UniprotStuff.java

/*
 * Copyright (C) 2010-2014  "Bio4j"
 *
 * This file is part of Bio4j
 *
 * Bio4j is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Affero General Public License as
 * published by the Free Software Foundation, either version 3 of the
 * License, or (at your option) any later version.
 * 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 Affero General Public License for more details.
 * You should have received a copy of the GNU Affero General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>
 */
package com.bio4j.neo4jdb.model.util;

/**
 * Class including constants related to Uniprot stuff
 * @author Pablo Pareja Tobes <ppareja@era7.com>
 */
public class UniprotStuff {

	public static final String ENTRY_TAG_NAME = "entry";
    public static final String ENTRY_ACCESSION_TAG_NAME = "accession";
    public static final String ENTRY_NAME_TAG_NAME = "name";
    public static final String ENTRY_MODIFIED_DATE_ATTRIBUTE = "modified";
    public static final String ENTRY_DATASET_ATTRIBUTE = "dataset";
    public static final String ENTRY_SEQUENCE_TAG_NAME = "sequence";

    public static final String KEYWORD_TAG_NAME = "keyword";
    public static final String KEYWORD_ID_ATTRIBUTE = "id";

    public static final String REFERENCE_TAG_NAME = "reference";
    public static final String CITATION_TAG_NAME = "citation";

    public static final String ORGANISM_TAG_NAME = "organism";
    public static final String ORGANISM_NAME_TAG_NAME = "name";
    public static final String ORGANISM_NAME_TYPE_ATTRIBUTE = "type";
    public static final String ORGANISM_SCIENTIFIC_NAME_TYPE = "scientific";
    public static final String ORGANISM_COMMON_NAME_TYPE = "common";
    public static final String ORGANISM_SYNONYM_NAME_TYPE = "synonym";

    public static final String DB_REFERENCE_TAG_NAME = "dbReference";
    public static final String DB_REFERENCE_TYPE_ATTRIBUTE = "type";
    public static final String DB_REFERENCE_ID_ATTRIBUTE = "id";
    public static final String DB_REFERENCE_VALUE_ATTRIBUTE = "value";
    public static final String DB_REFERENCE_PROPERTY_TAG_NAME = "property";

    public static final String INTERPRO_DB_REFERENCE_TYPE = "InterPro";
    public static final String INTERPRO_ENTRY_NAME = "entry name";

    public static final String GO_DB_REFERENCE_TYPE = "GO";
    public static final String EVIDENCE_TYPE_ATTRIBUTE = "evidence";
    
    public static final String SEQUENCE_MASS_ATTRIBUTE = "mass";
    public static final String SEQUENCE_LENGTH_ATTRIBUTE = "length";
    public static final String PROTEIN_TAG_NAME = "protein";
    public static final String PROTEIN_RECOMMENDED_NAME_TAG_NAME = "recommendedName";
    public static final String PROTEIN_FULL_NAME_TAG_NAME = "fullName";
    public static final String PROTEIN_SHORT_NAME_TAG_NAME = "shortName";
    public static final String GENE_TAG_NAME = "gene";
    public static final String GENE_NAME_TAG_NAME = "name";
    public static final String COMMENT_TAG_NAME = "comment";
    public static final String COMMENT_TYPE_ATTRIBUTE = "type";
    public static final String COMMENT_ALTERNATIVE_PRODUCTS_TYPE = "alternative products";
    public static final String COMMENT_SEQUENCE_CAUTION_TYPE = "sequence caution";
    public static final String SUBCELLULAR_LOCATION_TAG_NAME = "subcellularLocation";
    public static final String LOCATION_TAG_NAME = "location";
    public static final String COMMENT_TEXT_TAG_NAME = "text";
    public static final String FEATURE_TAG_NAME = "feature";
    public static final String FEATURE_TYPE_ATTRIBUTE = "type";
    public static final String FEATURE_DESCRIPTION_ATTRIBUTE = "description";
    public static final String STATUS_ATTRIBUTE = "status";
    public static final String FEATURE_REF_ATTRIBUTE = "ref";
    public static final String FEATURE_ID_ATTRIBUTE = "id";
    public static final String EVIDENCE_ATTRIBUTE = "evidence";
    public static final String FEATURE_LOCATION_TAG_NAME = "location";
    public static final String FEATURE_ORIGINAL_TAG_NAME = "original";
    public static final String FEATURE_VARIATION_TAG_NAME = "variation";
    public static final String FEATURE_POSITION_TAG_NAME = "position";
    public static final String FEATURE_LOCATION_BEGIN_TAG_NAME = "begin";
    public static final String FEATURE_LOCATION_END_TAG_NAME = "end";
    public static final String FEATURE_LOCATION_POSITION_ATTRIBUTE = "position";
    public static final String FEATURE_POSITION_POSITION_ATTRIBUTE = "position";
	
}