Annotation guidelines for the 'fulltext' model

Introduction

As mentioned elsewhere (TODO:link), there are several models that are used to analyze the contents of a PDF file. One of them is the fulltext model which attempts to recognize and struture items appearing in the body text of an article or a publication. This is different from for example the segmentation model which tries to recognize the general sections (title page, front, body, bibliography) and which is applied before the fulltext model.

Note: Whitespace is not important in the XML that Grobid uses. You can add newline characters and spaces to make the XML document more legible.

The fulltext model attempts to recognize the following objects:

  • paragraphs
  • section titles (not of the actual article or publication)
  • figures
  • tables
  • formulas
  • list items inside lists
  • markers: callouts to figures ("see Fig. 1"), tables, formulas and to bibliographical references (e.g. "Austin 2008(b)").

The following sections will give examples for each of the objects above and how they should be marked up. Note that the mark-up follows overall the TEI.

Analysis

Section titles

To indicate sub parts of an article, authors may have used section titles that subdivide the flow of the content into smaller chunks. These titles should appear on the same level as the paragraphs, formulas, etc. Here are some examples:

<head>CERAMIDE AND S1P BOTH TRIGGER AUTOPHAGY<lb/></head>
<head>1. Introduction<lb/></head>
<head>2 Background<lb/></head>
<head>B. Focusing an IACT<lb/></head>
<head>II. PROBLEM AND SOLUTION PROCEDURE<lb/></head>
<head>4 RESULTS<lb/></head>
<head>4.1 Image quality<lb/></head>
<head>Results<lb/></head>
<head>Patient characteristics<lb/></head>
<head>MATERIALS AND METHODS<lb/></head>
<head>Tissue samples<lb/></head>

Paragraphs

Paragraphs constitute the main bulk of most typical articles or publications and contain text which in turn may contain inline elements such as references (see below) or line breaks.

<p>Our group has investigated the correlation between sphingolipid metabolism, the<lb/>
  ...
  are able to induce autophagy in a breast cancer cell line. 3,4<lb/>
</p>

Note: The <lb/> (line break) elements are there because they have been recognized as such in the PDF in the text flow. However the fact that they are located within or outside a tagged paragraph or section title has no impact. Just be sure NOT to modify the order of the text flow and <lb/> as mentionned here.

Following the TEI, formulas should be on the same hierarchical level as paragraphs, and not be contained inside paragraphs:

<p>Exponentiation mixes. Our protocol will benefit from the exponentiation mix<lb/>
    ...
  MS i+1 . The first server takes the original list of PKs. The net effect is a list: <lb/>
</p>

<formula>(g x ρ(i) ·s ) i∈[n] ,<lb/> </formula>

<p>where:<lb/></p>

<formula>π =<lb/>
  [n]<lb/>
  1<lb/>
  ρ i , s =<lb/>
  [n]<lb/>
  1<lb/>
  s i ,<lb/>
</formula>

<p>and g s is also published by the last Teller.<lb/>
  ...
  (g s ) xi and finding the match.<lb/>
</p>

The next example illustrates similarly that in TEI list items should contained inside <list> elements which in turn are on the same hierarchical level as paragraphs and other block-level elements.

<p>The estimation of the eligible own funds and the SCR requires to carry out calculations <lb/>
  ...
  the following constraints:<lb/>
</p>

<list>
  <item>• updating the assets and liabilities model points;<lb/></item>

  <item>• constructing a set of economic scenarios under the risk-neutral probability and<lb/>
      checking its market-consistency;<lb/></item>
</list>

<p>The wild-type strain was Bristol N2. All animals were raised at<lb/>
  20uC. The following alleles and transgenes were used:<lb/>
</p>

<p>LGI: hda-3(ok1991)<lb/>
</p>

<p>LGII: hda-2(ok1479) <lb/>
</p>

Figures, tables and box

A photo, picture or other graphical representation (this could be a chart or another figure) and boxes, are to be marked up using the <figure> element. This element contains the title, the figure/table/boxed content/photo itself, captions, any legend or notes it may have.

Note that following the TEI, a table is maked as figure of type "table" (the actual <table> element appears in the table model applied in cascade) and a boxed content is marked as a figure of type "box".

The following XML sample shows one figure (<figure>) followed by two tables which are marked up as <figure type="table"> elements.

<figure>Figure 1. Hypothetical model for ceramide and S1P-induced autophagy and thei    consequences on cell fate. An<lb/>
  ...
  <lb/>
  ....
  promotes cell survival by inhibiting the induction of apoptosis.<lb/>
</figure>

<figure type="table"> Table 1 Clades of clownfishes used in this study<lb/>
  Clade name<lb/>
    Species<lb/>
  percula<lb/>
  A. ocellaris, A. percula, P. biaculeatus<lb/>
  Australian<lb/>
    A. akindynos, A. mccullochi<lb/>
  ...
  of clownfish species [19].<lb/>
</figure>

<figure type="table"> Table 1 The clinicopathological data of PDAC tissue samples<lb/>
  Sample<lb/>
  Age<lb/>
  Sex<lb/>
  Location a<lb/>
  Histology b<lb/>
  T<lb/>
  N<lb/>
  ...
  1<lb/>
  1<lb/>
  IVb<lb/>
  a<lb/>
  P ¼ primary lesion; Ph ¼ head; Pb ¼ body; Pt ¼ tail of the pancreas; LM ¼ liver metastatic lesion. b
    mod ¼ moderately; poor ¼ poorly differentiated tubular adenocarcinoma.<lb/>
  PDAC ¼ pancreatic ductal adenocarcinoma; FISH ¼ fluorescence in situ hybridisation; ISH ¼ in
    situ RNA hybridisation.<lb/>
</figure>

Boxed content, i.e. a box with additional content outside the flow of the general content, are tagged similarly with the element <figure type="box">.

Formulas

The label of the formula (usually its number) is tagged with the element <label>, as illustrated bellow:

<formula>
  σ α β =<lb/>
  1<lb/>
  3<lb/>
  ˙<lb/>
  R<lb/>
  R −<lb/>
  ˙<lb/>
  R<lb/>
  R<lb/>
  diag(0, 2, −1, −1),<lb/>
    <label>(10)</label>
  <lb/>
</formula>

List items

Following the TEI, list items (<item> elements) should be contained in a <list> element and must not occur within <p> elements. At this stage no difference is made between ordered and unordered lists.

List item markers such as hyphens, bullet points (for unordered lists) or numbers and letters (for ordered lists) should be contained within the <item> element.

<p>Introducing ballot identifiers has the appeal that it provides voters with a<lb/>
  very simple, direct and easy to understand way to confirm that their vote is<lb/>
  ...
  this observation that we exploit to counter this threat: we arrange for the voters<lb/>
  to learn their tracker numbers only after the information has been posted to the<lb/>
  WBB.<lb/>
  This paper presents a scheme that addresses both of these shortcomings by:<lb/>
</p>

<list>
  <item>– Guaranteeing that voters get unique trackers.<lb/></item>

  <item>– Arranging for voters to learn their tracker only after the votes and corre-<lb/>
  sponding tracking numbers have been posted (in the clear).<lb/></item>
</list>

<list>
    <item>1) The difficulty of identifying passages in a user&apos;s manual based on an individual word.<lb/></item>

  <item>2) The difficulty of distinguishing affirmative and negative sentences which mean   two different<lb/>
  features in the manual.<lb/></item>

  <item>3) The difficulty of retrieving appropriate passages for a query using words not appearing in the<lb/>
  manual.<lb/></item>
</list>

Markers (callouts to structures)

These elements appear as inline elements, inside <p>, <item>, or other elements containing and usual reference other parts of the document. They could be understood as links. Here is a list of currently supported markers:

  • <ref type="biblio"> a link to a bibliographical reference (of the type *see Austin 1982/b * )
  • <ref type="figure"> a pointer to a figure elsewhere in the document (Fig 5b, left)
  • <ref type="table"> a link to a table in the document
  • <ref type="box"> a link to some boxed content (a box with additional content, outside the flow of the general content)
  • <ref type="formula"> a link to a formula

Bibliographical reference markers (callouts)

The following excerpts show examples of markers (callouts) to bibliographical references introduced with numbers with or without brackets or parenthesis:

Harbaugh and Harbaugh <ref type="biblio">[7]</ref>
in Lolle et al. <ref type="biblio">1</ref>

Note that the bracket/parenthesis symbols are included in the tagged content.

Bellow, as the label within the brackets fully qualifies the reference, we don't further annotate the callout with the author names:

<p>The clinical entity of cervical flexion myelopa-<lb/>
  thy proposed in the 1960s by Reid <ref type="biblio">[16,17]</ref> and<lb/>
  Breig et al <ref type="biblio">[2,3]</ref> has been neglected for a long time.<lb/>
  ...
  groups of males and females controls.<lb/>
</p>

It is important to note that whenever there is an enumeration of several references, they should not be marked up as several references, using specific ref elements for each one, but just one element surrounding the whole group.

To highlight the diversity of bibliographical references, here are some more examples:

by <ref type="biblio">Greve et al. [1994]</ref> and <ref type="biblio">Koch et al.<lb/> [1994]</ref>
<ref type="biblio">[Whitham, 1954; Hogg and Pritchard,<lb/> 2004]</ref>
<ref type="biblio">[Abramowitz and Stegun,<lb/> 1964, see pp. 559 – 562] </ref>
<ref type="biblio">LEWANDOWSKI (1982b)</ref> has reported
<ref type="biblio">(STANCZYKOWSKA, 1977)</ref>
(e.g., <ref type="biblio">Bryant<lb/> &amp; Goswami, 1987</ref>) by<lb/>
<ref type="biblio">Smith and Matsoukas [1998]</ref> and <ref type="biblio">Khelifa and Hill [2006b]<lb/></ref>
by <ref type="biblio">Gal [1979]</ref> and<lb/> illustrated further recently by <ref type="biblio">Draper and Lund [2004]</ref>
<ref type="biblio">(ref. 1)</ref>

Note that strange style mixtures can be observed:

This was established in<lb/> <ref type="biblio">Thompson v. Lochert (1997)</ref> <ref type="biblio">[114]</ref> in which
such as receptors for IL-1β <ref type="biblio">(REFS 64,65)</ref>,<lb/> TNF <ref type="biblio">66</ref> and IFNγ <ref type="biblio">67</ref> .

Markers to tables and figures

The next example shows markers (callouts) to a table and a figure (as noted earlier, whitespace is not of importance for GROBID and can therefore be used liberally, like here to better show the tagging):

<p>The patient group comprised all six patients with<lb/>
  juvenile cervical
    flexion myelopathy admitted to<lb/>
  our hospital

  <ref type="table"> (Table 1) </ref>.

  In all of them, cervical flexion<lb/>
  ...
  alignment in the extended neck position

  <ref type="figure"> (Figure 3) </ref>.<lb/>

  Cervical MR imaging in the neutral neck position of<lb/>
  five of the six patients showed a straight cervical<lb/>
</p>

An example of callouts to two formulas (and a bibliographical entry):

<p>Here, Θ(y) denotes ...<lb/>
the semi-cylindrical drum. The dynamics of the avalanches of eqs.

  <ref type="formula">(1)</ref>

  and

  <ref type="formula">(2)</ref>

  is centered<lb/>
  around the angle ϕ d = tan b 0

  <ref type="biblio">[7]</ref>.<lb/>

  ...
  stochastic extension of the DMM:<lb/>
</p>

Markers to figure or table must contain enough information to identify precisely to which object we refere to. Here are some more short examples for figure markers:

<ref type="figure">(Supplementary Fig. 1<lb/> online)</ref>
<ref type="figure">(Fig. 5b, left)</ref>
<ref type="figure">Figure 2</ref> exemplifies
(10.3% of those analysed; <ref type="figure">Fig. 1a</ref>).

As for markers to bibliographical references, we group under the same element a conjunction/list of callouts:

In <ref type="figure">figs. 3 and 4</ref>