From 95d114a2cbdae056d12e9ec32d5939aeea4ee0d2 Mon Sep 17 00:00:00 2001
From: bniton <bartek.niton@gmail.com>
Date: Thu, 16 Nov 2017 13:22:40 +0100
Subject: [PATCH] Added BRAT configurations for COTHEC project.
---
configurations/COTHEC/annotation.conf | 35 +++++++++++++++++++++++++++++++++++
configurations/COTHEC/tools.conf | 71 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
configurations/COTHEC/visual.conf | 116 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
3 files changed, 222 insertions(+), 0 deletions(-)
create mode 100755 configurations/COTHEC/annotation.conf
create mode 100755 configurations/COTHEC/tools.conf
create mode 100755 configurations/COTHEC/visual.conf
diff --git a/configurations/COTHEC/annotation.conf b/configurations/COTHEC/annotation.conf
new file mode 100755
index 0000000..d8e2468
--- /dev/null
+++ b/configurations/COTHEC/annotation.conf
@@ -0,0 +1,35 @@
+# -*- Mode: Text; tab-width: 8; indent-tabs-mode: nil; coding: utf-8; -*-
+# vim:set ft=conf ts=2 sw=2 sts=2 autoindent:
+
+# Simple text-based definitions of entity, relation and event types
+# and event attributes for the BioNLP Shared Task 2011 EPI task.
+
+
+[entities]
+
+Mention
+
+[relations]
+
+Coref Arg1:Mention, Arg2:Mention, <REL-TYPE>:symmetric-transitive
+target Arg1:Mention, Arg2:Mention, <REL-TYPE>:symmetric
+indirect_aggregation Arg1:Mention, Arg2:Mention, <REL-TYPE>:symmetric
+indirect_composition Arg1:Mention, Arg2:Mention, <REL-TYPE>:symmetric
+indirect_bound Arg1:Mention, Arg2:Mention, <REL-TYPE>:symmetric
+indirect_other Arg1:Mention, Arg2:Mention, <REL-TYPE>:symmetric
+supporting_metareference Arg1:Mention, Arg2:Mention, <REL-TYPE>:symmetric
+supporting_comparison Arg1:Mention, Arg2:Mention, <REL-TYPE>:symmetric
+supporting_predicative Arg1:Mention, Arg2:Mention, <REL-TYPE>:symmetric
+supporting_other Arg1:Mention, Arg2:Mention, <REL-TYPE>:symmetric
+excluding_contrast Arg1:Mention, Arg2:Mention, <REL-TYPE>:symmetric
+excluding_ios Arg1:Mention, Arg2:Mention, <REL-TYPE>:symmetric
+excluding_polysemy Arg1:Mention, Arg2:Mention, <REL-TYPE>:symmetric
+excluding_other Arg1:Mention, Arg2:Mention, <REL-TYPE>:symmetric
+
+<OVERLAP> Arg1:Mention, Arg2:Mention, <OVL-TYPE>:contain|cross
+
+[events]
+
+
+[attributes]
+
diff --git a/configurations/COTHEC/tools.conf b/configurations/COTHEC/tools.conf
new file mode 100755
index 0000000..5d3ce61
--- /dev/null
+++ b/configurations/COTHEC/tools.conf
@@ -0,0 +1,71 @@
+[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
+
+[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
+#Wikipedia <URL>:http://en.wikipedia.org, <URLBASE>:http://en.wikipedia.org/?curid=%s
diff --git a/configurations/COTHEC/visual.conf b/configurations/COTHEC/visual.conf
new file mode 100755
index 0000000..d9e90ca
--- /dev/null
+++ b/configurations/COTHEC/visual.conf
@@ -0,0 +1,116 @@
+# -*- Mode: Text; tab-width: 8; indent-tabs-mode: nil; coding: utf-8; -*-
+# vim:set ft=conf ts=2 sw=2 sts=2 autoindent:
+
+# Note: this visual.conf is a combination of visual configurations for
+# a number of tasks that brat has been applied to. These settings are
+# here to provide defaults for new installations, and are not intended
+# to be used for reference or a starting point for creating new
+# visual.conf files. For simple, clean examples, see the visual.conf
+# files in subdirectories of configurations/.
+
+[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
+
+Mention | Mention | Men | M
+
+### Relation types
+
+Coref | Coreference | Coref | Co
+target | Target | Target | T
+indirect_aggregation | Indirect Aggregation | Aggregation | IAgr
+indirect_composition | Indirect Composition | Composition | IComp
+indirect_bound | Bound Anaphora | Bound | IB
+indirect_other | Indirect Other | Indirect Other | IOth
+supporting_metareference | Supporting Metareference | Metareference | SMet
+supporting_comparison | Supporting Comparison | Comparison | SComp
+supporting_predicative | Supporting Predicate | Predicate | SPred
+supporting_other | Supporting Other | Supporting Other | SOth
+excluding_contrast | Excluding Contrast | Contrast | ExCont
+excluding_ios | Excluding IOS | IOS | ExIOS
+excluding_polysemy | Excluding Polysemy | Polysemy | ExPol
+excluding_other | Excluding Other | Excluding Other | ExOth
+
+
+[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:#FFFF99, borderColor:darken
+ARC_DEFAULT color:black, arrowHead:triangle-5
+
+Equiv dashArray:3-3, arrowHead:none
+Part-of color:blue
+
+target color:blue
+indirect_aggregation color:#CB4D8D
+indirect_composition color:#DC352F
+indirect_bound color:#3EADE2
+indirect_other color:#529657
+supporting_metareference color:#E79B9F
+supporting_comparison color:#7FC7C3
+supporting_predicative color:#BB812D
+supporting_other color:#E9C006
+excluding_contrast color:#E0792C
+excluding_ios color:#BF302C
+excluding_polysemy color:#C7DD3C
+excluding_other color:#000000
+
+# entity span colors
+
+ATTRIBUTE_DEFAULT glyph:*
+
+Plant glyph:☘
+Pathological glyph:☠, position:left
+Developing glyph:↗
+Processed glyph:⚡
+
+[options]
+
+# Currently, only Arcs bundle is supported here
+# Possible values:
+# * none: do not bundle arcs
+# * all: bundle all arcs
+# * space: pack space, but do not bundle arcs
+# (actually, any value other than "none" and "all")
+Arcs bundle:all
--
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