NLP标注工具brat 配置文件说明

快速搭建brat

通过docker：

docker run --name=brat -d -p 38080:80 -e BRAT_USERNAME=brat -e BRAT_PASSWORD=brat -e BRAT_EMAIL=brat@example.com cassj/brat

启动会拉取镜像，耐心等待，然后打开IP:38080,使用brat，brat登录

braf 的四类配置文件

the configuration of an annotation project is controlled by four files:

annotation.conf: 标记类型 configuration
visual.conf: annotation显示配置
tools.conf: annotation工具配置
kb_shortcuts.conf: 键盘快捷键 keyboard shortcut tool configuration

annotation.conf

标记配置文件

# 实体类型

[entities]

# 每行一个实体类型

Protein

Simple_chemical

Complex

Organism

# 事件

[events]

# 事件名称  参数名称：参数类型

Gene_expression Theme:Protein

Binding Theme+:Protein

Positive_regulation Theme:<EVENT>|Protein, Cause?:<EVENT>|Protein

Negative_regulation Theme:<EVENT>|Protein, Cause?:<EVENT>|Protein

# 关系

[relations]

# 关系名称 关系的属性，syntax ARG:TYPE (where ARG are, by convention, Arg1 and Arg2)

Part-of Arg1:Protein, Arg2:Complex

Member-of Arg1:Protein, Arg2:Complex

# TODO: Should these really be called "Equivalent" instead of "Equiv"?

Equiv Arg1:Protein, Arg2:Protein, <REL-TYPE>:symmetric-transitive

Equiv Arg1:Simple_chemical, Arg2:Simple_chemical, <REL-TYPE>:symmetric-transitive

Equiv Arg1:Organism, Arg2:Organism, <REL-TYPE>:symmetric-transitive

# 属性定义

[attributes]

# 名称  参数

Negation        Arg:<EVENT>

Confidence        Arg:<EVENT>, Value:Possible|Likely|Certain

Visual configuration (visual.conf)

可视化configuration包含两部分

[labels]
[drawing]

The [labels] 定义标记类型UI上如何显示：

Simple_chemical | Simple chemical | Chemical

标记类型  |   全称  |  显示文字

使用"|"隔开，第一部分是里定义的

The [drawing] 用于定义显示样式，比如定义标记的颜色等

[labels]

Simple_chemical | Simple chemical | Chemical

Protein | Protein

Complex | Complex

Organism | Organism

Gene_expression | Gene expression | Expression | Expr

Binding | Binding

Regulation | Regulation

Positive_regulation | Positive regulation | +Regulation

Negative_regulation | Negative regulation | -Regulation

Phosphorylation | Phosphorylation | Phos

Equiv | Equiv

Theme  | Theme

Cause  | Cause

Participant | Participant

[drawing]

SPAN_DEFAULT	fgColor:black, bgColor:lightgreen, borderColor:darken

ARC_DEFAULT	color:black, arrowHead:triangle-5

ATTRIBUTE_DEFAULT	glyph:*

Protein	bgColor:#7fa2ff

Simple_chemical	bgColor:#8fcfff

Complex	bgColor:#8f97ff

Organism	bgColor:#ffccaa

Positive_regulation	bgColor:#e0ff00

Regulation	bgColor:#ffff00

Negative_regulation	bgColor:#ffe000

Cause	color:#007700

Equiv	dashArray:3-3, arrowHead:none

Negation	box:crossed, glyph:<NONE>, dashArray:<NONE>

Confidence	dashArray:3-6|3-3|-, glyph:<NONE>

工具栏配置 (tools.conf)

The annotation tool configuration file, tools.conf, is divided into the following sections:

[options]
[search]
[normalization]
[annotators]
[disambiguators]

These sections are all optional: an empty file is a vali

Option configuration ([options] section)

[options] 用来配置服务端如何处理分词、分局、验证、日志等:

Tokens tokenizer:VALUE, where VALUE=
- whitespace: split by whitespace characters in source text (only)
- ptblike: emulate Penn Treebank tokenization
- mecab: perform Japanese tokenization using MeCab
Sentences splitter:VALUE, where VALUE=
- regex: regular expression-based sentence splitting
- newline: split by newline characters in source text (only)
Validation validate:VALUE, where VALUE=
- all: perform full validation
- none: don't perform any validation
Annotation-log logfile:VALUE, where VALUE=
- <NONE>: no annotation logging
- NAME: log into file NAME (e.g. "/home/brat/work/annotation.log")

For example, the following [options] section gives the default brat configuration before v1.3:

[options]
Tokens	tokenizer:whitespace
Sentences	splitter:regex
Validation	validate:none
Annotation-log	logfile:

The following [options] section enables Japanese tokenization using MeCab, sentence splitting only by newlines, full validation, and annotation logging into the given file. (In setting Annotation-log logfile, remember to make sure the web server has appropriate write permissions to the file.)

[options]
Tokens	tokenizer:mecab
Sentences	splitter:newline
Validation	validate:all
Annotation-log	logfile:/home/brat/work/annotation.log

Normalization DB configuration ([normalization] section)

The [normalization] section defines the normalization resources that are available. For information on setting up normalization DBs, see the brat normalization documentation.

Each line in the [normalization] section has the following syntax:

    DBNAME     DB:DBPATH, <URL>:HOMEURL, <URLBASE>:ENTRYURL

Here, DB, <URL>, <URLBASE> and <PATH> are literal strings (they should appear as written here), while "DBNAME", "DBPATH", "HOMEURL" and "ENTRYURL" should be replaced with specific values appropriate for the database being configured:

DBNAME: sets the database name (e.g. "Wiki", "GO"). The name can be otherwise freely selected, but should not contain characters other than alphanumeric ("a"-"z", "A"-"Z", "0"-"9"), hyphen ("-") and underscore ("_"). This name will be used both in the brat UI and in the annotation file to identify the DB.
DBPATH (optional): provides the file system path to the normalization DB data on the server, relative to the brat server root. If DBPATH isn't set, the system assumes the DB can be found in the default location under the given DBNAME.
HOMEURL: sets the URL for the home page of the normalization resource (e.g. "http://en.wikipedia.org/wiki/"). Used both to identify the resource more specifically than DBNAME and to provide a link in the annotation UI for accessing the resource.
URLBASE (optional): sets a URL template (e.g. "http://en.wikipedia.org/?curid=%s") that can be filled in to generate a direct link in the annotation UI to an entry in the normalization resource. The value should contain the characters "%s" as a placeholder that will be replaced with the ID of the entry.

The following example shows examples of configured normalization DBs.

[normalization]
Wiki	DB:dbs/wiki, :http://en.wikipedia.org, :http://en.wikipedia.org/?curid=%s
UniProt	:http://www.uniprot.org/, :http://www.uniprot.org/uniprot/%s

The first line sets configuration for a database called "Wiki", found as "dbs/wiki" in the brat server directory, and the second for a DB called "UniProt", found in the default location for a DB with this name.

搜索配置 ([search] section)

The [search] 用来配置在线搜索，这样选中一个词语后，可以点击搜索链接进行搜索。

Each line in the [search] section contains the name used in the user interface for the search service, and a single key:value pair. The key should have the special value "" and its value should be the URL URL of the search service with the string to query for replaced by "%s".

The following example shows a simple [search] section.

[search]
Google	:http://www.google.com/search?q=%s
Wikipedia	:http://en.wikipedia.org/wiki/%s

When selecting a span or editing an annotation, these search options will then be shown in the brat annotation dialog.

Annotation tool configuration ([annotators] section)

The [annotators] section defines automatic annotation services that can be invoked from brat.

Each line in the [annotators] section contains a unique name for the service and key:value pairs defining the way it is presented in the user interface and the URL of the web service for the tool. Values should be given for "tool", "model" and "" (the first two are used for the user interface only).

The following example shows a simple [annotators] section.

[annotators]
SNER-CoNLL	tool:Stanford_NER, model:CoNLL, :http://example.com:80/tagger/

Disambiguation tool configuration ([disambiguators] section)

The [disambiguators] section defines automatic semantic class (annotation type) disambiguation services that can be invoked from brat.

Each line in the [disambiguators] section contains a unique name for the service and key:value pairs defining the way it is presented in the user interface and the URL of the web service for the tool. Values should be given for "tool", "model" and "" (the first two are used for the user interface only).

The following example shows a simple [disambiguators] section.

[disambiguators]
simsem-MUC	tool:simsem, model:MUC, :http://example.com:80/simsem/%s

As for search, the string to query for is identified by "%s" in the URL.

来看一个demo:

[options]

# Possible values for validate:

# - all: perform full validation

# - none: don't perform any validation

Validation	validate:all

# Possible values for tokenizer

# - ptblike: emulate Penn Treebank tokenization

# - mecab: perform Japanese tokenization using MeCab

# - whitespace: split by whitespace characters in source text (only)

Tokens	   tokenizer:whitespace

# Possible values for splitter:

# - regex  : regular expression-based sentence splitting

# - newline: split by newline characters in source text (only)

Sentences	splitter:newline

# Possible values for logfile:

# - <NONE> : no annotation logging

# - NAME : log into file NAME (e.g. "/home/brat/annotation.log")

Annotation-log logfile:<NONE>

[search]

# Search option configuration. Configured queries will be available in

# text span annotation dialogs. When selected on the UI, these open

# the given URL ("<URL>") with the string "%s" replaced with the

# selected text span.

Google       <URL>:http://www.google.com/search?q=%s

Wikipedia    <URL>:http://en.wikipedia.org/wiki/Special:Search?search=%s

UniProt      <URL>:http://www.uniprot.org/uniprot/?sort=score&query=%s

EntrezGene   <URL>:http://www.ncbi.nlm.nih.gov/gene?term=%s

GeneOntology <URL>:http://amigo.geneontology.org/cgi-bin/amigo/search.cgi?search_query=%s&action=new-search&search_constraint=term

ALC          <URL>:http://eow.alc.co.jp/%s

[annotators]

# Automatic annotation service configuration. The values of "tool" and

# "model" are required for the UI, and "<URL>" should be filled with

# the URL of the web service. See the brat documentation for more

# information.

# Examples:

# Random              tool:Random, model:Random, <URL>:http://localhost:47111/

# Stanford-CoNLL-MUC  tool:Stanford_NER, model:CoNLL+MUC, <URL>:http://127.0.0.1:47111/

# NERtagger-GENIA     tool:NERtagger, model:GENIA, <URL>:http://example.com:8080/tagger/

[disambiguators]

# Automatic semantic disambiguation service configuration. The values

# of "tool" and "model" are required for the UI, and "<URL>" should be

# filled with the URL of the web service. See the brat documentation

# for more information.

# Example:

# simsem-GENIA    tool:simsem, model:GENIA, <URL>:http://example.com:8080/tagger/%s

[normalization]

# Configuration for normalization against external resources. The

# resource name (first field of each line) should match that of a

# normalization DB on the brat server (see tools/norm_db_init.py),

# "<URL>" should be filled with the URL of the resource (preferably

# one providing a serach interface), and "<URLBASE>" should be a

# string containing "%s" that, when replacing "%s" with an ID in

# the external resource, becomes a link to a page representing

# the entry corresponding to the ID in that resource.

# Example

#UniProt    <URL>:http://www.uniprot.org/, <URLBASE>:http://www.uniprot.org/uniprot/%s

#GO    <URL>:http://www.geneontology.org/, <URLBASE>:http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:%s

#FMA    <URL>:http://fme.biostr.washington.edu/FME/index.html, <URLBASE>:http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=FMA&termId=FMA:%s

快捷键

选中标记后，键盘上按快捷键，可以快速切换选项

P       Protein

S Simple_chemical

X Complex

O Organism

C Cause

T Theme

作者：Jadepeng

出处：jqpeng的技术记事本--http://www.cnblogs.com/xiaoqi

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