The work presented in this paper is part of the project A2 (Sekimo) of the Research Group 437 Text-technological modelling of information funded by the German Research Foundation.[1]


There is a large amount of machine-readable structured linguistic documents (often XML annotated) available to the public as well as several NLP tools which allow for the analysis of linguistic data. Besides corpora annotated for several linguistic phenomena, external knowledge bases like lexical nets (WordNet, cf. Fellbaum, 1998 GermaNet, cf. Hamp and Feldweg, 1997) are an important source for linguistic studies. However, these resources are often heterogeneous in respect to both, the underlying schema of the output format and the functionality provided. Furthermore, their use for (semi-) automatic annotation can lead to the problem as to how to represent multi-dimensional, possibly overlapping markup - which often occurs when different linguistic annotation levels are unified (e.g. syllables vs. morphemes). Different methods for the annotation of multiple information levels have been developed: separation of multiple annotation levels in separate files, fragmentation or milestones (cf. Sperberg-McQueen and Burnard, 2002). In the Sekimo project different approaches for the integration of heterogeneous linguistic resources were developed and applied in the domain of anaphora resolution. For the task of anaphora resolution different types of information are necessary: POS, syntactic knowledge, world knowledge (e.g. in terms of an ontology) and the like. Therefore various linguistic resources such as parsers, dictionaries, wordnets or ontologies have to be combined. However, in most cases the output format of a linguistic resource A is not suitable as input format for a linguistic resource B, which means that a cascaded application of several resources is not possible. After experiences with a Prolog fact base approach (cf. section “Prolog-based architectures”) we have developed an XML-based abstract representation format similar to the standoff annotation model described by Thompson and McKelvie, 1997 which encodes the same textual data in separate files according to different document grammars addressing different relevant phenomena.

Information structuring can always be split up into a conceptual process and a technical realization. We follow the discussion in Goecke et al., 2008 and use the term level to refer to the information modelling concept (e.g., morphological structure, phrase structure) and the term layer for the technical realization, i.e. the XML markup. Levels and layers can be in different relations (1:1 relation, 1:n, m:1 or n:m) which can lead to overlapping markup in the layer structure. The annotation format described in Witt et al., 2005 solves this issue and ensures a 1:1 relation. For clarification issues we prefer the term multi-rooted trees in favor of multiple annotations when talking about the architecture used in our project because the different levels of annotation are stored in a single representation.

The remainder of this paper is structured as follows: At first we will give an overview of different approaches for integrating multiple annotated data, followed by a description of the Sekimo Generic Format (SGF) sketched out in section “The Sekimo Generic Format”. In section “Application of SGF” we will demonstrate how the SGF is used in the application domain of anaphora resolution. Finally, the paper closes with section “Conclusion and outlook” in which possible extensions and future work are discussed.

Different approaches to multiple annotated markup

There is a variety of approaches for dealing with multiple annotated data (or multiple hierarchies) already available. DeRose, 2004 summarizes some solutions (including both XML-based and non-XML-based approaches) with their respective strengths and weaknesses. We propose to group a selection of the available solutions into three categories:

  1. Prolog-based architectures.

  2. XML-related architectures.

  3. Graph-based architectures that follow the XML syntax.

The reason for this grouping is partially due to a chronological ordering (e.g. the roots of the Prolog-based architectures go back more than ten years) and partially because of the underlying technical foundation (e.g. the separation of XML-based and non-XML-based architectures). The last point is crucial with respect to the support in terms of tools (e.g. parsers, transformation processors, query tools) when it comes to the application of a specific architecture (cf. section “Application of SGF”).

Prolog-based architectures

In Sperberg-McQueen et al., 2000 and Sperberg-McQueen et al., 2002 an abstract representation format to represent meaning and interpretation of markup based on a Prolog fact base was introduced. Witt, 2002 extended this architecture for dealing with multiple annotated data. In this extension textual data and annotation are split up in order to avoid overlapping markup (cf. Bayerl et al., 2003 for a further discussion). The elements, attributes and text nodes of the annotation layers are stored as Prolog predicates which contain the following information (for details refer to Witt et al., 2005):

  • The type of node (element, attribute or text) as the name of the predicate.

  • The name of the annotation layer.

  • The absolute start and end positions of the annotated text sequence.

  • The position of the node in the document tree.

  • The name of the element or attribute.

  • The value of an attribute.

Each character in the text base (the primary data) can be addressed by its offset (its position) as shown in Figure 1. A single character has a start and end position and a step size of 1.

Figure 1: Addressing character positions

  T  h  i  s     i  s     a     s  e  n  t  e  n  c  e  .

On the basis of the Prolog fact base format, possible relationships between element instances of different annotation levels can be examined via Prolog predicates (cf. Durusau and O'Donnell, 2002 and Witt et al., 2005). As further option, a unified version can be created and exported back to XML where overlaps are handled by using milestones or fragments.

Although the conversion itself can be done very quickly (two implementations are available, one programmed in Python, another one in Perl), the fact remains that a conversion from XML to Prolog is necessary both for markup unification and for analysing relations between different annotation levels. The need for information about the position of each single character of the primary data - which is demanded for reconstructing the primary data - and the distributed storing of element and attribute information results in rather large Prolog fact bases: for the largest single text stored in our corpus a single annotation layer of 1.7 MB in size is converted to a 6.4 MB-size Prolog fact base, the combined three annotation layers that are used in our project (logical document structure, POS, anaphoric relations) result in a 14.3 MB-size Prolog fact base.

XML-related architectures

Several XML-related but non-XML-based approaches for storing multiple annotated data have been developed in recent years, including the Layered Markup and Annotation Language (LMNL, cf. Tennison, 2002, Cowan et al., 2006), TexMECS (cf. Huitfeldt and Sperberg-McQueen, 2001) and Generalized Ordered-Descendant Direct Acyclic Graphs (GODDAG, cf. Sperberg-McQueen and Huitfeldt, 2004) Multi-colored Trees (MCT, cf. Jagadish et al., 2004) or Delay Nodes (cf. Le Maitre, 2006). XCONCUR, formerly known as MuLaX (cf. Hilbert, 2005 and Hilbert et al., 2005) has been recently accompanied by XCONCUR-CL (cf. Schonefeld, 2007, Witt et al., 2007) as a constraint-based validation language.

Although some of these approaches (e.g. LMNL, TexMECS, XCONCUR) support inline annotation of multiple annotation layers, these documents can get very complex when dealing with a large number of annotation layers. As a drawback, both, design and implementation of most of these architectures, rely on the work of only a few people. Therefore, specifications such as XCONCUR roughly remain in the state of experimental markup languages lacking the support of the large number of tools that is available for XML-based solutions.

Graph-based architectures

A variety of graph-based architectures that use the XML syntax has been developed in recent years. Starting with the Annotation Graph (AG) model presented by Bird and Liberman, 1999 and Bird and Liberman, 2001, architectures such as the NITE Object Model (cf. Carletta et al., 2003) in conjunction with NITE-XML, ATLAS (cf. Bird et al., 2000; Laprun et al., 2002) and the ATLAS Interchange Format (AIF), the Linguistic Annotation Framework pivot format (cf. Ide and Romary, 2004) and the similar Potsdam Austauschformat für Linguistische Annotationen (PAULA, cf. Dipper, 2005), the Graph-based Format for Linguistic Annotation (GraF, cf. Ide and Suderman, 2007) or the Graph Exchange Language (GXL, cf. Holt et al., 2006, firstly used in the graph-based linguistic database HyGraphDB[2] to represent linguistic data structures) were published.

In principle, these graph-based formats allow the annotation of nearly every possible linguistic annotation. However, as these formats tend to split even single annotation layers into separate files (such as a markable/token file which delimits text spans used in annotation, a structure file for storing relations between annotation elements and a feature file which stores the former annotation), they are often used only as interchange formats. In addition, the higher complexity of computing graph structures in contrast to tree structures in combination with the fact that at least most single annotation layers can be structured in trees, leads to a certain inefficiency (cf. Dipper et al., 2007 who transform a standoff annotation into a an inline representation for efficient querying). Because our main focus was the development of a tool allowing for the comparison of different annotations we decided to implement an additional standoff format: The Sekimo Generic Format, SGF.

The Sekimo Generic Format

After the experiences made with the Prolog fact base format the decision was made to develop a similar representation based on XML. The initial goal was to use a native XML database as storage backend, however, during the development of the Sekimo Generic Format (SGF) several implementations were tested, including the use on a per-file basis, different native XML databases (e.g. eXist[3], Berkeley DB XML[4], Qizx/db[5], IBM DB2 Express-C 9.5[6]), and a relational database (MySQL[7], cf. section “SGF as import and export format”). In the following sections we will present SGF in detail. The annotation layers shown in Figure 2 and Figure 3 will serve for demonstration purposes. In section “Application of SGF” we will show a real world example from the domain of anaphora resolution.

Figure 2: Phrase structure annotation

<s xmlns=""
  xsi:schemaLocation=" phrase.xsd">

Figure 3: Syllable annotation

<syll xmlns=""
  xsi:schemaLocation=" syll.xsd">

The concept of SGF

SGF was developed for storing multiple annotated linguistic corpus data and examining relationships between elements derived from different annotation layers. The format consists of a base layer, providing the structure of an SGF instance and global attributes that are imported by the different annotation layers (cf. section “The base layer”). The use of metadata in SGF is described in section “Metadata” while section “Adding layers”, section “Disjoints and continuous segments” and section “Validation” deal with different aspects of the format. Finally, we will discuss processing and querying of SGF annotated data in section “Querying” and conclude with possible caveats of the format in section “Caveats and problems”.

Figure 4: Diagram of the corpus root element

SGF can be used in two different ways as shown in Figure 4:

  1. As a container format that contains optional meta data (cf. section “Metadata”) and the corpus data, i.e. the whole corpus is saved as a single SGF instance. This is the appropriate way when using SGF for storing small and medium sized corpora in conjunction with a native XML database (cf. Figure 5).

  2. On a per-file basis or when dealing with larger corpora a meta SGF file is used containing (again optional) metadata for and references to the actual corpus files (cf. Figure 6).

Figure 5: Storing a whole corpus in a single SGF instance

<corpus xmlns=""
  xsi:schemaLocation=" root.xsd">
  <corpusData xml:id="c1" type="text" sgfVersion="1.0">
    <!-- [...] -->
  <corpusData xml:id="c2" type="text" sgfVersion="1.0">
    <!-- [...] -->

Figure 6: Splitting up a whole corpus into multiple SGF instances (SGF meta file use)

<base:corpus xmlns=""
  xsi:schemaLocation=" ../xsd/root.xsd">
  <base:corpusDataRef xml:id="c1" uri="c1.xml" mime-type="text/xml"
  <base:corpusDataRef xml:id="c2" uri="c2.xml" mime-type="text/xml"
  <base:corpusDataRef xml:id="c3" uri="c3.xml" mime-type="text/xml"

In both cases the root element is the corpus element; underneath this a corpusDataRef element or a corpusData element can be inserted. The empty corpusDataRef element allows for referring to an external file containing a corpus entry via its uri attribute and for specifying the external data in terms of encoding and mime-types (respective attributes of the same name). In this case the root element of the corpus entry instances that are referenced by the SGF meta file should be the corpusData element (cf. section “The base layer”).

The base layer

The corpusData element is used for storing a single corpus entry containing optional metadata (cf. section “Metadata”), the primary data, the segmentation of the primary data, and zero or more respective annotation layer(s) (cf. section “Adding layers”). An example base layer is shown in Figure 8. The xml:id attribute is obligatory while the sgfVersion attribute is optional (with a default value of 1.0)

Figure 7: Diagram of the corpusData element

Figure 8: The SGF base layer

<corpusData xmlns=""
  xsi:schemaLocation=" root.xsd"
  xml:id="c1" type="text" sgfVersion="1.0">
  <primaryData start="0" end="19" xml:lang="en">
    <textualContent>This is a sentence.</textualContent>
    <checksum algorithm="md5">d15ba5f31fa7c797c093931328581664</checksum>

The corpusData element holds the type attribute which can be either set to the value text or multimodal while the primaryData child element contains either the textual primary data (i.e. the text that is used as basis for annotation) as text node of the textualContent element or a reference to a file containing the primary data (in case of larger texts or non-textual primary data) via a location child element (not shown in the example listing). In the latter case an optional checksum of the input file can be provided in the corresponding element to preserve integrity of primary data when dealing with multiple annotation resources. Note, that we do not handle any byte offset problems derived by different encodings (e.g. Latin 1 vs. UTF-16), therefore, the use of the encoding attribute is highly recommended.[8]

When using SGF for storing multimodal annotations, multiple primaryData elements are allowed. In this case, the attribute role has to be provided which marks exactly one primary data file as "master" while the other primary data files are marked as "slaves". The master primary data file sets the timeline, the slave files can be aligned to the master file via an optional offset attribute.


Metadata can be used in several locations in an SGF instance: as child element of the corpus element (for information regarding the whole corpus), underneath a corpusData entry (denoting metadata related to a single corpus entry and its annotation layer(s)), or as child of an annotation level. In the underlying XML schema description of the base layer the meta element is declared wrapper element for elements derived from a different namespace while the processContents attribute is set to lax, i.e. if an optional XML schema description for the referenced namespace is available it should be used for validation. In our case we use OLAC metadata (cf. Simons and Bird, 2003) which has turned out to be an adequate solution for a variety of linguistic data. Figure 10 shows an SGF instance containing OLAC metadata.

Adding layers

Several annotations of the primary data can be stored inside a corpusData element. Whenever an annotation layer is added, two steps have to be undertaken:

  1. The segments which delimit the annotated parts of the primary data are defined.

  2. A converted representation of the original annotation is stored.

The segments element consists of at least one segment. Each segment is defined by its start and end position in the character stream - similar to the Prolog fact base format discussed in section “Prolog-based architectures” (for an alternative definition of segments cf. section “Disjoints and continuous segments”). We use simple numeric attributes (defined as nonNegativInteger data type in the underlying XML Schema, cf. section “Validation” and XML Schema Part 2, 2004) for defining the start and end position - in contrast to the PAULA format (Dipper, 2005), which uses XLink (DeRose et al., 2001) and the XPointer framework (Grosso et al., 2003) to identify text spans. Because single characters have a step size of 1 (cf. Figure 1), empty elements use the same value for start and end position. An optional segment type attribute can be used to provide more information about the segment (available values are empty, char for character data, ws for whitespace characters, pun for punctuation characters, dur for duration in case of multimodal primary data and seg for referring to already defined segments, cf. section “Disjoints and continuous segments”).

Figure 10 shows the SGF representation of the two annotation layers given in Figure 2 and Figure 3. Note that a segment has to be defined only once, even if it is used in different annotation layers - in contrast to some other graph-based approaches (cf. section “Graph-based architectures”) which define the same character span separately for each annotation layer. This results in a smaller amount of segments that has to be defined even for a large number of annotation layers.

The annotation of the primary data is stored in the corresponding element. Following the terminological distinction between levels and layers (cf. section “Introduction”), each level element contains - in addition to optional metadata - exactly one layer element consisting of the markup representation of the corresponding annotation level. An annotation element may contain more than one level element, this mechanism can be used for subsuming annotation levels (e.g. when the corresponding elements are declared in the same document grammar). The layer element is a wrapper element containing elements derived from a different namespace, similar to the meta element (cf. section “Metadata”). However, while the value of the processContents attribute of the latter is set to lax, the value of the respective attribute of the layer element is set to strict, resulting in the fact that an XML schema has to be provided for each annotation layer (cf. section “Validation”).

Figure 9: Diagram of the level element

Figure 10: SGF instance containing two annotation layers

<corpus xmlns:xsi=""
  xsi:schemaLocation=" root.xsd"
  <corpusData xml:id="c1" type="text">
    <primaryData start="0" end="19" xml:lang="en">
      <textualContent>This is a sentence.</textualContent>
      <checksum algorithm="md5">d15ba5f31fa7c797c093931328581664</checksum>
      <segment xml:id="seg0" type="char" start="0" end="19" />
      <segment xml:id="seg1" type="char" start="0" end="4" />
      <segment xml:id="seg2" type="char" start="5" end="18" />
      <level xml:id="al1" priority="1">
          <olac:olac xmlns:olac=""
            <description>Phrase structure annotation.</description>
        <layer xmlns:phrase=""
          <phrase:s base:segment="seg0" xml:lang="en">
            <phrase:np base:segment="seg1">
              <phrase:pron base:segment="seg1" />
            <phrase:vp base:segment="seg2">
              <phrase:v base:segment="seg3" />
              <phrase:np base:segment="seg4">
                <phrase:det base:segment="seg5" />
                <phrase:n base:segment="seg6" />
      <level xml:id="al2" priority="1">
          <olac:olac xmlns:olac=""
            <description>Syllable annotation.</description>
        <layer xmlns:syll=""
          <syll:syll base:segment="seg0">
            <syll:s base:segment="seg1" />
            <syll:s base:segment="seg3" />
            <syll:s base:segment="seg5" />
            <syll:s base:segment="seg7" />
            <syll:s base:segment="seg8" />

As one can observe in Figure 11, SGF heavily makes use of XML's inherent ID/IDREF(S) mechanism to connect segments of the primary data with single or multiple annotation layers (displayed as solid red lines).

Figure 11: Use of XML's ID/IREF(S) mechanism in SGF

When comparing the two annotation layers with the namespace prefixes phrase and syll with their respective original representation given in Figure 2 and Figure 3, a second design goal of SGF is made visible: to conserve as much of the former annotation format as possible. Still, a conversion has to be made consisting of the following steps:

  • Elements with a mixed content model are converted into container elements.

  • Elements containing text nodes are converted into empty elements.

  • The base:segment attribute is added to former non-empty elements as an obligatory attribute (and as an optional attribute for empty elements).

The same conversion rules are applied to the underlying XSD (cf. section “Validation”). As shown in Figure 10 the hierarchy of elements and all attributes remain intact, i.e. there is no need for additional files such as structure files which are needed for the graph-based annotation formats discussed in section “Graph-based architectures”. However, this statement is only true as long as the XML-inherent tree structures are adequate.[9] An XSLT implementation is available for converting arbitrary inline annotation layers into their respective SGF representation while a second XSLT script merges different annotation layers according to the same primary data into a single SGF instance. Therefore, it is possible to add additional annotation elements to an already existing SGF instance at any time (as long as the primary data is not changed). Work has begun on a second implementation (written in Java).

Disjoints and continuous segments

Often segments consist of other segments making it possible to create new segments not only by defining their start and end positions but by referring to already defined segments using the segments attribute, too (cf. Figure 12). In order to distinguish if these newly established segments include all segments starting from the first referred segment up to the last referred one, or define a disjoint span, the attribute mode has to be set to the value continuous or disjoint, respectively. The example in Figure 12 shows a disjoint span.

Figure 12: Definition of a disjoint segment by referring to already established ones

<segment xml:id="seg6" type="seg" segments="seg1 seg3" mode="disjoint"/>;

Note that this feature of SGF could be used for conversion between SGF instances and architectures mentioned in section “XML-related architectures”, however, up to now it has been of theoretical use only.


An important aspect when dealing with multiple annotated data is the question of validating this data. In case of overlaps it is strictly impossible to provide a document grammar that is feasible for validating the unification of different annotation layers - even without the amount of work that has to be done for producing such a document grammar. Therefore, we propose that each annotation level is validated separately - in addition to the SGF instance as a whole - with a transformed version of its original document grammar. This conversion follows the conversion of the annotation layer described in section “Adding layers”.

We decided to use W3C XML Schema Description Language (XSD) (cf. XML Schema Part 1, 2004) as the underlying schema language for SGF for different reasons. As already stated, SGF relies heavily on two aspects:

  • ID/IDREF(S) mechanism, and

  • Namespace support.

While ID/IDREF(S) is already present in XML Document Type Definitions, DTDs lack real support for XML namespaces. Furthermore, SGF makes use of XML Schema data types (XML Schema Part 2, 2004) and when external document grammars (for annotation layers and metadata) are imported, the control of the processing of the imported document grammars is crucial (cf. section “SGF as import and export format” for the discussion of the Serengeti log functionality and the role of XML Schema's processContents attribute). Because of this we had to choose one of the XML schema languages available. XSD was favoured over RELAX NG (ISO/IEC 19757-2:2003) because of the better software support, e.g. with Saxon-SA[10] a schema-aware XSLT and XQuery engine is available which allows for the use of the id() and idref() functions for the task of comparing different annotation layers (cf. section “Analysing annotations”). Of course it would be possible to use simple string comparisons, however, XML IDs are usually indexed by the XSLT processor (for Saxon cf. and are for this reason - in most cases - much more efficient than the equivalent XPath expression using a string comparison predicate (cf. Kay 2008, p. 802-804.). This helps reducing processing costs when dealing with larger SGF instances, however, the downside is that the validation of each XSD associated takes some time (approximately one to two seconds in our case).

Apart from XSD validation, embedded Schematron (ISO/IEC 19757-3:2006) asserts are used as additional constraints, for example for refusing end positions of segments that are less than start positions (cf. Robertson, 2002). In the upcoming version 1.1 of XML Schema, the assert element will be used for fulfilling this task (XML Schema 1.1 Part 1, 2008).


One of the goals during the development of SGF has been the possibility of analyzing the relationships between elements of different layers. In contrast to the work described by Alink et al., 2006 and Alink et al., 2006a, which involves new standoff XPath axis steps, or the linguistic query language LPath, which extends the XPath 1.0 syntax and which was introduced by Bird et al., 2006, SGF uses unchanged XML-related specifications for querying data. Up to now we have employed XSLT 2.0, XPath 2.0 and XQuery 1.0 queries for typical tasks carried out in our project (cf. section “Application of SGF”). Bird et al., 2006 and Dipper et al., 2007 suggest different example queries to evaluate their architectures. By now, Q1 ("Find all sentences that include the word 'kam'"), Q2 ("Find all sentences that do not include the word 'kam'"), Q3 ("Find all NPs. Return the reference to that NP") and Q7 ("Find all pairs of anaphors and direct antecedents in which the anaphor is a personal pronoun") described in Dipper et al., 2007 were implemented. [11] Figure 13 shows Q7 for our corpus.

Figure 13: XQuery Q7 adapted for the corpus under investigation

declare boundary-space strip;
declare namespace base="";
declare namespace doc="";
declare namespace cnx="";
declare namespace chs="";
declare variable $doc := "ling-deu-003-sgf-noWS.xml";
<resultset file="{$doc}">
let $d := doc($doc)
for $s in $d//chs:semRel/chs:cospecLink[id(@phorIDRef)/
and @pos='PRON' and contains(@morpho,'Pers')]]

In addition, we have implemented Q8 ("Find all pairs of anaphors and antecedents and their respective parent(s) on the logical document layer"), for which it is necessary for the XQuery processor to traverse back to the segments, compare several segment elements and then to find the corresponding annotations. Most of the queries perform comparable to the respective inline queries referred to in Dipper et al., 2007, but in general they are difficult to compare since our corpus (six German scientific articles and eight German newspaper articles, containing 3,084 sentences, 56,203 tokens, 11,740 markables, 4,323 anaphoric relations, three annotation levels: logical document structure, POS, anaphoric relations) is different both in terms of size and annotation levels. Apart from Q7, most parts of the queries can be performed inline (which is a benefit of SGF over other architectures discussed in section “Graph-based architectures”), which allows us to abstain from converting SGF instances to inline representation prior to analyzing the relations (which was one of the motivations in developing SGF) as proposed by Dipper et al., 2007.

For a first evaluation we have chosen both the aforementioned complete corpus and our largest single text, a German scientific article comprising 157 paragraphs, 696 sentences, 12,345 token, 2,550 markables and 1,358 anaphoric relations (14,985 segments in total), annotated on the three annotation levels described above. All values are average results after five executions on two different machines:

  1. PC1: a Sun Fire V20z equipped with dual single core AMD Opteron 248 clocked at 2,2 GHz and 6 GB RAM running on Sun Solaris 10 (64bit) with Saxon-SA on Java 1.5.0_15 (2 GB RAM allocated for Java VM) and SWI-Prolog 5.6.21 (128 MB allocated as local stack limit).

  2. PC2: a standard PC equipped with a Intel dual core Core2Duo E6600 clocked at 2,99 GHz with 3.12 GB RAM running on Microsoft Windows XP SP3 (32bit) with Saxon-SA on Java 1.6.0_06 (1 GB RAM allocated for Java VM) and SWI-Prolog 5.6.57 (128 MB allocated as local stack limit).

Included in the XQuery results is the validation of five XSD files (-val parameter) and the output of an XML file (-o parameter) with a resultset root element and the corresponding query results underneath. For comparison, we evaluated the same queries for the Prolog fact base architecture used in the first project phase (cf. section “Prolog-based architectures”) on the same two machines. For the latter the amount of time for consulting the Prolog fact base containing the annotated data (14.3 MB in size, 3.37 sec on PC1; 2.94 sec on PC2) and the Prolog query file (4.3 KB in size, 0.0 sec on both machines) is not included in the results. The query results are output to a separate text file.

Table I

Evaluation results (in seconds). Average of five executions.

Query Prolog query results for single text (PC1 / PC2) XQuery results for single text (PC1 / PC2) XQuery results for whole corpus (PC1 / PC2)
Q1 0.22 / 0.054 4.612 / 1.244 9.609 / 4.162
Q2 13.502 / 4.554 5.161 / 1.234 9.390 / 4.357
Q3 0.084 / 0.03 4.035 / 1.219 9.556 / 4.084
Q7 30.66 / 7.798 5.764 / 1.481 11.669 / 5.35
Q8 84.16 / 24.738 15.379 / 11.134 152.683 / 114.525

Note that in contrast to the graph-based architectures described in section “Graph-based architectures”, the XQueries and their evaluation results depend on the annotation layers that are imported into the SGF base layer. This means that especially Q1, Q2 and Q3 are very fast because they can be performed inline in our corpus (i.e. both sentence and token information are descendants of the same annotation element - and the token element contains its textual content in its text attribute). For Q7, information derived from different annotation layers has to be taken into account, however, since only the id() function is used, the results are satisfactory as well. Q8 is the single XQuery that requires the identification of the respective segment element and the use of the idref() function afterwards in order to get the corresponding annotations. For these reasons, the advantage when using SGF over comparable architectures rises or drops depending on the imported annotation layers. To further reduce processing costs it is possible to use merged inline annotation layers (e.g. a logical document layer and a POS layer) as a combined, single SGF layer and use separate SGF layers only when overlaps occur. In this case the XML-inherent hierarchies can be used for (inline) analyzing of wide parts of the annotated data while a reversion to SGF's use of the ID/IDREF mechanism should only be made if not avoidable.

The performance figures for the Prolog fact base format show higher performance for simple queries but lower performance for more complex ones. These figures result from the fact that our corpus annotation makes heavy use of attributes, which leads to distributed information. We believe that a re-implemented Prolog fact base format could both reduce file size and speed up the querying.

Caveats and problems

Up to now, several former inline annotation layers have been converted into SGF and the format as such is quite stable (although minor changes may occur). Apart from the huge amount of markup that is necessary to do this kind of analysis, problems may arise when the annotation layers that are stored in SGF are exported back into their original inline representation. This is especially true when the annotation layers contain empty elements, for which it is impossible to provide the exact position in the original document tree (of course the base:segment attribute can be used for these elements as well; when a large number of empty elements appears in a row, the values of all their respective base:segment attributes would be identical). Although our largest SGF instance is at 6 MB including optional whitespace segments (4.8 MB without optional whitespace segments), it is still smaller than the respective Prolog fact base representation at 14.3 MB, cf. section “Prolog-based architectures”.

When it comes to queries, SGF relies on the imported annotation layers. For this reason, there is no standard set of queries available and the execution time cannot be easily predicted.

Application of SGF

Various application domains require the analysis of different information resources in order to answer a specific question. Alink et al., 2006, Alink et al., 2006a, for example, describe the analysis of multiple markup in the domain of digital forensics. In our project, we focus on linguistic phenomena, especially on anaphora resolution. Anaphora occurs when the interpretation of a linguistic unit (the anaphor) is dependent on the interpretation of another element in the previous context (the antecedent). The anaphor is often an abbreviated or reformulated reference to its antecedent and thus provides for the progression of discourse topics and discourse coherence. Anaphoric relations can be categorized according different axes (cf. Mitkov, 2002 for an overview): Type of anaphora (pronoun, NP, adverb, etc.), type of antecedent (e.g. nominal vs. abstract entity) and type of relation. In this paper, we will focus on nominal anaphora with nominal antecedents only. According the relation type, anaphoric relations may either express reference identity between the anaphor and its antecedent (Example 1) or the respective expressions are related via associative links (Example 2).

  1. I met a man yesterday. He told me a story. (example taken from Clark, 1977, p. 414)

  2. I looked into the room. The ceiling was very high. (example taken from Clark, 1977, p. 415)

In order to resolve anaphoric relations, different kinds of information have to be taken into account that are provided by different resources: POS tagger, Chunker, Parser, word net and ontologies. These resources provide information on gender or number agreement, noun phrases, grammatical function, lexico-semantic relations and domain or world knowledge. The resolution of the anaphoric relation given in Example 1 is dependent on agreement information of the pronoun he whereas the resolution of Example 2 requires the knowledge that a room typically has a ceiling which is provided in terminological nets such as WordNet (Fellbaum, 1998) or other ontological resources.[12]

We apply SGF for the integration of different resources and access to these data. In terms of levels and layers, each resource provides information for a specific level and this information is stored in a respective layer: A POS tagger provides information on part of speech tags and respective markup is generated in the tool's output file whereas access to a word net provides information on semantic relatedness of words in terms of distance between word's synsets. This information has to be stored and accessed for the anaphora resolution process. Figure 14 exemplifies the integration: Each resource is applied and the resulting markup is stored independently from the primary data. On the basis of the information stored in SGF it is possible to query the data, to create new markup layers, or to create inline versions of the markup and the primary data.

Figure 14: Application of multiple resources

Analysing annotations

In the application domain of anaphora resolution, a raw text document is taken as input and annotation layers are created for different levels. All layers are converted to SGF and can be analyzed afterwards. For the task of anaphora resolution, a set of antecedent candidates is created for each anaphoric element via an XSLT script (cf. Figure 16, an example candidate list is shown in Figure 17). The candidate list consists of several semRel elements each containing one anaphor element and several antecedentCandidate elements. Information on the relation type between anaphor and correct antecedent is stored as attribute information in the semRel element. The anaphor element describes properties of the anaphoric element whereas the antecedentCandidate elements describe information on the antecedent candidates. In both cases this information is stored in terms of attributes. Number or gender agreement can be computed from the morpho attribute. Additional information is given for part of speech (pos), grammatical function (syntax), dependency structure (dependHead), position of element in the whole document (position), the parent element on the logical document layer (docParent) as well as for the head noun both in surface form (text) and lemma (lemma). Together with other pieces of information a score for the most probable antecedent candidate can be computed (cf. Goecke et al. (to appear) for a similar approach). For the anaphora resolution system each anaphor-candidate-pair is interpreted as a feature vector which is used for training a classifier. Information on the correct antecedent candidate is necessary in order to classify positive and negative training examples (cf. Soon et al., 2001, Strube and Müller, 2003, Yang et al., 2004).

The annotated example sentence in Figure 15 is an extract of a German newspaper article that is part of our corpus. The content of the text excerpt is as follows:

Lurup ist ein sozialer Brennpunkt der Hansestadt, ein Vorort mit Einzelhäusern, aber auch vielen Wohnblocks im Westen der Stadt.

which is translated into:

Lurup is a social ghetto of the hanseatic city (Hansestadt), an outskirt with single unit houses but also many apartment blocks in the west of the city (Stadt).

In Figure 15 all levels that are used in the Sekimo project can be observed: the logical document structure (namespace prefix doc), the output of the commercial Parser/Tagger Machinese Syntax by Connexor Oy (namespace prefix cnx), the discourse entity level and the semantic relations level (namespace prefix chs). The segment seg1 delimits the whole text, while seg2 delimits a paragraph (containing a single sentence, cf. the doc:text and doc:para elements in the logical document layer and the cnx:sentece element in the cnx layer). The segments identified by seg1589 and seg1620 mark the two token (and respective discourse entities) "Hansestadt" and "Stadt". There is a cospecification relation (to be more specific: a hypernym relation) between these two discourse entities which is stored in the chs:cospecLink element located in the chs layer.

Figure 15: SGF instance of a German newspaper text (excerpt)

<corpus xmlns:xsi=""
  xsi:schemaLocation=" root.xsd"
  <corpusData xml:id="c15" type="text">
  <primaryData start="0" end="8208" fileref="c15-pd.txt" xml:lang="de">
  <checksum algorithm="md5">6ee0021b23c56b5917703746579e9ce8</checksum>
      <segment xml:id="seg1" type="char" start="0" end="8207"/>
      <segment xml:id="seg2" type="char" start="0" end="16"/>
      <segment xml:id="seg1577" type="char" start="4439" end="4567"/>
      <segment xml:id="seg1578" type="char" start="4439" end="4444"/>
      <segment xml:id="seg1589" type="char" start="4473" end="4487"/>
      <segment xml:id="seg1592" type="char" start="4477" end="4487"/>
      <segment xml:id="seg1620" type="seg" segments="seg1621 seg1623"/>
      <segment xml:id="seg1621" type="char" start="4557" end="4560"/>
      <segment xml:id="seg1623" type="char" start="4561" end="4566"/>
      <-- [...] -->
      <level xml:id="doc" priority="0">
        <meta><-- [...] --></meta>
        <layer xmlns:doc=""
          xsi:schemaLocation=" doc.xsd">
          <doc:text base:segment="seg1" xml:lang="de">
            <doc:para base:segment="seg2" skip="no"/>
            <-- [...] -->
      <level xml:id="cnx" priority="0">
        <meta><-- [...] --></meta>
        <layer xmlns:cnx=""
          xsi:schemaLocation=" cnx.xsd">
          <-- [...] -->
          <cnx:sentence base:segment="seg1577" id="w826" auto="no">
            <-- [...] -->
            <cnx:token base:segment="seg1578" text="Lurup" dependHead="w828"
              pos="N" syntax="@NH" lemma="lurup" dependValue="subj" morpho="NOM"
            <-- [...] -->
            <cnx:token base:segment="seg1592" text="Hansestadt" dependHead="w831"
              pos="N" syntax="@NH" lemma="hanse#stadt" dependValue="mod"
              morpho="FEM SG GEN" id="w833"/>
            <-- [...] -->
            <cnx:token base:segment="seg1621" text="der" dependHead="w848"
              pos="DET" syntax="@PREMOD" lemma="die" dependValue="det"
              morpho="Def FEM SG GEN" id="w847"/>
            <cnx:token base:segment="seg1623" text="Stadt" dependHead="w846"
              pos="N" syntax="@NH" lemma="stadt" dependValue="mod"
              morpho="FEM SG GEN" id="w848"/>
          <-- [...] -->
      <level xml:id="de" priority="1">
        <meta><-- [...] --></meta>
        <layer xmlns:chs=""
          xsi:schemaLocation=" chs.xsd">
          <-- [...] -->
          <chs:de base:segment="seg1589" deID="de226" headRef="w833" />
          <chs:de base:segment="seg1620" deID="de231" headRef="w848" deType="nom"/>
          <-- [...] -->
      <level xml:id="chs" priority="1">
        <meta><-- [...] --></meta>
        <layer xmlns:chs=""
            <-- [...] -->
            <chs:cospecLink id="sr86" relType="hypernym" phorIDRef="de231"
            <-- [...] -->

Apart from resources that have already been mentioned, further information is needed in order to create a suitable set of antecedent candidates for training and resolution. In general, a fixed search window in terms of markables (i.e. elements between which anaphoric relations can hold), sentences or paragraphs is chosen. This approach works well for pronoun anaphora due to the fact that pronouns tend to find their antecedents within a short distance (cf. Mitkov, 2002). However, for the resolution of non-pronominal definite noun phrases (definite descriptions) and the processing of long texts the application of a fixed search window is not feasible because definite descriptions tend to find their antecedents at a greater distance than pronouns. For the corpus under investigation that has been manually annotated for anaphoric relations (cf. Diewald et al. (submitted) for further information regarding the corpus and the annotation scheme), 26.8% of all non-pronominal anaphors (i.e. 20.9% of all anaphors in the corpus) find their antecedent at a distance of two or more paragraphs. We apply structural information to create candidate sets that include not only candidates at a short distance but also those at a larger distance. A small excerpt of the XSLT stylesheet that is used for the extraction is shown in Figure 16.

Figure 16: Excerpt of the XSLT stylesheet used for extracting candidates

<xsl:stylesheet xmlns:xsl="" version="2.0"
  <-- [...] -->
  <xsl:template match="chs:bridgingLink | chs:cospecLink">
    <xsl:variable name="link" select="."/>
      <xsl:attribute name="relationID" select="@id"/>
      <xsl:attribute name="type" select="local-name()"/>
      <xsl:for-each select="id(@phorIDRef)">
        <xsl:variable name="anaphoraPosition">
          <xsl:number level="single"/>
        <-- [...] -->
          <-- [...] -->
          <xsl:copy-of select="idref(id(@base:segment))[name()='cnx:token']/@*"/>
          <xsl:variable name="segstart" select="id(@base:segment)/@start"/>
          <xsl:variable name="segend" select="id(@base:segment)/@end"/>
          <xsl:for-each select="//element()[contains(name(),'doc')]">
            <xsl:if test="id(@base:segment)/@start <= $segstart and
            id(@base:segment)/@end >= $segend">
              <xsl:attribute name="docParent">
                <xsl:value-of select="name()"/>
                <xsl:number level="single"/>
        <xsl:for-each select="preceding-sibling::chs:de[position() <= $de_distance]">
          <xsl:variable name="antecedentPosition">
            <xsl:number level="single"/>
            <-- [...] -->

Because the segment element is the central and critical mechanism in SGF (cf. Figure 11) we have to use the id() and idref() XPath functions to analyze elements derived from different annotation layers. Figure 17 shows a result candidate list, extracted with a maximum distance of 10 discourse entities.

Figure 17: Candidate list extracted from the SGF instance

<candidateList xmlns=""
  maxDeDistance="10" filename="c15-sgf.xml">
  <-- [...] -->
  <semRel relationID="sr86" type="cospecLink" subtype="hyperonym" phorIDRef="de231"
    <anaphor base:segment="seg1623" deID="de231" headRef="w848" deType="nom"
      text="Stadt" dependHead="w846" pos="N" syntax="@NH" lemma="stadt"
      dependValue="mod" morpho="FEM SG GEN" id="w848" position="195" type="char"
      start="4557" end="4566" docParent="doc:para[13]"/>
    <antecedentCandidate base:segment="seg1560" deID="de221" headRef="w815"
      deType="nom" text="Kind" pos="N" syntax="@NH" lemma="kind"
      morpho="NEU SG NOM" id="w815" position="185" deDistance="10" type="char"
      start="4375" end="4403" docParent="doc:para[12]"/>
    <-- [...] -->
    <antecedentCandidate base:segment="seg1587" deID="de225" headRef="w831"
      deType="nom" text="Brennpunkt" dependHead="w828" pos="N" syntax="@NH"
      lemma="brenn#punkt" dependValue="comp" morpho="MSC SG NOM" id="w831"
      position="189" deDistance="6" type="char" start="4449" end="4472"
    <antecedentCandidate correctAntecendent="yes" base:segment="seg1592"
      deID="de226" headRef="w833" deType="nom" text="Hansestadt" dependHead="w831"
      pos="N" syntax="@NH" lemma="hanse#stadt" dependValue="mod"
      morpho="FEM SG GEN" id="w833" position="190" deDistance="5"
      type="char" start="4473" end="4487" docParent="doc:para[13]"/>
    <antecedentCandidate base:segment="seg1598" deID="de227" headRef="w836"
      deType="nom" text="Vorort" pos="N" syntax="@NH" lemma="vorort"
      morpho="MSC SG NOM" id="w836" position="191" deDistance="4" type="char"
      start="4489" end="4499" docParent="doc:para[13]"/>
    <antecedentCandidate base:segment="seg1602" deID="de228" headRef="w838"
      deType="nom" text="Einzelhäusern" dependHead="w836" pos="N" syntax="@NH"
      lemma="einzelhaus" dependValue="mod" morpho="NEU PL DAT" id="w838"
      position="192" deDistance="3" type="char" start="4504" end="4517"
    <-- [...] -->

For all antecedentCandidate elements (i.e. former chs:de elements) position and deDistance attributes have been added. Apart from the discourse structure that is used to model accessibility of antecedent candidates (cf. Polanyi, 1988), the logical document structure provides information on the hierarchical structure of texts by describing the organisation of the text document in terms of chapters, sections, paragraphs, and the like and is stored in the doc layer of the SGF instance.[13] Based on this information which can be accessed from DocBook, OpenDocument, or LaTeX, a layout-oriented presentation can be generated which is application independent. Especially for texts from e-publishing sources a set of logical document structure elements is easily available which can be used to identify different text segments. The influence of the logical document structure on the choice of an antecedent might be either (a) a direct influence on the markables (or antecedent life span) or (b) an influence on the search window (cf. Goecke and Witt, 2006). In our candidate list shown in Figure 17 the docParent attribute supplies information about the (virtual) parent element of the logical document layer, i.e. the element of the logical document layer that refers to a segment whose start position is lower or equal and whose end position is greater or equal to that of the segment referred to by the element analyzed.

Regarding the document structure, corpus evidence shows that some discourse entities are more prominent throughout the whole document than others, e.g. markables occurring in the abstract of a text might be accessible during the whole text whereas markables that occur in a footnote-structure are less likely as an antecedent for anaphoric elements in the main text. Corpus evidence shows that in a corpus consisting of 4323 anaphoric relations 65.3% of all anaphor-antecedent-pairs are located in the same segment. Regarding the remaining anaphor-antecedent-pairs, we expect markables described in hierarchically higher elements (e.g. subsection) to be much more prone to finding their antecedents in structuring elements of a higher level (section) than in a preceding but hierarchically lower segment (subsubsection). Thus, the influence on the search window may either enlarge the search window, i.e. the antecedent may be located outside the standard window (e.g. located in the whole paragraph or in a preceding one), or may narrow the search window, e.g. due to the start of a new chapter or section. Furthermore, the position of an antecedent candidate within a paragraph gives hints as to how likely that candidate is chosen as the correct one. An analysis of our corpus data shows that 50.2% of the antecedents are located paragraph-initial and 29.1% are located paragraph-final whereas only 20.2% are located in the middle of the paragraph. Thus in addition to the information regarding the search window, information on logical document structure might give cues for selecting the correct antecedent from a set of candidates.

SGF as import and export format

While the main reason for the development of SGF was analyzing relations between elements derived from different annotations (cf. section “Application of SGF”), the format is used in a another application in our project. The Serengeti web-based annotation tool described in Stührenberg et al., 2007 is currently enhanced to support different annotation schemes. This upcoming version of Serengeti will be used not only at Bielefeld University but also as an expert annotation tool in the AnaWiki project (cf. Poesio and Kruschwitz 2008) and will use SGF as its import and export format. For this reason, an SGF API (written in Perl) was implemented that allows the mapping of SGF to the relational MySQL database that is used as a backend for Serengeti.

During this development a log functionality was added to SGF ensuring that the information of added, deleted or modified data is not only stored in the Serengeti application but can be included in the exported SGF instance. A log can be stored as child element of an annotation level and contains at least one log entry, consisting of optional metadata and one or more action elements. The user responsible for the log entry is identified via a respective attribute, together with the time the entry was made (timestamp attribute). Each action is specified by its type attribute (add, delete, modify) and refers to the affected elements via an optional IDREF affectedItem attribute (not when the type attribute's value is set to add). The content of an action element is a sequence of elements from any namespace (otherwise modification of segments would not be possible), however, XML Schema's processContents attribute is set to skip, therefore, it is possible to use the same IDs several times (e.g. when modifying a segment element).

In addition, an SGF application for storing lexical chains was developed. SGF-LC, a lightweight XSD that is imported into the SGF base layer and that makes use of the attributes provided by the base layer is described in Waltinger et al., 2008 and is used as export format for the Scientific Workplace tool[14] developed by the project A4 (Indogram) of our Research Group.

Conclusion and outlook

In this paper we presented the Sekimo Generic Format (SGF) as an alternative approach for storing multiple annotated data amongst a variety of already established architectures and formats. SGF is used as an XML-based solution for storing and especially analyzing a corpus of multiple annotated documents (multi-rooted trees) in the linguistic application domain of anaphora resolution. Future work regarding our linguistic task of anaphora resolution focuses on the analysis of relations between logical document structure and the distribution of antecedent detection. On the technical side, we will adapt SGF to the upcoming version 1.1 of XML Schema, which includes assertions similar to the Schematron asserts used in the current version of SGF. Other possible developments include the implementation of converter scripts between SGF and some of the graph-based architectures mentioned and the further testing of the efficiency of SGF in large scale corpora using a wider set of sample queries.


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[1] More information about the project can be obtained at

[2] The HyGraphDB (cf. Gleim et al., 2007) has been developed as part of the X1 project of the collaborative research centre (CRC) 673 Alignment in Communication and of the Indogram project of the Research Group 437 Text-technological modelling of information.

[8] Relying on character offsets can be a source of trouble. For that reason one has to assure that whitespace differences between the textual primary data and annotation layers are normalized. Different whitespace normalizer tools were developed as part of our project.

[9] Of course it is possible to use graph-based annotation layers as well, however, the advantages of SGF over the formats discussed in section “Graph-based architectures” would be minimized in such cases (cf. section “Querying”).

[11] The other queries were not appropriate for the corpus under investigation.

[13] The logical document layer is a shortened variant of the DocBook schema (cf. Bayerl et al., 2003 for details).

Maik Stührenberg

Maik Stührenberg studied Computational Linguistics at Bielefeld University. He worked four years as research assistant at Giessen University in different text-technological projects (both funded by the German government and the German Research Foundation). He now works as a research assistant at Bielefeld University together with Andreas Witt, Dieter Metzing and Daniela Goecke in the Sekimo project of the Research Group Text-technological modelling of information funded by the German Research Foundation. His main research interests include specifications for structuring multiple annotated data and query languages and query processing.

Daniela Goecke

Daniela Goecke studied Computational Linguistics at Bielefeld University. She finished her master thesis in cooperation with IBM Scientific Center Heidelberg and worked four years at Philips Speech Processing Aachen. She now works as a research assistant at Bielefeld University together with Andreas Witt, Dieter Metzing and Maik Stührenberg in the Sekimo project of the Research Group 437 Text-technological modelling of information funded by the German Research Foundation. Her main research topics are the unification of text-technological resources and anaphora resolution.