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OpenOmics 0.8.8 documentation
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OpenOmics 0.8.8 documentation

Using OpenOmics Python API

  • Installation
  • Getting started
  • Loading a multi-omics dataset
  • External annotation databases
  • Creating biological interaction networks
  • Preparing data for downstream analyses

API Reference

  • MultiOmics data
    • ClinicalData
    • CopyNumberVariation
    • DNAMethylation
    • Expression
    • LncRNA
    • MessengerRNA
    • MicroRNA
    • MultiOmics
    • Protein
    • SomaticMutation
  • Annotation interfaces
    • Annotatable
    • Database
  • Genomic databases
    • BioMartManager
    • EnsemblGeneSequences
    • EnsemblGenes
    • EnsemblSNP
    • EnsemblSomaticVariation
    • EnsemblTranscriptSequences
    • GTEx
    • NONCODE
    • ProteinAtlas
    • RNAcentral
    • TANRIC
  • Sequence databases
    • GENCODE
    • MirBase
    • SequenceDatabase
  • Interaction databases
    • BioGRID
    • GeneMania
    • Interactions
    • LncBase
    • LncRNA2Target
    • LncReg
    • MiRTarBase
    • NPInter
    • STRING
    • StarBase
    • TargetScan
    • lncRInter
    • lncRNome
  • Disease databases
    • DisGeNet
    • DiseaseAssociation
    • HMDD
    • LncRNADisease
    • MalaCards
    • OMIM
  • Ontology databases
    • dfs_path
    • filter_dfs_paths
    • flatten
    • flatten_list
    • traverse_predecessors
    • write_taxonomy
    • GeneOntology
    • HumanPhenotypeOntology
    • Ontology
  • Utilities
    • get_pkg_data_filename
    • read_gtf

MISC

  • Frequently Asked Questions (FAQ)

Contributing and releases

  • Contributing
  • Release history

DiseaseAssociation¶

class openomics.database.disease.DiseaseAssociation(path, file_resources=None, **kwargs)[source][source]¶

Bases: openomics.database.base.Database

Methods Summary

get_disease_assocs([index])

param index

Methods Documentation

abstract get_disease_assocs(index='gene_name')[source][source]¶
Parameters

index –

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