List of available queries

Here is the list of available services.

Warning: some of these methods are only available to the users of the Java library!

  1. convertId
  2. getChildren
  3. getFramework
  4. getJavaLibraryVersion
  5. getOWLTerm
  6. getOWLTerms
  7. getOWLTree
  8. getParents
  9. getServicesInfo
  10. getServicesVersion
  11. getStringTermById (deprecated)
  12. getStringTermsByIds (deprecated)
  13. getStringTree (deprecated)
  14. getTerm
  15. getTermById (deprecated)
  16. getTermByIdOWL (deprecated)
  17. getTerms
  18. getTermsByIds (deprecated)
  19. getTermsByIdsOWL (deprecated)
  20. getTree
  21. getTree (deprecated)
  22. getTreeOWL (deprecated)
  23. getXMLTerm
  24. getXMLTerms
  25. getXMLTree
  26. isChildOf
  27. isChildOf (deprecated)
  28. isDirectChildOf
  29. isDirectChildOf (deprecated)
  30. isLibraryUpdated
  31. isObsolete
  32. isObsolete (deprecated)
  33. isRoot
  34. isRoot (deprecated)
  35. sayHi
  36. search
  37. searchOWL
  38. searchPossibleCompletions
  39. searchPossibleCompletionsOWL
  40. searchString
  41. searchStringPossibleCompletions
  42. searchStringTermDetails
  43. searchStringTermMath
  44. searchStringTermName
  45. searchStringTermSynonyms
  46. searchTermDetails
  47. searchTermDetailsOWL
  48. searchTermMath
  49. searchTermMathOWL
  50. searchTermName
  51. searchTermNameOWL
  52. searchTermSynonyms
  53. searchTermSynonymsOWL

Details of the queries

convertId

Converts an unofficial SBO identifier (Integer) into an official one (String). For example, converts '192' into 'SBO:0000192'. Only converts the identifier, doesn't check if it actually exists in the ontology!

Returns
string - official version of an SBO identifier (can be null if the identifier is invalid for SBO use)
Parameter Type Description
identifier integer integer version of an SBO identifier

getChildren

Retrieves the list of direct children of the given SBO term.

Returns
list of strings - list of identifiers of the children of the given term
Parameter Type Description
identifier string official identifier of a SBO term (for example: 'SBO:0000055')

getFramework

Retrieves the value of the framework (its identifier) given an SBO expression identifier.

Returns
string - SBO identifier of a term from the "modelling framework" branch
Parameter Type Description
identifier string official identifier of a SBO term (for example: 'SBO:0000055')

getJavaLibraryVersion

Retrieves the latest version of the Java library available.

Returns
string - latest version of the Java library available

getOWLTerm

Retrieves the OWL of a term, given its identifier.

Returns
string - OWL version of the term
Parameter Type Description
identifier string official identifier of a SBO term (for example: 'SBO:0000055')

getParents

Retrieves the list of direct parents of the given SBO term.

Returns
list of strings - list of identifiers of the parents of the given term
Parameter Type Description
identifier string official identifier of a SBO term (for example: 'SBO:0000055')

getOWLTerms

Retrieves the OWL version of a list of terms, given their identifiers.

Returns
string - OWL version of the list of terms
Parameter Type Description
identifiers list of strings list of official identifiers of SBO terms (for example: 'SBO:0000055')

getOWLTree

Retrieves in the OWL format, the subtree starting from the term which identifier is given in parameter.

Returns
string - OWL version of the subtree starting from the given term
Parameter Type Description
identifier string official identifier of a SBO term (for example: 'SBO:0000055')

getServicesInfo

Retrieves some information about these Web Services.

Returns
string - information about the Web Services

getServicesVersion

Retrieves the current version of these Web Services.

Returns
string - Current version of the Web Services

getStringTermById

This method is now deprecated! Instead, please use: getXMLTerm(String)

Retrieves the XML version of a term, given its identifier. This identifier is not the official one, it is only composed of integers.

Returns
string - XML version of the term
Parameter Type Description
identifier integer unofficial integer identifier (which should not be used) of a SBO term

getStringTermsByIds

This method is now deprecated! Instead, please use: getXMLTerms(List<String>)

Retrieves the XML version of a list of terms, given their identifiers. These identifiers are not the official ones, they are only composed of integers.

Returns
list of strings - XML version of the list of terms
Parameter Type Description
identifiers list of integers list of unofficial integer identifiers (which should not be used) of SBO terms

getStringTree

This method is now deprecated! Instead, please use: getXMLTree(String)

Retrieves the subtree starting from the given term. This identifier is not the official one, it is only composed of integers. The format returned is OWL.

Returns
list of strings - XML version of the subtree
Parameter Type Description
identifier integer unofficial integer identifier (which should not be used) of a SBO term

getTerm

Retrieves the Term corresponding to the given identifier.

Returns
Term - Term corresponding to the given identifier, can be null if the identifier is invalid or doesn't exist
Parameter Type Description
identifier string SBO term identifier, for example: 'SBO:0000192'

getTermById

This method is now deprecated! Instead, please use: getTerm(String)

Retrieves the Term corresponding to the given identifier. This identifier is not the official one, it is only composed of integers.

Returns
Term - the Term corresponding to the given identifier
Parameter Type Description
identifier int unofficial integer identifier (which should not be used) of a SBO term

getTermByIdOWL

This method is now deprecated! Instead, please use: getOWLTerm(String)

Retrieves the OWL version of a term, given its identifier. This identifier is not the official one, it is only composed of integers.

Returns
string - OWL version of the term
Parameter Type Description
identifier integer unofficial integer identifier (which should not be used) of a SBO term

getTerms

Retrieves the list of Term corresponding to the given identifiers. The returned list can contain less values than the list of identifiers given, if some identifiers are not valid or don't exist.

Returns
list of terms - list of terms corresponding to the valid and existing given identifiers (can be null or empty as well)
Parameter Type Description
identifiers list of strings list of SBO term identifiers (an SBO identifier looks like: 'SBO:0000192')

getTermsByIds

This method is now deprecated! Instead, please use: getTerms(List<String>)

Retrieves the list of Term corresponding to the given identifiers. These identifiers are not the official ones, they are only composed of integers. The returned list can contain less values than the list of identifiers given, if some identifiers are not valid or don't exist.

Returns
list of terms - list of terms corresponding to the valid and existing given identifiers (can be null or empty as well)
Parameter Type Description
identifiers list of integers list of unofficial integer identifiers (which should not be used) of SBO terms

getTermsByIdsOWL

This method is now deprecated! Instead, please use: getOWLTerms(List<String>)

Retrieves the OWL version of a list of terms, given their identifiers. These identifiers are not the official ones, they are only composed of integers.

Returns
string - OWL version of the list of terms
Parameter Type Description
identifiers list of integers list of unofficial integer identifiers (which should not be used) of SBO terms

getTree

Retrieves the list of Term which composed the subtree starting with the term corresponding to the given identifier.

Returns
list of terms - list of Term
Parameter Type Description
identifier string identifier of a SBO term (for example: 'SBO:0000055')

getTree

This method is now deprecated! Instead, please use: getTree(String)

Retrieves the list of Term which composed the subtree starting with the term corresponding to the given identifier. This identifier is not the official one, it is only composed of integers.

Returns
list of terms - list of Term
Parameter Type Description
identifier integer unofficial integer identifier (which should not be used) of a SBO term

getTreeOWL

This method is now deprecated! Instead, please use: getOWLTree(String)

Retrieves in the OWL format, the subtree starting from the term which identifier is given in parameter. This identifier is not the official one, it is only composed of integers.

Returns
string - OWL version of the subtree starting from the given term
Parameter Type Description
identifier integer unofficial integer identifier (which should not be used) of a SBO term

getXMLTerm

Retrieves the XML version of a term, given its identifier.

Returns
string - XML version of the term
Parameter Type Description
identifier string official identifier of a SBO term (for example: 'SBO:0000055')

getXMLTerms

Retrieves the XML version of a list of terms, given their identifiers.

Returns
list of strings - XML version of the list of terms
Parameter Type Description
identifiers list of strings list of official identifiers of SBO terms (for example: 'SBO:0000055')

getXMLTree

Retrieves the subtree starting from the given term. The format returned is OWL.

Returns
list of strings - XML version of the subtree
Parameter Type Description
identifier string official identifier of a SBO term (for example: 'SBO:0000055')

isChildOf

Checks if one term is a child (even indirect) of a second term.

Returns
boolean - answer to the question: is this term child of that other one?
Parameters Type Description
child string official identifier of a SBO term (for example: 'SBO:0000055'), supposedly the child
parent string official identifier of a SBO term (for example: 'SBO:0000055'), supposedly the parent

isChildOf

This method is now deprecated! Instead, please use: isChildOf(String, String)

Checks if one term is a child (even indirect) of a second term.

Returns
boolean - answer to the question: is this term child of that other one?
Parameters Type Description
child integer unofficial integer identifier (which should not be used) of a SBO term
parent integer unofficial integer identifier (which should not be used) of a SBO term

isDirectChildOf

Checks if one term is a direct child of a second term.

Returns
boolean - answer to the question: is this term a direct child of that other one?
Parameters Type Description
child string official identifier of a SBO term (for example: 'SBO:0000055'), supposedly the child
parent string official identifier of a SBO term (for example: 'SBO:0000055'), supposedly the parent

isDirectChildOf

This method is now deprecated! Instead, please use: isDirectChildOf(String, String)

Checks if one term is a direct child of a second term.

Returns
boolean - answer to the question: is this term a direct child of that other one?
Parameters Type Description
child integer unofficial integer identifier (which should not be used) of a SBO term, supposedly the child
parent integer unofficial integer identifier (which should not be used) of a SBO term, supposedly the parent

isLibraryUpdated

Tests if the Java library used is the latest available.

Returns
boolean - is your library the latest available?

isObsolete

checks if a term is obsolete or not.

Returns
boolean - answer to the question: is this term obsolete?
Parameter Type Description
identifier string official identifier of a SBO term (for example: 'SBO:0000055')

isObsolete

This method is now deprecated! Instead, please use: isObsolete(String)

checks if a term is obsolete or not.

Returns
boolean - answer to the question: is this term obsolete?
Parameter Type Description
identifier integer unofficial integer identifier (which should not be used) of a SBO term

isRoot

Checks if a term is root or not.

Returns
boolean - answer to the question: is this term root?
Parameter Type Description
identifier string official identifier of a SBO term (for example: 'SBO:0000055')

isRoot

This method is now deprecated! Instead, please use: isRoot(String)

Checks if a term is root or not.

Returns
boolean - answer to the question: is this term root?
Parameter Type Description
identifier integer unofficial integer identifier (which should not be used) of a SBO term

sayHi

Returns to the user the sentence he sent. This method can be used for testing purposes.

Returns
string -
Parameter Type Description
sentence string whatever

search

Global search on the whole content of the ontology.

Returns
list of terms - list of Term matching the query
Parameter Type Description
query string word or sentence

searchOWL

Retrieves the list of terms which related information (name, synonym, definition, comment, mathML) contain the given parameter. The format returned is OWL. The search is case insensitive.

Returns
string - OWL version of the list of terms matching the query
Parameter Type Description
query string word or sentence which is part of the related information of terms

searchPossibleCompletions

Retrieves the list of Term which name contains the word(s) given in parameter. For example: "hill" will return "Hill coefficient", "Hill constant", "Hill-type rate law, reduced form", ... The search is case insensitive.

Returns
list of terms - list of Term (can be null or empty)
Parameter Type Description
element string word or sentence which is part of the name of terms

searchPossibleCompletionsOWL

Retrieves the OWL version of the list of terms which name contains the word(s) given in parameter. For example: "hill" will return "Hill coefficient", "Hill constant", "Hill-type rate law, reduced form", ... The search is case insensitive.

Returns
string - OWL version of the list of terms matching the search
Parameter Type Description
word string word or sentence which is part of the name of terms

searchString

Retrieves the list of terms which related information (name, synonym, definition, comment, mathML) contain the given parameter. The format returned is XML. The search is case insensitive.

Returns
list of strings - XML version of the list of terms matching the query
Parameter Type Description
query string word or sentence which is part of the related information of terms

searchStringPossibleCompletions

Retrieves the list of terms which name contains the given parameter. The format returned is XML. The search is case insensitive.

Returns
list of strings - set of XML version of terms matching the query
Parameter Type Description
query string word or sentence which is part of the name of terms

searchStringTermDetails

Retrieves the list of terms which details contain the given parameter. The format returned is XML. The search is case insensitive.

Returns
list of strings - XML version of the list of terms matching the query
Parameter Type Description
query string word or sentence which is part of the synonym of terms

searchStringTermMath

Retrieves the list of terms which MathML contain the given parameter. The format returned is XML. The search is case insensitive.

Returns
list of strings - XML version of the list of terms matching the query
Parameter Type Description
query string word or sentence which is part of the synonym of terms

searchStringTermName

Retrieves the list of terms which name contain the given parameter. The format returned is XML. The search is case insensitive.

Returns
list of strings - XML version of the list of terms matching the query
Parameter Type Description
query string word or sentence which is part of the name of terms

searchStringTermSynonyms

Retrieves the list of terms which synonym(s) contain the given parameter. The format returned is XML. The search is case insensitive.

Returns
list of strings - XML version of the list of terms matching the query
Parameter Type Description
query string word or sentence which is part of the synonym of terms

searchTermDetails

Searches for the occurrence of the given parameter in the details (comment and definition) of terms from the ontology.

Returns
list of terms - list of Term containing in their comment or definition, the given parameter
Parameter Type Description
query string word or sentence which is part of the details of terms

searchTermDetailsOWL

Retrieves the list of terms which details contain the given parameter. The format returned is OWL. The search is case insensitive.

Returns
string - OWL version of the list of term matching the query
Parameter Type Description
query string word or sentence which is part of the details of terms

searchTermMath

Searches for the occurrence of the word given in parameter in the MathML of terms in the ontology.

Returns
list of terms - list of Term containing the given parameter in their MathML
Parameter Type Description
query string word or sentence which is part of the MathML of terms

searchTermMathOWL

Retrieves the list of terms which MathML contain the given parameter. The format returned is OWL. The search is case insensitive.

Returns
string - OWL version of the list of term matching the query
Parameter Type Description
query string word or sentence which is part of the MathML of terms

searchTermName

Searches for the occurrence of the word given in parameter in the name of terms of the ontology.

Returns
list of terms - list of Term containing the given parameter in their name
Parameter Type Description
query string word or sentence which is part of the name of terms

searchTermNameOWL

Retrieves the list of terms which name contain the given parameter. The format returned is OWL. The search is case insensitive.

Returns
string - OWL version of the list of terms matching the query
Parameter Type Description
query string word or sentence which is part of the name of terms

searchTermSynonyms

Retrieves the list of Term with a synonym containing the word(s) given in parameter.

Returns
list of terms - list of Term (can be null or empty)
Parameter Type Description
query string word or sentence which is part of the synonym of terms

searchTermSynonymsOWL

Retrieves the list of terms which synonym contains the given parameter. The format returned is OWL. The search is case insensitive.

Returns
string - OWL version of the list of term matching the query
Parameter Type Description
query string word or sentence which is part of the synonym of terms