diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/IProtDAO.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/IProtDAO.java index 2cdb864f9d53b454f5ac769d203a6e9ce3691a3d..4b1d3874adb35e4eb2fe545ac8f5728675e46450 100644 --- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/IProtDAO.java +++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/IProtDAO.java @@ -21,8 +21,10 @@ import net.lemnik.eodsql.DataSet; import net.lemnik.eodsql.Select; import net.lemnik.eodsql.Update; +import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Database; import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Experiment; import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ModificationType; +import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinReference; import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Sample; import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Sequence; @@ -36,13 +38,6 @@ public interface IProtDAO extends BaseQuery @Select("select * from modification_types") public DataSet<ModificationType> listModificationTypes(); - @Select("select * from sequences where amino_acid_sequence = ?{1}") - public Sequence tryToGetSequenceBySequenceString(String sequence); - - @Select("insert into sequences (amino_acid_sequence, checksum) " - + "values (?{1.sequence}, ?{1.checksum}) returning id") - public long createSequence(Sequence sequence); - @Select("select * from experiments where perm_id = ?{1}") public Experiment tryToGetExperimentByPermID(String permID); @@ -55,11 +50,18 @@ public interface IProtDAO extends BaseQuery @Select("insert into samples (expe_id, perm_id) values (?{1}, ?{2}) returning id") public long createSample(long experimentID, String samplePermID); + @Select("select * from databases where name_and_version = ?{1}") + public Database tryToGetDatabaseByName(String name); + + @Select("insert into databases (name_and_version) values (?{1}) returning id") + public long createDatabase(String databaseName); + @Select("select * from data_sets where perm_id = ?{1}") public ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.DataSet tryToGetDataSetByPermID(String permID); - @Select("insert into data_sets (expe_id, samp_id, perm_id) values (?{1}, ?{2}, ?{3}) returning id") - public long createDataSet(long experimentID, Long sampleID, String dataSetPermID); + @Select("insert into data_sets (expe_id, samp_id, perm_id, db_id) " + + "values (?{1}, ?{2}, ?{3}, ?{4}) returning id") + public long createDataSet(long experimentID, Long sampleID, String dataSetPermID, long databaseID); @Update("insert into probability_fdr_mappings (dase_id, probability, false_discovery_rate) " + "values (?{1}, ?{2}, ?{3})") @@ -75,7 +77,26 @@ public interface IProtDAO extends BaseQuery @Update("insert into modifications (pept_id, moty_id, pos, mass) values (?{1}, ?{2}, ?{3}, ?{4})") public void createModification(long peptideID, long modificationTypeID, int position, double mass); + + @Select("select * from protein_references where uniprot_id = ?{1}") + public ProteinReference tryToGetProteinReference(String uniprotID); + + @Select("insert into protein_references (uniprot_id, description) values (?{1}, ?{2}) returning id") + public long createProteinReference(String uniprotID, String description); + + @Update("update protein_references set description = ?{2} where id = ?{1}") + public void updateProteinReferenceDescription(long proteinReferenceID, String description); + + @Select("select * from sequences where prre_id = ?{1} and db_id = ?{2}") + public Sequence tryToGetSequenceByReferenceAndDatabase(long referenceID, long databaseID); + + @Select("insert into sequences (db_id, prre_id, amino_acid_sequence, checksum) " + + "values (?{1.databaseID}, ?{1.proteinReferenceID}, ?{1.sequence}, ?{1.checksum}) " + + "returning id") + public long createSequence(Sequence sequence); + + @Update("insert into identified_proteins (prot_id, sequ_id) values (?{1}, ?{2})") + public void createIdentifiedProtein(long proteinID, long sequenceID); - @Update("insert into identified_proteins (prot_id, sequ_id, description) values (?{1}, ?{2}, ?{3})") - public void createIdentifiedProtein(long proteinID, Long sequenceID, String description); } + diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetHandler.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetHandler.java index 2125be965accddfe2f7b63bd22975c405afbab17..76db67b026928ce4e0420fc7d5c2c9b0306537eb 100644 --- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetHandler.java +++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetHandler.java @@ -40,6 +40,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation; import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.AminoAcidMass; import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.AnnotatedProtein; import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.DataSet; +import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Database; import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Experiment; import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ModificationType; import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Peptide; @@ -48,6 +49,7 @@ import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Protein; import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinAnnotation; import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinGroup; import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinProphetDetails; +import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinReference; import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinSummary; import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinSummaryDataFilter; import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Sample; @@ -67,6 +69,55 @@ public class ResultDataSetHandler implements IDataSetHandler private static final String DATABASE_OWNER = "database.owner"; private static final String DATABASE_PASSWORD = "database.password"; + private static final class ProteinDescription + { + private final String uniprotID; + private final String description; + private final String sequence; + + public ProteinDescription(String proteinDescription) + { + String[] items = proteinDescription.split("\\\\"); + uniprotID = tryToGetUniprotID(items); + description = tryToGetValue(items, "DE"); + sequence = tryToGetValue(items, "SEQ"); + } + + public final String getUniprotID() + { + return uniprotID; + } + + public final String getDescription() + { + return description; + } + + public final String getSequence() + { + return sequence; + } + + private String tryToGetUniprotID(String[] items) + { + return items == null || items.length == 0 ? null : items[0].trim(); + } + + private String tryToGetValue(String[] items, String key) + { + for (String item : items) + { + int indexOfEqualSign = item.indexOf('='); + if (indexOfEqualSign > 0 + && item.substring(0, indexOfEqualSign).trim().equalsIgnoreCase(key)) + { + return item.substring(indexOfEqualSign + 1).trim(); + } + } + return null; + } + } + private final IDataSetHandler delegator; private final Unmarshaller unmarshaller; private final IProtDAO dao; @@ -130,12 +181,35 @@ public class ResultDataSetHandler implements IDataSetHandler dataSetInfo.getSample().getPermId(); Experiment experiment = getOrCreateExperiment(dataSetInfo.getExperiment().getPermId()); Sample sample = getOrCreateSample(experiment, dataSetInfo.getSample().getPermId()); - DataSet ds = getOrCreateDataSet(experiment, sample, dataSetInfo.getDataSetCode()); + String referenceDatabase = summary.getSummaryHeader().getReferenceDatabase(); + Database database = getOrGreateDatabase(referenceDatabase); + DataSet ds = getOrCreateDataSet(experiment, sample, database, dataSetInfo.getDataSetCode()); addToDatabase(ds, summary); return dataSets; } - private DataSet getOrCreateDataSet(Experiment experiment, Sample sample, String dataSetPermID) + private Database getOrGreateDatabase(String databaseNameAndVersion) + { + int indexOfLastSlash = databaseNameAndVersion.lastIndexOf('/'); + String nameOrVersion; + if (indexOfLastSlash < 0) + { + nameOrVersion = databaseNameAndVersion; + } else + { + nameOrVersion = databaseNameAndVersion.substring(indexOfLastSlash + 1); + } + Database database = dao.tryToGetDatabaseByName(nameOrVersion); + if (database == null) + { + database = new Database(); + database.setNameAndVersion(nameOrVersion); + database.setId(dao.createDatabase(database.getNameAndVersion())); + } + return database; + } + + private DataSet getOrCreateDataSet(Experiment experiment, Sample sample, Database database, String dataSetPermID) { DataSet dataSet = dao.tryToGetDataSetByPermID(dataSetPermID); if (dataSet == null) @@ -144,7 +218,11 @@ public class ResultDataSetHandler implements IDataSetHandler dataSet.setPermID(dataSetPermID); long experimentID = experiment.getId(); dataSet.setExperimentID(experimentID); - dataSet.setId(dao.createDataSet(experimentID, sample.getId(), dataSetPermID)); + long sampleID = sample.getId(); + dataSet.setSampleID(sampleID); + long databaseID = database.getId(); + dataSet.setDatabaseID(databaseID); + dataSet.setId(dao.createDataSet(experimentID, sampleID, dataSetPermID, databaseID)); } return dataSet; } @@ -193,29 +271,26 @@ public class ResultDataSetHandler implements IDataSetHandler private void addToDatabase(DataSet dataSet, ProteinSummary summary) { long dataSetID = dataSet.getId(); + Long databaseID = dataSet.getDatabaseID(); createProbabilityToFDRMapping(dataSetID, summary); Iterable<ModificationType> modificationTypes = dao.listModificationTypes(); + System.out.println(modificationTypes); List<ProteinGroup> proteinGroups = summary.getProteinGroups(); - int maxGroupSize = 0; - String maxGroupName = null; for (ProteinGroup proteinGroup : proteinGroups) { double probability = proteinGroup.getProbability(); List<Protein> proteins = proteinGroup.getProteins(); - if (maxGroupSize < proteins.size()) - { - maxGroupSize = proteins.size(); - maxGroupName = proteinGroup.getGroupNumber(); - } - for (Protein protein : proteins) + if (proteins.isEmpty() == false) { + // only the first protein is added. All other proteins are ignored. + Protein protein = proteins.get(0); ProteinAnnotation annotation = protein.getAnnotation(); long proteinID = dao.createProtein(dataSetID, probability); - dao.createIdentifiedProtein(proteinID, null, annotation.getDescription()); + createIdentifiedProtein(proteinID, databaseID, annotation.getDescription()); for (AnnotatedProtein annotatedProtein : protein.getIndistinguishableProteins()) { String description = annotatedProtein.getAnnotation().getDescription(); - dao.createIdentifiedProtein(proteinID, null, description); + createIdentifiedProtein(proteinID, databaseID, description); } List<Peptide> peptides = protein.getPeptides(); for (Peptide peptide : peptides) @@ -238,7 +313,6 @@ public class ResultDataSetHandler implements IDataSetHandler } } } - System.out.println("maximum group size: " + maxGroupSize + ", name:" + maxGroupName); } private void createProbabilityToFDRMapping(long dataSetID, ProteinSummary summary) @@ -264,20 +338,35 @@ public class ResultDataSetHandler implements IDataSetHandler } throw new UserFailureException("Missing Protein Prophet details."); } - - private Sequence getOrCreateSequence(Peptide peptide) + + private void createIdentifiedProtein(long proteinID, long databaseID, String proteinDescription) { - String s = peptide.getSequence(); - Sequence sequence = dao.tryToGetSequenceBySequenceString(s); - if (sequence == null) + ProteinDescription protDesc = new ProteinDescription(proteinDescription); + String uniprotID = protDesc.getUniprotID(); + String description = protDesc.getDescription(); + ProteinReference proteinReference = dao.tryToGetProteinReference(uniprotID); + if (proteinReference == null) { - sequence = new Sequence(s); - long id = dao.createSequence(sequence); - sequence.setId(id); + proteinReference = new ProteinReference(); + proteinReference.setUniprotID(uniprotID); + proteinReference.setDescription(description); + proteinReference.setId(dao.createProteinReference(uniprotID, description)); + } else if (description.equals(proteinReference.getDescription()) == false) + { + dao.updateProteinReferenceDescription(proteinReference.getId(), description); + } + Sequence sequence = + dao.tryToGetSequenceByReferenceAndDatabase(proteinReference.getId(), databaseID); + if (sequence == null || protDesc.getSequence().equals(sequence.getSequence()) == false) + { + sequence = new Sequence(protDesc.getSequence()); + sequence.setDatabaseID(databaseID); + sequence.setProteinReferenceID(proteinReference.getId()); + sequence.setId(dao.createSequence(sequence)); } - return sequence; + dao.createIdentifiedProtein(proteinID, sequence.getId()); } - + private ModificationType findModificationType(Iterable<ModificationType> modificationTypes, double mass) { diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/DataSet.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/DataSet.java index dccbf4331bd5d601b0eee6259e85f6f63265fa8c..59fab841a383fbac05b3442087cc52843e9f4cbe 100644 --- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/DataSet.java +++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/DataSet.java @@ -30,6 +30,9 @@ public class DataSet extends AbstractDTOWithIDAndPermID @ResultColumn("expe_id") private Long experimentID; + + @ResultColumn("db_id") + private Long databaseID; public final Long getSampleID() { @@ -50,4 +53,14 @@ public class DataSet extends AbstractDTOWithIDAndPermID { this.experimentID = experimentID; } + + public final Long getDatabaseID() + { + return databaseID; + } + + public final void setDatabaseID(Long databaseID) + { + this.databaseID = databaseID; + } } diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/Database.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/Database.java new file mode 100644 index 0000000000000000000000000000000000000000..e94351743b9bc08f344cc47ad2d4bd1788329379 --- /dev/null +++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/Database.java @@ -0,0 +1,41 @@ +/* + * Copyright 2009 ETH Zuerich, CISD + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +package ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto; + +import net.lemnik.eodsql.ResultColumn; + +/** + * + * + * @author Franz-Josef Elmer + */ +public class Database extends AbstractDTOWithID +{ + @ResultColumn("name_and_version") + private String nameAndVersion; + + public final String getNameAndVersion() + { + return nameAndVersion; + } + + public final void setNameAndVersion(String nameAndVersion) + { + this.nameAndVersion = nameAndVersion; + } + +} diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/ModificationType.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/ModificationType.java index 5fa9ebcad1f708bcdddf681ebab33211cadb7fef..0bdcdcc5a5feb06f0ae1f509d57c57ea81832e4c 100644 --- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/ModificationType.java +++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/ModificationType.java @@ -27,9 +27,12 @@ public class ModificationType extends AbstractDTOWithID { private String code; + @ResultColumn("amino_acid") + private String aminoAcid; + private double mass; - @ResultColumn("delta_mass") + @ResultColumn("mass_tolerance") private double deltaMass; public final String getCode() @@ -42,6 +45,16 @@ public class ModificationType extends AbstractDTOWithID this.code = code; } + public final String getAminoAcid() + { + return aminoAcid; + } + + public final void setAminoAcid(String aminoAcid) + { + this.aminoAcid = aminoAcid; + } + public final double getMass() { return mass; @@ -70,7 +83,7 @@ public class ModificationType extends AbstractDTOWithID @Override public String toString() { - return code + "=(" + mass + "\u00b1" + deltaMass + ")"; + return code + "=(" + aminoAcid + ":" + mass + "\u00b1" + deltaMass + ")"; } diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/ProteinReference.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/ProteinReference.java new file mode 100644 index 0000000000000000000000000000000000000000..f38ce5c1812ddb9796049aa1b8a39ae6db0c02c2 --- /dev/null +++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/ProteinReference.java @@ -0,0 +1,53 @@ +/* + * Copyright 2009 ETH Zuerich, CISD + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +package ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto; + +import net.lemnik.eodsql.ResultColumn; + +/** + * + * + * @author Franz-Josef Elmer + */ +public class ProteinReference extends AbstractDTOWithID +{ + @ResultColumn("uniprot_id") + private String uniprotID; + + @ResultColumn("description") + private String description; + + public final String getUniprotID() + { + return uniprotID; + } + + public final void setUniprotID(String uniprotID) + { + this.uniprotID = uniprotID; + } + + public final String getDescription() + { + return description; + } + + public final void setDescription(String description) + { + this.description = description; + } +} diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/Sequence.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/Sequence.java index b91127644c6cf281a03c72baea289819f1b424d2..cb861ba3d7c8b224ef2a5609a2eb46663cb353ed 100644 --- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/Sequence.java +++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/Sequence.java @@ -25,6 +25,12 @@ import net.lemnik.eodsql.ResultColumn; */ public class Sequence extends AbstractDTOWithID { + @ResultColumn("database_id") + private long databaseID; + + @ResultColumn("protein_reference_id") + private long proteinReferenceID; + @ResultColumn("amino_acid_sequence") private String sequence; @@ -42,6 +48,26 @@ public class Sequence extends AbstractDTOWithID calculateChecksum(); } + public final long getDatabaseID() + { + return databaseID; + } + + public final void setDatabaseID(long databaseID) + { + this.databaseID = databaseID; + } + + public final long getProteinReferenceID() + { + return proteinReferenceID; + } + + public final void setProteinReferenceID(long proteinDescriptionID) + { + this.proteinReferenceID = proteinDescriptionID; + } + public final String getSequence() { return sequence; diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/Dict.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/Dict.java index 6dfb6b712e0346fe3c42e83e2fa02da85ec86a2a..f63ff120ff97d9d834f47b2c1fcbb8ae6a718782 100644 --- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/Dict.java +++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/Dict.java @@ -26,6 +26,7 @@ public class Dict public static final String QUERY_MENU_TITLE = "query_menu_title"; public static final String SELECTED_EXPERIMENT_LABEL = "selected_experiment_label"; + public static final String UNIPROT_ID = "uniprot_id"; public static final String PROTEIN_DESCRIPTION = "protein_description"; public static final String FALSE_DISCOVERY_RATE = "false_discovery_rate"; public static final String DATA_SET = "data_set"; diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowserGrid.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowserGrid.java index 8528a2e36e1f7e757f237e956a2416ffee8ca38e..b78fab56adba44ba35334861e915745053cad321 100644 --- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowserGrid.java +++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowserGrid.java @@ -21,6 +21,7 @@ import java.util.List; import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback; import ch.systemsx.cisd.openbis.generic.client.web.client.application.GenericConstants; import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext; +import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.DispatcherHelper; import ch.systemsx.cisd.openbis.generic.client.web.client.application.renderer.LinkRenderer; import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.columns.framework.IColumnDefinitionKind; import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.AbstractSimpleBrowserGrid; @@ -73,11 +74,12 @@ class ProteinByExperimentBrowserGrid extends AbstractSimpleBrowserGrid<ProteinIn super(viewContext.getCommonViewContext(), BROWSER_ID, GRID_ID, false); specificViewContext = viewContext; setDisplayTypeIDGenerator(PhosphoNetXDisplayTypeIDGenerator.PROTEIN_BY_EXPERIMENT_BROWSER_GRID); - registerLinkClickListenerFor(ProteinColDefKind.DATA_SET.id(), + registerLinkClickListenerFor(ProteinColDefKind.DESCRIPTION.id(), new ICellListener<ProteinInfo>() { public void handle(ProteinInfo rowItem) { + DispatcherHelper.dispatchNaviEvent(ProteinViewer.createTabItemFactory(viewContext, rowItem)); System.out.println(rowItem.getDataSetPermID()); } }); @@ -100,7 +102,7 @@ class ProteinByExperimentBrowserGrid extends AbstractSimpleBrowserGrid<ProteinIn protected ColumnDefsAndConfigs<ProteinInfo> createColumnsDefinition() { ColumnDefsAndConfigs<ProteinInfo> definitions = super.createColumnsDefinition(); - definitions.setGridCellRendererFor(ProteinColDefKind.DATA_SET.id(), LinkRenderer.createLinkRenderer()); + definitions.setGridCellRendererFor(ProteinColDefKind.DESCRIPTION.id(), LinkRenderer.createLinkRenderer()); return definitions; } diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinViewer.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinViewer.java new file mode 100644 index 0000000000000000000000000000000000000000..4537c98a83939617eacca41ef8754a0ce6bbd7b5 --- /dev/null +++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinViewer.java @@ -0,0 +1,109 @@ +/* + * Copyright 2009 ETH Zuerich, CISD + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +package ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application; + +import java.util.LinkedHashMap; +import java.util.Map; +import java.util.Set; + +import com.extjs.gxt.ui.client.widget.ContentPanel; + +import ch.systemsx.cisd.openbis.generic.client.web.client.application.GenericConstants; +import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext; +import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.DatabaseModificationAwareComponent; +import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.DefaultTabItem; +import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.IDatabaseModificationObserver; +import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.ITabItem; +import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.ITabItemFactory; +import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.AbstractViewer; +import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.PropertyValueRenderers; +import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.property.PropertyGrid; +import ch.systemsx.cisd.openbis.generic.client.web.client.dto.Experiment; +import ch.systemsx.cisd.openbis.generic.client.web.client.dto.Invalidation; +import ch.systemsx.cisd.openbis.generic.client.web.client.dto.Sample; +import ch.systemsx.cisd.openbis.generic.shared.basic.TechId; +import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind; +import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Person; +import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleProperty; +import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType; +import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync; +import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ProteinInfo; + +/** + * + * + * @author Franz-Josef Elmer + */ +public class ProteinViewer extends ContentPanel implements IDatabaseModificationObserver +{ + private static final String PREFIX = "protein-viewer_"; + + public static final String ID_PREFIX = GenericConstants.ID_PREFIX + PREFIX; + + static ITabItemFactory createTabItemFactory(final IViewContext<IPhosphoNetXClientServiceAsync> viewContext, final ProteinInfo proteinInfo) + { + return new ITabItemFactory() + { + public String getId() + { + return createWidgetID(proteinInfo.getId()); + } + + public ITabItem create() + { + ProteinViewer viewer = new ProteinViewer(viewContext, proteinInfo.getId()); + DatabaseModificationAwareComponent c = new DatabaseModificationAwareComponent(viewer, viewer); + return DefaultTabItem.create("Protein: " + proteinInfo.getDescription(), c, viewContext, false); + } + }; + } + + static String createWidgetID(TechId proteinID) + { + return ID_PREFIX + proteinID.getId(); + } + + private final IViewContext<IPhosphoNetXClientServiceAsync> viewContext; + private final TechId proteinID; + private final String widgetID; + + private ProteinViewer(IViewContext<IPhosphoNetXClientServiceAsync> viewContext, + TechId proteinID) + { + widgetID = createWidgetID(proteinID); + this.viewContext = viewContext; + this.proteinID = proteinID; + } + + private void createUI() + { + final Map<String, Object> properties = new LinkedHashMap<String, Object>(); + final PropertyGrid propertyGrid = new PropertyGrid(viewContext, properties.size()); + properties.put("ID", proteinID); + add(propertyGrid); + } + + public DatabaseModificationKind[] getRelevantModifications() + { + return new DatabaseModificationKind[0]; + } + + public void update(Set<DatabaseModificationKind> observedModifications) + { + } + +} diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/columns/ProteinColDefKind.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/columns/ProteinColDefKind.java index cbb616bec46a32ae87654d29fda17701cd13acdf..8cebe67bd2c15ffaf62d79be997443b2ecfdd51a 100644 --- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/columns/ProteinColDefKind.java +++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/columns/ProteinColDefKind.java @@ -26,14 +26,22 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.Protein */ public enum ProteinColDefKind implements IColumnDefinitionKind<ProteinInfo> { - DESCRIPTION(new AbstractColumnDefinitionKind<ProteinInfo>(Dict.PROTEIN_DESCRIPTION) + UNIPROT_ID(new AbstractColumnDefinitionKind<ProteinInfo>(Dict.UNIPROT_ID) { @Override public String tryGetValue(ProteinInfo entity) { - return entity.getDescription(); + return entity.getUniprotID(); } }), + DESCRIPTION(new AbstractColumnDefinitionKind<ProteinInfo>(Dict.PROTEIN_DESCRIPTION) + { + @Override + public String tryGetValue(ProteinInfo entity) + { + return entity.getDescription(); + } + }), FALSE_DISCOVERY_RATE(new AbstractColumnDefinitionKind<ProteinInfo>(Dict.FALSE_DISCOVERY_RATE) { @Override @@ -48,14 +56,6 @@ public enum ProteinColDefKind implements IColumnDefinitionKind<ProteinInfo> return entity.getFalseDiscoveryRate(); } }), - DATA_SET(new AbstractColumnDefinitionKind<ProteinInfo>(Dict.DATA_SET) - { - @Override - public String tryGetValue(ProteinInfo entity) - { - return entity.getDataSetPermID(); - } - }), ; private final AbstractColumnDefinitionKind<ProteinInfo> columnDefinitionKind; diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/ProteinInfo.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/ProteinInfo.java index 8b3d16e92a32642270b5472610cf4d515cb6764b..6d9f08723eb50f80550ee28432abc5a377f5af2f 100644 --- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/ProteinInfo.java +++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/ProteinInfo.java @@ -29,6 +29,8 @@ public class ProteinInfo implements IsSerializable { private TechId id; + private String uniprotID; + private String dataSetPermID; private String description; @@ -65,6 +67,16 @@ public class ProteinInfo implements IsSerializable this.falseDiscoveryRate = falseDiscoveryRate; } + public final String getUniprotID() + { + return uniprotID; + } + + public final void setUniprotID(String uniprotID) + { + this.uniprotID = uniprotID; + } + public final String getDescription() { return description; diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/public/phosphonetx-dictionary.js b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/public/phosphonetx-dictionary.js index c44e230eec8852d8b61a6c5c50a51b637217bc47..78641fcc60f6062ec52b1a86ce1418dadc94ac64 100644 --- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/public/phosphonetx-dictionary.js +++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/public/phosphonetx-dictionary.js @@ -6,6 +6,7 @@ var phosphonetx = { selected_experiment_label: "Experiment", // Protein grid + uniprot_id: "UniProt ID", protein_description: "Protein", false_discovery_rate: "FDR", diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/ListProteinOriginalDataProvider.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/ListProteinOriginalDataProvider.java index a70d321e237d77716133d91c628862deb07fa239..417ce243e8239e0972cee95cb26c9c819ff296bc 100644 --- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/ListProteinOriginalDataProvider.java +++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/ListProteinOriginalDataProvider.java @@ -52,6 +52,7 @@ class ListProteinOriginalDataProvider implements IOriginalDataProvider<ProteinIn { ProteinInfo proteinInfo = new ProteinInfo(); proteinInfo.setId(new TechId(protein.getId())); + proteinInfo.setUniprotID(protein.getUniprotID()); proteinInfo.setDescription(protein.getDescription()); proteinInfo.setFalseDiscoveryRate(protein.getFalseDiscoveryRate()); proteinInfo.setDataSetPermID(protein.getDataSetPermID()); diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/IProteinQueryDAO.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/IProteinQueryDAO.java index 7442ebc0ff6e06539771008cefe80382827ff430..38249baf882e57f793a7a47df25c181bdc697bcc 100644 --- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/IProteinQueryDAO.java +++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/IProteinQueryDAO.java @@ -34,9 +34,11 @@ public interface IProteinQueryDAO extends BaseQuery public DataSet<ProbabilityFDRMapping> getProbabilityFDRMapping(long dataSetID); @Select("select ip.id as id, d.id as data_set_id, d.perm_id as data_set_perm_id, " - + "p.id as protein_id, p.probability, ip.description " + + "p.id as protein_id, p.probability, pr.uniprot_id, pr.description " + "from identified_proteins as ip left join proteins as p on ip.prot_id = p.id " + "left join data_sets as d on p.dase_id = d.id " - + "left join experiments as e on d.expe_id = e.id where e.perm_id = ?{1}") + + "left join experiments as e on d.expe_id = e.id, " + + "sequences as s left join protein_references as pr on s.prre_id = pr.id " + + "where e.perm_id = ?{1} and ip.sequ_id = s.id") public DataSet<IdentifiedProtein> listProteinsByExperiment(String experimentPermID); } diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/IdentifiedProtein.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/IdentifiedProtein.java index 4bd201ca83a3b3419be38b75936e26075148e197..a9128f0f92e5cd730b7d7da9b2b1b64dccb803f3 100644 --- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/IdentifiedProtein.java +++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/IdentifiedProtein.java @@ -37,6 +37,9 @@ public class IdentifiedProtein @ResultColumn("protein_id") private long proteinID; + @ResultColumn("uniprot_id") + private String uniprotID; + @ResultColumn("description") private String description; @@ -65,6 +68,16 @@ public class IdentifiedProtein this.dataSetPermID = dataSetPermID; } + public final String getUniprotID() + { + return uniprotID; + } + + public final void setUniprotID(String uniprotID) + { + this.uniprotID = uniprotID; + } + public final String getDescription() { return description; diff --git a/rtd_phosphonetx/source/sql/postgresql/001/data-001.sql b/rtd_phosphonetx/source/sql/postgresql/001/data-001.sql index 553fa004bbd6cfd282f7ebc1babd0cf800eab0c8..1a3d84dde88a4a7abffceff0077a576e411676d8 100644 --- a/rtd_phosphonetx/source/sql/postgresql/001/data-001.sql +++ b/rtd_phosphonetx/source/sql/postgresql/001/data-001.sql @@ -2,7 +2,7 @@ INSERT INTO MODIFICATION_TYPES (CODE ,DESCRIPTION ,MASS -,DELTA_MASS) +,MASS_TOLERANCE) values ('UNKNOWN' ,'Unknown mass' @@ -13,11 +13,13 @@ values INSERT INTO MODIFICATION_TYPES (CODE ,DESCRIPTION +,AMINO_ACID ,MASS -,DELTA_MASS) +,MASS_TOLERANCE) values ('115' ,'Mass around 115' +,'N' ,115 ,2 ); @@ -25,11 +27,13 @@ values INSERT INTO MODIFICATION_TYPES (CODE ,DESCRIPTION +,AMINO_ACID ,MASS -,DELTA_MASS) +,MASS_TOLERANCE) values ('147' ,'Mass around 147' +,'M' ,147 ,2 ); @@ -37,11 +41,13 @@ values INSERT INTO MODIFICATION_TYPES (CODE ,DESCRIPTION +,AMINO_ACID ,MASS -,DELTA_MASS) +,MASS_TOLERANCE) values ('160' ,'Mass around 160' +,'C' ,160 ,2 ); diff --git a/rtd_phosphonetx/source/sql/postgresql/001/schema-001.dez b/rtd_phosphonetx/source/sql/postgresql/001/schema-001.dez index 67676c87598d9a6e800837f877799315f4833c28..93452b4964129b72a8a21ad03a6a90d12924bcf7 100644 --- a/rtd_phosphonetx/source/sql/postgresql/001/schema-001.dez +++ b/rtd_phosphonetx/source/sql/postgresql/001/schema-001.dez @@ -4,14 +4,14 @@ <VERSION> <PROJECTSETTINGS> <PROJECTFILENAME>D:\User\felmer\dev-workspace\rtd_phosphonetx\source\sql\postgresql\phosphonetx.dez</PROJECTFILENAME> -<MODIFIED>2009-06-30</MODIFIED> +<MODIFIED>2009-07-06</MODIFIED> <CREATED>2009-06-29</CREATED> <CREATED2></CREATED2> <PROJECTNAME></PROJECTNAME> <DESCRIPTION></DESCRIPTION> <AUTHOR></AUTHOR> <COPYRIGHT></COPYRIGHT> -<LASTGENERATEDFILES>D:\User\felmer\dev-workspace\rtd_phosphonetx\source\sql\postgresql\001\schema-001.sql;D:\User\felmer\dev-workspace\rtd_phosphonetx\targets\drop.sql;C:\Documents and Settings\felmer\My Documents\CreateDBLog_200906301.txt</LASTGENERATEDFILES> +<LASTGENERATEDFILES>N:\user\cisd\felmer\phosphonetx\schema-001.sql;N:\user\cisd\felmer\phosphonetx\drop.sql;C:\Users\felmer\Documents\CreateDBLog_200907062.txt</LASTGENERATEDFILES> </PROJECTSETTINGS> <CONNECTIONSETTINGS> <SQLFILE>D:\User\felmer\dev-workspace\rtd_phosphonetx\source\sql\postgresql\001\schema-001.sql</SQLFILE> @@ -20,7 +20,7 @@ </CONNECTIONSETTINGS> <DATADICT> <DBID>postgresql8</DBID> -<LASTID>97</LASTID> +<LASTID>135</LASTID> <DDSETTINGS> <PKCONNAMETEMPLATE>PK_%table%</PKCONNAMETEMPLATE> <FKCONNAMETEMPLATE>%relname%</FKCONNAMETEMPLATE> @@ -57,23 +57,11 @@ <IGNORECOMMENTS>0</IGNORECOMMENTS> <USESCHEMANAMES>0</USESCHEMANAMES> <UCONNAMETEMPLATE></UCONNAMETEMPLATE> -<SQLCREATEFILE>D:\User\felmer\dev-workspace\rtd_phosphonetx\source\sql\postgresql\001\schema-001.sql</SQLCREATEFILE> -<SQLDROPFILE>D:\User\felmer\dev-workspace\rtd_phosphonetx\targets\drop.sql</SQLDROPFILE> +<SQLCREATEFILE>N:\user\cisd\felmer\phosphonetx\schema-001.sql</SQLCREATEFILE> +<SQLDROPFILE>N:\user\cisd\felmer\phosphonetx\drop.sql</SQLDROPFILE> </DDSETTINGS> <DOMAINS> <DOMAIN> -<NAME>BINARY_DATA</NAME> -<ID>3</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<DT> -<DTLISTNAME>BYTEA</DTLISTNAME> -<SD>0</SD> -<INC>1</INC> -</DT> -</DOMAIN> -<DOMAIN> <NAME>CHECKSUM</NAME> <ID>4</ID> <POSNR>0</POSNR> @@ -186,6 +174,19 @@ <INC>1</INC> </DT> </DOMAIN> +<DOMAIN> +<NAME>UNIPROT_ACCESSION_NUMBER</NAME> +<ID>109</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<DT> +<DTLISTNAME>CHARACTER VARYING</DTLISTNAME> +<LE>40</LE> +<SD>0</SD> +<INC>1</INC> +</DT> +</DOMAIN> </DOMAINS> <ENTITIES> <ENT> @@ -399,7 +400,7 @@ <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> -<ATTRLASTID>5</ATTRLASTID> +<ATTRLASTID>6</ATTRLASTID> <IDXLASTID>3</IDXLASTID> <TRGLASTID>1</TRGLASTID> <CONLASTID>2</CONLASTID> @@ -496,6 +497,34 @@ </NNCON> </ATTR> <ATTR> +<NAME>DB_ID</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> +<ID>6</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<DOMAINID>12</DOMAINID> +<DT> +<DTLISTNAME>BIGINT</DTLISTNAME> +<SD>0</SD> +<INC>1</INC> +</DT> +<NNCON> +<NAME></NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<VALUE>1</VALUE> +<CONLEVEL>1</CONLEVEL> +<CONTYPE>5</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>6</ATTRIBUTEID> +</ATTRIBUTEIDS> +</NNCON> +</ATTR> +<ATTR> <NAME>PERM_ID</NAME> <ID>3</ID> <POSNR>0</POSNR> @@ -787,7 +816,7 @@ <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> -<ATTRLASTID>6</ATTRLASTID> +<ATTRLASTID>7</ATTRLASTID> <IDXLASTID>1</IDXLASTID> <TRGLASTID>1</TRGLASTID> <CONLASTID>2</CONLASTID> @@ -873,6 +902,20 @@ </DT> </ATTR> <ATTR> +<NAME>AMINO_ACID</NAME> +<ID>7</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<DOMAINID>-1</DOMAINID> +<DT> +<DTLISTNAME>CHARACTER</DTLISTNAME> +<LE>1</LE> +<SD>0</SD> +<INC>1</INC> +</DT> +</ATTR> +<ATTR> <NAME>MASS</NAME> <ID>5</ID> <POSNR>0</POSNR> @@ -886,7 +929,7 @@ </DT> </ATTR> <ATTR> -<NAME>DELTA_MASS</NAME> +<NAME>MASS_TOLERANCE</NAME> <ID>6</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -994,6 +1037,7 @@ </ATTR> <ATTR> <NAME>SEQUENCE</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> <ID>10</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -1327,7 +1371,7 @@ <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> -<ATTRLASTID>4</ATTRLASTID> +<ATTRLASTID>6</ATTRLASTID> <IDXLASTID>1</IDXLASTID> <TRGLASTID>1</TRGLASTID> <CONLASTID>1</CONLASTID> @@ -1372,6 +1416,62 @@ </NNCON> </ATTR> <ATTR> +<NAME>DB_ID</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> +<ID>5</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<DOMAINID>12</DOMAINID> +<DT> +<DTLISTNAME>BIGINT</DTLISTNAME> +<SD>0</SD> +<INC>1</INC> +</DT> +<NNCON> +<NAME></NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<VALUE>1</VALUE> +<CONLEVEL>1</CONLEVEL> +<CONTYPE>5</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>5</ATTRIBUTEID> +</ATTRIBUTEIDS> +</NNCON> +</ATTR> +<ATTR> +<NAME>PRRE_ID</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> +<ID>6</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<DOMAINID>12</DOMAINID> +<DT> +<DTLISTNAME>BIGINT</DTLISTNAME> +<SD>0</SD> +<INC>1</INC> +</DT> +<NNCON> +<NAME></NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<VALUE>1</VALUE> +<CONLEVEL>1</CONLEVEL> +<CONTYPE>5</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>6</ATTRIBUTEID> +</ATTRIBUTEIDS> +</NNCON> +</ATTR> +<ATTR> <NAME>AMINO_ACID_SEQUENCE</NAME> <ID>3</ID> <POSNR>0</POSNR> @@ -1519,24 +1619,8 @@ <SD>0</SD> <INC>1</INC> </DT> -</ATTR> -<ATTR> -<NAME>DESCRIPTION</NAME> -<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> -<ID>4</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<DOMAINID>6</DOMAINID> -<DT> -<DTLISTNAME>CHARACTER VARYING</DTLISTNAME> -<LE>2000</LE> -<SD>0</SD> -<INC>1</INC> -</DT> <NNCON> <NAME></NAME> -<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> <ID>1</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -1545,7 +1629,7 @@ <CONLEVEL>1</CONLEVEL> <CONTYPE>5</CONTYPE> <ATTRIBUTEIDS> -<ATTRIBUTEID>4</ATTRIBUTEID> +<ATTRIBUTEID>5</ATTRIBUTEID> </ATTRIBUTEIDS> </NNCON> </ATTR> @@ -1553,6 +1637,7 @@ </ENT> <ENT> <NAME>ABUNDANCES</NAME> +<NAMETEMPLATE>PK_%table%</NAMETEMPLATE> <ID>91</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -1577,6 +1662,7 @@ <ATTRIBUTES> <ATTR> <NAME>ID</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> <ID>2</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -1604,6 +1690,7 @@ </ATTR> <ATTR> <NAME>PROT_ID</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> <ID>3</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -1631,6 +1718,7 @@ </ATTR> <ATTR> <NAME>SAMP_ID</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> <ID>4</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -1658,6 +1746,7 @@ </ATTR> <ATTR> <NAME>ABTY_ID</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> <ID>5</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -1685,6 +1774,7 @@ </ATTR> <ATTR> <NAME>VALUE</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> <ID>6</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -1714,6 +1804,7 @@ </ENT> <ENT> <NAME>PROBABILITY_FDR_MAPPINGS</NAME> +<NAMETEMPLATE>PK_%table%</NAMETEMPLATE> <ID>96</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -1738,6 +1829,7 @@ <ATTRIBUTES> <ATTR> <NAME>ID</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> <ID>2</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -1765,6 +1857,7 @@ </ATTR> <ATTR> <NAME>DASE_ID</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> <ID>5</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -1792,6 +1885,7 @@ </ATTR> <ATTR> <NAME>PROBABILITY</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> <ID>3</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -1819,6 +1913,7 @@ </ATTR> <ATTR> <NAME>FALSE_DISCOVERY_RATE</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> <ID>4</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -1846,96 +1941,330 @@ </ATTR> </ATTRIBUTES> </ENT> -</ENTITIES> -<SUBCATEGORIES> -</SUBCATEGORIES> -<TEXTAREAS> -</TEXTAREAS> -<GROUPBOXES> -</GROUPBOXES> -<STAMPS> -</STAMPS> -<SEQUENCES> -</SEQUENCES> -<PROCEDURES> -</PROCEDURES> -<VIEWS> -</VIEWS> -<RELATIONSHIPS> -<REL> -<NAME>DA_EX_FK</NAME> -<NAMETEMPLATE>DA_EX_FK</NAMETEMPLATE> -<ID>29</ID> +<ENT> +<NAME>PROTEIN_REFERENCES</NAME> +<NAMETEMPLATE>PK_%table%</NAMETEMPLATE> +<ID>98</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> -<PARENTOBJECTID>16</PARENTOBJECTID> -<CHILDOBJECTID>17</CHILDOBJECTID> -<CARDINALITY>0</CARDINALITY> -<RELTYPE>1</RELTYPE> -<MANDATORYPARENT>1</MANDATORYPARENT> -<UPDATERULE>0</UPDATERULE> -<DELETERULE>0</DELETERULE> -<CONSTRAINT> -<NAME>DA_EX_FK</NAME> -<NAMETEMPLATE>DA_EX_FK</NAMETEMPLATE> +<ATTRLASTID>4</ATTRLASTID> +<IDXLASTID>2</IDXLASTID> +<TRGLASTID>1</TRGLASTID> +<CONLASTID>2</CONLASTID> +<PKCON> +<NAME>PK_PROTEIN_REFERENCES</NAME> +<NAMETEMPLATE>PK_%table%</NAMETEMPLATE> <ID>1</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> <CONLEVEL>2</CONLEVEL> -<CONTYPE>4</CONTYPE> +<CONTYPE>3</CONTYPE> <ATTRIBUTEIDS> -<ATTRIBUTEID>4</ATTRIBUTEID> +<ATTRIBUTEID>2</ATTRIBUTEID> </ATTRIBUTEIDS> -</CONSTRAINT> -<PAIRS> -<PAIR> -<NAME></NAME> -<ID>0</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<KEYID>2</KEYID> -<FOREIGNKEYID>4</FOREIGNKEYID> -</PAIR> -</PAIRS> -</REL> -<REL> -<NAME>DA_SA_FK</NAME> -<NAMETEMPLATE>DA_SA_FK</NAMETEMPLATE> -<ID>30</ID> +</PKCON> +<ATTRIBUTES> +<ATTR> +<NAME>ID</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> +<ID>2</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> -<PARENTOBJECTID>24</PARENTOBJECTID> -<CHILDOBJECTID>17</CHILDOBJECTID> -<CARDINALITY>0</CARDINALITY> -<RELTYPE>1</RELTYPE> -<MANDATORYPARENT>1</MANDATORYPARENT> -<UPDATERULE>0</UPDATERULE> -<DELETERULE>0</DELETERULE> -<CONSTRAINT> -<NAME>DA_SA_FK</NAME> -<NAMETEMPLATE>DA_SA_FK</NAMETEMPLATE> +<DOMAINID>-1</DOMAINID> +<DT> +<DTLISTNAME>BIGSERIAL</DTLISTNAME> +<SD>0</SD> +<INC>1</INC> +</DT> +<NNCON> +<NAME></NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> <ID>1</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> -<CONLEVEL>2</CONLEVEL> -<CONTYPE>4</CONTYPE> +<VALUE>1</VALUE> +<CONLEVEL>1</CONLEVEL> +<CONTYPE>5</CONTYPE> <ATTRIBUTEIDS> -<ATTRIBUTEID>5</ATTRIBUTEID> +<ATTRIBUTEID>2</ATTRIBUTEID> </ATTRIBUTEIDS> -</CONSTRAINT> -<PAIRS> -<PAIR> -<NAME></NAME> -<ID>0</ID> +</NNCON> +</ATTR> +<ATTR> +<NAME>UNIPROT_ID</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> +<ID>3</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> -<KEYID>2</KEYID> +<DOMAINID>109</DOMAINID> +<DT> +<DTLISTNAME>CHARACTER VARYING</DTLISTNAME> +<LE>40</LE> +<SD>0</SD> +<INC>1</INC> +</DT> +<NNCON> +<NAME></NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<VALUE>1</VALUE> +<CONLEVEL>1</CONLEVEL> +<CONTYPE>5</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>3</ATTRIBUTEID> +</ATTRIBUTEIDS> +</NNCON> +</ATTR> +<ATTR> +<NAME>DESCRIPTION</NAME> +<ID>4</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<DOMAINID>6</DOMAINID> +<DT> +<DTLISTNAME>CHARACTER VARYING</DTLISTNAME> +<LE>2000</LE> +<SD>0</SD> +<INC>1</INC> +</DT> +</ATTR> +</ATTRIBUTES> +<INDEXES> +<INDEX> +<NAME>IDX_PROTEIN_REFERENCES_1</NAME> +<NAMETEMPLATE>IDX_%table%_%counter%</NAMETEMPLATE> +<ID>2</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<RELID>0</RELID> +<AUTOIDXTYPE>0</AUTOIDXTYPE> +<IDXCOLS> +<IDXCOL> +<NAME>UNIPROT_ID</NAME> +<ID>0</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<IDXCOLATTRID>3</IDXCOLATTRID> +</IDXCOL> +</IDXCOLS> +</INDEX> +</INDEXES> +<CONSTRAINTS> +<CONSTRAINT> +<NAME>TUC_PROTEIN_REFERENCES_1</NAME> +<NAMETEMPLATE>TUC_%table%_%counter%</NAMETEMPLATE> +<ID>2</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<CONLEVEL>2</CONLEVEL> +<CONTYPE>2</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>3</ATTRIBUTEID> +</ATTRIBUTEIDS> +</CONSTRAINT> +</CONSTRAINTS> +</ENT> +<ENT> +<NAME>DATABASES</NAME> +<NAMETEMPLATE>PK_%table%</NAMETEMPLATE> +<ID>110</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<ATTRLASTID>3</ATTRLASTID> +<IDXLASTID>1</IDXLASTID> +<TRGLASTID>1</TRGLASTID> +<CONLASTID>2</CONLASTID> +<PKCON> +<NAME>PK_DATABASES</NAME> +<NAMETEMPLATE>PK_%table%</NAMETEMPLATE> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<CONLEVEL>2</CONLEVEL> +<CONTYPE>3</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>2</ATTRIBUTEID> +</ATTRIBUTEIDS> +</PKCON> +<ATTRIBUTES> +<ATTR> +<NAME>ID</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> +<ID>2</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<DOMAINID>-1</DOMAINID> +<DT> +<DTLISTNAME>BIGSERIAL</DTLISTNAME> +<SD>0</SD> +<INC>1</INC> +</DT> +<NNCON> +<NAME></NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<VALUE>1</VALUE> +<CONLEVEL>1</CONLEVEL> +<CONTYPE>5</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>2</ATTRIBUTEID> +</ATTRIBUTEIDS> +</NNCON> +</ATTR> +<ATTR> +<NAME>NAME_AND_VERSION</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> +<ID>3</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<DOMAINID>11</DOMAINID> +<DT> +<DTLISTNAME>CHARACTER VARYING</DTLISTNAME> +<LE>200</LE> +<SD>0</SD> +<INC>1</INC> +</DT> +<NNCON> +<NAME></NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<VALUE>1</VALUE> +<CONLEVEL>1</CONLEVEL> +<CONTYPE>5</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>3</ATTRIBUTEID> +</ATTRIBUTEIDS> +</NNCON> +</ATTR> +</ATTRIBUTES> +<CONSTRAINTS> +<CONSTRAINT> +<NAME>TUC_DATABASES_1</NAME> +<NAMETEMPLATE>TUC_%table%_%counter%</NAMETEMPLATE> +<ID>2</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<CONLEVEL>2</CONLEVEL> +<CONTYPE>2</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>3</ATTRIBUTEID> +</ATTRIBUTEIDS> +</CONSTRAINT> +</CONSTRAINTS> +</ENT> +</ENTITIES> +<SUBCATEGORIES> +</SUBCATEGORIES> +<TEXTAREAS> +</TEXTAREAS> +<GROUPBOXES> +</GROUPBOXES> +<STAMPS> +</STAMPS> +<SEQUENCES> +</SEQUENCES> +<PROCEDURES> +</PROCEDURES> +<VIEWS> +</VIEWS> +<RELATIONSHIPS> +<REL> +<NAME>DA_EX_FK</NAME> +<NAMETEMPLATE>DA_EX_FK</NAMETEMPLATE> +<ID>29</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<PARENTOBJECTID>16</PARENTOBJECTID> +<CHILDOBJECTID>17</CHILDOBJECTID> +<CARDINALITY>0</CARDINALITY> +<RELTYPE>1</RELTYPE> +<MANDATORYPARENT>1</MANDATORYPARENT> +<UPDATERULE>0</UPDATERULE> +<DELETERULE>0</DELETERULE> +<CONSTRAINT> +<NAME>DA_EX_FK</NAME> +<NAMETEMPLATE>DA_EX_FK</NAMETEMPLATE> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<CONLEVEL>2</CONLEVEL> +<CONTYPE>4</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>4</ATTRIBUTEID> +</ATTRIBUTEIDS> +</CONSTRAINT> +<PAIRS> +<PAIR> +<NAME></NAME> +<ID>0</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<KEYID>2</KEYID> +<FOREIGNKEYID>4</FOREIGNKEYID> +</PAIR> +</PAIRS> +</REL> +<REL> +<NAME>DA_SA_FK</NAME> +<NAMETEMPLATE>DA_SA_FK</NAMETEMPLATE> +<ID>30</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<PARENTOBJECTID>24</PARENTOBJECTID> +<CHILDOBJECTID>17</CHILDOBJECTID> +<CARDINALITY>0</CARDINALITY> +<RELTYPE>1</RELTYPE> +<MANDATORYPARENT>1</MANDATORYPARENT> +<UPDATERULE>0</UPDATERULE> +<DELETERULE>0</DELETERULE> +<CONSTRAINT> +<NAME>DA_SA_FK</NAME> +<NAMETEMPLATE>DA_SA_FK</NAMETEMPLATE> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<CONLEVEL>2</CONLEVEL> +<CONTYPE>4</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>5</ATTRIBUTEID> +</ATTRIBUTEIDS> +</CONSTRAINT> +<PAIRS> +<PAIR> +<NAME></NAME> +<ID>0</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<KEYID>2</KEYID> <FOREIGNKEYID>5</FOREIGNKEYID> </PAIR> </PAIRS> @@ -2146,7 +2475,7 @@ <CHILDOBJECTID>47</CHILDOBJECTID> <CARDINALITY>0</CARDINALITY> <RELTYPE>1</RELTYPE> -<MANDATORYPARENT>0</MANDATORYPARENT> +<MANDATORYPARENT>1</MANDATORYPARENT> <UPDATERULE>0</UPDATERULE> <DELETERULE>0</DELETERULE> <CONSTRAINT> @@ -2330,6 +2659,123 @@ </PAIR> </PAIRS> </REL> +<REL> +<NAME>DATABASES_SEQUENCES</NAME> +<NAMETEMPLATE>%parent%_%child%</NAMETEMPLATE> +<ID>111</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<PARENTOBJECTID>110</PARENTOBJECTID> +<CHILDOBJECTID>25</CHILDOBJECTID> +<CARDINALITY>0</CARDINALITY> +<RELTYPE>1</RELTYPE> +<MANDATORYPARENT>1</MANDATORYPARENT> +<UPDATERULE>0</UPDATERULE> +<DELETERULE>0</DELETERULE> +<CONSTRAINT> +<NAME>DATABASES_SEQUENCES</NAME> +<NAMETEMPLATE>%relname%</NAMETEMPLATE> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<CONLEVEL>2</CONLEVEL> +<CONTYPE>4</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>5</ATTRIBUTEID> +</ATTRIBUTEIDS> +</CONSTRAINT> +<PAIRS> +<PAIR> +<NAME></NAME> +<ID>0</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<KEYID>2</KEYID> +<FOREIGNKEYID>5</FOREIGNKEYID> +</PAIR> +</PAIRS> +</REL> +<REL> +<NAME>PROTEIN_REFERENCES_SEQUENCES</NAME> +<NAMETEMPLATE>%parent%_%child%</NAMETEMPLATE> +<ID>112</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<PARENTOBJECTID>98</PARENTOBJECTID> +<CHILDOBJECTID>25</CHILDOBJECTID> +<CARDINALITY>0</CARDINALITY> +<RELTYPE>1</RELTYPE> +<MANDATORYPARENT>1</MANDATORYPARENT> +<UPDATERULE>0</UPDATERULE> +<DELETERULE>0</DELETERULE> +<CONSTRAINT> +<NAME>PROTEIN_REFERENCES_SEQUENCES</NAME> +<NAMETEMPLATE>%relname%</NAMETEMPLATE> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<CONLEVEL>2</CONLEVEL> +<CONTYPE>4</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>6</ATTRIBUTEID> +</ATTRIBUTEIDS> +</CONSTRAINT> +<PAIRS> +<PAIR> +<NAME></NAME> +<ID>0</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<KEYID>2</KEYID> +<FOREIGNKEYID>6</FOREIGNKEYID> +</PAIR> +</PAIRS> +</REL> +<REL> +<NAME>DATABASES_DATA_SETS</NAME> +<NAMETEMPLATE>%parent%_%child%</NAMETEMPLATE> +<ID>125</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<PARENTOBJECTID>110</PARENTOBJECTID> +<CHILDOBJECTID>17</CHILDOBJECTID> +<CARDINALITY>0</CARDINALITY> +<RELTYPE>1</RELTYPE> +<MANDATORYPARENT>1</MANDATORYPARENT> +<UPDATERULE>0</UPDATERULE> +<DELETERULE>0</DELETERULE> +<CONSTRAINT> +<NAME>DATABASES_DATA_SETS</NAME> +<NAMETEMPLATE>%relname%</NAMETEMPLATE> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<CONLEVEL>2</CONLEVEL> +<CONTYPE>4</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>6</ATTRIBUTEID> +</ATTRIBUTEIDS> +</CONSTRAINT> +<PAIRS> +<PAIR> +<NAME></NAME> +<ID>0</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<KEYID>2</KEYID> +<FOREIGNKEYID>6</FOREIGNKEYID> +</PAIR> +</PAIRS> +</REL> </RELATIONSHIPS> <SUBCATEGORYCONNECTIONS> </SUBCATEGORYCONNECTIONS> @@ -2392,7 +2838,7 @@ <W>205</W> <H>78</H> <L>15</L> -<T>452</T> +<T>442</T> <BRUSH>0,16777215</BRUSH> <PEN>0,1,4,0</PEN> <FONT>Arial,8,,0,clWindowText,0</FONT> @@ -2416,7 +2862,7 @@ <ID>17</ID> <DIAGRAMID>1</DIAGRAMID> <W>141</W> -<H>93</H> +<H>108</H> <L>297</L> <T>24</T> <BRUSH>0,16777215</BRUSH> @@ -2441,9 +2887,9 @@ <ENTC> <ID>20</ID> <DIAGRAMID>1</DIAGRAMID> -<W>209</W> -<H>108</H> -<L>574</L> +<W>237</W> +<H>123</H> +<L>533</L> <T>603</T> <BRUSH>0,16777215</BRUSH> <PEN>0,1,4,0</PEN> @@ -2457,7 +2903,7 @@ <W>187</W> <H>93</H> <L>274</L> -<T>452</T> +<T>442</T> <BRUSH>0,16777215</BRUSH> <PEN>0,1,4,0</PEN> <FONT>Arial,8,,0,clWindowText,0</FONT> @@ -2494,9 +2940,9 @@ <ID>25</ID> <DIAGRAMID>1</DIAGRAMID> <W>250</W> -<H>78</H> -<L>533</L> -<T>452</T> +<H>108</H> +<L>735</L> +<T>289</T> <BRUSH>0,16777215</BRUSH> <PEN>0,1,4,0</PEN> <FONT>Arial,8,,0,clWindowText,0</FONT> @@ -2506,9 +2952,9 @@ <ENTC> <ID>47</ID> <DIAGRAMID>1</DIAGRAMID> -<W>168</W> -<H>93</H> -<L>615</L> +<W>142</W> +<H>78</H> +<L>533</L> <T>289</T> <BRUSH>0,16777215</BRUSH> <PEN>0,1,4,0</PEN> @@ -2534,8 +2980,34 @@ <DIAGRAMID>1</DIAGRAMID> <W>245</W> <H>93</H> -<L>538</L> -<T>166</T> +<L>457</L> +<T>176</T> +<BRUSH>0,16777215</BRUSH> +<PEN>0,1,4,0</PEN> +<FONT>Arial,8,,0,clWindowText,0</FONT> +<TR>0</TR> +<AS>1</AS> +</ENTC> +<ENTC> +<ID>98</ID> +<DIAGRAMID>1</DIAGRAMID> +<W>255</W> +<H>78</H> +<L>730</L> +<T>442</T> +<BRUSH>0,16777215</BRUSH> +<PEN>0,1,4,0</PEN> +<FONT>Arial,8,,0,clWindowText,0</FONT> +<TR>0</TR> +<AS>1</AS> +</ENTC> +<ENTC> +<ID>110</ID> +<DIAGRAMID>1</DIAGRAMID> +<W>252</W> +<H>63</H> +<L>733</L> +<T>107</T> <BRUSH>0,16777215</BRUSH> <PEN>0,1,4,0</PEN> <FONT>Arial,8,,0,clWindowText,0</FONT> @@ -2560,7 +3032,7 @@ <FROMRELATIVEX>5000</FROMRELATIVEX> <FROMRELATIVEY>4921</FROMRELATIVEY> <TORELATIVEX>5000</TORELATIVEX> -<TORELATIVEY>3333</TORELATIVEY> +<TORELATIVEY>2870</TORELATIVEY> <POINTS> <POINT> <X>646</X> @@ -2588,7 +3060,7 @@ <FROMRELATIVEX>5000</FROMRELATIVEX> <FROMRELATIVEY>5000</FROMRELATIVEY> <TORELATIVEX>5000</TORELATIVEX> -<TORELATIVEY>4194</TORELATIVEY> +<TORELATIVEY>3611</TORELATIVEY> <POINTS> <POINT> <X>151</X> @@ -2620,7 +3092,7 @@ <POINTS> <POINT> <X>367</X> -<Y>545</Y> +<Y>535</Y> </POINT> <POINT> <X>367</X> @@ -2642,20 +3114,20 @@ <FONT>Arial,8,,0,clWindowText,0</FONT> <PEN>1,1,4,0</PEN> <FROMRELATIVEX>5000</FROMRELATIVEX> -<FROMRELATIVEY>5000</FROMRELATIVEY> +<FROMRELATIVEY>4390</FROMRELATIVEY> <TORELATIVEX>5000</TORELATIVEX> <TORELATIVEY>5000</TORELATIVEY> <POINTS> <POINT> -<X>573</X> +<X>532</X> <Y>657</Y> </POINT> <POINT> -<X>541</X> +<X>494</X> <Y>657</Y> </POINT> <POINT> -<X>541</X> +<X>494</X> <Y>657</Y> </POINT> <POINT> @@ -2688,7 +3160,7 @@ </POINT> <POINT> <X>367</X> -<Y>451</Y> +<Y>441</Y> </POINT> </POINTS> </RELC> @@ -2704,15 +3176,15 @@ <POINTS> <POINT> <X>367</X> -<Y>117</Y> +<Y>132</Y> </POINT> <POINT> <X>367</X> -<Y>142</Y> +<Y>210</Y> </POINT> <POINT> <X>367</X> -<Y>142</Y> +<Y>210</Y> </POINT> <POINT> <X>367</X> @@ -2728,7 +3200,7 @@ <FROMRELATIVEX>5000</FROMRELATIVEX> <FROMRELATIVEY>5000</FROMRELATIVEY> <TORELATIVEX>5000</TORELATIVEX> -<TORELATIVEY>4194</TORELATIVEY> +<TORELATIVEY>5000</TORELATIVEY> <POINTS> <POINT> <X>457</X> @@ -2743,7 +3215,7 @@ <Y>328</Y> </POINT> <POINT> -<X>614</X> +<X>532</X> <Y>328</Y> </POINT> </POINTS> @@ -2753,26 +3225,26 @@ <DIAGRAMID>1</DIAGRAMID> <FONT>Arial,8,,0,clWindowText,0</FONT> <PEN>1,1,4,0</PEN> -<FROMRELATIVEX>6640</FROMRELATIVEX> -<FROMRELATIVEY>5000</FROMRELATIVEY> 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+<KEYID>2</KEYID> +<FOREIGNKEYID>4</FOREIGNKEYID> +</PAIR> +</PAIRS> +</REL> +<REL> +<NAME>PR_SE_FK</NAME> +<NAMETEMPLATE>PR_SE_FK</NAMETEMPLATE> +<ID>39</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<PARENTOBJECTID>25</PARENTOBJECTID> +<CHILDOBJECTID>23</CHILDOBJECTID> +<CARDINALITY>0</CARDINALITY> +<RELTYPE>1</RELTYPE> +<MANDATORYPARENT>0</MANDATORYPARENT> +<UPDATERULE>0</UPDATERULE> +<DELETERULE>0</DELETERULE> +<CONSTRAINT> +<NAME>PR_SE_FK</NAME> +<NAMETEMPLATE>PR_SE_FK</NAMETEMPLATE> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<CONLEVEL>2</CONLEVEL> +<CONTYPE>4</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>5</ATTRIBUTEID> +</ATTRIBUTEIDS> +</CONSTRAINT> +<PAIRS> +<PAIR> +<NAME></NAME> +<ID>0</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<KEYID>2</KEYID> +<FOREIGNKEYID>5</FOREIGNKEYID> +</PAIR> +</PAIRS> +</REL> +<REL> +<NAME>PR_PS_FK</NAME> +<NAMETEMPLATE>PR_PS_FK</NAMETEMPLATE> +<ID>41</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<PARENTOBJECTID>22</PARENTOBJECTID> +<CHILDOBJECTID>23</CHILDOBJECTID> +<CARDINALITY>0</CARDINALITY> +<RELTYPE>1</RELTYPE> +<MANDATORYPARENT>0</MANDATORYPARENT> +<UPDATERULE>0</UPDATERULE> +<DELETERULE>0</DELETERULE> +<CONSTRAINT> +<NAME>PR_PS_FK</NAME> +<NAMETEMPLATE>PR_PS_FK</NAMETEMPLATE> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<CONLEVEL>2</CONLEVEL> +<CONTYPE>4</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>6</ATTRIBUTEID> +</ATTRIBUTEIDS> +</CONSTRAINT> +<PAIRS> +<PAIR> +<NAME></NAME> +<ID>0</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<KEYID>2</KEYID> +<FOREIGNKEYID>6</FOREIGNKEYID> +</PAIR> +</PAIRS> +</REL> +<REL> +<NAME>ABUNDANCES_TYPES_PROTEINS</NAME> +<NAMETEMPLATE>ABUNDANCES_TYPES_PROTEINS</NAMETEMPLATE> +<ID>43</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<PARENTOBJECTID>14</PARENTOBJECTID> +<CHILDOBJECTID>23</CHILDOBJECTID> +<CARDINALITY>0</CARDINALITY> +<RELTYPE>1</RELTYPE> +<MANDATORYPARENT>0</MANDATORYPARENT> +<UPDATERULE>0</UPDATERULE> +<DELETERULE>0</DELETERULE> +<CONSTRAINT> +<NAME>ABUNDANCES_TYPES_PROTEINS</NAME> +<NAMETEMPLATE>ABUNDANCES_TYPES_PROTEINS</NAMETEMPLATE> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<CONLEVEL>2</CONLEVEL> +<CONTYPE>4</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>8</ATTRIBUTEID> +</ATTRIBUTEIDS> +</CONSTRAINT> +<PAIRS> +<PAIR> +<NAME></NAME> +<ID>0</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<KEYID>2</KEYID> +<FOREIGNKEYID>8</FOREIGNKEYID> +</PAIR> +</PAIRS> +</REL> +<REL> +<NAME>ABUNDANCES_TYPES_PEPTIDES</NAME> +<NAMETEMPLATE>ABUNDANCES_TYPES_PEPTIDES</NAMETEMPLATE> +<ID>44</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<PARENTOBJECTID>14</PARENTOBJECTID> +<CHILDOBJECTID>21</CHILDOBJECTID> +<CARDINALITY>0</CARDINALITY> +<RELTYPE>1</RELTYPE> +<MANDATORYPARENT>0</MANDATORYPARENT> +<UPDATERULE>0</UPDATERULE> +<DELETERULE>0</DELETERULE> +<CONSTRAINT> +<NAME>ABUNDANCES_TYPES_PEPTIDES</NAME> +<NAMETEMPLATE>ABUNDANCES_TYPES_PEPTIDES</NAMETEMPLATE> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<CONLEVEL>2</CONLEVEL> +<CONTYPE>4</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>8</ATTRIBUTEID> +</ATTRIBUTEIDS> +</CONSTRAINT> +<PAIRS> +<PAIR> +<NAME></NAME> +<ID>0</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<KEYID>2</KEYID> +<FOREIGNKEYID>8</FOREIGNKEYID> +</PAIR> +</PAIRS> +</REL> +<REL> +<NAME>DATA_SETS_PROTEINS</NAME> +<NAMETEMPLATE>DATA_SETS_PROTEINS</NAMETEMPLATE> +<ID>46</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<PARENTOBJECTID>17</PARENTOBJECTID> +<CHILDOBJECTID>23</CHILDOBJECTID> +<CARDINALITY>0</CARDINALITY> +<RELTYPE>1</RELTYPE> +<MANDATORYPARENT>1</MANDATORYPARENT> +<UPDATERULE>0</UPDATERULE> +<DELETERULE>0</DELETERULE> +<CONSTRAINT> +<NAME>DATA_SETS_PROTEINS</NAME> +<NAMETEMPLATE>DATA_SETS_PROTEINS</NAMETEMPLATE> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<CONLEVEL>2</CONLEVEL> +<CONTYPE>4</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>10</ATTRIBUTEID> +</ATTRIBUTEIDS> +</CONSTRAINT> +<PAIRS> +<PAIR> +<NAME></NAME> +<ID>0</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<KEYID>2</KEYID> +<FOREIGNKEYID>10</FOREIGNKEYID> +</PAIR> +</PAIRS> +</REL> +</RELATIONSHIPS> +<SUBCATEGORYCONNECTIONS> +</SUBCATEGORYCONNECTIONS> +</DATADICT> +</VERSION> +<VERSION> +<VERSIONINFO> +<VERSIONNUMBER>2</VERSIONNUMBER> +<VERSIONLABEL>Version 2009-06-29 1</VERSIONLABEL> +<VERSIONDATE>2009-06-29 11:02</VERSIONDATE> <VERSIONCOMMENTS></VERSIONCOMMENTS> <VERSIONTYPE>DB</VERSIONTYPE> <VERSIONTYPEDESC>Data dictionary only (no diagrams)</VERSIONTYPEDESC> @@ -4176,7 +7053,7 @@ <SCHEMA></SCHEMA> <DESC></DESC> <ATTRLASTID>10</ATTRLASTID> -<IDXLASTID>5</IDXLASTID> +<IDXLASTID>7</IDXLASTID> <TRGLASTID>1</TRGLASTID> <CONLASTID>1</CONLASTID> <PKCON> @@ -4366,6 +7243,26 @@ </IDXCOL> </IDXCOLS> </INDEX> +<INDEX> +<NAME>IDX_PROTEINS_3</NAME> +<NAMETEMPLATE>IDX_PROTEINS_3</NAMETEMPLATE> +<ID>6</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<RELID>0</RELID> +<AUTOIDXTYPE>0</AUTOIDXTYPE> +<IDXCOLS> +<IDXCOL> +<NAME>DASE_ID</NAME> +<ID>0</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<IDXCOLATTRID>10</IDXCOLATTRID> +</IDXCOL> +</IDXCOLS> +</INDEX> </INDEXES> </ENT> <ENT> @@ -4681,21 +7578,6 @@ <STAMPS> </STAMPS> <SEQUENCES> -<SEQUENCE> -<NAME>SEQ</NAME> -<ID>10</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<INCREMENT>1</INCREMENT> -<SEED>0</SEED> -<MAX>NOMAXVALUE</MAX> -<MIN>NOMINVALUE</MIN> -<CACHE></CACHE> -<CACHECODE></CACHECODE> -<CYCLE></CYCLE> -<ORDER></ORDER> -</SEQUENCE> </SEQUENCES> <PROCEDURES> </PROCEDURES> @@ -5216,16 +8098,16 @@ </VERSION> <VERSION> <VERSIONINFO> -<VERSIONNUMBER>2</VERSIONNUMBER> -<VERSIONLABEL>Version 2009-06-29 1</VERSIONLABEL> -<VERSIONDATE>2009-06-29 11:02</VERSIONDATE> +<VERSIONNUMBER>3</VERSIONNUMBER> +<VERSIONLABEL>Version 2009-06-29 2</VERSIONLABEL> +<VERSIONDATE>2009-06-29 12:29</VERSIONDATE> <VERSIONCOMMENTS></VERSIONCOMMENTS> <VERSIONTYPE>DB</VERSIONTYPE> <VERSIONTYPEDESC>Data dictionary only (no diagrams)</VERSIONTYPEDESC> </VERSIONINFO> <DATADICT> <DBID>postgresql8</DBID> -<LASTID>46</LASTID> +<LASTID>48</LASTID> <DDSETTINGS> <PKCONNAMETEMPLATE>PK_%table%</PKCONNAMETEMPLATE> <FKCONNAMETEMPLATE>%relname%</FKCONNAMETEMPLATE> @@ -5382,6 +8264,7 @@ <ENTITIES> <ENT> <NAME>ABUNDANCES_TYPES</NAME> +<NAMETEMPLATE>PK_%table%</NAMETEMPLATE> <ID>14</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -5490,6 +8373,7 @@ </ENT> <ENT> <NAME>EXPERIMENTS</NAME> +<NAMETEMPLATE>PK_%table%</NAMETEMPLATE> <ID>16</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -6073,6 +8957,7 @@ </ENT> <ENT> <NAME>MODIFICATION_TYPES</NAME> +<NAMETEMPLATE>PK_%table%</NAMETEMPLATE> <ID>20</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -6439,6 +9324,7 @@ </ENT> <ENT> <NAME>PROTEIN_STATISTICS</NAME> +<NAMETEMPLATE>PK_%table%</NAMETEMPLATE> <ID>22</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -6542,6 +9428,7 @@ </ATTR> <ATTR> <NAME>DASE_ID</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> <ID>10</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -6606,33 +9493,6 @@ </DT> </ATTR> <ATTR> -<NAME>DESCRIPTION</NAME> -<ID>7</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<DOMAINID>6</DOMAINID> -<DT> -<DTLISTNAME>CHARACTER VARYING</DTLISTNAME> -<LE>2000</LE> -<SD>0</SD> -<INC>1</INC> -</DT> -<NNCON> -<NAME></NAME> -<ID>1</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<VALUE>1</VALUE> -<CONLEVEL>1</CONLEVEL> -<CONTYPE>5</CONTYPE> -<ATTRIBUTEIDS> -<ATTRIBUTEID>7</ATTRIBUTEID> -</ATTRIBUTEIDS> -</NNCON> -</ATTR> -<ATTR> <NAME>ABUNDANCE</NAME> <ID>9</ID> <POSNR>0</POSNR> @@ -6711,6 +9571,7 @@ </ENT> <ENT> <NAME>SAMPLES</NAME> +<NAMETEMPLATE>PK_%table%</NAMETEMPLATE> <ID>24</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -6831,6 +9692,7 @@ </ENT> <ENT> <NAME>SEQUENCES</NAME> +<NAMETEMPLATE>PK_%table%</NAMETEMPLATE> <ID>25</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -6880,14 +9742,120 @@ </NNCON> </ATTR> <ATTR> -<NAME>AMINO_ACID_SEQUENCE</NAME> +<NAME>AMINO_ACID_SEQUENCE</NAME> +<ID>3</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<DOMAINID>9</DOMAINID> +<DT> +<DTLISTNAME>TEXT</DTLISTNAME> +<SD>0</SD> +<INC>1</INC> +</DT> +<NNCON> +<NAME></NAME> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<VALUE>1</VALUE> +<CONLEVEL>1</CONLEVEL> +<CONTYPE>5</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>3</ATTRIBUTEID> +</ATTRIBUTEIDS> +</NNCON> +</ATTR> +<ATTR> +<NAME>CHECKSUM</NAME> +<ID>4</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<DOMAINID>4</DOMAINID> +<DT> +<DTLISTNAME>CHARACTER VARYING</DTLISTNAME> +<LE>8</LE> +<SD>0</SD> +<INC>1</INC> +</DT> +<NNCON> +<NAME></NAME> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<VALUE>1</VALUE> +<CONLEVEL>1</CONLEVEL> +<CONTYPE>5</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>4</ATTRIBUTEID> +</ATTRIBUTEIDS> +</NNCON> +</ATTR> +</ATTRIBUTES> +</ENT> +<ENT> +<NAME>SPECTRA</NAME> +<NAMETEMPLATE>PK_%table%</NAMETEMPLATE> +<ID>26</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<ATTRLASTID>3</ATTRLASTID> +<IDXLASTID>1</IDXLASTID> +<TRGLASTID>1</TRGLASTID> +<CONLASTID>1</CONLASTID> +<PKCON> +<NAME>PK_SPECTRA</NAME> +<NAMETEMPLATE>PK_SPECTRA</NAMETEMPLATE> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<CONLEVEL>2</CONLEVEL> +<CONTYPE>3</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>2</ATTRIBUTEID> +</ATTRIBUTEIDS> +</PKCON> +<ATTRIBUTES> +<ATTR> +<NAME>ID</NAME> +<ID>2</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<DOMAINID>-1</DOMAINID> +<DT> +<DTLISTNAME>BIGSERIAL</DTLISTNAME> +<SD>0</SD> +<INC>1</INC> +</DT> +<NNCON> +<NAME></NAME> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<VALUE>1</VALUE> +<CONLEVEL>1</CONLEVEL> +<CONTYPE>5</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>2</ATTRIBUTEID> +</ATTRIBUTEIDS> +</NNCON> +</ATTR> +<ATTR> +<NAME>DATA</NAME> <ID>3</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> -<DOMAINID>9</DOMAINID> +<DOMAINID>3</DOMAINID> <DT> -<DTLISTNAME>TEXT</DTLISTNAME> +<DTLISTNAME>BYTEA</DTLISTNAME> <SD>0</SD> <INC>1</INC> </DT> @@ -6905,48 +9873,21 @@ </ATTRIBUTEIDS> </NNCON> </ATTR> -<ATTR> -<NAME>CHECKSUM</NAME> -<ID>4</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<DOMAINID>4</DOMAINID> -<DT> -<DTLISTNAME>CHARACTER VARYING</DTLISTNAME> -<LE>8</LE> -<SD>0</SD> -<INC>1</INC> -</DT> -<NNCON> -<NAME></NAME> -<ID>1</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<VALUE>1</VALUE> -<CONLEVEL>1</CONLEVEL> -<CONTYPE>5</CONTYPE> -<ATTRIBUTEIDS> -<ATTRIBUTEID>4</ATTRIBUTEID> -</ATTRIBUTEIDS> -</NNCON> -</ATTR> </ATTRIBUTES> </ENT> <ENT> -<NAME>SPECTRA</NAME> -<ID>26</ID> +<NAME>IDENTIFIED_PROTEINS</NAME> +<ID>47</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> -<ATTRLASTID>3</ATTRLASTID> +<ATTRLASTID>4</ATTRLASTID> <IDXLASTID>1</IDXLASTID> <TRGLASTID>1</TRGLASTID> <CONLASTID>1</CONLASTID> <PKCON> -<NAME>PK_SPECTRA</NAME> -<NAMETEMPLATE>PK_SPECTRA</NAMETEMPLATE> +<NAME>PK_IDENTIFIED_PROTEINS</NAME> +<NAMETEMPLATE>PK_IDENTIFIED_PROTEINS</NAMETEMPLATE> <ID>1</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -6985,14 +9926,14 @@ </NNCON> </ATTR> <ATTR> -<NAME>DATA</NAME> +<NAME>PROT_ID</NAME> <ID>3</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> -<DOMAINID>3</DOMAINID> +<DOMAINID>12</DOMAINID> <DT> -<DTLISTNAME>BYTEA</DTLISTNAME> +<DTLISTNAME>BIGINT</DTLISTNAME> <SD>0</SD> <INC>1</INC> </DT> @@ -7010,6 +9951,33 @@ </ATTRIBUTEIDS> </NNCON> </ATTR> +<ATTR> +<NAME>DESCRIPTION</NAME> +<ID>4</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<DOMAINID>6</DOMAINID> +<DT> +<DTLISTNAME>CHARACTER VARYING</DTLISTNAME> +<LE>2000</LE> +<SD>0</SD> +<INC>1</INC> +</DT> +<NNCON> +<NAME></NAME> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<VALUE>1</VALUE> +<CONLEVEL>1</CONLEVEL> +<CONTYPE>5</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>4</ATTRIBUTEID> +</ATTRIBUTEIDS> +</NNCON> +</ATTR> </ATTRIBUTES> </ENT> </ENTITIES> @@ -7535,6 +10503,45 @@ </PAIR> </PAIRS> </REL> +<REL> +<NAME>PROTEINS_IDENTIFIED_PROTEINS</NAME> +<NAMETEMPLATE>PROTEINS_IDENTIFIED_PROTEINS</NAMETEMPLATE> +<ID>48</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<PARENTOBJECTID>23</PARENTOBJECTID> +<CHILDOBJECTID>47</CHILDOBJECTID> +<CARDINALITY>0</CARDINALITY> +<RELTYPE>1</RELTYPE> +<MANDATORYPARENT>1</MANDATORYPARENT> +<UPDATERULE>0</UPDATERULE> +<DELETERULE>0</DELETERULE> +<CONSTRAINT> +<NAME>PROTEINS_IDENTIFIED_PROTEINS</NAME> +<NAMETEMPLATE>PROTEINS_IDENTIFIED_PROTEINS</NAMETEMPLATE> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<CONLEVEL>2</CONLEVEL> +<CONTYPE>4</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>3</ATTRIBUTEID> +</ATTRIBUTEIDS> +</CONSTRAINT> +<PAIRS> +<PAIR> +<NAME></NAME> +<ID>0</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<KEYID>2</KEYID> +<FOREIGNKEYID>3</FOREIGNKEYID> +</PAIR> +</PAIRS> +</REL> </RELATIONSHIPS> <SUBCATEGORYCONNECTIONS> </SUBCATEGORYCONNECTIONS> @@ -7542,16 +10549,16 @@ </VERSION> <VERSION> <VERSIONINFO> -<VERSIONNUMBER>3</VERSIONNUMBER> -<VERSIONLABEL>Version 2009-06-29 2</VERSIONLABEL> -<VERSIONDATE>2009-06-29 12:29</VERSIONDATE> +<VERSIONNUMBER>4</VERSIONNUMBER> +<VERSIONLABEL>Version 2009-06-30</VERSIONLABEL> +<VERSIONDATE>2009-06-30 09:00</VERSIONDATE> <VERSIONCOMMENTS></VERSIONCOMMENTS> <VERSIONTYPE>DB</VERSIONTYPE> <VERSIONTYPEDESC>Data dictionary only (no diagrams)</VERSIONTYPEDESC> </VERSIONINFO> <DATADICT> <DBID>postgresql8</DBID> -<LASTID>48</LASTID> +<LASTID>97</LASTID> <DDSETTINGS> <PKCONNAMETEMPLATE>PK_%table%</PKCONNAMETEMPLATE> <FKCONNAMETEMPLATE>%relname%</FKCONNAMETEMPLATE> @@ -7668,7 +10675,7 @@ </DT> </DOMAIN> <DOMAIN> -<NAME>SEQUENCE</NAME> +<NAME>LONG_SEQUENCE</NAME> <ID>9</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -7704,6 +10711,19 @@ <INC>1</INC> </DT> </DOMAIN> +<DOMAIN> +<NAME>SHORT_SEQUENCE</NAME> +<ID>69</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<DT> +<DTLISTNAME>CHARACTER VARYING</DTLISTNAME> +<LE>1000</LE> +<SD>0</SD> +<INC>1</INC> +</DT> +</DOMAIN> </DOMAINS> <ENTITIES> <ENT> @@ -8078,127 +11098,26 @@ <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> -<IDXCOLATTRID>5</IDXCOLATTRID> -</IDXCOL> -</IDXCOLS> -</INDEX> -</INDEXES> -<CONSTRAINTS> -<CONSTRAINT> -<NAME>TUC_DATA_SETS_1</NAME> -<NAMETEMPLATE>TUC_DATA_SETS_1</NAMETEMPLATE> -<ID>2</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<CONLEVEL>2</CONLEVEL> -<CONTYPE>2</CONTYPE> -<ATTRIBUTEIDS> -<ATTRIBUTEID>3</ATTRIBUTEID> -</ATTRIBUTEIDS> -</CONSTRAINT> -</CONSTRAINTS> -</ENT> -<ENT> -<NAME>IDENTIFICATION_DATA</NAME> -<NAMETEMPLATE>IX_FK_IDENTIFICATION_DATA_SPECTRA</NAMETEMPLATE> -<ID>18</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<ATTRLASTID>4</ATTRLASTID> -<IDXLASTID>2</IDXLASTID> -<TRGLASTID>1</TRGLASTID> -<CONLASTID>1</CONLASTID> -<PKCON> -<NAME>PK_IDENTIFICATION_DATA</NAME> -<NAMETEMPLATE>PK_IDENTIFICATION_DATA</NAMETEMPLATE> -<ID>1</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<CONLEVEL>2</CONLEVEL> -<CONTYPE>3</CONTYPE> -<ATTRIBUTEIDS> -<ATTRIBUTEID>2</ATTRIBUTEID> -</ATTRIBUTEIDS> -</PKCON> -<ATTRIBUTES> -<ATTR> -<NAME>ID</NAME> -<ID>2</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<DOMAINID>-1</DOMAINID> -<DT> -<DTLISTNAME>BIGSERIAL</DTLISTNAME> -<SD>0</SD> -<INC>1</INC> -</DT> -<NNCON> -<NAME></NAME> -<ID>1</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<VALUE>1</VALUE> -<CONLEVEL>1</CONLEVEL> -<CONTYPE>5</CONTYPE> -<ATTRIBUTEIDS> -<ATTRIBUTEID>2</ATTRIBUTEID> -</ATTRIBUTEIDS> -</NNCON> -</ATTR> -<ATTR> -<NAME>SPEC_ID</NAME> -<ID>3</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<DOMAINID>12</DOMAINID> -<DT> -<DTLISTNAME>BIGINT</DTLISTNAME> -<SD>0</SD> -<INC>1</INC> -</DT> -</ATTR> -<ATTR> -<NAME>SPECTRA_COUNT</NAME> -<ID>4</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<DOMAINID>7</DOMAINID> -<DT> -<DTLISTNAME>INTEGER</DTLISTNAME> -<SD>0</SD> -<INC>1</INC> -</DT> -</ATTR> -</ATTRIBUTES> -<INDEXES> -<INDEX> -<NAME>IX_FK_IDENTIFICATION_DATA_SPECTRA</NAME> -<NAMETEMPLATE>IX_FK_IDENTIFICATION_DATA_SPECTRA</NAMETEMPLATE> -<ID>2</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<RELID>0</RELID> -<AUTOIDXTYPE>0</AUTOIDXTYPE> -<IDXCOLS> -<IDXCOL> -<NAME>SPEC_ID</NAME> -<ID>0</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<IDXCOLATTRID>3</IDXCOLATTRID> +<IDXCOLATTRID>5</IDXCOLATTRID> </IDXCOL> </IDXCOLS> </INDEX> </INDEXES> +<CONSTRAINTS> +<CONSTRAINT> +<NAME>TUC_DATA_SETS_1</NAME> +<NAMETEMPLATE>TUC_DATA_SETS_1</NAMETEMPLATE> +<ID>2</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<CONLEVEL>2</CONLEVEL> +<CONTYPE>2</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>3</ATTRIBUTEID> +</ATTRIBUTEIDS> +</CONSTRAINT> +</CONSTRAINTS> </ENT> <ENT> <NAME>MODIFICATIONS</NAME> @@ -8541,7 +11460,7 @@ <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> -<ATTRLASTID>9</ATTRLASTID> +<ATTRLASTID>10</ATTRLASTID> <IDXLASTID>5</IDXLASTID> <TRGLASTID>1</TRGLASTID> <CONLASTID>1</CONLASTID> @@ -8612,14 +11531,15 @@ </NNCON> </ATTR> <ATTR> -<NAME>SEQU_ID</NAME> -<ID>4</ID> +<NAME>SEQUENCE</NAME> +<ID>10</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> -<DOMAINID>12</DOMAINID> +<DOMAINID>69</DOMAINID> <DT> -<DTLISTNAME>BIGINT</DTLISTNAME> +<DTLISTNAME>CHARACTER VARYING</DTLISTNAME> +<LE>1000</LE> <SD>0</SD> <INC>1</INC> </DT> @@ -8633,37 +11553,11 @@ <CONLEVEL>1</CONLEVEL> <CONTYPE>5</CONTYPE> <ATTRIBUTEIDS> -<ATTRIBUTEID>4</ATTRIBUTEID> +<ATTRIBUTEID>10</ATTRIBUTEID> </ATTRIBUTEIDS> </NNCON> </ATTR> <ATTR> -<NAME>ABTY_ID</NAME> -<ID>8</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<DOMAINID>12</DOMAINID> -<DT> -<DTLISTNAME>BIGINT</DTLISTNAME> -<SD>0</SD> -<INC>1</INC> -</DT> -</ATTR> -<ATTR> -<NAME>IDDA_ID</NAME> -<ID>6</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<DOMAINID>12</DOMAINID> -<DT> -<DTLISTNAME>BIGINT</DTLISTNAME> -<SD>0</SD> -<INC>1</INC> -</DT> -</ATTR> -<ATTR> <NAME>CHARGE</NAME> <ID>7</ID> <POSNR>0</POSNR> @@ -8689,42 +11583,9 @@ </ATTRIBUTEIDS> </NNCON> </ATTR> -<ATTR> -<NAME>ABUNDANCE</NAME> -<ID>9</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<DOMAINID>8</DOMAINID> -<DT> -<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME> -<SD>0</SD> -<INC>1</INC> -</DT> -</ATTR> </ATTRIBUTES> <INDEXES> <INDEX> -<NAME>IX_FK_PEPTIDES_IDENTIFICATION_DATA</NAME> -<NAMETEMPLATE>IX_FK_PEPTIDES_IDENTIFICATION_DATA</NAMETEMPLATE> -<ID>3</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<RELID>0</RELID> -<AUTOIDXTYPE>0</AUTOIDXTYPE> -<IDXCOLS> -<IDXCOL> -<NAME>IDDA_ID</NAME> -<ID>0</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<IDXCOLATTRID>6</IDXCOLATTRID> -</IDXCOL> -</IDXCOLS> -</INDEX> -<INDEX> <NAME>IX_FK_PEPTIDES_PROTEINS</NAME> <NAMETEMPLATE>IX_FK_PEPTIDES_PROTEINS</NAMETEMPLATE> <ID>4</ID> @@ -8744,89 +11605,16 @@ </IDXCOL> </IDXCOLS> </INDEX> -<INDEX> -<NAME>IX_FK_PEPTIDES_SEQUENCES</NAME> -<NAMETEMPLATE>IX_FK_PEPTIDES_SEQUENCES</NAMETEMPLATE> -<ID>5</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<RELID>0</RELID> -<AUTOIDXTYPE>0</AUTOIDXTYPE> -<IDXCOLS> -<IDXCOL> -<NAME>SEQU_ID</NAME> -<ID>0</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<IDXCOLATTRID>4</IDXCOLATTRID> -</IDXCOL> -</IDXCOLS> -</INDEX> </INDEXES> </ENT> <ENT> -<NAME>PROTEIN_STATISTICS</NAME> -<NAMETEMPLATE>PK_%table%</NAMETEMPLATE> -<ID>22</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<ATTRLASTID>2</ATTRLASTID> -<IDXLASTID>1</IDXLASTID> -<TRGLASTID>1</TRGLASTID> -<CONLASTID>1</CONLASTID> -<PKCON> -<NAME>PK_PROTEIN_STATISTICS</NAME> -<NAMETEMPLATE>PK_PROTEIN_STATISTICS</NAMETEMPLATE> -<ID>1</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<CONLEVEL>2</CONLEVEL> -<CONTYPE>3</CONTYPE> -<ATTRIBUTEIDS> -<ATTRIBUTEID>2</ATTRIBUTEID> -</ATTRIBUTEIDS> -</PKCON> -<ATTRIBUTES> -<ATTR> -<NAME>ID</NAME> -<ID>2</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<DOMAINID>-1</DOMAINID> -<DT> -<DTLISTNAME>BIGSERIAL</DTLISTNAME> -<SD>0</SD> -<INC>1</INC> -</DT> -<NNCON> -<NAME></NAME> -<ID>1</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<VALUE>1</VALUE> -<CONLEVEL>1</CONLEVEL> -<CONTYPE>5</CONTYPE> -<ATTRIBUTEIDS> -<ATTRIBUTEID>2</ATTRIBUTEID> -</ATTRIBUTEIDS> -</NNCON> -</ATTR> -</ATTRIBUTES> -</ENT> -<ENT> <NAME>PROTEINS</NAME> <NAMETEMPLATE>IX_FK_PROTEINS_DATA_SETS</NAMETEMPLATE> <ID>23</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> -<ATTRLASTID>10</ATTRLASTID> +<ATTRLASTID>11</ATTRLASTID> <IDXLASTID>7</IDXLASTID> <TRGLASTID>1</TRGLASTID> <CONLASTID>1</CONLASTID> @@ -8898,46 +11686,7 @@ </NNCON> </ATTR> <ATTR> -<NAME>SEQU_ID</NAME> -<ID>5</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<DOMAINID>12</DOMAINID> -<DT> -<DTLISTNAME>BIGINT</DTLISTNAME> -<SD>0</SD> -<INC>1</INC> -</DT> -</ATTR> -<ATTR> -<NAME>ABTY_ID</NAME> -<ID>8</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<DOMAINID>12</DOMAINID> -<DT> -<DTLISTNAME>BIGINT</DTLISTNAME> -<SD>0</SD> -<INC>1</INC> -</DT> -</ATTR> -<ATTR> -<NAME>PRST_ID</NAME> -<ID>6</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<DOMAINID>12</DOMAINID> -<DT> -<DTLISTNAME>BIGINT</DTLISTNAME> -<SD>0</SD> -<INC>1</INC> -</DT> -</ATTR> -<ATTR> -<NAME>ABUNDANCE</NAME> +<NAME>PROBABILITY</NAME> <ID>9</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -8948,52 +11697,25 @@ <SD>0</SD> <INC>1</INC> </DT> -</ATTR> -</ATTRIBUTES> -<INDEXES> -<INDEX> -<NAME>IX_FK_PROTEINS_SEQUENCES</NAME> -<NAMETEMPLATE>IX_FK_PROTEINS_SEQUENCES</NAMETEMPLATE> -<ID>3</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<RELID>0</RELID> -<AUTOIDXTYPE>0</AUTOIDXTYPE> -<IDXCOLS> -<IDXCOL> -<NAME>SEQU_ID</NAME> -<ID>0</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<IDXCOLATTRID>5</IDXCOLATTRID> -</IDXCOL> -</IDXCOLS> -</INDEX> -<INDEX> -<NAME>IX_FK_PROTEINS_PROTEIN_STATISTICS</NAME> -<NAMETEMPLATE>IX_FK_PROTEINS_PROTEIN_STATISTICS</NAMETEMPLATE> -<ID>5</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<RELID>0</RELID> -<AUTOIDXTYPE>0</AUTOIDXTYPE> -<IDXCOLS> -<IDXCOL> -<NAME>PRST_ID</NAME> -<ID>0</ID> +<NNCON> +<NAME></NAME> +<ID>1</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> -<IDXCOLATTRID>6</IDXCOLATTRID> -</IDXCOL> -</IDXCOLS> -</INDEX> +<VALUE>1</VALUE> +<CONLEVEL>1</CONLEVEL> +<CONTYPE>5</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>9</ATTRIBUTEID> +</ATTRIBUTEIDS> +</NNCON> +</ATTR> +</ATTRIBUTES> +<INDEXES> <INDEX> -<NAME>IDX_PROTEINS_3</NAME> -<NAMETEMPLATE>IDX_PROTEINS_3</NAMETEMPLATE> +<NAME>IDX_PROTEINS_1</NAME> +<NAMETEMPLATE>IDX_PROTEINS_1</NAMETEMPLATE> <ID>6</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -9241,19 +11963,19 @@ </ATTRIBUTES> </ENT> <ENT> -<NAME>SPECTRA</NAME> +<NAME>IDENTIFIED_PROTEINS</NAME> <NAMETEMPLATE>PK_%table%</NAMETEMPLATE> -<ID>26</ID> +<ID>47</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> -<ATTRLASTID>3</ATTRLASTID> +<ATTRLASTID>5</ATTRLASTID> <IDXLASTID>1</IDXLASTID> <TRGLASTID>1</TRGLASTID> <CONLASTID>1</CONLASTID> <PKCON> -<NAME>PK_SPECTRA</NAME> -<NAMETEMPLATE>PK_SPECTRA</NAMETEMPLATE> +<NAME>PK_IDENTIFIED_PROTEINS</NAME> +<NAMETEMPLATE>PK_IDENTIFIED_PROTEINS</NAMETEMPLATE> <ID>1</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -9267,6 +11989,7 @@ <ATTRIBUTES> <ATTR> <NAME>ID</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> <ID>2</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -9292,14 +12015,15 @@ </NNCON> </ATTR> <ATTR> -<NAME>DATA</NAME> +<NAME>PROT_ID</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> <ID>3</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> -<DOMAINID>3</DOMAINID> +<DOMAINID>12</DOMAINID> <DT> -<DTLISTNAME>BYTEA</DTLISTNAME> +<DTLISTNAME>BIGINT</DTLISTNAME> <SD>0</SD> <INC>1</INC> </DT> @@ -9317,21 +12041,218 @@ </ATTRIBUTEIDS> </NNCON> </ATTR> +<ATTR> +<NAME>SEQU_ID</NAME> +<ID>5</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<DOMAINID>12</DOMAINID> +<DT> +<DTLISTNAME>BIGINT</DTLISTNAME> +<SD>0</SD> +<INC>1</INC> +</DT> +</ATTR> +<ATTR> +<NAME>DESCRIPTION</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> +<ID>4</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<DOMAINID>6</DOMAINID> +<DT> +<DTLISTNAME>CHARACTER VARYING</DTLISTNAME> +<LE>2000</LE> +<SD>0</SD> +<INC>1</INC> +</DT> +<NNCON> +<NAME></NAME> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<VALUE>1</VALUE> +<CONLEVEL>1</CONLEVEL> +<CONTYPE>5</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>4</ATTRIBUTEID> +</ATTRIBUTEIDS> +</NNCON> +</ATTR> </ATTRIBUTES> </ENT> <ENT> -<NAME>IDENTIFIED_PROTEINS</NAME> -<ID>47</ID> +<NAME>ABUNDANCES</NAME> +<ID>91</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> -<ATTRLASTID>4</ATTRLASTID> +<ATTRLASTID>6</ATTRLASTID> <IDXLASTID>1</IDXLASTID> <TRGLASTID>1</TRGLASTID> <CONLASTID>1</CONLASTID> <PKCON> -<NAME>PK_IDENTIFIED_PROTEINS</NAME> -<NAMETEMPLATE>PK_IDENTIFIED_PROTEINS</NAMETEMPLATE> +<NAME>PK_ABUNDANCES</NAME> +<NAMETEMPLATE>PK_ABUNDANCES</NAMETEMPLATE> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<CONLEVEL>2</CONLEVEL> +<CONTYPE>3</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>2</ATTRIBUTEID> +</ATTRIBUTEIDS> +</PKCON> +<ATTRIBUTES> +<ATTR> +<NAME>ID</NAME> +<ID>2</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<DOMAINID>-1</DOMAINID> +<DT> +<DTLISTNAME>BIGSERIAL</DTLISTNAME> +<SD>0</SD> +<INC>1</INC> +</DT> +<NNCON> +<NAME></NAME> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<VALUE>1</VALUE> +<CONLEVEL>1</CONLEVEL> +<CONTYPE>5</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>2</ATTRIBUTEID> +</ATTRIBUTEIDS> +</NNCON> +</ATTR> +<ATTR> +<NAME>PROT_ID</NAME> +<ID>3</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<DOMAINID>12</DOMAINID> +<DT> +<DTLISTNAME>BIGINT</DTLISTNAME> +<SD>0</SD> +<INC>1</INC> +</DT> +<NNCON> +<NAME></NAME> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<VALUE>1</VALUE> +<CONLEVEL>1</CONLEVEL> +<CONTYPE>5</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>3</ATTRIBUTEID> +</ATTRIBUTEIDS> +</NNCON> +</ATTR> +<ATTR> +<NAME>SAMP_ID</NAME> +<ID>4</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<DOMAINID>12</DOMAINID> +<DT> +<DTLISTNAME>BIGINT</DTLISTNAME> +<SD>0</SD> +<INC>1</INC> +</DT> +<NNCON> +<NAME></NAME> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<VALUE>1</VALUE> +<CONLEVEL>1</CONLEVEL> +<CONTYPE>5</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>4</ATTRIBUTEID> +</ATTRIBUTEIDS> +</NNCON> +</ATTR> +<ATTR> +<NAME>ABTY_ID</NAME> +<ID>5</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<DOMAINID>12</DOMAINID> +<DT> +<DTLISTNAME>BIGINT</DTLISTNAME> +<SD>0</SD> +<INC>1</INC> +</DT> +<NNCON> +<NAME></NAME> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<VALUE>1</VALUE> +<CONLEVEL>1</CONLEVEL> +<CONTYPE>5</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>5</ATTRIBUTEID> +</ATTRIBUTEIDS> +</NNCON> +</ATTR> +<ATTR> +<NAME>VALUE</NAME> +<ID>6</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<DOMAINID>8</DOMAINID> +<DT> +<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME> +<SD>0</SD> +<INC>1</INC> +</DT> +<NNCON> +<NAME></NAME> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<VALUE>1</VALUE> +<CONLEVEL>1</CONLEVEL> +<CONTYPE>5</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>6</ATTRIBUTEID> +</ATTRIBUTEIDS> +</NNCON> +</ATTR> +</ATTRIBUTES> +</ENT> +<ENT> +<NAME>PROBABILITY_FDR_MAPPINGS</NAME> +<ID>96</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<ATTRLASTID>5</ATTRLASTID> +<IDXLASTID>1</IDXLASTID> +<TRGLASTID>1</TRGLASTID> +<CONLASTID>1</CONLASTID> +<PKCON> +<NAME>PK_PROBABILITY_FDR_MAPPINGS</NAME> +<NAMETEMPLATE>PK_PROBABILITY_FDR_MAPPINGS</NAMETEMPLATE> <ID>1</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -9351,7 +12272,33 @@ <DESC></DESC> <DOMAINID>-1</DOMAINID> <DT> -<DTLISTNAME>BIGSERIAL</DTLISTNAME> +<DTLISTNAME>BIGSERIAL</DTLISTNAME> +<SD>0</SD> +<INC>1</INC> +</DT> +<NNCON> +<NAME></NAME> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<VALUE>1</VALUE> +<CONLEVEL>1</CONLEVEL> +<CONTYPE>5</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>2</ATTRIBUTEID> +</ATTRIBUTEIDS> +</NNCON> +</ATTR> +<ATTR> +<NAME>DASE_ID</NAME> +<ID>5</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<DOMAINID>12</DOMAINID> +<DT> +<DTLISTNAME>BIGINT</DTLISTNAME> <SD>0</SD> <INC>1</INC> </DT> @@ -9365,19 +12312,19 @@ <CONLEVEL>1</CONLEVEL> <CONTYPE>5</CONTYPE> <ATTRIBUTEIDS> -<ATTRIBUTEID>2</ATTRIBUTEID> +<ATTRIBUTEID>5</ATTRIBUTEID> </ATTRIBUTEIDS> </NNCON> </ATTR> <ATTR> -<NAME>PROT_ID</NAME> +<NAME>PROBABILITY</NAME> <ID>3</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> -<DOMAINID>12</DOMAINID> +<DOMAINID>8</DOMAINID> <DT> -<DTLISTNAME>BIGINT</DTLISTNAME> +<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME> <SD>0</SD> <INC>1</INC> </DT> @@ -9396,15 +12343,14 @@ </NNCON> </ATTR> <ATTR> -<NAME>DESCRIPTION</NAME> +<NAME>FALSE_DISCOVERY_RATE</NAME> <ID>4</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> -<DOMAINID>6</DOMAINID> +<DOMAINID>8</DOMAINID> <DT> -<DTLISTNAME>CHARACTER VARYING</DTLISTNAME> -<LE>2000</LE> +<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME> <SD>0</SD> <INC>1</INC> </DT> @@ -9519,45 +12465,6 @@ </PAIRS> </REL> <REL> -<NAME>ID_SP_FK</NAME> -<NAMETEMPLATE>ID_SP_FK</NAMETEMPLATE> -<ID>31</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<PARENTOBJECTID>26</PARENTOBJECTID> -<CHILDOBJECTID>18</CHILDOBJECTID> -<CARDINALITY>0</CARDINALITY> -<RELTYPE>1</RELTYPE> -<MANDATORYPARENT>0</MANDATORYPARENT> -<UPDATERULE>0</UPDATERULE> -<DELETERULE>0</DELETERULE> -<CONSTRAINT> -<NAME>ID_SP_FK</NAME> -<NAMETEMPLATE>ID_SP_FK</NAMETEMPLATE> -<ID>1</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<CONLEVEL>2</CONLEVEL> -<CONTYPE>4</CONTYPE> -<ATTRIBUTEIDS> -<ATTRIBUTEID>3</ATTRIBUTEID> -</ATTRIBUTEIDS> -</CONSTRAINT> -<PAIRS> -<PAIR> -<NAME></NAME> -<ID>0</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<KEYID>2</KEYID> -<FOREIGNKEYID>3</FOREIGNKEYID> -</PAIR> -</PAIRS> -</REL> -<REL> <NAME>MO_PE_FK</NAME> <NAMETEMPLATE>MO_PE_FK</NAMETEMPLATE> <ID>32</ID> @@ -9636,45 +12543,6 @@ </PAIRS> </REL> <REL> -<NAME>PE_ID_FK</NAME> -<NAMETEMPLATE>PE_ID_FK</NAMETEMPLATE> -<ID>35</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<PARENTOBJECTID>18</PARENTOBJECTID> -<CHILDOBJECTID>21</CHILDOBJECTID> -<CARDINALITY>0</CARDINALITY> -<RELTYPE>1</RELTYPE> -<MANDATORYPARENT>0</MANDATORYPARENT> -<UPDATERULE>0</UPDATERULE> -<DELETERULE>0</DELETERULE> -<CONSTRAINT> -<NAME>PE_ID_FK</NAME> -<NAMETEMPLATE>PE_ID_FK</NAMETEMPLATE> -<ID>1</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<CONLEVEL>2</CONLEVEL> -<CONTYPE>4</CONTYPE> -<ATTRIBUTEIDS> -<ATTRIBUTEID>6</ATTRIBUTEID> -</ATTRIBUTEIDS> -</CONSTRAINT> -<PAIRS> -<PAIR> -<NAME></NAME> -<ID>0</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<KEYID>2</KEYID> -<FOREIGNKEYID>6</FOREIGNKEYID> -</PAIR> -</PAIRS> -</REL> -<REL> <NAME>PE_PR_FK</NAME> <NAMETEMPLATE>PE_PR_FK</NAMETEMPLATE> <ID>36</ID> @@ -9714,22 +12582,22 @@ </PAIRS> </REL> <REL> -<NAME>PE_SE_FK</NAME> -<NAMETEMPLATE>PE_SE_FK</NAMETEMPLATE> -<ID>37</ID> +<NAME>DATA_SETS_PROTEINS</NAME> +<NAMETEMPLATE>DATA_SETS_PROTEINS</NAMETEMPLATE> +<ID>46</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> -<PARENTOBJECTID>25</PARENTOBJECTID> -<CHILDOBJECTID>21</CHILDOBJECTID> +<PARENTOBJECTID>17</PARENTOBJECTID> +<CHILDOBJECTID>23</CHILDOBJECTID> <CARDINALITY>0</CARDINALITY> <RELTYPE>1</RELTYPE> <MANDATORYPARENT>1</MANDATORYPARENT> <UPDATERULE>0</UPDATERULE> <DELETERULE>0</DELETERULE> <CONSTRAINT> -<NAME>PE_SE_FK</NAME> -<NAMETEMPLATE>PE_SE_FK</NAMETEMPLATE> +<NAME>DATA_SETS_PROTEINS</NAME> +<NAMETEMPLATE>DATA_SETS_PROTEINS</NAMETEMPLATE> <ID>1</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -9737,7 +12605,7 @@ <CONLEVEL>2</CONLEVEL> <CONTYPE>4</CONTYPE> <ATTRIBUTEIDS> -<ATTRIBUTEID>4</ATTRIBUTEID> +<ATTRIBUTEID>10</ATTRIBUTEID> </ATTRIBUTEIDS> </CONSTRAINT> <PAIRS> @@ -9748,27 +12616,27 @@ <SCHEMA></SCHEMA> <DESC></DESC> <KEYID>2</KEYID> -<FOREIGNKEYID>4</FOREIGNKEYID> +<FOREIGNKEYID>10</FOREIGNKEYID> </PAIR> </PAIRS> </REL> <REL> -<NAME>PR_SE_FK</NAME> -<NAMETEMPLATE>PR_SE_FK</NAMETEMPLATE> -<ID>39</ID> +<NAME>PROTEINS_IDENTIFIED_PROTEINS</NAME> +<NAMETEMPLATE>PROTEINS_IDENTIFIED_PROTEINS</NAMETEMPLATE> +<ID>48</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> -<PARENTOBJECTID>25</PARENTOBJECTID> -<CHILDOBJECTID>23</CHILDOBJECTID> +<PARENTOBJECTID>23</PARENTOBJECTID> +<CHILDOBJECTID>47</CHILDOBJECTID> <CARDINALITY>0</CARDINALITY> <RELTYPE>1</RELTYPE> -<MANDATORYPARENT>0</MANDATORYPARENT> +<MANDATORYPARENT>1</MANDATORYPARENT> <UPDATERULE>0</UPDATERULE> <DELETERULE>0</DELETERULE> <CONSTRAINT> -<NAME>PR_SE_FK</NAME> -<NAMETEMPLATE>PR_SE_FK</NAMETEMPLATE> +<NAME>PROTEINS_IDENTIFIED_PROTEINS</NAME> +<NAMETEMPLATE>PROTEINS_IDENTIFIED_PROTEINS</NAMETEMPLATE> <ID>1</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -9776,7 +12644,7 @@ <CONLEVEL>2</CONLEVEL> <CONTYPE>4</CONTYPE> <ATTRIBUTEIDS> -<ATTRIBUTEID>5</ATTRIBUTEID> +<ATTRIBUTEID>3</ATTRIBUTEID> </ATTRIBUTEIDS> </CONSTRAINT> <PAIRS> @@ -9787,27 +12655,27 @@ <SCHEMA></SCHEMA> <DESC></DESC> <KEYID>2</KEYID> -<FOREIGNKEYID>5</FOREIGNKEYID> +<FOREIGNKEYID>3</FOREIGNKEYID> </PAIR> </PAIRS> </REL> <REL> -<NAME>PR_PS_FK</NAME> -<NAMETEMPLATE>PR_PS_FK</NAMETEMPLATE> -<ID>41</ID> +<NAME>SEQUENCES_IDENTIFIED_PROTEINS</NAME> +<NAMETEMPLATE>SEQUENCES_IDENTIFIED_PROTEINS</NAMETEMPLATE> +<ID>50</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> -<PARENTOBJECTID>22</PARENTOBJECTID> -<CHILDOBJECTID>23</CHILDOBJECTID> +<PARENTOBJECTID>25</PARENTOBJECTID> +<CHILDOBJECTID>47</CHILDOBJECTID> <CARDINALITY>0</CARDINALITY> <RELTYPE>1</RELTYPE> <MANDATORYPARENT>0</MANDATORYPARENT> <UPDATERULE>0</UPDATERULE> <DELETERULE>0</DELETERULE> <CONSTRAINT> -<NAME>PR_PS_FK</NAME> -<NAMETEMPLATE>PR_PS_FK</NAMETEMPLATE> +<NAME>SEQUENCES_IDENTIFIED_PROTEINS</NAME> +<NAMETEMPLATE>SEQUENCES_IDENTIFIED_PROTEINS</NAMETEMPLATE> <ID>1</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -9815,7 +12683,7 @@ <CONLEVEL>2</CONLEVEL> <CONTYPE>4</CONTYPE> <ATTRIBUTEIDS> -<ATTRIBUTEID>6</ATTRIBUTEID> +<ATTRIBUTEID>5</ATTRIBUTEID> </ATTRIBUTEIDS> </CONSTRAINT> <PAIRS> @@ -9826,27 +12694,27 @@ <SCHEMA></SCHEMA> <DESC></DESC> <KEYID>2</KEYID> -<FOREIGNKEYID>6</FOREIGNKEYID> +<FOREIGNKEYID>5</FOREIGNKEYID> </PAIR> </PAIRS> </REL> <REL> -<NAME>ABUNDANCES_TYPES_PROTEINS</NAME> -<NAMETEMPLATE>ABUNDANCES_TYPES_PROTEINS</NAMETEMPLATE> -<ID>43</ID> +<NAME>SAMPLES_ABUNDANCES</NAME> +<NAMETEMPLATE>SAMPLES_ABUNDANCES</NAMETEMPLATE> +<ID>92</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> -<PARENTOBJECTID>14</PARENTOBJECTID> -<CHILDOBJECTID>23</CHILDOBJECTID> +<PARENTOBJECTID>24</PARENTOBJECTID> +<CHILDOBJECTID>91</CHILDOBJECTID> <CARDINALITY>0</CARDINALITY> <RELTYPE>1</RELTYPE> -<MANDATORYPARENT>0</MANDATORYPARENT> +<MANDATORYPARENT>1</MANDATORYPARENT> <UPDATERULE>0</UPDATERULE> <DELETERULE>0</DELETERULE> <CONSTRAINT> -<NAME>ABUNDANCES_TYPES_PROTEINS</NAME> -<NAMETEMPLATE>ABUNDANCES_TYPES_PROTEINS</NAMETEMPLATE> +<NAME>SAMPLES_ABUNDANCES</NAME> +<NAMETEMPLATE>SAMPLES_ABUNDANCES</NAMETEMPLATE> <ID>1</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -9854,7 +12722,7 @@ <CONLEVEL>2</CONLEVEL> <CONTYPE>4</CONTYPE> <ATTRIBUTEIDS> -<ATTRIBUTEID>8</ATTRIBUTEID> +<ATTRIBUTEID>4</ATTRIBUTEID> </ATTRIBUTEIDS> </CONSTRAINT> <PAIRS> @@ -9865,27 +12733,27 @@ <SCHEMA></SCHEMA> <DESC></DESC> <KEYID>2</KEYID> -<FOREIGNKEYID>8</FOREIGNKEYID> +<FOREIGNKEYID>4</FOREIGNKEYID> </PAIR> </PAIRS> </REL> <REL> -<NAME>ABUNDANCES_TYPES_PEPTIDES</NAME> -<NAMETEMPLATE>ABUNDANCES_TYPES_PEPTIDES</NAMETEMPLATE> -<ID>44</ID> +<NAME>ABUNDANCES_TYPES_ABUNDANCES</NAME> +<NAMETEMPLATE>ABUNDANCES_TYPES_ABUNDANCES</NAMETEMPLATE> +<ID>93</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> <PARENTOBJECTID>14</PARENTOBJECTID> -<CHILDOBJECTID>21</CHILDOBJECTID> +<CHILDOBJECTID>91</CHILDOBJECTID> <CARDINALITY>0</CARDINALITY> <RELTYPE>1</RELTYPE> -<MANDATORYPARENT>0</MANDATORYPARENT> +<MANDATORYPARENT>1</MANDATORYPARENT> <UPDATERULE>0</UPDATERULE> <DELETERULE>0</DELETERULE> <CONSTRAINT> -<NAME>ABUNDANCES_TYPES_PEPTIDES</NAME> -<NAMETEMPLATE>ABUNDANCES_TYPES_PEPTIDES</NAMETEMPLATE> +<NAME>ABUNDANCES_TYPES_ABUNDANCES</NAME> +<NAMETEMPLATE>ABUNDANCES_TYPES_ABUNDANCES</NAMETEMPLATE> <ID>1</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -9893,7 +12761,7 @@ <CONLEVEL>2</CONLEVEL> <CONTYPE>4</CONTYPE> <ATTRIBUTEIDS> -<ATTRIBUTEID>8</ATTRIBUTEID> +<ATTRIBUTEID>5</ATTRIBUTEID> </ATTRIBUTEIDS> </CONSTRAINT> <PAIRS> @@ -9904,27 +12772,27 @@ <SCHEMA></SCHEMA> <DESC></DESC> <KEYID>2</KEYID> -<FOREIGNKEYID>8</FOREIGNKEYID> +<FOREIGNKEYID>5</FOREIGNKEYID> </PAIR> </PAIRS> </REL> <REL> -<NAME>DATA_SETS_PROTEINS</NAME> -<NAMETEMPLATE>DATA_SETS_PROTEINS</NAMETEMPLATE> -<ID>46</ID> +<NAME>PROTEINS_ABUNDANCES</NAME> +<NAMETEMPLATE>PROTEINS_ABUNDANCES</NAMETEMPLATE> +<ID>94</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> -<PARENTOBJECTID>17</PARENTOBJECTID> -<CHILDOBJECTID>23</CHILDOBJECTID> +<PARENTOBJECTID>23</PARENTOBJECTID> +<CHILDOBJECTID>91</CHILDOBJECTID> <CARDINALITY>0</CARDINALITY> <RELTYPE>1</RELTYPE> <MANDATORYPARENT>1</MANDATORYPARENT> <UPDATERULE>0</UPDATERULE> <DELETERULE>0</DELETERULE> <CONSTRAINT> -<NAME>DATA_SETS_PROTEINS</NAME> -<NAMETEMPLATE>DATA_SETS_PROTEINS</NAMETEMPLATE> +<NAME>PROTEINS_ABUNDANCES</NAME> +<NAMETEMPLATE>PROTEINS_ABUNDANCES</NAMETEMPLATE> <ID>1</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -9932,7 +12800,7 @@ <CONLEVEL>2</CONLEVEL> <CONTYPE>4</CONTYPE> <ATTRIBUTEIDS> -<ATTRIBUTEID>10</ATTRIBUTEID> +<ATTRIBUTEID>3</ATTRIBUTEID> </ATTRIBUTEIDS> </CONSTRAINT> <PAIRS> @@ -9943,27 +12811,27 @@ <SCHEMA></SCHEMA> <DESC></DESC> <KEYID>2</KEYID> -<FOREIGNKEYID>10</FOREIGNKEYID> +<FOREIGNKEYID>3</FOREIGNKEYID> </PAIR> </PAIRS> </REL> <REL> -<NAME>PROTEINS_IDENTIFIED_PROTEINS</NAME> -<NAMETEMPLATE>PROTEINS_IDENTIFIED_PROTEINS</NAMETEMPLATE> -<ID>48</ID> +<NAME>DATA_SETS_PROBABILITY_FDR_MAPPINGS</NAME> +<NAMETEMPLATE>DATA_SETS_PROBABILITY_FDR_MAPPINGS</NAMETEMPLATE> +<ID>97</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> -<PARENTOBJECTID>23</PARENTOBJECTID> -<CHILDOBJECTID>47</CHILDOBJECTID> +<PARENTOBJECTID>17</PARENTOBJECTID> +<CHILDOBJECTID>96</CHILDOBJECTID> <CARDINALITY>0</CARDINALITY> <RELTYPE>1</RELTYPE> <MANDATORYPARENT>1</MANDATORYPARENT> <UPDATERULE>0</UPDATERULE> <DELETERULE>0</DELETERULE> <CONSTRAINT> -<NAME>PROTEINS_IDENTIFIED_PROTEINS</NAME> -<NAMETEMPLATE>PROTEINS_IDENTIFIED_PROTEINS</NAMETEMPLATE> +<NAME>DATA_SETS_PROBABILITY_FDR_MAPPINGS</NAME> +<NAMETEMPLATE>DATA_SETS_PROBABILITY_FDR_MAPPINGS</NAMETEMPLATE> <ID>1</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -9971,7 +12839,7 @@ <CONLEVEL>2</CONLEVEL> <CONTYPE>4</CONTYPE> <ATTRIBUTEIDS> -<ATTRIBUTEID>3</ATTRIBUTEID> +<ATTRIBUTEID>5</ATTRIBUTEID> </ATTRIBUTEIDS> </CONSTRAINT> <PAIRS> @@ -9982,7 +12850,7 @@ <SCHEMA></SCHEMA> <DESC></DESC> <KEYID>2</KEYID> -<FOREIGNKEYID>3</FOREIGNKEYID> +<FOREIGNKEYID>5</FOREIGNKEYID> </PAIR> </PAIRS> </REL> @@ -9993,16 +12861,16 @@ </VERSION> <VERSION> <VERSIONINFO> -<VERSIONNUMBER>4</VERSIONNUMBER> -<VERSIONLABEL>Version 2009-06-30</VERSIONLABEL> -<VERSIONDATE>2009-06-30 09:00</VERSIONDATE> +<VERSIONNUMBER>5</VERSIONNUMBER> +<VERSIONLABEL>Version 2009-07-06</VERSIONLABEL> +<VERSIONDATE>2009-07-06 13:15</VERSIONDATE> <VERSIONCOMMENTS></VERSIONCOMMENTS> <VERSIONTYPE>DB</VERSIONTYPE> <VERSIONTYPEDESC>Data dictionary only (no diagrams)</VERSIONTYPEDESC> </VERSIONINFO> <DATADICT> <DBID>postgresql8</DBID> -<LASTID>97</LASTID> +<LASTID>135</LASTID> <DDSETTINGS> <PKCONNAMETEMPLATE>PK_%table%</PKCONNAMETEMPLATE> <FKCONNAMETEMPLATE>%relname%</FKCONNAMETEMPLATE> @@ -10039,23 +12907,11 @@ <IGNORECOMMENTS>0</IGNORECOMMENTS> <USESCHEMANAMES>0</USESCHEMANAMES> <UCONNAMETEMPLATE></UCONNAMETEMPLATE> -<SQLCREATEFILE>D:\User\felmer\dev-workspace\rtd_phosphonetx\source\sql\postgresql\001\schema-001.sql</SQLCREATEFILE> -<SQLDROPFILE>D:\User\felmer\dev-workspace\rtd_phosphonetx\targets\drop.sql</SQLDROPFILE> +<SQLCREATEFILE>N:\user\cisd\felmer\phosphonetx\schema-001.sql</SQLCREATEFILE> +<SQLDROPFILE>N:\user\cisd\felmer\phosphonetx\drop.sql</SQLDROPFILE> </DDSETTINGS> <DOMAINS> <DOMAIN> -<NAME>BINARY_DATA</NAME> -<ID>3</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<DT> -<DTLISTNAME>BYTEA</DTLISTNAME> -<SD>0</SD> -<INC>1</INC> -</DT> -</DOMAIN> -<DOMAIN> <NAME>CHECKSUM</NAME> <ID>4</ID> <POSNR>0</POSNR> @@ -10156,14 +13012,27 @@ </DT> </DOMAIN> <DOMAIN> -<NAME>SHORT_SEQUENCE</NAME> -<ID>69</ID> +<NAME>SHORT_SEQUENCE</NAME> +<ID>69</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<DT> +<DTLISTNAME>CHARACTER VARYING</DTLISTNAME> +<LE>1000</LE> +<SD>0</SD> +<INC>1</INC> +</DT> +</DOMAIN> +<DOMAIN> +<NAME>UNIPROT_ACCESSION_NUMBER</NAME> +<ID>109</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> <DT> <DTLISTNAME>CHARACTER VARYING</DTLISTNAME> -<LE>1000</LE> +<LE>40</LE> <SD>0</SD> <INC>1</INC> </DT> @@ -10381,7 +13250,7 @@ <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> -<ATTRLASTID>5</ATTRLASTID> +<ATTRLASTID>6</ATTRLASTID> <IDXLASTID>3</IDXLASTID> <TRGLASTID>1</TRGLASTID> <CONLASTID>2</CONLASTID> @@ -10478,6 +13347,33 @@ </NNCON> </ATTR> <ATTR> +<NAME>DB_ID</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> +<ID>6</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<DOMAINID>12</DOMAINID> +<DT> +<DTLISTNAME>BIGINT</DTLISTNAME> +<SD>0</SD> +<INC>1</INC> +</DT> +<NNCON> +<NAME></NAME> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<VALUE>1</VALUE> +<CONLEVEL>1</CONLEVEL> +<CONTYPE>5</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>6</ATTRIBUTEID> +</ATTRIBUTEIDS> +</NNCON> +</ATTR> +<ATTR> <NAME>PERM_ID</NAME> <ID>3</ID> <POSNR>0</POSNR> @@ -10769,7 +13665,7 @@ <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> -<ATTRLASTID>6</ATTRLASTID> +<ATTRLASTID>7</ATTRLASTID> <IDXLASTID>1</IDXLASTID> <TRGLASTID>1</TRGLASTID> <CONLASTID>2</CONLASTID> @@ -10855,6 +13751,20 @@ </DT> </ATTR> <ATTR> +<NAME>AMINO_ACID</NAME> +<ID>7</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<DOMAINID>-1</DOMAINID> +<DT> +<DTLISTNAME>CHARACTER</DTLISTNAME> +<LE>1</LE> +<SD>0</SD> +<INC>1</INC> +</DT> +</ATTR> +<ATTR> <NAME>MASS</NAME> <ID>5</ID> <POSNR>0</POSNR> @@ -10868,7 +13778,7 @@ </DT> </ATTR> <ATTR> -<NAME>DELTA_MASS</NAME> +<NAME>MASS_TOLERANCE</NAME> <ID>6</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -10976,6 +13886,7 @@ </ATTR> <ATTR> <NAME>SEQUENCE</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> <ID>10</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -11307,7 +14218,7 @@ <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> -<ATTRLASTID>4</ATTRLASTID> +<ATTRLASTID>6</ATTRLASTID> <IDXLASTID>1</IDXLASTID> <TRGLASTID>1</TRGLASTID> <CONLASTID>1</CONLASTID> @@ -11352,6 +14263,60 @@ </NNCON> </ATTR> <ATTR> +<NAME>DB_ID</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> +<ID>5</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<DOMAINID>12</DOMAINID> +<DT> +<DTLISTNAME>BIGINT</DTLISTNAME> +<SD>0</SD> +<INC>1</INC> +</DT> +<NNCON> +<NAME></NAME> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<VALUE>1</VALUE> +<CONLEVEL>1</CONLEVEL> +<CONTYPE>5</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>5</ATTRIBUTEID> +</ATTRIBUTEIDS> +</NNCON> +</ATTR> +<ATTR> +<NAME>PRRE_ID</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> +<ID>6</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<DOMAINID>12</DOMAINID> +<DT> +<DTLISTNAME>BIGINT</DTLISTNAME> +<SD>0</SD> +<INC>1</INC> +</DT> +<NNCON> +<NAME></NAME> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<VALUE>1</VALUE> +<CONLEVEL>1</CONLEVEL> +<CONTYPE>5</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>6</ATTRIBUTEID> +</ATTRIBUTEIDS> +</NNCON> +</ATTR> +<ATTR> <NAME>AMINO_ACID_SEQUENCE</NAME> <ID>3</ID> <POSNR>0</POSNR> @@ -11497,21 +14462,6 @@ <SD>0</SD> <INC>1</INC> </DT> -</ATTR> -<ATTR> -<NAME>DESCRIPTION</NAME> -<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> -<ID>4</ID> -<POSNR>0</POSNR> -<SCHEMA></SCHEMA> -<DESC></DESC> -<DOMAINID>6</DOMAINID> -<DT> -<DTLISTNAME>CHARACTER VARYING</DTLISTNAME> -<LE>2000</LE> -<SD>0</SD> -<INC>1</INC> -</DT> <NNCON> <NAME></NAME> <ID>1</ID> @@ -11522,7 +14472,7 @@ <CONLEVEL>1</CONLEVEL> <CONTYPE>5</CONTYPE> <ATTRIBUTEIDS> -<ATTRIBUTEID>4</ATTRIBUTEID> +<ATTRIBUTEID>5</ATTRIBUTEID> </ATTRIBUTEIDS> </NNCON> </ATTR> @@ -11530,6 +14480,7 @@ </ENT> <ENT> <NAME>ABUNDANCES</NAME> +<NAMETEMPLATE>PK_%table%</NAMETEMPLATE> <ID>91</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -11554,6 +14505,7 @@ <ATTRIBUTES> <ATTR> <NAME>ID</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> <ID>2</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -11580,13 +14532,149 @@ </ATTR> <ATTR> <NAME>PROT_ID</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> <ID>3</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> -<DOMAINID>12</DOMAINID> +<DOMAINID>12</DOMAINID> +<DT> +<DTLISTNAME>BIGINT</DTLISTNAME> +<SD>0</SD> +<INC>1</INC> +</DT> +<NNCON> +<NAME></NAME> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<VALUE>1</VALUE> +<CONLEVEL>1</CONLEVEL> +<CONTYPE>5</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>3</ATTRIBUTEID> +</ATTRIBUTEIDS> +</NNCON> +</ATTR> +<ATTR> +<NAME>SAMP_ID</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> +<ID>4</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<DOMAINID>12</DOMAINID> +<DT> +<DTLISTNAME>BIGINT</DTLISTNAME> +<SD>0</SD> +<INC>1</INC> +</DT> +<NNCON> +<NAME></NAME> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<VALUE>1</VALUE> +<CONLEVEL>1</CONLEVEL> +<CONTYPE>5</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>4</ATTRIBUTEID> +</ATTRIBUTEIDS> +</NNCON> +</ATTR> +<ATTR> +<NAME>ABTY_ID</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> +<ID>5</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<DOMAINID>12</DOMAINID> +<DT> +<DTLISTNAME>BIGINT</DTLISTNAME> +<SD>0</SD> +<INC>1</INC> +</DT> +<NNCON> +<NAME></NAME> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<VALUE>1</VALUE> +<CONLEVEL>1</CONLEVEL> +<CONTYPE>5</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>5</ATTRIBUTEID> +</ATTRIBUTEIDS> +</NNCON> +</ATTR> +<ATTR> +<NAME>VALUE</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> +<ID>6</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<DOMAINID>8</DOMAINID> +<DT> +<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME> +<SD>0</SD> +<INC>1</INC> +</DT> +<NNCON> +<NAME></NAME> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<VALUE>1</VALUE> +<CONLEVEL>1</CONLEVEL> +<CONTYPE>5</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>6</ATTRIBUTEID> +</ATTRIBUTEIDS> +</NNCON> +</ATTR> +</ATTRIBUTES> +</ENT> +<ENT> +<NAME>PROBABILITY_FDR_MAPPINGS</NAME> +<NAMETEMPLATE>PK_%table%</NAMETEMPLATE> +<ID>96</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<ATTRLASTID>5</ATTRLASTID> +<IDXLASTID>1</IDXLASTID> +<TRGLASTID>1</TRGLASTID> +<CONLASTID>1</CONLASTID> +<PKCON> +<NAME>PK_PROBABILITY_FDR_MAPPINGS</NAME> +<NAMETEMPLATE>PK_PROBABILITY_FDR_MAPPINGS</NAMETEMPLATE> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<CONLEVEL>2</CONLEVEL> +<CONTYPE>3</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>2</ATTRIBUTEID> +</ATTRIBUTEIDS> +</PKCON> +<ATTRIBUTES> +<ATTR> +<NAME>ID</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> +<ID>2</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<DOMAINID>-1</DOMAINID> <DT> -<DTLISTNAME>BIGINT</DTLISTNAME> +<DTLISTNAME>BIGSERIAL</DTLISTNAME> <SD>0</SD> <INC>1</INC> </DT> @@ -11600,13 +14688,14 @@ <CONLEVEL>1</CONLEVEL> <CONTYPE>5</CONTYPE> <ATTRIBUTEIDS> -<ATTRIBUTEID>3</ATTRIBUTEID> +<ATTRIBUTEID>2</ATTRIBUTEID> </ATTRIBUTEIDS> </NNCON> </ATTR> <ATTR> -<NAME>SAMP_ID</NAME> -<ID>4</ID> +<NAME>DASE_ID</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> +<ID>5</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> @@ -11626,19 +14715,20 @@ <CONLEVEL>1</CONLEVEL> <CONTYPE>5</CONTYPE> <ATTRIBUTEIDS> -<ATTRIBUTEID>4</ATTRIBUTEID> +<ATTRIBUTEID>5</ATTRIBUTEID> </ATTRIBUTEIDS> </NNCON> </ATTR> <ATTR> -<NAME>ABTY_ID</NAME> -<ID>5</ID> +<NAME>PROBABILITY</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> +<ID>3</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> -<DOMAINID>12</DOMAINID> +<DOMAINID>8</DOMAINID> <DT> -<DTLISTNAME>BIGINT</DTLISTNAME> +<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME> <SD>0</SD> <INC>1</INC> </DT> @@ -11652,13 +14742,14 @@ <CONLEVEL>1</CONLEVEL> <CONTYPE>5</CONTYPE> <ATTRIBUTEIDS> -<ATTRIBUTEID>5</ATTRIBUTEID> +<ATTRIBUTEID>3</ATTRIBUTEID> </ATTRIBUTEIDS> </NNCON> </ATTR> <ATTR> -<NAME>VALUE</NAME> -<ID>6</ID> +<NAME>FALSE_DISCOVERY_RATE</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> +<ID>4</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> @@ -11678,25 +14769,26 @@ <CONLEVEL>1</CONLEVEL> <CONTYPE>5</CONTYPE> <ATTRIBUTEIDS> -<ATTRIBUTEID>6</ATTRIBUTEID> +<ATTRIBUTEID>4</ATTRIBUTEID> </ATTRIBUTEIDS> </NNCON> </ATTR> </ATTRIBUTES> </ENT> <ENT> -<NAME>PROBABILITY_FDR_MAPPINGS</NAME> -<ID>96</ID> +<NAME>PROTEIN_REFERENCES</NAME> +<NAMETEMPLATE>PK_%table%</NAMETEMPLATE> +<ID>98</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> -<ATTRLASTID>5</ATTRLASTID> -<IDXLASTID>1</IDXLASTID> +<ATTRLASTID>4</ATTRLASTID> +<IDXLASTID>2</IDXLASTID> <TRGLASTID>1</TRGLASTID> -<CONLASTID>1</CONLASTID> +<CONLASTID>2</CONLASTID> <PKCON> -<NAME>PK_PROBABILITY_FDR_MAPPINGS</NAME> -<NAMETEMPLATE>PK_PROBABILITY_FDR_MAPPINGS</NAMETEMPLATE> +<NAME>PK_PROTEIN_REFERENCES</NAME> +<NAMETEMPLATE>PK_PROTEIN_REFERENCES</NAMETEMPLATE> <ID>1</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -11710,6 +14802,7 @@ <ATTRIBUTES> <ATTR> <NAME>ID</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> <ID>2</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> @@ -11735,14 +14828,16 @@ </NNCON> </ATTR> <ATTR> -<NAME>DASE_ID</NAME> -<ID>5</ID> +<NAME>UNIPROT_ID</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> +<ID>3</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> -<DOMAINID>12</DOMAINID> +<DOMAINID>109</DOMAINID> <DT> -<DTLISTNAME>BIGINT</DTLISTNAME> +<DTLISTNAME>CHARACTER VARYING</DTLISTNAME> +<LE>40</LE> <SD>0</SD> <INC>1</INC> </DT> @@ -11756,19 +14851,98 @@ <CONLEVEL>1</CONLEVEL> <CONTYPE>5</CONTYPE> <ATTRIBUTEIDS> -<ATTRIBUTEID>5</ATTRIBUTEID> +<ATTRIBUTEID>3</ATTRIBUTEID> </ATTRIBUTEIDS> </NNCON> </ATTR> <ATTR> -<NAME>PROBABILITY</NAME> -<ID>3</ID> +<NAME>DESCRIPTION</NAME> +<ID>4</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> -<DOMAINID>8</DOMAINID> +<DOMAINID>6</DOMAINID> <DT> -<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME> +<DTLISTNAME>CHARACTER VARYING</DTLISTNAME> +<LE>2000</LE> +<SD>0</SD> +<INC>1</INC> +</DT> +</ATTR> +</ATTRIBUTES> +<INDEXES> +<INDEX> +<NAME>IDX_PROTEIN_REFERENCES_1</NAME> +<NAMETEMPLATE>IDX_PROTEIN_REFERENCES_1</NAMETEMPLATE> +<ID>2</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<RELID>0</RELID> +<AUTOIDXTYPE>0</AUTOIDXTYPE> +<IDXCOLS> +<IDXCOL> +<NAME>UNIPROT_ID</NAME> +<ID>0</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<IDXCOLATTRID>3</IDXCOLATTRID> +</IDXCOL> +</IDXCOLS> +</INDEX> +</INDEXES> +<CONSTRAINTS> +<CONSTRAINT> +<NAME>TUC_PROTEIN_REFERENCES_1</NAME> +<NAMETEMPLATE>TUC_PROTEIN_REFERENCES_1</NAMETEMPLATE> +<ID>2</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<CONLEVEL>2</CONLEVEL> +<CONTYPE>2</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>3</ATTRIBUTEID> +</ATTRIBUTEIDS> +</CONSTRAINT> +</CONSTRAINTS> +</ENT> +<ENT> +<NAME>DATABASES</NAME> +<NAMETEMPLATE>PK_%table%</NAMETEMPLATE> +<ID>110</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<ATTRLASTID>3</ATTRLASTID> +<IDXLASTID>1</IDXLASTID> +<TRGLASTID>1</TRGLASTID> +<CONLASTID>2</CONLASTID> +<PKCON> +<NAME>PK_DATABASES</NAME> +<NAMETEMPLATE>PK_DATABASES</NAMETEMPLATE> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<CONLEVEL>2</CONLEVEL> +<CONTYPE>3</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>2</ATTRIBUTEID> +</ATTRIBUTEIDS> +</PKCON> +<ATTRIBUTES> +<ATTR> +<NAME>ID</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> +<ID>2</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<DOMAINID>-1</DOMAINID> +<DT> +<DTLISTNAME>BIGSERIAL</DTLISTNAME> <SD>0</SD> <INC>1</INC> </DT> @@ -11782,19 +14956,21 @@ <CONLEVEL>1</CONLEVEL> <CONTYPE>5</CONTYPE> <ATTRIBUTEIDS> -<ATTRIBUTEID>3</ATTRIBUTEID> +<ATTRIBUTEID>2</ATTRIBUTEID> </ATTRIBUTEIDS> </NNCON> </ATTR> <ATTR> -<NAME>FALSE_DISCOVERY_RATE</NAME> -<ID>4</ID> +<NAME>NAME_AND_VERSION</NAME> +<NAMETEMPLATE>NN_%column%</NAMETEMPLATE> +<ID>3</ID> <POSNR>0</POSNR> <SCHEMA></SCHEMA> <DESC></DESC> -<DOMAINID>8</DOMAINID> +<DOMAINID>69</DOMAINID> <DT> -<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME> +<DTLISTNAME>CHARACTER VARYING</DTLISTNAME> +<LE>1000</LE> <SD>0</SD> <INC>1</INC> </DT> @@ -11808,11 +14984,26 @@ <CONLEVEL>1</CONLEVEL> <CONTYPE>5</CONTYPE> <ATTRIBUTEIDS> -<ATTRIBUTEID>4</ATTRIBUTEID> +<ATTRIBUTEID>3</ATTRIBUTEID> </ATTRIBUTEIDS> </NNCON> </ATTR> </ATTRIBUTES> +<CONSTRAINTS> +<CONSTRAINT> +<NAME>TUC_DATABASES_1</NAME> +<NAMETEMPLATE>TUC_DATABASES_1</NAMETEMPLATE> +<ID>2</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<CONLEVEL>2</CONLEVEL> +<CONTYPE>2</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>3</ATTRIBUTEID> +</ATTRIBUTEIDS> +</CONSTRAINT> +</CONSTRAINTS> </ENT> </ENTITIES> <SUBCATEGORIES> @@ -12114,7 +15305,7 @@ <CHILDOBJECTID>47</CHILDOBJECTID> <CARDINALITY>0</CARDINALITY> <RELTYPE>1</RELTYPE> -<MANDATORYPARENT>0</MANDATORYPARENT> +<MANDATORYPARENT>1</MANDATORYPARENT> <UPDATERULE>0</UPDATERULE> <DELETERULE>0</DELETERULE> <CONSTRAINT> @@ -12298,6 +15489,123 @@ </PAIR> </PAIRS> </REL> +<REL> +<NAME>DATABASES_SEQUENCES</NAME> +<NAMETEMPLATE>DATABASES_SEQUENCES</NAMETEMPLATE> +<ID>111</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<PARENTOBJECTID>110</PARENTOBJECTID> +<CHILDOBJECTID>25</CHILDOBJECTID> +<CARDINALITY>0</CARDINALITY> +<RELTYPE>1</RELTYPE> +<MANDATORYPARENT>1</MANDATORYPARENT> +<UPDATERULE>0</UPDATERULE> +<DELETERULE>0</DELETERULE> +<CONSTRAINT> +<NAME>DATABASES_SEQUENCES</NAME> +<NAMETEMPLATE>DATABASES_SEQUENCES</NAMETEMPLATE> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<CONLEVEL>2</CONLEVEL> +<CONTYPE>4</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>5</ATTRIBUTEID> +</ATTRIBUTEIDS> +</CONSTRAINT> +<PAIRS> +<PAIR> +<NAME></NAME> +<ID>0</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<KEYID>2</KEYID> +<FOREIGNKEYID>5</FOREIGNKEYID> +</PAIR> +</PAIRS> +</REL> +<REL> +<NAME>PROTEIN_REFERENCES_SEQUENCES</NAME> +<NAMETEMPLATE>PROTEIN_REFERENCES_SEQUENCES</NAMETEMPLATE> +<ID>112</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<PARENTOBJECTID>98</PARENTOBJECTID> +<CHILDOBJECTID>25</CHILDOBJECTID> +<CARDINALITY>0</CARDINALITY> +<RELTYPE>1</RELTYPE> +<MANDATORYPARENT>1</MANDATORYPARENT> +<UPDATERULE>0</UPDATERULE> +<DELETERULE>0</DELETERULE> +<CONSTRAINT> +<NAME>PROTEIN_REFERENCES_SEQUENCES</NAME> +<NAMETEMPLATE>PROTEIN_REFERENCES_SEQUENCES</NAMETEMPLATE> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<CONLEVEL>2</CONLEVEL> +<CONTYPE>4</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>6</ATTRIBUTEID> +</ATTRIBUTEIDS> +</CONSTRAINT> +<PAIRS> +<PAIR> +<NAME></NAME> +<ID>0</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<KEYID>2</KEYID> +<FOREIGNKEYID>6</FOREIGNKEYID> +</PAIR> +</PAIRS> +</REL> +<REL> +<NAME>DATABASES_DATA_SETS</NAME> +<NAMETEMPLATE>DATABASES_DATA_SETS</NAMETEMPLATE> +<ID>125</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<PARENTOBJECTID>110</PARENTOBJECTID> +<CHILDOBJECTID>17</CHILDOBJECTID> +<CARDINALITY>0</CARDINALITY> +<RELTYPE>1</RELTYPE> +<MANDATORYPARENT>1</MANDATORYPARENT> +<UPDATERULE>0</UPDATERULE> +<DELETERULE>0</DELETERULE> +<CONSTRAINT> +<NAME>DATABASES_DATA_SETS</NAME> +<NAMETEMPLATE>DATABASES_DATA_SETS</NAMETEMPLATE> +<ID>1</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<CONLEVEL>2</CONLEVEL> +<CONTYPE>4</CONTYPE> +<ATTRIBUTEIDS> +<ATTRIBUTEID>6</ATTRIBUTEID> +</ATTRIBUTEIDS> +</CONSTRAINT> +<PAIRS> +<PAIR> +<NAME></NAME> +<ID>0</ID> +<POSNR>0</POSNR> +<SCHEMA></SCHEMA> +<DESC></DESC> +<KEYID>2</KEYID> +<FOREIGNKEYID>6</FOREIGNKEYID> +</PAIR> +</PAIRS> +</REL> </RELATIONSHIPS> <SUBCATEGORYCONNECTIONS> </SUBCATEGORYCONNECTIONS> diff --git a/rtd_phosphonetx/source/sql/postgresql/001/schema-001.png b/rtd_phosphonetx/source/sql/postgresql/001/schema-001.png index 5d464e41e1b4665432a3a9b085edae9e62fb03ac..5e33190f05fa966110216608caa6a372a567fb6d 100644 Binary files a/rtd_phosphonetx/source/sql/postgresql/001/schema-001.png and b/rtd_phosphonetx/source/sql/postgresql/001/schema-001.png differ diff --git a/rtd_phosphonetx/source/sql/postgresql/001/schema-001.sql b/rtd_phosphonetx/source/sql/postgresql/001/schema-001.sql index 8bba1d6bd7d3238f3f7c07abe25bc7151d64b78b..564e02e3e181fcdfb61c3d0c66437e594bea7953 100644 --- a/rtd_phosphonetx/source/sql/postgresql/001/schema-001.sql +++ b/rtd_phosphonetx/source/sql/postgresql/001/schema-001.sql @@ -1,12 +1,12 @@ /* ---------------------------------------------------------------------- */ /* Script generated with: DeZign for Databases v5.2.2 */ /* Target DBMS: PostgreSQL 8 */ -/* Project file: phosphonetx.dez */ +/* Project file: schema-001.dez */ /* Project name: */ /* Author: */ /* Script type: Database creation script */ -/* Created on: 2009-06-30 09:00 */ -/* Model version: Version 2009-06-30 */ +/* Created on: 2009-07-06 13:30 */ +/* Model version: Version 2009-07-06 1 */ /* ---------------------------------------------------------------------- */ @@ -14,8 +14,6 @@ /* Domains */ /* ---------------------------------------------------------------------- */ -CREATE DOMAIN BINARY_DATA AS BYTEA; - CREATE DOMAIN CHECKSUM AS CHARACTER VARYING(8); CREATE DOMAIN CODE AS CHARACTER VARYING(40); @@ -34,6 +32,8 @@ CREATE DOMAIN TECH_ID AS BIGINT; CREATE DOMAIN SHORT_SEQUENCE AS CHARACTER VARYING(1000); +CREATE DOMAIN UNIPROT_ACCESSION_NUMBER AS CHARACTER VARYING(40); + /* ---------------------------------------------------------------------- */ /* Tables */ /* ---------------------------------------------------------------------- */ @@ -69,6 +69,7 @@ CREATE TABLE DATA_SETS ( ID BIGSERIAL NOT NULL, EXPE_ID TECH_ID NOT NULL, SAMP_ID TECH_ID NOT NULL, + DB_ID TECH_ID NOT NULL, PERM_ID CODE NOT NULL, CONSTRAINT PK_DATA_SETS PRIMARY KEY (ID), CONSTRAINT TUC_DATA_SETS_1 UNIQUE (PERM_ID) @@ -103,8 +104,9 @@ CREATE TABLE MODIFICATION_TYPES ( ID BIGSERIAL NOT NULL, CODE CODE NOT NULL, DESCRIPTION SHORT_DESCRIPTION, + AMINO_ACID CHARACTER(1), MASS REAL_NUMBER, - DELTA_MASS REAL_NUMBER, + MASS_TOLERANCE REAL_NUMBER, CONSTRAINT PK_MODIFICATION_TYPES PRIMARY KEY (ID), CONSTRAINT TUC_MODIFICATION_TYPES_1 UNIQUE (CODE) ); @@ -154,6 +156,8 @@ CREATE TABLE SAMPLES ( CREATE TABLE SEQUENCES ( ID BIGSERIAL NOT NULL, + DB_ID TECH_ID NOT NULL, + PRRE_ID TECH_ID NOT NULL, AMINO_ACID_SEQUENCE LONG_SEQUENCE NOT NULL, CHECKSUM CHECKSUM NOT NULL, CONSTRAINT PK_SEQUENCES PRIMARY KEY (ID) @@ -166,8 +170,7 @@ CREATE TABLE SEQUENCES ( CREATE TABLE IDENTIFIED_PROTEINS ( ID BIGSERIAL NOT NULL, PROT_ID TECH_ID NOT NULL, - SEQU_ID TECH_ID, - DESCRIPTION DESCRIPTION NOT NULL, + SEQU_ID TECH_ID NOT NULL, CONSTRAINT PK_IDENTIFIED_PROTEINS PRIMARY KEY (ID) ); @@ -196,6 +199,31 @@ CREATE TABLE PROBABILITY_FDR_MAPPINGS ( CONSTRAINT PK_PROBABILITY_FDR_MAPPINGS PRIMARY KEY (ID) ); +/* ---------------------------------------------------------------------- */ +/* Add table "PROTEIN_REFERENCES" */ +/* ---------------------------------------------------------------------- */ + +CREATE TABLE PROTEIN_REFERENCES ( + ID BIGSERIAL NOT NULL, + UNIPROT_ID UNIPROT_ACCESSION_NUMBER NOT NULL, + DESCRIPTION DESCRIPTION, + CONSTRAINT PK_PROTEIN_REFERENCES PRIMARY KEY (ID), + CONSTRAINT TUC_PROTEIN_REFERENCES_1 UNIQUE (UNIPROT_ID) +); + +CREATE INDEX IDX_PROTEIN_REFERENCES_1 ON PROTEIN_REFERENCES (UNIPROT_ID); + +/* ---------------------------------------------------------------------- */ +/* Add table "DATABASES" */ +/* ---------------------------------------------------------------------- */ + +CREATE TABLE DATABASES ( + ID BIGSERIAL NOT NULL, + NAME_AND_VERSION SHORT_DESCRIPTION NOT NULL, + CONSTRAINT PK_DATABASES PRIMARY KEY (ID), + CONSTRAINT TUC_DATABASES_1 UNIQUE (NAME_AND_VERSION) +); + /* ---------------------------------------------------------------------- */ /* Foreign key constraints */ /* ---------------------------------------------------------------------- */ @@ -206,6 +234,9 @@ ALTER TABLE DATA_SETS ADD CONSTRAINT DA_EX_FK ALTER TABLE DATA_SETS ADD CONSTRAINT DA_SA_FK FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID); +ALTER TABLE DATA_SETS ADD CONSTRAINT DATABASES_DATA_SETS + FOREIGN KEY (DB_ID) REFERENCES DATABASES (ID); + ALTER TABLE MODIFICATIONS ADD CONSTRAINT MO_PE_FK FOREIGN KEY (PEPT_ID) REFERENCES PEPTIDES (ID); @@ -218,6 +249,12 @@ ALTER TABLE PEPTIDES ADD CONSTRAINT PE_PR_FK ALTER TABLE PROTEINS ADD CONSTRAINT DATA_SETS_PROTEINS FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID); +ALTER TABLE SEQUENCES ADD CONSTRAINT DATABASES_SEQUENCES + FOREIGN KEY (DB_ID) REFERENCES DATABASES (ID); + +ALTER TABLE SEQUENCES ADD CONSTRAINT PROTEIN_REFERENCES_SEQUENCES + FOREIGN KEY (PRRE_ID) REFERENCES PROTEIN_REFERENCES (ID); + ALTER TABLE IDENTIFIED_PROTEINS ADD CONSTRAINT PROTEINS_IDENTIFIED_PROTEINS FOREIGN KEY (PROT_ID) REFERENCES PROTEINS (ID);