MapFace - A Graphical Editor for MetaMap Transfer (MMTx)

The MMTx program [1] tokenizes free text of medical documents into phrases and maps UMLS concepts [3] to the medical concepts identified within these phrases. Due to the complexity of this task, it is still necessary to correct parts of the tokenization as well as the mapping of UMLS concepts. To correct these results with the help of the MapFace editor ensures the quality of the output, which in turn improves the output of subsequent tasks using this information as input.

Besides correcting the information provided by the MMTx program, MapFace serves the purpose of visualizing these results in a transparent and intelligible way. Phrases or medical concepts can be selected in the text, whereupon the corresponding information is displayed. Visualizing the semantic information is accomplished by color-coding the semantic types and highlighting the text accordingly. In addition, MapFace provides information about relations between the constructs in the text. The visualization of the acquired information is important for knowledge engineers in order to better understand the medical text, thus ensuring the quality of further transformation processes leading to a stable, computer-executable model.

Example
An arbitrary sentence of a medical document could be:

The MMTx program tokenizes the sentence into phrase chunks and maps the text to medical concepts available in the UMLS Metathesaurus:

Corrections accomplished by means of the MapFace edior:

• Splitting the phrase chunk "with mild asthma inhaled steroids"
• Coosing the correct UMLs concept in case of an ambiguous mapping;
• Merging the concept chunks "five" and "years" to a single chunk and assingning a UMLS concept matching the text "age".

User Interface

The user interface of MapFace is divided into three different panes: the editor pane, the candidates pane, and the annotation scheme pane.

Components of the MapFace GUI

The Editor Pane

The main window of the Graphical User Interface of MapFace is the editor pane. It displays the text of the document. This is where the user can select some text and process it by means of the MMTx program. In addition, the user can select the concepts or phrases of processed text by double-clicking the text chunk of the concept or phrase in the editor, whereupon a list of best matching UMLS concept candidates will be displayed in the candidates view.

Example above (phrases delimited by brackets)

The Candidates Pane

The candidates pane contains three different views, the candidates view, the concept relations view, and the semantic relations view.
The main view of the candidates pane is the candidates view. It provides information about the best matching UMLS concept candidates for a given text chunk and possibilities for editing. Therefore the candidates view displays a list of candidates detected by the MMTx program for a selected concept chunk or phrase chunk in the editor, together with their semantic types, semantic collections [2], and semantic groups [4].

UMLS concept candidates for the text chunk "woman"

The concept relations view displays a list of all relations between the concept candidate selected in the candidates view and the UMLS concepts affiliated to concept chunks in the same section of the text.
The semantic relations view provides a list of all relations between the semantic type of the UMLS concept candidate selected in the candidates view and the semantic types occurring in the same section of the text.

Semantic relations of the concept chunk "Ovarian cancer"
 

The Annotation Scheme Pane

The annotation scheme pane of the basic MapFace program contains two different views, the semantic collections view, and the XML elements view.
The semantic collections view contains a list of all semantic types, grouped by semantic collections [2], each associated with a different color. Here the user can select semantic types of interest, which will highlight every text chunk in the editor assotiated with these semantic types.
The XML elements view contains all names of XML tags occurring in the XML document that is being processed. By selecting an XML element in the view, the corresponding text chunk of the guideline is highlighted in the editor.

Software Prototype

>> Download MapFace editor (size: 30,8 MB)
Filename: mapface_2.0.zip (build #50)
Needed application: MMTx V2.4C, Windows, Java JRE 5

Papers

Theresia Gschwandtner, Katharina Kaiser, Patrick Martini, Silvia Miksch: Easing Semantically Enriched Information Retrieval - An Interactive Semi-Automatic Annotation System for Medical Documents. International Journal of Human-Computer Studies (IJHCS), Special Issue on Human Computer Interaction for Medicine (HCI4MED), accepted. [bibtex]

Theresia Gschwandtner, Katharina Kaiser, Silvia Miksch: MapFace - A Graphical Editor to Support the Semantic Annotation of Medical Text. In Proc. of the Junior Scientist Conference 2008 (JSC'08), H. Kaiser, R. Kirner (Eds.), Vienna, Austria, p. 91 - 92, November 2008. [bibtex]

Theresia Gschwandtner, Katharina Kaiser, Patrick Martini, Silvia Miksch: MapFace - An Aid for Medical Experts to Easily Annotate Documents with MetaMap Transfer. In Proc. of the Workshop on Human-Computer Interaction for Medicine and Health Care (HCI4MED'08) at BCS HCI 2008, Liverpool, UK, September 2, 2008. [bibtex]

Katharina Kaiser, Theresia Gschwandtner, Patrick Martini: MapFace - An Editor for MetaMap Transfer (MMTx). In Proc. of the 21st IEEE International Symposium on Computer-based Medical Systems (CBMS 2008), Jyväskylä, Finland, p. 150 - 152, IEEE Computer Society, June 2008. [bibtex]

Theresia Gschwandtner: MapFace - A Graphical Editor for MetaMap Transfer (MMTx); Master's thesis. Supervisors: S. Miksch, K. Kaiser; Vienna University of Technology, Institute of Software Technology and Interactive Systems, Vienna, Austria, 2008. [bibtex]

References
[1] Alan R. Aronson (2001): Effective Mapping of Biomedical Text to the UMLS Metathesaurus: The MetaMap Program, in: Proc. of the Annual AMIA Symposium 2001, 17-21.
[2] Zong Chen, Yehoshua Perl, Michael Halper, James Geller, Huanying Gu (2002): Partitioning the UMLS Semantic Network, in: IEEE Transactions on Information Technology in Biomedicine, Number: 2, Volume: 6, 102-108.
[3] Donald A. Lindberg, Betsy L. Humphreys, Alexa T. McCray (1993): The Unified Medical Language System, in: Methods of Information in Medicine, Number 4, Volume 32, 281-291.
[4] Alexa T. McCray, Anita Burgun, Olivier Bodenreider (2001): Aggregating UMLS Semantic Types for Reducing Conceptual Complexity, in: Proceedings from the Medinfo 2001 World Congress on Medical Informatics, Volume: 84 Studies in Health Technology and Informatics, 216-220, IOS Press.