org.ncbo.stanford.server.beans
Interface NCBOWebserviceEndpoint

All Superinterfaces:

Remote

public interface NCBOWebserviceEndpoint
extends Remote

The endpoint interface for NCBO webservices. It is used to implement a JSR-181 ejb3 endpoint implementation.Client uses the jaxrpc-mapping file and the endpoint interface to consume these services.

Method Summary

StringList	getAssociationsForOntology(String ontologyDisplayLabel) Get all existing associations/relations for an ontlogy in the NCBO library.
StringList	getAttributesForOntology(String ontologyDisplayLabel) Get all existing attributes like definition.synonym etc for an ontlogy in the NCBO library.
SearchBeanResultList	getAttributeValueContains(StringList ontologyDisplayLabel, String searchStr, StringList attributeName, boolean includeObsolete) Search for class/type by searching the attribute value contains.
SearchBeanResultList	getAttributeValueEndsWith(StringList ontologyDisplayLabel, String searchStr, StringList attributeName, boolean includeObsolete) Search for class/type by searching the attribute value ends with.
SearchBeanResultList	getAttributeValueSoundsLike(StringList ontologyDisplayLabel, String searchStr, StringList attributeName, boolean includeObsolete) Search for class/type by searching the attribute value sounds like(double metaphone).
SearchBeanResultList	getAttributeValueStartsWith(StringList ontologyDisplayLabel, String searchStr, StringList attributeName, boolean includeObsolete) Search for class/type by searching the attribute value starts with.
AssociationBeanResultList	getChildNodes(String ontologyDisplayLabel, String focusNodeId, StringList associationName) Get the child nodes and related relations/associations given an ontology label.
String	getHierarchyToRootImageUrl(String ontologyDisplayLabel, String focusNodeId, StringList associationName) Get an image url like http://www.bioontology.org/graphs/webservice/1.jpg for hierarchy to root of a class/type.
NCBOOntologyList	getNCBOOntologies() Get All ontologies in the NCBO library.
NCBOOntologyList	getNCBOOntologiesByCategory(String categoryName) Get an NCBO ontology given the category.
NCBOOntology	getNCBOOntology(String ontologyDisplayLabel) Get an NCBO ontology given the primary identifier, displaylabel.
String	getNetworkNeighborhoodImageUrl(String ontologyDisplayLabel, String focusNodeId, StringList associationName) Get an image url like http://www.bioontology.org/graphs/webservice/1.jpg for a network neighborhood of a class/type.
NodeBeanResult	getNode(String ontologyDisplayLabel, String focusNodeId) Get a Node given an id of a class/type.
SearchBeanResultList	getNodeIdContains(StringList ontologyDisplayLabel, String searchStr, boolean includeObsolete) Search for class/type id that contains a string in a list of ontologies.
SearchBeanResultList	getNodeIdEndsWith(StringList ontologyDisplayLabel, String searchStr, boolean includeObsolete) Search for class/type id that ends with a string in a list of ontologies.
SearchBeanResultList	getNodeIdExactMatch(StringList ontologyDisplayLabel, String searchStr, boolean includeObsolete) Search for class/type id that matches exactly with a string in a list of ontologies.
SearchBeanResultList	getNodeIdStartsWith(StringList ontologyDisplayLabel, String searchStr, boolean includeObsolete) Search for class/type id that starts with a string in a list of ontologies.
SearchBeanResultList	getNodeNameContains(StringList ontologyDisplayLabel, String searchStr, boolean includeObsolete) Search for class/type name that contains the search string given a list of ontologies.
SearchBeanResultList	getNodeNameEndsWith(StringList ontologyDisplayLabel, String searchStr, boolean includeObsolete) Search for class/type name that ends with a string in a list of ontologies.
SearchBeanResultList	getNodeNameExactMatch(StringList ontologyDisplayLabel, String searchStr, boolean includeObsolete) Search for class/type name that matches exactly with the serach string given a list of ontologies.
SearchBeanResultList	getNodeNameSoundsLike(StringList ontologyDisplayLabel, String searchStr, boolean includeObsolete) Search for class/type name that sounds like(double metaphone) the search string in a list of ontologies.
SearchBeanResultList	getNodeNameStartsWith(StringList ontologyDisplayLabel, String searchStr, boolean includeObsolete) Search for class/type name that starts with a string in a list of ontologies.
AssociationBeanResultList	getParentNodes(String ontologyDisplayLabel, String focusNodeId, StringList associationName) Get the parent nodes and related relations/associations given an ontology label.
AssociationBeanResult	getTopLevelNodes(String ontologyDisplayLabel) Get the top level nodes and related relations/associations given an ontology label

Method Detail

getNCBOOntologies

NCBOOntologyList getNCBOOntologies()
                                   throws RemoteException

Get All ontologies in the NCBO library.

Returns:

a list of NCBOOntology. NCBOOntologyList .

Throws:

RemoteException

getNCBOOntology

NCBOOntology getNCBOOntology(String ontologyDisplayLabel)
                             throws RemoteException

Get an NCBO ontology given the primary identifier, displaylabel.

Parameters:

ontologyDisplayLabel - The unique identifier of the ontology in the NCBO library.

Returns:

NCBOOntology.A wrapped array of NCBOOntology.

Throws:

RemoteException

getNCBOOntologiesByCategory

NCBOOntologyList getNCBOOntologiesByCategory(String categoryName)
                                             throws RemoteException

Get an NCBO ontology given the category. NCBOOntology.

Parameters:

categoryName - The name of a valid category in the NCBO library.

Returns:

NCBOOntologyList.A wrapped array of NCBOOntology.

Throws:

RemoteException

getNode

NodeBeanResult getNode(String ontologyDisplayLabel,
                       String focusNodeId)
                       throws RemoteException

Get a Node given an id of a class/type.

Parameters:

ontologyDisplayLabel - The unique identifier of the ontology in the NCBO library.

focusNodeId. - The node that is being queried.

Returns:

NodeBeanResult. Information about this class/type along with it's attributes and values

Throws:

RemoteException

getTopLevelNodes

AssociationBeanResult getTopLevelNodes(String ontologyDisplayLabel)
                                       throws RemoteException

Get the top level nodes and related relations/associations given an ontology label

Parameters:

ontologyDisplayLabel - The unique identifier of the ontology in the NCBO library.

Returns:

AssociationBeanResult. Wrapped array of nodes and associations .

Throws:

RemoteException

getParentNodes

AssociationBeanResultList getParentNodes(String ontologyDisplayLabel,
                                         String focusNodeId,
                                         StringList associationName)
                                         throws RemoteException

Get the parent nodes and related relations/associations given an ontology label.

Parameters:

ontologyDisplayLabel - The unique identifier of the ontology in the NCBO library.

focusNodeId. - The node that is being queried.

associationName. - A wrapped array of associations taht need to be queried. If empty or null all associations will be queried.

Returns:

AssociationBeanResultList. Wrapped Array of nodes and associations .

Throws:

RemoteException

getChildNodes

AssociationBeanResultList getChildNodes(String ontologyDisplayLabel,
                                        String focusNodeId,
                                        StringList associationName)
                                        throws RemoteException

Get the child nodes and related relations/associations given an ontology label.

Parameters:

ontologyDisplayLabel - The unique identifier of the ontology in the NCBO library.

focusNodeId. - The node that is being queried.

associationName. - A wrapped array of associations taht need to be queried. If empty or null all associations will be queried.

Returns:

AssociationBeanResult. Wrapped Array of nodes and associations.

Throws:

RemoteException

getAssociationsForOntology

StringList getAssociationsForOntology(String ontologyDisplayLabel)
                                      throws RemoteException

Get all existing associations/relations for an ontlogy in the NCBO library. given an ontology label.

Parameters:

ontologyDisplayLabel - The unique identifier of the ontology in the NCBO library.

Returns:

StringList. Wrapped Array of strings of association names.

Throws:

RemoteException

getAttributesForOntology

StringList getAttributesForOntology(String ontologyDisplayLabel)
                                    throws RemoteException

Get all existing attributes like definition.synonym etc for an ontlogy in the NCBO library. given an ontology label.

Parameters:

ontologyDisplayLabel - The unique identifier of the ontology in the NCBO library.

Returns:

StringList. Wrapped Array of strings of attribute names .

Throws:

RemoteException

getNodeNameStartsWith

SearchBeanResultList getNodeNameStartsWith(StringList ontologyDisplayLabel,
                                           String searchStr,
                                           boolean includeObsolete)
                                           throws RemoteException

Search for class/type name that starts with a string in a list of ontologies.

Parameters:

ontologyDisplayLabel - A wrapped array of labels. Label is the unique identifier of the ontology in the NCBO library.

searchStr. - The search string

includeObsolete. - A boolean indicating whether or not to search obsolte/inactive class/type

Returns:

SearchBeanResultList. Wrapped Array of nodes resulting from the search.

Throws:

RemoteException

getNodeNameSoundsLike

SearchBeanResultList getNodeNameSoundsLike(StringList ontologyDisplayLabel,
                                           String searchStr,
                                           boolean includeObsolete)
                                           throws RemoteException

Search for class/type name that sounds like(double metaphone) the search string in a list of ontologies.

Parameters:

ontologyDisplayLabel - The unique identifier of the ontology in the NCBO library.

searchStr. - The search string

includeObsolete. - A boolean indicating whether or not to search obsolte/inactive class/type

Returns:

SearchBeanResultList. Wrapped Array of nodes resulting from the search.

Throws:

RemoteException

getNodeNameEndsWith

SearchBeanResultList getNodeNameEndsWith(StringList ontologyDisplayLabel,
                                         String searchStr,
                                         boolean includeObsolete)
                                         throws RemoteException

Search for class/type name that ends with a string in a list of ontologies.

Parameters:

ontologyDisplayLabel - The unique identifier of the ontology in the NCBO library.

searchStr. - The search string. part of the name of class/type.

includeObsolete. - A boolean indicating whether or not to search obsolte/inactive class/type

Returns:

SearchBeanResultList. Wrapped Array of nodes resulting from the search.

Throws:

RemoteException

getNodeNameExactMatch

SearchBeanResultList getNodeNameExactMatch(StringList ontologyDisplayLabel,
                                           String searchStr,
                                           boolean includeObsolete)
                                           throws RemoteException

Search for class/type name that matches exactly with the serach string given a list of ontologies.

Parameters:

ontologyDisplayLabel - The unique identifier of the ontology in the NCBO library.

searchStr. - The search string. part of the name of class/type

includeObsolete. - A boolean indicating whether or not to search obsolte/inactive class/type

Returns:

SearchBeanResultList. Wrapped Array of nodes resulting from the search.

Throws:

RemoteException

getNodeNameContains

SearchBeanResultList getNodeNameContains(StringList ontologyDisplayLabel,
                                         String searchStr,
                                         boolean includeObsolete)
                                         throws RemoteException

Search for class/type name that contains the search string given a list of ontologies.

Parameters:

ontologyDisplayLabel - The unique identifier of the ontology in the NCBO library.

searchStr. - The search string. part of the name of class/type

includeObsolete. - A boolean indicating whether or not to search obsolte/inactive class/type

Returns:

SearchBeanResultList. Wrapped Array of nodes resulting from the search.

Throws:

RemoteException

getNodeIdStartsWith

SearchBeanResultList getNodeIdStartsWith(StringList ontologyDisplayLabel,
                                         String searchStr,
                                         boolean includeObsolete)
                                         throws RemoteException

Search for class/type id that starts with a string in a list of ontologies.

Parameters:

ontologyDisplayLabel - The unique identifier of the ontology in the NCBO library.

searchStr. - The search string which is part of the id.

includeObsolete. - A boolean indicating whether or not to search obsolte/inactive class/type

Returns:

SearchBeanResultList. Wrapped Array of nodes resulting from the search.

Throws:

RemoteException

getNodeIdEndsWith

SearchBeanResultList getNodeIdEndsWith(StringList ontologyDisplayLabel,
                                       String searchStr,
                                       boolean includeObsolete)
                                       throws RemoteException

Search for class/type id that ends with a string in a list of ontologies.

Parameters:

ontologyDisplayLabel - The unique identifier of the ontology in the NCBO library.

searchStr. - The search string which is part of the id.

includeObsolete. - A boolean indicating whether or not to search obsolte/inactive class/type

Returns:

SearchBeanResultList. Wrapped Array of nodes resulting from the search.

Throws:

RemoteException

getNodeIdExactMatch

SearchBeanResultList getNodeIdExactMatch(StringList ontologyDisplayLabel,
                                         String searchStr,
                                         boolean includeObsolete)
                                         throws RemoteException

Search for class/type id that matches exactly with a string in a list of ontologies.

Parameters:

ontologyDisplayLabel - The unique identifier of the ontology in the NCBO library.

searchStr. - The search string which is part of the id.

includeObsolete. - A boolean indicating whether or not to search obsolte/inactive class/type

Returns:

SearchBeanResultList. Wrapped Array of nodes resulting from the search.

Throws:

RemoteException

getNodeIdContains

SearchBeanResultList getNodeIdContains(StringList ontologyDisplayLabel,
                                       String searchStr,
                                       boolean includeObsolete)
                                       throws RemoteException

Search for class/type id that contains a string in a list of ontologies.

Parameters:

ontologyDisplayLabel - The unique identifier of the ontology in the NCBO library.

searchStr. - The search string which is part of the id.

includeObsolete. - A boolean indicating whether or not to search obsolte/inactive class/type

Returns:

SearchBeanResultList. Wrapped Array of nodes resulting from the search SearchBeanResultList.

Throws:

RemoteException

getAttributeValueStartsWith

SearchBeanResultList getAttributeValueStartsWith(StringList ontologyDisplayLabel,
                                                 String searchStr,
                                                 StringList attributeName,
                                                 boolean includeObsolete)
                                                 throws RemoteException

Search for class/type by searching the attribute value starts with. Attribute includes synonyms,definitions.comments etc that contains a string in a list of ontologies.

Parameters:

ontologyDisplayLabel - The unique identifier of the ontology in the NCBO library.

searchStr. - The search string which is part of the id.

includeObsolete. - A boolean indicating whether or not to search obsolte/inactive class/type

Returns:

SearchBeanResultList. Wrapped Array of nodes resulting from the search.

Throws:

RemoteException

getAttributeValueEndsWith

SearchBeanResultList getAttributeValueEndsWith(StringList ontologyDisplayLabel,
                                               String searchStr,
                                               StringList attributeName,
                                               boolean includeObsolete)
                                               throws RemoteException

Search for class/type by searching the attribute value ends with. attribute includes synonyms,definitions.comments etc that contains a string in a list of ontologies.

Parameters:

ontologyDisplayLabel - The unique identifier of the ontology in the NCBO library.

searchStr. - The search string which is part of the id.

includeObsolete. - A boolean indicating whether or not to search obsolte/inactive class/type

Returns:

SearchBeanResultList. Wrapped Array of nodes resulting from the search.

Throws:

RemoteException

getAttributeValueContains

SearchBeanResultList getAttributeValueContains(StringList ontologyDisplayLabel,
                                               String searchStr,
                                               StringList attributeName,
                                               boolean includeObsolete)
                                               throws RemoteException

Search for class/type by searching the attribute value contains. attribute includes synonyms,definitions.comments etc that contains a string in a list of ontologies.

Parameters:

ontologyDisplayLabel - The unique identifier of the ontology in the NCBO library.

searchStr. - The search string which is part of the id.

includeObsolete. - A boolean indicating whether or not to search obsolte/inactive class/type

Returns:

SearchBeanResultList. Wrapped Array of nodes resulting from the search.

Throws:

RemoteException

getAttributeValueSoundsLike

SearchBeanResultList getAttributeValueSoundsLike(StringList ontologyDisplayLabel,
                                                 String searchStr,
                                                 StringList attributeName,
                                                 boolean includeObsolete)
                                                 throws RemoteException

Search for class/type by searching the attribute value sounds like(double metaphone). attribute includes synonyms,definitions.comments etc that contains a string in a list of ontologies.

Parameters:

ontologyDisplayLabel - The unique identifier of the ontology in the NCBO library.

searchStr. - The search string which is part of the id.

includeObsolete. - A boolean indicating whether or not to search obsolte/inactive class/type

Returns:

SearchBeanResultList. Wrapped Array of nodes resulting from the search.

Throws:

RemoteException

getNetworkNeighborhoodImageUrl

String getNetworkNeighborhoodImageUrl(String ontologyDisplayLabel,
                                      String focusNodeId,
                                      StringList associationName)
                                      throws RemoteException

Get an image url like http://www.bioontology.org/graphs/webservice/1.jpg for a network neighborhood of a class/type. This returns a maximum graph of 50 nodes.

Parameters:

ontologyDisplayLabel - The unique identifier of the ontology in the NCBO library.

focusNodeId. - The node that is being gaphed.

associationName. - A wrapped array of associations taht need to be queried. If empty or null all associations will be considered

Returns:

String representing the url

Throws:

RemoteException

getHierarchyToRootImageUrl

String getHierarchyToRootImageUrl(String ontologyDisplayLabel,
                                  String focusNodeId,
                                  StringList associationName)
                                  throws RemoteException

Get an image url like http://www.bioontology.org/graphs/webservice/1.jpg for hierarchy to root of a class/type. This returns a maximum graph of 50 nodes.

Parameters:

ontologyDisplayLabel - The unique identifier of the ontology in the NCBO library.

focusNodeId. - The node that is being gaphed.

associationName. - A wrapped array of associations taht need to be queried. If empty or null all associations will be considered

Returns:

String representing the url

Throws:

RemoteException