HasProperty.from_link = HasRoleInSubsystem.from_link
Feature HasProperty Property (many-to-many)	FeatureAlias IsAliasOf Feature (many-to-many)	HasProperty.from_link = IsAliasOf.to_link
Feature HasProperty Property (many-to-many)	Family IsFamilyForFeature Feature (many-to-many)	HasProperty.from_link = IsFamilyForFeature.to_link
Feature HasProperty Property (many-to-many)	Feature IsLocatedIn Contig (many-to-many)	HasProperty.from_link = IsLocatedIn.from_link
Feature HasProperty Property (many-to-many)	CDD IsPresentOnProteinOf Feature (many-to-many)	HasProperty.from_link = IsPresentOnProteinOf.to_link
Feature HasProperty Property (many-to-many)	PDB IsProteinForFeature Feature (many-to-many)	HasProperty.from_link = IsProteinForFeature.to_link
Feature HasProperty Property (many-to-many)	SynonymGroup IsSynonymGroupFor Feature (many-to-many)	HasProperty.from_link = IsSynonymGroupFor.to_link
Feature HasProperty Property (many-to-many)	Feature IsTargetOfAnnotation Annotation (one-to-many)	HasProperty.from_link = IsTargetOfAnnotation.from_link
Feature HasProperty Property (many-to-many)	Property	Property.id = HasProperty.to_link
Feature HasRoleInSubsystem Subsystem (many-to-many)	SSCell ContainsFeature Feature (many-to-many)	HasRoleInSubsystem.from_link = ContainsFeature.to_link
Feature HasRoleInSubsystem Subsystem (many-to-many)	Feature	Feature.id = HasRoleInSubsystem.from_link
Feature HasRoleInSubsystem Subsystem (many-to-many)	Genome HasFeature Feature (one-to-many)	HasRoleInSubsystem.from_link = HasFeature.to_link
Feature HasRoleInSubsystem Subsystem (many-to-many)	Subsystem HasGenomeSubset GenomeSubset (one-to-many)	HasRoleInSubsystem.to_link = HasGenomeSubset.from_link
Feature HasRoleInSubsystem Subsystem (many-to-many)	Feature HasProperty Property (many-to-many)	HasRoleInSubsystem.from_link = HasProperty.from_link
Feature HasRoleInSubsystem Subsystem (many-to-many)	Subsystem HasRoleSubset RoleSubset (one-to-many)	HasRoleInSubsystem.to_link = HasRoleSubset.from_link
Feature HasRoleInSubsystem Subsystem (many-to-many)	Subsystem HasSSCell SSCell (one-to-many)	HasRoleInSubsystem.to_link = HasSSCell.from_link
Feature HasRoleInSubsystem Subsystem (many-to-many)	FeatureAlias IsAliasOf Feature (many-to-many)	HasRoleInSubsystem.from_link = IsAliasOf.to_link
Feature HasRoleInSubsystem Subsystem (many-to-many)	Family IsFamilyForFeature Feature (many-to-many)	HasRoleInSubsystem.from_link = IsFamilyForFeature.to_link
Feature HasRoleInSubsystem Subsystem (many-to-many)	Feature IsLocatedIn Contig (many-to-many)	HasRoleInSubsystem.from_link = IsLocatedIn.from_link
Feature HasRoleInSubsystem Subsystem (many-to-many)	CDD IsPresentOnProteinOf Feature (many-to-many)	HasRoleInSubsystem.from_link = IsPresentOnProteinOf.to_link
Feature HasRoleInSubsystem Subsystem (many-to-many)	PDB IsProteinForFeature Feature (many-to-many)	HasRoleInSubsystem.from_link = IsProteinForFeature.to_link
Feature HasRoleInSubsystem Subsystem (many-to-many)	SynonymGroup IsSynonymGroupFor Feature (many-to-many)	HasRoleInSubsystem.from_link = IsSynonymGroupFor.to_link
Feature HasRoleInSubsystem Subsystem (many-to-many)	Feature IsTargetOfAnnotation Annotation (one-to-many)	HasRoleInSubsystem.from_link = IsTargetOfAnnotation.from_link
Feature HasRoleInSubsystem Subsystem (many-to-many)	Role OccursInSubsystem Subsystem (many-to-many)	HasRoleInSubsystem.to_link = OccursInSubsystem.to_link
Feature HasRoleInSubsystem Subsystem (many-to-many)	Genome ParticipatesIn Subsystem (many-to-many)	HasRoleInSubsystem.to_link = ParticipatesIn.to_link
Feature HasRoleInSubsystem Subsystem (many-to-many)	Subsystem	Subsystem.id = HasRoleInSubsystem.to_link
Subsystem HasRoleSubset RoleSubset (one-to-many)	RoleSubset ConsistsOfRoles Role (many-to-many)	HasRoleSubset.to_link = ConsistsOfRoles.from_link
Subsystem HasRoleSubset RoleSubset (one-to-many)	Subsystem HasGenomeSubset GenomeSubset (one-to-many)	HasRoleSubset.from_link = HasGenomeSubset.from_link
Subsystem HasRoleSubset RoleSubset (one-to-many)	Feature HasRoleInSubsystem Subsystem (many-to-many)	HasRoleSubset.from_link = HasRoleInSubsystem.to_link
Subsystem HasRoleSubset RoleSubset (one-to-many)	Subsystem HasSSCell SSCell (one-to-many)	HasRoleSubset.from_link = HasSSCell.from_link
Subsystem HasRoleSubset RoleSubset (one-to-many)	Role OccursInSubsystem Subsystem (many-to-many)	HasRoleSubset.from_link = OccursInSubsystem.to_link
Subsystem HasRoleSubset RoleSubset (one-to-many)	Genome ParticipatesIn Subsystem (many-to-many)	HasRoleSubset.from_link = ParticipatesIn.to_link
Subsystem HasRoleSubset RoleSubset (one-to-many)	RoleSubset	RoleSubset.id = HasRoleSubset.to_link
Subsystem HasRoleSubset RoleSubset (one-to-many)	Subsystem	Subsystem.id = HasRoleSubset.from_link
Subsystem HasSSCell SSCell (one-to-many)	SSCell ContainsFeature Feature (many-to-many)	HasSSCell.to_link = ContainsFeature.from_link
Subsystem HasSSCell SSCell (one-to-many)	Subsystem HasGenomeSubset GenomeSubset (one-to-many)	HasSSCell.from_link = HasGenomeSubset.from_link
Subsystem HasSSCell SSCell (one-to-many)	Feature HasRoleInSubsystem Subsystem (many-to-many)	HasSSCell.from_link = HasRoleInSubsystem.to_link
Subsystem HasSSCell SSCell (one-to-many)	Subsystem HasRoleSubset RoleSubset (one-to-many)	HasSSCell.from_link = HasRoleSubset.from_link
Subsystem HasSSCell SSCell (one-to-many)	Genome IsGenomeOf SSCell (one-to-many)	HasSSCell.to_link = IsGenomeOf.to_link
Subsystem HasSSCell SSCell (one-to-many)	Role IsRoleOf SSCell (one-to-many)	HasSSCell.to_link = IsRoleOf.to_link
Subsystem HasSSCell SSCell (one-to-many)	Role OccursInSubsystem Subsystem (many-to-many)	HasSSCell.from_link = OccursInSubsystem.to_link
Subsystem HasSSCell SSCell (one-to-many)	Genome ParticipatesIn Subsystem (many-to-many)	HasSSCell.from_link = ParticipatesIn.to_link
Subsystem HasSSCell SSCell (one-to-many)	SSCell	SSCell.id = HasSSCell.to_link
Subsystem HasSSCell SSCell (one-to-many)	Subsystem	Subsystem.id = HasSSCell.from_link
Compound IsAComponentOf Reaction (many-to-many)	Role Catalyzes Reaction (many-to-many)	IsAComponentOf.to_link = Catalyzes.to_link
Compound IsAComponentOf Reaction (many-to-many)	Compound	Compound.id = IsAComponentOf.from_link
Compound IsAComponentOf Reaction (many-to-many)	Compound HasCompoundName CompoundName (many-to-many)	IsAComponentOf.from_link = HasCompoundName.from_link
Compound IsAComponentOf Reaction (many-to-many)	Compound IsIdentifiedByCAS CompoundCAS (many-to-many)	IsAComponentOf.from_link = IsIdentifiedByCAS.from_link
Compound IsAComponentOf Reaction (many-to-many)	Reaction	Reaction.id = IsAComponentOf.to_link
FeatureAlias IsAliasOf Feature (many-to-many)	SSCell ContainsFeature Feature (many-to-many)	IsAliasOf.to_link = ContainsFeature.to_link
FeatureAlias IsAliasOf Feature (many-to-many)	Feature	Feature.id = IsAliasOf.to_link
FeatureAlias IsAliasOf Feature (many-to-many)	FeatureAlias	FeatureAlias.id = IsAliasOf.from_link
FeatureAlias IsAliasOf Feature (many-to-many)	Genome HasFeature Feature (one-to-many)	IsAliasOf.to_link = HasFeature.to_link
FeatureAlias IsAliasOf Feature (many-to-many)	Feature HasProperty Property (many-to-many)	IsAliasOf.to_link = HasProperty.from_link
FeatureAlias IsAliasOf Feature (many-to-many)	Feature HasRoleInSubsystem Subsystem (many-to-many)	IsAliasOf.to_link = HasRoleInSubsystem.from_link
FeatureAlias IsAliasOf Feature (many-to-many)	Family IsFamilyForFeature Feature (many-to-many)	IsAliasOf.to_link = IsFamilyForFeature.to_link
FeatureAlias IsAliasOf Feature (many-to-many)	Feature IsLocatedIn Contig (many-to-many)	IsAliasOf.to_link = IsLocatedIn.from_link
FeatureAlias IsAliasOf Feature (many-to-many)	CDD IsPresentOnProteinOf Feature (many-to-many)	IsAliasOf.to_link = IsPresentOnProteinOf.to_link
FeatureAlias IsAliasOf Feature (many-to-many)	PDB IsProteinForFeature Feature (many-to-many)	IsAliasOf.to_link = IsProteinForFeature.to_link
FeatureAlias IsAliasOf Feature (many-to-many)	SynonymGroup IsSynonymGroupFor Feature (many-to-many)	IsAliasOf.to_link = IsSynonymGroupFor.to_link
FeatureAlias IsAliasOf Feature (many-to-many)	Feature IsTargetOfAnnotation Annotation (one-to-many)	IsAliasOf.to_link = IsTargetOfAnnotation.from_link
Family IsFamilyForFeature Feature (many-to-many)	SSCell ContainsFeature Feature (many-to-many)	IsFamilyForFeature.to_link = ContainsFeature.to_link
Family IsFamilyForFeature Feature (many-to-many)	Family	Family.id = IsFamilyForFeature.from_link
Family IsFamilyForFeature Feature (many-to-many)	Feature	Feature.id = IsFamilyForFeature.to_link
Family IsFamilyForFeature Feature (many-to-many)	Genome HasFeature Feature (one-to-many)	IsFamilyForFeature.to_link = HasFeature.to_link
Family IsFamilyForFeature Feature (many-to-many)	Feature HasProperty Property (many-to-many)	IsFamilyForFeature.to_link = HasProperty.from_link
Family IsFamilyForFeature Feature (many-to-many)	Feature HasRoleInSubsystem Subsystem (many-to-many)	IsFamilyForFeature.to_link = HasRoleInSubsystem.from_link
Family IsFamilyForFeature Feature (many-to-many)	FeatureAlias IsAliasOf Feature (many-to-many)	IsFamilyForFeature.to_link = IsAliasOf.to_link
Family IsFamilyForFeature Feature (many-to-many)	Feature IsLocatedIn Contig (many-to-many)	IsFamilyForFeature.to_link = IsLocatedIn.from_link
Family IsFamilyForFeature Feature (many-to-many)	CDD IsPresentOnProteinOf Feature (many-to-many)	IsFamilyForFeature.to_link = IsPresentOnProteinOf.to_link
Family IsFamilyForFeature Feature (many-to-many)	PDB IsProteinForFeature Feature (many-to-many)	IsFamilyForFeature.to_link = IsProteinForFeature.to_link
Family IsFamilyForFeature Feature (many-to-many)	SynonymGroup IsSynonymGroupFor Feature (many-to-many)	IsFamilyForFeature.to_link = IsSynonymGroupFor.to_link
Family IsFamilyForFeature Feature (many-to-many)	Feature IsTargetOfAnnotation Annotation (one-to-many)	IsFamilyForFeature.to_link = IsTargetOfAnnotation.from_link
Genome IsGenomeOf SSCell (one-to-many)	Genome ComesFrom Source (many-to-many)	IsGenomeOf.from_link = ComesFrom.from_link
Genome IsGenomeOf SSCell (one-to-many)	GenomeSubset ConsistsOfGenomes Genome (many-to-many)	IsGenomeOf.from_link = ConsistsOfGenomes.to_link
Genome IsGenomeOf SSCell (one-to-many)	SSCell ContainsFeature Feature (many-to-many)	IsGenomeOf.to_link = ContainsFeature.from_link
Genome IsGenomeOf SSCell (one-to-many)	Genome	Genome.id = IsGenomeOf.from_link
Genome IsGenomeOf SSCell (one-to-many)	Genome HasContig Contig (one-to-many)	IsGenomeOf.from_link = HasContig.from_link
Genome IsGenomeOf SSCell (one-to-many)	Genome HasFeature Feature (one-to-many)	IsGenomeOf.from_link = HasFeature.from_link
Genome IsGenomeOf SSCell (one-to-many)	Subsystem HasSSCell SSCell (one-to-many)	IsGenomeOf.to_link = HasSSCell.to_link
Genome IsGenomeOf SSCell (one-to-many)	Role IsRoleOf SSCell (one-to-many)	IsGenomeOf.to_link = IsRoleOf.to_link
Genome IsGenomeOf SSCell (one-to-many)	Genome ParticipatesIn Subsystem (many-to-many)	IsGenomeOf.from_link = ParticipatesIn.from_link
Genome IsGenomeOf SSCell (one-to-many)	SSCell	SSCell.id = IsGenomeOf.to_link
Compound IsIdentifiedByCAS CompoundCAS (many-to-many)	Compound	Compound.id = IsIdentifiedByCAS.from_link
Compound IsIdentifiedByCAS CompoundCAS (many-to-many)	CompoundCAS	CompoundCAS.id = IsIdentifiedByCAS.to_link
Compound IsIdentifiedByCAS CompoundCAS (many-to-many)	Compound HasCompoundName CompoundName (many-to-many)	IsIdentifiedByCAS.from_link = HasCompoundName.from_link
Compound IsIdentifiedByCAS CompoundCAS (many-to-many)	Compound IsAComponentOf Reaction (many-to-many)	IsIdentifiedByCAS.from_link = IsAComponentOf.from_link
Role IsIdentifiedByEC RoleEC (many-to-many)	Role Catalyzes Reaction (many-to-many)	IsIdentifiedByEC.from_link = Catalyzes.from_link
Role IsIdentifiedByEC RoleEC (many-to-many)	RoleSubset ConsistsOfRoles Role (many-to-many)	IsIdentifiedByEC.from_link = ConsistsOfRoles.to_link
Role IsIdentifiedByEC RoleEC (many-to-many)	Role IsRoleOf SSCell (one-to-many)	IsIdentifiedByEC.from_link = IsRoleOf.from_link
Role IsIdentifiedByEC RoleEC (many-to-many)	Role OccursInSubsystem Subsystem (many-to-many)	IsIdentifiedByEC.from_link = OccursInSubsystem.from_link
Role IsIdentifiedByEC RoleEC (many-to-many)	Role	Role.id = IsIdentifiedByEC.from_link
Role IsIdentifiedByEC RoleEC (many-to-many)	RoleEC	RoleEC.id = IsIdentifiedByEC.to_link
Role IsIdentifiedByEC RoleEC (many-to-many)	Role RoleOccursIn Diagram (many-to-many)	IsIdentifiedByEC.from_link = RoleOccursIn.from_link
Feature IsLocatedIn Contig (many-to-many)	SSCell ContainsFeature Feature (many-to-many)	IsLocatedIn.from_link = ContainsFeature.to_link
Feature IsLocatedIn Contig (many-to-many)	Contig	Contig.id = IsLocatedIn.to_link
Feature IsLocatedIn Contig (many-to-many)	Feature	Feature.id = IsLocatedIn.from_link
Feature IsLocatedIn Contig (many-to-many)	Genome HasContig Contig (one-to-many)	IsLocatedIn.to_link = HasContig.to_link
Feature IsLocatedIn Contig (many-to-many)	Genome HasFeature Feature (one-to-many)	IsLocatedIn.from_link = HasFeature.to_link
Feature IsLocatedIn Contig (many-to-many)	Feature HasProperty Property (many-to-many)	IsLocatedIn.from_link = HasProperty.from_link
Feature IsLocatedIn Contig (many-to-many)	Feature HasRoleInSubsystem Subsystem (many-to-many)	IsLocatedIn.from_link = HasRoleInSubsystem.from_link
Feature IsLocatedIn Contig (many-to-many)	FeatureAlias IsAliasOf Feature (many-to-many)	IsLocatedIn.from_link = IsAliasOf.to_link
Feature IsLocatedIn Contig (many-to-many)	Family IsFamilyForFeature Feature (many-to-many)	IsLocatedIn.from_link = IsFamilyForFeature.to_link
Feature IsLocatedIn Contig (many-to-many)	Contig IsMadeUpOf Sequence (one-to-many)	IsLocatedIn.to_link = IsMadeUpOf.from_link
Feature IsLocatedIn Contig (many-to-many)	CDD IsPresentOnProteinOf Feature (many-to-many)	IsLocatedIn.from_link = IsPresentOnProteinOf.to_link
Feature IsLocatedIn Contig (many-to-many)	PDB IsProteinForFeature Feature (many-to-many)	IsLocatedIn.from_link = IsProteinForFeature.to_link
Feature IsLocatedIn Contig (many-to-many)	SynonymGroup IsSynonymGroupFor Feature (many-to-many)	IsLocatedIn.from_link = IsSynonymGroupFor.to_link
Feature IsLocatedIn Contig (many-to-many)	Feature IsTargetOfAnnotation Annotation (one-to-many)	IsLocatedIn.from_link = IsTargetOfAnnotation.from_link
Contig IsMadeUpOf Sequence (one-to-many)	Contig	Contig.id = IsMadeUpOf.from_link
Contig IsMadeUpOf Sequence (one-to-many)	Genome HasContig Contig (one-to-many)	IsMadeUpOf.from_link = HasContig.to_link
Contig IsMadeUpOf Sequence (one-to-many)	Feature IsLocatedIn Contig (many-to-many)	IsMadeUpOf.from_link = IsLocatedIn.to_link
Contig IsMadeUpOf Sequence (one-to-many)	Sequence	Sequence.id = IsMadeUpOf.to_link
CDD IsPresentOnProteinOf Feature (many-to-many)	CDD	CDD.id = IsPresentOnProteinOf.from_link
CDD IsPresentOnProteinOf Feature (many-to-many)	SSCell ContainsFeature Feature (many-to-many)	IsPresentOnProteinOf.to_link = ContainsFeature.to_link
CDD IsPresentOnProteinOf Feature (many-to-many)	Feature	Feature.id = IsPresentOnProteinOf.to_link
CDD IsPresentOnProteinOf Feature (many-to-many)	Genome HasFeature Feature (one-to-many)	IsPresentOnProteinOf.to_link = HasFeature.to_link
CDD IsPresentOnProteinOf Feature (many-to-many)	Feature HasProperty Property (many-to-many)	IsPresentOnProteinOf.to_link = HasProperty.from_link
CDD IsPresentOnProteinOf Feature (many-to-many)	Feature HasRoleInSubsystem Subsystem (many-to-many)	IsPresentOnProteinOf.to_link = HasRoleInSubsystem.from_link
CDD IsPresentOnProteinOf Feature (many-to-many)	FeatureAlias IsAliasOf Feature (many-to-many)	IsPresentOnProteinOf.to_link = IsAliasOf.to_link
CDD IsPresentOnProteinOf Feature (many-to-many)	Family IsFamilyForFeature Feature (many-to-many)	IsPresentOnProteinOf.to_link = IsFamilyForFeature.to_link
CDD IsPresentOnProteinOf Feature (many-to-many)	Feature IsLocatedIn Contig (many-to-many)	IsPresentOnProteinOf.to_link = IsLocatedIn.from_link
CDD IsPresentOnProteinOf Feature (many-to-many)	PDB IsProteinForFeature Feature (many-to-many)	IsPresentOnProteinOf.to_link = IsProteinForFeature.to_link
CDD IsPresentOnProteinOf Feature (many-to-many)	SynonymGroup IsSynonymGroupFor Feature (many-to-many)	IsPresentOnProteinOf.to_link = IsSynonymGroupFor.to_link
CDD IsPresentOnProteinOf Feature (many-to-many)	Feature IsTargetOfAnnotation Annotation (one-to-many)	IsPresentOnProteinOf.to_link = IsTargetOfAnnotation.from_link
PDB IsProteinForFeature Feature (many-to-many)	SSCell ContainsFeature Feature (many-to-many)	IsProteinForFeature.to_link = ContainsFeature.to_link
PDB IsProteinForFeature Feature (many-to-many)	PDB DocksWith Ligand (many-to-many)	IsProteinForFeature.from_link = DocksWith.from_link
PDB IsProteinForFeature Feature (many-to-many)	Feature	Feature.id = IsProteinForFeature.to_link
PDB IsProteinForFeature Feature (many-to-many)	Genome HasFeature Feature (one-to-many)	IsProteinForFeature.to_link = HasFeature.to_link
PDB IsProteinForFeature Feature (many-to-many)	Feature HasProperty Property (many-to-many)	IsProteinForFeature.to_link = HasProperty.from_link
PDB IsProteinForFeature Feature (many-to-many)	Feature HasRoleInSubsystem Subsystem (many-to-many)	IsProteinForFeature.to_link = HasRoleInSubsystem.from_link
PDB IsProteinForFeature Feature (many-to-many)	FeatureAlias IsAliasOf Feature (many-to-many)	IsProteinForFeature.to_link = IsAliasOf.to_link
PDB IsProteinForFeature Feature (many-to-many)	Family IsFamilyForFeature Feature (many-to-many)	IsProteinForFeature.to_link = IsFamilyForFeature.to_link
PDB IsProteinForFeature Feature (many-to-many)	Feature IsLocatedIn Contig (many-to-many)	IsProteinForFeature.to_link = IsLocatedIn.from_link
PDB IsProteinForFeature Feature (many-to-many)	CDD IsPresentOnProteinOf Feature (many-to-many)