MetaMapLite ReSTful client

Introduction

This client provides a reference implementation of a client for MetaMapLite ReSTful service at the URL: https://ii.nlm.nih.gov/metamaplite/rest/annotate . An interactive form that uses the ReST service is at https://ii.nlm.nih.gov/metamaplite/rest

Where to get the ReST Client

The MetaMapLite ReST client is available at: https://data.lhncbc.nlm.nih.gov/public/ii/tools/MetaMap/download/metamaplite/mmlrestclient.py

Available document input and result output formats

Document Input Formats

freetext: Unstructured text
sli: Single Line Delimited Input
sldiwi: Single Line Delimited Input with ID: Each line contains id and text separated by a separator (pipe) symbol
pubmed: PubMed XML document format
medline: Medline document format

Result Output Formats

brat: Brat Standoff format
mmi: MetaMap Indexing
full: piped separated representation
json: json representation of full format
cui: list UMLS concept identifiers found

Example of use

Example of input with docformat sldiwi and output mmi:

Txt001|Written informed consent.
Txt002|Age 18 years or older.
Txt003|informed consent.
Txt004|Male or female.

The client is invoked like this when specifying document format sldiwi and result format mmi:

python mmlrestclient.py \
    https://ii.nlm.nih.gov/metamaplite/rest/annotate \
    inputfile \
    --output outputfile \
    --docformat sldiwi \
    --resultformat mmi

Output looks like this with mmi :

Txt004|MMI|1.38|Female Phenotype|C1705498|[qlco]|"Female"-text-0-"female"-NN-0|8/6|x.x.x
Txt004|MMI|1.38|Female, Self-Report|C1705497|[qlco]|"Female"-text-0-"female"-NN-0|8/6|x.x.x
Txt004|MMI|1.38|Females|C0086287|[orga]|"Female"-text-0-"female"-NN-0|8/6|x.x.x
Txt004|MMI|1.38|Male Gender, Self Report|C1706180|[qlco]|"Male"-text-0-"Male"-NN-0|0/4|x.x.x
Txt004|MMI|1.38|Male Phenotype|C1706428|[qlco]|"Male"-text-0-"Male"-NN-0|0/4|x.x.x
Txt004|MMI|1.38|Male, Self-Reported|C1706429|[orga]|"Male"-text-0-"Male"-NN-0|0/4|x.x.x
Txt004|MMI|1.38|Males|C0086582|[orga]|"Male"-text-0-"Male"-NN-0|0/4|x.x.x
Txt004|MMI|1.38|Woman|C0043210|[popg]|"female"-text-0-"female"-NN-0|8/6|x.x.x
Txt003|MMI|9.21|Informed Consent|C0021430|[rnlw]|"Informed Consent"-text-0-"informed consent"-JJ-0|0/16|I01.880.604.473.650.718;I01.880.604.583.427;N03.706.437.650.312;N03.706.535.489
Txt002|MMI|0.46|Age|C0001779|[orga]|"Age"-text-0-"Age"-NNP-0|0/3|
Txt002|MMI|0.46|Age:Time:Point in time:^Patient:Quantitative|C1114365|[clna]|"Age"-text-0-"Age"-NNP-0|0/3|
Txt002|MMI|0.46|year|C0439234|[tmco]|"years"-text-0-"years"-NNS-0|7/5|
Txt001|MMI|0.46|ActClass - consent|C1554192|[idcn]|"consent"-text-0-"consent"-NN-0|17/7|
Txt001|MMI|0.46|Consent|C1511481|[ftcn]|"Consent"-text-0-"consent"-NN-0|17/7|
Txt001|MMI|0.46|Consent:Finding:Point in time:{Setting}:Document:Patient|C2923685|[clna]|"Consent"-text-0-"consent"-NN-0|17/7|
Txt001|MMI|0.46|Written - Consent Mode|C1547186|[idcn]|"Written"-text-0-"Written"-NNP-0|0/7|
Txt001|MMI|0.46|written - ParticipationMode|C1576874|[ftcn]|"written"-text-0-"Written"-NNP-0|0/7|