惊！brat安装后进行标注-实战，并且通过一行代码自动标注为BIO格式，便于模型训练-and 错误解决

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篇首语：本文由小常识网(cha138.com)小编为大家整理，主要介绍了惊！brat安装后进行标注-实战，并且通过一行代码自动标注为BIO格式，便于模型训练-and 错误解决相关的知识，希望对你有一定的参考价值。

安装可查看文章：https://blog.csdn.net/weixin_42565135/article/details/119460805

安装后可以继续看下文哦

目录

流程

1.首先是数据集的处理

2.将要标注的数据导入

三.实战标注过程

四.模型

1.自动标注的流程及结果展示

2.写代码标注：也很简单，这里说说思路

3.模型训练

输入实体识别模型中可以直接训练，不同模型的输入可能不相同，稍微修改数据样式即可

为什么选择brat标注工具。在刚开始进行标注时，是选择的stanford npl工具进行标注的，那个对英文的数据集标注效果是不错的，但进行尝试后发现，比如人工智能这个词，会将人工标注为形容词 智能标注为实体，而且在进行实体识别模型训练的时候，大多数模型需要对标签进行处理，采用的是BIO的标注方式：

  • B，即Begin，表示开始
  • I，即Intermediate，表示中间
  • O，即Other，表示其他，用于标记无关字符

而且在一些知识图谱构建的比赛中也是提到了使用brat进行标注，这样参考的资料也多一些

流程

1.首先是数据集的处理

因为是爬取的英文论文中数据，属于非结构化数据，在实验中计划先取2000条数据进行标注。这2000条数据在一个csv文件中，因此要对数据进行清理，并将每一篇摘要保存到一个txt文件中，每一行为一句话。

import csv
with open('/home/jtt/ai-ner/2021-scopus.csv') as f:
    csv_write = csv.reader(f)
    for i, row in enumerate(csv_write):
        if i == 10:
            break
        else:
            name_='/home/jtt/ai-ner/2021-'+str(i+1)+'.txt'
            ff = open(name_, 'a')
           # resul=row[1].split('.')
           # print(len(resul))

            list_ret = list()
            for s_str in row[1].split('.'):  # 对输入进行处理  (用英文结尾句号.来划分句子)
                s_str = s_str.replace('\\n', '')  # 去掉句子中的\\n换行

                if '?' in s_str:
                    list_ret.extend(s_str.split('?'))
                elif '!' in s_str:
                    list_ret.extend(s_str.split('!'))
                else:
                    list_ret.append(s_str)
            for xx,xc in enumerate(list_ret):
                #print(xc.strip(),'\\n')
                if xc.strip()!='':
                    tmp=xc.strip()+'.\\n'
                    ff.write(tmp)

            ff.close()

print('okokokoo')

2.将要标注的数据导入

下面有坑【解决方法是将新建文件家ainer移动到/var/www/html/brat/data下面在标注的时候才能找到，要不咋也找不到文件，即导入的数据得放在/var/www/html/brat/data下】：在主目录/var/www/html/brat下新建文件夹ainer[命令：mkdir ainer],将主目录下的annotation.conf和visual.conf两个文件复制到新建文件夹ainer中【命令：cp annotation.conf /var/www/html/brat/ainer/annotation.conf和cp visual.conf /var/www/html/brat/ainer/visual.conf】；

jtt@jtt-System-Product-Name:/var/www/html/brat$ cd ainer
jtt@jtt-System-Product-Name:/var/www/html/brat/ainer$ ls
annotation.conf  visual.conf
将包含txt数据集的文件夹放置到安装文件下一个data的目录下， 
jtt@jtt-System-Product-Name:/var/www/html/brat/ainer$ mkdir data

jtt@jtt-System-Product-Name:~/ai-ner$ mv  all-txt /var/www/html/brat/ainer/data/ 

jtt@jtt-System-Product-Name:~$ cd /var/www/html/brat/ainer/data/
jtt@jtt-System-Product-Name:/var/www/html/brat/ainer/data$ ls
all-txt
然后使用命令：

find 文件夹名称 -name '*.txt'|sed -e 's|\\.txt|.ann|g'|xargs touch，其意思是对每个txt文件都创建一个空的标引文件.ann，因为BRAT是要求的collection中，每个txt文件是必须有一个对应的.ann文件的，方便放置标引内容，这个ann文件的格式也挺规范。

jtt@jtt-System-Product-Name:/var/www/html/brat/ainer/data$ find all-txt -name '*.txt'|sed -e 's|\\.txt|.ann|g'|xargs touch

jtt@jtt-System-Product-Name:/var/www/html/brat/ainer/data$ ls
all-txt
jtt@jtt-System-Product-Name:/var/www/html/brat/ainer/data$ cd all-txt
jtt@jtt-System-Product-Name:/var/www/html/brat/ainer/data/all-txt$ ls
2021-10.ann  2021-2.ann  2021-4.ann  2021-6.ann  2021-8.ann
2021-10.txt  2021-2.txt  2021-4.txt  2021-6.txt  2021-8.txt
2021-1.ann   2021-3.ann  2021-5.ann  2021-7.ann  2021-9.ann
2021-1.txt   2021-3.txt  2021-5.txt  2021-7.txt  2021-9.txt

3.标注

在自己要标注的数据目录添加配置文件annotation.conf，编辑标引规范，就是写明白自己标注的都有哪些命名实体、哪些语义关系。eg:

[entities]

OTH

LOC

NAME

ORG

TIME

TIL

NUM

[relations]

[events]

[attributes]

jtt@jtt-System-Product-Name:~$ cd /var/www/html/brat/ainer
jtt@jtt-System-Product-Name:/var/www/html/brat/ainer$ ls
annotation.conf  data  visual.conf
jtt@jtt-System-Product-Name:/var/www/html/brat/ainer$ vi annotation.conf

点击键盘 i  进行实体类别编辑，如下修改

Method-tech
Area-subject
Time
Other

关系
Applyied Arg1:Method-tech,Arg2:Area-subject
Associate Arg1:Method-tech,Arg2:Method-tech
Associate2 Arg1:Area-subject,Arg2:Area-subject
Emergence Arg1:Method-tech,Arg2:Time

Located            Arg1:Other, Arg2:Other
Geographical_part  Arg1:Other,    Arg2:Other
Family             Arg1:Person, Arg2:Other
Employment         Arg1:Other, Arg2:Other
Ownership          Arg1:Other, Arg2:Other

属性
Merge-time Arg:<RELATION>

点击esc退出编辑
光标到最后输入：wq即可返回命令界面

点击BRAT页面，用自己的账号登录，从页面上直接进入collection中，找到文件进行标引。

命名实体标引直接用光标拖拽，关系标引用鼠标将一个实体指向另一个实体即可。

jtt@jtt-System-Product-Name:~$ cd /var/www/html/brat
jtt@jtt-System-Product-Name:/var/www/html/brat$ python2 standalone.py
Serving brat at http://127.0.0.1:8001

现在遇到一个问题：找不到要标注的数据在哪里，然后通过代码测试 总算找到了。之后将配置文件和数据移动到了正确位置中。【这就是坑-跳出来了】总结：在data中新建一个文件夹/var/www/html/brat/data/all-txt，里面包含文本/.ann/以及配置文件annotation.conf 和  visual.conf

jtt@jtt-System-Product-Name:/var/www/html/brat$ cd data
jtt@jtt-System-Product-Name:/var/www/html/brat/data$ ls
6.ann  6.txt  examples  tutorials

移动：jtt@jtt-System-Product-Name:/var/www/html/brat/ainer/data$ mv all-txt /var/www/html/brat/data/

jtt@jtt-System-Product-Name:/var/www/html/brat$ cd data
jtt@jtt-System-Product-Name:/var/www/html/brat/data$ ls
6.ann  6.txt  all-txt  examples  tutorials
jtt@jtt-System-Product-Name:/var/www/html/brat/data$ rm 6.ann
jtt@jtt-System-Product-Name:/var/www/html/brat/data$ rm 6.txt
jtt@jtt-System-Product-Name:/var/www/html/brat/data$ ls
all-txt  examples  tutorials

ok了

接下来将配置文件重新修改一下

jtt@jtt-System-Product-Name:/var/www/html/brat$ vi annotation.conf

修改完成后进行标注

可以看到图中有了数据了

三.实战标注过程

选择要标注的实体，直接弹出框框进行标注，最后可以将标注好的数据导出

四.模型

根据标注的结果转化成BIO标注，选择bert-bilstm-crf模型进行标注。

怎么标注呢

1.自动标注的流程及结果展示

进入目录/var/www/html/brat/tools;

输入：python anntoconll.py 要进行BIO标注的文本文件

ok

eg：

ann文件标注了两个实体：T1    Method-tech 4 12    COVID-19
                                           T2    Other 225 237    intelligence

运行代码：python anntoconll.py /var/www/html/brat/data/all-txt/2021-1.txt

生成了标注后的文件：文件名.conll

结果：

2.写代码标注：也很简单，这里说说思路

根据标注的.ann文件，找到是实体的标注

第一个识别的标为B，判断如果他后面的词还是实体，就给标注为I

当不是实体的其他标为O

3.模型训练

输入实体识别模型中可以直接训练，不同模型的输入可能不相同，稍微修改数据样式即可

错误解决

正常的配置文件，在实体标注时可以，在bio标注时报错。同样在bio标注时正确，在实体识别时报错，究其原因及解决办法--如下

原因：

py文件中代码报错

解决办法：

在brat/server/src/sspostproc.py文件中，实体标注时代码：

jtt@jtt-System-Product-Name:~$ cd /var/www/html/brat
jtt@jtt-System-Product-Name:/var/www/html/brat$ python2 standalone.py
Serving brat at http://127.0.0.1:8001

文件内容为

#!/usr/bin/env python

# Python version of geniass-postproc.pl. Originally developed as a
# heuristic postprocessor for the geniass sentence splitter, drawing
# in part on Yoshimasa Tsuruoka's medss.pl.

from __future__ import with_statement

import re

INPUT_ENCODING = "UTF-8"
OUTPUT_ENCODING = "UTF-8"
DEBUG_SS_POSTPROCESSING = False

__initial = []

# TODO: some cases that heuristics could be improved on
# - no split inside matched quotes
# - "quoted." New sentence
# - 1 mg .\\nkg(-1) .

# breaks sometimes missing after "?", "safe" cases
__initial.append((re.compile(r'\\b([a-z]+\\?) ([A-Z][a-z]+)\\b'), r'\\1\\n\\2'))
# breaks sometimes missing after "." separated with extra space, "safe" cases
__initial.append((re.compile(r'\\b([a-z]+ \\.) ([A-Z][a-z]+)\\b'), r'\\1\\n\\2'))

# join breaks creating lines that only contain sentence-ending punctuation
__initial.append((re.compile(r'\\n([.!?]+)\\n'), r' \\1\\n'))

# no breaks inside parens/brackets. (To protect against cases where a
# pair of locally mismatched parentheses in different parts of a large
# document happen to match, limit size of intervening context. As this
# is not an issue in cases where there are no interveining brackets,
# allow an unlimited length match in those cases.)

__repeated = []

# unlimited length for no intevening parens/brackets
__repeated.append((re.compile(r'(\\([^\\[\\]\\(\\)]*)\\n([^\\[\\]\\(\\)]*\\))'),r'\\1 \\2'))
__repeated.append((re.compile(r'(\\[[^\\[\\]\\(\\)]*)\\n([^\\[\\]\\(\\)]*\\])'),r'\\1 \\2'))
# standard mismatched with possible intervening
__repeated.append((re.compile(r'(\\([^\\(\\)]0,250)\\n([^\\(\\)]0,250\\))'), r'\\1 \\2'))
__repeated.append((re.compile(r'(\\[[^\\[\\]]0,250)\\n([^\\[\\]]0,250\\])'), r'\\1 \\2'))
# nesting to depth one
__repeated.append((re.compile(r'(\\((?:[^\\(\\)]|\\([^\\(\\)]*\\))0,250)\\n((?:[^\\(\\)]|\\([^\\(\\)]*\\))0,250\\))'), r'\\1 \\2'))
__repeated.append((re.compile(r'(\\[(?:[^\\[\\]]|\\[[^\\[\\]]*\\])0,250)\\n((?:[^\\[\\]]|\\[[^\\[\\]]*\\])0,250\\])'), r'\\1 \\2'))

__final = []

# no break after periods followed by a non-uppercase "normal word"
# (i.e. token with only lowercase alpha and dashes, with a minimum
# length of initial lowercase alpha).
__final.append((re.compile(r'\\.\\n([a-z]3[a-z-]0,[ \\.\\:\\,\\;])'), r'. \\1'))

# no break in likely species names with abbreviated genus (e.g.
# "S. cerevisiae"). Differs from above in being more liberal about
# separation from following text.
__final.append((re.compile(r'\\b([A-Z]\\.)\\n([a-z]3,)\\b'), r'\\1 \\2'))

# no break in likely person names with abbreviated middle name
# (e.g. "Anton P. Chekhov", "A. P. Chekhov"). Note: Won't do
# "A. Chekhov" as it yields too many false positives.
__final.append((re.compile(r'\\b((?:[A-Z]\\.|[A-Z][a-z]3,) [A-Z]\\.)\\n([A-Z][a-z]3,)\\b'), r'\\1 \\2'))

# no break before CC ..
__final.append((re.compile(r'\\n((?:and|or|but|nor|yet) )'), r' \\1'))

# or IN. (this is nothing like a "complete" list...)
__final.append((re.compile(r'\\n((?:of|in|by|as|on|at|to|via|for|with|that|than|from|into|upon|after|while|during|within|through|between|whereas|whether) )'), r' \\1'))

# no sentence breaks in the middle of specific abbreviations
__final.append((re.compile(r'\\b(e\\.)\\n(g\\.)'), r'\\1 \\2'))
__final.append((re.compile(r'\\b(i\\.)\\n(e\\.)'), r'\\1 \\2'))
__final.append((re.compile(r'\\b(i\\.)\\n(v\\.)'), r'\\1 \\2'))

# no sentence break after specific abbreviations
__final.append((re.compile(r'\\b(e\\. ?g\\.|i\\. ?e\\.|i\\. ?v\\.|vs\\.|cf\\.|Dr\\.|Mr\\.|Ms\\.|Mrs\\.)\\n'), r'\\1 '))

# or others taking a number after the abbrev
__final.append((re.compile(r'\\b([Aa]pprox\\.|[Nn]o\\.|[Ff]igs?\\.)\\n(\\d+)'), r'\\1 \\2'))

# no break before comma (e.g. Smith, A., Black, B., ...)
__final.append((re.compile(r'(\\.\\s*)\\n(\\s*,)'), r'\\1 \\2'))

def refine_split(s):
    """
    Given a string with sentence splits as newlines, attempts to
    heuristically improve the splitting. Heuristics tuned for geniass
    sentence splitting errors.
    """

    if DEBUG_SS_POSTPROCESSING:
        orig = s

    for r, t in __initial:
        s = r.sub(t, s)

    for r, t in __repeated:
        while True:
            n = r.sub(t, s)
            if n == s: break
            s = n

    for r, t in __final:
        s = r.sub(t, s)

    # Only do final comparison in debug mode.
    if DEBUG_SS_POSTPROCESSING:
        # revised must match original when differences in space<->newline
        # substitutions are ignored
        r1 = orig.replace('\\n', ' ')
        r2 = s.replace('\\n', ' ')
        if r1 != r2:
            print >> sys.stderr, "refine_split(): error: text mismatch (returning original):\\nORIG: '%s'\\nNEW:  '%s'" % (orig, s)
            s = orig

    return s

if __name__ == "__main__":
    import sys
    import codecs

    # for testing, read stdin if no args
    if len(sys.argv) == 1:
        sys.argv.append('/dev/stdin')

    for fn in sys.argv[1:]:
        try:
            with codecs.open(fn, encoding=INPUT_ENCODING) as f:
                s = "".join(f.read())
                sys.stdout.write(refine_split(s).encode(OUTPUT_ENCODING))
        except Exception, e:
            print >> sys.stderr, "Failed to read", fn, ":", e

BIO标注时代码：

jtt@jtt-System-Product-Name:~$ cd /var/www/html/brat/tools
jtt@jtt-System-Product-Name:/var/www/html/brat/tools$  python anntoconll.py /var/www/html/brat/data/2021-pre2000/2021-1.txt


内容为

#!/usr/bin/env python

# Python version of geniass-postproc.pl. Originally developed as a
# heuristic postprocessor for the geniass sentence splitter, drawing
# in part on Yoshimasa Tsuruoka's medss.pl.



import re

INPUT_ENCODING = "UTF-8"
OUTPUT_ENCODING = "UTF-8"
DEBUG_SS_POSTPROCESSING = False

__initial = []

# TODO: some cases that heuristics could be improved on
# - no split inside matched quotes
# - "quoted." New sentence
# - 1 mg .\\nkg(-1) .

# breaks sometimes missing after "?", "safe" cases
__initial.append((re.compile(r'\\b([a-z]+\\?) ([A-Z][a-z]+)\\b'), r'\\1\\n\\2'))
# breaks sometimes missing after "." separated with extra space, "safe" cases
__initial.append((re.compile(r'\\b([a-z]+ \\.) ([A-Z][a-z]+)\\b'), r'\\1\\n\\2'))

# join breaks creating lines that only contain sentence-ending punctuation
__initial.append((re.compile(r'\\n([.!?]+)\\n'), r' \\1\\n'))

# no breaks inside parens/brackets. (To protect against cases where a
# pair of locally mismatched parentheses in different parts of a large
# document happen to match, limit size of intervening context. As this
# is not an issue in cases where there are no interveining brackets,
# allow an unlimited length match in those cases.)

__repeated = []

# unlimited length for no intevening parens/brackets
__repeated.append(
    (re.compile(r'(\\([^\\[\\]\\(\\)]*)\\n([^\\[\\]\\(\\)]*\\))'), r'\\1 \\2'))
__repeated.append(
    (re.compile(r'(\\[[^\\[\\]\\(\\)]*)\\n([^\\[\\]\\(\\)]*\\])'), r'\\1 \\2'))
# standard mismatched with possible intervening
__repeated.append(
    (re.compile(r'(\\([^\\(\\)]0,250)\\n([^\\(\\)]0,250\\))'), r'\\1 \\2'))
__repeated.append(
    (re.compile(r'(\\[[^\\[\\]]0,250)\\n([^\\[\\]]0,250\\])'), r'\\1 \\2'))
# nesting to depth one
__repeated.append(
    (re.compile(r'(\\((?:[^\\(\\)]|\\([^\\(\\)]*\\))0,250)\\n((?:[^\\(\\)]|\\([^\\(\\)]*\\))0,250\\))'),
     r'\\1 \\2'))
__repeated.append(
    (re.compile(r'(\\[(?:[^\\[\\]]|\\[[^\\[\\]]*\\])0,250)\\n((?:[^\\[\\]]|\\[[^\\[\\]]*\\])0,250\\])'),
     r'\\1 \\2'))

__final = []

# no break after periods followed by a non-uppercase "normal word"
# (i.e. token with only lowercase alpha and dashes, with a minimum
# length of initial lowercase alpha).
__final.append((re.compile(r'\\.\\n([a-z]3[a-z-]0,[ \\.\\:\\,\\;])'), r'. \\1'))

# no break in likely species names with abbreviated genus (e.g.
# "S. cerevisiae"). Differs from above in being more liberal about
# separation from following text.
__final.append((re.compile(r'\\b([A-Z]\\.)\\n([a-z]3,)\\b'), r'\\1 \\2'))

# no break in likely person names with abbreviated middle name
# (e.g. "Anton P. Chekhov", "A. P. Chekhov"). Note: Won't do
# "A. Chekhov" as it yields too many false positives.
__final.append(
    (re.compile(r'\\b((?:[A-Z]\\.|[A-Z][a-z]3,) [A-Z]\\.)\\n([A-Z][a-z]3,)\\b'),
     r'\\1 \\2'))

# no break before CC ..
__final.append((re.compile(r'\\n((?:and|or|but|nor|yet) )'), r' \\1'))

# or IN. (this is nothing like a "complete" list...)
__final.append((re.compile(
    r'\\n((?:of|in|by|as|on|at|to|via|for|with|that|than|from|into|upon|after|while|during|within|through|between|whereas|whether) )'), r' \\1'))

# no sentence breaks in the middle of specific abbreviations
__final.append((re.compile(r'\\b(e\\.)\\n(g\\.)'), r'\\1 \\2'))
__final.append((re.compile(r'\\b(i\\.)\\n(e\\.)'), r'\\1 \\2'))
__final.append((re.compile(r'\\b(i\\.)\\n(v\\.)'), r'\\1 \\2'))

# no sentence break after specific abbreviations
__final.append(
    (re.compile(r'\\b(e\\. ?g\\.|i\\. ?e\\.|i\\. ?v\\.|vs\\.|cf\\.|Dr\\.|Mr\\.|Ms\\.|Mrs\\.)\\n'),
     r'\\1 '))

# or others taking a number after the abbrev
__final.append(
    (re.compile(r'\\b([Aa]pprox\\.|[Nn]o\\.|[Ff]igs?\\.)\\n(\\d+)'), r'\\1 \\2'))

# no break before comma (e.g. Smith, A., Black, B., ...)
__final.append((re.compile(r'(\\.\\s*)\\n(\\s*,)'), r'\\1 \\2'))


def refine_split(s):
    """Given a string with sentence splits as newlines, attempts to
    heuristically improve the splitting.

    Heuristics tuned for geniass sentence splitting errors.
    """

    if DEBUG_SS_POSTPROCESSING:
        orig = s

    for r, t in __initial:
        s = r.sub(t, s)

    for r, t in __repeated:
        while True:
            n = r.sub(t, s)
            if n == s:
                break
            s = n

    for r, t in __final:
        s = r.sub(t, s)

    # Only do final comparison in debug mode.
    if DEBUG_SS_POSTPROCESSING:
        # revised must match original when differences in space<->newline
        # substitutions are ignored
        r1 = orig.replace('\\n', ' ')
        r2 = s.replace('\\n', ' ')
        if r1 != r2:
            print("refine_split(): error: text mismatch (returning original):\\nORIG: '%s'\\nNEW:  '%s'" % (orig, s), file=sys.stderr)
            s = orig

    return s


if __name__ == "__main__":
    import sys
    import codecs

    # for testing, read stdin if no args
    if len(sys.argv) == 1:
        sys.argv.append('/dev/stdin')

    for fn in sys.argv[1:]:
        try:
            with codecs.open(fn, encoding=INPUT_ENCODING) as f:
                s = "".join(f.read())
                sys.stdout.write(refine_split(s).encode(OUTPUT_ENCODING))
        except Exception as e:
            print("Failed to read", fn, ":", e, file=sys.stderr)

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