GitHub - clips/MBSP: Memory-based shallow parser for Python

MBSP is a text analysis system based on the TiMBL and MBT memory based learning applications developed at CLiPS and ILK. It provides tools for Tokenization and Sentence Splitting, Part of Speech Tagging, Chunking, Lemmatization, Relation Finding and Prepositional Phrase Attachment. The general English version of MBSP has been trained on data from the Wall Street Journal corpus.

Download

MBSP for Python (1.4) | download (.zip, 24MB)

Requires: Python 2.5+ on Unix | Mac | Cygwin.
Licensed under GPL
Releases: 1.4 | 1.3 | 1.2 | 1.1
Authors:
Vincent Van Asch (vincent.vanasch at uantwerpen.be),
Tom De Smedt (tom at organisms.be)

Reference: Daelemans, W., & Van den Bosch, A. (2005).
Memory-based language processing. Cambridge University Press, Cambridge, UK.
ISBN-13: 9780521808903 | ISBN-10: 0521808901

SHA256 checksum of the .zip:
62be10ece640404058b607d9f15493a2a98d55b7e3a3d9becc6ed5854fa800bc

Introduction

Quick overview

MBSP parses a string of characters into words and sentences, and determines the grammatical structure of the sentence. It is a Python module, so you'll need Python to run it (already installed on Mac OS X).

The module uses a client-server architecture for performance. It includes binaries (TiMBL, MBT and MBLEM) precompiled for Mac OS X, so on Mac it works out-of-the-box. Otherwise, if you're on a Unix system, the module has a setup.py file that should compile everything for you. Go to the terminal and type:

cd MBSP
python setup.py

If that doesn't work you'll need to follow the steps in the installation instructions.

Put the MBSP folder in the same folder as your Python script and import the module. By default, the servers are configured to start automatically. Once they are up and running you can use the parse() command to analyze texts:

import MBSP
print MBSP.parse('cats with hats')
>>> cats/NNS/I-NP/O/O/A1/cat with/IN/I-PP/B-PNP/O/P1/with hats/NNS/I-NP/I-PNP/O/P1/hat

Each word has been tagged with grammatical information. For example, MBSP determined that cats is a plural noun (NNS). It has a prepositional noun phrase (PNP) attached to it (A1 is the anchor of P1), so the hats go with the cats. For a human this might seem pretty straightforward, but consider that without any analysis, for a machine the sentence is just a sequence of characters with no meaning.

The tag codes may seem cryptic at first, but consider that it is more concise to say NNS than PLURAL NOUN over and over. The tag codes are common in natural language processing, it's a good idea to get acquainted with them.

Something went wrong? Probably the servers didn't have enough time to start:

MBSP.start(timeout=120)
print(MBSP.parse('cats with hats'))

The output of the parse() command is a tagged string that can be manipulated in many ways.
With the split() command it can be transformed into a tree of linked Python objects:

s = MBSP.parse('black cats with striped hats')
s = MBSP.split(s)
for sentence in s:
    for chunk in sentence.chunks:
        print([word.lemma for word in chunk.words], chunk.attachments)
>>> [u'black', u'cat'] [Chunk('with striped hats/PNP')]
>>> [u'with'] []
>>> [u'striped', u'hat'] []

With the xml() command it can be transformed into an XML string for processing outside of Python:

s = parse('black cats with striped hats')
print xml(s)

Purpose

MBSP stands for "Memory-Based Shallow Parser". Shallow parsing (i.e. automatic discovery of a sentence constituents) is an important component of many text analysis systems, in applications such as information extraction and summary generation. The Memory-Based Learning (MBL) approach has the advantage of avoiding the need for manual definition of patterns (for example, using regular expression syntax) and of being reusable across different corpora and sublanguages.

MBSP is a so-called lazy learner: it keeps all the initial training data available (including exceptions which may sometimes be productive). This technique has been shown to achieve higher accuracy than eager (or greedy) methods for many language processing tasks. For the Wall Street Journal corpus (WSJ), accuracy (Fβ=1) is 96.4% for part-of-speech tagging, 93.8% for NP chunking, 94.7% for VP chunking, 77.1% for SBJ detection, 79.0% for OBJ detection, and 82.7% for PP-attachment. MBSP is based on the IB1-IG and IGTREE algorithms bundled in our MBL software package, called TiMBL.

Reference: Daelemans, W., Buchholz, S., & Veenstra, J. (1999).
Memory-Based Shallow Parsing. In: Proceedings of CoNLL, Bergen, Norway.

The parser provides functionality for tokenization and sentence splitting, part-of-speech tagging, chunking, relation finding, prepositional phrase attachment and lemmatization.

Tokenization: splits sentence periods and punctuation marks from words.
Tagging: assigns part-of-speech tags to words (e.g. cat → noun → NN, eat → verb → VB).
Chunking: assigns chunk tags to groups of words (e.g. the black cat → noun phrase → NP).
Relation finder: finds relations between chunks, sentence subject, object and predicates.
PNP finder: finds prepositional noun phrases (e.g. under the table).
PP-attachment: finds prepositional noun phrase anchors (e.g. eat pizza → with fork).
Lemmatization: finds word lemmata (e.g. was → be).

Grammar basics

Sentences are made up of words. Words have a syntactic role (noun, verb, adjective, ...) depending on their location in the sentence. For example, can can be a verb or a noun, depending on the context (the can, I can).

Sentence: the basic unit of writing, expected to have a subject and a predicate.
Word: a string of characters that expresses a meaningful concept.
Token: a specific word with grammatical tags: the can/NN, I can/VB.
Chunk: a group of words (phrase) that contains a single thought (e.g. a sumptuous banquet).
Head: the word that determines the syntactic type of the chunk: the black cat → NP.
Subject: the person/thing doing or being, usually a noun phrase (NP): the cat is black.
Predicate: the remainder of the sentence tells us what the subject does: the cat sits on the mat.
Clause: subject + predicate.
Argument: a chunk that is related to a verb in a clause, i.e. subject and object.
Object: the person/thing affected by the action: the cat eats fish. Poor fish.
Preposition: temporal, spatial or logical relationship: the cat sits on the mat.
Copula: a word used to link subject and predicate, typically the verb to be.
Lemma: canonical form of a word: run, runs, running are part of a lexeme, run is the lemma.
POS: part-of-speech, the syntactic role that a word or phrase plays in a sentence, e.g. adjective = JJ.

Acknowledgements

This version of MBSP has been developed by the computational linguistics group of CLiPS (Computational Linguistics & Psycholinguistics, department of Linguistics, University of Antwerp, Belgium) on the basis of earlier versions developed at the University of Antwerp and Tilburg University.

Contributing authors: Walter Daelemans, Jakub Zavrel, Sabine Buchholz, Jorn Veenstra, Antal van den Bosch, Ko van der Sloot, Bertjan Busser, Erik F. Tjong Kim Sang, Jo Meyhi, Vincent Van Asch, Tom De Smedt.

For reference you can use:
De Smedt T., Van Asch V. & Daelemans, W. (2010). Memory-based Shallow Parser for Python.
CLiPS Technical Report Series (CTRS), vol. 2. ISSN 2033-3544. [PDF]

Installation

MBSP is a Python module. On Mac OS X, the Python programming language is already installed. On other systems you need to download and install it yourself, if necessary. MBSP works with Python 2.5, but support for processes is better in version 2.6. It should also work with version 2.4.

MBSP is bundled with three required dependencies written in C/C++ (TiMBL 6.1.5, MBT 3.1.3 and MBLEM). Binaries have been precompiled for Mac OS X 10.5, but these may not work on your machine. In that case you need to compile binaries manually from the source code.

Compiling with setup.py

The module comes with a setup.py script that compiles the C/C++ binaries automatically. If this works for you, you're in luck – no manual compilation is necessary. Also, if you run setup.py with the install argument, it will first compile the binaries and then install a copy of MBSP in Python's /site-packages folder so that the module is available in any Python script.

> cd MBSP
> python setup.py install

Compiling from source

You'll need a gcc compiler. On Windows you'll need cygwin.
In the cygwin installer (setup.exe), be sure to select the "devel" packages for installation.

Building MBLEM

Go to the MBSP/mblem folder.
Delete all files with a ".o" extension + the current executable binary mblem_english_bmt.
From the command line, do make in the MBSP/mblem folder:

> cd MBSP/mblem
> make

Building TiMBL

Go to the MBSP/timbl folder.
Uncompress the source code from the timbl-6.1.5.tar archive.
From the command line, do configure and make in the MBSP/timbl/timbl-6.1.5 folder:

> cd MBSP/timbl/timbl-6.1.5
> ./configure --enable-shared=no --enable-static=no --prefix=[FOLDER]
> make install

[FOLDER] is an absolute path to the folder where Timbl will be built.
The Timbl executable will be in [FOLDER]/bin → copy it to MBSP/timbl.
Now build MBT in the same [FOLDER] location:

Building MBT

Go to the MBSP/mbt folder.
Uncompress the source code from the mbt-3.1.3.tar archive.
From the command line, do configure and make in the MBSP/mbt/mbt-3.1.3 folder:

> cd MBSP/mbt/mbt-3.1.3
> ./configure --enable-shared=no --enable-static=no --prefix=[FOLDER]
> make install

The Mbt executable will be in [FOLDER] → copy it to MBSP/mbt.
Delete the build [FOLDER], it is no longer needed.

Module folder location

To be able to import MBSP in your scripts, Python needs to know where the module is located.
There are three basic ways to accomplish this:

Put the MBSP folder in the same folder as your script.
Put the MBSP folder in the standard location for modules so it is available to all scripts.
The standard location depends on your operating system, for example:
/Library/Python/2.5/site-packages/ on Mac,
/usr/lib/python2.5/site-packages/ on Unix,
c:\python25\Lib\site-packages\ on Windows.
Add the location of MBSP to the sys.path list in your script, before importing it:

>>> MODULE = '/users/tom/desktop/MBSP'
>>> import sys; if MODULE not in sys.path: sys.path.append(MODULE)
>>> import MBSP

Memory usage

MBSP starts four data servers that require quite a bit of memory (CHUNK: 80MB, LEMMA: 10MB, RELATION: 160MB, PREPOSITION: 210MB). Only the CHUNK server (which gives you the part-of-speech tags) is mandatory. The optional servers can be disabled in config.py to reduce the memory usage, for example:

servers = ['chunk', 'lemma']

Multithreading

MBSP can be configured to work with multithreading, which can increase performance by 25% - 200%. MBSP.config.threading needs to be set to True. You also need to build the newer TiMBL 6.3+, MBT 3.2+ and TimblServer 2+ from source. The installation instructions are mostly the same:

TimblServer can be compiled in the same way as MBT.
Put the TimblServer executable in MBSP/timbl instead of the Timbl executable.

Older systems may complain that pkg-config is outdated. In this case, before building Timbl, compile pkg-config 0.25+ (http://pkgconfig.freedesktop.org) from source with: sudo ./configure; sudo make; sudo make install

We have precompiled versions of TimblServer which may also work on your system (in that case you don't need to install from source): download for Mac OS X 10.5 | Ubuntu 10.04 (64-bit).

Parser

MBSP uses a client-server architecture. This way, the corpus data is loaded only once (during server startup) and stays available while the servers sleep in the background. Before tagging jobs can be sent to the parser, the servers have to be started. By default, this will happen automatically when you import MBSP in your script. Otherwise, the start() command starts the four servers (named CHUNK, LEMMA, RELATION and PREPOSITION). The started() command yields True if a given server has been started. The stop() command will stop the servers.

MBSP.start(timeout=60)

MBSP.started(name=ALL) # CHUNK | LEMMA | RELATION | PREPOSITION

MBSP.stop()

The parse() command takes a string of sentences and returns a tagged Unicode string.
Sentences in the output are separated by newline characters.

MBSP.parse(string,
     tokenize = True,
         tags = True,
       chunks = True,
    relations = True,
      anchors = True,
      lemmata = True,
     encoding = 'utf-8')

For example:

print(MBSP.parse('I ate pizza with a fork.'))

>>> I/PRP/I-NP/O/NP-SBJ-1/O/i
    ate/VBD/I-VP/O/VP-1/A1/eat
    pizza/NN/I-NP/O/NP-OBJ-1/O/pizza
    with/IN/I-PP/B-PNP/O/P1/with
    a/DT/I-NP/I-PNP/O/P1/a
    fork/NN/I-NP/I-PNP/O/P1/fork ././O/O/O/O/.

Each token (i.e. tagged word) in a sentence has a number of annotations: tags</span><span class="inline_code">=True includes the word part-of-speech tag, chunks the chunk tag + PNP tag (prepositional noun phrase), relations the chunk relation tag, anchors the PNP anchor tag. With tokenize set to False, no tokenization is carried out (so the input string is expected to be tokenized). The encoding parameter defines the character encoding of the input string, "utf-8" is fine in most cases.

Parser tags

Let's examine the word ate and the tags assigned by the parser in the example above:


word	part-of-speech	chunk	pnp	relation	anchor	lemma
ate	VBD	I-VP	O	VP-1	A1	eat

The word's part-of-speech tag is VBD, which means that it is a verb in the past tense. The word occurs in a VP chunk, a verb phrase. It is not part of a prepositional noun phrase. It's relation tag is VP-1, which means it is linked to the words tagged as NP-SBJ-1 (I, the sentence subject) and NP-OBJ-1 (pizza, the sentence object). Its anchor tag is A1, meaning it is the anchor of the prepositional noun phrase P1, with a fork. How did I eat pizza? → with a fork. The base form or lemma of ate is eat.

Common part-of-speech tags include NN (noun), JJ (adjective) and VB (verb).
Common chunk tags include NP (noun phrase) and VP (verb phrase).
Common relations include SBJ (subject) and OBJ (object).

The MBSP tags page gives an overview of all the possible tags generated by the parser.

A description and an example can also be acquired with the taginfo() command:

>>> description, example = MBSP.taginfo('NN')
>>> print(description, example)

('noun, singular or mass', 'tiger, chair, laughter')

Parser shortcuts

Below is a set of concise commands that internally call parse() with the required parameters.

The tag() command returns a string annotated with part-of-speech tags.
The chunk() command returns a string annotated with part-of-speech, chunk and PNP tags.
The lemma() command takes a single word and returns its lemma.
The nouns(), verbs() or adjectives() command returns a list of nouns, verbs or adjectives retrieved from the given string.

MBSP.tokenize(string)

MBSP.tag(string, tokenize=True, lemmata=False)

MBSP.chunk(string, tokenize=True, lemmata=False)

MBSP.lemma(word)

MBSP.nouns(string, lemmatize=False)
MBSP.verbs(string, lemmatize=False)
MBSP.adjectives(string, lemmatize=False)

Like parse(), all of these commands have an optional encoding parameter that is "utf-8" by default.

Parser output

The output of the parse() command is a string of sentences in which each token has been annotated with the requested tags. The pprint() command (extra p is for pretty) gives a good overview of the tags:

s = MBSP.parse('I eat pizza.')
MBSP.pprint(s)

>>>    WORD   TAG    CHUNK   ROLE   ID     PNP    ANCHOR   LEMMA
          I   PRP    NP      SBJ    1      -      -        i
        eat   VBP    VP      -      1      -      -        eat
      pizza   NN     NP      OBJ    1      -      -        pizza
          .   .      -       -      -      -      -        .

The output string is in fact a TokenString object that behaves as a Python string, but with extra functionality. Most notably it has a TokenString.split() method that yields a TokenList object: a list of sentences, where each sentence is a list of tokens, in which each token is a list of tags. This is useful when you want to extend the parser and need to make some modifications to the output.

If you want to analyze the output (i.e. examine the relations between words and groups of words), it is more convenient to construct a parse tree from the output.

Tokenizer

MBSP includes a regular expressions-based tokenizer that divides sequences of characters into words and sentences. Special care is given to punctuation marks. We need to guess which punctuation marks are part of a word (e.g. periods in abbreviations) and which mark word and sentence breaks. Once tokenized, the parser can then determine categories for words (tokens) in the string.

MBSP.tokenizer.split(string, tags=False, citations=False, replace={}, ignore=[])

The split() command returns a list of Unicode strings where punctuation marks have been split from words as individual tokens. Each string in the list is a sentence. By default, all SGML-tags (i.e. anything wrapped in <...>) are stripped from the input string. With citations=True, sentences in quoted citations are kept together. The replace dictionary is used to map unicode quotes and ellipsis to standard quotes and periods. The ignore list defines ranges of words that require special attention (for example, abbreviations and URL's – see below).

For example:

MBSP.tokenizer.split('The U.N. is considering banning "defamation of religion." The U.N. president said such a move would not limit free speech.')
[u'The U.N. is considering banning " defamation of religion . "',
 u'The U.N. president said such a move would not limit free speech .']

Tokenization process

In the simplest case, words are marked by spaces. A number of exceptions are then handled:

Handle missing space: punctuation inside a word can indicate a missing space.
Handle punctuation: punctuation marks at the head or tail of a word can indicate a sentence break, the start of a citation, the start of an explanation in parenthesis. In this case the punctuation is split from the word. Punctuation that is part of the word (e.g. 5p.m.) needs to be kept intact.
Handle contractions: apostrophes in contractions (he's) and possessives (father's) mark word boundaries. The suffix is split from the word.
Handle lists: list item markers such as 1. 1) * - a. a) at the start of a new line indicate the start of a new sentence, even if the previous sentence did not end with a period.
Handle hyphenation: hyphens at the end of a line mark words that have been split across lines: mar- + ket becomes market, Great- + Britain becomes Great-Britain.
Handle sentence breaks: periods, exclamation marks, question marks and ellipsis end a sentence if they are followed by a capitalized letter. Parenthesis and quotes can be part of the sentence even if the period precedes it.

Tokenizer word ranges

The tokenizer defines a Range class for matching sets of words: all abbreviations, all numeric strings, all hyperlinks, etc. The Range class is a list of known words enriched with regular expression patterns. In the example below, an abbreviation range is created that matches U.K., U.N. and any single letter abbreviation (as in T. De Smedt).

abbreviations = MBSP.tokenizer.Range(['U.K.', 'U.N.'])
abbreviations.patterns.append(re.compile('^[A-Za-z]\.$'))
print 'U.K.' in abbreviations, 'T.' in abbreviations
>>> True True

Custom ranges can be passed to the ignore parameter of the split() command.
By default, split() will use a list of predefined ranges:

MBSP.tokenizer.ignore = [abbreviations, numeric, URI, entities, biomedical]

Predefined ranges:

Abbreviations: the simple rule is that every point is a sentence break. This is 93.2% correct for Brown corpus [1]. Fixing decimal points, single letter abbreviations, alternating letters and capital letter followed by consonants (Dept.) improves sentence break correctness to 97.7%. Additionally, the abbreviations range defines a list of other well-known abbreviations.
Numeric: matches anything starting with a digit followed by a chain of digits and .,:/ separators. The range will also recognize units of measurement (length, mass, volume, time, epoch, temperature, storage capacity, data transfer rate, percentage): US$100, 1.2MB, 31/12/2010, ...
URI: matches URL's, links and e-mail addresses.
Entities: matches HTML and Unicode entities.
Biomedical: guesses biomedical-specific words, such as 1',2'-trifenol.

Tokenizer modes

The tokenizer can be configured in different modes. By default it uses Penn Treebank specifications for tokenization and uses special corrections for biomedical use.

MBSP.tokenizer.PENN_TREEBANK = True
MBSP.tokenizer.BIOMEDICAL = True

In Penn Treebank mode, only % is split from numbers and contractions are not substituted: won't becomes wo n't instead of will not. In biomedical mode, less magic is used when finding missing spaces so that 3(R),3a(S),6a(R)-bis-tetrahydrofuranylurethane is not split at the comma or the parenthesis.

Lemmatizer

MBSP uses the MBLEM C module for word lemmatization. MBLEM (Memory-Based Lematization) transforms a word form into a canonical lexical form: was → be, booking → book.

>>> print MBSP.lemmatize("The cats were sleeping.", tokenize=True)

the cat be sleep .

The goal of lemmatization is to provide better (generalizable) lexical information that can be used by other components in the pipeline, and (possibly) also for indexing the processed text in a search engine. Lemmatization is not to be confused with stemming, in which frequent suffixes such as -ing and -ed are simply removed: having is stemmed to hav, while it is lemmatized to have.

Lemmatization process

Words can have more than one lemma. The lemmatizer's task is to find the most suitable:

Find lemmata: determines for each word in a sentence which lemmata it could be mapped to. The word saw is lemmatized to the noun lemma saw and the verb lemma see. In case of producing more than one lemma, the lemmatizer is unable to determine which lemma is appropriate in the current sentence, as it does not use context.
Disambiguate: consults the output of the part-of-speech tagger. If the tagger has identified saw as a past-tense verb form (VBD), MBLEM concludes that the appropriate lemma is see, and selects this one as the correct output. MBLEM therefore always generates a single lemma per word.

MBLEM is trained on the CELEX English lexical database, and will simply retrieve the lemmatizations of words that occur in the database. Words in the text that are not in CELEX (so-called "unknown" words, typically constituting 5% of the words in a text) are lemmatized by analogy to stored word lemmatizations.

Reference: Van den Bosch, A., & Daelemans, W. (1999).
Memory-based morphological analysis, In: Proceedings of the 37th annual meeting of the Association for Computational Linguistics on Computational Linguistics, pp. 285-292.

PP-attacher

A shallow parsing approach sometimes has its shortcomings, an important one being that prepositional phrases, which contain important semantic information for interpreting events (e.g. I sleep vs. I sleep under a bridge), are left unattached. MBSP comes with a memory-based PP-attacher (MBPA) trained on sections 2 through 21 of the Penn Treebank II Wall Street Journal corpus (WSJ). It will link PNP chunks to other “anchor” chunks.

With the PP-attacher enabled, performance is slower but you gain a lot of useful information.

s = MBSP.parse('I sleep under a bridge', anchors=True)
s = MBSP.split(s)
print(s[0].pnp)
print(s[0].pnp[0].anchor)

>>> [Chunk('under a bridge/PNP')]
>>> sleep

PP-attachment process

A PNP-chunk can be attached to different candidate chunks. However, there is a semantic difference between I eat pizza with olives and I eat pizza with olives. Which one is correct? And which one is correct here: I eat pizza with a fork or I eat pizza with a fork?

Find prepositional noun phrases: these are retrieved by a regular expression-like algorithm. All PP + NP sequences are considered to be PNP’s. Two exceptions: PP + “ + NP (e.g. in “modest amounts”) and PP + VBG + NP (in making paper) are also considered PNP’s.
Classify: the core of the PP-attacher is a memory-based classifier. Candidate anchors are the NP’s and VP’s of the sentence that are not part of the PNP itself. For example, I eat a pizza with olives induces three classification tasks (I-with, eat-with, pizza-with) in which the machine learner will have to decide if the pair suggests a true anchor or not – taking into account the distance to the candidate anchor and intermediary punctuation, the number of intermediary NP’s, and so on.
Heuristic decision making: when the classifier identifies multiple anchor candidates, an extra step is taken to pick one unique anchor, using a baseline and entropy algorithm (details are summarized in the reference paper).

In 50% of the cases a noun phrase (NP) is chosen as anchor, in about 45% a verb phrase (VP).

Reference: Van Asch, V., & Daelemans, W. (2009).
Prepositional Phrase Attachment in Shallow Parsing. In: Proceedings of the 7th International Conference on Recent Advances in Natural Language Processing (RANLP), pp. 12-17.

Parse trees

A parse tree stores a parsed string as a network of linked Python objects that can be traversed to analyze the sentences in the string. The output of the parser can be passed to the split() command, which produces a Text object. Essentially, a Text is a list of Sentence objects. Each Sentence consists of Word objects. Word objects are also grouped in Chunk objects, which are related to other Chunk objects in various ways.

MBSP.split(parsed_string, token=[WORD, POS, CHUNK, PNP, RELATION, ANCHOR, LEMMA])

We'll run the sentence "The cat sat on the mat." through the parse tree:

s = MBSP.parse('The cat sat on the mat.')
s = MBSP.split(s)
print(repr(s))

[Sentence(
 """The/DT/B-NP/O/NP-SBJ-1/O/the
  cat/NN/I-NP/O/NP-SBJ-1/O/cat
  sat/VBD/B-VP/O/VP-1/A1/sit
  on/IN/B-PP/B-PNP/PP-CLR/P1/on
  the/DT/B-NP/I-PNP/NP-CLR/P1/the
  mat/NN/I-NP/I-PNP/NP-CLR/P1/mat
  ././O/O/O/O/.""")]

print(s[0].chunks)

>>> [Chunk('The cat/NP-SBJ-1'),
     Chunk('sat/VP-1'),
     Chunk('on/PP-CLR'),
     Chunk('the mat/NP-CLR')]

Text

A Text is a list of Sentence objects.

text = MBSP.Text(parsed_string, token=[WORD, POS, CHUNK, PNP, REL, ANCHOR, LEMMA])

text = MBSP.Text.from_xml(xml)

text.string                # 'The cat sat on the mat .'
text.sentences             # [Sentence('The cat sat on the mat .')]
text.append(sentence)
text.copy()

text.xml

Since Text behaves as a Python list it is easy to traverse all the contained sentences:

for sentence in text:
    print(sentence)

Sentence

A Sentence is a list of Word objects, with attributes and methods that organize words in Chunk objects.

sentence = MBSP.Sentence(string="", token=[WORD,POS,CHUNK,PNP,REL,ANCHOR,LEMMA])

sentence = MBSP.Sentence.from_xml(xml)

sentence.parent            # Slices refer to the sentence they are part of.
sentence.id                # Unique for each sentence.
sentence.start             # 0
sentence.stop              # 6
sentence.token             # [WORD, POS, CHUNK, PNP, REL, ANCHOR, LEMMA]

sentence.string            # 'The cat sat on the mat .'
sentence.words             # [Word('The/DT'), Word('cat/NN'), ... ]
sentence.lemmata           # [u'the', u'cat', u'sit', u'on', u'the', u'mat', u'.']
sentence.tagged            # [(u'The', u'DT'), (u'cat', u'NN'), ... ]
sentence.parts_of_speech   # [u'DT', u'NN', u'VBD', u'IN', u'DT', u'NN', u'.']

sentence.chunks            # [Chunk('The cat/NP-SBJ-1'), Chunk('sat/VP-1'), ... ]
sentence.subjects          # [Chunk('The cat/NP-SBJ-1')]
sentence.objects           # []
sentence.verbs             # [Chunk('sat/VP-1')]
sentence.relations         # {'SBJ': {1: Chunk('the cat/NP-SBJ-1')},
                           #   'VP': {1: Chunk('sat/VP-1')},
                           #  'OBJ': {}}

sentence.pnp               # [Chunk('on the mat/PNP')]
sentence.anchors           # [Chunk('sat/VP-1')]

sentence.constituents(pnp=False)

sentence.get(index, tag=LEMMA)
sentence.loop(tag1, tag2, ...)
sentence.indexof(value, tag=WORD)

sentence.slice(start, stop)
sentence.copy()

sentence.xml
sentence.nltk_tree()

Sentence.constituents() returns an in-order list of Word and Chunk objects.
With pnp=True, also groups into PNPChunk objects whenever possible.
Sentence.get() returns the requested tag of the word at the given index.
The tag can be WORD, LEMMA, POS, CHUNK, PNP, RELATION, ROLE, ANCHOR or a custom word tag.
Sentence.loop() is an iterator over a list of tuples containing the requested tags for each word.
Sentence.indexof() returns the indices of words for which the given tag equals the given value.
For example, Sentence.indexof("NN*", tag=POS) returns a list of indices of the words whose part-of-speech is NN, NNS, NNP or NNPS.
Sentence.slice() returns a new, partial sentence starting with the word at index start and containing all the words up to (before) index stop.

Creating a sentence

Normally, a sentence is constructed from the output of the parse() command. Since this output is a TokenString which stores the order in which tags appear in a token, Sentence can figure out how to construct a parse tree by itself. If you want to construct sentences from a different source, you need to specify the token parameter in the constructor, or use Sentence.append() to add words manually. If you have tokens in a slash-formatted string like MBSP (e.g. "cats/NNS/I-NP/O/O/O/cat") you can use Sentence.parse_token(), which returns the arguments for Sentence.append().

sentence.append(word,
       lemma = None,
        type = None,
       chunk = None,
        role = None,
    relation = None,
         pnp = None,
      anchor = None,
         iob = None,
      custom = {})

sentence.parse_token(token, tags=[WORD, POS, CHUNK, PNP, REL, ANCHOR, LEMMA])

For example:

s = MBSP.Sentence('cats/NNS', token=[MBSP.WORD, MBSP.POS])
print(s.words)

>>> [Word('cats/NNS')]

s = MBSP.Sentence()
s.append(word='cats', lemma='cat', type='NNS', chunk='NP')
print(s.words)

>>> [Word('cats/NNS')]

s = MBSP.Sentence()
s.append(*s.parse_token('cats/NNS/I-NP/O/O/O/cat'))
print(s.words)

>>> [Word('cats/NNS')]

Sentence words

A Sentence is made up of Word objects, which are also grouped in Chunk objects:

word = MBSP.Word(sentence, string, lemma=None, type=None, index=0)

word.sentence              # Sentence object (e.g. 'The cat sat on the mat .')
word.index                 # 2
word.string                # 'sat'
word.lemma                 # 'sit'
word.type                  # 'VBD'
word.chunk                 # Chunk('sat/VP-1').
word.pnp                   # None

word.custom_tags           # User-defined tags, e.g. {SENTIMENT: 'lazy'}

word.tags()                # ['sat', 'VBD', 'B-VP', 'O', 'VP-1', 'O', 'sit']

Word.type is an alias for Word.part_of_speech.
Word.pnp is an alias for Word.prepositional_noun_phrase.
The word.custom_tags is a dictionary of additional, user-defined tags that can occur when the parser has been extended. If the word has (for example) an additional sentiment tag, it is also available as Word.sentiment.
The Word.tags() method returns a list of token tags as they appear in the output of the parser.
The order of tags is determined by the Sentence.token attribute.

Sentence chunks

A Chunk is a list of Word objects that belong together.
Chunks can be part of a PNPChunk, which starts with a PP chunk followed by NP chunks.

chunk = MBSP.Chunk(sentence, words=[], type=None, role=None, relation=None)

chunk.sentence             # Sentence object (e.g. 'The cat sat on the mat .')
chunk.start                # 0
chunk.stop                 # 2

chunk.string               # 'The cat'
chunk.words                # [Word('The/DT'), Word('cat/NN')]
chunk.lemmata              # ['the', 'cat']
chunk.tagged               # [(u'The', u'DT'), (u'cat', u'NN')]
chunk.head                 # Word('cat/NN')

chunk.type                 # 'NP'
chunk.role                 # 'SBJ'
chunk.relation             # 1
chunk.relations            # [(1, u'SBJ')]
chunk.related              # [Chunk('sat/VP-1')]
chunk.subject              # None
chunk.object               # None
chunk.verb                 # Chunk('sat/VP-1')
chunk.modifiers            # []
chunk.conjunctions         # []

chunk.pnp                  # None
chunk.anchor               # None
chunk.attachments          # [Chunk('on the mat/PNP')]

chunk.append(word)

chunk.previous(type=None)  # None
chunk.next(type=None)      # Chunk('sat/VP-1')
chunk.nearest(type="VP")   # Chunk('sat/VP-1')

Chunk.head yields the last (i.e. principal) Word in the chunk.
Chunk.relations contains all relations the chunk is involved in.
Some chunks (about 15%) have multiple relations, for example functioning as both SBJ and OBJ, or being the OBJ of multiple VP chunks.
For VP chunks, `Chunk.modifiers is a list of nearby adjectives and adverbs with no relations.
For example: in 'the cat really wants out', really and out are ADVP with no relations.
The parse tree will assume that they have something to do with the VP wants.
What does the cat want? → out.
How badly does the cat want out? → really.
`Chunk.conjunctions is a list of chunks linked by "and" or "or" to this chunk.
For example: in 'going up and down', the up chunk has conjunctions: [(Chunk('down'), AND)].
Chunk.pnp is an alias for the parent Chunk.prepositional_noun_phrase`.
`Chunk.attachments contains related prepositional noun phrases
`Chunk.anchor references the chunk that is the anchor of this PNP.

Prepositional noun phrases

PNPChunk is a subclass of Chunk, it has the same attributes and methods.
It groups multiple chunks in a prepositional noun phrase (PNP).

pnp = MBSP.PNPChunk(sentence, words=[], type=None, role=None, relation=None)

pnp.string                 # 'on the mat'
pnp.chunks                 # [Chunk('on/PP-CLR'), Chunk('the mat/NP-CLR')]
pnp.preposition            # Chunk('on/PP-CLR')
pnp.anchor                 # Chunk('sat/VP-1')

pnp.guess_anchor()         # Returns the nearest VP chunk.

Words and chunks that are part of a PNP will have their Word.pnp and Chunk.pnp attribute set.
All the prepositional noun phrases in a sentence can be retrieved with `Sentence.pnp.

Clients and servers

MBSP uses a client-server architecture so that the data only has to be loaded once. From then on it is available as a server that can be contacted with the TCP protocol. MBSP has a Client and a Server class that communicate using the Python socket module. Server is a wrapper around `subprocess.Popen and starts TiMBL or MBT as a background process.

MBSP starts four servers:


Name	Address	Process	Description
`MBSP.CHUNK	localhost:6061	MBT	Server for finding part-of-speech and chunk tags.
`MBSP.LEMMA	localhost:6062	TiMBL	Server used by MBLEM to find word lemmata.
`MBSP.RELATION	localhost:6063	TiMBL	Server for finding verb-argument chunk relations.
`MBSP.PREPOSITION	localhost:6064	TiMBL	Server for finding PNP anchors.

TiMBL: memory-based learning is an elegantly simple and robust machine-learning method applicable to a wide range of tasks in Natural Language Processing.

http://ilk.uvt.nl/timbl/

MBT: a memory-based tagger-generator and tagger in one. MBT can, for instance, be used to generate part-of-speech taggers or chunkers for natural language processing. http://ilk.uvt.nl/mbt/

Client

The Client base class can be used to contact a TiMBL or MBT server running at a given host address, at a given TCP communication port. Client is then subclassed with `Timbl and Mbt classes.

client = MBSP.Client(
        host = LOCALHOST,
        port = 6060,
        name = None,
         log = False,
     request = lambda v:v.strip()+'\n',
    response = lambda v:v)

client.name
client.host
client.port
client.connected # True after Client.connect() is called.

client.connect()
client.send(request, timeout=None)
client.disconnect()

Client.connect() raises a ServerConnectionError if the server can't be contacted.
ServerConnectionError.code can contain additional information, such as CONNECTION_RESET_BY_PEER, CONNECTION_REFUSED or BROKEN_PIPE.
Client.send() prepares the request, sends it to the server and returns the response. Client.send() raises a ClientDisconnectedError if Client.connect() is not called first.
If timeout is given and no response is returned in the given time, a ClientTimeoutError is raised.
Make sure to clean up with `Client.disconnect() when the client is no longer needed.

Request and response formatters

Note the request and response parameters in the Client constructor. These are formatter functions that will be called by Client.send() to 1) prepare the data before sending it to the server and 2) to clean up the server response before returning it.

For example, if we send a raw request to the chunk server:

>>> chunker = MBSP.Client(port=6061)
>>> print chunker.send('cat')

cat/NN/I-NP -utt-

The MBT server's response ends with a delimiter which we may want to clean from the output.
This can be achieved by using a response formatter:

>>> chunker = MBSP.Client(port=6061, response=lambda v: v.rstrip(' -utt-\n'))
>>> print chunker.send('cat')

cat/NN/I-NP

Note: in reality, MBT's delimiter is a utt tag (so utt enclosed in < and >) but in this example we use -utt- instead to avoid the browser thinking it's a HTML-tag.

TiMBL and MBT client

MBSP has a Timbl and a Mbt class: subclasses of Client, with the right request and response formatters.

timbl = MBSP.Timbl(host=LOCALHOST, port=6060, name=None, log=False, verbosity=[])

mbt = MBSP.Mbt(host=LOCALHOST, port=6060, name=None, log=False)

TiMBL's output depends on the way the server verbosity (+v) is configured. In MBSP it typically it yields a category string: "CATEGORY {NP-SBJ} ". Depending on the verbosity it can also yield different output. For example, verbosity option +v di+db yields a ** category-distance-distribution string:
"CATEGORY {VP} DISTRIBUTION { VP 3.11506, n-VP 2.58232 } DISTANCE {2.02066} ".

The TiMBL client has an additional verbosity parameter which can be used to format the response:

>>> timbl = MBSP.Timbl(port=6064, verbosity=['di','db'])
>>> print timbl.send('0 0 2 - eat VBP pizza NN with fork NN 1 0')

['VP', 2.0206599999999999, {'VP': 3.1150600000000002, 'n-VP': 2.5823200000000002}]

The server at port 6064 is the preposition server, which loads with option +v di+db, so responses include distance and distribution metrics. The TiMBL client in this example sets the right verbosity options so that distance is correctly parsed as a float, and distribution as a dictionary.

See the TiMBL manual for all verbosity options.

Client batch requests

Since the servers are multithreaded, multiple request can be sent at the same time to speed up the lookup process. MBSP's client module has a client.batch() command to achieve this. It takes a list of requests (i.e. instances) and a "client definition". This definition is a tuple with the necessary parameters that allows the batch() command to generate threaded Client objects. The client.define() command can be used to generate the tuple.

MBSP.client.batch(instances, client, timeout=None, retries=1)

MBSP.client.define(client, host=LOCALHOST, port=6060, name=None, log=False)

For example:

>>> from MBSP.client import batch, define, Mbt
>>> print batch(['cat', 'sat', 'mat'], client=define(Mbt, port=6061))

['cat/NN/I-NP', 'sat/VBN/I-VP', 'mat/NN/I-NP']

Client request log

If config.log=True, all client requests and server responses are logged. This is useful for evaluation. Also, when logs are enabled, a cached request can be reused without having to contact the server. The performance hit is negligible however – except for very repetitive texts.

The log is a dictionary indexed by server name (CHUNK, LEMMA, RELATION and PREPOSITION).
Each individual server log in the dictionary is an ordered dictionary that stores the last 1000 requests.

MBSP.client.log

For example:

>>> MBSP.config.log = True
>>> MBSP.parse('I eat pizza with a fork.')
>>> print MBSP.client.log[MBSP.RELATION]

{'-1 0 0 eat VBP - - - - - - - I PRP NP VBP VP ?': 'CATEGORY {NP-SBJ}\n',
  '1 0 0 eat VBP - - - eat VBP VP - pizza NN NP NN PNP ?': 'CATEGORY {NP-OBJ}\n',
  '2 0 0 eat VBP eat VBP VP pizza NN NP - fork NN PNP - - ?': 'CATEGORY {-}\n'}

Three requests were sent to the relation server to find the sentence SBJ and OBJ.
More complex sentences require more lookup requests and more complex request with more instance features require more time.

Server

MBSP has a Server class that is used to start TiMBL or MBT as a background process. A server can be queried by creating a client. Typically, servers run locally on your own machine (e.g. at "localhost") but they can also be configured to work with an IP-address over a network. You can also create new servers from scratch and work with their responses in Python code.

server = MBSP.Server(
        name,
        host = LOCALHOST,
        port = 6060,
     process = TIMBL,
        ping = None,
    features = {})

server.name                # LEMMA
server.host                # LOCALHOST
server.port                # 6062
server.process             # TIMBL
server.features            # {'-f': '/models/em.data', '-m': 'M', '-w': 2, '-k-: 5}
server.ping                # ('c = = = = = = = = = = = = = = = = = = = B ?\n',
                           #  'CATEGORY {ABB-X}\n')

server.program             # The shell command used to start the process.
server.pid                 # Process id, needed when stop() is called.

server.started             # True when ping request yields ping response.

server.start(timeout=60)
server.stop()

Server.features specifies the training data file and various options (see the TiMBL manual).
Server.start() raises a ServerTimeoutError when the server doesn't start in the given time.
Server.start() will continually check Server.started until it returns True.
Server.started determines if the server is up and running by sending a ping request.
Server.ping is a tuple with a sample request and its desired (e.g. correct) response.
If it is None, Server.started just sends "x ?" and accepts whatever response.
Sending a sample request and validating the response is the only safe way to figure out you are addressing the right server.

Stopping a server

When a server is stopped, the background process is killed. The Server.pid process id is stored as a temporary file so that MBSP can retrieve which servers are up and running across Python sessions – you don't need to stop and restart a server each time you run a new Python script.

If the process id is lost (for example, the system did a cleanup of temporary files), the server background process will have to be killed manually. The server module has a force_quit() that terminates all running TiMBL and MBT processes:

MBSP.server.force_quit(processes=(TIMBL, MBT))

This only works on Unix-systems though. Otherwise, the TiMBL and MBT processes will have to be terminated manually from the Windows Task Manager or Mac OS X's Activity Monitor.

MBSP can also be configured to automatically stop its servers when Python exits.

Configuration

A number of settings in config.py can be adjusted. Most notably, IP addresses for the servers (CHUNK, LEMMA, RELATION, PREPOSITION) can be defined in the config.hosts list, so MBSP can be configured to work over a network.

By default, the servers will start automatically when MBSP is imported. Servers are always started at localhost, i.e. the config.hosts list contains the addresses needed for the clients. So if your MBSP is set up to contact servers over a network, config.autostart should be set to False so that no servers are started on your own machine. Servers can also be configured to stop automatically when Python exits, by setting config.</span><span class="inline_code">autostop to True.

The config.log option controls whether client requests and the servers' responses are logged in the MBSP.client.log dictionary.

config.py options

Option	Default	Description
`MODULE`	`os.path.dirname(os.path.abspath(__file__))`	MBSP folder path.
`LOCALHOST `	`'localhost' `	Localhost IP address.
hosts	`[LOCALHOST, LOCALHOST, LOCALHOST, LOCALHOST]`	Server IP addresses.
`ports`	`[6061, 6062, 6063, 6064] `	Server ports.
`autostart `	`True `	Automatically start servers?
`autostop `	`False `	Automatically stop servers?
`log `	`False `	Log server requests?
`verbose`	`True `	Server startup message?
`paths `	{'timbl': MODULE+'/timbl/Timbl'), 'mbt': MODULE+'/mbt/Mbt'), 'mblem': MODULE+'/mblem/mblem_english_bmt'), 'models': MODULE+'/models')}	Binaries and training data.
`threading`	`False`	See installation instructions.
`encoding `	`'utf-8' `	Default character encoding.

Command-line interface

The parser can be run from the command-line by invoking mbsp.py inside the MBSP library folder. The parsed output is printed in the terminal window. Note that the servers will not be started automatically, so you have to start them manually:

> cd MBSP
> python mbsp.py start
> python mbsp.py parse -f camelot.txt
> python mbsp.py parse -s "It's only a model."
> python mbsp.py parse xml -s 'It is a silly place.'
> python mbsp.py stop

Command-line options

If no options are given a full parse is executed (i.e. tokenization, tagging, chunking, relations, prepositions and lemmata). Otherwise, you need to explicitly list every required option:


-O	--tokenize	Tokenize the input.
`-T	--tags `	Parse part-of-speech tags.
`-C	--chunks `	Parse chunks and PNP tags.
`-R	--relations`	Find verb/predicate relations.
`-A	--anchors`	Find PP-attachments.
`-L	--lemmata `	Find word lemmata.
`-f	--file`	Input filename.
-s	`--string`	Input string.
`-e	--encoding`	Specify character encoding (utf-8 by default).
`-v`	--version	Current version of MBSP.

Short options can be concatenated, e.g.: python mbsp.py parse -OTL -f camelot.txt

Extending MBSP

Event framework

MBSP has a built-in event framework that offers a convenient way to customize the module. For example, each completed step in the parser fires an event. A user-defined event handler can be assigned to an event, instead of messing around in the source code.

Server event handlers take a Server object as input. Events are fired when a server is registered in a Servers group (see below), or when a server is successfully started or stopped.

def event_handler(server):
    return None

MBSP.events.server.on_register = event_handler
MBSP.events.server.on_start = event_handler
MBSP.events.server.on_stop = event_handler

Parser event handlers take a TokenString object (see below) as input and return the modified TokenString. Events are fired when each step in the parsing process is completed (for example, tokenization is done).

def event_handler(tokenstring):
    return tokenstring

MBSP.events.parser.on_tokenize = event_handler
MBSP.events.parser.on_parse_tags_and_chunks = event_handler
MBSP.events.parser.on_parse_prepositions = event_handler
MBSP.events.parser.on_parse_relations = event_handler
MBSP.events.parser.on_parse_pp_attachments = event_handler
MBSP.events.parser.on_lemmatize = event_handler

Customizing the parser

Suppose you need to correct some part-of-speech tags. Since the part-of-speech tag influences the relation and anchor tag annotation, you'd need to do this somewhere halfway down the parsing process. This is possible by injecting an event handler – without modifying the source code and thus keeping it easy to install package updates:

>>> def my_tagger_chunker(tokenstring):
>>>     T = tokenstring.split()
>>> i = T.tags.index(MBSP.PART_OF_SPEECH)
>>> for sentence in T:
>>> for token in sentence:
>>> print token[i] # modify POS-tag here
>>> return T.join()
>>>
>>> MBSP.events.parser.on_parse_tags_and_chunks = my_tagger_chunker

Since the output of the event handler is then processed further, it needs to maintain the order of tags and it can't delete tags (they are still needed by the parser to determine other tags).

Customizing the parser output

The output of the parse() command is a string of sentences in which each token has been annotated with the requested tags. This string is in fact a TokenString object that behaves as a Python string, but with extra functionality. Most notably, it has a TokenString.split() method that yields a TokenList object: a list of sentences, where each sentence is a list of tokens, in which each token is a list of tags.

tokenstring = MBSP.TokenString(string, tags=[WORD])

tokenstring.tags              # [WORD, POS, CHUNK, PNP, RELATION, ANCHOR, LEMMA]
tokenstring.split(sep=TOKENS) # Yields a TokenList.
tokenstring.copy()

tokenlist = MBSP.TokenList(sentences, tags)

tokenlist.tags
tokenlist.tags.insert(i, tag, values=None)
tokenlist.tags.append(tag, values=None)
tokenlist.tags.remove(tag)
tokenlist.tags.pop(i)
tokenlist.tags.swap(tag1, tag2)

tokenlist.join()              # Yields a TokenString.
tokenlist.copy()
tokenlist.reduce(tags=[])
tokenlist.filter(
        word = None,
         tag = None,
       chunk = None,
    relation = None,
      anchor = None,
       lemma = None)

The TokenString facilitates the conversion from a tagged string to a list – where tokens can then be manipulated. The TokenList.tags list not only stores the order of tags in each token, it also keeps the tokens in synch. If you delete an item from TokenList.tags, all tokens in each sentence are automatically modified as well. In the same way, TokenList.tags.append() has an additional values parameter where you can enter the values of the new tag for each token in each sentence ( by default, O).

For example:

>>> s = MBSP.parse('I eat pizza')
>>> s = s.split()
>>> s.tags.append('semantic', values=[['person', 'action', 'food']])
>>> s = s.join()
>>> print s

I/PRP/I-NP/O/NP-SBJ-1/O/i/person eat/VBP/I-VP/O/VP-1/O/eat/action
pizza/NN/I-NP/O/NP-OBJ-1/O/pizza/food

When you create a parse tree from this output, the semantic tag will end up in Word.custom_tags.

If you want to insert a tag from one TokenString into another, you can use TokenString1.tags.pop(). It extracts (and removes) the tag value from each token. You can use this return value for the values parameter in the other TokenString2.tags.append().

TokenList.reduce() returns a copy with the given tags removed from all tokens.
TokenList.filter() returns a list of all tokens that match the given criteria. Wildcards can be used at the head, tail or middle of a constraint:

>>> s = MBSP.parse('I eat pizzas with a fork.')
>>> print s.split().filter(tag="NN*")

[[u'pizzas', u'NNS', u'I-NP', u'O', u'NP-OBJ-1', u'O', u'pizza'],
 [u'fork', u'NN', u'I-NP', u'I-PNP', u'O', u'P1', u'fork']]

Customizing the servers

MBSP's servers are grouped in a Servers object: a Python list with some additional functionality:

Servers can automatically start and stop a server (i.e. Server object) that is added to the group.
Servers will check that all servers in the group use a different port and a different name.
When a server is added, its Server.group attribute will refer to the Servers object.
When a server is added, the on_register event will be fired.

servers = MBSP.Servers(start=False, stop=False)

servers.append(server)

servers.[server_name]      # Retrieve a server by name.

servers.started            # True when all servers in the group have started.
servers.start(timeout=60)
servers.stop()

The correct way to install a custom server is to add it to the module's active_servers group to ensure that it is started and stopped together with the other servers (e.g. when MBSP.stop() is called).

Assume we have a tagger trained for biomedical use that overrides the default part-of-speech tags:

>>> import MBSP
>>> MBSP.active_servers.append(
>>>    MBSP.Server(
>>>            name = 'biomedical_pos',
>>>            port = 6065,
>>>         process = MBSP.MBT,
>>>        features = {'-s' : 'biopos/biopos.settings')}))

We can contact the server with an event, after MBSP is done tagging and chunking:

def update_pos(tokenstring):
>>>     client = MBSP.Mbt(port=6065)
>>>     s1 = tokenstring.split()
>>>     s2 = s1.reduce([MBSP.WORD])
>>>     s2 = MBSP.TokenString(client.send(s2.join()), tags=[MBSP.WORD, MBSP.POS])
>>>     s2 = s2.split()
>>>     s2.tags.append(MBSP.CHUNK, values=s1.tags.pop(s1.tags.index(MBSP.CHUNK)))
>>>     client.disconnect()
>>>     return s2.join()
>>>
>>> MBSP.events.parser.on_parse_tags_and_chunks = update_pos

We have installed a new server and then contact it in the update_pos() event, right after MBSP has finished tagging and chunking with the default servers. The event extracts the original words in the sentence and feeds them to our biomedical MBT server. We append the original chunk tags to the updated output and pass it back to MBSP. MBSP will continue to look for relations and prepositions with the updated tags.

Replacing a default server before it starts

Assume you want to replace a default server with one of your own. If MBSP's servers are configured to start automatically, there is no way to stop them from loading before you can replace them. The way to do this is to disable MBSP's autostart feature, add replacement servers to active_servers, and then implement your own autostart in your own script.

Exporting to XML and NLTK

With the xml() command the output of the parse() command can be dumped as an XML string:

MBSP.xml(string, token=[WORD, POS, CHUNK, PNP, RELATION, ANCHOR, LEMMA])

MBSP.Text.xml           # Returns the Text as an XML string.

MBSP.Text.from_xml(xml) # Returns a new Text from the given XML string.

The XML output is a <text> element consisting of one or more <sentence> elements. Each <sentence> has a unique idattribute, a token descriptor and consists of <chunk> and <chink> elements. A <chunk> can have a type attribute (e.g.NP, VP) and/or a relation attribute (e.g. SBJ). In this case it can also have an of attribute with the id of the related VPchunk. A <chunk type=”PNP”> element can also have an of attribute, with the anchor of the chunk to which it is attached. A <chunk> consists of <word> elements, or other <chunk> elements in the case of a PNP. A <word> element contains the actual word and can have a type attribute (e.g. NN) and a lemma attribute. If MBSP was extended with custom tags these will be listed in the <sentence> token attribute and as <word> attributes.

For example:

s = MBSP.parse('I eat pizza with a fork.')
print(MBSP.xml(s))

<?xml version="1.0" encoding="UTF-8"?>
<text>
<sentence id="1"

token="word, part-of-speech, chunk, preposition, relation, anchor, lemma">

<chunk type="NP" relation="SBJ" of="1.1">

<word type="PRP" lemma="i">I</word>

</chunk>

<chunk type="VP" id="1.1" anchor="1.A1">

<word type="VBP" lemma="eat">eat</word>

</chunk>

<chunk type="NP" relation="OBJ" of="1.1">

<word type="NN" lemma="pizza">pizza</word>

</chunk>

<chunk type="PNP" of="1.A1">

<chunk type="PP">

<word type="IN" lemma="with">with</word>

</chunk>

<chunk type="NP">

<word type="DT" lemma="a">a</word>

<word type="NN" lemma="fork">fork</word>

</chunk>

</chunk>

<chink>

<word type="." lemma=".">.</word>

</chink>
</sentence>
</text>

Exporting to NLTK

The MBSP.tree module has an nltk_tree() command that returns an nltk.tree.Tree object from the given MBSP.Sentence object. This way the output from MBSP can be integrated into NLTK for further processing.

s = MBSP.parse('I eat pizza with a fork.')
s = MBSP.split(s)
print MBSP.tree.nltk_tree(s.sentences[0])

>>> (S
      (NP (PRP I))
      (VP (VBP eat) (PNP (PP (IN with)) (NP (DT a) (NN fork))))
      (NP (NN pizza)))

NLTK needs to be installed on your system for this to work.

Exporting to GraphViz

The MBSP.tree module has a graphviz_dot() command that returns a string in the DOT language (a simple way to describe graphs) from the given MBSP.Sentence object. DOT files can be visualized with GraphViz, a free application for drawing graphs and exporting them as images (PDF, PNG, ...)

>>> s = MBSP.parse('I eat pizza with a fork.')
>>> s = MBSP.split(s)
>>> f = open('pizza.dot', 'w')
>>> f.write(MBSP.tree.graphviz_dot(s.sentences[0])
>>> f.close()

When pizza.dot is then openend in GraphViz it displays the following syntax tree:

Licensing

MBSP uses a duel license model and offers licenses for two distinct purposes – commercial and open source development.

Open source: for open source purposes MBSP uses the GNU General Public License version 3 (GPLv3). It requires that you contribute to the open source community by placing your application that uses MBSP under an open source license (e.g. GPLv3). This option secures all users the rights to obtain the application's full source code, modify it, and redistribute it.

Commercial: for commercial purposes you can directly contact prof. Walter Daelemans (walter.daelemans at uantwerpen.be). This requires that you contribute to the continued development of the product by purchasing a commercial license. This option secures you the right to distribute your application under the license terms of your choice

Name		Name	Last commit message	Last commit date
Latest commit History 13 Commits
examples		examples
manual		manual
mblem		mblem
mbt		mbt
models		models
pl		pl
prepositions		prepositions
timbl		timbl
.gitignore		.gitignore
LICENSE.txt		LICENSE.txt
README.MD		README.MD
__init__.py		__init__.py
cache.py		cache.py
client.py		client.py
config.py		config.py
mbsp.py		mbsp.py
relationfinder.py		relationfinder.py
server.py		server.py
setup.py		setup.py
tags.py		tags.py
tokenizer.py		tokenizer.py
tree.py		tree.py

License

clips/MBSP

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Documentation

Introduction

Quick overview

Purpose

Grammar basics

Acknowledgements

Installation

Compiling with setup.py

Compiling from source

Building MBLEM

Building TiMBL

Building MBT

Module folder location

Memory usage

Multithreading

Parser

Parser tags

Parser shortcuts

Parser output

Tokenizer

Tokenization process

Tokenizer word ranges

Tokenizer modes

Lemmatizer

Lemmatization process

PP-attacher

PP-attachment process

Parse trees

Text

Sentence

Creating a sentence

Sentence words

Sentence chunks

Prepositional noun phrases

Clients and servers

Client

Request and response formatters

TiMBL and MBT client

Client batch requests

Client request log

Server

Stopping a server

Configuration

config.py options

Command-line interface

Command-line options

Extending MBSP

Event framework

Customizing the parser

Customizing the parser output

Customizing the servers

Replacing a default server before it starts

Exporting to XML and NLTK

Exporting to NLTK

Exporting to GraphViz

Licensing

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