From 95e385520364ca897fee9f7d2322040d046f308e Mon Sep 17 00:00:00 2001
From: bill-baumgartner <bill.baumgartner@gmail.com>
Date: Fri, 17 Apr 2015 13:48:55 -0600
Subject: [PATCH] updated README with maven pom info and RDF generation
 instructions

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 1 file changed, 141 insertions(+)

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 # datasource
 A library of code for parsing (mostly biomedical) data source files and converting their contents to RDF
+
+This library contains file parsers for files from many different biomedical databases. It also contains
+code that uses a file parser as input and outputs RDF. The structure of the RDF is described in:
+```
+KaBOB: Ontology-Based Semantic Integration of Biomedical Databases
+Kevin M Livingston, Michael Bada, William A Baumgartner, Lawrence E Hunter
+BMC Bioinformatics (accepted)
+``` 
+
+## Use with Java 1.8
+```
+Note: This code was developed using Java 1.7. There have been reports that the
+project won't build using Java 1.8.
+```
+
+
+## Maven signature if only using the file parser API
+```xml
+<dependency>
+	<groupId>edu.ucdenver.ccp</groupId>
+	<artifactId>datasource-fileparsers</artifactId>
+	<version>0.5</version>
+</dependency>
+
+<repository>
+	<id>bionlp-sourceforge</id>
+	<url>http://svn.code.sf.net/p/bionlp/code/repo/</url>
+</repository>
+```
+
+## Maven signature if interested in generating RDF of parsed file content
+```xml
+<dependency>
+	<groupId>edu.ucdenver.ccp</groupId>
+	<artifactId>datasource-rdfizer</artifactId>
+	<version>0.5</version>
+</dependency>
+
+<repository>
+	<id>bionlp-sourceforge</id>
+	<url>http://svn.code.sf.net/p/bionlp/code/repo/</url>
+</repository>
+```
+
+## Bulk RDF Generation 
+This library has been built to work easily with distributed resource management
+systems such as Oracle Grid Engine or Torque. All this really means is that there
+is a script available that will kick of RDF generation for a specific file parser
+based on an integer argument. 
+
+#### Integer -to- File mappings
+To see the integer-to-file mappings, 
+run edu.ucdenver.ccp.datasource.rdfizer.rdf.ice.FileDataSource.main()
+Note that due to licensing issues, some files are not available for download directly.
+The resources denoted in italics below must be manually obtained in order to be used.
+Those resources not listed in italics are capable of being automatically downloaded at
+RDF generation time.
+```
+*1 ==> DIP*
+*2 ==> HPRD_ID_MAPPINGS*
+*3 ==> TRANSFAC_GENE*
+*4 ==> TRANSFAC_MATRIX*
+*5 ==> GAD*
+6 ==> PHARMGKB_DISEASE
+7 ==> PHARMGKB_GENE
+*8 ==> PHARMGKB_RELATION*
+9 ==> PHARMGKB_DRUG
+10 ==> DRUGBANK
+11 ==> HGNC
+12 ==> HOMOLOGENE
+13 ==> IREFWEB
+14 ==> MGI_ENTREZGENE
+15 ==> MGI_MGIPHENOGENO
+16 ==> MGI_MRKLIST
+17 ==> MGI_MRKREFERENCE
+18 ==> MGI_MRKSEQUENCE
+19 ==> MGI_MRKSWISSPROT
+20 ==> MIRBASE
+*21 ==> OMIM*
+22 ==> RGD_GENES
+23 ==> RGD_GENE_MP
+24 ==> RGD_GENE_RDO
+25 ==> RGD_GENE_NBO
+26 ==> RGD_GENE_PW
+27 ==> PREMOD_HUMAN
+28 ==> PREMOD_MOUSE
+29 ==> PR_MAPPINGFILE
+30 ==> REACTOME_UNIPROT2PATHWAYSTID
+31 ==> REFSEQ_RELEASECATALOG
+32 ==> NCBIGENE_GENE2REFSEQ
+33 ==> NCBIGENE_GENEINFO
+34 ==> NCBIGENE_MIM2GENE
+35 ==> NCBIGENE_REFSEQUNIPROTCOLLAB
+36 ==> GOA
+37 ==> UNIPROT_SWISSPROT
+38 ==> UNIPROT_IDMAPPING
+39 ==> UNIPROT_TREMBL_SPARSE
+40 ==> INTERPRO_NAMESDAT
+41 ==> INTERPRO_INTERPRO2GO
+42 ==> INTERPRO_PROTEIN2IPR
+```
+
+While this is very convenient when dealing with some job schedulers, 
+it also allows for easy execution of single RDF generation jobs. For
+example, to generate RDF for the MirBase database file (index = 20):
+
+```
+export DATA_DIR=[BASE_DIRECTORY_WHERE_DATA_FILES_TO_PARSE_LIVE]
+export RDF_DIR=[BASE_DIRECTORY_WHERE_RDF_WILL_BE_WRITTEN]
+mkdir $DATA_DIR
+mkdir $RDF_DIR
+export DATE=[TODAYS_DATE_TO_TIMESTAMP_THE_DATA e.g. 2015-04-16]
+cd datasource
+mvn clean install
+mvn -f datasource-rdfizer/scripts/pom-rdf-gen.xml exec:exec -DstartStage=20 \
+-DnumStages=1 -DbaseSourceDir=$DATA_DIR -DbaseRdfDir=$RDF_DIR -DcompressRdf=true \
+-DoutputRecordLimit=-1 -Ddate=$DATE > rdfgen.log 2>&1
+```
+
+Note: you may need to adjust the Java Heap size in pom-rdf-gen.xml depending on the 
+memory limitations of your hardware.
+
+#### Species-specific subsets
+It can sometime be beneficial to limit RDF output to a specific species or group of species.
+Doing so can improve RDF generation time as well as limit the number of triples produced when
+parsing a file. Some of the file parsers are *species-aware* and there are two pre-built scripts
+that allow for RDF generation using species-specific subsets.
+
+```
+For human, use: datasource-rdfizer/scripts/pom-rdf-gen-9606.xml
+
+For human plus seven model organisms, use: datasource-rdfizer/scripts/pom-rdf-gen-modelorgs.xml
+The seven model organisms are: fly, rat, mouse, yeast, worm, arabidopsis, zebrafish
+```
+
+As mentioned above, note that when a taxon-aware file parser is used, some extra data is downloaded that ensures 
+mappings from biological concepts to taxon identifiers are present. This download can be time 
+consuming due to one of the files being very large, but it is a one-time cost.
+
+
+  
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