Sample of Data

Here is a sample of tagging from PMID 7379042. The bolded word in the second line of the abstract body, "N-2-fluorenylacetamide", is POS-tagged as a singular common noun (NN) and entity-tagged as a substance. 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 presented in the .mrg file (text)
• a screenshot of that part of the abstract in the interactive HTML view.

Abstract text (pm07379042.cyp)

Cancer Lett. 1980 Apr;9(2):123-31.  

Characterization of the guinea pig liver microsomal 2-fluorenylamine and
N-2-fluorenylacetamide N-hydroxylase.

Razzouk C, Mercier M, Roberfroid M.

Many reports in the literature have indicated that the guinea-pig is resistant
to the carcinogenic effect of N-2-fluorenylacetamide (2FAA); this refractoriness
has been attributed to its lack of N-hydroxylating enzymes. The present
communication, however, supports the results of contradictory reports which
demonstrate that guinea-pig liver microsomes are in fact able to N-hydroxylate
both 2-fluorenamine and 2FAA. The guinea-pig N-hydroxylase activity toward
2-fluorenamine is found to be even greater than the reported activity in the rat
and hamster. It is similarly inhibited by 3-methylcholanthrene (3MC),
7,8-benzoflavone (7,8 BF) or miconazole. Activity toward N-2-fluorenacetamide is
present in the microsomal preparation from the control guinea-pig. There is
slight activation by SKF525A, paraoxon (PX) or sodium fluoride. Under optimum
conditions, in the presence of both paraoxon and sodium fluoride, activity is
equivalent to that of rat liver microsomal enzymes.

PMID: 7379042 [PubMed - indexed for MEDLINE]

Standoff annotations (pm07379042.cyp.ann)

     <Annotation type="substance" span="304..326" confidence="1.0" annotator="rchoi" id="61">
      <Annotation type="NN" span="304..326" confidence="1.0" annotator="stippich" id="62"/>
     </Annotation>

Token file (pm07379042.tkn)

cyp    pm07379042.cyp   61  substance  304   326  e   41  N-2-fluorenylacetamide
cyp    pm07379042.cyp   62  NN         304   326  w   41  N-2-fluorenylacetamide

Merged-data treebank file (pm07379042.mrg)

;sentence 3 Span:194..415
;Many reports in the literature have indicated that the guinea-pig is
;resistant  to the carcinogenic effect of N-2-fluorenylacetamide (2FAA); this
;refractoriness  has been attributed to its lack of N-hydroxylating enzymes.
;[304..326]:substance:"N-2-fluorenylacetamide"
;[328..332]:substance:"2FAA"
;[391..414]:substance:"N-hydroxylating enzymes"
(SENT
  (S
    (S
      (NP-SBJ
        (NP (JJ:[194..198] Many) (NNS:[199..206] reports))
        (PP (IN:[207..209] in)
          (NP (DT:[210..213] the) (NN:[214..224] literature))))
      (VP (VBP:[225..229] have)
        (VP (VBN:[230..239] indicated)
          (SBAR (IN:[240..244] that)
            (S
              (NP-SBJ (DT:[245..248] the) (NN:[249..255] guinea)
                      (HYPH:[255..256] -) (NN:[256..259] pig))
              (VP (VBZ:[260..262] is)
                (ADJP-PRD (JJ:[263..272] resistant)
                  (PP (TO:[274..276] to)
                    (NP
                      (NP (DT:[277..280] the) (JJ:[281..293] carcinogenic)
                          (NN:[294..300] effect))
                      (PP (IN:[301..303] of)
                        (NP
                          (NP (NN:[304..326] N-2-fluorenylacetamide))

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