How was annotation performed?
Experienced medical doctors used a linguistic annotation tool to annotate entities.
We present a new corpus comprising annotations of medical entities in case reports, originating from PubMed Central's open access library. In the case reports, we annotate cases, conditions, findings, factors and negation modifiers. Moreover, where applicable, we annotate relations between these entities. As such, this is the first corpus of this kind made available to the scientific community in English. It enables the initial investigation of automatic information extraction from case reports through tasks like Named Entity Recognition, Relation Extraction and (sentence/paragraph) relevance detection. Additionally, we present four strong baseline systems for the detection of medical entities made available through the annotated dataset.
The automatic processing of medical texts and documents plays an increasingly important role in the recent development of the digital health area. To enable dedicated Natural Language Processing (NLP) that is highly accurate with respect to medically relevant categories, manually annotated data from this domain is needed. One category of high interest and relevance are medical entities. Only very few annotated corpora in the medical domain exist. Many of them focus on the relation between chemicals and diseases or proteins and diseases, such as the BC5CDR corpus BIBREF0, the Comparative Toxicogenomics Database BIBREF1, the FSU PRotein GEne corpus BIBREF2 or the ADE (adverse drug effect) corpus BIBREF3. The NCBI Disease Corpus BIBREF4 contains condition mention annotations along with annotations of symptoms. Several new corpora of annotated case reports were made available recently. grouin-etal-2019-clinical presented a corpus with medical entity annotations of clinical cases written in French, copdPhenotype presented a corpus focusing on phenotypic information for chronic obstructive pulmonary disease while 10.1093/database/bay143 presented a corpus focusing on identifying main finding sentences in case reports. The corpus most comparable to ours is the French corpus of clinical case reports by grouin-etal-2019-clinical. Their annotations are based on UMLS semantic types. Even though there is an overlap in annotated entities, semantic classes are not the same. Lab results are subsumed under findings in our corpus and are not annotated as their own class. Factors extend beyond gender and age and describe any kind of risk factor that contributes to a higher probability of having a certain disease. Our corpus includes additional entity types. We annotate conditions, findings (including medical findings such as blood values), factors, and also modifiers which indicate the negation of other entities as well as case entities, i. e., entities specific to one case report. An overview is available in Table TABREF3.