Entrez

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

# BioMedQuery.Entrez.esearch — Method.

esearch(search_dict)

Request list of UIDs matiching a query - see NCBI Entrez:Esearch

Arguments

• search_dic::Dict: dictionary specifying search criteria

Output

• ::String: XML response from NCBI

Example

search_dic = Dict("db"=>"pubmed", "term" => search_term,
"retstart" => 0, "retmax"=>5, "tool" =>"BioJulia",
"email" => "email")
esearch_response = esearch(search_dic)

Note

• email must be a valid email address (otherwise pubmed will block you)
• search_term corresponds to a valid PubMed Search. It may contain one or more filtering criteria using AND/OR.

For instance:

search_term = (asthma[MeSH Terms]) AND ("2001/01/29"[Date - Publication] : "2010"[Date - Publication]).

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EFetch

# BioMedQuery.Entrez.efetch — Method.

efetch(fetch_dic, id_list)

Retrieve data records from a list of UIDs - see NCBI Entrez: EFetch

Arguments

• fetch_dic::Dict - Dictionary specifying fetch criteria
• id_list::Array - List of ids e.g those embedded in response from esearch

Results

• ::String - XML response from NCBI

Example

# get the list of ids
if !haskey(esearch_dict, "IdList")
  error("Error: IdList not found")
end

ids = []

for id_node in esearch_dict["IdList"][1]["Id"]
  push!(ids, id_node)
end

# define the fetch dictionary
fetch_dic = Dict("db"=>"pubmed","tool" =>"BioJulia",
"email" => email, "retmode" => "xml", "rettype"=>"null")

# fetch
efetch_response = efetch(fetch_dic, ids)

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ELink

# BioMedQuery.Entrez.elink — Method.

elink(elink_dict)

Lists, checks or returns UIDs linked to an input list of UIDs in the same or different Entrez database. For more info see NCBI Entrez:ELink

Arguments

• elink_dict::Dict: dictionary specifying elink inputs as credentials, ids...

Output

• ::String: XML response from NCBI

Example

pmid = "19304878"
elink_dict = Dict("dbfrom" =>"pubmed", "id" => pmid,
                  "linkname" => "pubmed_pubmed", "email"=>email)
elink_response = elink(elink_dict)

source

ESummary

# BioMedQuery.Entrez.esummary — Method.

esummary(esummary_dict)

Return document summaries for a list of input UIDs. For more info see NCBI Entrez:ESummary

Arguments

• esummary_dict::Dict: dictionary specifying esummary inputs as credentials, ids...

Output

• ::String: XML response from NCBI

Example

pmid = "30367"
esummary_dict = Dict("db" =>"pubmed", "id" => pmid, "email"=>email)
esummary_response = esummary(esummary_dict)

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EParse

# BioMedQuery.Entrez.eparse — Method.

eparse(response::String)

Converts NCBI XML response into a Julia dictionary

source

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

# BioMedQuery.Entrez.DB.all_pmids — Method.

all_pmids(db)

Return all PMIDs stored in the article table of the input database

source

All MESH descriptors for an article

# BioMedQuery.Entrez.DB.get_article_mesh — Method.

get_article_mesh(db, pmid)

Get the all mesh-descriptors associated with a give article

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