Entrezpy tutorials

Esearch

Esearch searches the specified Entrez database for data records matching the query. It can return the found UIDs or a WebEnv/query_key referencing for the UIDs

• Esearch returning UIDs
• Esearch returning History server reference to UIDs

Conduit

The Conduit module facilitates creating pipelines to link individual Eutils request, i.e. linking the results of an Esearch to the corresponding nucleotide data records.

• Conduit pipelines
• Linking within and between Entrezpy databases

Extending entrezpy

entrezpy can be extended by inheriting its base classes. This will be the case when the final step is to fetch data records and do something with them, e.g. processing them for a database or parsing for specific information.

• Fetching publication information from Entrez
  • Overview
  • PubMed data structure
  • Simple Conduit pipeline to fetch PubMed Records
  • How to store PubMed data records
  • Defining PubmedResult and PubmedAnalyzer
  • Putting everything together
• Fetching sequence metadata from Entrez
  • Overview
  • Docsum data structure
  • Simple Conduit pipeline to fetch Docsum Records
  • How to store Docsum data records
  • Putting everything together