Welcome to PhenomeDB’s documentation

PhenomeDB (/fee-gnome-dee-bee/) is a platform for harmonising and integrating metabolomics data across multiple projects.

PhenomeDB was developed by the informatics team at the National Phenome Centre at Imperial College London.

Getting started

Please see the following guides for installing and using PhenomeDB

Contents:

Installation
- Local/desktop Docker installation
- Python installatiion
- Running the tests
- Building the docs
Settings
- Local Python Installation
- Docker installation
- TEST
- DB
- WEBSERVER
- API
- REDIS
- R
- SMTP
- DATA
- API_KEYS
- LOGGING
- PIPELINES
Usage
- Tasks
- The Apache-Airflow interface
- Tasks and Pipelines
- Command line interface
- Importing analytical data and sample metadata
- Harmonising sample metadata
- Importing compound metadata
- Harmonising annotation metadata
- Creating and executing queries
- Scaling, normalisation, and batch correction
- Running analyses
API
Development
- Core platform architecture
- Adding tasks
- Building the docker images
phenomedb.analysis
- AnalysisTask
- NPYCTask
- RAnalysisTask
- RunMWAS
- RunNPYCReport
- RunPCA
- RunPCPR2
- RunWilcoxonRankTest
- RunXCMS
phenomedb.batch_correction
- RunCombatCorrection
- RunDBnormCorrection
- RunNPYCBatchCorrection
- RunNPYCBatchCorrectionReportsForExistingCorrectedFeatureDataset
- RunNormResidualsMM
- SaveBatchCorrection
phenomedb.base_view
- PhenomeDBBaseView
phenomedb.cache
- Cache
- CreateSavedQueryDataframeCache
- CreateSavedQuerySummaryStatsCache
- CreateTaskViewCache
- MoveTaskOutputToCache
- RemoveUntransformedDataFromCache
phenomedb.compounds
- AddMissingClassyFireClasses
- CleanROIFile
- CompoundTask
- ExportCompoundsToCSV
- ImportBrukerBiLISACompounds
- ImportBrukerBiQuantCompounds
- ImportCompoundsFromCSV
- ImportROICompounds
- ImportStandardsV1
- ParseHMDBXMLtoCSV
- ParseKEGGtoPubchemCIDTask
- UpdateCompoundRefs
phenomedb.database
- get_beta_database_session()
- get_database_session()
- get_db_session()
- get_test_database_session()
phenomedb.imports
- Main import tasks
phenomedb.metadata
- Overview of the HarmoniseMetadataField task
phenomedb.models
- AnnotatedFeature
- Annotation
- AnnotationCompound
- AnnotationEvidence
- AnnotationEvidenceFileUpload
- AnnotationMethod
- Assay
- ChemicalStandardDataset
- ChemicalStandardPeakList
- Compound
- CompoundClass
- CompoundClassCompound
- CompoundExternalDB
- DataRepository
- EvidenceType
- ExternalDB
- FeatureDataset
- FeatureMetadata
- HarmonisedAnnotatedFeature
- HarmonisedAnnotation
- HarmonisedDataset
- HarmonisedMetadataField
- Laboratory
- MetadataField
- MetadataValue
- MissingImportData
- OntologyRef
- OntologySource
- Pipeline
- Project
- Protocol
- ProtocolParameter
- Publication
- Sample
- SampleAssay
- SampleAssayFeatures
- SampleAssayProtocol
- SavedQuery
- Subject
- TaskRun
- Unit
phenomedb.pipeline_factory
- Overview
- User Interface
- Python API
phenomedb.pipelines
- BasicSetup
- BatchCorrectionAssessmentPipelineGenerator
- DynamicPipelineTask
- GenerateSingleTaskPipelines
- ImportAllMetabolightsPipelineGenerator
- PipelineGeneratorTask
- RebuildPipelinesFromDB
- RunBatchCorrectionAssessmentPipeline
- RunMWASMulti
phenomedb.query_factory
- MetadataFilter
- ProjectRoleFilter
- QueryFactory
- QueryFilter
- QueryMatch
- QuerySubFilter
phenomedb.task
- CreateAnnotationMethod
- CreateAssay
- CreateHarmonisedMetadataField
- CreateLab
- CreateProject
- CreateUnit
- ManualSQL
- Task
phenomedb.utilities
- CustomEncoder
- breakdown_annotation_id()
- breakdown_compound_class_id()
- configure_logging()
- flatten_model_for_search()
- get_date()
- get_module_and_class_name()
- get_npyc_enum_from_value()
- is_number()
- isfloat()
- isint()
- round_decimals_down()
- round_decimals_up()
- send_tls_email()
- serialise_unserialise()
- total_size()
phenomedb.views

Indices and tables