MedTator

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MedTator Settings

MEM: {{ get_metator_mem() }} MB
Import
GUI

Sentence Splitting Algorithm :

Linking marks selection between editor and concept list :

 
Filter: {{ anns.length }} files
  • {{ v_ann._filename }}
    {{ anns[v_ann.idx].tags.length }}

Load schema file first

Drop Annotation File(s) / Folder Here
(.xml / .txt)

  • All Tags
    {{ count_n_tags(null) }}
  • {{ etag.shortcut }}
    {{ count_n_tags(etag) }}
  • {{ ltag.shortcut }}
    {{ count_n_tags(ltag) }}
Tag ID Spans Text Attributes
{{ tag.tag }}
{{ tag.id }} {{ tag._annotator }} DOCUMENT {{ tag.spans }} LINK {{ tag.text }}
{{ attlist.name }} *  
Creating a Link Tag {{ linking_tag.tag }}
 - {{ attlist.name }}

Corpus Files

# TXT File Name   XML File Name
{{ txt_ann_idx + 1 }} {{ txt_ann._filename }} {{ get_new_xml_filename(txt_xmls[txt_ann_idx].fn) }} Download

Export Preview

IAA:

Tag Name
F1
OVERALL
 
{{ to_fixed(iaa_dict.all.f1) }}
{{ etag.name }}
 
{{ to_fixed(iaa_dict.tag[etag.name].f1) }}

Text Matched Files: {{ iaa_dict.stat.matched_hashcodes.length }}

Duplicated Files: {{ iaa_dict.stat.duplicates.length }}

Unmatched Files: {{ iaa_dict.stat.unmatched.length }}

Annotation Files

File names
OVERALL {{ iaa_display_tag_name }}   F1
A: {{ iaa_dict.ann[v_ann.ann_hashcode].anns[0]._filename }}
B: {{ iaa_dict.ann[v_ann.ann_hashcode].anns[1]._filename }}
GS: {{ iaa_gs_dict[v_ann.ann_hashcode].ann._filename }}
 
{{ to_fixed(get_rst(iaa_dict.ann[v_ann.ann_hashcode].rst)['f1']) }}
AB: {{ get_rst(iaa_dict.ann[v_ann.ann_hashcode].rst).cm.tp }} A+: {{ get_rst(iaa_dict.ann[v_ann.ann_hashcode].rst).cm.fp }} B+: {{ get_rst(iaa_dict.ann[v_ann.ann_hashcode].rst).cm.fn }}
OVERALL {{ iaa_display_tag_name }} in GS: {{ count_gs_tags(v_ann.ann_hashcode) }}

Annotated Tags

A {{ iaa_dict.ann[iaa_display_hashcode].anns[0]._filename }}
B {{ iaa_dict.ann[iaa_display_hashcode].anns[1]._filename }}
{{ iaa_gs_dict[iaa_display_hashcode].ann._filename }}
{{ tag_name }} AB: {{ tag_rst.cm.tp }} A+: {{ tag_rst.cm.fp }} B+: {{ tag_rst.cm.fn }}
{{ tag_name }} Total: {{ count_iaa_gs_tag_notnull(iaa_gs_dict[iaa_display_hashcode].rst[tag_name]) }}  
 

IAA:

Overall Cohen's Kappa: {{ to_fixed(iaa_dict.all.cohen_kappa.kappa) }}     Percentage Agreement: {{ to_fixed(iaa_dict.all.cohen_kappa.Po) }}
TP: {{ iaa_dict.all.cm.tp }}   FP: {{ iaa_dict.all.cm.fp }}   FN: {{ iaa_dict.all.cm.fn }}   N: {{ iaa_dict.all.cohen_kappa.N }}
Po: {{ to_fixed(iaa_dict.all.cohen_kappa.Po) }}   Pe: {{ to_fixed(iaa_dict.all.cohen_kappa.Pe) }}   SEk: {{ to_fixed(iaa_dict.all.cohen_kappa.SE_k) }}   95% CI: {{ to_fixed(iaa_dict.all.cohen_kappa.lower) }}, {{ to_fixed(iaa_dict.all.cohen_kappa.upper) }}
  Annotator B
    {{ tag_def.name }} EMPTY Pb
Annotator A {{ tag_def_row.name }} {{ iaa_dict.tag[tag_def_row.name].cm.tp }}   {{ iaa_dict.tag[tag_def_row.name].cm.fp }} {{ to_fixed(iaa_dict.all.cohen_kappa.Pes.b[tag_def_row.name]) }}
EMPTY {{ iaa_dict.tag[tag_def_col.name].cm.fn }} 0 {{ to_fixed(iaa_dict.all.cohen_kappa.Pes.b['_EMPTY_']) }}
Pa {{ to_fixed(iaa_dict.all.cohen_kappa.Pes.a[tag_def_col.name]) }} {{ to_fixed(iaa_dict.all.cohen_kappa.Pes.a['_EMPTY_']) }}

Summary

{{ stat_item[0] }}:
{{ stat_item[1] }}

Document Summary

File Name Total {{ tag_def.name }} {{ tag_def.name }}
{{ stat.file_name }} {{ stat.file_name }} {{ stat._total_tags }} {{ stat[tag_def.name] }} {{ stat[tag_def.name] }} {{ stat[tag_def.name] }} {{ stat[tag_def.name] }}

Annotated Tags

{{ tag_def.name }}
{{ hint_dict[tag_def.name].texts.length }}
-
{{ hint_dict[tag_def.name].nc_dict.count }} DOC-LEVEL
{{ fn_v }} {{ fn }}
{{ hint_dict[tag_def.name].text_dict[text].count }} {{ text }}
{{ fn_v }} {{ fn }}
{{ hovered_tag._annotator }} {{ hovered_tag.tag }}.{{ hovered_tag.id }} {{ hovered_tag.spans }}
SCHEMA NAME
ENTITY TAGS - RELATION TAGS - {{ tags.length }} tag(s) | Tag
TAG NAME
ANN.TYPE
ATTRIBUTE
TYPE
DEFAULT
DEFAULT
ITEMS ({{ att.values.length }})

You can click the "New" button to create an empty annotation schema.
Or click the "Open" button to open an existing schema file to edit.

Once the schema design is finished, you can download it as a DTD format file for backup, or use it directly in annotation.
The specification of the annotation schema file can be found in MedTator Wiki.

For more schema samples, you can check MedTator sample schemas on GitHub repo.