phenomedb.models

class phenomedb.models.AnnotatedFeature(**kwargs)
class phenomedb.models.Annotation(**kwargs)
class MultiCompoundOperator(value)

An enumeration.

class phenomedb.models.AnnotationCompound(**kwargs)
class phenomedb.models.AnnotationEvidence(**kwargs)
class phenomedb.models.AnnotationEvidenceFileUpload(**kwargs)
class phenomedb.models.AnnotationMethod(**kwargs)
class phenomedb.models.Assay(**kwargs)
class QuantificationType(value)

An enumeration.

class phenomedb.models.ChemicalStandardDataset(**kwargs)
class phenomedb.models.ChemicalStandardPeakList(**kwargs)
class phenomedb.models.Compound(**kwargs)
class phenomedb.models.CompoundClass(**kwargs)
class CompoundClassType(value)

An enumeration.

class phenomedb.models.CompoundClassCompound(**kwargs)
class phenomedb.models.CompoundExternalDB(**kwargs)
class phenomedb.models.DataRepository(**kwargs)
class phenomedb.models.EvidenceType(**kwargs)
class phenomedb.models.ExternalDB(**kwargs)
class phenomedb.models.FeatureDataset(**kwargs)
class CorrectionType(value)

An enumeration.

class Type(value)

An enumeration.

class phenomedb.models.FeatureMetadata(**kwargs)

Feature Metadata

class phenomedb.models.HarmonisedAnnotatedFeature(**kwargs)
class phenomedb.models.HarmonisedAnnotation(**kwargs)

Annotation

class MultiCompoundOperator(value)

An enumeration.

class phenomedb.models.HarmonisedDataset(**kwargs)
class Type(value)

An enumeration.

class phenomedb.models.HarmonisedMetadataField(**kwargs)

Metadata Harmonised Field

class HarmonisedMetadataFieldDatatype(value)

An enumeration.

class phenomedb.models.Laboratory(**kwargs)
class phenomedb.models.MetadataField(**kwargs)
class phenomedb.models.MetadataValue(**kwargs)
class phenomedb.models.MissingImportData(**kwargs)
class phenomedb.models.OntologyRef(**kwargs)
class phenomedb.models.OntologySource(**kwargs)
class phenomedb.models.Pipeline(**kwargs)
class phenomedb.models.Project(**kwargs)

Project represents the information about the project being analysed

class phenomedb.models.Protocol(**kwargs)
class phenomedb.models.ProtocolParameter(**kwargs)
class phenomedb.models.Publication(**kwargs)
class phenomedb.models.Sample(**kwargs)

Sampling Event

class phenomedb.models.SampleAssay(**kwargs)

Sampling Event Assay

class phenomedb.models.SampleAssayFeatures(**kwargs)

Sampling Event Assay

class phenomedb.models.SampleAssayProtocol(**kwargs)
class phenomedb.models.SavedQuery(**kwargs)

SavedQuery object

Parameters:

  • id (int) – Primary Key

  • name (str) – The name of the SavedQuery

  • description (str) – The description of the SavedQuery

  • json (dict) – The definition of the SavedQuery in JSON format

  • project_short_label (str) – A short label that will be displayed in downstream analyses

  • code_string (str) – The SQLAlchemy representation of the query

  • created_by (str) – The user who created the query

  • date_added (datetime.datetime) – The data the query was added

  • type (phenomedb.models.SavedQuery.Type) – The Type, whether ‘custom’ or ‘preset’, only used by the UI

  • cache_state (dict) – The current cache state of the query result dataframes

class Type(value)

An enumeration.

class phenomedb.models.Subject(**kwargs)
class phenomedb.models.TaskRun(**kwargs)
class Status(value)

An enumeration.

class phenomedb.models.Unit(**kwargs)