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Table 6 Syntactic patterns for propagating event labels to other candidate bacteria-location (or trigger-location) pairs, with examples where B, B1 and B2 are bacteria annotations, and L1 and L2 are location annotations

From: Unsupervised inference of implicit biomedical events using context triggers

 Propagation patternsDescriptions and examples
1NestingGiven the phrase “apple and lettuce surfaces” with its four nested location annotations: apple surfaces, lettuce surfaces, apple, and lettuce, if bacteria B is found to be located in “apple and lettuce surfaces”, we identify four events by associating B with each of the four location mentions, as illustrated in Fig. 4.
2CoordinationGiven the two coordinated location mentions “tryptic soy broth” and “nutrient broth”, if bacteria B is found to be located in “tryptic soy broth”, we also identify the pair of B and “nutrient broth” as an event, as illustrated in Fig. 4.
3AppositionIn the example “[methicillin-resistant Staphylococcus aureus] B1([MRSA] B2)colonization in a [skilled nursing facility] L1([SNF] L2)”, we first identify the intra-clause event B1-L1 using a trigger pattern, and then propagate it to additional three events B2-L1, B2-L2, and B1-L2, based on the apposition relations between B1 and B2 and between L1 and L2, as captured by their syntactic dependencies.
4Location hierarchyTwo geographical location mentions are sometimes connected via a comma when they have a clear hierarchical relationship, such as “in [Georgia] L1, [USA] L2” and “residents of [Olmsted Country] L3, [Minnesota] L4”. In this case, we propagate an event relation for a smaller region to that for a larger one.
5Participle- prepositionIn the example “[Israeli travelers]L1 returning from [Nepal]L2 were diagnosed with [S. Paratyphi A]B1 bacteremia”, we first identify the intra-clause event B1-L1 using a trigger pattern, and then propagate it to B1-L2 through the participle-preposition relation between L1 and L2. This pattern can also be applied to two locations connected by a single preposition such as “in the [Hospital S. Camillo De Lellis]L1of [Roma]L2”.
  1. Note that these patterns are applied to entity pairs of the same type, i.e., bacteria-bacteria or location-location pairs. B, B1, and B2 in boldface refer to bacteria entities. L, L1, L2, L3, and L4 in boldface refer to location entities