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
- Relationships
- Role Catalyzes Reaction (many-to-many)
- Genome ComesFrom Source (many-to-many)
- GenomeSubset ConsistsOfGenomes Genome (many-to-many)
- RoleSubset ConsistsOfRoles Role (many-to-many)
- SSCell ContainsFeature Feature (many-to-many)
- PDB DocksWith Ligand (many-to-many)
- Genome HasContig Contig (one-to-many)
- Genome HasFeature Feature (one-to-many)
- Subsystem HasGenomeSubset GenomeSubset (one-to-many)
- Feature HasProperty Property (many-to-many)
- Feature HasRoleInSubsystem Subsystem (many-to-many)
- Subsystem HasRoleSubset RoleSubset (one-to-many)
- Subsystem HasSSCell SSCell (one-to-many)
- Compound IsAComponentOf Reaction (many-to-many)
- Coupling IsEvidencedBy PCH (one-to-many)
- Family IsFamilyForFeature Feature (many-to-many)
- Genome IsGenomeOf SSCell (one-to-many)
- Feature IsLocatedIn Contig (many-to-many)
- Contig IsMadeUpOf Sequence (one-to-many)
- PDB IsProteinForFeature Feature (many-to-many)
- Role IsRoleOf SSCell (one-to-many)
- SynonymGroup IsSynonymGroupFor Feature (one-to-many)
- Feature IsTargetOfAnnotation Annotation (one-to-many)
- SproutUser IsTrustedBy SproutUser (many-to-many)
- SproutUser MadeAnnotation Annotation (one-to-many)
- Role OccursInSubsystem Subsystem (many-to-many)
- Genome ParticipatesIn Subsystem (many-to-many)
- Feature ParticipatesInCoupling Coupling (many-to-many)
- Role RoleOccursIn Diagram (many-to-many)
- PCH UsesAsEvidence Feature (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
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
Relations for Compound
| Compound | ||
| Field | Type | Description |
|---|---|---|
| id | name-string | Unique identifier for this Compound. |
| label | name-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 | ||
| Field | Type | Description |
|---|---|---|
| id | name-string | Unique identifier for this Compound. |
| cas-id | name-string | Chemical Abstract Service ID for this compound (optional). |
- Index idx0
- This index allows the user to find the compound corresponding to the specified CAS ID.
- cas-id
- Index idx1
- id
| CompoundName | ||
| Field | Type | Description |
|---|---|---|
| id | name-string | Unique identifier for this Compound. |
| name | name-string | Descriptive name for the compound. A compound may have several names. |
| name-priority | int | Priority of a compound name. The name with the loweset priority is the main name of this compound. |
- Index idx0
- This index allows the user to find the compound corresponding to the specified name.
- name
- Index idx1
- This index allows the user to access the compound names in priority order.
- id, name-priority
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
Coupling
A coupling is a relationship between two features. The features are physically close on the contig, and there is evidence that they generally belong together. The key of this entity is formed by combining the coupled feature IDs with a space.
Relationships for Coupling
Relations for Coupling
| Coupling | ||
| Field | Type | Description |
|---|---|---|
| id | id-string | Unique identifier for this Coupling. |
| score | int | A number based on the set of PCHs (pairs of close homologs). A PCH indicates that two genes near each other on one genome are very similar to genes near each other on another genome. The score only counts PCHs for which the genomes are very different. (In other words, we have a pairing that persists between different organisms.) A higher score implies a stronger meaning to the clustering. |
- Index idx0 (unique)
- Primary index for Coupling.
- 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
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
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)
- Family IsFamilyForFeature Feature (many-to-many)
- Feature IsLocatedIn Contig (many-to-many)
- PDB IsProteinForFeature Feature (many-to-many)
- SynonymGroup IsSynonymGroupFor Feature (one-to-many)
- Feature IsTargetOfAnnotation Annotation (one-to-many)
- Feature ParticipatesInCoupling Coupling (many-to-many)
- PCH UsesAsEvidence Feature (many-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) |
| feature-type | 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. |
- Index idx0 (unique)
- Primary index for Feature.
- id
| FeatureAlias | ||
| Field | Type | Description |
|---|---|---|
| id | id-string | Unique identifier for this Feature. |
| alias | medium-string | Alternative name for this feature. A feature can have many aliases. |
- Index idx0
- This index allows the user to find the feature corresponding to the specified alias name.
- alias
- Index idx1
- 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 reflect 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
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
| GenomeGroups | ||
| Field | Type | Description |
|---|---|---|
| id | name-string | Unique identifier for this Genome. |
| group-name | name-string | The group identifies a special grouping of organisms that would be displayed on a particular page or of particular interest to a research group or web site. A single genome can belong to multiple such groups or none at all. |
- Index idx0
- 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
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
PCH
A PCH (physically close homolog) connects a clustering (which is a pair of physically close features on a contig) to a second pair of physically close features that are similar to the first. Essentially, the PCH is a relationship between two clusterings in which the first clustering's features are similar to the second clustering's features. The simplest model for this would be to simply relate clusterings to each other; however, not all physically close pairs qualify as clusterings, so we relate a clustering to a pair of features. The key a unique ID number.
Relationships for PCH
Relations for PCH
| PCH | ||
| Field | Type | Description |
|---|---|---|
| id | counter | Unique identifier for this PCH. |
| used | boolean | TRUE if this PCH is used in scoring the attached clustering, else FALSE. If a clustering has a PCH for a particular genome and many similar genomes are present, then a PCH will probably exist for the similar genomes as well. When this happens, only one of the PCHs will be scored: the others are considered duplicates of the same evidence. |
- Index idx0 (unique)
- Primary index for PCH.
- 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
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
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
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 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. |
| abbr | name-string | Abbreviated name for the role, generally non-unique, but useful in column headings for HTML tables. |
- Index idx0 (unique)
- Primary index for Role.
- id
| RoleEC | ||
| Field | Type | Description |
|---|---|---|
| id | string | Unique identifier for this Role. |
| EC | string | EC code for this role. |
- Index idx0
- This index allows the user to find the role corresponding to an EC number.
- EC
- Index idx1
- 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
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
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
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
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
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
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
Coupling IsEvidencedBy PCH
Each Coupling relates to multiple PCHs.
This relationship connects a functional coupling to the physically close homologs (PCHs) which affirm that the coupling is meaningful.
| IsEvidencedBy | ||
| Field | Type | Description |
|---|---|---|
| from-link | id-string | id of the source Coupling. |
| to-link | counter | id of the target PCH. |
- Index idxFrom
- from-link
- Index idxTo (unique)
- 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
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
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.
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 (unique)
- 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. |
| 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
Feature ParticipatesInCoupling Coupling
Each Feature relates to multiple Couplings. Each Coupling relates to multiple Features.
This relationship connects a feature to all the functional couplings in which it participates. A functional coupling is a recognition of the fact that the features are close to each other on a chromosome, and similar features in other genomes also tend to be close.
| ParticipatesInCoupling | ||
| Field | Type | Description |
|---|---|---|
| from-link | id-string | id of the source Feature. |
| to-link | id-string | id of the target Coupling. |
| pos | int | Ordinal position of the feature in the coupling. Currently, this is either "1" or "2". |
- Index idxFrom
- from-link
- Index idxTo
- This index enables the application to view the features of a coupling in the proper order. The order influences the way the PCHs are examined.
- to-link, pos
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
PCH UsesAsEvidence Feature
Each PCH relates to multiple Features. Each Feature relates to multiple PCHs.
This relationship connects a PCH to the features that represent its evidence. Each PCH is connected to a parent coupling that relates two features on a specific genome. The PCH's evidence that the parent coupling is functional is the existence of two physically close features on a different genome that correspond to the features in the coupling. Those features are found on the far side of this relationship.
| UsesAsEvidence | ||
| Field | Type | Description |
|---|---|---|
| from-link | counter | id of the source PCH. |
| to-link | id-string | id of the target Feature. |
| pos | int | Ordinal position of the feature in the coupling that corresponds to our target feature. There is a one-to-one correspondence between the features connected to the PCH by this relationship and the features connected to the PCH's parent coupling. The ordinal position is used to decode that relationship. Currently, this field is either "1" or "2". |
- Index idxFrom
- This index enables the application to view the features of a PCH in the proper order.
- from-link, pos
- 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 |
| 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 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 IsAComponentOf Reaction (many-to-many) | Compound.id = IsAComponentOf.from_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 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) | 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) | 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 (one-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) | Feature ParticipatesInCoupling Coupling (many-to-many) | ContainsFeature.to_link = ParticipatesInCoupling.from_link |
| SSCell ContainsFeature Feature (many-to-many) | SSCell | SSCell.id = ContainsFeature.from_link |
| SSCell ContainsFeature Feature (many-to-many) | PCH UsesAsEvidence Feature (many-to-many) | ContainsFeature.to_link = UsesAsEvidence.to_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 |
| Coupling | Coupling IsEvidencedBy PCH (one-to-many) | Coupling.id = IsEvidencedBy.from_link |
| Coupling | Feature ParticipatesInCoupling Coupling (many-to-many) | Coupling.id = ParticipatesInCoupling.to_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 | Family IsFamilyForFeature Feature (many-to-many) | Feature.id = IsFamilyForFeature.to_link |
| Feature | Feature IsLocatedIn Contig (many-to-many) | Feature.id = IsLocatedIn.from_link |
| Feature | PDB IsProteinForFeature Feature (many-to-many) | Feature.id = IsProteinForFeature.to_link |
| Feature | SynonymGroup IsSynonymGroupFor Feature (one-to-many) | Feature.id = IsSynonymGroupFor.to_link |
| Feature | Feature IsTargetOfAnnotation Annotation (one-to-many) | Feature.id = IsTargetOfAnnotation.from_link |
| Feature | Feature ParticipatesInCoupling Coupling (many-to-many) | Feature.id = ParticipatesInCoupling.from_link |
| Feature | PCH UsesAsEvidence Feature (many-to-many) | Feature.id = UsesAsEvidence.to_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 |
| 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) | 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) | PDB IsProteinForFeature Feature (many-to-many) | HasFeature.to_link = IsProteinForFeature.to_link |
| Genome HasFeature Feature (one-to-many) | SynonymGroup IsSynonymGroupFor Feature (one-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 |
| Genome HasFeature Feature (one-to-many) | Feature ParticipatesInCoupling Coupling (many-to-many) | HasFeature.to_link = ParticipatesInCoupling.from_link |
| Genome HasFeature Feature (one-to-many) | PCH UsesAsEvidence Feature (many-to-many) | HasFeature.to_link = UsesAsEvidence.to_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) | 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) | PDB IsProteinForFeature Feature (many-to-many) | HasProperty.from_link = IsProteinForFeature.to_link |
| Feature HasProperty Property (many-to-many) | SynonymGroup IsSynonymGroupFor Feature (one-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) | Feature ParticipatesInCoupling Coupling (many-to-many) | HasProperty.from_link = ParticipatesInCoupling.from_link |
| Feature HasProperty Property (many-to-many) | Property | Property.id = HasProperty.to_link |
| Feature HasProperty Property (many-to-many) | PCH UsesAsEvidence Feature (many-to-many) | HasProperty.from_link = UsesAsEvidence.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) | 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) | PDB IsProteinForFeature Feature (many-to-many) | HasRoleInSubsystem.from_link = IsProteinForFeature.to_link |
| Feature HasRoleInSubsystem Subsystem (many-to-many) | SynonymGroup IsSynonymGroupFor Feature (one-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) | Feature ParticipatesInCoupling Coupling (many-to-many) | HasRoleInSubsystem.from_link = ParticipatesInCoupling.from_link |
| Feature HasRoleInSubsystem Subsystem (many-to-many) | Subsystem | Subsystem.id = HasRoleInSubsystem.to_link |
| Feature HasRoleInSubsystem Subsystem (many-to-many) | PCH UsesAsEvidence Feature (many-to-many) | HasRoleInSubsystem.from_link = UsesAsEvidence.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) | Reaction | Reaction.id = IsAComponentOf.to_link |
| Coupling IsEvidencedBy PCH (one-to-many) | Coupling | Coupling.id = IsEvidencedBy.from_link |
| Coupling IsEvidencedBy PCH (one-to-many) | PCH | PCH.id = IsEvidencedBy.to_link |
| Coupling IsEvidencedBy PCH (one-to-many) | Feature ParticipatesInCoupling Coupling (many-to-many) | IsEvidencedBy.from_link = ParticipatesInCoupling.to_link |
| Coupling IsEvidencedBy PCH (one-to-many) | PCH UsesAsEvidence Feature (many-to-many) | IsEvidencedBy.to_link = UsesAsEvidence.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) | Feature IsLocatedIn Contig (many-to-many) | IsFamilyForFeature.to_link = IsLocatedIn.from_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 (one-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 |
| Family IsFamilyForFeature Feature (many-to-many) | Feature ParticipatesInCoupling Coupling (many-to-many) | IsFamilyForFeature.to_link = ParticipatesInCoupling.from_link |
| Family IsFamilyForFeature Feature (many-to-many) | PCH UsesAsEvidence Feature (many-to-many) | IsFamilyForFeature.to_link = UsesAsEvidence.to_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 |
| 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) | 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) | PDB IsProteinForFeature Feature (many-to-many) | IsLocatedIn.from_link = IsProteinForFeature.to_link |
| Feature IsLocatedIn Contig (many-to-many) | SynonymGroup IsSynonymGroupFor Feature (one-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 |
| Feature IsLocatedIn Contig (many-to-many) | Feature ParticipatesInCoupling Coupling (many-to-many) | IsLocatedIn.from_link = ParticipatesInCoupling.from_link |
| Feature IsLocatedIn Contig (many-to-many) | PCH UsesAsEvidence Feature (many-to-many) | IsLocatedIn.from_link = UsesAsEvidence.to_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 |
| 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) | 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) | SynonymGroup IsSynonymGroupFor Feature (one-to-many) | IsProteinForFeature.to_link = IsSynonymGroupFor.to_link |
| PDB IsProteinForFeature Feature (many-to-many) | Feature IsTargetOfAnnotation Annotation (one-to-many) | IsProteinForFeature.to_link = IsTargetOfAnnotation.from_link |
| PDB IsProteinForFeature Feature (many-to-many) | PDB | PDB.id = IsProteinForFeature.from_link |
| PDB IsProteinForFeature Feature (many-to-many) | Feature ParticipatesInCoupling Coupling (many-to-many) | IsProteinForFeature.to_link = ParticipatesInCoupling.from_link |
| PDB IsProteinForFeature Feature (many-to-many) | PCH UsesAsEvidence Feature (many-to-many) | IsProteinForFeature.to_link = UsesAsEvidence.to_link |
| Role IsRoleOf SSCell (one-to-many) | Role Catalyzes Reaction (many-to-many) | IsRoleOf.from_link = Catalyzes.from_link |
| Role IsRoleOf SSCell (one-to-many) | RoleSubset ConsistsOfRoles Role (many-to-many) | IsRoleOf.from_link = ConsistsOfRoles.to_link |
| Role IsRoleOf SSCell (one-to-many) | SSCell ContainsFeature Feature (many-to-many) | IsRoleOf.to_link = ContainsFeature.from_link |
| Role IsRoleOf SSCell (one-to-many) | Subsystem HasSSCell SSCell (one-to-many) | IsRoleOf.to_link = HasSSCell.to_link |
| Role IsRoleOf SSCell (one-to-many) | Genome IsGenomeOf SSCell (one-to-many) | IsRoleOf.to_link = IsGenomeOf.to_link |
| Role IsRoleOf SSCell (one-to-many) | Role OccursInSubsystem Subsystem (many-to-many) | IsRoleOf.from_link = OccursInSubsystem.from_link |
| Role IsRoleOf SSCell (one-to-many) | Role | Role.id = IsRoleOf.from_link |
| Role IsRoleOf SSCell (one-to-many) | Role RoleOccursIn Diagram (many-to-many) | IsRoleOf.from_link = RoleOccursIn.from_link |
| Role IsRoleOf SSCell (one-to-many) | SSCell | SSCell.id = IsRoleOf.to_link |
| SynonymGroup IsSynonymGroupFor Feature (one-to-many) | SSCell ContainsFeature Feature (many-to-many) | IsSynonymGroupFor.to_link = ContainsFeature.to_link |
| SynonymGroup IsSynonymGroupFor Feature (one-to-many) | Feature | Feature.id = IsSynonymGroupFor.to_link |
| SynonymGroup IsSynonymGroupFor Feature (one-to-many) | Genome HasFeature Feature (one-to-many) | IsSynonymGroupFor.to_link = HasFeature.to_link |
| SynonymGroup IsSynonymGroupFor Feature (one-to-many) | Feature HasProperty Property (many-to-many) | IsSynonymGroupFor.to_link = HasProperty.from_link |
| SynonymGroup IsSynonymGroupFor Feature (one-to-many) | Feature HasRoleInSubsystem Subsystem (many-to-many) | IsSynonymGroupFor.to_link = HasRoleInSubsystem.from_link |
| SynonymGroup IsSynonymGroupFor Feature (one-to-many) | Family IsFamilyForFeature Feature (many-to-many) | IsSynonymGroupFor.to_link = IsFamilyForFeature.to_link |
| SynonymGroup IsSynonymGroupFor Feature (one-to-many) | Feature IsLocatedIn Contig (many-to-many) | IsSynonymGroupFor.to_link = IsLocatedIn.from_link |
| SynonymGroup IsSynonymGroupFor Feature (one-to-many) | PDB IsProteinForFeature Feature (many-to-many) | IsSynonymGroupFor.to_link = IsProteinForFeature.to_link |
| SynonymGroup IsSynonymGroupFor Feature (one-to-many) | Feature IsTargetOfAnnotation Annotation (one-to-many) | IsSynonymGroupFor.to_link = IsTargetOfAnnotation.from_link |
| SynonymGroup IsSynonymGroupFor Feature (one-to-many) | Feature ParticipatesInCoupling Coupling (many-to-many) | IsSynonymGroupFor.to_link = ParticipatesInCoupling.from_link |
| SynonymGroup IsSynonymGroupFor Feature (one-to-many) | SynonymGroup | SynonymGroup.id = IsSynonymGroupFor.from_link |
| SynonymGroup IsSynonymGroupFor Feature (one-to-many) | PCH UsesAsEvidence Feature (many-to-many) | IsSynonymGroupFor.to_link = UsesAsEvidence.to_link |
| Feature IsTargetOfAnnotation Annotation (one-to-many) | Annotation | Annotation.id = IsTargetOfAnnotation.to_link |
| Feature IsTargetOfAnnotation Annotation (one-to-many) | SSCell ContainsFeature Feature (many-to-many) | IsTargetOfAnnotation.from_link = ContainsFeature.to_link |
| Feature IsTargetOfAnnotation Annotation (one-to-many) | Feature | Feature.id = IsTargetOfAnnotation.from_link |
| Feature IsTargetOfAnnotation Annotation (one-to-many) | Genome HasFeature Feature (one-to-many) | IsTargetOfAnnotation.from_link = HasFeature.to_link |
| Feature IsTargetOfAnnotation Annotation (one-to-many) | Feature HasProperty Property (many-to-many) | IsTargetOfAnnotation.from_link = HasProperty.from_link |
| Feature IsTargetOfAnnotation Annotation (one-to-many) | Feature HasRoleInSubsystem Subsystem (many-to-many) | IsTargetOfAnnotation.from_link = HasRoleInSubsystem.from_link |
| Feature IsTargetOfAnnotation Annotation (one-to-many) | Family IsFamilyForFeature Feature (many-to-many) | IsTargetOfAnnotation.from_link = IsFamilyForFeature.to_link |
| Feature IsTargetOfAnnotation Annotation (one-to-many) | Feature IsLocatedIn Contig (many-to-many) | IsTargetOfAnnotation.from_link = IsLocatedIn.from_link |
| Feature IsTargetOfAnnotation Annotation (one-to-many) | PDB IsProteinForFeature Feature (many-to-many) | IsTargetOfAnnotation.from_link = IsProteinForFeature.to_link |
| Feature IsTargetOfAnnotation Annotation (one-to-many) | SynonymGroup IsSynonymGroupFor Feature (one-to-many) | IsTargetOfAnnotation.from_link = IsSynonymGroupFor.to_link |
| Feature IsTargetOfAnnotation Annotation (one-to-many) | SproutUser MadeAnnotation Annotation (one-to-many) | IsTargetOfAnnotation.to_link = MadeAnnotation.to_link |
| Feature IsTargetOfAnnotation Annotation (one-to-many) | Feature ParticipatesInCoupling Coupling (many-to-many) | IsTargetOfAnnotation.from_link = ParticipatesInCoupling.from_link |
| Feature IsTargetOfAnnotation Annotation (one-to-many) | PCH UsesAsEvidence Feature (many-to-many) | IsTargetOfAnnotation.from_link = UsesAsEvidence.to_link |
| SproutUser IsTrustedBy SproutUser (many-to-many) | SproutUser MadeAnnotation Annotation (one-to-many) | IsTrustedBy.to_link = MadeAnnotation.from_link |
| SproutUser IsTrustedBy SproutUser (many-to-many) | SproutUser | IsTrustedBy.to_link = SproutUser.id |
| Ligand | PDB DocksWith Ligand (many-to-many) | Ligand.id = DocksWith.to_link |
| SproutUser MadeAnnotation Annotation (one-to-many) | Annotation | Annotation.id = MadeAnnotation.to_link |
| SproutUser MadeAnnotation Annotation (one-to-many) | Feature IsTargetOfAnnotation Annotation (one-to-many) | MadeAnnotation.to_link = IsTargetOfAnnotation.to_lin |