A Silver Standard Corpus of Human Phenotype-Gene Relations
Table 1: The final number of abstracts retrieved, number of phenotype and gene annotations extracted and the number of known, unknown and total of relations extracted between phenotype and genes, for Query 1 and 2.
['[BOLD] Query', '[BOLD] Abstracts', '[BOLD] Annotations  [BOLD] Phenotype', '[BOLD] Annotations  [BOLD] Gene', '[BOLD] Relations  [BOLD] Known', '[BOLD] Relations  [BOLD] Unknown', '[BOLD] Relations  [BOLD] Total']
We opted by searching per gene and not human phenotype or the combination of both terms because this approach was the one that retrieved abstracts with the higher number of gene and human phenotype annotations, in the following NER and RE phases. We removed the abstracts that did not check the conditions of being written in English, with a correct XML format and content. The abstracts retrieved by Query 1 were not specific enough for human phenotype-gene relations and therefore about half of them did not contained entities from both types, which we addressed in Query 2, increasing from about 2.5 relations per abstract to about 3.0 relations per abstract. Using a distant supervision approach, with the HPO file that links phenotypic abnormalities to genes, we were able to classify a relation with Known or Unknown. For this end, we extract pairs of entities, of gene and human phenotype, by co-occurrence in the same sentence (Example 2).