Sample of Data

Here is a sample of tagging from PMID 10661623. The bolded word in the first line of the abstract body, "K-ras2", is POS-tagged as a singular common noun (NN) and entity-tagged as a gene (in either DNA or RNA; labelled "gene-rna"). The following sections show

• the whole abstract as it appears in our corpus as a text file.
• the standoff annotation of that token from the .ann annotation file (XML). The POS annotation is nested inside the entity annotation.
• the annotation as captured in the .tkn file (tab-delimited text). Annotations are listed in order of the beginning of their span, and then by decreasing scope: file, paragraph, sentence (or "section"), entity, POS.
• the treebank, POS, and entity data (as of release 0.9) as presented in the .mrg file (text)
• a screenshot of that part of the abstract in the interactive HTML view (v0.9 only).

Abstract text (pm10661623.bma)

Anal Cell Pathol  1999;19(1):39-46 

K-ras2 activation and genome instability increase proliferation and size of FAP
adenomas.

Rapallo A, Sciutto A, Geido E, Orecchia R, Infusini E, Pujic N, d'Amore ES,
Monaco R, Risio M, Rossini FP, Giaretti W.

Laboratory of Biophysics and Cytometry, National Cancer Institute, Genoa, Italy.

The possible role of K-ras2 mutations and aneuploidy toward increase of
proliferation and adenoma size in Familial Adenomatous Polyposis (FAP) adenomas
is not known. The present study addresses these issues by investigating 147
colorectal adenomas obtained from four FAP patients. The majority of adenomas
had size lower than or equal to 10 mm (86%), low grade dysplasia (63%), and were
preferentially located in the right colon (60%). Normal mucosa samples were
obtained from 19 healthy donors. Three synchronous adenocarcinomas were also
investigated. K-ras2 mutation spectrum was analysed by PCR and Sequence Specific
Oligonucleotide (SSO) hybridization, while flow cytometry (FCM) was used for
evaluating degree of DNA ploidy and S-phase fraction. Overall, incidences of
K-ras2 mutations, DNA aneuploidy and high S-phase values (>7.2%) were 6.6%, 5.4%
and 10.5%, respectively. In particular, among the adenomas with size lower than
5 mm, K-ras2 mutation and DNA aneuploidy frequencies were only slightly above
1%. Statistically significant correlations were found between K-ras2 and size,
DNA ploidy and size and K-ras2 and S-phase (p < 0.001). In particular, among the
wild type K-ras2 adenomas, high S-phase values were detected in 8% of the cases
versus 57% among the K-ras2 mutated adenomas (p = 0.0005). The present series of
FAP adenomas indicates that K-ras2 activation and gross genomic changes play a
role toward a proliferative gain and tumour growth in size.

PMID: 10661623 [PubMed - indexed for MEDLINE]

Standoff annotations (pm10661623.bma.ann)

     <Annotation type="gene-rna" span="361..367" confidence="1.0" annotator="Sabrina" id="83">
      <Annotation type="NN" span="361..367" confidence="1.0" annotator="manocchi" id="84"/>
     </Annotation>

Token file (pm10661623.tkn)

o2san  pm10661623.bma   86  gene-rna   361   367  e   81  K-ras2
o2san  pm10661623.bma	87  NN         361   367  w   81  K-ras2

Merged-data treebank file (pm10661623.mrg)

;sentence 4 Span:340..507
;The possible role of K-ras2 mutations and aneuploidy toward increase of 
;proliferation and adenoma size in Familial Adenomatous Polyposis (FAP)
;adenomas  is not known.
;[361..367]:gene-rna:"K-ras2"
[...]
(SENT
  (S
    (NP-SBJ-1
      (NP (DT:[340..343] The) (JJ:[344..352] possible) (NN:[353..357] role))
      (PP (IN:[358..360] of)
        (NP
          (NP
            (NP (NN:[361..367] K-ras2) (NNS:[368..377] mutations))
[...]

HTML view (source_file_1361_28710.src.html, source_file_1361_28710.src.js*)

(* The filenames in the HTML view are derived from our annotation tracking system, but the HTML interface lists them by PMID.)