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