SequenceOntology

java.lang.Object
- org.sbolstandard.core2.SequenceOntology

```
public class SequenceOntology
extends Object
```
This class provides methods for accessing Sequence Ontology (SO) terms and querying about their relationships.

Version:

2.1

Author:

Zhen Zhang, Tramy Nguyen, Nicholas Roehner, Chris Myers

Field Summary

Fields
Modifier and Type	Field and Description
`static URI`	`CDS` A contiguous sequence which begins with, and includes, a start codon, and ends with, and includes, a stop codon (SO:0000316).
`static URI`	`CIRCULAR` A quality of a nucleotide polymer that has no terminal nucleotide residues.
`static URI`	`DNA` An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone.
`static URI`	`DOUBLE` A stand attribute that it indicates it is composed of a double strand.
`static URI`	`ENGINEERED_GENE` A gene that is engineered (SO:0000280).
`static URI`	`ENGINEERED_REGION` A region that is engineered (SO:0000804).
`static URI`	`FIVE_PRIME_UTR` A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein (SO:0000204).
`static URI`	`GENE` A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript.
`static URI`	`INSULATOR` A transcriptional cis regulatory region that, when located between a CM and a gene's promoter, prevents the CRM from modulating that genes expression (SO:0000627)
`static URI`	`LINEAR` A quality of a nucleotide polymer that has a 3'-terminal residue and a 5'-terminal residue.
`static URI`	`MRNA` Messenger RNA is the intermediate molecule between DNA and protein.
`static URI`	`NAMESPACE` Namespace of the Sequence Ontology (http://identifiers.org/so/).
`static URI`	`OPERATOR` A regulatory element of an operon to which activators or repressors bind, thereby effecting translation of genes in that operon (SO:0000057).
`static URI`	`ORIGIN_OF_REPLICATION` The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies (SO:0000296).
`static URI`	`PRIMER_BINDING_SITE` Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription (SO:0005850)
`static URI`	`PROMOTER` A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery (SO:0000167).
`static URI`	`RESTRICTION_ENZYME_RECOGNITION_SITE` Represents a region of a DNA molecule which is a nucleotide region (usually a palindrome) that is recognized by a restriction enzyme (SO:0001687).
`static URI`	`RIBOSOME_ENTRY_SITE` Region in mRNA where ribosome assembles (SO:0000139)
`static URI`	`RNA` An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a D-ribose ring connected to a phosphate backbone.
`static URI`	`SEQUENCE_FEATURE` Any extent of continuous biological sequence.
`static URI`	`SGRNA` A small RNA oligo, typically about 20 bases, that guides the cas nuclease to a target DNA sequence in the CRISPR/cas mutagenesis method.
`static URI`	`SINGLE` A stand attribute that it indicates it is composed of a single strand.
`static URI`	`STRAND_ATTRIBUTE` Attributes added to describe the different kinds of replicon.
`static URI`	`TERMINATOR` The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription (SO:0000141).
`static URI`	`TOPOLOGY_ATTRIBUTE` Attributes added to describe the different kinds of replicon.

Constructor Summary

Constructors
Constructor and Description

SequenceOntology()
Construct an SO ontology and reads the OBO definition file, if it has not been read in before.

Constructors
Constructor and Description
`SequenceOntology()` Construct an SO ontology and reads the OBO definition file, if it has not been read in before.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`Set<String>`	`getDescendantNamesOf(String parentId)` Returns the set of child names that are descendants of a given parent ID.
`Set<String>`	`getDescendantNamesOf(URI parentURI)` Returns the set of child names that are descendants of a given parent URI.
`Set<String>`	`getDescendantsOf(String parentId)` Returns the set of child IDs that are descendants of the given parent ID.
`Set<String>`	`getDescendantsOf(URI parentURI)` Returns the set of child IDs that are descendants of the given parent URI.
`Set<URI>`	`getDescendantURIsOf(String parentId)` Returns the set of child URIs that are descendants of the given parent ID.
`Set<URI>`	`getDescendantURIsOf(URI parentURI)` Returns the set of child URIs that are descendants of the given parent URI.
`String`	`getId(String stanzaName)` Returns the ID of the stanza whose name matches the given stanza name.
`String`	`getId(URI termURI)` Returns the extracted ID of the given term's URI.
`String`	`getName(String stanzaId)` Returns the name field of the stanza that matches the ID referred by the given stanza URI.
`String`	`getName(URI termURI)` Returns the name field of the stanza that matches the ID for the given term URI.
`URI`	`getURIbyId(String stanzaId)` Creates a URI by appending the given stanza ID to the end of the Sequence Ontology (SO) namespace，i.e.
`URI`	`getURIbyName(String stanzaName)` Returns the URI that is composed of the Sequence Ontology (SO) namespace, i.e.
`boolean`	`isDescendantOf(String Id1, String Id2)` Returns `true` if the stanza with Id1 is a descendant of the stanza with Id2.
`boolean`	`isDescendantOf(URI childURI, URI parentURI)` Returns `true` if the stanza with childURI is a descendant of the stanza with parentURI.

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - NAMESPACE
```
public static final URI NAMESPACE
```
    Namespace of the Sequence Ontology (http://identifiers.org/so/).
  - PROMOTER
```
public static final URI PROMOTER
```
    A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery (SO:0000167).
  - OPERATOR
```
public static final URI OPERATOR
```
    A regulatory element of an operon to which activators or repressors bind, thereby effecting translation of genes in that operon (SO:0000057).
  - CDS
```
public static final URI CDS
```
    A contiguous sequence which begins with, and includes, a start codon, and ends with, and includes, a stop codon (SO:0000316).
  - FIVE_PRIME_UTR
```
public static final URI FIVE_PRIME_UTR
```
    A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein (SO:0000204).
  - TERMINATOR
```
public static final URI TERMINATOR
```
    The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription (SO:0000141).
  - INSULATOR
```
public static final URI INSULATOR
```
    A transcriptional cis regulatory region that, when located between a CM and a gene's promoter, prevents the CRM from modulating that genes expression (SO:0000627)
  - ORIGIN_OF_REPLICATION
```
public static final URI ORIGIN_OF_REPLICATION
```
    The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies (SO:0000296).
  - PRIMER_BINDING_SITE
```
public static final URI PRIMER_BINDING_SITE
```
    Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription (SO:0005850)
  - RIBOSOME_ENTRY_SITE
```
public static final URI RIBOSOME_ENTRY_SITE
```
    Region in mRNA where ribosome assembles (SO:0000139)
  - GENE
```
public static final URI GENE
```
    A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions (SO:0000704)
  - MRNA
```
public static final URI MRNA
```
    Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns (SO:0000234)
  - RESTRICTION_ENZYME_RECOGNITION_SITE
```
public static final URI RESTRICTION_ENZYME_RECOGNITION_SITE
```
    Represents a region of a DNA molecule which is a nucleotide region (usually a palindrome) that is recognized by a restriction enzyme (SO:0001687).
  - ENGINEERED_GENE
```
public static final URI ENGINEERED_GENE
```
    A gene that is engineered (SO:0000280).
  - ENGINEERED_REGION
```
public static final URI ENGINEERED_REGION
```
    A region that is engineered (SO:0000804).
  - SEQUENCE_FEATURE
```
public static final URI SEQUENCE_FEATURE
```
    Any extent of continuous biological sequence. (SO:0000110).
  - SGRNA
```
public static final URI SGRNA
```
    A small RNA oligo, typically about 20 bases, that guides the cas nuclease to a target DNA sequence in the CRISPR/cas mutagenesis method. (SO:0001998).
  - STRAND_ATTRIBUTE
```
public static final URI STRAND_ATTRIBUTE
```
    Attributes added to describe the different kinds of replicon. (SO:0000983).
  - SINGLE
```
public static final URI SINGLE
```
    A stand attribute that it indicates it is composed of a single strand. (SO:0000984).
  - DOUBLE
```
public static final URI DOUBLE
```
    A stand attribute that it indicates it is composed of a double strand. (SO:0000985).
  - TOPOLOGY_ATTRIBUTE
```
public static final URI TOPOLOGY_ATTRIBUTE
```
    Attributes added to describe the different kinds of replicon. (SO:0000986).
  - LINEAR
```
public static final URI LINEAR
```
    A quality of a nucleotide polymer that has a 3'-terminal residue and a 5'-terminal residue. (SO:0000987).
  - CIRCULAR
```
public static final URI CIRCULAR
```
    A quality of a nucleotide polymer that has no terminal nucleotide residues. (SO:0000988).
  - DNA
```
public static final URI DNA
```
    An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone. (SO:0000352).
  - RNA
```
public static final URI RNA
```
    An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a D-ribose ring connected to a phosphate backbone. (SO:0000356).
- Constructor Detail
  - SequenceOntology
```
public SequenceOntology()
```
    Construct an SO ontology and reads the OBO definition file, if it has not been read in before.
- Method Detail
  - getId
```
public final String getId(URI termURI)
```
    Returns the extracted ID of the given term's URI.
    
    Parameters:
    
    termURI - the identity URI of a term
    
    Returns:
    
    the extracted ID of the given term's URI
  - getId
```
public final String getId(String stanzaName)
```
    Returns the ID of the stanza whose name matches the given stanza name. If multiple matches are found, only the first matching one is returned.
    
    Parameters:
    
    stanzaName - the name of a stanza
    
    Returns:
    
    the matching stanza ID, or null if no match is found.
  - getName
```
public final String getName(URI termURI)
```
    Returns the name field of the stanza that matches the ID for the given term URI.
    
    Parameters:
    
    termURI - the identity URI of a term
    
    Returns:
    
    the name field of the stanza whose ID is referred to by the given term URI.
  - getName
```
public final String getName(String stanzaId)
```
    Returns the name field of the stanza that matches the ID referred by the given stanza URI.
    
    Parameters:
    
    stanzaId - the ID of a stanza
    
    Returns:
    
    the name field of the stanza that matches the ID referred by the given stanza URI, or null if this no match was found
  - getURIbyName
```
public final URI getURIbyName(String stanzaName)
```
    Returns the URI that is composed of the Sequence Ontology (SO) namespace, i.e. "http://identifiers.org/so/", followed by the ID of an SO term, of the stanza whose name matches the given name. If multiple matches are found, only the first matching one is returned.
    
    Parameters:
    
    stanzaName - the name of a term
    
    Returns:
    
    the URI of the given SO name
  - getURIbyId
```
public final URI getURIbyId(String stanzaId)
```
    Creates a URI by appending the given stanza ID to the end of the Sequence Ontology (SO) namespace，i.e. "http://identifiers.org/so/".
    
    Parameters:
    
    stanzaId - the ID of a stanza
    
    Returns:
    
    the created URI
  - isDescendantOf
```
public boolean isDescendantOf(String Id1,
                              String Id2)
```
    Returns true if the stanza with Id1 is a descendant of the stanza with Id2.
    
    Parameters:
    
    Id1 - ID of the first stanza
    
    Id2 - ID of the second stanza
    
    Returns:
    
    true if the stanza with Id1 is a descendant of the stanza with Id2, or false otherwise
  - isDescendantOf
```
public final boolean isDescendantOf(URI childURI,
                                    URI parentURI)
```
    Returns true if the stanza with childURI is a descendant of the stanza with parentURI. This method first extracts IDs for the child and parent, and then passes them to isDescendantOf(String, String).
    
    Parameters:
    
    childURI - the URI of the child stanza
    
    parentURI - the URI of the parent stanza
    
    Returns:
    
    true if the stanza with childURI is a descendant of the stanza with parentURI, or false otherwise
  - getDescendantsOf
```
public Set<String> getDescendantsOf(String parentId)
```
    Returns the set of child IDs that are descendants of the given parent ID. This set excludes the given parent ID.
    
    Parameters:
    
    parentId - the ID of the parent stanza
    
    Returns:
    
    the set of child IDs that are descendants of the given parent ID
  - getDescendantsOf
```
public final Set<String> getDescendantsOf(URI parentURI)
```
    Returns the set of child IDs that are descendants of the given parent URI. This set excludes the given parent ID.
    
    Parameters:
    
    parentURI - the URI of the parent stanza
    
    Returns:
    
    the set of child IDs that are descendants of the given parent URI
  - getDescendantURIsOf
```
public final Set<URI> getDescendantURIsOf(String parentId)
```
    Returns the set of child URIs that are descendants of the given parent ID. This set excludes the given parent URI.
    
    Parameters:
    
    parentId - the ID of the parent stanza
    
    Returns:
    
    the set of child URIs that are descendants of the given parent ID.
  - getDescendantURIsOf
```
public final Set<URI> getDescendantURIsOf(URI parentURI)
```
    Returns the set of child URIs that are descendants of the given parent URI. This set excludes the given parent URI.
    
    Parameters:
    
    parentURI - the URI of the parent stanza
    
    Returns:
    
    the set of child URIs that are descendants of the given parent URI
  - getDescendantNamesOf
```
public final Set<String> getDescendantNamesOf(String parentId)
```
    Returns the set of child names that are descendants of a given parent ID. This set excludes the given parent name.
    
    Parameters:
    
    parentId - the ID of the parent stanza
    
    Returns:
    
    the set of child names that are descendants of a given parent ID.
  - getDescendantNamesOf
```
public final Set<String> getDescendantNamesOf(URI parentURI)
```
    Returns the set of child names that are descendants of a given parent URI. This set excludes the given parent name.
    
    Parameters:
    
    parentURI - the URI of the parent stanza
    
    Returns:
    
    the set of child names that are descendants of a given parent URI

Class SequenceOntology

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

NAMESPACE

PROMOTER

OPERATOR

CDS

FIVE_PRIME_UTR

TERMINATOR

INSULATOR

ORIGIN_OF_REPLICATION

PRIMER_BINDING_SITE

RIBOSOME_ENTRY_SITE

GENE

MRNA

RESTRICTION_ENZYME_RECOGNITION_SITE

ENGINEERED_GENE

ENGINEERED_REGION

SEQUENCE_FEATURE

SGRNA

STRAND_ATTRIBUTE

SINGLE

DOUBLE

TOPOLOGY_ATTRIBUTE

LINEAR

CIRCULAR

DNA

RNA

Constructor Detail

SequenceOntology

Method Detail

getId

getId

getName

getName

getURIbyName

getURIbyId

isDescendantOf

isDescendantOf

getDescendantsOf

getDescendantsOf

getDescendantURIsOf

getDescendantURIsOf

getDescendantNamesOf

getDescendantNamesOf