PubChemInlineURIFactory.java example

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/**

Copyright (C) SYSTAP, LLC 2006-2015.  All rights reserved.

Contact:
     SYSTAP, LLC
     2501 Calvert ST NW #106
     Washington, DC 20008
     licenses@systap.com

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; version 2 of the License.

This program 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 General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 */
package com.blazegraph.vocab.pubchem;

import com.bigdata.rdf.internal.InlineIntegerURIHandlerMap;
import com.bigdata.rdf.internal.InlinePrefixedFixedWidthIntegerURIHandler;
import com.bigdata.rdf.internal.InlinePrefixedIntegerURIHandler;
import com.bigdata.rdf.internal.InlinePrefixedSuffixedIntegerURIHandler;
import com.bigdata.rdf.internal.InlineURIFactory;
import com.bigdata.rdf.internal.InlineURIHandler;

/**
 * {@link InlineURIFactory} for the {@link PubChemVocabularyDecl} to load the PubChem data from {@link https://pubchem.ncbi.nlm.nih.gov/rdf/}.
 * 
 * Include by adding the line below to your namespace properties.  It is intended to be used with {@link PubChemVocabulary}.
 * 
 * <code> 
 * com.bigdata.rdf.store.AbstractTripleStore.inlineURIFactory=com.blazegraph.vocab.pubchem.PubChemInlineURIFactory
 * </code>
 * 
 * 
 * @author beebs
 *
 */
public class PubChemInlineURIFactory extends InlineURIFactory {

	/*
	 * See https://pubchem.ncbi.nlm.nih.gov/rdf/
	 * 
	 * http://rdf.ncbi.nlm.nih.gov/pubchem/compound/CID60823
	 * http://rdf.ncbi.nlm.nih.gov/pubchem/substance/SID8032774
	 * http://rdf.ncbi.nlm.nih.gov/pubchem/bioassay/AID1788
	 * http://rdf.ncbi.nlm.nih.gov/pubchem/protein/GI124375976
	 * http://rdf.ncbi.nlm.nih.gov/pubchem/conserveddomain/PSSMID132758
	 * http://rdf.ncbi.nlm.nih.gov/pubchem/gene/GID367
	 * http://rdf.ncbi.nlm.nih.gov/pubchem/biosystem/BSID82991
	 * http://rdf.ncbi.nlm.nih.gov/pubchem/reference/PMID10395478
	 */

	/*
	 * http://purl.obolibrary.org/obo/CHEBI_74763
	 * http://purl.obolibrary.org/obo/PR_
	 * http://www.bioassayontology.org/bao#BAO_0002877
	 * http://semanticscience.org/resource/CHEMINF_
	 * http://purl.obolibrary.org/obo/IAO_0000136
	 * http://purl.obolibrary.org/obo/OBI_0000299
	 */

	/*
	 * http://rdf.ncbi.nlm.nih.gov/pubchem/compound/CID
	 * http://rdf.ncbi.nlm.nih.gov/pubchem/substance/SID
	 * http://rdf.ncbi.nlm.nih.gov/pubchem/bioassay/AID
	 * http://rdf.ncbi.nlm.nih.gov/pubchem/protein/GI
	 * http://rdf.ncbi.nlm.nih.gov/pubchem/conserveddomain/PSSMID
	 * http://rdf.ncbi.nlm.nih.gov/pubchem/gene/GID
	 * http://rdf.ncbi.nlm.nih.gov/pubchem/biosystem/BSID
	 * http://rdf.ncbi.nlm.nih.gov/pubchem/reference/PMID
	 * http://purl.obolibrary.org/obo/CHEBI_74763
	 * http://semanticscience.org/resource/CHEMINF_
	 * 
	 * Fixed width
	 * 
	 * http://www.bioassayontology.org/bao#BAO_0002877 fixed width 7
	 * http://purl.obolibrary.org/obo/PR_000005253 //fixed width 9
	 * http://purl.obolibrary.org/obo/IAO_0000136 //fixed width 7
	 * http://purl.obolibrary.org/obo/OBI_0000299 //fixed width 7
	 */
	public final static String[] uris = {
			"http://rdf.ncbi.nlm.nih.gov/pubchem/compound/", // 1
			"http://rdf.ncbi.nlm.nih.gov/pubchem/substance/", // 2
			"http://rdf.ncbi.nlm.nih.gov/pubchem/bioassay/", // 3
			"http://rdf.ncbi.nlm.nih.gov/pubchem/protein/", // 4
			"http://rdf.ncbi.nlm.nih.gov/pubchem/conserveddomain/", // 5
			"http://rdf.ncbi.nlm.nih.gov/pubchem/gene/", // 6
			"http://rdf.ncbi.nlm.nih.gov/pubchem/biosystem/", // 7
			"http://rdf.ncbi.nlm.nih.gov/pubchem/reference/", // 8
			"http://semanticscience.org/resource/",  // 9
			};

	public final static String[] localNames = { "CID", // 1
			"SID", // 2
			"AID", // 3
			"GI", // 4
			"PSSMID", // 5
			"GID", // 6
			"BSID", // 7
			"PMID", // 8
			"CHEMINF_" //9
			};

	/*
	 * http://rdf.ncbi.nlm.nih.gov/pubchem/descriptor/
	 * 
	 * descriptor:CID5606223_Compound_Identifier ,
	 * descriptor:CID5606223_Covalent_Unit_Count ,
	 * descriptor:CID5606223_Defined_Atom_Stereo_Count ,
	 * descriptor:CID5606223_Defined_Bond_Stereo_Count ,
	 * descriptor:CID5606223_Exact_Mass ,
	 * descriptor:CID5606223_Hydrogen_Bond_Acceptor_Count ,
	 * descriptor:CID5606223_Hydrogen_Bond_Donor_Count ,
	 * descriptor:CID5606223_IUPAC_InChI , descriptor:CID5606223_Isomeric_SMILES
	 * , descriptor:CID5606223_Isotope_Atom_Count ,
	 * descriptor:CID5606223_Molecular_Formula ,
	 * descriptor:CID5606223_Molecular_Weight ,
	 * descriptor:CID5606223_Mono_Isotopic_Weight ,
	 * descriptor:CID5606223_Non-hydrogen_Atom_Count ,
	 * descriptor:CID5606223_Preferred_IUPAC_Name ,
	 * descriptor:CID5606223_Rotatable_Bond_Count ,
	 * descriptor:CID5606223_Structure_Complexity , descriptor:CID5606223_TPSA ,
	 * descriptor:CID5606223_Tautomer_Count ,
	 * descriptor:CID5606223_Total_Formal_Charge ,
	 * descriptor:CID5606223_Undefined_Atom_Stereo_Count ,
	 * descriptor:CID5606223_Undefined_Bond_Stereo_Count ,
	 * descriptor:CID5606223_XLogP3-AA .
	 */
	public static final String[] descriptorSuffix = { "_XLogP3-AA",
			"_Undefined_Bond_Stereo_Count", "_Undefined_Atom_Stereo_Count",
			"_Total_Formal_Charge", "_Tautomer_Count", "_TPSA",
			"_Structure_Complexity", "_Rotatable_Bond_Count",
			"_Preferred_IUPAC_Name", "_Non-hydrogen_Atom_Count",
			"_Mono_Isotopic_Weight", "_Molecular_Weight", "_Molecular_Formula",
			"_Isotope_Atom_Count", "_Isomeric_SMILES", "_IUPAC_InChI",
			"_Hydrogen_Bond_Donor_Count", "_Hydrogen_Bond_Acceptor_Count",
			"_Exact_Mass", "_Defined_Bond_Stereo_Count",
			"_Defined_Atom_Stereo_Count", "_Covalent_Unit_Count",
			"_Compound_Identifier", "_Canonical_SMILES" };

	
	public static final String descriptorPrefix = "CID";
	public static final String descriptorNS = "http://rdf.ncbi.nlm.nih.gov/pubchem/descriptor/";
	
	public static final String oboNS = "http://purl.obolibrary.org/obo/";

	public PubChemInlineURIFactory() {

		super();

		for (int i = 0; i < uris.length; i++) {
			addHandler(new InlinePrefixedIntegerURIHandler(uris[i],
					localNames[i]));
		}

		// http://www.bioassayontology.org/bao#BAO_0002877 fixed width 7
		addHandler(new InlinePrefixedFixedWidthIntegerURIHandler(
				"http://www.bioassayontology.org/bao#", "BAO_", 7));

		{
			// Create a map of Handlers for the
			// "http://purl.obolibrary.org/obo/"
			// namespace

			final InlineIntegerURIHandlerMap oboMap = new InlineIntegerURIHandlerMap(
					oboNS);

			int i = 0;
			// http://purl.obolibrary.org/obo/CHEBI_13453 
			InlineURIHandler handler = new InlinePrefixedIntegerURIHandler(
					oboNS, "CHEBI_", i);

			oboMap.addHandlerForNS(i++, handler);

			// http://purl.obolibrary.org/obo/PR_000005253 //fixed width 9
			handler = new InlinePrefixedFixedWidthIntegerURIHandler(
					oboNS, "PR_", 9, i);

			oboMap.addHandlerForNS(i++, handler);

			// http://purl.obolibrary.org/obo/IAO_0000136 //fixed width 7
			handler = new InlinePrefixedFixedWidthIntegerURIHandler(
					oboNS, "IAO_", 7, i);
			oboMap.addHandlerForNS(i++, handler);

			// http://purl.obolibrary.org/obo/OBI_0000299 //fixed width 7
			handler = new InlinePrefixedFixedWidthIntegerURIHandler(
					oboNS, "OBI_", 7, i);
			oboMap.addHandlerForNS(i++, handler);

			// Add the OBO Map Handler for the base namespace
			addHandler(oboMap);

		}
		
		{

			// Now we want to a namespace with multiple different inline
			// URI Handlers based on local name variations.
			final InlineIntegerURIHandlerMap hMap = new InlineIntegerURIHandlerMap(
					descriptorNS);

			for (int i = 0; i < descriptorSuffix.length; i++) {
				final InlineURIHandler h = new InlinePrefixedSuffixedIntegerURIHandler(
						descriptorNS, descriptorPrefix, descriptorSuffix[i], i);

				// Add the handler to the namespace map
				hMap.addHandlerForNS(i, h);
			}

			// Add the handler map for the base namespace URI
			addHandler(hMap);

		}

	}
}