Extract list of Persons and Organizations using Stanford NER Tagger in NLTK

I am trying to extract list of persons and organizations using Stanford Named Entity Recognizer (NER) in Python NLTK. When I run:

from nltk.tag.stanford import NERTagger
st = NERTagger('/usr/share/stanford-ner/classifiers/all.3class.distsim.crf.ser.gz',
               '/usr/share/stanford-ner/stanford-ner.jar') 
r=st.tag('Rami Eid is studying at Stony Brook University in NY'.split())
print(r)

the output is:

[('Rami', 'PERSON'), ('Eid', 'PERSON'), ('is', 'O'), ('studying', 'O'),
('at', 'O'), ('Stony', 'ORGANIZATION'), ('Brook', 'ORGANIZATION'),
('University', 'ORGANIZATION'), ('in', 'O'), ('NY', 'LOCATION')]

what I want is to extract from this list all persons and organizations in this form:

Rami Eid
Sony Brook University

I tried to loop through the list of tuples:

for x,y in i:
        if y == 'ORGANIZATION':
            print(x)

But this code only prints every entity one per line:

Sony 
Brook 
University

With real data there can be more than one organizations, persons in one sentence, how can I put the limits between different entities?

Solution 1:

Thanks to the link discovered by @Vaulstein, it is clear that the trained Stanford tagger, as distributed (at least in 2012) does not chunk named entities. From the accepted answer:

Many NER systems use more complex labels such as IOB labels, where codes like B-PERS indicates where a person entity starts. The CRFClassifier class and feature factories support such labels, but they're not used in the models we currently distribute (as of 2012)

You have the following options:

Collect runs of identically tagged words; e.g., all adjacent words tagged PERSON should be taken together as one named entity. That's very easy, but of course it will sometimes combine different named entities. (E.g. New York, Boston [and] Baltimore is about three cities, not one.) Edit: This is what Alvas's code does in the accepted anwser. See below for a simpler implementation.
Use nltk.ne_recognize(). It doesn't use the Stanford recognizer but it does chunk entities. (It's a wrapper around an IOB named entity tagger).
Figure out a way to do your own chunking on top of the results that the Stanford tagger returns.
Train your own IOB named entity chunker (using the Stanford tools, or the NLTK's framework) for the domain you are interested in. If you have the time and resources to do this right, it will probably give you the best results.

Edit: If all you want is to pull out runs of continuous named entities (option 1 above), you should use itertools.groupby:

from itertools import groupby
for tag, chunk in groupby(netagged_words, lambda x:x[1]):
    if tag != "O":
        print("%-12s"%tag, " ".join(w for w, t in chunk))

If netagged_words is the list of (word, type) tuples in your question, this produces:

PERSON       Rami Eid
ORGANIZATION Stony Brook University
LOCATION     NY

Note again that if two named entities of the same type occur right next to each other, this approach will combine them. E.g. New York, Boston [and] Baltimore is about three cities, not one.

Solution 2:

IOB/BIO means Inside, Outside, Beginning (IOB), or sometimes aka Beginning, Inside, Outside (BIO)

The Stanford NE tagger returns IOB/BIO style tags, e.g.

[('Rami', 'PERSON'), ('Eid', 'PERSON'), ('is', 'O'), ('studying', 'O'),
('at', 'O'), ('Stony', 'ORGANIZATION'), ('Brook', 'ORGANIZATION'),
('University', 'ORGANIZATION'), ('in', 'O'), ('NY', 'LOCATION')]

The ('Rami', 'PERSON'), ('Eid', 'PERSON') are tagged as PERSON and "Rami" is the Beginning or a NE chunk and "Eid" is the inside. And then you see that any non-NE will be tagged with "O".

The idea to extract continuous NE chunk is very similar to Named Entity Recognition with Regular Expression: NLTK but because the Stanford NE chunker API doesn't return a nice tree to parse, you have to do this:

def get_continuous_chunks(tagged_sent):
    continuous_chunk = []
    current_chunk = []

    for token, tag in tagged_sent:
        if tag != "O":
            current_chunk.append((token, tag))
        else:
            if current_chunk: # if the current chunk is not empty
                continuous_chunk.append(current_chunk)
                current_chunk = []
    # Flush the final current_chunk into the continuous_chunk, if any.
    if current_chunk:
        continuous_chunk.append(current_chunk)
    return continuous_chunk

ne_tagged_sent = [('Rami', 'PERSON'), ('Eid', 'PERSON'), ('is', 'O'), ('studying', 'O'), ('at', 'O'), ('Stony', 'ORGANIZATION'), ('Brook', 'ORGANIZATION'), ('University', 'ORGANIZATION'), ('in', 'O'), ('NY', 'LOCATION')]

named_entities = get_continuous_chunks(ne_tagged_sent)
named_entities = get_continuous_chunks(ne_tagged_sent)
named_entities_str = [" ".join([token for token, tag in ne]) for ne in named_entities]
named_entities_str_tag = [(" ".join([token for token, tag in ne]), ne[0][1]) for ne in named_entities]

print named_entities
print
print named_entities_str
print
print named_entities_str_tag
print

[out]:

[[('Rami', 'PERSON'), ('Eid', 'PERSON')], [('Stony', 'ORGANIZATION'), ('Brook', 'ORGANIZATION'), ('University', 'ORGANIZATION')], [('NY', 'LOCATION')]]

['Rami Eid', 'Stony Brook University', 'NY']

[('Rami Eid', 'PERSON'), ('Stony Brook University', 'ORGANIZATION'), ('NY', 'LOCATION')]

But please note the limitation that if two NEs are continuous, then it might be wrong, nevertheless i still can't think of any example where two NEs are continuous without any "O" between them.

As @alexis suggested, it's better to convert the stanford NE output into NLTK trees:

from nltk import pos_tag
from nltk.chunk import conlltags2tree
from nltk.tree import Tree

def stanfordNE2BIO(tagged_sent):
    bio_tagged_sent = []
    prev_tag = "O"
    for token, tag in tagged_sent:
        if tag == "O": #O
            bio_tagged_sent.append((token, tag))
            prev_tag = tag
            continue
        if tag != "O" and prev_tag == "O": # Begin NE
            bio_tagged_sent.append((token, "B-"+tag))
            prev_tag = tag
        elif prev_tag != "O" and prev_tag == tag: # Inside NE
            bio_tagged_sent.append((token, "I-"+tag))
            prev_tag = tag
        elif prev_tag != "O" and prev_tag != tag: # Adjacent NE
            bio_tagged_sent.append((token, "B-"+tag))
            prev_tag = tag

    return bio_tagged_sent


def stanfordNE2tree(ne_tagged_sent):
    bio_tagged_sent = stanfordNE2BIO(ne_tagged_sent)
    sent_tokens, sent_ne_tags = zip(*bio_tagged_sent)
    sent_pos_tags = [pos for token, pos in pos_tag(sent_tokens)]

    sent_conlltags = [(token, pos, ne) for token, pos, ne in zip(sent_tokens, sent_pos_tags, sent_ne_tags)]
    ne_tree = conlltags2tree(sent_conlltags)
    return ne_tree

ne_tagged_sent = [('Rami', 'PERSON'), ('Eid', 'PERSON'), ('is', 'O'), 
('studying', 'O'), ('at', 'O'), ('Stony', 'ORGANIZATION'), 
('Brook', 'ORGANIZATION'), ('University', 'ORGANIZATION'), 
('in', 'O'), ('NY', 'LOCATION')]

ne_tree = stanfordNE2tree(ne_tagged_sent)

print ne_tree

[out]:

  (S
  (PERSON Rami/NNP Eid/NNP)
  is/VBZ
  studying/VBG
  at/IN
  (ORGANIZATION Stony/NNP Brook/NNP University/NNP)
  in/IN
  (LOCATION NY/NNP))

Then:

ne_in_sent = []
for subtree in ne_tree:
    if type(subtree) == Tree: # If subtree is a noun chunk, i.e. NE != "O"
        ne_label = subtree.label()
        ne_string = " ".join([token for token, pos in subtree.leaves()])
        ne_in_sent.append((ne_string, ne_label))
print ne_in_sent

[out]:

[('Rami Eid', 'PERSON'), ('Stony Brook University', 'ORGANIZATION'), ('NY', 'LOCATION')]

Extract list of Persons and Organizations using Stanford NER Tagger in NLTK

Solution 1:

Solution 2:

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