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tools.conf
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[options]
# Possible values for validate:
# - all: perform full validation
# - none: don't perform any validation
Validation validate:none
# 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:regex
# 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
PubMed <URL>:http://www.ncbi.nlm.nih.gov/pubmed?term=%s
# SDRF supported ontologies
EFO <URL>:https://www.ebi.ac.uk/ols4/search?lang=en&q=%s&ontology=efo
Unimod <URL>:http://www.ebi.ac.uk/ols4/search?q=%s&ontology=unimod
PSI-MS <URL>:http://www.ebi.ac.uk/ols4/search?q=%s&ontology=ms
Cell line <URL>:http://www.ebi.ac.uk/ols4/search?q=%s&ontology=clo
PSI-MOD <URL>:http://www.ebi.ac.uk/ols4/search?q=%s&ontology=mod
DAO <URL>:http://www.ebi.ac.uk/ols4/search?q=%s&ontology=fbbt
Cell Ontology <URL>:http://www.ebi.ac.uk/ols4/search?q=%s&ontology=pcl
Plant Ontology <URL>:http://www.ebi.ac.uk/ols4/search?q=%s&ontology=po
Uberon <URL>:http://www.ebi.ac.uk/ols4/search?q=%s&ontology=uberon
Zebrafish anatomy <URL>:http://www.ebi.ac.uk/ols4/search?q=%s&ontology=zfa
Zebrafish developmental stages <URL>:http://www.ebi.ac.uk/ols4/search?q=%s&ontology=zfs
FlyBase Developmental Ontology <URL>:http://www.ebi.ac.uk/ols4/search?q=%s&ontology=fbdv
Rat strain <URL>:http://www.ebi.ac.uk/ols4/search?q=%s&ontology=rs
CHEBI <URL>:http://www.ebi.ac.uk/ols4/search?q=%s&ontology=chebi
Taxonomy <URL>:http://www.ebi.ac.uk/ols4/search?q=%s&ontology=ncbitaxon
PATO <URL>:http://www.ebi.ac.uk/ols4/search?q=%s&ontology=pato
PRIDE <URL>:http://www.ebi.ac.uk/ols4/search?q=%s&ontology=pride
MONDO <URL>:http://www.ebi.ac.uk/ols4/search?q=%s&ontology=mondo
[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.
#Taxonomy <URL>:https://www.ncbi.nlm.nih.gov/taxonomy/, <URLBASE>:https://www.ncbi.nlm.nih.gov/taxonomy/?term=%s
# Example
#UniProt <URL>:http://www.uniprot.org/, <URLBASE>:http://www.uniprot.org/uniprot/%s
# GO <URL>:https://www.ebi.ac.uk/QuickGO, <URLBASE>:https://www.ebi.ac.uk/QuickGO/term/GO:%s
# CP <URL>:https://www.ebi.ac.uk/complexportal, <URLBASE>:https://www.ebi.ac.uk/complexportal/complex/%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