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#
# tDiary : plugin/bio.rb
#
# Copyright (C) 2003 KATAYAMA Toshiaki <k@bioruby.org>
# Mitsuteru C. Nakao <n@bioruby.org>
# Itoshi NIKAIDO <itoshi@gsc.riken.go.jp>
# Takeya KASUKAWA <kasukawa@gsc.riken.go.jp>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2 of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
# $Id: tdiary.rb,v 1.3 2003/03/17 04:24:47 k Exp $
#
=begin
== What's this?
This is a plugin for the ((<tDiary|URL:http://www.tdiary.org/>)) to create
various links for biological resources from your diary.
tDiary is an extensible web diary application written in Ruby.
== How to install
Just copy this file under the tDiary's plugin directory as bio.rb.
== Usage
--- pubmed(pmid, comment = nil)
Create a link to NCBI Entrez reference database by using PubMed ID.
See ((<URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi>)) for more
information.
* tDiary style
* <%= pubmed 12345 %>
* <%= pubmed 12345, 'hogehoge' %>
* RD style
* ((% pubmed 12345 %))
* ((% pubmed 12345, 'hogehoge' %))
--- biofetch(db, entry_id)
Create a link to the BioFetch detabase entry retrieval system.
See ((<URL:http://biofetch.bioruby.org/>)) for more information.
* tDiary style
* <%= biofetch 'genbank', 'AA2CG' %>
* RD style
* ((% biofetch 'genbank', 'AA2CG' %))
--- amigo(go_id, comment = nil)
Create a link to the AmiGO GO term browser by using GO ID.
See ((<URL:http://www.godatabase.org/cgi-bin/go.cgi>)) for more
information.
* tDiary style
* <%= amigo '0003673' %>
* <%= amigo '0003673', 'The root of GO' %>
* RD style
* ((% amigo 0003673 %))
* ((% amigo 0003673, 'The root of GO' %))
--- fantom(id, comment = nil)
Create a link to FANTOM database by using Clone ID.
You can use RIKEN clone ID, Rearray ID, Seq ID and Accession Number.
See ((<URL:http://fantom2.gsc.riken.go.jp/db/>)) for more information.
* tDiary style
* <%= fantom 12345 %>
* <%= fantom 12345, 'hogehoge' %>
* RD style
* ((% fantom 12345 %))
* ((% fantom 12345, 'hogehoge' %))
--- rtps(id, comment = nil)
Create a link to FANTOM RTPS database by using Clone ID.
You can use only RTPS ID.
See ((<URL:http://fantom2.gsc.riken.go.jp/RTPS/>)) for more information.
* tDiary style
* <%= rtps 12345 %>
* <%= rtps 12345, 'hogehoge' %>
* RD style
* ((% rtps 12345 %))
* ((% rtps 12345, 'hogehoge' %))
== References
* Analysis of the mouse transcriptome based on functional annotation of
60,770 full-length cDNAs, The FANTOM Consortium and the RIKEN Genome
Exploration Research Group Phase I & II Team, Nature 420:563-573, 2002
* Functional annotation of a full-length mouse cDNA collection,
The RIKEN Genome Exploration Research Group Phase II Team and
the FANTOM Consortium, Nature 409:685-690, 2001
=end
def pubmed(pmid, comment = nil)
pmid = pmid.to_s.strip
url = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi"
url << "?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=#{pmid}"
if comment
%Q[<a href="#{url}">#{comment.to_s.strip}</a>]
else
%Q[<a href="#{url}">PMID:#{pmid}</a>]
end
end
def biofetch(db, entry_id)
url = "http://biofetch.bioruby.org/"
%Q[<a href="#{url}?db=#{db};id=#{entry_id};style=raw">#{db}:#{entry_id}</a>]
end
def amigo(go_id = '0003673', comment = nil)
go_id = go_id.to_s.strip
url = "http://www.godatabase.org/cgi-bin/go.cgi?query=#{go_id};view=query;action=query;search_constraint=terms"
comment = "AmiGO:#{go_id}" unless comment
%Q[<a href="#{url}">#{comment}</a>]
end
def fantom(id, comment = nil)
id = id.to_s.strip
url = "http://fantom2.gsc.riken.go.jp/db/link/id.cgi"
url << "?id=#{id}"
if comment
%Q[<a href="#{url}">#{comment.to_s.strip}</a>]
else
%Q[<a href="#{url}">FANTOM DB:#{id}</a>]
end
end
def rtps(id, comment = nil)
id = id.to_s.strip
url = "http://fantom2.gsc.riken.go.jp/RTPS/link/id.cgi"
url << "?id=#{id}"
if comment
%Q[<a href="#{url}">#{comment.to_s.strip}</a>]
else
%Q[<a href="#{url}">FANTOM RTPS DB:#{id}</a>]
end
end
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