This repository contains a synthetic corpus of clinical cases enriched with PHI expressions, named the MEDDOCAN corpus.
The final collection of 1,000 clinical cases that make up the corpus have around 33 thousand sentences, with an average of around 33 sentences per clinical case. The MEDDOCAN corpus contains around 495 thousand words, with an average of 494 words per clinical case, slightly less than for the records of the i2b2 de-identification longitudinal corpus (617 tokens per record). The MEDDOCAN corpus is distributed in plain text in UTF8 encoding, where each clinical case is stored as a single text file, and PHI annotations are released in the popular BRAT format, which makes visualization of results straightforward.
In this repository:
script/ CODALAB-Evaluation-Script/ COBALAB version of the original evaluation script for the MEDDOCAN task. Format-Converter-Script/ Script to convert files between MEDDOCAN-Brat, MEDDOCAN-XML, and i2b2 formats.
In Zenodo:
corpus/ `Train`, `development`, and `test` data sets, both `BRAT` standoff format and `i2b2` format. guidelines/ Annotation guidelines. IAA/ Inter-annotator agreement report, along with the data and the scripts used to calculate it.
The SPACCC corpus was created after collecting 1,000 clinical cases from SciELO (Scientific Electronic Library Online), an electronic library that gathers electronic publications of complete full text articles from scientific journals of Latin America, South Africa and Spain (http://www.scielo.org).
A clinician classified those cases into those that were similar to real clinical texts in terms of structure and content and those that were not suitable for this task. Figure legends were automatically removed and, in case multiple clinical cases were listed, these were split into single clinical cases.
The manual annotation of the entire corpus was carried out in a three-step approach. First, an initial annotation
process was carried out on an adapted version of the AnnotateIt tool. The resulting annotations were then exported,
trailing whitespaces were removed and double annotations of the same string were send as an alert to the human annotators
for revision/correction. Then, the annotations were uploaded into the BRAT annotation tool, which was slightly less
efficient for mention labeling in terms of manual annotation speed. The human annotators performed afterwards a final
revision of the annotations in BRAT, in order to correct mistakes and to add potentially missing annotation mentions.
Finally the senior annotator did a last round of annotation revision of the entire corpus.
Annotations created for SPACCC_MEDDOCAN are provided in BRAT standoff format; i.e. the annotations are stored separately
(in an .ann file) from the document text (a .txt file).
These two files are associated by their base name; their file name without suffix is the same, for example, the file
es-S0004-06142005000200009-1.ann contains the annotations for the file es-S0004-06142005000200009-1.txt.
See http://brat.nlplab.org/standoff.html for further details on the brat standoff format.
The MEDDOCAN annotation scheme defines a total of 29 granular entity types grouped into more general parent classes.
See guidelines in guidelines/ folder for further details.
The annotation guidelines describe the criteria that have been followed to annotate the corpus, along with illustrative examples.
The annotation process of the MEDDOCAN corpus was inspired initially by previous annotation schemes and corpora used for the i2b2 de-identification tracks, revising the guidelines used for these tracks, translating certain characteristics into Spanish and adapting them to the specificities and needs of our document collection and legislative framework. This adaptation was carried out in collaboration with practicing physicians, a team of annotators and the University Hospital 12 de Octubre.
The adaptation, translation, and refinement of the guidelines was carried out on several random sample sets of the MEDDOCAN corpus and connected to an iterative process of annotation consistency analysis through inter-annotator agreement (IAA) calculation until a high annotation quality on terms of IAA was reached.
Three cycles of refinement and IAA analysis were needed in order to reach the quality criteria required for this track, being
in line with similar scores obtained for instance for i2b2. The final version of the used 28 pages annotation guidelines can
be found in the guidelines/ directory.
Guidelines have been written and developed in Spanish and are only available in Spanish.
The final, inter-annotator agreement measure obtained for this corpus was calculated on a set of 50 records that were double annotated (blinded) by two different expert annotators, reaching a pairwise agreement of 98% on the exact entity mention comparison level together with the corresponding mention type labels.
See the inter-annotator agreement report (Informe_interagreement_CNIO_PlanTL_SEAD.pdf) included in folder IAAin Zenodo for
further details.
Montserrat Marimon ([email protected])
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