Background¶

Caution

LAF-Fabric has a successor: Text-Fabric. LAF-Fabric stays around in order to run legacy notebooks. It is recommended to use Text-Fabric for new work.

What is LAF/GrAF¶

LAF/GrAF is a framework for representing linguistic source material plus associated annotations. LAF, Linguistic Annotation Framework is an ISO standard (24612:2012) that describes the organization of the data. GrAF, Graph Annotation Framework, is a set of schemas for the XML-annotations in a LAF resource.

Despite the L of linguistics, there is nothing particularly linguistic to LAF. LAF describes data that comes as a linearly ordered primary data stream (audio, video, text, or anything that has a one dimensional order), in which regions can be defined. Annotations are key=value pairs or feature structures in general, which conform to the joint definition of TEI Feature Structures and ISO 24610). Between the primary data and the annotations is a graph of nodes and edges. Some nodes are linked to regions of primary data. Some nodes are linked to other nodes by means of edges. An annotation may refer to a node or to an edge, but not both.

So, features target the primary data through annotations. Annotations can be labeled and they can be organized in annotation spaces.

Data¶

Although this tool is written to deal with LAF resources in general, it has been developed with a particular LAF resource in mind: the ETCBC4 Text database of the Hebrew Bible, now a dataset archived at DANS-EASY. Here is a quick link to the ETCBC4 features

The SHEBANQ project has converted this database from a special text database format into LAF (the conversion code is in the package emdros2laf, which is included in LAF-Fabric), and the resulting LAF resource is a file set of 1.64 GB, being predominantly linguistic annotations. It is this LAF resource that is the reference context for LAF-Fabric.

A compiled version of this LAF resource, suitable for working with LAF-Fabric, is included in the dataset. Also the original data has been included, so you can also run EMDROS tools on the data in conjunction with LAF-Fabric. LAF-Fabric even contains a notebook that integrates the use of EMDROS MQL with the proper LAF processing.

Existing tools for LAF/GrAF resources¶

There is an interesting Python module (POIO, Graf-python) that can read generic GrAF resources. It exposes an API to work with the graph and annotations of such resources. However, when feeding it a resource with 430 k words and 2 GB of annotation material, the performance is such that the graph does not fit into memory of a laptop. Clearly, the tool has been developed for bunches of smaller GrAF documents, and not for single documents with a half million words words and gigabytes of annotation material.

LAF-Fabric¶

This program seeks to remedy that situation. Its aim is to provide a framework on top of which you can write Python notebooks that perform analytic tasks on big GrAF resources. It achieves this goal by compiling xml into compact binary data, both on disk and in RAM and by selective loading of features. The binary data loads very fast. Only selected features will be loaded, and after loading they will be blown up into data structures that facilitate fast lookup of values.

With LAF-Fabric you can add an additional annotation package to the basic resource. You can also switch easily between additional packages without any need for recompiling the basic resource. The annotations in the extra package may define new annotation spaces, but they can also declare themselves in the spaces that exist in the basic source. Features in the extra annotation package that coincide with existent features, override the existing ones, in the sense that for targets where they define a different value, the one of the added annotation package is taken. Where the additional package does not provide values, the original values are used.

With this device it becomes possible for you to include a set of corrections to the original features. Or alternatively, you can include the results of your own work, whether manual or algorithmic or both, with the original data. You can then do what-if research on the combination.

The notebook annox_workflow demonstrates this workflow.

Interactive notebooks¶

LAF-Fabric is designed to work within iPython notebooks. That is a great environment to run tasks interactively, exploring the data as you go, and visualizing your intermediate results at the moment they become available. Last but not least, you can add documentation to notebooks and share them with your colleagues. As an example, look at the gender notebook notebook by which you can draw a graph of the percentage of masculine and feminine words in each chapter of the Hebrew Bible. More involved notebooks can be found at the laf-fabric-nbs repository and the study repo.

Rationale¶

The paradigms for biblical research are becoming data-driven. If you work in that field, you need increasingly sophisticated ways to get qualitative and quantitative data out of your texts. You, as a researcher, are in the best position to define what you need. You can even fulfill those needs if you or someone else in your group has basic programming experience.

LAF-Fabric is a stepping stone for teams in digital humanities to the wonderful world of computing. With it you extract data from your resources of interest and feed it into your other tools.

See for example the notebook cooccurrences, which codes in less than a page an extraction of data tables relevant to the study of linguistic variation in the Hebrew Bible. These tables are suitable for subsequent data analysis by means of the open source statistics toolkit R.

An other example is the notebook proper, which outputs a visualization of the text of the Hebrew Bible in which the syntactic structure of the text is visible plus the the genders of all the proper nouns. With this visualization it becomes possible to discern genealogies from other genres with the unaided eye, even without being able to read a letter of Hebrew.

Digging deeper into syntax, the notebook trees_etcbc4 produces syntax trees for all sentences in the Hebrew Bible.

The code of LAF-Fabric is on github, including example notebooks and extra annotation packages. You are invited to develop your own notebooks and share them, either through data archives or directly through github, or the notebook viewer. In doing so, you (together) will create a truly state-of-the-art research tool, adapted to your scholarly needs of analysis, review and publication.

Implementation highlights¶

There are several ideas involved in compiling a LAF resource into something that is compact, fast loadable, and amenable to efficient computing.

1. Replace nodes and edges and regions by integers.
2. Store relationships between integers in arrays, that is, Python arrays.
3. Store relationships between integers and sets of integers also in arrays.
4. Keep individual features separate.
5. Compress data when writing it to disk.

Use of integers In LAF the pieces of data are heavily connected, and the connections are expressed by means of XML identifiers. In the compiled version we get rid of all XML identifiers. Instead, we will represent everything that comes in great quantities by integers: regions, nodes, edges. But feature names and values, annotation labels and spaces will be kept as is.

Relationships between integers as Python arrays In Python, an array is a C-like structure of memory slots of fixed size. You do not have arrays of arrays, nor arrays with mixed types. This makes array handling very efficient, especially loading data from disk and saving it to disk. Moreover, the amount of space in memory needed is like in C, without the overhead a scripting language usually adds to its data types.

There is an other advantage: a mapping normally consists of two columns of numbers, and numbers in the left column map to numbers in the right column. In the case of arrays of integers, we can leave out the left column: it is the array index, and does not have to be stored.

Relationships between integers as Python arrays If we want to map numbers to sets of numbers, we need to be more tricky, because we cannot store sets of numbers directly in the slots of an array. What we do instead is: we build two arrays, the first array points to data records in the second array. A data record in the second array consists of a number giving the length of the record, followed by that number of integers. The function arrayify() in laf.lib takes a list of items and turns it in a double array.

Keep individual features separate A feature is a mapping from either nodes or edges to string values. Features are organized by the annotations they occur in, since these annotations have a label and occur in an annotation space. We let features inherit the label and the space of their annotations. Within space and label, features are distinguished by name. And the part of a feature that addresses edges is kept separate from the part that addresses nodes.

So an individual feature is identified by annotation space, annotation label, feature name, and kind (node or edge). For example, in the Hebrew Bible data, we have the feature:

etcbc4:ft.sp (node)


with annotation space etcbc4, annotation label ft, feature name sp (part of speech), and kind node. The data of this feature is a mapping that assigns a string value to each of the 426,555 word nodes. So this individual feature represents a significant chunk of data.

The individual features together take up the bulk of the compiled data. Here is a break down of the compiled data:

features                         150 MB
graph (nodes, edges, regions)     17 MB
LAF XML identifiers mappings      59 MB
precomputed data for node order    8 MB
extra annotation package           1 MB
--------------------------------+------
total                            269 MB


Most notebooks require only a limited set of individual features. So when we run tasks and switch between them, we swap feature data in and out. The design of LAF-fabric is such that feature data is neatly chunked per individual feature.

Note

Here is the reason that we do not have an overall table for feature values, identified by integers. We miss some compression here, but with a global feature value mapping, we would burden every task with a significant amount of memory. Moreover, the functionality of extra annotation packages is easier to implement when individual features are cleanly separable.

Note

Features coming from the source and features coming from the extra annotation package will be combined before the you can touch them in tasks. This merging occurs late in the process, even after the loading of features by LAF-fabric. Only at the point in time when a task declares the names of the API methods (see API() in laf.fabric) the feature data coming from main source and annox will be assembled into objects. Yet the underlying tables will not mixed, so that features do not have to be unloaded and reloaded when you change your annox. The price is a small overhead for each feature lookup: it will be looked up first in the annox data, and only if it is not found there, in the main data.

Author¶

This work has been undertaken first in November 2013 by Dirk Roorda, working for Data Archiving and Networked Services (DANS) and The Language Archive (TLA). The work has been triggered by the execution of the SHEBANQ project together with the researchers Wido van Peursen, Oliver Glanz and Janet Dyk at the Eep Talstra Centre for Bible and Computing (ETCBC), VU University.

Thanks to Martijn Naaijer and Gino Kalkman for first and on-going experiments with LAF-Fabric.

History¶

2014-07-31 Publication of the ETCBC4 dataset in DANS-EASY.

2014-02-16 A new github repository, study, has been created by our associate programmer Judith Gottschalk. This repository will host the actual notebooks written for and by the ETCBC people. The LAF-Fabric repository will only host example/tutorial notebooks.

2014-01-17 Joint presentation with Martijn Naaijer at CLIN (Computational Linguistics In the Netherlands).

2013-12-18 Demonstration on the StandOff Markup and GrAF workshop (CLARIN-D) in Köln.

2013-12-12 Demonstration for the ETCBC team Amsterdam. Updated the slides.

2013-12-09 Abstract sent to CLIN (Computational Linguistics In the Netherlands) accepted. To be delivered 2014-01-17.

2013-11-26 Vitamin Talk to the TLA team Nijmegen. Here are the slides.