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BioModels Database

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BioModels Web Services

List of available queries

  1. getAllCuratedModelsId
  2. getAllModelsId
  3. getAllNonCuratedModelsId
  4. getAuthorsByModelId
  5. getDateLastModifByModelId
  6. getEncodersByModelId
  7. getModelById (deprecated)
  8. getModelNameById
  9. getModelSBMLById
  10. getModelsIdByChEBI
  11. getModelsIdByChEBIId
  12. getModelsIdByGO
  13. getModelsIdByGOId
  14. getModelsIdByName
  15. getModelsIdByPerson
  16. getModelsIdByPublication
  17. getModelsIdByTaxonomy
  18. getModelsIdByTaxonomyId
  19. getModelsIdByUniprot
  20. getModelsIdByUniprotId
  21. getModelsIdByUniprotIds
  22. getPublicationByModelId
  23. getSimpleModelById
  24. getSimpleModelsByChEBIIds
  25. getSimpleModelsByIds
  26. getSimpleModelsByReactomeIds
  27. getSimpleModelsByUniprotIds
  28. getSimpleModelsRelatedWithChEBI
  29. getSubModelSBML
  30. helloBioModels
  31. setEndPoint
  32. setProperty

Details of the queries

getAllCuratedModelsId

Retrieves the identifiers of all the published curated models.

Returns
array of strings - list of model identifiers

getAllModelsId

Retrieves the identifiers of all the published models.

Returns
array of strings - list of model identifiers

getAllNonCuratedModelsId

Retrieves the identifiers of all the published non-curated models.

Returns
array of strings - list of model identifiers

getAuthorsByModelId

Retrieves the name of the authors of the publication associated with a given model.

Returns
array of strings - names of the publication's authors, or 'null' if the provided identifier is not valid or the model does not exist
Parameter Type Description
modelId string model identifier (e.g. BIOMD0000000408 or MODEL1201250000)

getDateLastModifByModelId

Retrieves the date of last modification of a given model.

Returns
string - date of last modification (expressed according to ISO 8601), or 'null' if the provided identifier is not valid or the model does not exist
Parameter Type Description
modelId string model identifier (e.g. BIOMD0000000408 or MODEL1201250000)

getEncodersByModelId

Retrieves the name of the encoders of a given model.

Returns
array of strings - names of the model's encoders, or 'null' if the provided identifier is not valid or the model does not exist
Parameter Type Description
modelId string model identifier (e.g. BIOMD0000000408 or MODEL1201250000)

getModelById

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

Retrieves the SBML form of a model (in a string) given its identifier.

Returns
string - SBML model in a string, or 'null' if the provided identifier is not valid or the model does not exist
Parameter Type Description
id string model identifier (e.g. BIOMD0000000408 or MODEL1201250000)

getModelNameById

Retrieves the name of a model name given its identifier.

Returns
string - model name, or 'null' if the provided identifier is not valid or the model does not exist
Parameter Type Description
id string model identifier (e.g. BIOMD0000000408 or MODEL1201250000)

getModelSBMLById

Retrieves the SBML form of a model (in a string) given its identifier.

Returns
string - SBML model in a string, or 'null' if the provided identifier is not valid or the model does not exist
Parameter Type Description
id string model identifier (e.g. BIOMD0000000408 or MODEL1201250000)

getModelsIdByChEBI

Retrieves the identifiers of all models which are associated to some ChEBI terms. This relies on the method 'getLiteEntity' of the ChEBI Web Services (cf. http://www.ebi.ac.uk/chebi/webServices.do).

Returns
array of strings - list of models identifiers
Parameter Type Description
text string ChEBI identifier (e.g. CHEBI:4991) or name or synonym

getModelsIdByChEBIId

Retrieves the identifiers of all the models which are annotated with a given ChEBI term.

Returns
array of strings - list of models identifiers
Parameter Type Description
ChEBIId string identifier of a ChEBI term (e.g. CHEBI:4991)

getModelsIdByGO

Retrieves the models which are associated to the provided Gene Ontology text.

Returns
array of strings - list of models identifiers
Parameter Type Description
text string free (GO based) text

getModelsIdByGOId

Retrieves the models which are annotated with the given Gene Ontology term.

Returns
array of strings - list of models identifiers
Parameter Type Description
GOId string Gene Ontology identifier (e.g. GO:0006915)

getModelsIdByName

Retrieves the models' identifiers which name includes the given keyword.

Returns
array of strings - list of models identifiers
Parameter Type Description
modelName string part of a model name

getModelsIdByPerson

Retrieves the identifiers of all models which have a given person as author or encoder.

Returns
array of strings - list of models identifiers
Parameter Type Description
personName string author's or encoder's name

getModelsIdByPublication

Retrieves the identifiers of all models related to one (or more) publication(s).

Returns
array of strings - list of model identifiers
Parameter Type Description
publicationIdOrText string publication identifier (PMID or DOI) or text which occurs in the publication's title or abstract

getModelsIdByTaxonomy

Retrieves the models which are associated to the provided Taxonomy text.

Returns
array of strings - list of models identifiers
Parameter Type Description
text string free (Taxonomy based) text

getModelsIdByTaxonomyId

Retrieves the models which are annotated with the given taxon.

Returns
array of strings - list of models identifiers
Parameter Type Description
taxonomyId string Taxonomy identifier (e.g. 9606)

getModelsIdByUniprot

Retrieves all the models which are associated to the provided UniProt text.

Returns
array of strings - list of models identifiers
Parameter Type Description
text string free UniProt based text

getModelsIdByUniprotId

Retrieves all the models which are annotated with a given UniProt record.

Returns
array of strings - list of models identifiers
Parameter Type Description
uniprotId string

getModelsIdByUniprotIds

Retrieves all the models which are annotated with the given UniProt records.

Returns
array of strings - list of models identifiers
Parameter Type Description
uniprotIds array of strings

getPublicationByModelId

Retrieves the publication's identifier of a given model.

Returns
string - publication identifier (can be a PMID, DOI or URL), or 'null' if the provided identifier is not valid or the model does not exist
Parameter Type Description
modelId string model identifier (e.g. BIOMD0000000408 or MODEL1201250000)

getSimpleModelById

Retrieves the main information (identifier, name, publication identifier and date of last modification) about a given model.

Returns
string - simple XML representation of the main information about the model, or 'null' if the provided identifier is not valid or the model does not exist
Parameter Type Description
id string model identifier (e.g. BIOMD0000000408 or MODEL1201250000)

getSimpleModelsByChEBIIds

Retrieves the models which are annotated with the given ChEBI terms.

Returns
string - all models annotated with the provided ChEBI identifiers, as a TreeMap (which uses ChEBI identifiers as keys)
Parameter Type Description
ChEBIIds array of strings identifiers of a ChEBI terms (e.g. CHEBI:4991)

getSimpleModelsByIds

Retrieves the main information (identifier, name, publication identifier and date of last modification, ...) about given models.

Returns
string - simple XML representation of the main information about the models
Parameter Type Description
ids array of strings

getSimpleModelsByReactomeIds

Retrieves all the models which are annotated with the given Reactome records.

Returns
string - models annotated with the provided Reactome identifiers, as a TreeMap (which uses Reactome identifiers as keys)
Parameter Type Description
ReactomeIds array of strings list of Reactome identifiers (e.g. REACT_1590)

getSimpleModelsByUniprotIds

Retrieves all the models which are annotated with the given UniProt records.

Returns
string - all the models annotated with the provided UniProt records, as a TreeMap (which uses UniProt identifiers as keys)
Parameter Type Description
UniProtIds array of strings list of UniProt identifiers (e.g. P12345)

getSimpleModelsRelatedWithChEBI

Retrieves all the models which are annotated with ChEBI terms.

Returns
string - all models annotated with ChEBI terms, as a TreeMap (which uses ChEBI identifiers as keys)

getSubModelSBML

Generates the minimal sub-model of a given model in the database including all selected components.

Returns
string - sub-model encoded in SBML
Parameters Type Description
modelId string identifier of the model from which the sub-model will be extracted
elementsIds array of strings identifiers of the selected elements. Currently only supports identifiers from compartments, species, and reactions.

helloBioModels

Checks if the web services are working properly.

Returns
string - "Hello BioModels", if the call is a success

setEndPoint (only available from the Java library)

Sets the address of the web services endpoint.

A default endpoint is provided, so the usage of this method is only useful if you wish to use our testing services instead of the production ones.

Returns
void
Parameter Type Description
address string URL of the web services endpoint to be used

setProperty (only available from the Java library)

Sets the values of environmental variables (useful for things such as proxy, ...).

Returns
void
Parameters Type Description
propertyName string name of the property
value string value of the property

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