| 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 | |