UMLS

Search the Unified Medical Language System (UMLS), for more details visit the REST API.

Searching the UMLS requires approved credentials. You can sign up [here]](https://uts.nlm.nih.gov//license.html)

Import

using BioMedQuery.UMLS

Credentials

# BioMedQuery.UMLS.Credentials — Type.

Credentials(user, psswd)

source

Search the UMLS

# BioMedQuery.UMLS.search_umls — Method.

search_umls(c::Credentials, query)

Search UMLS Rest API. For more info see UMLS_API

Arguments

  • c::Credentials: UMLS username and password
  • query: UMLS query containing the search term
  • version: Optional - defaults to current

Output

  • result_pages: Array, where each entry is a dictionary containing a page of

results. e.g

Dict{AbstractString,Any} with 3 entries: "pageSize" => 25 "pageNumber" => 1 "result" => Dict{AbstractString,Any}("classType"=>"searchResults","result…

Examples


julia credentials = Credentials(user, psswd) tgt = get_tgt(credentials) term = "obesity" query = Dict("string"=>term, "searchType"=>"exact" ) all_results= search_umls(tgt, query) ```


<a target='_blank' href='https://github.com/bcbi/BioMedQuery.jl/tree/6784d8728ec34959a797e41b8178c17a1243251d/src/UMLS/UMLS.jl#L97-L129' class='documenter-source'>source</a><br>


<a id='Best-match-CUI-1'></a>

## Best match CUI

<a id='BioMedQuery.UMLS.best_match_cui-Tuple{Any}' href='#BioMedQuery.UMLS.best_match_cui-Tuple{Any}'>#</a>
**`BioMedQuery.UMLS.best_match_cui`** &mdash; *Method*.

best_match_cui(result_pages)


Retrive the best match from array of all result pages

###Example

```julia
cui = BioMedQuery.UMLS.best_match_cui(all_results)

source

Semantic types of a CUI

# BioMedQuery.UMLS.get_semantic_type — Method.

get_semantic_type(c::Credentials, cui)

Return an array of the semantic types associated with a cui

Example

credentials = Credentials(user, psswd)
tgt = get_tgt(credentials)
cui = "C0028754"
sm = BioMedQuery.UMLS.get_semantic_type(tgt, cui)

source

Semantic Network Database

# BioMedQuery.UMLS.populate_net_mysql — Method.

populate_net_mysql(config; sn_version, mysql_version)

Populate and return a MySQL database with the UMLS Semantic Network Structure

Arguments:

  • config:Dict(): Dictionary containing MySQL database information
  • sn_version: Version of the Semantic Network (defaults to 2015AB). Available

versions include: 2015AB (planning to include future releases)

  • mysql_version: Supported and default version is mysql5_6

Example:

host="localhost"
username="root"
password=""
umls_sn_dbname="umls_sn"
overwrite_db=true

db_config = Dict(:host=>host,
                 :dbname=>umls_sn_dbname,
                 :username=>username,
                 :pswd=>password,
                 :overwrite=>overwrite_db)
umls_sn_db= populate_net_mysql(db_config)

source

Schema

The schema of the MySQL database of the semantic network is the following:

Note:

The previous function uses the original scripts that are part of MetamorphoSys (part of the mmsys.zip downloaded here), and the current Relational ASCII (CVS) files for the UMLS Semantic Network (obtained here)

For useful information on loading your Semantic Network files into an Oracle or MySQL database, please consult the on-line documentation at:

http://www.nlm.nih.gov/research/umls/implementation_resources/scripts/index.html