diff --git a/assembly/pom.xml b/assembly/pom.xml index 9ce2ed904..3a21a9944 100644 --- a/assembly/pom.xml +++ b/assembly/pom.xml @@ -5,7 +5,7 @@ psimi-master psidev.psi.mi - 1.8.6-SNAPSHOT + 1.9.6-SNAPSHOT 4.0.0 @@ -79,13 +79,6 @@ zip distribution - - psidev.psi.mi - psi25-xml-rdf - ${project.version} - zip - distribution - psidev.psi.mi psimitab-organism diff --git a/calimocho-solr/pom.xml b/calimocho-solr/pom.xml index 5be5babda..f9dd3c0e3 100644 --- a/calimocho-solr/pom.xml +++ b/calimocho-solr/pom.xml @@ -4,7 +4,7 @@ psimi-master psidev.psi.mi - 1.8.6 + 1.9.6-SNAPSHOT calimocho-solr diff --git a/calimocho-tab/pom.xml b/calimocho-tab/pom.xml index b7228d4e9..16b5e17d1 100644 --- a/calimocho-tab/pom.xml +++ b/calimocho-tab/pom.xml @@ -3,7 +3,7 @@ psidev.psi.mi psimi-master - 1.8.6 + 1.9.6-SNAPSHOT 4.0.0 diff --git a/calimocho-xgmml/pom.xml b/calimocho-xgmml/pom.xml index 2dbc3de8d..f77254a28 100644 --- a/calimocho-xgmml/pom.xml +++ b/calimocho-xgmml/pom.xml @@ -3,7 +3,7 @@ psidev.psi.mi psimi-master - 1.8.6 + 1.9.6-SNAPSHOT 4.0.0 diff --git a/calimocho-xml/pom.xml b/calimocho-xml/pom.xml index 53f8ae224..3161f975c 100644 --- a/calimocho-xml/pom.xml +++ b/calimocho-xml/pom.xml @@ -3,7 +3,7 @@ psidev.psi.mi psimi-master - 1.8.6 + 1.9.6-SNAPSHOT 4.0.0 @@ -23,7 +23,7 @@ psidev.psi.mi psi25-xml - 1.8.6 + 1.9.6-SNAPSHOT diff --git a/calimocho/pom.xml b/calimocho/pom.xml index af542f29e..a9055c96e 100644 --- a/calimocho/pom.xml +++ b/calimocho/pom.xml @@ -3,7 +3,7 @@ psidev.psi.mi psimi-master - 1.8.6 + 1.9.6-SNAPSHOT 4.0.0 diff --git a/pom.xml b/pom.xml index e9862da51..7de4c68f7 100644 --- a/pom.xml +++ b/pom.xml @@ -5,7 +5,7 @@ psidev.psi.mi psimi-master pom - 1.8.6 + 1.9.6-SNAPSHOT PSI Base build file @@ -23,7 +23,6 @@ calimocho-xgmml calimocho-xml psi25-xml - psi25-xml-rdf psimi-enricher psimi-examples psimitab-organism @@ -195,10 +194,10 @@ maven-compiler-plugin - 2.3.2 + 3.8.1 - 1.5 - 1.5 + 1.6 + 1.6 **/test/**/*.java diff --git a/psi25-xml-rdf/pom.xml b/psi25-xml-rdf/pom.xml deleted file mode 100644 index 11f756913..000000000 --- a/psi25-xml-rdf/pom.xml +++ /dev/null @@ -1,87 +0,0 @@ - - - - psidev.psi.mi - psimi-master - 1.8.6 - - - 4.0.0 - - psi25-xml-rdf - jar - 1.8.6 - - PSI :: RDF converter - - - - - - org.apache.maven.plugins - maven-assembly-plugin - - - - - - - psidev.psi.mi - psi25-xml - ${project.version} - - - - - org.biopax.paxtools - psimi-converter - 4.1.1 - - - org.biopax.paxtools - paxtools-core - 4.1.1 - - - org.biopax.paxtools - paxtools-jena-io - 4.1.1 - - - org.biopax.validator - biopax-validator-core - 2.0.0 - - - lucene - lucene - - - - - org.biopax - miriam-lib - 3.0.4 - - - - - com.hp.hpl.jena - jena - 2.6.4 - - - - - - - intact.nexus - IntAct Nexus - http://www.ebi.ac.uk/intact/maven/nexus/content/groups/public/ - - - biopax-release - http://www.biopax.org/m2repo/releases/ - - - diff --git a/psi25-xml-rdf/src/main/assembly/descriptor.xml b/psi25-xml-rdf/src/main/assembly/descriptor.xml deleted file mode 100644 index 31b8d1dbd..000000000 --- a/psi25-xml-rdf/src/main/assembly/descriptor.xml +++ /dev/null @@ -1,34 +0,0 @@ - - distribution - false - - - zip - - - - - - README* - LICENSE* - NOTICE* - - - - target - / - - *.jar - - - - - - /lib - false - runtime - - - diff --git a/psi25-xml-rdf/src/main/java/org/hupo/psi/mi/rdf/BioPaxUriFixer.java b/psi25-xml-rdf/src/main/java/org/hupo/psi/mi/rdf/BioPaxUriFixer.java deleted file mode 100644 index 5255e8d3c..000000000 --- a/psi25-xml-rdf/src/main/java/org/hupo/psi/mi/rdf/BioPaxUriFixer.java +++ /dev/null @@ -1,136 +0,0 @@ -/** - * Copyright 2011 The European Bioinformatics Institute, and others. - * - * 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 org.hupo.psi.mi.rdf; - -import org.apache.commons.lang.StringUtils; -import org.biopax.paxtools.io.jena.JenaIOHandler; -import org.biopax.paxtools.model.BioPAXLevel; -import org.biopax.paxtools.model.Model; -import org.biopax.paxtools.model.level3.SimplePhysicalEntity; -import org.biopax.paxtools.model.level3.Xref; -import org.biopax.validator.utils.Normalizer; - -import java.io.*; -import java.util.HashMap; -import java.util.Map; -import java.util.Set; - -/** - * @author Bruno Aranda (baranda@ebi.ac.uk) - * @version $Id$ - */ -public class BioPaxUriFixer { - - private static final String NEW_LINE = System.getProperty("line.separator"); - private static final String IDENTIFIERS_ORG = "http://identifiers.org/"; - private BioPAXLevel biopaxLevel; - - public BioPaxUriFixer(BioPAXLevel biopaxLevel) { - this.biopaxLevel = biopaxLevel; - } - - public void fixBioPaxUris(Model model, Writer writer) throws IOException { - model.getNameSpacePrefixMap().clear(); - - Map mappings = new HashMap(); - mappings.put("psi-mi", "mi"); - mappings.put("rcsb pdb", "pdb"); - - fixXrefs(model, mappings); - - Map idMappings = calculateIdMapings(model); - - new Normalizer().normalize(model); - - OutputStream baos = new ByteArrayOutputStream(); - - new JenaIOHandler(this.biopaxLevel).convertToOWL(model, baos); - - fixURIs(idMappings, new StringReader(baos.toString()), writer); - - // close OutputStream - baos.close(); - } - - private void fixURIs(Map idMappings, Reader reader, Writer writer) throws IOException { - BufferedReader in = new BufferedReader(reader); - String line; - while ((line = in.readLine()) != null) { - - if (line.contains("Reference")) { - for (Map.Entry protMapEntry : idMappings.entrySet()) { - if (line.contains(protMapEntry.getKey())) { - line = line.replaceAll(protMapEntry.getKey(), protMapEntry.getValue()); - } - } - } - - if (line.contains("urn:miriam:")) { - String[] tokens = line.split("urn:miriam:"); - // hack : only take first word - if (tokens[1].contains(" <")){ - int index = tokens[1].indexOf(" <"); - String uriToFix = tokens[1].substring(0, index); - tokens[1] = StringUtils.replaceOnce(uriToFix, ":", "/")+tokens[1].substring(index); - } - else { - tokens[1] = StringUtils.replaceOnce(tokens[1], ":", "/"); - } - - line = StringUtils.join(tokens, IDENTIFIERS_ORG); - } - - writer.write(line + NEW_LINE); - } - - // close bufferReader - in.close(); - } - - private Map calculateIdMapings(Model model) { - Map idMappings = new HashMap(); - - final Set proteins = model.getObjects(SimplePhysicalEntity.class); - - for (SimplePhysicalEntity protein : proteins) { - final String protRefId = protein.getEntityReference().getRDFId(); - - for (Xref xref : protein.getXref()) { - if ("uniprotkb".equals(xref.getDb())) { - String newId = IDENTIFIERS_ORG + "uniprot/" + xref.getId(); - idMappings.put(protRefId, newId); - break; - } else if ("chebi".equals(xref.getDb())) { - String newId = IDENTIFIERS_ORG + xref.getDb() + "/" + xref.getId(); - idMappings.put(protRefId, newId); - break; - } - } - } - return idMappings; - } - - private void fixXrefs(Model model, Map mappings) { - final Set xrefs = model.getObjects(Xref.class); - - for (Xref xref : xrefs) { - if (mappings.containsKey(xref.getDb())) { - xref.setDb(mappings.get(xref.getDb())); - } - } - } - -} diff --git a/psi25-xml-rdf/src/main/java/org/hupo/psi/mi/rdf/PsimiRdfConverter.java b/psi25-xml-rdf/src/main/java/org/hupo/psi/mi/rdf/PsimiRdfConverter.java deleted file mode 100644 index 40a71c82b..000000000 --- a/psi25-xml-rdf/src/main/java/org/hupo/psi/mi/rdf/PsimiRdfConverter.java +++ /dev/null @@ -1,214 +0,0 @@ -/** - * Copyright 2011 The European Bioinformatics Institute, and others. - * - * 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 org.hupo.psi.mi.rdf; - -import com.hp.hpl.jena.ontology.OntModel; -import com.hp.hpl.jena.ontology.OntModelSpec; -import com.hp.hpl.jena.rdf.arp.JenaReader; -import com.hp.hpl.jena.rdf.model.ModelFactory; -import com.hp.hpl.jena.rdf.model.RDFReader; -import com.hp.hpl.jena.rdf.model.RDFWriter; -import org.biopax.paxtools.controller.PropertyEditor; -import org.biopax.paxtools.io.jena.JenaIOHandler; -import org.biopax.paxtools.model.BioPAXLevel; -import org.biopax.paxtools.model.Model; -import org.mskcc.psibiopax.converter.PSIMIBioPAXConverter; -import psidev.psi.mi.xml.PsimiXmlReader; -import psidev.psi.mi.xml.PsimiXmlReaderException; -import psidev.psi.mi.xml.converter.ConverterContext; -import psidev.psi.mi.xml.model.Entry; -import psidev.psi.mi.xml.model.EntrySet; - -import java.io.*; -import java.util.Arrays; -import java.util.Iterator; - -/** - * @author Bruno Aranda (baranda@ebi.ac.uk) - * @version $Id$ - */ -public class PsimiRdfConverter { - - public PsimiRdfConverter() { - - } - - public void convert(EntrySet entrySet, RdfFormat format, Writer writer) throws IOException { - convert(entrySet, format.getName(), writer); - } - - public void convert(Reader reader, RdfFormat format, Writer writer) throws IOException, PsimiXmlReaderException { - convert(reader, format.getName(), writer); - } - - public void convert(EntrySet entrySet, RdfFormat format, OutputStream os) throws IOException { - convert(entrySet, format.getName(), os); - } - - public void convert(InputStream is, RdfFormat format, OutputStream os) throws IOException, PsimiXmlReaderException { - convert(new InputStreamReader(is), format.getName(), new OutputStreamWriter(os)); - } - - public void convert(EntrySet entrySet, String format, OutputStream os) throws IOException { - convert(entrySet, format, new OutputStreamWriter(os)); - } - - public void convert(InputStream is, String format, Writer writer) throws IOException, PsimiXmlReaderException { - convert(new InputStreamReader(is), format, writer); - } - - public void convert(Reader reader, String format, Writer writer) throws IOException, PsimiXmlReaderException { - PsimiXmlReader xmlReader = new PsimiXmlReader(); - EntrySet entrySet = xmlReader.read(reader); - convert(entrySet, format, writer); - } - - public void convert(EntrySet entrySet, String format, Writer writer) { - - if (format.startsWith("BioPAX")) { - BioPAXLevel biopaxLevel; - - if (format.equals(RdfFormat.BIOPAX_L2.getName())) { - biopaxLevel = BioPAXLevel.L2; - } else { - biopaxLevel = BioPAXLevel.L3; - } - - try { - convertToBioPAXAndFixURIs(entrySet, biopaxLevel, writer); - } catch (IOException e) { - throw new RuntimeException("Problem converting EntrySet to BioPAX", e); - } - } else { - final String baseUri = "http://org.hupo.psi.mi"; - - OntModel jenaModel = convertToJena(entrySet); - - final RDFWriter rdfWriter = jenaModel.getWriter(format); - rdfWriter.setProperty("xmlbase", baseUri); - jenaModel.setNsPrefix("", baseUri); - - rdfWriter.write(jenaModel, writer, baseUri); - } - - try { - writer.flush(); - } catch (IOException e) { - throw new RuntimeException("Problem flushing writer", e); - } - } - - public OntModel convertToJena(EntrySet entrySet) { - StringWriter sw = new StringWriter(); - - try { - convertToBioPAXAndFixURIs(entrySet, BioPAXLevel.L3, sw); - StringReader stringReader = new StringReader(sw.toString()); - OntModel model = createJenaModel(stringReader, "http://org.hupo.psi.mi"); - - // close reader and writer - stringReader.close(); - sw.close(); - - return model; - } catch (IOException e) { - throw new RuntimeException("Problem converting EntrySet to BioPAX", e); - } - } - - public Model convertToBioPAX(EntrySet entrySet, BioPAXLevel biopaxLevel) { - StringWriter sw = new StringWriter(); - - try { - convertToBioPAXAndFixURIs(entrySet, biopaxLevel, sw); - - Model model = new JenaIOHandler(biopaxLevel).convertFromOWL(new ByteArrayInputStream(sw.toString().getBytes())); - - //close writer - sw.close(); - - return model; - - } catch (IOException e) { - throw new RuntimeException("Problem converting EntrySet to BioPAX", e); - } - } - - private EntrySet mergeEntriesIfNecessary(EntrySet entrySet){ - if (entrySet == null){ - return null; - } - - if (entrySet.getEntries().size() > 1){ - Iterator entryIterator = entrySet.getEntries().iterator(); - - Entry originalEntry = entryIterator.next(); - - while (entryIterator.hasNext()){ - Entry newEntry = entryIterator.next(); - - originalEntry.getExperiments().addAll(newEntry.getExperiments()); - originalEntry.getInteractors().addAll(newEntry.getInteractors()); - originalEntry.getInteractions().addAll(newEntry.getInteractions()); - } - - return new EntrySet(Arrays.asList(originalEntry), entrySet.getLevel(), entrySet.getVersion(), entrySet.getMinorVersion()); - } - - return entrySet; - } - - private void convertToBioPAXAndFixURIs(EntrySet entrySet, BioPAXLevel biopaxLevel, Writer writer) throws IOException { - OutputStream os = new ByteArrayOutputStream(); - - PSIMIBioPAXConverter biopaxConverter = new PSIMIBioPAXConverter(biopaxLevel); - biopaxConverter.convert(mergeEntriesIfNecessary(entrySet), os); - - String biopaxOutput = os.toString(); - - // close outputStream - os.close(); - - if (!biopaxOutput.isEmpty()) { - ByteArrayInputStream byteInputStream = new ByteArrayInputStream(biopaxOutput.getBytes()); - // fix the biopax non-dereferenciable URIs - Model model = new JenaIOHandler(biopaxLevel).convertFromOWL(byteInputStream); - - BioPaxUriFixer fixer = new BioPaxUriFixer(biopaxLevel); - - fixer.fixBioPaxUris(model, writer); - - // close byteInputStream - byteInputStream.close(); - } - } - - private OntModel createJenaModel(Reader reader, String baseUri) { - OntModel model = ModelFactory.createOntologyModel(OntModelSpec.OWL_DL_MEM); - - final RDFReader rdfReader = new JenaReader(); - rdfReader.read(model, reader, baseUri); - return model; - } - - public void close(){ - // remove current value for threadlocal - PropertyEditor.checkRestrictions.remove(); - // removed current value for xml converterContext - ConverterContext.remove(); - } - -} diff --git a/psi25-xml-rdf/src/main/java/org/hupo/psi/mi/rdf/RdfFormat.java b/psi25-xml-rdf/src/main/java/org/hupo/psi/mi/rdf/RdfFormat.java deleted file mode 100644 index 515717fb8..000000000 --- a/psi25-xml-rdf/src/main/java/org/hupo/psi/mi/rdf/RdfFormat.java +++ /dev/null @@ -1,30 +0,0 @@ -package org.hupo.psi.mi.rdf; - -/** - * @author Bruno Aranda (baranda@ebi.ac.uk) - * @version $Id$ - */ -public enum RdfFormat { - - BIOPAX_L2("BioPAX.L2"), - BIOPAX_L3("BioPAX.L3"), - RDF_XML("RDF/XML"), - RDF_XML_ABBREV("RDF/XML-ABBREV"), - N_TRIPLE("N-TRIPLE"), - TURTLE("TURTLE"), - N3("N3"), - N3_PP("N3-PP"), - N3_PLAIN("N3-PLAIN"), - N3_TRIPLE("N3-TRIPLE"); - - private String name; - - private RdfFormat(String name) { - this.name = name; - } - - public String getName() { - return name; - } -} - diff --git a/psi25-xml-rdf/src/test/java/org/hupo/psi/mi/rdf/Playground.java b/psi25-xml-rdf/src/test/java/org/hupo/psi/mi/rdf/Playground.java deleted file mode 100644 index 87f2c8660..000000000 --- a/psi25-xml-rdf/src/test/java/org/hupo/psi/mi/rdf/Playground.java +++ /dev/null @@ -1,33 +0,0 @@ -/** - * Copyright 2011 The European Bioinformatics Institute, and others. - * - * 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 org.hupo.psi.mi.rdf; - -import java.io.InputStream; - -/** - * @author Bruno Aranda (baranda@ebi.ac.uk) - * @version $Id$ - */ -public class Playground { - - public static void main(String[] args) throws Exception { - InputStream is = Playground.class.getResourceAsStream("/META-INF/simple-nary-interaction.xml"); - - PsimiRdfConverter converter = new PsimiRdfConverter(); - converter.convert(is, RdfFormat.BIOPAX_L2, System.out); - } - -} diff --git a/psi25-xml-rdf/src/test/resources/META-INF/simple-nary-interaction.xml b/psi25-xml-rdf/src/test/resources/META-INF/simple-nary-interaction.xml deleted file mode 100644 index 5e3f71dc5..000000000 --- a/psi25-xml-rdf/src/test/resources/META-INF/simple-nary-interaction.xml +++ /dev/null @@ -1,326 +0,0 @@ - - - - - European Bioinformatics Institute - - - - - - - - - - - Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United - Kingdom - - http://www.ebi.ac.uk - - - - - - mansour-2001-1 - Characterization of functional interactions among the Escherichia coli mismatch repair - proteins using a bacterial two-hybrid assay. - - - - - - - - - - - - - - - yeast - Saccharomyces cerevisiae - - - - - - two hybrid - two hybrid - 2H - two-hybrid - 2h - - - - - - - - - - - predetermined - predetermined participant - - - - - - - - - Mansour CA., Doiron KM., Cupples CG. - claire@vax2.concordia.ca - Interaction was checked by assaying for beta-galactosidase. - - fig 1a - 2001 - Mutat. Res. (0027-5107) - - - - - - - mutl_ecoli - DNA mismatch repair protein mutL - mutL - b4170 - - - - - - - - - - - protein - protein - - - - - - - - - - ecoli - Escherichia coli - - - - MPIQVLPPQLANQIAAGEVVERPASVVKELVENSLDAGATRIDIDIERGGAKLIRIRDNGCGIKKDELALALARHATSKIASLDDLEAIISLGFRGEALASISSVSRLTLTSRTAEQQEAWQAYAEGRDMNVTVKPAAHPVGTTLEVLDLFYNTPARRKFLRTEKTEFNHIDEIIRRIALARFDVTINLSHNGKIVRQYRAVPEGGQKERRLGAICGTAFLEQALAIEWQHGDLTLRGWVADPNHTTPALAEIQYCYVNGRMMRDRLINHAIRQACEDKLGADQQPAFVLYLEIDPHQVDVNVHPAKHEVRFHQSRLVHDFIYQGVLSVLQQQLETPLPLDDEPQPAPRSIPENRVAAGRNHFAEPAAREPVAPRYTPAPASGSRPAAPWPNAQPGYQKQQGEVYRQLLQTPAPMQKLKAPEPQEPALAANSQSFGRVLTIVHSDCALLERDGNISLLSLPVAERWLRQAQLTPGEAPVCAQPLLIPLRLKVSAEEKSALEKAQSALAELGIDFQSDAQHVTIRAVPLPLRQQNLQILIPELIGYLAKQSVFEPGNIAQWIARNLMSEHAQWSMAQAITLLADVERLCPQLVKTPPGGLLQSVDLHPAIKALKDE - - - - - vsr_ecoli - Very short patch repair protein - vsr - b1960 - - - - - - - - - protein - protein - - - - - - - - - - ecoli - Escherichia coli - - - - ADVHDKATRSKNMRAIATRDTAIEKRLASLLTGQGLAFRVQDASLPGRPDFVVDEYRCVIFTHGCFWHHHHCYLFKVPATRTEFWLEKIGKNVERDRRDISRLQELGWRVLIVWECALRGREKLTDEALTERLEEWICGEGASAQIDTQGIHLLA - - - - - muts_ecoli - DNA mismatch repair protein mutS - mutS - fdv - b2733 - - - - - - - - - - - protein - protein - - - - - - - - - - ecoli - Escherichia coli - - - - MSAIENFDAHTPMMQQYLRLKAQHPEILLFYRMGDFYELFYDDAKRASQLLDISLTKRGASAGEPIPMAGIPYHAVENYLAKLVNQGESVAICEQIGDPATSKGPVERKVVRIVTPGTISDEALLQERQDNLLAAIWQDSKGFGYATLDISSGRFRLSEPADRETMAAELQRTNPAELLYAEDFAEMSLIEGRRGLRRRPLWEFEIDTARQQLNLQFGTRDLVGFGVENAPRGLCAAGCLLQYAKDTQRTTLPHIRSITMEREQDSIIMDAATRRNLEITQNLAGGAENTLASVLDCTVTPMGSRMLKRWLHMPVRDTRVLLERQQTIGALQDFTAGLQPVLRQVGDLERILARLALRTARPRDLARMRHAFQQLPELRAQLETVDSAPVQALREKMGEFAELRDLLERAIIDTPPVLVRDGGVIASGYNEELDEWRALADGATDYLERLEVRERERTGLDTLKVGFNAVHGYYIQISRGQSHLAPINYMRRQTLKNAERYIIPELKEYEDKVLTSKGKALALEKQLYEELFDLLLPHLEALQQSASALAELDVLVNLAERAYTLNYTCPTFIDKPGIRITEGRHPVVEQVLNEPFIANPLNLSPQRRMLIITGPNMGGKSTYMRQTALIALMAYIGSYVPAQKVEIGPIDRIFTRVGAADDLASGRSTFMVEMTETANILHNATEYSLVLMDEIGRGTSTYDGLSLAWACAENLANKIKALTLFATHYFELTQLPEKMEGVANVHLDALEHGDTIAFMHSVQDGAASKSYGLAVAALAGVPKEVIKRARQKLRELESISPNAAATQVDGTQMSLLSVPEETSPAVEALENLDPDSLTPRQALEWIYRLKSLV - - - - - - - vsr-mutl-1 - Y2H: bait = Vsr, prey= MutL - - - - - - 2 - - - - - - 6 - - - unspecified role - unspecified role - - - - - - - - - - bait - bait - - - - - - - - - - - - 4 - - - unspecified role - unspecified role - - - - - - - - - - prey - prey - - - - - - - - - - 7 - - - unspecified role - unspecified role - - - - - - - - - - prey - prey - - - - - - - - - - - - physical interaction - physical interaction - aggregation - - - - - - - - 0.0 - - - - - diff --git a/psi25-xml/pom.xml b/psi25-xml/pom.xml index d7babdc69..0943fe172 100755 --- a/psi25-xml/pom.xml +++ b/psi25-xml/pom.xml @@ -3,14 +3,14 @@ psidev.psi.mi psimi-master - 1.8.6 + 1.9.6-SNAPSHOT 4.0.0 psi25-xml jar - 1.8.6 + 1.9.6-SNAPSHOT PSI :: PSI-MI XML 2.5 Library @@ -35,6 +35,7 @@ org.apache.maven.plugins maven-jar-plugin + 3.2.0 ${project.build.outputDirectory}/META-INF/MANIFEST.MF @@ -125,20 +126,20 @@ + - org.apache.commons - com.springsource.org.apache.commons.logging - 1.1.1 + commons-logging + commons-logging + 1.2 true - org.apache.log4j - com.springsource.org.apache.log4j - 1.2.15 + org.apache.logging.log4j + log4j-jcl + 2.16.0 true - org.osgi diff --git a/psimi-enricher/pom.xml b/psimi-enricher/pom.xml index 110a28eee..318065945 100644 --- a/psimi-enricher/pom.xml +++ b/psimi-enricher/pom.xml @@ -4,7 +4,7 @@ psidev.psi.mi psimi-master - 1.8.6 + 1.9.6-SNAPSHOT psimi-enricher diff --git a/psimi-examples/pom.xml b/psimi-examples/pom.xml index 84712a0bc..de1c5a104 100644 --- a/psimi-examples/pom.xml +++ b/psimi-examples/pom.xml @@ -4,14 +4,14 @@ psidev.psi.mi psimi-master - 1.8.6 + 1.9.6-SNAPSHOT 4.0.0 psimi-examples jar - 1.8.6 + 1.9.6-SNAPSHOT PSI :: PSI-MI Examples diff --git a/psimitab-organism/pom.xml b/psimitab-organism/pom.xml index 2679a5f85..508e16905 100755 --- a/psimitab-organism/pom.xml +++ b/psimitab-organism/pom.xml @@ -5,12 +5,12 @@ psidev.psi.mi psimi-master - 1.8.6 + 1.9.6-SNAPSHOT psimitab-organism jar - 1.8.6 + 1.9.6-SNAPSHOT PSI :: Computation of organism tree from MITAB25 diff --git a/psimitab-parser/pom.xml b/psimitab-parser/pom.xml index 06523477c..3422a245a 100755 --- a/psimitab-parser/pom.xml +++ b/psimitab-parser/pom.xml @@ -3,14 +3,14 @@ psidev.psi.mi psimi-master - 1.8.6 + 1.9.6-SNAPSHOT 4.0.0 psimitab jar - 1.8.6 + 1.9.6-SNAPSHOT PSI :: PSI-MI TABular format tools http://psidev.sf.net diff --git a/psimitab-search/pom.xml b/psimitab-search/pom.xml index 97a6c88aa..532ad16a4 100755 --- a/psimitab-search/pom.xml +++ b/psimitab-search/pom.xml @@ -3,14 +3,14 @@ psidev.psi.mi psimi-master - 1.8.6 + 1.9.6-SNAPSHOT 4.0.0 psimitab-search jar - 1.8.6 + 1.9.6-SNAPSHOT PSI :: PSI-MI TABular Search