MTIWrapper

Julia wrapper to the Medical Text Indexer Java API

Travis CI	Coverage	License

Install

using Pkg
Pkg.add("https://github.com/bcbi/MTIWrapper.jl.git")

Usage

using MTIWrapper

Install mti Java API

mti_dir = "./"
MTIWrapper.install_web_api(mti_dir)

Compose a file to send to MTI from dataframe

input_file = MTIWrapper.abstracts_to_request_file(df, out_file, uid_column = :pmid, abstract_column= :abstract_text)

Send a batch query

MTIWrapper.mti_batch_query(mti_dir, ENV["NCBI_EMAIL"], ENV["UMLS_USER"], ENV["UMLS_PSSWD"], 
                           input_file, output_file)

Load results into a DataFrame

header = ["uid","term", "cui", "score", "type", "misc", "location", "path"]
df = CSV.read(output_file, header = header, datarow=3, delim='|')

MTI Output

Detail

Source

Format: PMID|Term|CUI|Score|Type|Misc|Location|Path(s)

PMID - PubMed assigned unique identifier. If freetext, this is "0".

Term - MeSH Term. If the term has an asterisk ("*") at the beginning, it denotes that the term was identified as coming from the Title section of a document. This is an optional output item and requires the "-starMHTI" option being specified.

CUI - Concept Unique Identifier for the MeSH Term.

Score - MTI score for this term.

Type - Type of the term: MH - MeSH Heading HM - Heading Mapped to ET - Entry Term NM - Supplemental Concept SH - MeSH SubHeading CT - MeSH CheckTag

Misc - If ET, this explains the replacement. If not, blank.

Location - If term comes from MMI, we have location information showing where the term came from within the text. "TI" - Title, "AB" - Abstract or "TI;AB" - comes from both Title and Abstract.

Path(s) - One or more designators showing which of the pathways recommended the term.

        MM - MetaMap's MMI
        RC - PubMed Related Citations
        TG - John Wilbur's Trigram Method