## 4 Lung Cancer Named Entity Recognition
### Corpus Annotation  
The corpus has been manually annotated using the Brat ([[https://brat.nlplab.org/](https://brat.nlplab.org/)]([https://brat.nlplab.org/](https://brat.nlplab.org/))) tool. It is composed of clinical notes from lung cancer patients from _\"Hospital Universitario Puer de Hierro, Madrid, Spain\"_, with every clinical note being introduced anonymously. The corpus contains the following labeled entities:  
* **Cancer entity:** this entity captures both the cancer type (_carcinoma, adenocarcinoma, cancer, etc.)_ together with the anatomical location (_left lung, right lung, right lobe, etc.)_. For instance: _\"Patient diagnosed with right lung adenocarcinoma\"_. In the annotation process the more detailed description will be used. Thus in the sentence, _\"Patient  
Figure 2: Approach to extract lung cancer diagnosis.  
diagnosed with small cell lung cancer\"_, the concept \"Small cell lung cancer\" will be annotated instead of _\"lung cancer\"_.
* **Cancer stage:** staging is the process of finding out how much cancer is in a person's body and where it's located. The cancer stage can be expressed on a scale that ranges from I to IV. Stage I indicates the initial stage and stage IV, the most advanced stage of cancer. The cancer staging can also be done using the TNM notation: Tumor (T), Nearby(N), and Metastasis(M). As a consequence, we have annotated both scales. On the one hand, entities such as _stage II and stage IV_ are annotated as a stage entity while expressions such as _cT3 cN3 cM1_ and _T3 N2 M0_ are annotated as TNM entity.
* **Dates:** Represents dates and time expressions mentioned in clinical notes. Date entity is a crucial concept to obtain the natural history of the patient. Only explicit dates are annotated.
* **Events**: This entity is used to represent events such as _being diagnosed, being treated, treatment start, begin clinical trial, etc._. In the sentence _\"Patient diagnosed with lung cancer, begins treatment with chemotherapy on 5 December 2019_, there are two events (shown in bold).
* **Family members**: represents concepts about family members of a patient. This entity commonly appears together with cancer concepts in the family antecedents, (_e.g., \"**Mother** diagnosed with lung cancer in 2007)\"_. This entity is used to differentiate between a cancer concept associated to a patient, and one associated to a family member.
* **Treatment**: The kind of treatment ranging from chemotherapy, radiotherapy, and surgery will be included. These treatments will be annotated separately. This tag is only used to annotate generic mentions to treatments, without mentioning the specific drug, as in the case of sentences such as: _\"Patient with lung cancer, with chemotherapy in October 2018\"_.
* **Drug**: This entity is used to annotate particular names of drugs related to any kind of treatment, such as in the sentence: _Lung cancer patient, treated with Carboplatin on October 2018_.  
Table 1 shows a summary of the number of annotations for each entity. Two domain experts annotated the corpus previously described. The inter-annotator agreement was 0.89 measured by Cohen's Kappa.