Annotation guidelines¶

The first step of the annotation process is to generate training data from unlabeled documents based on the current models. The procedure is explained in details in training_data. GROBID will create the training data corresponding to these documents in the right TEI format and with pre-annotations. The annotation work then consists of manually checking the produced annotations and adding the missing ones.

Warning

It is very important not to modify the text content in these generated files, not adding spaces or other characters, but only adding or moving XML tags.

When the training data has been manually corrected, move the file under the repository resouces/dataset/${model}/corpus/ for retraining, or under resouces/dataset/${model}/evaluation/ if the annotated data should be used for evaluation only. To see the different evaluation options, see GROBID documentation on training and evaluating.

Note

the exact directory where the data is picked up could be also a final under corpus. Please check the description under each model definition, below.

In this document we describe the annotation guidelines for the following models:

Quantities model - STABLE
Units model - STABLE
Values model - STABLE
Quantified objects CRF model / substance CRF model - Work in progress

Quantities model¶

The Quantities model is the first model of the chain and segment text into units and values. This model pick up the training data from resouces/dataset/${model}/corpus.

Currently it supports three types of measurements:

single value (or atomic value),
continuous values in intervals (or range of values),
lists of discrete values.

Note

At the present time we do not distinguish between conjunctive and disjunctive lists.

Unit type vocabulary¶

The list of unit types (temperature, pressure, length, etc.) is controlled and based on SI definition. This controlled vocabulary contains currently around 50 types. The unit types are provided in the file `src/main/java/org/grobid/core/utilities/UnitUtilities.java` and they are used to get the right transformation.

Note

at the moment we do not support disambiguation of overlapping units.

The given names of the unit types has to be used when annotating measurement.

Note

In the future, the list of units should however not be controlled and GROBID should support units never seen before. For now it is admitted to annotate with UNKNOWN in case of doubt about the type.

Examples:

m^2/kg (specific surface area)
kD (dissociation constant)
rad.m^-2, in issue #51
others in issue #53

Atomic values¶

We can distinguish two kinds of atomic values expressions:

Atomic values with units¶

Following TEI, the numeric value is identified with the element `<num>` and the unit with the element `<measure>` where the unit type is given by the attribute `@type`. The indicate of the unit name by the attribute `@unit` is optional: if present it might be used to augment the unit lexicon if not yet represented in the lexicon. A global `<measure>` element encodes the complete measurement (composed by the numeric value and the unit) associated with the measurement type given by the attribute `@type` `value`.

Example 1:

We monitored nutritional behaviour of amateur ski-mountaineering athletes during <measure type="value"><num>4</num>
<measure type="TIME" unit="day">days</measure></measure> prior to a major competition to compare it with official
recommendations and with the athletes' beliefs.

Example 2:

... <measure type="value"><num>20</num> <measure type="ENERGY" unit="MJ">MJ</measure></measure> (<measure
type="value"><num>4,800</num> <measure type="ENERGY" unit="kcal">kcal</measure></measure>) for the shorter race route...

A percentage (and similar expression per mil and per ten thousand) has a unit type Unit_Type.FRACTION:

<measure type="value"><num>5</num> <measure type="FRACTION" unit="%">%</measure></measure> of fat mass...

Atomic value without unit¶

They correspond to a count (implicit Unit_Type.COUNT). The numeric value is encoded with element <num> and the global <measure> element indicating the measurement type is added.

For example:

consists of <measure type="value"><num>two</num></measure> different race routes

The implicit Unit_Type.COUNT type will be infer by this particular encoding. Not that this encoding is only relevant to countable quantities.

Intervals¶

An interval introduces a range of values. We can distinguish two kinds of interval expressions:

1. Bounded value¶

Interval defined by a lower bound value and an upper bound value:

team races that can last from <measure type="interval"><num atLeast="4">4</num> to more than <num atMost="12">12</num>
<measure type="TIME" unit="hour">h</measure></measure>

If the unit is mentioned twice, both units are annotated, example for 3 AU ≤ rh <~ 5 AU:

<measure type="interval"><num atLeast="3">3</num> <measure type="LENGTH" unit="AU">AU</measure> ≤ r h <num atMost="5">5</num> <measure type="LENGTH" unit="AU">AU</measure></measure>

Note that an interval can be introduced by only one boundary value:

A rotor shaft according to any one of the preceding claims having a diameter of at least <measure type="interval"><num
atLeast="1">1</num><measure type="LENGTH" unit="m">m</measure></measure>

[..]sky positions lie within a <measure type="interval"><num atMost="7">7</num> <measure type="ANGLE" unit="°">°</measure>
</measure> radius of other planets[..]

2. Base and differential value¶

Take the example

4 women and 15 men, 30± 10 years, 176±7 cm, 70±9 kg, 15±5 % of fat mass, VO2max: 50±8 ml·kg−1·min−1 and 21 of race A

after two “counts”, four measurements express intervals following this form.

<measure type="value"><num>4</num></measure> women and <measure type="value"><num>15</num></measure> men,

Similarly as in the previous interval case, an attribute in element <num>, here @type, characterizes the base value and the differential/range value.

<measure type="interval"><num type="base">30</num> ± <num type="range">10</num><measure type="TIME" unit="year">years</measure></measure>,
<measure type="interval"><num type="base">176</num> ± <num type="range">7</num><measure type="LENGTH" unit="cm">cm</measure></measure>,
<measure type="interval"><num type="base">70</num> ± <num type="range">9</num> <measure type="MASS" unit="kg">kg</measure></measure>,
<measure type="interval"><num type="base">15</num> ± <num type="range">5</num> <measure type="FRACTION" unit="%">%</measure></measure> of fat mass

If the quantity is expressed only in term of range (without base) it can be implicitly assumed that the base=0, see example ± 10 years

<measure type="interval">± <num type="range">10</num><measure type="TIME" unit="year">years</measure></measure>

If the interval has a base without a range, it’s annotated with only the base (issue #64 <https://github.com/kermitt2/grobid-quantities/issues/64>):

a certain temperature interval1 around <measure type="interval"><num type="base">4 0</num> <measure type="TEMPERATURE" unit="°C">°C</measure></measure>

Notes about intervals¶

Interval markers such as more than, less than, and so on, are left outside the annotation when it’s possible (see issue #35). Example:
```
more than <measure type="interval"> <num atLeast="2">2</num> </measure>
```

An interval can be bounded with quantities expressed in different unit multiples (see issue #45). For the sentence radii between 10 µm and 1 cm the result will be:

grains with radii between <measure type="interval"><num atLeast="10">10</num> <measure type="LENGTH" unit="µm">µm</measure> and <num atMost="1">1</num> <measure type="LENGTH" unit="cm">cm</measure></measure>

The From ... to markers are not necessarily introducing an interval, example:

the rate was reduced from <measure type="value"><num>1.87</num></measure> to <measure type="value"><num>0.82</num></measure>

When interval boundaries are given alphabetically, the <num> attribute must be converted in numbers:

between <measure type="interval"><num atLeast="1">one</num> and <num atMost="10">ten</num></measure>

Rational numbers are writter with a slash (/) (issue #66 <https://github.com/kermitt2/grobid-quantities/issues/66>)

at least <measure type="interval"><num atLeast="2/3">two-thirds</num></measure> of wins for their favourite team

Lists¶

Lists introduce series of values. The unit can be expressed per value or for several values at the same time. A <measure> element encloses the whole list of values including their units:

<measure type="list"><measure type="ENERGY" unit="cm^-1">cm-1</measure>: <num>3440</num>(br), <num>1662</num>,
<num>1632</num>, <num>1575</num>, <num>1536</num>, <num>1498</num>, <num>1411</num>, <num>1370</num>, <num>1212</num>,
<num>1006</num>, <num>826</num>, <num>751</num></measure>

<measure type="list"><num>1.27</num> <measure type="LENGTH" unit="Å">Å</measure> for 1H5Y, <num>1.52</num>
<measure type="LENGTH" unit="Å">Å</measure> for 1KA9, and <num>1.69</num> <measure type="LENGTH" unit="Å">Å</measure>
</measure> for 1THF

List can be disjunctive, conjunctive, or a combination. We do not distinguish the different kinds of list at the present time:

batches of <measure type="list"><num>three</num> or <num>four</num></measure> observations

for flexural samples the size is <measure type="list"><num>100</num> <measure type="LENGTH" unit="mm">mm</measure>
 x <num>100</num> <measure type="LENGTH" unit="mm">mm</measure> x <num>400</num> <measure type="LENGTH" unit="mm">mm
 </measure></measure>

If there are no intermediary values, it’s an argument for deciding to annotate an element as a list, for example this ranked list (issue #65 <https://github.com/kermitt2/grobid-quantities/issues/65>):

for every lower position in the general classification the prize money was more or less halved between
 the first <measure type="value"><num>seven</num></measure> ranked riders: from <measure type="list">
 <measure type="CURRENCY" unit="euro">€</measure> <num>450,000</num> for the winner over <measure type=
 "CURRENCY" unit="euro">€</measure> <num>200,000</num> for the runner-up to <measure type="CURRENCY"
 unit="euro">€</measure> <num>100,000</num> for the third ranked rider, and so on to
 <measure type="CURRENCY" unit="euro">€</measure> <num>11,500</num></measure> for the rider ranked in seventh place.

Additional items¶

Dates¶

Dates are time measurements, they are thus also encoded in the training data as a complement to the other _TIME_ expressions involving time units. In TEI P5, the dates are marked with a specific element <date> which can be contained in an element <measure>. The encoding is then straightforward for atomic values (with attribute @when), intervals (with attribute @from-iso and @to-iso in case on min-max intervals) and lists:

Comet C/2013 A1 (Siding Spring) will have a close encounter with Mars on <measure type="value"><date when=
"2014-10-19">October 19, 2014</date></measure>.

The arrival time of these particles spans a <measure type="interval"><num type="range">20</num>-<measure
type="TIME" unit="min">minute</measure> time interval centered at <date type="base" when="2014-10-19T20:09">
October 19, 2014 at 20:09 TDB</date></measure>


Observations took place from <measure type="interval"><date from-iso="2014-10-19">October 19, 2014</date> to
<date to-iso="2014-10-25">October 25, 2014</date></measure>.

the emergence of this sport in the <measure type="interval"><date from-iso="1980" to-iso="1989">1980 s</date>
</measure>


Observations were performed on <measure type="list"><date when="2013-10-29">October 29, 2013</date>, on <date
when="2014-01-21">Jan 21, 2014</date>, and on <date when="2014-03-11">March 11, 2014</date></measure>.

Time tag (and difference with Date tag)¶

if only the part of a date is expressed (for example the time of a day), but we can infer the date, a complete date is implicit and the context can make it being fully quantified.

For example 20:10 UTC will be annotated:

<measure type="value"><date when="2014-10-19T20:10Z">20:10 UTC</date></measure>

With UTC inside the annotation which is important to know exactly the “time” measure.

for a time expression not linked to a date, like the expression of an “hour”, it’s appropriate to annotate with the tag <time>, to distinguish from the <date> case (see issue #48):

To sleep well, relax everyday at <measure type="value"><time when="21:00:00">21:00</time></measure>

It consists of infusing the [...] drugs in the following order: leucovorin between <measure type="interval"><time from-iso="10:30:00">10 h 30</time> and <time to-iso="21:20:00">21 h 20</time></measure> [...]

Special cases¶

Frozen quantity expressions like decade or Room temperature

Room temperature (Raumtemperatur, température ambiante, …) is used very frequently in chemistry and related fields. It can be considered as 20 °C (293 Kelvin), although not defined in a standard manner (https://de.wikipedia.org/wiki/Raumtemperatur).
```
<measure type="value"><measure type="TEMPERATURE">Raumtemperatur</measure></measure>
```

Decade (issue #52 )

over  <measure type="interval"><num atLeast="2">two</num> <measure type="TIME" >decades</measure></measure>

Miscellaneous / Examples¶

Plus (+) and minus (-) signs¶

The + and - signs must be put inside the <num> tag. Examples:

a recent study [...] showed that cycling efficiency was lower (<measure type="value"><num>−11</num><measure type="FRACTION" unit="%">%</measure></measure>) and energy cost of running was greater (<measure type="value"><num>+11</num><measure type="FRACTION" unit="%">%</measure></measure>) in the master compared with young triathletes

Units without values¶

Case where it’s not annotated: When we refer to the units as such, to express something about the units, we are not using the units to quantify something with a value:

and r H are the geocentric and heliocentric distances in cm and AU, respectively, and F comet and F

Like here for the units: cm and AU.

Case where it’s annotated: We could have units expressed without values, when the value is implicit:

that can extend <measure type="interval"><measure type="LENGTH" unit="mm">millimeters</measure></measure> or even <measure type="interval"><measure type="LENGTH" unit="cm">centimeters</measure></measure> from the cell body

here the value of millimeters and centimeters is unspecified (e.g. equivalent to several), but we have a quantity and more precisely an interval. See issue #31

Imprecise quantifiers¶

When used with units, quantifers like few, several, a couple, a large amount of is annotated, and whatever quantifies even imprecisely :

the reference solution becomes distinct from the ballistic solution only a <measure type="value"><num>couple</num> of <measure type="TIME" unit="week">weeks</measure></measure> before the encounter.

Determiners are left outside (a <measure type=”value”><num>couple</num> of <measure type=”TIME” unit=”week”>weeks</measure></measure>). See issue #34

X-fold¶

Quantifiers like two-fold, sevenfold meaning “two times/part”, “seven times/part” are annotated, to capture the full expression of quantity including this notion of “part”:

allowing a <measure type="value"><num>sevenfold</num></measure> compaction of the length

LUCA-HisF displays a clear <measure type="value"><num>two-fold</num></measure> symmetry

Constants¶

Precise number (for example c , the speed of light in vacuum) and imprecise numbers (for example π which has an infinite number of decimals) are annotated. See issue #37

Example:

`decelerating from <num>5</num><measure type="VELOCITY" unit="% c">% c</measure>`

Exponents for powers of ten¶

Exponents notation might be lost in documents, for example 10 power -6 in pdf becomes 10 −6. The correct exponents are written in the attribute when there is one, 10 power -6 will be written 10^-6. Example in interval:

<measure type="interval"><num atMost="10^-6">10 −6</num></measure>

See issue #38

Numbers which seems to be only tags but are in fact quantifying¶

For example expressions like at day 21 or between day 56 and day 91, which are really quantifying and for which range queries can be expressed.

OCR errors¶

OCR errors are annotated as if they were the correct sequences, since they are realistic noise. For example:

20 aC -> <measure type="value"><num>20</num> <measure type="TEMPERATURE" unit="°C">°C</measure></measure>
2.5 • -> <measure type="value"><num>2.5</num><measure type="ANGLE" unit="°">°</measure></measure>

Out of scope¶

Only expressions of quantities are annotated, which can use numbers or alphabetical words.

Some numbers are also used for other stuff like markers, call-out, section number, identifiers, index, reference expressions, formula parameters, ill-encoded characters, etc. and all these cases are out of scope. See issue #36

Some sequences not annotated (not commented)¶

Markers, call-out, section number, numerical bullet points, identifiers, index, reference expressions, formula parameters

Examples:

Reference markers:

lower than those derived by Vaubaillon et al. (2014) and Moorhead et al. (2014) computing the corresponding impact probabilities (Milani et al. 2005)

Figure/table titles, and other numbers who don’t quantify anything:

Figure 1 shows the residuals of C/2013 A1's observations
[Figure 1 about here.]
Table 1 contains the orbital elements of the computed solution.
our new orbit solution (JPL solution 46)

Inline formulas, like:

a minimum point of ∆v 2 = |∆v| 2 under the constraint that the particle reaches Mars, i.e., (ξ, ζ)(r, β, ∆v) = (0, 0).

Some sequences to be commented out¶

Ill-encoded characters

Examples:

Sequence that would be usually annotated but contain encoding problems / characters in the free unicode range, like:

񮽙񮽙  

Case not yet supported¶

The following cases are not annotated at this stage. The sentence when these cases occur should be put in comments for the moment.

Sigma estimation

We selected the A 1 uncertainty so that its range would span from 0 au/d 2 to twice the nominal value at 3&#x3C3;.

Intervals embedded in intervals

[..]only Mars is near enough that the orbital motion can extend a single viewing window from 45 days to as much as 60 to 90 days.

For the wide scenario the uncertainty goes from 45 min down to 1–2 min.

Note: one possibility would be to only mark the external boundaries of the interval.

[..]only Mars is near enough that the orbital motion can extend a single viewing window from <measure type="interval">
<num atLeast="45">45</num><measure type="TIME" unit="day">days</measure> to as much as 60 to <num atMost="90">90</num>
<measure type="TIME" unit="day">days</measure></measure>.

For the wide scenario the uncertainty goes from <measure type="interval"><num atLeast="45">45</num>
<measure type="TIME" unit="days">min</measure> down to 1–<num atMost="2">2</num> <measure type="TIME" unit="min">min</measure></measure>.

List of intervals

No significant difference in running and total times was observed between the age groups 25 to 34 and 35 to 44 years

Atomic value expressed with different values and units

The current Hawaii Ironman triathlon record is 8:54:202 for females

[a] male athlete was able to finish [an] ultra-marathon in a time of 19 h 44 min

Unit embedded in numerical value

For example 92°.5 wich would require to embed <measure> in <num> (issue #49). Or also 126 withdrawals out of 162 riders.

Discontinuous cases

Interval quantities whith base and range multiplied as a whole by a power of ten (see issue #42):

A1 (Siding Spring) will pass Mars with a close approach distance of 1.35 ± 0.05 × 10 5 km

or like:

The gas production rates, Q(CO 2 ) = (3.52> ± 0.03) × 10 26 molecules s −1

Other cases

This process takes place between t = 30[ 12 h] and t = 140[ 12 h]

Various examples¶

XML examples (ended with the name of the file between brackets)

Note that only <measure type="value"><num>47 out of the 76</num></measure> patients experienced a first accident.[hal-00643787.training.tei.xml]

Branson Sonifier W-250D, <measure type="value"><num>2 x 2</num> <measure type="TIME" unit="min">min</measure></measure> in <measure type="value"><num>15</num> <measure type="TIME" unit="s">sec</measure></measure> intervals. [hal-00924047.training.tei.xml]

ranging from <measure type="interval"><num atLeast="1.14">1.14</num> <measure type="LENGTH" unit="Å">Å</measure> to <num atMost="1.43">1.43</num> <measure type="LENGTH" unit="Å">Å</measure></measure>.[hal-00924047.training.tei.xml]

the emission maxima shifted from <measure type="value"><num>345</num> <measure type="LENGTH" unit="nm">nm</measure></measure> to <measure type="value"><num>325</num> <measure type="LENGTH" unit="nm">nm</measure></measure> [hal-00924047.training.tei.xml]

[...] (<measure type="list"><num>72</num> for compressive test and <num>72</num></measure> for flexural test) [hal-00962359]

Patients with SS have a <measure type="interval"><num atLeast="20">20</num>-<num atMost="40">40 fold</num></measure> increased risk of developing lymphoma [hal-00987664]

Units CRF model¶

The Units model is used to parse chunks of text recognised as units from the Quantity CRF model. The data handled as unit is modelled based on the SI representation of unit, which models any unit as a triple: prefix, base and pow. For example m^2 can be represented as [-, m, 2]. Complex units are naturally supported: m^3/kg*s can be rewritten as [(-, m, 3)(k, g, -1)(-, s, -1)].

There are 3 labels for this model:

<prefix> represent the unit prefix, for example k for kilo, G for giga and so on and so forth. The definition of these prefix is in the prefix dictionary under resources/lexicon/${lang}/prefix.txt.
<base> carry out the unit base information. For NON-SI units the entire unit should be contained as <base>.
<pow> contains information about the exponents and divisions. It’s used to correctly assign exponent values and to revert the sign to blocks in the denominator.

The training data follows a simple structure, see an example on how cm is represented:

<units>
  <unit><prefix>c</prefix><base>m</base></unit>
</units>

General principles:

in complex units the division mark should be labelled as <pow>, for example:
```
<unit><base>m</base><pow>/</pow><base>s</base></unit>
```
the indication of a power, like ^ should be taken out of the <pow> label, for example m/s^4 should be annotated as:
```
<unit><base>m</base><pow>/</pow><base>s</base>^<pow>4</pow></unit>
```
non-SI units are added in the <base> as anticipated above:
```
<unit><base>miles</base></unit>
```
denominator written with subsequent division marks, like cal/kg/m/days, which means cal/(kg*m*days), all the / should be annotated:
```
<unit><base>cal</base><pow>/</pow><base>kg</base><pow>/</pow><base>m</base><pow>/</pow><base>days</base></unit>
```
in general numerator / den1 den2 den3 is equivalent to numerator/(den1*den2*den3). Groups by parenthesis are not supported.

Values CRF model¶

The Values model is used to parse chunks of text recognised as values from the Quantity CRF model.

The Values model uses the following labels:

<number> identify numeric values
<exp> identify the exponent in the base-E expressions (written as e and corresponding to the constant Euler's number 2.71828)
<base> identify the base of the base-N representation
<pow> identify the exponent for base-N or base-E expressions
<time> represent date and time expressions
<alpha> identify values expressed in alphabetic

This labels are combined to recognise this type of values:

numeric value:
```
<value><number>2</number></value>
```
alphabetic value:
```
<value><alpha>two</number></value>
```
power with base-10 expression, discussed in #7. Example:
```
<value><base>10</base>^<pow>-5</pow></value>
```
The <base> and <pow> should contains only values. Additional markers (like x, ^, x) should be left out. The <base> label should contains expression of the “base”, usually 10 but could be set to different values.

For example:
```
<value><number>1</number> × <base>10</base> <pow>−7</pow></value>
```
Euler’s number based expressions, discussed in: #8. Example:
```
<value><number>1.2</number>e^<exp>-5</exp></value>
```
e or E should be left out, because is a constant and does not have variability.

time and date expressions, discussed in #12

<value><time>2001 August</time></value>

Quantified objects CRF model¶

Currently work in progress The quantified object (or substance) is the object for which the measurement is expressed. For example A mixture of 10kg of silicon nitride powder. The object is the silicon nitride powder which is attached to the measurement of 10 with unit Kg.

Cf. issue #19

The quantified object model currently rely on a simplistic approach that involve the dependency parsing of the sentence and the identification of the head in the phrase with some heuristic.

In this section we discuss the guidelines for annotating training data used for a CRF model to replace the current implementation.

In the training data are identified the measurement (and their type) and the quantified object.

For example:

<p>A mixture of 10kg of silicon nitride powder.</p>

can be annotated as:

<p>A mixtured of <measure type="value" ptr="#1235324324321">10kg</measure> of <quantifiedObject id="1235324324321">silicon nitride powder</quantified Object>.</p>

The quantified object is identified by its ID and linked to the measure via the attribute ptr=”#ID”.

Note

This implementation allows the linking of objects directly attached on the left or right of the measurement, for the time being far entities are not supported.

How to annotate?

Annotating the quantifiedObject is a complicated task, because it requires a clear definition to avoid misunderstanding. Firstly the question each annotator should ask is “What is being measured?”.