visual.conf
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# -*- Mode: Text; tab-width: 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.
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]
# 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, 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>