CLinkaRT @ Evalita 2023

Linking a Lab Result to its Test Event in the Clinical Domain

CLinkaRT at EVALITA 2023 is a relation extraction task based on clinical cases taken from the E3C corpus, i.e. on Italian written documents reporting statements of a clinical practice (thus including, for example, the reasons for a clinical visit, the physical exams undertaken, the assessment of the patient’s diagnosis and subsequent treatments).

The task consists in identifying test results and measurements and linking them to the textual mentions of the laboratory tests and measurements from which they were obtained.

Main

Organization

Contact and submissions

clinkart@fbk.eu


Important dates

Available here


For participants


Task Description

Laboratory tests are a common step in the disease and disorder diagnosis processes and, as a part of them, they are documented in clinical narratives. The main goal of the CLinkaRT task is finding test results and measurements and linking them to the textual mentions of laboratory tests and measurements from which they were obtained. For this, both elements need to be identified in text and then the relation between them needs to be created.

Laboratory tests and measurements and their results provide interesting information on the patients’ status in a certain time of the development of the disorder but have been given little attention in the last years. The task also brings up a new data treatment perspective since the extraction of lab values and vital signs cannot be handled as a named entity recognition task, as it requires interpreting numeric values and ranges.

In the following example, the test event is marked in blue and the result is marked in red:

Both the test events and the results are defined as text strings. All test events are single-token strings (i.e. only the syntactic head is considered, following the THYME framework), while results may be represented by multitoken strings (i.e. a whole syntactic chunk). There are not discontinuous spans nor nested entities.

All relations are of the type PERTAINS (see the red arrows in the examples) and can be one-to-one, one-to-many and many-to-one.

The annotation of pertains-to relations is strictly based on tokens (the target, in particular, must necessarily consist of one token, while the source consists of one or more token) and on sentences (source and target of a relation must belong to the same sentence).

In order to reduce the noise that might be introduced by mismatching pre-processing, participants to the Clinkart task are strongly encouraged to use the same (automatic) tokenization and sentence splitting that has been used when the data have been (manually) annotated (which is distributed together with the annotated data and the test data).

Data

Test dataset

Language: Italian

Documents: 80

Source: E3C corpus

Download - May 12th


Training dataset

Language: Italian

Documents: 83

Tokens: 28,856

Annotated Relations: 658

Source: E3C corpus

Download 



Data format

All annotation data are made available to participants in a format that owes a lot to  the PubTator format.  The annotated data consists of a straightforward tab-delimited text file:


<DOCID>|t|<TEXT>

<DOCID>  REL  <RML_START>-<RML_END>  <EVENT_START>-<EVENT_END>  <RML_TEXT>  <EVENT_TEXT>

<DOCID>  REL  <RML_START>-<RML_END>  <EVENT_START>-<EVENT_END>  <RML_TEXT>  <EVENT_TEXT>


<DOCID>|t|<TEXT>

<DOCID>  REL  <RML_START>-<RML_END>  <EVENT_START>-<EVENT_END>  <RML_TEXT>  <EVENT_TEXT>


Where:


For example:

100509|t|Donna, 87 anni, ipertiroidismo subclinico, artrosi, osteoporosi (fratture T10-T11), ipovisus, AH in terapia steroidea cronica; ipertensione; scompenso cardiaco diastolico; un ricovero per EPA. Recente embolia polmonare, da allora in TAO. Recentemente agitazione e dolore resistente a paracetamolo. All’ECG RS 66 bpm, deviazione assiale sinistra, BBD incompleto. Chest Pain Score e Wells Score bassi. All’ecocardiogramma FE 55%. PA 160/90 mmHg. Giordano positivo, dolore paravertebrale bilateralmente. Dopo caduta accidentale vivo dolore a livello dorsale. Al quadro rx crolli vertebrali da T6 a T8 con pregresso crollo di T12. Procrastinata la chifoplastica e prescritto un busto, iniziava cauta fisioterapia. Videat oculistico e continuazione della terapia steroidea. Prescrizione di teriparatide e vitamina D.

100509     REL     309-315     306-308     66 bpm     RS

100509     REL     393-398     387-392     bassi      Score

100509     REL     393-398     373-378     bassi      Score

100509     REL     423-426     420-422     55%        FE

100509     REL     431-442     428-430     160/90 mmHg     PA

100509     REL     453-461     444-452     positivo     Giordano

Use of data for model training

The CLinkaRT training data are part of the E3C corpus, which is released under CC-BY-NC-4.0 licence. 

There are no restriction in the use of additional data for model training. The training data released for the TESTLINK twin task can be used, as well as any other datasets participants might consider useful. Nonetheless, all data used for training purposes must to be specified in the system report.

Evaluation

Evaluation procedure

The task has been defined as a relation extraction (RE) task in which the elements taking part in the relation as well as the directionality of the relation are considered. Participating systems are provided with raw text from clinical cases as input and asked to return a list of entity mention pairs for which a relationship exists in the text. For example, given the document reported below:

100854|t|Un maschio di 25 anni dopo una partita di calcetto si è presentato in PS per paralisi degli AAII. Gli ematochimici evidenziavano marcata ipokaliemia: <1.5 Mmol/L; dopo esecuzione di supplementazione di potassio il pz veniva dimesso. Pochi giorni più tardi il pz si ripresentava in PS per una recidiva e veniva ricoverato. Veniva eseguito TSH con riscontro di tireotossicosi senza sintomi di ipertiroidismo: TSH <0.005 mUI/L, FT4 44.9 ng/L. Veniva impostata terapia tireostatica e somministrato K+ con risposta clinica. Sono stati effettuati RMN, rachicentesi e dosaggio enzimi muscolari per ricerca di diagnosi differenziali. È stato proposto anche test genetico.

The systems output includes both the document in input and the annotated relations as follows:

100854|t|Un maschio di 25 anni dopo una partita di calcetto si è presentato in PS per paralisi degli AAII. Gli ematochimici evidenziavano marcata ipokaliemia: <1.5 Mmol/L; dopo esecuzione di supplementazione di potassio il pz veniva dimesso. Pochi giorni più tardi il pz si ripresentava in PS per una recidiva e veniva ricoverato. Veniva eseguito TSH con riscontro di tireotossicosi senza sintomi di ipertiroidismo: TSH <0.005 mUI/L, FT4 44.9 ng/L. Veniva impostata terapia tireostatica e somministrato K+ con risposta clinica. Sono stati effettuati RMN, rachicentesi e dosaggio enzimi muscolari per ricerca di diagnosi differenziali. È stato proposto anche test genetico.

100854     REL     150-161   137-148   <1.5 Mmol/L   ipokaliemia

100854     REL     411-423   407-410   <0.005 mUI/L  TSH

100854     REL     429-438   425-428   44.9 ng/L     FT4

 In the annotated relations, the mention text span (e.g., <1.5 Mmol/L, ipokaliemia) can be set but it is not used for evaluation. 

Participants are allowed to submit up to two different runs.

We measure RE performance by standard Precision, Recall and F1 measure, in which a relation prediction is considered correct if the start and end character offsets of the two related entity mentions and their order of both in the relation are correct. To perform this evaluation the scorer of BioCreative V CDR task is used, i.e.

>  eval_relation.sh  PubTator   gold_file  prediction_file

Where:

PubTator: input files format

gold_file: contains the gold standard annotations

prediction_file: contains the predicted annotations