Web Services documentation

Here is the list of all the services available.

We will be pleased to add any other queries that you would need.

List of available queries

  1. checkRegExp
  2. convertURL
  3. convertURLs
  4. convertURN
  5. convertURNs
  6. getDataEntries (deprecated)
  7. getDataEntries (deprecated)
  8. getDataEntry (deprecated)
  9. getDataResources
  10. getDataTypeAllURIs (deprecated)
  11. getDataTypeDef
  12. getDataTypePattern
  13. getDataTypeSynonyms
  14. getDataTypeURI (deprecated)
  15. getDataTypeURI
  16. getDataTypeURIs (deprecated)
  17. getDataTypeURIs
  18. getDataTypeURL (deprecated)
  19. getDataTypeURLs (deprecated)
  20. getDataTypeURN (deprecated)
  21. getDataTypeURNs (deprecated)
  22. getDataTypesId
  23. getDataTypesName
  24. getJavaLibraryVersion
  25. getLocation
  26. getLocations
  27. getLocations
  28. getLocationsWithToken
  29. getMiriamURI
  30. getName
  31. getNames
  32. getOfficialDataTypeURI
  33. getOfficialURI (deprecated)
  34. getResourceInfo
  35. getResourceInstitution
  36. getResourceLocation
  37. getServicesInfo
  38. getServicesVersion
  39. getURI (deprecated)
  40. getURI
  41. getURIs
  42. getURL (deprecated)
  43. getURN (deprecated)
  44. isDeprecated

Details of the queries

checkRegExp

Checks if the identifier given follows the regular expression of the data collection (also provided).

Returns
string - "true" if the identifier follows the regular expression, "false" otherwise
Parameters Type Description
identifier string internal identifier used by the data collection
datatype string name, synonym or MIRIAM URI of a data collection

convertURL

Converts an Identifiers.org URL into its equivalent MIRIAM URN.

This performs a check of the identifier based on the recorded regular expression.

Returns
string - the MIRIAM URN corresponding to the provided Identifiers.org URL or 'null' if the provided URL is invalid
Parameter Type Description
url string an Identifiers.org URL

convertURLs

Converts a list of Identifiers.org URLs into their equivalent MIRIAM URNs.

This performs a check of the identifier based on the recorded regular expression.

If a URL is invalid, 'null' is returned for this URL.

If the size of the list of URLs exceeds 200, 'null' is returned.

Returns
array of strings - a list of MIRIAM URNs corresponding to the provided Identifiers.org URLs
Parameter Type Description
urls array of strings a list of Identifiers.org URLs

convertURN

Converts a MIRIAM URI into its equivalent Identifiers.org URL.

This takes care of any necessary conversion, for example in the case the URI provided is obsolete.

Returns
string - the Identifiers.org URL corresponding to the provided MIRIAM URI or 'null' if the provided URI does not exist
Parameter Type Description
uri string a MIRIAM URI

convertURNs

Converts a list of MIRIAM URIs into their equivalent Identifiers.org URLs.

This takes care of any necessary conversion, for example in the case a URI provided is obsolete.

If a URI is invalid, 'null' is returned for this URI.

If the size of the list of URIs exceeds 200, 'null' is returned.

Returns
array of strings - a list of Identifiers.org URLs corresponding to the provided URIs
Parameter Type Description
uris array of strings a list of MIRIAM URIs

getDataEntries

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

Retrieves the physical locationS (URLs) of web pageS about the data-entry.

Returns
array of strings - physical locationS of web pageS about the data-entry
Parameters Type Description
nickname string name (can be a synonym) or URN or URL of a data collection (examples: "ChEBI", "UniProt")
id string identifier of an element (examples: "GO:0045202", "P62158")

getDataEntries

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

Retrieves the physical locationS (URLs) of web pageS about the data-entry.

Returns
array of strings - physical locationS of web pageS about the data-entry
Parameter Type Description
uri string MIRIAM URI of an element (example: 'urn:miriam:obo.go:GO%3A0045202')

getDataEntry

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

Retrieves the physical location (URL) of a web page about the data-entry, using a specific resource.

Returns
string - physical location of a web page about the data-entry, using a specific resource
Parameters Type Description
uri string MIRIAM URI of an element (example: 'urn:miriam:obo.go:GO%3A0045202')
resource string internal identifier of a resource (example: 'MIR:00100005')

getDataResources

Retrieves all the physical locations (URLs) of the services providing the data collection (web page).

Returns
array of strings - array of strings containing all the address of the main page of the resources of the data collection
Parameter Type Description
nickname string name (can be a synonym) or URL or URN of a data collection name (or synonym) or URI (URL or URN)

getDataTypeAllURIs

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

Retrieves all the URIs (URNs and URLs) of the data collection

Returns
array of strings - all the URIs (URLs and URNs) of the data collection including all the deprecated ones
Parameter Type Description
name string name of a data collection (examples: "ChEBI", "UniProt")

getDataTypeDef

Retrieves the definition of a data collection.

Returns
string - definition of the data collection
Parameter Type Description
nickname string name or URI (URN or URL) of a data collection

getDataTypePattern

Retrieves the pattern (regular expression) used by the identifiers within a data collection.

Returns
string - pattern of the data collection
Parameter Type Description
nickname string data collection name (or synonym) or URI (URL or URN)

getDataTypeSynonyms

Retrieves all the synonym names of a data collection (this list includes the original name).

Returns
array of strings - all the synonym names of the data collection
Parameter Type Description
name string name or synonym of a data collection

getDataTypeURI

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

Retrieves the unique (official) URL or URN of the data collection (example: "http://www.taxonomy.org/", "urn:lsid:uniprot.org").

Returns
string - unique URL or URN of the data collection
Parameters Type Description
name string name of the data collection (examples: "ChEBI", "UniProt")
type string type of the URI the user wants to retrieve ('URN' or 'URL')

getDataTypeURI

Retrieves the unique (official) URI of a data collection (example: "urn:miriam:uniprot").

Returns
string - unique URI of the data collection
Parameter Type Description
name string name or synonym of a data collection (examples: "UniProt")

getDataTypeURIs

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

Retrieves all the URLs or URNs of the data collection (examples: "urn:miriam:uniprot", "http://www.taxonomy.org/") including all the deprecated ones.

Returns
array of strings - all the URIs (URLs or URNs) of the data collection including all the deprecated ones
Parameters Type Description
name string name of the data collection (examples: "ChEBI", "UniProt")
type string type of the URI the user wants to recover ('URN' or 'URL')

getDataTypeURIs

Retrieves all the URIs of a data collection, including all the deprecated ones (examples: "urn:miriam:uniprot", "http://www.uniprot.org/", "urn:lsid:uniprot.org:uniprot", ...).

Returns
array of strings - all the URIs of a data collection (including the deprecated ones)
Parameter Type Description
name string name (or synonym) of the data collection (examples: "ChEBI", "UniProt")

getDataTypeURL

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

Retrieves the unique (official) URL (not a physical URL but a URI) of the data collection (example: "http://www.taxonomy.org/").

Returns
string - unique URL of the data collection
Parameter Type Description
name string name of a data collection (examples: "ChEBI", "UniProt")

getDataTypeURLs

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

Retrieves the unique (official) URL (not a physical URL but a URI) of the data collection (example: "http://www.taxonomy.org/") and all the deprecated ones.

Returns
array of strings - unique URL of the data collection and all the deprecated ones
Parameter Type Description
name string name of a data collection (examples: "ChEBI", "UniProt")

getDataTypeURN

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

Retrieves the unique official URN of a data collection (example: urn:miriam:uniprot).

Returns
string - unique (official) URN of the data collection
Parameter Type Description
name string name primary name (or synonym) of a data collection (examples: "ChEBI", "UniProt", "GO")

getDataTypeURNs

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

Retrieves the unique (official) URN of the data collection (example: "urn:miriam:uniprot") and all the deprecated ones.

Returns
array of strings - unique URN and all the deprecated ones
Parameter Type Description
name string name or synonym of a data collection (examples: "ChEBI", "UniProt")

getDataTypesId

Retrieves the internal identifier (stable and perennial) of all the data collections (for example: "MIR:00000005").

Returns
array of strings - list of the identifier of all the data collections

getDataTypesName

Retrieves the list of names of all the data collections available.

Returns
array of strings - list of the name of all the data collections

getJavaLibraryVersion

Retrieves the latest version of the Java library available.

Returns
string - latest version of the Java library available

getLocation

Retrieves the physical location (URL) of a web page providing knowledge about a specific entity, using a specific resource.

Returns
string - physical location of a web page providing knowledge about the given entity, using a specific resource
Parameters Type Description
uri string MIRIAM URI of an entity (example: 'urn:miriam:obo.go:GO%3A0045202')
resource string internal identifier of a resource (example: 'MIR:00100005')

getLocations

Retrieves the (non obsolete) physical locationS (URLs) of web pageS providing knowledge about an entity.

If the URI is not recognised or the data collection does not exist, an empty array is returned.

If the identifier is invalid for the data collection, 'null' is returned.

All special characters in the data entry part of the URLs are properly encoded.

Returns
array of strings - physical locationS of web pageS providing knowledge about the given entity
Parameters Type Description
nickname string name (can be a synonym) or URI of a data collection (examples: "Gene Ontology", "UniProt")
id string identifier of an entity within the given data collection (examples: "GO:0045202", "P62158")

getLocations

Retrieves the (non obolete) physical locationS (URLs) of web pageS providing knowledge about a specific entity.

If the URI is not recognised or the data collection does not exist, an empty array is returned.

If the identifier is invalid for the data collection, 'null' is returned.

All special characters in the data entry part of the URLs are properly encoded.

Returns
array of strings - physical locationS of web pageS providing knowledge about the given entity
Parameter Type Description
uri string MIRIAM URI of an entity (example: 'urn:miriam:obo.go:GO%3A0045202')

getLocationsWithToken

Retrieves the list of (non obsolete) generic physical locations (URLs) of web pageS providing the dataset of a given data collection.

Warning: those URLs cannot be directly used! They contain a token which needs to be replaced by an actual data entry identifier.

If the data collection is not recognised or does not exist, 'null' is returned.

Returns
array of strings - list of (non obsolete) generic physical locations (URLs) of web pageS providing the dataset of a given data collection
Parameters Type Description
nickname string name (can be a synonym) or URI of a data collection (examples: "Gene Ontology", "UniProt", "urn:miriam:biomodels.db")
token string placeholder which will be put in the URLs at the location of the data entry identifier (default: $id)

getMiriamURI

Transforms a MIRIAM URI into its official equivalent (to transform obsolete URIs into current valid ones).

The parameter can be an obsolete URI (URN or URL), but the returned one will always be a URN.

This process involve a percent-encoding of all reserved characters (like ':').

Returns
string - the official URI corresponding to the deprecated one (for example: "urn:miriam:obo.chebi:CHEBI%3A17891") or 'null' if the URN does not exist
Parameter Type Description
uri string deprecated URI (URN or URL), example: "http://www.ebi.ac.uk/chebi/#CHEBI:17891"

getName

Retrieves the common name of a data collection.

Returns
string - the common name of the data collection
Parameter Type Description
uri string URI (URL or URN) of a data collection

getNames

Retrieves all the names (with synonyms) of a data collection.

Returns
array of strings - the common name of the data collection and all the synonyms
Parameter Type Description
uri string URI (URL or URN) of a data collection

getOfficialDataTypeURI

Retrieves the official URI (it will always be a URN) of a data collection.

Returns
string - the official URI of the data collection
Parameter Type Description
nickname string name (can be a synonym) or MIRIAM URI (even deprecated one) of a data collection (for example: "ChEBI", "http://www.ebi.ac.uk/chebi/", ...)

getOfficialURI

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

Retrieves the official URI (it will always be URN) of a data collection corresponding to the deprecated one.

Returns
string - the official URI corresponding to the deprecated one
Parameter Type Description
uri string deprecated URI (URN or URL) of a data collection

getResourceInfo

Retrieves the general information about a precise resource of a data collection.

Returns
string - general information about a resource
Parameter Type Description
id string identifier of a resource (example: "MIR:00100005")

getResourceInstitution

Retrieves the institution which manages a precise resource of a data collection.

Returns
string - institution which manages a resource
Parameter Type Description
id string identifier of a resource (example: "MIR:00100005")

getResourceLocation

Retrieves the location of the servers of a location.

Returns
string - location of the servers of a resource
Parameter Type Description
id string identifier of a resource (example: "MIR:00100005")

getServicesInfo

Retrieves some information about these Web Services.

Returns
string - information about the Web Services

getServicesVersion

Retrieves the current version of MIRIAM Web Services.

Returns
string - Current version of the Web Services

getURI

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

Retrieves the unique URI (URL or URN) of the data-entry (example: "urn:miriam:obo.go:GO%3A0045202").

Returns
string - unique URI of the data-entry
Parameters Type Description
name string name of a data collection (examples: "ChEBI", "UniProt")
id string identifier of an element (examples: "GO:0045202", "P62158")
type string type of the URI the user wants to recover ('URN' or 'URL')

getURI

Retrieves the unique URI of a specific entity (example: "urn:miriam:obo.go:GO%3A0045202").

If the data collection does not exist (or is not recognised), an empty String is returned.

If the identifier is invalid for the given data collection, 'null' is returned.

Returns
string - unique MIRIAM URI of a given entity
Parameters Type Description
name string name of a data collection (examples: "ChEBI", "UniProt")
id string identifier of an entity within the data collection (examples: "GO:0045202", "P62158")

getURIs

Retrieves the unique URIs for a list of specific entities (example: "urn:miriam:obo.go:GO%3A0045202").

If a data collection does not exist (or is not recognised), an empty String is returned for this data collection.

If an identifier is invalid for the given data collection, 'null' is returned for this data collection.

If the provided lists do not have the same size, 'null' is returned.

If the size of any list exceeds 200, 'null' is returned.

Returns
array of strings - list of MIRIAM URIs
Parameters Type Description
names array of strings list of data collection names (examples: "ChEBI", "UniProt")
ids array of strings list of entities identifiers (examples: "GO:0045202", "P62158")

getURL

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

Retrieves unique URL of the data-entry (example: "urn:miriam:obo.go:GO%3A0045202").

Returns
string - unique URN of the data-entry
Parameters Type Description
name string name of a data collection (examples: "ChEBI", "UniProt")
id string identifier of an element (examples: "GO:0045202", "P62158")

getURN

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

Retrieves the unique URN of the data-entry (example: "urn:miriam:uniprot:P62158").

Returns
string - unique URN of the data-entry
Parameters Type Description
name string name of a data collection (examples: "ChEBI", "UniProt")
id string identifier of an element (examples: "GO:0045202", "P62158")

isDeprecated

Says if a URI of a data collection is deprecated.

Returns
string - answer ("true" or "false") to the question: is this URI deprecated?
Parameter Type Description
uri string (URN or URL) of a data collection