Class

com.johnsnowlabs.nlp.training

PubTator

Related Doc: package training

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case class PubTator() extends Product with Serializable

The PubTator format includes medical papers’ titles, abstracts, and tagged chunks.

For more information see PubTator Docs and MedMentions Docs.

readDataset is used to create a Spark DataFrame from a PubTator text file.

Example

import com.johnsnowlabs.nlp.training.PubTator

val pubTatorFile = "./src/test/resources/corpus_pubtator_sample.txt"
val pubTatorDataSet = PubTator().readDataset(ResourceHelper.spark, pubTatorFile)
pubTatorDataSet.show(1)
+--------+--------------------+--------------------+--------------------+-----------------------+---------------------+-----------------------+
|  doc_id|      finished_token|        finished_pos|        finished_ner|finished_token_metadata|finished_pos_metadata|finished_label_metadata|
+--------+--------------------+--------------------+--------------------+-----------------------+---------------------+-----------------------+
|25763772|[DCTN4, as, a, mo...|[NNP, IN, DT, NN,...|[B-T116, O, O, O,...|   [[sentence, 0], [...| [[word, DCTN4], [...|   [[word, DCTN4], [...|
+--------+--------------------+--------------------+--------------------+-----------------------+---------------------+-----------------------+
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  1. new PubTator()

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  11. final def notify(): Unit

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  12. final def notifyAll(): Unit

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  13. def readDataset(spark: SparkSession, path: String, isPaddedToken: Boolean = true): DataFrame

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  14. final def synchronized[T0](arg0: ⇒ T0): T0

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