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medgen

what is medgen?

medgen provides functions for annotating Medical Genetics information: genes and conditions from the NCBI MedGen databases (https://bitbucket.org/invitae/medgen-mysql). For example, the Gene2Condition service uses annotations from this database for annotating diseases associated with a specific gene, including the mode of inheritance and extensive phenotypic descriptions from MedGen linked data sources including OMIM and HPO (Human Phenotype Ontology). Use of MedGen extends from variant level details provided by ClinVar all the way to disease descriptions used in hospital medical record systems (SNOMED) and billing systems (ICD9).

Depends

medgen-python uses either a local or hosted set of https://bitbucket.org/invitae/medgen-mysql databases. See requirements.txt for the list of python required packages.

support and licensing

medgen python is a free and open source library provided by Invitae under the [Apache 2.0 License](http://www.apache.org/licenses/), a copy of which is included within the repository.

All questions, concerns, support, and curse words should be directed to package maintainers Andrew McMurry (AndyMC@apache.org) and BioMed contributors ( BioMed@invitae.com ).

Contributions to this library are encouraged via fork and pull request. Diffs may be accepted when attached to nicely written emails.

api-shell

virtualenv ve
source ve/bin/activate
pip install -r bin/requirements.txt
./api-shell
whos

API Functional documentation

type "whos" to see a list of supported API functions.
type "function?" to see the docstring for a given function.

API (frequency used, not extensive list)

  • ClinvarPubmeds?
  • ClinvarAccession?
  • Concept?
  • Define?
  • Relate?
  • DiseaseName?
  • DiseaseParents?
  • DiseaseSubtypes?
  • Gene?
  • Gene2PubMed?
  • GeneID?
  • GeneInfo?
  • GeneNamePreferred?
  • GeneSynonyms?
  • Gene2ConditionSource?
  • Gene2Function?
  • Gene2LocusDB?
  • GeneName?
  • GeneNamePreferred?
  • Gene2PubMed?
  • GeneSynonyms?
  • MedGenDB?
  • PMID2Article?
  • PMCID2Article?
  • SQLData?

SQLData classes

SQLData? MedGenDB? ClinVarDB? GeneDB? HugoDB? PubMedDB?