cothec / brat4ref

Commit 95d114a2cbdae056d12e9ec32d5939aeea4ee0d2

Authored by Bartłomiej Nitoń
1 parent 9484ca64

Added BRAT configurations for COTHEC project.

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Showing 3 changed files with 222 additions and 0 deletions
configurations/COTHEC/annotation.conf 0 → 100755
  View file @95d114a
  1 +# -*- Mode: Text; tab-width: 8; indent-tabs-mode: nil; coding: utf-8; -*-
  2 +# vim:set ft=conf ts=2 sw=2 sts=2 autoindent:
  3 +
  4 +# Simple text-based definitions of entity, relation and event types
  5 +# and event attributes for the BioNLP Shared Task 2011 EPI task.
  6 +
  7 +
  8 +[entities]
  9 +
  10 +Mention
  11 +
  12 +[relations]
  13 +
  14 +Coref Arg1:Mention, Arg2:Mention, <REL-TYPE>:symmetric-transitive
  15 +target Arg1:Mention, Arg2:Mention, <REL-TYPE>:symmetric
  16 +indirect_aggregation Arg1:Mention, Arg2:Mention, <REL-TYPE>:symmetric
  17 +indirect_composition Arg1:Mention, Arg2:Mention, <REL-TYPE>:symmetric
  18 +indirect_bound Arg1:Mention, Arg2:Mention, <REL-TYPE>:symmetric
  19 +indirect_other Arg1:Mention, Arg2:Mention, <REL-TYPE>:symmetric
  20 +supporting_metareference Arg1:Mention, Arg2:Mention, <REL-TYPE>:symmetric
  21 +supporting_comparison Arg1:Mention, Arg2:Mention, <REL-TYPE>:symmetric
  22 +supporting_predicative Arg1:Mention, Arg2:Mention, <REL-TYPE>:symmetric
  23 +supporting_other Arg1:Mention, Arg2:Mention, <REL-TYPE>:symmetric
  24 +excluding_contrast Arg1:Mention, Arg2:Mention, <REL-TYPE>:symmetric
  25 +excluding_ios Arg1:Mention, Arg2:Mention, <REL-TYPE>:symmetric
  26 +excluding_polysemy Arg1:Mention, Arg2:Mention, <REL-TYPE>:symmetric
  27 +excluding_other Arg1:Mention, Arg2:Mention, <REL-TYPE>:symmetric
  28 +
  29 +<OVERLAP> Arg1:Mention, Arg2:Mention, <OVL-TYPE>:contain|cross
  30 +
  31 +[events]
  32 +
  33 +
  34 +[attributes]
  35 +
configurations/COTHEC/tools.conf 0 → 100755
  View file @95d114a
  1 +[options]
  2 +
  3 +# Possible values for validate:
  4 +# - all: perform full validation
  5 +# - none: don't perform any validation
  6 +Validation validate:all
  7 +
  8 +# Possible values for tokenizer
  9 +# - ptblike: emulate Penn Treebank tokenization
  10 +# - mecab: perform Japanese tokenization using MeCab
  11 +# - whitespace: split by whitespace characters in source text (only)
  12 +Tokens tokenizer:whitespace
  13 +
  14 +# Possible values for splitter:
  15 +# - regex : regular expression-based sentence splitting
  16 +# - newline: split by newline characters in source text (only)
  17 +Sentences splitter:newline
  18 +
  19 +# Possible values for logfile:
  20 +# - <NONE> : no annotation logging
  21 +# - NAME : log into file NAME (e.g. "/home/brat/annotation.log")
  22 +Annotation-log logfile:<NONE>
  23 +
  24 +[search]
  25 +
  26 +# Search option configuration. Configured queries will be available in
  27 +# text span annotation dialogs. When selected on the UI, these open
  28 +# the given URL ("<URL>") with the string "%s" replaced with the
  29 +# selected text span.
  30 +
  31 +#Google <URL>:http://www.google.com/search?q=%s
  32 +#Wikipedia <URL>:http://en.wikipedia.org/wiki/Special:Search?search=%s
  33 +
  34 +[annotators]
  35 +
  36 +# Automatic annotation service configuration. The values of "tool" and
  37 +# "model" are required for the UI, and "<URL>" should be filled with
  38 +# the URL of the web service. See the brat documentation for more
  39 +# information.
  40 +
  41 +# Examples:
  42 +# Random tool:Random, model:Random, <URL>:http://localhost:47111/
  43 +# Stanford-CoNLL-MUC tool:Stanford_NER, model:CoNLL+MUC, <URL>:http://127.0.0.1:47111/
  44 +# NERtagger-GENIA tool:NERtagger, model:GENIA, <URL>:http://example.com:8080/tagger/
  45 +
  46 +[disambiguators]
  47 +
  48 +# Automatic semantic disambiguation service configuration. The values
  49 +# of "tool" and "model" are required for the UI, and "<URL>" should be
  50 +# filled with the URL of the web service. See the brat documentation
  51 +# for more information.
  52 +
  53 +# Example:
  54 +# simsem-GENIA tool:simsem, model:GENIA, <URL>:http://example.com:8080/tagger/%s
  55 +
  56 +[normalization]
  57 +
  58 +# Configuration for normalization against external resources. The
  59 +# resource name (first field of each line) should match that of a
  60 +# normalization DB on the brat server (see tools/norm_db_init.py),
  61 +# "<URL>" should be filled with the URL of the resource (preferably
  62 +# one providing a serach interface), and "<URLBASE>" should be a
  63 +# string containing "%s" that, when replacing "%s" with an ID in
  64 +# the external resource, becomes a link to a page representing
  65 +# the entry corresponding to the ID in that resource.
  66 +
  67 +# Example
  68 +#UniProt <URL>:http://www.uniprot.org/, <URLBASE>:http://www.uniprot.org/uniprot/%s
  69 +#GO <URL>:http://www.geneontology.org/, <URLBASE>:http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:%s
  70 +#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
  71 +#Wikipedia <URL>:http://en.wikipedia.org, <URLBASE>:http://en.wikipedia.org/?curid=%s
configurations/COTHEC/visual.conf 0 → 100755
  View file @95d114a
  1 +# -*- Mode: Text; tab-width: 8; indent-tabs-mode: nil; coding: utf-8; -*-
  2 +# vim:set ft=conf ts=2 sw=2 sts=2 autoindent:
  3 +
  4 +# Note: this visual.conf is a combination of visual configurations for
  5 +# a number of tasks that brat has been applied to. These settings are
  6 +# here to provide defaults for new installations, and are not intended
  7 +# to be used for reference or a starting point for creating new
  8 +# visual.conf files. For simple, clean examples, see the visual.conf
  9 +# files in subdirectories of configurations/.
  10 +
  11 +[labels]
  12 +
  13 +# Label definitions for display. The labels are separated by pipe
  14 +# characters "|".
  15 +
  16 +# The first label must correspond to the form found first in other
  17 +# configuration files. As this form must be valid for use in e.g. the
  18 +# BioNLP ST standoff format, it must have only ASCII alphanumerics,
  19 +# "_" or "-" (i.e. match '^[a-zA-Z0-9_-]$').
  20 +
  21 +# Labels other than the first define forms that are presented to the
  22 +# user in the annotation interface, with the first form being the
  23 +# preferred full form and the others abbreviations that will be used
  24 +# if fuller forms do not fit in the given space. These have no format
  25 +# restrictions and can contain e.g. space (this tends to make the
  26 +# first and second columns identical for most terms, which do not
  27 +# contain space). Surrounding space is ignored.
  28 +
  29 +### Entity types
  30 +
  31 +Mention | Mention | Men | M
  32 +
  33 +### Relation types
  34 +
  35 +Coref | Coreference | Coref | Co
  36 +target | Target | Target | T
  37 +indirect_aggregation | Indirect Aggregation | Aggregation | IAgr
  38 +indirect_composition | Indirect Composition | Composition | IComp
  39 +indirect_bound | Bound Anaphora | Bound | IB
  40 +indirect_other | Indirect Other | Indirect Other | IOth
  41 +supporting_metareference | Supporting Metareference | Metareference | SMet
  42 +supporting_comparison | Supporting Comparison | Comparison | SComp
  43 +supporting_predicative | Supporting Predicate | Predicate | SPred
  44 +supporting_other | Supporting Other | Supporting Other | SOth
  45 +excluding_contrast | Excluding Contrast | Contrast | ExCont
  46 +excluding_ios | Excluding IOS | IOS | ExIOS
  47 +excluding_polysemy | Excluding Polysemy | Polysemy | ExPol
  48 +excluding_other | Excluding Other | Excluding Other | ExOth
  49 +
  50 +
  51 +[drawing]
  52 +
  53 +# Other aspects of visual presentation. The format is label (form used
  54 +# in other configurations, first of the labels) of the annotation
  55 +# separated by tab from comma-separated key:value pairs. The recognized
  56 +# keys, their values and purpose are:
  57 +# - fgColor : any HTML color specification (e.g. "black"), sets
  58 +# the color of a span text in the visualization.
  59 +# - bgColor : any HTML color specification (e.g. "white"), sets
  60 +# the color of a span "box" background in the visualization.
  61 +# - borderColor : any HTML color specification (e.g. "black"), sets
  62 +# the color of a span "box" border in the visualization.
  63 +# Also supports special value "darken", which specifies to
  64 +# use a darker shade of bgColor for the border.
  65 +# - color : any HTML color specification (e.g. "black"), sets
  66 +# the color of an arc in the visualization.
  67 +# - dashArray : any valid SVG stroke-dasharray specification using
  68 +# dashes (instead of commas or space) as separators
  69 +# (e.g. "3-3"), sets the dash/dot pattern for lines
  70 +# in the span/arc visualization ("-" works for solid
  71 +# line)
  72 +# The special labels "SPAN_DEFAULT" and "ARC_DEFAULT" are recognized
  73 +# as setting defaults that will be used for types without specific
  74 +# settings. It is not necessary to define all aspects of the
  75 +# visualization (e.g. just Color can be given): defaults will be
  76 +# used for unspecified cases.
  77 +
  78 +
  79 +SPAN_DEFAULT fgColor:black, bgColor:#FFFF99, borderColor:darken
  80 +ARC_DEFAULT color:black, arrowHead:triangle-5
  81 +
  82 +Equiv dashArray:3-3, arrowHead:none
  83 +Part-of color:blue
  84 +
  85 +target color:blue
  86 +indirect_aggregation color:#CB4D8D
  87 +indirect_composition color:#DC352F
  88 +indirect_bound color:#3EADE2
  89 +indirect_other color:#529657
  90 +supporting_metareference color:#E79B9F
  91 +supporting_comparison color:#7FC7C3
  92 +supporting_predicative color:#BB812D
  93 +supporting_other color:#E9C006
  94 +excluding_contrast color:#E0792C
  95 +excluding_ios color:#BF302C
  96 +excluding_polysemy color:#C7DD3C
  97 +excluding_other color:#000000
  98 +
  99 +# entity span colors
  100 +
  101 +ATTRIBUTE_DEFAULT glyph:*
  102 +
  103 +Plant glyph:☘
  104 +Pathological glyph:☠, position:left
  105 +Developing glyph:↗
  106 +Processed glyph:⚡
  107 +
  108 +[options]
  109 +
  110 +# Currently, only Arcs bundle is supported here
  111 +# Possible values:
  112 +# * none: do not bundle arcs
  113 +# * all: bundle all arcs
  114 +# * space: pack space, but do not bundle arcs
  115 +# (actually, any value other than "none" and "all")
  116 +Arcs bundle:all