simple_bioc 0.0.1
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- checksums.yaml +7 -0
- data/.gitignore +18 -0
- data/Gemfile +4 -0
- data/LICENSE +20 -0
- data/LICENSE.txt +22 -0
- data/README.md +29 -0
- data/Rakefile +8 -0
- data/lib/simple_bioc/annotation.rb +11 -0
- data/lib/simple_bioc/bioc_reader.rb +102 -0
- data/lib/simple_bioc/bioc_writer.rb +93 -0
- data/lib/simple_bioc/collection.rb +15 -0
- data/lib/simple_bioc/document.rb +29 -0
- data/lib/simple_bioc/location.rb +10 -0
- data/lib/simple_bioc/node.rb +12 -0
- data/lib/simple_bioc/node_base.rb +14 -0
- data/lib/simple_bioc/passage.rb +29 -0
- data/lib/simple_bioc/relation.rb +14 -0
- data/lib/simple_bioc/sentence.rb +20 -0
- data/lib/simple_bioc/version.rb +3 -0
- data/lib/simple_bioc.rb +14 -0
- data/simple_bioc.gemspec +27 -0
- data/spec/simple_bioc_spec.rb +14 -0
- data/xml/BioC.dtd +146 -0
- data/xml/PMID-8557975-simplified-sentences-tokens.xml +492 -0
- data/xml/PMID-8557975-simplified-sentences.xml +49 -0
- data/xml/abbr.key +71 -0
- data/xml/abbr.xml +1 -0
- data/xml/ascii.key +29 -0
- data/xml/ascii.xml +3 -0
- data/xml/everything-sentence.xml +1 -0
- data/xml/everything.key +8 -0
- data/xml/everything.xml +1 -0
- data/xml/lemma.key +51 -0
- data/xml/lemma.xml +1 -0
- data/xml/pos.key +49 -0
- data/xml/pos.xml +1 -0
- data/xml/sentence.key +36 -0
- data/xml/sentence.xml +1 -0
- metadata +153 -0
data/xml/pos.key
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pos key
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collection: 10 random PubMed documents with ASCII text split into
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sentences and tokens by the MedPost tokenizer
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Original source sentence.xml
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source: PubMed
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date: yyyymmdd. Date documents downloaded from PubMed
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document: Title and possibly abstract from a PubMed reference
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id: PubMed id
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passage: Either title or abstract
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infon["type"]: "title" or "abstract"
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offset: The original Unicode byte offsets were not updated after
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the ASCII conversion.
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PubMed is extracted from an XML file, so literal offsets
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would not be useful. Title has an offset of zero, while
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the abstract is assumed to begin after the title and one
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space. These offsets at least sequence the abstract after
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the title.
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sentence: One sentence of the passage as determined by the
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MedPost sentence splitter
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offset: A document offset to where the sentence begins in the
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passage. Sum of the passage offset and the local offset
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within the passage.
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annotation: tokens in the sentence with their part-of-speech.
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the annotations are of "type" "token"
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infon["POS"]: The Penn Treebank part of speech tag as determined
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by the MedPost biomedical part-of-speech tagger
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location: offset: A document offset to where the annotated text
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begins in the sentence. Sum of the sentence
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offset and the local offset within the
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sentence.
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length: The length of the token.
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text: ASCII text of the token.
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