1、下载、解压brat
https://github.com/nlplab/brat/releases/tag/v1.3p1
tar xzf brat-v1.3_Crunchy_Frog.tar.gz
2、系统安装httpd
centos6
开启httpd：service httpd start
重启httpd：service httpd restart
关闭httpd：service httpd stop
3、进入brat目录，执行安装
./install.sh
安装过程中会提示输入用户名、密码、邮箱信息，用户名和密码用于web浏览器用户登录。
4、添加用户
找到brat/config.py 对应的行，增加：
USER_PASSWORD = { 'admn': 'admin', 'test': 'test', # (add USERNAME:PASSWORD pairs below this line.) }
4、配置支持中文
vim /var/www/html/brat/server/src/projectconfig.py
找到n = re.sub(r'[^a-zA-Z0-9_-]', '_', n)这一行并修改：
n = re.sub(u'[^a-zA-Zu4e00-u9fa5<>,0-9_-]', '_', n)
5、增加测试文件
在data/目录新建hero测试目录，然后在hero目录里面新建文档test1.txt,test2.txt,test3.txt，随便写点内容进去，然后在brat目录下执行命令：
find data -name '*.txt' | sed -e 's|.txt|.ann|g' | xargs touch
6、开启服务
在centos中启动 brat ：cd brat-v1.3_Crunchy_Frog 运行python standalone.py
7、在web中访问
http://192.168.2.190:8001/index.xhtml
备注：
在data目录下创建diag目录，此目录下添加配置文件，annotation.conf文件为实体和关系对应的英文名称，visual.conf为实体和关系对应的中文名称
kwz目录为kwz标注人员分配的标注文件，里面是.txt和.ann文件
下面贴出具体的配置文件内容
annotation.conf
# Simple text-based definitions of hierarchial ontologies of # (physical) entity types, relation types, event types, and # attributes. # This is a minimal example configuration, based (loosely) on some # ACE'05 entity, relation and event definitions # (http://projects.ldc.upenn.edu/ace/annotation/2005Tasks.html). # Please edit this according to the needs of your annotation. [entities] # Definition of entities. # Format is a simple list with one type per line. ThemeDisease ThemeOperation ICD -------------------- DiagnosticBasisSymptom DiagnosticBasisRiskFactors DiagnosticBasisExamination DiagnosticBasisExaminationResult DifferentialDiagnoses -------------------- StandardTimeOfHospitalization NecessaryExaminationAdmission OptionalExaminationAdmission DrugForTreatment Treatment IndicationForTreatment ContraindicationForTreatment -------------------- Complications DrugBeforeTreatment MeasureBeforeTreatment ExaminationBeforeTreatment -------------------- !AboutOperation OperationName DataOfOperation AnesthesiaMode DrugDuringOperation SurgicalApproach InstrumentUsedInOperation InstrumentIntoBody BloodTransfusionDuringOperation ExaminationDuringTreatment DrugAfterTreatment MeasureAfterTreatment ExaminationAfterTreatment -------------------- InformedConsent -------------------- Delete [relations] # Definition of (binary) relations. # Format in brief: one relation per line, with first space-separated # field giving the relation type and the rest of the line the # comma-separated arguments in ROLE:TYPE format. The roles are # typically "Arg1" and "Arg2". #Located Arg1:Person, Arg2:GPE #Geographical_part Arg1:GPE, Arg2:GPE #Family Arg1:Person, Arg2:Person #Employment Arg1:Person, Arg2:GPE #Ownership Arg1:Person, Arg2:Organization #Origin Arg1:Organization, Arg2:GPE #Alias Arg1:Person, Arg2:Person, <REL-TYPE>:symmetric-transitive DiagnosticBasisExaminationDiagnosticBasisExaminationResult Arg1:DiagnosticBasisExamination,Arg2:DiagnosticBasisExaminationResult IndicationForTreatmentTreatment Arg1:IndicationForTreatment,Arg2:Treatment IndicationForTreatmentDrugForTreatment Arg1:IndicationForTreatment,Arg2:DrugForTreatment IndicationForTreatmentDrugBeforeTreatment Arg1:IndicationForTreatment,Arg2:DrugBeforeTreatment IndicationForTreatmentMeasureBeforeTreatment Arg1:IndicationForTreatment,Arg2:MeasureBeforeTreatment IndicationForTreatmentDrugAfterTreatment Arg1:IndicationForTreatment,Arg2:DrugAfterTreatment IndicationForTreatmentMeasureAfterTreatment Arg1:IndicationForTreatment,Arg2:MeasureAfterTreatment IndicationForTreatmentOperationName Arg1:IndicationForTreatment,Arg2:OperationName DrugForTreatmentClassItemDrugForTreatment Arg1:DrugForTreatment,Arg2:DrugForTreatment ComplicationsTreatment Arg1:Complications,Arg2:Treatment ComplicationsDrugForTreatment Arg1:Complications,Arg2:DrugForTreatment ComplicationsDrugBeforeTreatment Arg1:Complications,Arg2:DrugBeforeTreatment ComplicationsMeasureBeforeTreatment Arg1:Complications,Arg2:MeasureBeforeTreatment ComplicationsDrugAfterTreatment Arg1:Complications,Arg2:DrugAfterTreatment ComplicationsMeasureAfterTreatment Arg1:Complications,Arg2:MeasureAfterTreatment ThemeDiseaseDiagnosticBasisSymptom Arg1:ThemeDisease,Arg2:DiagnosticBasisSymptom ThemeDiseaseDiagnosticBasisRiskFactors Arg1:ThemeDisease,Arg2:DiagnosticBasisRiskFactors ThemeDiseaseDiagnosticBasisExamination Arg1:ThemeDisease,Arg2:DiagnosticBasisExamination ThemeDiseaseDiagnosticBasisExaminationResult Arg1:ThemeDisease,Arg2:DiagnosticBasisExaminationResult ThemeDiseaseDifferentialDiagnoses Arg1:ThemeDisease,Arg2:DifferentialDiagnoses ContraindicationForTreatmentTreatment Arg1:ContraindicationForTreatment,Arg2:Treatment ContraindicationForTreatmentDrugForTreatment Arg1:ContraindicationForTreatment,Arg2:DrugForTreatment ContraindicationForTreatmentDrugBeforeTreatment Arg1:ContraindicationForTreatment,Arg2:DrugBeforeTreatment ContraindicationForTreatmentMeasureBeforeTreatment Arg1:ContraindicationForTreatment,Arg2:MeasureBeforeTreatment ContraindicationForTreatmentDrugAfterTreatment Arg1:ContraindicationForTreatment,Arg2:DrugAfterTreatment ContraindicationForTreatmentMeasureAfterTreatment Arg1:ContraindicationForTreatment,Arg2:MeasureAfterTreatment ContraindicationForTreatmentOperationName Arg1:ContraindicationForTreatment,Arg2:OperationName ThemeDiseaseICD Arg1:ThemeDisease,Arg2:ICD ThemeOperationICD Arg1:ThemeOperation,Arg2:ICD [events] # Definition of events. # Format in brief: one event per line, with first space-separated # field giving the event type and the rest of the line the # comma-separated arguments in ROLE:TYPE format. Arguments may be # specified as either optional (by appending "?" to role) or repeated # (by appending either "*" for "0 or more" or "+" for "1 or more"). # this is a macro definition, used for brevity <POG>=Person|Organization|GPE # the "!" before a type specifies that it cannot be used for annotation # (hierarchy structure only.) # !Life # Be-born Person-Arg:Person, Place-Arg?:GPE # Marry Person-Arg{2}:Person, Place-Arg?:GPE # Divorce Person-Arg{2}:Person, Place-Arg?:GPE # Die Person-Arg:Person, Agent-Arg?:<POG>, Place-Arg?:GPE # Report Reporter-Arg:<POG>, Event-Arg:<EVENT> [attributes] # Definition of entity and event attributes. # Format in brief: first tab-separated field is attribute name, second # a set of key-value pairs. The latter must define "Arg:" which # specifies what the attribute can attach to (typically "<EVENT>"). # If no other keys are defined, the attribute is binary (present or # absent). If "Value:" with multiple alternatives is defined, the # attribute can have one of the given values. Individual Arg:<ENTITY> Mention Arg:<ENTITY>, Value:Name|Nominal|Other Negation Arg:<EVENT> Confidence Arg:<EVENT>, Value:High|Neutral|Low
visual.conf：
# -*- Mode: Text; tab- 8; indent-tabs-mode: nil; coding: utf-8; -*- # vim:set ft=conf ts=2 sw=2 sts=2 autoindent: [labels] # Label definitions for display. The labels are separated by pipe # characters "|". # The first label must correspond to the form found first in other # configuration files. As this form must be valid for use in e.g. the # BioNLP ST standoff format, it must have only ASCII alphanumerics, # "_" or "-" (i.e. match '^[a-zA-Z0-9_-]$'). # Labels other than the first define forms that are presented to the # user in the annotation interface, with the first form being the # preferred full form and the others abbreviations that will be used # if fuller forms do not fit in the given space. These have no format # restrictions and can contain e.g. space (this tends to make the # first and second columns identical for most terms, which do not # contain space). Surrounding space is ignored. ### Entity types #Person | Person #Organization | Organization | Org #GPE | Geo-political entity | GPE ThemeDisease | 临床路径适用疾病 ThemeOperation | 临床路径适用手术或操作 ICD | ICD编码 DiagnosticBasisSymptom | 诊断依据临床表现 DiagnosticBasisRiskFactors | 诊断依据危险因素 DiagnosticBasisExamination | 诊断相关检查 DiagnosticBasisExaminationResult | 诊断依据检查结果 DifferentialDiagnoses | 鉴别诊断 StandardTimeOfHospitalization | 标准住院日 NecessaryExaminationAdmission | 入院必需检查 OptionalExaminationAdmission | 入院可选检查 DrugForTreatment | 治疗药物 Treatment | 治疗方式 IndicationForTreatment | 治疗适应症 ContraindicationForTreatment | 治疗禁忌症 Complications | 需要处理的并发症 DrugBeforeTreatment | 治疗前药物 MeasureBeforeTreatment | 治疗前处置 ExaminationBeforeTreatment | 治疗前检查 AboutOperation | 手术相关 OperationName | 手术名称 DataOfOperation | 手术日 AnesthesiaMode | 麻醉方式 DrugDuringOperation | 术中用药 SurgicalApproach | 手术入路 InstrumentUsedInOperation | 使用的器械或耗材 InstrumentIntoBody | 植介入器械 BloodTransfusionDuringOperation | 手术输血情况 ExaminationDuringTreatment | 治疗中检查或监测 DrugAfterTreatment | 治疗后药物 MeasureAfterTreatment | 治疗后处置 ExaminationAfterTreatment | 治疗后检查 InformedConsent | 必要的知情同意文书 Delete | 删除重复文档 ### Event types Be-born | Be born Transfer-ownership | Transfer ownership Transfer-money | Transfer money Start-org | Start org Merge-org | Merge org End-org | End org ### Relation types Geographical_part | Geographical part | Geo part Employment | Employment | Employ DiagnosticBasisExaminationDiagnosticBasisExaminationResult | 诊断相关检查-诊断依据检查结果 IndicationForTreatmentTreatment | 治疗适应症-治疗方式 IndicationForTreatmentDrugForTreatment | 治疗适应症-治疗药物 IndicationForTreatmentDrugBeforeTreatment | 治疗适应症-治疗前药物 IndicationForTreatmentMeasureBeforeTreatment | 治疗适应症-治疗前处置 IndicationForTreatmentDrugAfterTreatment | 治疗适应症-治疗后药物 IndicationForTreatmentMeasureAfterTreatment | 治疗适应症-治疗后处置 IndicationForTreatmentOperationName | 治疗适应症-手术名称 DrugForTreatmentClassItemDrugForTreatment | 治疗药物-大类-细项-治疗药物 ComplicationsTreatment | 治疗适应症-治疗方式 ComplicationsDrugForTreatment | 治疗适应症-治疗药物 ComplicationsDrugBeforeTreatment | 需要处理的并发症-治疗前药物 ComplicationsMeasureBeforeTreatment | 需要处理的并发症-治疗前处置 ComplicationsDrugAfterTreatment | 需要处理的并发症-治疗后药物 ComplicationsMeasureAfterTreatment | 需要处理的并发症-治疗后处置 ThemeDiseaseDiagnosticBasisSymptom | 临床路径适用疾病-诊断依据临床表现 ThemeDiseaseDiagnosticBasisRiskFactors | 临床路径适用疾病-诊断依据危险因素 ThemeDiseaseDiagnosticBasisExamination | 临床路径适用疾病-诊断相关检查 ThemeDiseaseDiagnosticBasisExaminationResult | 临床路径适用疾病-诊断依据检查结果 ThemeDiseaseDifferentialDiagnoses | 临床路径适用疾病-鉴别诊断 ContraindicationForTreatmentTreatment | 治疗禁忌症-治疗方式 ContraindicationForTreatmentDrugForTreatment | 治疗禁忌症-治疗药物 ContraindicationForTreatmentDrugBeforeTreatment | 治疗禁忌症-治疗前药物 ContraindicationForTreatmentMeasureBeforeTreatment | 治疗禁忌症-治疗前处置 ContraindicationForTreatmentDrugAfterTreatment | 治疗禁忌症-治疗后药物 ContraindicationForTreatmentMeasureAfterTreatment | 治疗禁忌症-治疗后处置 ContraindicationForTreatmentOperationName | 治疗禁忌症-手术名称 ThemeDiseaseICD | 临床路径适用疾病-ICD编码 ThemeOperationICD | 临床路径适用手术或操作-ICD编码 ### Role types Agent-Arg | Agent Artifact-Arg | Artifact Beneficiary-Arg | Beneficiary Buyer-Arg | Buyer Event-Arg | Event Giver-Arg | Giver Money-Arg | Money Org-Arg | Org Person-Arg | Person Place-Arg | Place Recipient-Arg | Recipient Reporter-Arg | Reporter Seller-Arg | Seller [drawing] # Other aspects of visual presentation. The format is label (form used # in other configurations, first of the labels) of the annotation # separated by tab from comma-separated key:value pairs. The recognized # keys, their values and purpose are: # - fgColor : any HTML color specification (e.g. "black"), sets # the color of a span text in the visualization. # - bgColor : any HTML color specification (e.g. "white"), sets # the color of a span "box" background in the visualization. # - borderColor : any HTML color specification (e.g. "black"), sets # the color of a span "box" border in the visualization. # Also supports special value "darken", which specifies to # use a darker shade of bgColor for the border. # - color : any HTML color specification (e.g. "black"), sets # the color of an arc in the visualization. # - dashArray : any valid SVG stroke-dasharray specification using # dashes (instead of commas or space) as separators # (e.g. "3-3"), sets the dash/dot pattern for lines # in the span/arc visualization ("-" works for solid # line) # The special labels "SPAN_DEFAULT" and "ARC_DEFAULT" are recognized # as setting defaults that will be used for types without specific # settings. It is not necessary to define all aspects of the # visualization (e.g. just Color can be given): defaults will be # used for unspecified cases. SPAN_DEFAULT fgColor:black, bgColor:lightgreen, borderColor:darken ARC_DEFAULT color:black, dashArray:-, arrowHead:triangle-5, labelArrow:none # color scheme from # http://www.colourlovers.com/palette/314275/marmalade_skies # 20663F 259959 ABD406 FFD412 FF821C Person bgColor:#FF821C Organization bgColor:#a7c2ff GPE bgColor:#FFD412 Money bgColor:#007000, fgColor:white Alias dashArray:3-3, arrowHead:none Individual glyph:(I) Mention glyph:(N)|(n)|(o), position:left Negation box:crossed, glyph:<NONE>, dashArray:<NONE> Confidence glyph:↑|↔|↓