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INSTALL
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INSTALL
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Installation and usage guide
A. Requirements
OpenJDK 1.8 or later (https://www.oracle.com/)
SAXON 9 or later (https://saxon.sourceforge.net/)
MMCIF Dictionary Suite (http://mmcif.wwpdb.org/)
BMRBxTool (https://github.com/yokochi47/BMRBxTool)
Raptor RDF Syntax Library (http://librdf.org/raptor/)
OpenLink Virtuoso (https://virtuoso.openlinksw.com/ or https://sourceforge.net/projects/virtuoso/)
and
BMRB/XML documents validated by the same version of BMRBxTool
B. Retrieve mmCIF dictionary (NMR-STAR.dic) and update XML schema
Please edit MMCIF_DS_DIR in schema/update_schema.sh
% cd dic2xsd
% update_schema.sh
Then, you will find the following files...
NMR-STAR.dic : mmCIF dictionary patched by PDBj-BMRB.
schema/mmcif_nmr-star.xsd : XML schema derived from NMR-STAR.dic.
C. Translate XML schema to BMRB/OWL
Please edit path for MMCIF Dictionary Suite (MMCIF_DS_DIR) in schema/update_schema.sh
% cd xsd2owl
% bmrbx2owl.sh
schema/mmcif_nmr-star.owl: BMRB/OWL derived from XML schema.
D. Translate XML schema to BMRB/XML->RDF XSLT code
% cd xsd2xml2rdf
% bmrbx2xml2rdf.sh
schema/bmrbx2rdf.xsl : BMRB/XML->RDF XSLT code
E. Translate BMRB/XML to BMRB/RDF
Please edit path for BMRBxTool (BMRBX_TOOL_HOME) in scripts/xtool-home.sh
% bmr2rdf.sh
To refresh all RDF files,
% bmr2rdf.sh -u no
F. Validate BMRB/RDF
To validate all RDF files,
% bmrchk_rdf.sh
G. OPTION: Starting Virtuoso (RDF data server over HTTP)
Please set environment variable VIRTUOSO_HOME that points Virtuoso directory.
If you drop current db and restart virtuoso database,
% init_virtuoso.sh
To load all RDF data inio Virtuoso,
% bmr2virtuoso.sh
H. Compress RDF files (gzip)
% bmrzip_rdf.sh
H. OPTION: Generate compressed NT files
% bmr2nt.sh
I. Other files and directories
update_rsrc.sh : same as to run update_schma.sh, bmrbx2owl.sh and bmrbx2xml2rdf.sh
bm[rs]zip_rdf.sh : compress RDF files.
chkrdflinks.sh : count rdf links to external information resources.
schema/bmrb-owl.xsl : BMRB/OWL->HTML XSLT code.
schema/bmrb-rdf*.xsl : BMRB/RDF->HTML XSLT codes.
scripts/* : utility shell scripts.
start_virtuoso.sh : script for starting Virtuoso server.
virtuoso.ini : configuration file for Virtuoso server.
Please fill <path_here>/BMRBoTool
and copy the file in /usr/local/virtuoso-opensource/var/lib/virtuoso/db.
run_sparql.sh : shell script for SPARQL query.
queries : includes example SPARQL (ca_all.sparql, cacb_all.sparql and ca_ph_5.5_or_lower.sparql).
You will find next directories after executing the translation scripts.
bmr_rdf_raw : includes BMRB/RDF files (uncompressed)
bmr_rdf_rel : includes update information files
bmr_rdf_err : includes XSLT error logs (disappears if no errors)
bmr_rdf_doc : includes BMRB/RDF files (compressed RDF/XML)
bmr_rdf_ntz : includes BMRB/RDF files (compressed N-Triples)
J. As for Metabolomics database
% bms2rdf.sh
% bmschk_rdf.sh
% bms2virtuoso.sh
% bmszip_rdf.sh
K. ### An interactive script executing all processes above ###
% run_all.sh
L. Questions or comment
Please contact to system maintainer (Masashi Yokochi) at PDBj-BMRB:
yokochi@protein.osaka-u.ac.jp
Copyright 2013-2019 PDBj-BMRB, Institute for Protein Research, Osaka University