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PubTator.key
A BioC format for PubTator and other NER tools (i.e., tmChem, DNorm, tmVar, SR4GN or GenNorm) developed at the Biomedical Text Mining group at NCBI
The goal of this collection is to provide easy access to the text and bio-concept annotations for PMC articles.
collection: a group of PubMed documents, each document is organized into title, abstract and other passages
source: PubMed, PubMed Central, etc.
date: Document download date
document: abstract, full-text article, free-text document, etc.
id: PubMed ID (or other ID in a given collection) of the document
passage: Title, abstract and other passages
infon["type"]: "title", "abstract" and other passages
offset: Title has an offset of zero, while the other passages (e.g., abstract) are assumed to begin after the previous passages and one space
text: Text of the passage
annotation: One bio-concept of the passage as determined by the tmChem, DNorm, tmVar, SR4GN or GenNorm
infon["type"]: The type of bioconcept, e.g. "Gene", "Species", "Disease", "Chemical" or "Mutation"
infon["MeSH"]: The bio-concept identifier in MeSH as detected by DNorm or tmChem
infon["OMIM"]: The bio-concept identifier in OMIM as detected by DNorm
infon["NCBI_Gene"]: The bio-concept identifier in NCBI Gene as detected by GenNorm
infon["NCBI_Taxonomy"]: The bio-concept identifier in NCBI Taxonomy as detected by SR4GN
infon["ChEBI"]: The bio-concept identifier in ChEBI as detected by tmChem
infon["tmVar"]: The intelligent key generated artificially for the mention detected by tmVar (<Sequence type>|<Mutation type>|<Wild type>|<Mutation position>|<Mutant>)
location: location of the mention including the global document "offset" where a bio-concept is located and the "length" of the mention
text: Mention of the bio-concept
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