entrez.md

Julia interface to Entrez Utilities API.

For executables that use this package to search PubMed, see the sister package PubMedMiner

Import Module

using BioMedQuery.Entrez

The following E-utils functions have been implemented:

• ESearch
• EFetch
• ELink
• ESummary

The following utility functions are available to handle and store NCBI responses

• EParse - Convert XML response to Julia Dict
• Saving NCBI Responses to XML
• Saving EFetch to a SQLite database
• Saving EFetch to a MySQL database

The following utility functions are available to query the database

• All PMIDs
• All MESH descriptors for an article

ESearch

CurrentModule = BioMedQuery.Entrez

esearch(search_dict)

EFetch

efetch(fetch_dic, id_list)

ELink

elink(elink_dict)

ESummary

esummary(esummary_dict)

EParse

eparse(ncbi_response::ASCIIString)

Saving NCBI Responses to XML

You can save directly the XML String to file using the XMLconvert Package

###Example

    XMLconvert.xmlASCII2file(efetch_response, "./efetch.xml")

Saving EFetch to a SQLite database

save_efetch_sqlite(efetch_dict, db_config, verbose)

Saving EFetch to a MySQL database

save_efetch_mysql(efetch_dict, db_config, verbose)

The following schema has been used to store the results. If you are interested in having this module store additional fields, feel free to open an issue

All PMIDs

all_pmids(db)

All MESH descriptors for an article

get_article_mesh(db, pmid::Integer)