Concept_Profile_GeneOntology_input00 A Skos formated dictionary/thesaurus of predefined concepts. 2014-04-11 13:48:01.261 UTC @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . @prefix skos: <http://www.w3.org/2004/02/skos/core#> . @prefix dct: <http://purl.org/dc/terms/> . @prefix emco: <http://rdf.biosemantics.org/emco/> . @prefix emco15: <http://rdf.biosemantics.org/emco/v1.5/> . @prefix concepts: <http://rdf.biosemantics.org/emco/v1.5/concepts/> . @prefix prop: <http://rdf.biosemantics.org/emco/properties/> . @prefix datatype: <http://rdf.biosemantics.org/emco/datatypes/> . @prefix semtype: <http://rdf.biosemantics.org/emco/semtypes/> . @prefix vocab: <http://rdf.biosemantics.org/emco/v1.5/vocabularies/> . prop:prefLabel_CI rdfs:subPropertyOf skos:prefLabel . prop:prefLabel_NO rdfs:subPropertyOf skos:prefLabel . prop:prefLabel_CI_NO rdfs:subPropertyOf skos:prefLabel . prop:altLabel_CI rdfs:subPropertyOf skos:altLabel . prop:altLabel_NO rdfs:subPropertyOf skos:altLabel . prop:altLabel_CI_NO rdfs:subPropertyOf skos:altLabel . vocab:default rdfs:comment "ErasmusMC ontology file" ; dct:title "Anni2_1_June2009" ; a skos:ConceptScheme . vocab:MSH dct:title "MeSH" ; a skos:ConceptScheme . vocab:SNOMEDCT dct:title "SNOMED Clinical Terms" ; a skos:ConceptScheme . semtype:T47 skos:topConceptOf vocab:default ; rdfs:label "Disease or Syndrome" ; skos:definition "A condition which alters or interferes with a normal process, state, or activity of an organism. It is usually characterized by the abnormal functioning of one or more of the host's systems, parts, or organs. Included here is a complex of symptoms descriptive of a disorder." ; a skos:Concept . concepts:C9187 skos:inScheme vocab:default ; prop:altLabel_CI_NO "Coccidiosis"@es ; prop:prefLabel_CI_NO "Coccidiosis" ; skos:notation "C0009187"^^datatype:umls-notation-datatype ; rdfs:label "Coccidiosis" ; skos:definition "Protozoan infection found in animals and man. It is caused by several different genera of COCCIDIA." ; skos:broader semtype:T47 ; a skos:Concept ; skos:inScheme vocab:MSH , vocab:SNOMEDCT . concepts:C24530 skos:inScheme vocab:default ; prop:altLabel_CI_NO "Malaria NOS" , "Plasmodium Infections" , "Remittent Fever" , "Paludism" , "Plasmodiosis" , "Malarial fever" , "Malaria (disorder)" , "Marsh Fever" , "Malaria"@es ; prop:prefLabel_CI "Malaria" ; skos:notation "C0024530"^^datatype:umls-notation-datatype ; rdfs:label "test" ; skos:broader concepts:C9187 , semtype:T47 ; a skos:Concept ; skos:inScheme vocab:MSH , vocab:SNOMEDCT . concepts:C3031092 skos:inScheme vocab:default ; prop:altLabel_NO "myelocytomatosis viral oncogene homolog (avian)" , "myelocytomatosis oncogene" , "Transcription factor p64" , "Myc proto-oncogene protein" , "v-myc myelocytomatosis viral oncogene homolog (avian)" , "Myc2" , "myc proto-oncogene protein" , "Transcription factor p-64" , "Myc-2" ; skos:notation "120208"^^datatype:gd-notation-datatype , "3130"^^datatype:gd-notation-datatype , "31092"^^datatype:ho-notation-datatype , "NM"^^datatype:rq-notation-datatype , "17869"^^datatype:eg-notation-datatype , "24577"^^datatype:eg-notation-datatype , "4609"^^datatype:eg-notation-datatype , "3130"^^datatype:rgd-notation-datatype , "190080"^^datatype:om-notation-datatype , "7553"^^datatype:hg-notation-datatype , "P01106"^^datatype:sp-notation-datatype , "P01108"^^datatype:sp-notation-datatype , "P09416"^^datatype:sp-notation-datatype , "Q6WDF7"^^datatype:sp-notation-datatype , "Hs.202453"^^datatype:ug-notation-datatype , "97250"^^datatype:mgi-notation-datatype , "1368308"^^datatype:af-notation-datatype , "1424942"^^datatype:af-notation-datatype , "202431"^^datatype:af-notation-datatype , "239931"^^datatype:af-notation-datatype ; rdfs:label "MYC" ; skos:prefLabel "MYC" , "C-MYC" , "Myc" , "Niard" , "Nird" , "c-Myc" , "c-myc" , "Myc-II" ; skos:broader semtype:T116 ; a skos:Concept ; skos:inScheme vocab:GENE , vocab:HOMOLOGENE . concepts:C3003921 skos:inScheme vocab:default ; prop:altLabel_NO "v-myc myelocytomatosis viral oncogene homolog 1, lung carcinoma derived (avian)" , "oncogene lmyc" , "l-myc-1 proto-oncogene" , "Lmyc1" , "myc-related gene from lung cancer" , "Oncogene MYC, lung carcinoma-derived" , "l-myc protein" , "Lmyc-1" , "Mycl1" , "L-myc-1 proto-oncogene protein" , "v-myc myelocytomatosis viral oncogene homolog 1, lung carcinoma derived (avian) (mapped)" , "v-myc avian myelocytomatosis viral oncogene homolog 1, lung carcinoma derived" , "MYCL-1" , "Mycl-1" ; prop:prefLabel_NO "MYCL1" ; skos:notation "120706"^^datatype:gd-notation-datatype , "1588591"^^datatype:gd-notation-datatype , "3921"^^datatype:ho-notation-datatype , "NM"^^datatype:rq-notation-datatype , "16918"^^datatype:eg-notation-datatype , "298506"^^datatype:eg-notation-datatype , "4610"^^datatype:eg-notation-datatype , "1588591"^^datatype:rgd-notation-datatype , "164850"^^datatype:om-notation-datatype , "7555"^^datatype:hg-notation-datatype , "P10166"^^datatype:sp-notation-datatype , "P12524"^^datatype:sp-notation-datatype , "Q6TLI1"^^datatype:sp-notation-datatype , "Hs.437922"^^datatype:ug-notation-datatype , "96799"^^datatype:mgi-notation-datatype , "1422087"^^datatype:af-notation-datatype , "1422088"^^datatype:af-notation-datatype , "214058"^^datatype:af-notation-datatype ; rdfs:label "MYCL1" ; skos:prefLabel "LMYC" , "MYCL" , "MYCL" , "MYCL-I" , "Lmyc-I" , "Mycl-I" ; skos:broader semtype:T116 ; a skos:Concept ; skos:inScheme vocab:GENE , vocab:HOMOLOGENE . concepts:C3003922 skos:inScheme vocab:default ; prop:altLabel_NO "v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian) (mapped)" , "v-myc myelocytomatosis viral related oncogene, neuroblastoma derived" , "v-myc avian myelocytomatosis viral related oncogene, neuroblastoma derived" , "Nmyc-1" , "neuroblastoma-derived v-myc avian myelocytomatosis viral related oncogene" , "v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)" , "N-MYC PROTO-ONCOGENE PROTEIN" , "Nmyc1" , "neuroblastoma MYC oncogene" , "pp65/67" , "oncogene NMYC" , "Oncogene NMYC" , "N-myc proto-oncogene protein" ; skos:notation "120527"^^datatype:gd-notation-datatype , "1584995"^^datatype:gd-notation-datatype , "3922"^^datatype:ho-notation-datatype , "NM"^^datatype:rq-notation-datatype , "18109"^^datatype:eg-notation-datatype , "298894"^^datatype:eg-notation-datatype , "4613"^^datatype:eg-notation-datatype , "1584995"^^datatype:rgd-notation-datatype , "164840"^^datatype:om-notation-datatype , "7559"^^datatype:hg-notation-datatype , "P03966"^^datatype:sp-notation-datatype , "Q53XS5"^^datatype:sp-notation-datatype , "Q63379"^^datatype:sp-notation-datatype , "Hs.25960"^^datatype:ug-notation-datatype , "97357"^^datatype:mgi-notation-datatype , "1417155"^^datatype:af-notation-datatype , "1425922"^^datatype:af-notation-datatype , "1425923"^^datatype:af-notation-datatype , "209756"^^datatype:af-notation-datatype , "209757"^^datatype:af-notation-datatype , "211377"^^datatype:af-notation-datatype , "234376"^^datatype:af-notation-datatype ; rdfs:label "MYCN" ; skos:prefLabel "MYCN" , "Mycn" , "N-myc" , "ODED" , "MODED" , "Nmyc" , "NMYC" , "Nmyc-I" ; skos:broader semtype:T116 ; a skos:Concept ; skos:inScheme vocab:GENE , vocab:HOMOLOGENE . concepts:C3020128 skos:inScheme vocab:default ; prop:altLabel_NO "neural cell adhesion molecule L1" , "NEURAL CELL ADHESION MOLECULE L1" , "Neural cell adhesion molecule L1" , "N-CAML1" , "L1cam" , "MIC5" , "antigen identified by monoclonal antibody R1" , "L1 cell adhesion molecule (hydrocephalus, stenosis of aqueduct of Sylvius 1, MASA (mental retardation, aphasia, shuffling gait and adducted thumbs) syndrome, spastic paraplegia 1)" , "CD171 antigen" , "HSAS1" , "S10" , "CAML1" , "NCAM-L1" , "MIC5" , "L1 cell adhesion molecule" , "SPG1" , "CD171" , "N-CAM L1" , "neural cell adhesion molecule L-I" , "neural cell adhesion molecule L-1" , "NEURAL CELL ADHESION MOLECULE L-I" , "NEURAL CELL ADHESION MOLECULE L-1" , "Neural cell adhesion molecule L-I" , "Neural cell adhesion molecule L-1" , "N-CAML-1" , "MIC-5" , "antigen identified by monoclonal antibody R-I" , "antigen identified by monoclonal antibody R-1" , "HSAS-1" , "CAML-1" , "NCAM-L-1" , "MIC-5" , "SPG-1" , "CD-171" , "N-CAM L-I" , "N-CAM L-1" ; prop:prefLabel_NO "L1CAM" ; skos:notation "120133"^^datatype:gd-notation-datatype , "120526"^^datatype:gd-notation-datatype , "619777"^^datatype:gd-notation-datatype , "20128"^^datatype:ho-notation-datatype , "NM"^^datatype:rq-notation-datatype , "16728"^^datatype:eg-notation-datatype , "3897"^^datatype:eg-notation-datatype , "50687"^^datatype:eg-notation-datatype , "619777"^^datatype:rgd-notation-datatype , "308840"^^datatype:om-notation-datatype , "6470"^^datatype:hg-notation-datatype , "P11627"^^datatype:sp-notation-datatype , "P32004"^^datatype:sp-notation-datatype , "Q05695"^^datatype:sp-notation-datatype , "Hs.522818"^^datatype:ug-notation-datatype , "96721"^^datatype:mgi-notation-datatype , "1369213"^^datatype:af-notation-datatype , "1421958"^^datatype:af-notation-datatype , "1450435"^^datatype:af-notation-datatype , "204584"^^datatype:af-notation-datatype , "204585"^^datatype:af-notation-datatype ; rdfs:label "L1CAM" ; skos:prefLabel "HSAS" , "MASA" , "N-CAML-I" , "MIC-V" , "HSAS-I" , "CAML-I" , "NCAM-L-I" , "MIC-V" , "SPG-I" ; skos:broader semtype:T116 ; a skos:Concept ; skos:inScheme vocab:GENE , vocab:HOMOLOGENE . concepts:C3000168 skos:inScheme vocab:default ; prop:altLabel_NO "CD54 antigen" , "intercellular adhesion molecule I" , "intercellular adhesion molecule1" , "Icam-1" , "CD-54" , "BB-2" , "Intercellular adhesion molecule I" , "Intercellular adhesion molecule1" , "Intercellular adhesion molecule-I" ; prop:prefLabel_NO "ICAM-1" ; skos:notation "120076"^^datatype:gd-notation-datatype , "2857"^^datatype:gd-notation-datatype , "168"^^datatype:ho-notation-datatype , "NM"^^datatype:rq-notation-datatype , "15894"^^datatype:eg-notation-datatype , "25464"^^datatype:eg-notation-datatype , "3383"^^datatype:eg-notation-datatype , "2857"^^datatype:rgd-notation-datatype , "147840"^^datatype:om-notation-datatype , "5344"^^datatype:hg-notation-datatype , "Q00238"^^datatype:sp-notation-datatype , "Q15463"^^datatype:sp-notation-datatype , "Hs.643447"^^datatype:ug-notation-datatype , "1387202"^^datatype:af-notation-datatype , "1424067"^^datatype:af-notation-datatype , "1427805"^^datatype:af-notation-datatype , "1427806"^^datatype:af-notation-datatype , "202637"^^datatype:af-notation-datatype , "202638"^^datatype:af-notation-datatype , "215485"^^datatype:af-notation-datatype ; rdfs:label "ICAM1" ; skos:prefLabel "ICAM-I" , "Icam-I" , "BB-II" ; skos:broader semtype:T116 ; a skos:Concept ; skos:inScheme vocab:GENE , vocab:HOMOLOGENE . 2014-03-21 13:04:42.508 UTC db_properties00 mysql.user=root mysql.password=amrishsql mysql.url=jdbc:mysql://localhost:3306/mydb mysql.driver=com.mysql.jdbc.Driver 2014-05-12 09:23:12.452 UTC Please load a file in as seen in the example where the user, password, url (which is the database it should use), and driver is stated. 2014-05-12 14:03:22.531 UTC Path_Peregrine_Indexer00 F:/School/Stage2/peregrine/ 2014-06-15 17:31:44.152 UTC Give the full path where the production.properties and peregrine-skos-cli.jar files are located of the Peregrine Indexer Tool. path/to/ production.properties path/to/ peregrine-skos-cli.jar 2014-06-15 17:43:06.759 UTC endPeregrine_Indexertable_name0ontology0Input2propertyString0Path0 The nested workflow Peregrine Indexer uses a java peregrine skos cli.jar file to index the occurrence of concepts in documents. The Peregrine indexer program can be downloaded from trac.nbic.nl/biosemantics/downloads. Install LVG2013Lite. See: https://trac.nbic.nl/biosemantics/wiki/Peregrine%20SKOS%20CLI Copy properties file from production.properties which can be downloaded from: https://trac.nbic.nl/biosemantics/wiki/Peregrine%20SKOS%20CLI Change lvg.properties LVG_DIR=/home/path/to/lvg2013lite/ This file can be found in: /home/path/to/lvg2013lite/data/config/lvg.properties Change the normalizer.lvg.properties and normalizer.lvg.binaryCache properties to point to the LVG installation path. normalizer.lvg.properties =/home/path/to/lvg2013lite/data/config/config/lvg.properties normalizer.lvg.binaryCahce=/home/path/to/lvg2013lite/standartNormCache2013.bin Have MySQL installed with a database called mydb or please create one. Have mysql-connector-java-5.1.28-bin.jar or better placed in the local JAR files. 2014-06-11 11:57:41.849 UTC net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeCalculate_Uncertainty_Coefficientconcept_pairs1corrected_contingency_values2timestamp0propertyString0 A nested workflow to calculate the Uncertainty coefficient with the contingency table values of the concept pairs. The calculated values are afterwards inserted into the uncertainty coefficient SQL table. The row with the same concepts in column name concept_uri_1 is the concept profile. The values in the columns name concept_uri_2 are the concepts that are used for calculating the uncertainty coefficient (similarity measure). Example of the constructed SQL table: 1 A A UC value of concept pair AA 2 A B UC value of concept pair AB 3 A C UC value of concept pair AC Example of a concept profile made of concept A: A | |__UC value__A |__UC value__B |__UC value__C 2014-06-11 12:23:10.770 UTC net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeCalculate_Contingency_Tabletable_name0propertyString0outputlist11corrected_contingency_values22 A nested workflow that retrieves the values of a 2x2 contingency table and puts the co-occurrence of made concept pairs into the SQL table TableName_co_occurrence. This is done by creating concept pairs which is retrieved from the Sql table TableName_occurrence. This contingency table consits out of a matrix where two concepts co-occur, concept A only occurs and not concept B, concept B occurs and not concept A and neither concepts occur in literature. Example of a 2x2 contingency table of concept pair A B: B Not B A AB A not A B not A not B This is calculated for every possible concept pair. 2014-06-11 12:13:17.153 UTC net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeCalculate_Inner_Productconcept_pairs1timestamp0propertyString0 A nested workflow to calculate the inner product between concept profile pairs for concept profile matching. The calculated values are afterwards inserted into the inner product SQL table. Example of calculating the inner product between two concept profiles: A B | | |__UC value__A x A__UC value__| | + | |__UC value__B x B__UC value__| | | |__UC value__C D__UC value__| The inner product of the two concept profile A and B is the common concept multplied between each other and added: (UC value AA x UC value BA) + (UC value AB x UC value BB) = inner product 2014-06-11 12:37:47.216 UTC net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeCreate_Tablesdb_properties0timeStamp00 This nested workflows creates the necessary tables for inserting the generated values. The following tables are created: - Co-occurrence table - Occurrence table - Uncertainty coefficient table - Inner product table - Summary table 2014-06-11 11:53:41.270 UTC net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGet_Summary_Tabletimestamp0propertyString0resultList11 A nested workflow to retrieve the calculated co-occurrence, occurrence, uncertainty coefficient and inner product values. These values are inserted into one table to summarize and quick access. 2014-06-11 10:55:51.663 UTC net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGet_abstractspropertyString0db_results22 A nested workflow to retrieve abstracts from a sql table. This table is assumed to have atleast two columns consisting out of pmid and abstract text. 2014-06-11 11:04:59.773 UTC net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokePeregrine_Indexertable_nameCreate_TablestimeStampPeregrine_IndexerontologyOntology_inputPeregrine_IndexerInputGet_abstractsdb_resultsPeregrine_IndexerpropertyStringdb_propertiesPeregrine_IndexerPathPath_Peregrine_IndexerCalculate_Uncertainty_Coefficientconcept_pairsCalculate_Contingency_TableoutputlistCalculate_Uncertainty_Coefficientcorrected_contingency_valuesCalculate_Contingency_Tablecorrected_contingency_valuesCalculate_Uncertainty_CoefficienttimestampCreate_TablestimeStampCalculate_Uncertainty_CoefficientpropertyStringdb_propertiesCalculate_Contingency_Tabletable_nameCreate_TablestimeStampCalculate_Contingency_TablepropertyStringdb_propertiesCalculate_Inner_Productconcept_pairsCalculate_Contingency_TableoutputlistCalculate_Inner_ProducttimestampCreate_TablestimeStampCalculate_Inner_ProductpropertyStringdb_propertiesCreate_Tablesdb_propertiesdb_propertiesGet_Summary_TabletimestampCreate_TablestimeStampGet_Summary_TablepropertyStringdb_propertiesGet_abstractspropertyStringdb_propertiesendGet_Summary_TableresultList 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cf0e0e58-2e01-4b6b-b690-abdcf02c5e29 2014-03-31 13:03:01.42 UTC ea0d3514-021d-4416-a92c-e847e8cb3b05 2014-04-14 12:34:34.807 UTC 8cbbae64-7fff-4d96-aca0-f37c13057cca 2014-04-10 10:59:19.754 UTC 0fa5ae93-fe58-4958-a86a-4118f2b82cb8 2014-06-11 11:57:44.520 UTC 7f5909ba-e457-4017-827e-28756be2a2db 2014-05-12 11:34:18.819 UTC 85eb7ca4-2261-4b6b-8dbc-e983dfffad06 2014-04-25 08:42:27.977 UTC 1407f28f-2b20-4a4b-987f-0e8a978fd069 2014-04-14 12:19:58.355 UTC 71c0ae47-08a2-42e7-8b61-368228badc87 2014-04-09 11:38:19.412 UTC 393c3128-043d-4598-aeab-8d8a7ff26f25 2014-04-25 09:09:37.203 UTC 2eb0f038-4ecd-440b-b39e-f188243e37c0 2014-03-26 17:23:46.827 UTC 65061b5e-4240-4e5d-bea5-395adf42981f 2014-03-20 10:20:03.284 UTC 921d4091-ab1d-4a97-ae19-f89b54d5d6f1 2014-06-11 11:53:44.5 UTC 7fa1d021-c166-4f12-abe3-eae08e6e8c38 2014-04-02 11:21:12.430 UTC f2fcd097-92b8-4fdc-a7d4-b2577d4ac7f8 2014-03-11 10:22:44.507 UTC 7a09384c-cf1e-4b6c-856b-36abc5e2981f 2014-04-11 11:26:47.475 UTC 4b062ff7-3737-457c-9079-3e0e7a9c45f9 2014-05-21 16:11:02.255 UTC 5404ca4a-6824-47f0-b99d-3bac2972d3b3 2014-04-09 08:25:23.468 UTC 529b0a59-d5b5-4a86-9f68-176441054011 2014-03-21 10:47:02.223 UTC bb263958-6955-44d3-b785-8b8cb552ca4e 2014-04-09 11:48:16.918 UTC dbdc039a-a221-43bc-a79a-b24724697451 2014-04-11 11:20:16.786 UTC 7309ae74-fe52-47cb-8faa-0255373b31bb 2014-05-12 09:26:43.227 UTC 392cb15c-a3dd-490e-93d2-ac28fd03b6a5 2014-03-19 13:03:01.757 UTC c59ee9c4-e463-48c7-a0f2-c9b65cdfb83b 2014-06-10 15:53:56.13 UTC 2140fe4d-db70-420e-9ca2-595da9e5f8cf 2014-04-10 14:40:42.779 UTC 45dd4291-684e-43c3-bfa6-ae2a37ee87ce 2014-05-02 15:40:52.743 UTC Requirements: Have MySQL installed with a database called mydb or please create one. Have a mysql connector file. This can be downloaded from mysql.com. Rename the downloaded file to mysql-connector-java.jar and place it in the the local lib file of Taverna as written on the dependencies tab. Choose this dependency by rightclicking a beanshell script and selecting it for the whole workflow as system classloader. Download the Peregrine SKOS CLI from: https://trac.nbic.nl/biosemantics/downloads Install LVG2013Lite. See: https://trac.nbic.nl/biosemantics/wiki/Peregrine%20SKOS%20CLI Change lvg.properties LVG_DIR=/home/path/to/lvg2013lite/ This file can be found in: /home/path/to/lvg2013lite/data/config/lvg.properties Copy properties file from production.properties which can be found on: https://trac.nbic.nl/biosemantics/wiki/Peregrine%20SKOS%20CLI Change the normalizer.lvg.properties and normalizer.lvg.binaryCache properties to point to the LVG installation path. This file can be obtained from https://trac.nbic.nl/biosemantics/wiki/Peregrine%20SKOS%20CLI Have Peregrine indexer installed locally and give it the correct path in the component named "Indexer_tool". Which can be found in the nested workflow named Peregrine indexer. If using a Windows machine please install cygwin. Set cygwin in the $PATH of the environment variabale. Go to taverna File --> preferences --> Tool invocation --> set modify on explicit locations --> edit a default local to Shell: C:\Windows\system32\cmd.exe /c and save that. -->Set Modify on: symbolic locations --> edit --> choose default local and save. When using a unix environment make sure the default local is set Shell into /bin/sh -c. Please make sure this is also set into the indexer tool part. Have JAVA_HOME C:\Program Files\jdk 1.7.0 in environment variabale when using Windows. The nested workflow Get_abstract uses a sql command to retrieve abstracts which assumes are located in the database mydb. If this is not the case, please change the database in the SQL value. 2014-06-11 11:56:14.761 UTC d0997741-9889-48a1-af06-9b4601e6876d 2014-05-01 13:36:53.145 UTC 1e32cd62-6709-4253-8812-b7f7823f323f 2014-03-19 12:39:25.755 UTC 513c4d46-b511-4a6d-9b9f-9f046720c2b7 2014-03-27 14:40:34.469 UTC 0a9fc708-f04c-4b3b-9c2b-3077d360a004 2014-03-26 16:58:01.18 UTC eed395e4-da87-432e-9a6f-1db669dd1c0c 2014-03-27 10:27:04.552 UTC 74f97370-a9b5-40a6-98ae-e263c8f9debe 2014-03-27 16:59:33.565 UTC 5ed05d10-6606-4eb6-a549-f0acd558a5e1 2014-03-12 16:27:46.614 UTC a116a99e-7b24-4fcb-949c-434c185de7c4 2014-06-10 09:39:52.374 UTC bc510c1b-3918-4a2e-ad6b-83fd94a3fdcd 2014-04-10 12:48:04.773 UTC 867e8a5a-c59f-4c68-8e3b-11e1f3d811d4 2014-04-09 08:32:47.874 UTC 448d9b98-3eb9-4ead-921c-3baef48a0efe 2014-03-21 13:36:17.856 UTC 936c0da5-18d3-4670-842e-b6de7827f6be 2014-04-10 14:22:40.555 UTC c912b1cf-361c-4414-8d15-535730449e20 2014-05-02 15:09:58.330 UTC 7f57bf70-4232-4af9-82bd-c524120cf7fe 2014-03-20 10:27:13.607 UTC b73de25f-87f0-4b09-a0d3-c339d340f8c0 2014-06-10 11:16:06.229 UTC 93512370-e9f6-49b6-ba46-4482dae8c38e 2014-05-02 16:40:23.354 UTC 474781e2-4053-4460-9062-2c102596efdf 2014-05-12 13:04:27.927 UTC 558f78ee-316b-45d1-b74d-08d613b59f81 2014-06-10 15:32:38.405 UTC 05fc1170-1530-4218-b74c-7f19168686bf 2014-06-11 10:55:52.360 UTC ecc3b293-9ddf-4063-8645-7215221ef342 2014-03-04 17:15:26.661 UTC ee149ce2-e3ba-465e-9c63-04b297aa5059 2014-03-04 16:18:24.468 UTC 90225384-5852-4768-ba1d-cb7671b920da 2014-03-19 09:49:54.0 UTC 4792a9cb-3d7e-4327-8c8e-4e499b8f4f28 2014-03-11 15:47:23.615 UTC 5110b42a-7d69-4212-82a9-7adefe6d3c21 2014-06-15 16:21:38.370 UTC 224d82d5-73dd-4dce-baea-8ad1341e9152 2014-04-11 12:18:58.687 UTC ad0d25ec-2b96-4307-bf18-4b95f1c7740c 2014-04-11 11:31:27.283 UTC 8e44e788-4fc5-447f-bde6-9bdf3be24bd0 2014-03-18 12:02:18.860 UTC 5fddb0b2-585d-466c-a72a-00031f0cceef 2014-03-18 10:47:26.114 UTC 0fa803bd-3469-415e-89a7-039489d3480c 2014-03-17 10:45:38.163 UTC b7956990-8189-4f16-bf37-da3363361e3e 2014-05-05 12:45:22.875 UTC 05687d54-4107-43c2-aa91-0b7b706756db 2014-06-11 09:03:42.795 UTC 0d50bbee-3571-4315-b7d7-44342273a8b9 2014-04-10 08:33:00.501 UTC 71f14995-6503-40d5-8948-2d64864e36d2 2014-03-12 15:28:10.329 UTC 344da505-68bc-47c1-ba68-afd6a55ebf7e 2014-03-21 10:16:16.121 UTC 53b52fe4-2b10-4717-b7c6-5bbcef46b206 2014-04-15 14:29:31.643 UTC bbc1a00b-a48b-44f5-a291-597d30838c76 2014-05-12 13:36:37.252 UTC 4a392f2b-0aab-4721-94f6-f7b73d5dbc96 2014-03-27 09:49:33.460 UTC 2d213aed-77c4-40d7-a3f9-b06ce1f93960 2014-04-09 08:37:09.195 UTC 7f6d900b-1832-4b86-b7f4-08c039b9edd2 2014-03-03 15:06:51.165 UTC b04f1761-c23c-4c94-96fe-9f5952836a36 2014-06-15 17:43:07.239 UTC 1ffc7cc7-bd8c-49e0-92ff-0ca02090bca3 2014-03-31 13:45:49.982 UTC d98af7c3-005b-4c4c-be87-3cedc55890d3 2014-03-19 16:15:51.545 UTC 5b411999-5685-47eb-b8cd-49837b0d4621 2014-03-27 09:19:58.748 UTC 4c4cec6d-8632-4576-a6e9-571c6b0c6236 2014-03-11 14:45:15.59 UTC nestedpropertyString00 Please load a file in as seen in the example where the user, password, url (which is the database it should use), and driver is stated. 2014-06-11 11:59:30.901 UTC mysql.user=root mysql.password=amrishsql mysql.url=jdbc:mysql://localhost:3306/mydb mysql.driver=com.mysql.jdbc.Driver 2014-05-12 09:36:25.325 UTC db_resultsExecute_SQL_Querysql0propertyString0resultList22net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity sql 0 text/plain java.lang.String true params 1 text/plain java.lang.String true propertyString 0 text/plain java.lang.String true resultList 2 2 xmlresults 0 0 system mysql-connector-java.jar net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker UserNameHere 2014-05-12 09:40:09.625 UTC net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokesql_valuevalue00 SQL code for using the abstracts with their corresponding pubmed id. 2014-06-11 11:58:55.226 UTC net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity SELECT pmid, abstract_text FROM mydb.abstracts LIMIT 50 ; net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExecute_SQL_Querysqlsql_valuevalueExecute_SQL_QuerypropertyStringpropertyStringdb_resultsExecute_SQL_QueryresultList nested 2014-05-08 17:44:28.277 UTC 6830ad2e-b9bd-4907-8a40-dd10863cd570 2014-05-21 16:10:52.487 UTC dd77b156-bebc-4183-952c-2e2fe4f1cc96 2014-05-12 09:38:33.591 UTC 00987503-eb35-484e-a701-05958e3fb254 2014-05-12 09:40:51.404 UTC 8aa3f84f-3b34-4860-b383-4e023cbf1c66 2014-05-12 09:39:08.438 UTC 39c6af3b-223f-4ff5-bd6f-aa2e6899ad80 2014-05-12 09:39:42.53 UTC 29a8b7aa-9837-4483-8e93-896c111c3780 2014-05-08 17:54:18.980 UTC 48169015-d279-400c-9a11-e0e9748f312b 2014-05-12 09:45:01.638 UTC c614eadc-67ae-45d9-9f65-96ced3bb0c45 2014-05-12 11:36:32.316 UTC 1bf0a549-ef7b-4c62-b298-fbcac4792269 2014-06-11 11:59:30.999 UTC 08396e51-5a76-4ec0-be54-fecd90bf6e0d 2014-06-10 08:43:12.865 UTC 1607252e-3503-4b77-9617-ed429023613a 2014-05-12 09:26:40.211 UTC c7bbc90c-8116-494b-ba64-8769830aff55 2014-05-12 09:36:58.375 UTC 67c5c3e5-fa09-4524-931f-b09f47abad5f 2014-05-12 08:36:52.574 UTC 1a3144fd-9bb3-474a-8760-ced1e79cbf60 2014-06-10 08:34:23.241 UTC Peregrine indexerontology00 A Skos formated dictionary/thesaurus of predefined concepts. 2014-05-01 14:22:40.779 UTC @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . @prefix skos: <http://www.w3.org/2004/02/skos/core#> . @prefix dct: <http://purl.org/dc/terms/> . @prefix emco: <http://rdf.biosemantics.org/emco/> . @prefix emco15: <http://rdf.biosemantics.org/emco/v1.5/> . @prefix concepts: <http://rdf.biosemantics.org/emco/v1.5/concepts/> . @prefix prop: <http://rdf.biosemantics.org/emco/properties/> . @prefix datatype: <http://rdf.biosemantics.org/emco/datatypes/> . @prefix semtype: <http://rdf.biosemantics.org/emco/semtypes/> . @prefix vocab: <http://rdf.biosemantics.org/emco/v1.5/vocabularies/> . prop:prefLabel_CI rdfs:subPropertyOf skos:prefLabel . prop:prefLabel_NO rdfs:subPropertyOf skos:prefLabel . prop:prefLabel_CI_NO rdfs:subPropertyOf skos:prefLabel . prop:altLabel_CI rdfs:subPropertyOf skos:altLabel . prop:altLabel_NO rdfs:subPropertyOf skos:altLabel . prop:altLabel_CI_NO rdfs:subPropertyOf skos:altLabel . vocab:default rdfs:comment "ErasmusMC ontology file" ; dct:title "Anni2_1_June2009" ; a skos:ConceptScheme . vocab:MSH dct:title "MeSH" ; a skos:ConceptScheme . vocab:SNOMEDCT dct:title "SNOMED Clinical Terms" ; a skos:ConceptScheme . semtype:T47 skos:topConceptOf vocab:default ; rdfs:label "Disease or Syndrome" ; skos:definition "A condition which alters or interferes with a normal process, state, or activity of an organism. It is usually characterized by the abnormal functioning of one or more of the host's systems, parts, or organs. Included here is a complex of symptoms descriptive of a disorder." ; a skos:Concept . concepts:C9187 skos:inScheme vocab:default ; prop:altLabel_CI_NO "Coccidiosis"@es ; prop:prefLabel_CI_NO "Coccidiosis" ; skos:notation "C0009187"^^datatype:umls-notation-datatype ; rdfs:label "Coccidiosis" ; skos:definition "Protozoan infection found in animals and man. It is caused by several different genera of COCCIDIA." ; skos:broader semtype:T47 ; a skos:Concept ; skos:inScheme vocab:MSH , vocab:SNOMEDCT . concepts:C24530 skos:inScheme vocab:default ; prop:altLabel_CI_NO "Malaria NOS" , "Plasmodium Infections" , "Remittent Fever" , "Paludism" , "Plasmodiosis" , "Malarial fever" , "Malaria (disorder)" , "Marsh Fever" , "Malaria"@es ; prop:prefLabel_CI "Malaria" ; skos:notation "C0024530"^^datatype:umls-notation-datatype ; rdfs:label "test" ; skos:broader concepts:C9187 , semtype:T47 ; a skos:Concept ; skos:inScheme vocab:MSH , vocab:SNOMEDCT . concepts:C3031092 skos:inScheme vocab:default ; prop:altLabel_NO "myelocytomatosis viral oncogene homolog (avian)" , "myelocytomatosis oncogene" , "Transcription factor p64" , "Myc proto-oncogene protein" , "v-myc myelocytomatosis viral oncogene homolog (avian)" , "Myc2" , "myc proto-oncogene protein" , "Transcription factor p-64" , "Myc-2" ; skos:notation "120208"^^datatype:gd-notation-datatype , "3130"^^datatype:gd-notation-datatype , "31092"^^datatype:ho-notation-datatype , "NM"^^datatype:rq-notation-datatype , "17869"^^datatype:eg-notation-datatype , "24577"^^datatype:eg-notation-datatype , "4609"^^datatype:eg-notation-datatype , "3130"^^datatype:rgd-notation-datatype , "190080"^^datatype:om-notation-datatype , "7553"^^datatype:hg-notation-datatype , "P01106"^^datatype:sp-notation-datatype , "P01108"^^datatype:sp-notation-datatype , "P09416"^^datatype:sp-notation-datatype , "Q6WDF7"^^datatype:sp-notation-datatype , "Hs.202453"^^datatype:ug-notation-datatype , "97250"^^datatype:mgi-notation-datatype , "1368308"^^datatype:af-notation-datatype , "1424942"^^datatype:af-notation-datatype , "202431"^^datatype:af-notation-datatype , "239931"^^datatype:af-notation-datatype ; rdfs:label "MYC" ; skos:prefLabel "MYC" , "C-MYC" , "Myc" , "Niard" , "Nird" , "c-Myc" , "c-myc" , "Myc-II" ; skos:broader semtype:T116 ; a skos:Concept ; skos:inScheme vocab:GENE , vocab:HOMOLOGENE . concepts:C3003921 skos:inScheme vocab:default ; prop:altLabel_NO "v-myc myelocytomatosis viral oncogene homolog 1, lung carcinoma derived (avian)" , "oncogene lmyc" , "l-myc-1 proto-oncogene" , "Lmyc1" , "myc-related gene from lung cancer" , "Oncogene MYC, lung carcinoma-derived" , "l-myc protein" , "Lmyc-1" , "Mycl1" , "L-myc-1 proto-oncogene protein" , "v-myc myelocytomatosis viral oncogene homolog 1, lung carcinoma derived (avian) (mapped)" , "v-myc avian myelocytomatosis viral oncogene homolog 1, lung carcinoma derived" , "MYCL-1" , "Mycl-1" ; prop:prefLabel_NO "MYCL1" ; skos:notation "120706"^^datatype:gd-notation-datatype , "1588591"^^datatype:gd-notation-datatype , "3921"^^datatype:ho-notation-datatype , "NM"^^datatype:rq-notation-datatype , "16918"^^datatype:eg-notation-datatype , "298506"^^datatype:eg-notation-datatype , "4610"^^datatype:eg-notation-datatype , "1588591"^^datatype:rgd-notation-datatype , "164850"^^datatype:om-notation-datatype , "7555"^^datatype:hg-notation-datatype , "P10166"^^datatype:sp-notation-datatype , "P12524"^^datatype:sp-notation-datatype , "Q6TLI1"^^datatype:sp-notation-datatype , "Hs.437922"^^datatype:ug-notation-datatype , "96799"^^datatype:mgi-notation-datatype , "1422087"^^datatype:af-notation-datatype , "1422088"^^datatype:af-notation-datatype , "214058"^^datatype:af-notation-datatype ; rdfs:label "MYCL1" ; skos:prefLabel "LMYC" , "MYCL" , "MYCL" , "MYCL-I" , "Lmyc-I" , "Mycl-I" ; skos:broader semtype:T116 ; a skos:Concept ; skos:inScheme vocab:GENE , vocab:HOMOLOGENE . concepts:C3003922 skos:inScheme vocab:default ; prop:altLabel_NO "v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian) (mapped)" , "v-myc myelocytomatosis viral related oncogene, neuroblastoma derived" , "v-myc avian myelocytomatosis viral related oncogene, neuroblastoma derived" , "Nmyc-1" , "neuroblastoma-derived v-myc avian myelocytomatosis viral related oncogene" , "v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)" , "N-MYC PROTO-ONCOGENE PROTEIN" , "Nmyc1" , "neuroblastoma MYC oncogene" , "pp65/67" , "oncogene NMYC" , "Oncogene NMYC" , "N-myc proto-oncogene protein" ; skos:notation "120527"^^datatype:gd-notation-datatype , "1584995"^^datatype:gd-notation-datatype , "3922"^^datatype:ho-notation-datatype , "NM"^^datatype:rq-notation-datatype , "18109"^^datatype:eg-notation-datatype , "298894"^^datatype:eg-notation-datatype , "4613"^^datatype:eg-notation-datatype , "1584995"^^datatype:rgd-notation-datatype , "164840"^^datatype:om-notation-datatype , "7559"^^datatype:hg-notation-datatype , "P03966"^^datatype:sp-notation-datatype , "Q53XS5"^^datatype:sp-notation-datatype , "Q63379"^^datatype:sp-notation-datatype , "Hs.25960"^^datatype:ug-notation-datatype , "97357"^^datatype:mgi-notation-datatype , "1417155"^^datatype:af-notation-datatype , "1425922"^^datatype:af-notation-datatype , "1425923"^^datatype:af-notation-datatype , "209756"^^datatype:af-notation-datatype , "209757"^^datatype:af-notation-datatype , "211377"^^datatype:af-notation-datatype , "234376"^^datatype:af-notation-datatype ; rdfs:label "MYCN" ; skos:prefLabel "MYCN" , "Mycn" , "N-myc" , "ODED" , "MODED" , "Nmyc" , "NMYC" , "Nmyc-I" ; skos:broader semtype:T116 ; a skos:Concept ; skos:inScheme vocab:GENE , vocab:HOMOLOGENE . concepts:C3020128 skos:inScheme vocab:default ; prop:altLabel_NO "neural cell adhesion molecule L1" , "NEURAL CELL ADHESION MOLECULE L1" , "Neural cell adhesion molecule L1" , "N-CAML1" , "L1cam" , "MIC5" , "antigen identified by monoclonal antibody R1" , "L1 cell adhesion molecule (hydrocephalus, stenosis of aqueduct of Sylvius 1, MASA (mental retardation, aphasia, shuffling gait and adducted thumbs) syndrome, spastic paraplegia 1)" , "CD171 antigen" , "HSAS1" , "S10" , "CAML1" , "NCAM-L1" , "MIC5" , "L1 cell adhesion molecule" , "SPG1" , "CD171" , "N-CAM L1" , "neural cell adhesion molecule L-I" , "neural cell adhesion molecule L-1" , "NEURAL CELL ADHESION MOLECULE L-I" , "NEURAL CELL ADHESION MOLECULE L-1" , "Neural cell adhesion molecule L-I" , "Neural cell adhesion molecule L-1" , "N-CAML-1" , "MIC-5" , "antigen identified by monoclonal antibody R-I" , "antigen identified by monoclonal antibody R-1" , "HSAS-1" , "CAML-1" , "NCAM-L-1" , "MIC-5" , "SPG-1" , "CD-171" , "N-CAM L-I" , "N-CAM L-1" ; prop:prefLabel_NO "L1CAM" ; skos:notation "120133"^^datatype:gd-notation-datatype , "120526"^^datatype:gd-notation-datatype , "619777"^^datatype:gd-notation-datatype , "20128"^^datatype:ho-notation-datatype , "NM"^^datatype:rq-notation-datatype , "16728"^^datatype:eg-notation-datatype , "3897"^^datatype:eg-notation-datatype , "50687"^^datatype:eg-notation-datatype , "619777"^^datatype:rgd-notation-datatype , "308840"^^datatype:om-notation-datatype , "6470"^^datatype:hg-notation-datatype , "P11627"^^datatype:sp-notation-datatype , "P32004"^^datatype:sp-notation-datatype , "Q05695"^^datatype:sp-notation-datatype , "Hs.522818"^^datatype:ug-notation-datatype , "96721"^^datatype:mgi-notation-datatype , "1369213"^^datatype:af-notation-datatype , "1421958"^^datatype:af-notation-datatype , "1450435"^^datatype:af-notation-datatype , "204584"^^datatype:af-notation-datatype , "204585"^^datatype:af-notation-datatype ; rdfs:label "L1CAM" ; skos:prefLabel "HSAS" , "MASA" , "N-CAML-I" , "MIC-V" , "HSAS-I" , "CAML-I" , "NCAM-L-I" , "MIC-V" , "SPG-I" ; skos:broader semtype:T116 ; a skos:Concept ; skos:inScheme vocab:GENE , vocab:HOMOLOGENE . concepts:C3000168 skos:inScheme vocab:default ; prop:altLabel_NO "CD54 antigen" , "intercellular adhesion molecule I" , "intercellular adhesion molecule1" , "Icam-1" , "CD-54" , "BB-2" , "Intercellular adhesion molecule I" , "Intercellular adhesion molecule1" , "Intercellular adhesion molecule-I" ; prop:prefLabel_NO "ICAM-1" ; skos:notation "120076"^^datatype:gd-notation-datatype , "2857"^^datatype:gd-notation-datatype , "168"^^datatype:ho-notation-datatype , "NM"^^datatype:rq-notation-datatype , "15894"^^datatype:eg-notation-datatype , "25464"^^datatype:eg-notation-datatype , "3383"^^datatype:eg-notation-datatype , "2857"^^datatype:rgd-notation-datatype , "147840"^^datatype:om-notation-datatype , "5344"^^datatype:hg-notation-datatype , "Q00238"^^datatype:sp-notation-datatype , "Q15463"^^datatype:sp-notation-datatype , "Hs.643447"^^datatype:ug-notation-datatype , "1387202"^^datatype:af-notation-datatype , "1424067"^^datatype:af-notation-datatype , "1427805"^^datatype:af-notation-datatype , "1427806"^^datatype:af-notation-datatype , "202637"^^datatype:af-notation-datatype , "202638"^^datatype:af-notation-datatype , "215485"^^datatype:af-notation-datatype ; rdfs:label "ICAM1" ; skos:prefLabel "ICAM-I" , "Icam-I" , "BB-II" ; skos:broader semtype:T116 ; a skos:Concept ; skos:inScheme vocab:GENE , vocab:HOMOLOGENE . 2014-05-01 13:27:51.940 UTC Input22 Give a list with sublist. Each sublist consist out of two elements. Such as [ [ Document_URI, Abstract_URI] ]. For an example please load in the file named: input value for full CPGP. Which can be found under the files tab on MyExperiment. 2014-05-01 14:22:24.867 UTC 2014-05-01 14:21:52.278 UTC table_name00 2014_04_30_21_24_30 2014-05-01 13:33:43.886 UTC Needs the correct table name given for writing the values. The tablename needs to be the same as the one that is created. 2014-05-02 15:02:59.945 UTC propertyString00 Please load a file in as seen in the example where the user, password, url (which is the database it should use), and driver is stated. 2014-06-11 12:01:06.826 UTC mysql.user=root mysql.password=amrishsql mysql.url=jdbc:mysql://localhost:3306/mydb mysql.driver=com.mysql.jdbc.Driver 2014-06-11 12:00:51.795 UTC Path00 Give the full path where the production.properties and peregrine-skos-cli.jar files are located. path/to/ production.properties path/to/ peregrine-skos-cli.jar 2014-06-15 17:42:28.228 UTC F:/School/Stage2/peregrine/ 2014-06-15 17:40:54.119 UTC outputBeanshell_SQL_query_generator_Concept_Doc_occurrencetable_name0concept_occurence_document0out100 A Beanshell script that generates a Sql statement to INSERT the concept URI and document URI in the table named after the timestamp/tablename the workflow started. It uses a database called mydb. If there is not a database/schema named mydb, please create one. 2014-05-01 14:28:50.45 UTC net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity table_name 0 text/plain java.lang.String true concept_occurence_document 0 text/plain java.lang.String true out1 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_extract_uri_doc_and_abstractInput1abstracts00doc_uri00 A Beanshell script which loops through the input to seperate the Document URIs and Abstract URIs. 2014-03-21 13:07:52.147 UTC net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity Input 1 text/plain java.lang.String true doc_uri 0 0 abstracts 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_remove_dot_and_correct_doc_uri_in_con_docdoc_uri1concept_occurence_document0out100 A Beanshell script that replaces the temp created Taverna file with the correct Document URI. 2014-04-11 13:53:30.291 UTC net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity concept_occurence_document 0 text/plain java.lang.String true doc_uri 1 text/plain java.lang.String true out1 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExecute_SQL_Update_INSERT_INTO_occurrence_tablesql0propertyString0resultList00 Executes the SQL statement generated by the Beanshell script: "Sql_beanshell_query_generator_Concept_occ_Doc" which insert the concept and document URI into the table named 'timestamp'_occurence. 2014-05-01 14:29:19.326 UTC net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity sql 0 text/plain java.lang.String true params 1 text/plain java.lang.String true propertyString 0 text/plain java.lang.String true resultList 0 0 workflow net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker UserNameHere 2014-05-12 11:39:07.643 UTC net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokePeregrine_Indexer_toolontology0abstract_content1path0concept_per_document00 Uses a jar peregrine program to index which concept occurs in what document. Change the commands to : java -Dperegrine.config.location=your/path/to/peregrine/production.properties -jar path/to/peregrine-skos-cli.jar ontology abstract_content out1 When using a Windows machine please install cygwin. Set cygwin in the $PATH of the environment variabale. Go to Location tab select radiobutton "Select an symbolic location" and default . Press Manage locations and go to explicit locations --> edit a default local to Shell: C:\Windows\system32\cmd.exe /c and save that. -->Set Modify on: symbolic locations --> pick default --> edit and choose default local and save. When using a unix environment make sure the default local is set Shell into /bin/sh -c and link command to: /bin/ln -s %%PATH_TO_ORIGINAL%% %%TARGET_NAME%%. Save settings by clicking apply . 2014-06-11 12:11:02.104 UTC net.sf.taverna.t2.activitiesexternal-tool-activity1.4net.sf.taverna.t2.activities.externaltool.ExternalToolActivity default 789663B8-DA91-428A-9F7D-B3F3DA185FD4 default local <?xml version="1.0" encoding="UTF-8"?> <localInvocation><shellPrefix>C:\Windows\system32\cmd.exe /c</shellPrefix></localInvocation> 6c76743e-a600-4f7e-832f-6d0e284a1a29 java -Dperegrine.config.location=%%pwd%%production.properties -jar %%pwd%%peregrine-skos-cli.jar ontology abstract_content concept_per_document 1200 1800 pwd abstract_content abstract_content true false false windows-1252 false true false path pwd false false false windows-1252 false false false ontology ontology true false false windows-1252 false false false concept_per_document concept_per_document false false false false 0 false net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSplit_string_into_string_list_by_regular_expressionstring0regex0split11 Uses Regex to split string into string list. 2014-03-21 13:10:43.967 UTC net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity string 0 'text/plain' java.lang.String true regex 0 'text/plain' java.lang.String true split 1 1 workflow org.embl.ebi.escience.scuflworkers.java.SplitByRegex UserNameHere 2014-03-11 10:44:03.209 UTC net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeregex_valuevalue00 Regex value of enter. 2014-05-01 14:27:23.340 UTC net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity [\n] net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_SQL_query_generator_Concept_Doc_occurrencetable_nametable_nameBeanshell_SQL_query_generator_Concept_Doc_occurrenceconcept_occurence_documentBeanshell_remove_dot_and_correct_doc_uri_in_con_docout1Beanshell_extract_uri_doc_and_abstractInputInputBeanshell_remove_dot_and_correct_doc_uri_in_con_docdoc_uriBeanshell_extract_uri_doc_and_abstractdoc_uriBeanshell_remove_dot_and_correct_doc_uri_in_con_docconcept_occurence_documentSplit_string_into_string_list_by_regular_expressionsplitExecute_SQL_Update_INSERT_INTO_occurrence_tablesqlBeanshell_SQL_query_generator_Concept_Doc_occurrenceout1Execute_SQL_Update_INSERT_INTO_occurrence_tablepropertyStringpropertyStringPeregrine_Indexer_toolontologyontologyPeregrine_Indexer_toolabstract_contentBeanshell_extract_uri_doc_and_abstractabstractsPeregrine_Indexer_toolpathPathSplit_string_into_string_list_by_regular_expressionstringPeregrine_Indexer_toolconcept_per_documentSplit_string_into_string_list_by_regular_expressionregexregex_valuevalueoutputExecute_SQL_Update_INSERT_INTO_occurrence_tableresultList 3674dfd2-59e3-4a0b-9355-9c89beb5d437 2014-05-12 08:26:10.414 UTC 7a8efe41-e6c8-4b99-8e20-d005bd0db003 2014-06-11 12:01:06.934 UTC ea1540f5-3320-4fd4-aae0-1a7233b7f828 2014-06-10 16:00:54.719 UTC Peregrine indexer 2014-04-25 08:41:57.947 UTC 68476bab-0e32-4f6a-8e9d-f50804088938 2014-06-10 08:28:55.760 UTC 8054095d-ff1d-434d-8db7-73e0d92521ab 2014-05-01 14:56:49.352 UTC c54ca59d-de52-4b86-8f4d-6f34db8e1cda 2014-06-15 17:43:35.549 UTC 5fae11dd-f324-4db1-a120-a04debed40f6 2014-06-11 08:50:56.448 UTC c45a8012-d1be-44b9-b9f1-5d547075682c 2014-05-12 11:39:52.208 UTC 7a8e521a-ce70-464f-b5be-b38496ea9a7a 2014-05-02 15:03:12.106 UTC 899b13f9-9169-42a4-8c8f-c6c8437c9b72 2014-06-15 17:42:28.355 UTC 87fe3bfb-dcd3-4cf3-bca5-a4ddcf8d3b32 2014-05-05 09:43:02.878 UTC 28b58762-e9a5-4336-ae8c-0de8bbde97cf 2014-05-08 13:28:53.205 UTC ef75149c-93d4-4a53-938d-598b34c547c0 2014-04-25 08:43:19.286 UTC 7013adf6-1cff-4da4-a4f4-1dc8348cdefb 2014-05-08 12:48:10.297 UTC 2c3c56e4-87ff-48c8-a895-54c7eabeca9f 2014-05-01 14:29:30.621 UTC 65c07cb7-552e-414e-b0d9-d691dee366dc 2014-06-10 08:32:43.599 UTC To be able to run this workflow it is necessary to have the following ready. The Peregrine indexer program which can be downloaded from: trac.nbic.nl/biosemantics/downloads. Install LVG2013Lite. See: https://trac.nbic.nl/biosemantics/wiki/Peregrine%20SKOS%20CLI Copy properties file from production.properties which can be downloaded from: https://trac.nbic.nl/biosemantics/wiki/Peregrine%20SKOS%20CLI Change lvg.properties LVG_DIR=/home/path/to/lvg2013lite/ This file can be found in: /home/path/to/lvg2013lite/data/config/lvg.properties Change the normalizer.lvg.properties and normalizer.lvg.binaryCache properties to point to the LVG installation path. normalizer.lvg.properties =/home/path/to/lvg2013lite/data/config/config/lvg.properties normalizer.lvg.binaryCahce=/home/path/to/lvg2013lite/standartNormCache2013.bin Have MySQL installed with a database called mydb or please create one. Have mysql-connector-java-5.1.28-bin.jar or better placed in the local JAR files. Have a table created with the following sql statement: CREATE TABLE mydb.YourTableName_occurence( concept_doc_id INT NOT NULL AUTO_INCREMENT, concept_uri VARCHAR(255) NULL, doc_uri VARCHAR(255) NULL, PRIMARY KEY (concept_doc_id)); 2014-05-05 09:43:00.319 UTC 68bfb5a4-5361-40f7-b1e8-e9d2285f985d 2014-05-01 13:36:50.25 UTC 7d302e8e-e49f-46c2-9620-cbc9a8acd7c3 2014-05-01 13:38:12.169 UTC ddac8804-8407-4785-beae-b2d5ce0a80e3 2014-05-08 15:23:53.460 UTC e13584ce-2e64-4486-8ae5-e6e2c08f20d5 2014-05-01 14:22:50.934 UTC Amrish Mahes 2014-05-01 14:47:30.600 UTC f746b38a-fa7c-4188-b916-8b157d2cbfd3 2014-05-21 16:13:01.500 UTC fe4de177-331a-46bc-919c-0b60de007289 2014-05-01 13:29:11.726 UTC 58b4fc1a-33f4-45d0-8a33-f87356cc96e1 2014-04-25 08:42:29.100 UTC 21d0d9ac-38df-4c79-a6a3-95e6abd02e8f 2014-05-21 16:04:24.164 UTC 685e7713-6183-4320-a76a-f4bfd8d87b60 2014-06-10 16:00:27.639 UTC 417fb3f9-90d0-4da1-9b1b-71687090d140 2014-06-11 12:11:48.558 UTC eb47dba0-b920-4535-b634-e4db661210b5 2014-06-15 17:29:43.252 UTC 64734dc3-1155-4296-aefe-58117c4e2e63 2014-05-12 13:39:42.471 UTC Create Tablesdb_properties00 mysql.user=root mysql.password=amrishsql mysql.url=jdbc:mysql://localhost:3306/mydb mysql.driver=com.mysql.jdbc.Driver 2014-06-11 12:42:50.723 UTC Please load a file in as seen in the example where the user, password, url (which is the database it should use), and driver is stated. 2014-06-11 12:42:39.196 UTC timeStampBeanshell_get_timestamptimeStamp00 A Beanshell script which retreives the time the program started. As in year, month, day, hour, minutes and seconds in military time. 2014-04-11 13:57:49.999 UTC net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity timeStamp 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_SQL_Create_TablestimeStamp0Table_sql00 A Beanshell script for creating the tables. 2014-06-15 17:25:33.10 UTC net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity timeStamp 0 text/plain java.lang.String true Table_sql 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExecute_SQL_UpdatepropertyString0sql0net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity sql 0 text/plain java.lang.String true params 1 text/plain java.lang.String true propertyString 0 text/plain java.lang.String true resultList 0 0 workflow net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker UserNameHere 2014-06-15 16:25:51.599 UTC net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSplit_string_into_string_list_by_regular_expressionregex0string0split11net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity string 0 'text/plain' java.lang.String true regex 0 'text/plain' java.lang.String true split 1 l('text/plain') 1 workflow org.embl.ebi.escience.scuflworkers.java.SplitByRegex net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeregex_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity [\n] net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_SQL_Create_TablestimeStampBeanshell_get_timestamptimeStampExecute_SQL_UpdatepropertyStringdb_propertiesExecute_SQL_UpdatesqlSplit_string_into_string_list_by_regular_expressionsplitSplit_string_into_string_list_by_regular_expressionregexregex_valuevalueSplit_string_into_string_list_by_regular_expressionstringBeanshell_SQL_Create_TablesTable_sqltimeStampBeanshell_get_timestamptimeStamp 1c464dba-d276-4ea4-8e3d-e37f4893e7d0 2014-06-15 16:54:44.837 UTC f3183def-03f7-46b5-a971-9b5ca2eb1ad3 2014-04-25 09:32:55.418 UTC 1582f59b-8bd9-43ce-9f83-644f97d954c7 2014-05-12 12:01:29.197 UTC 50075aae-f1e4-44c2-9c80-ab5c8bd3f4e3 2014-06-15 16:33:07.624 UTC 9635824a-e4f1-4881-97e5-929978878075 2014-06-11 08:57:20.555 UTC 86079042-0398-4522-b766-79a51a2061b6 2014-04-25 09:34:08.496 UTC f70ead12-638d-4210-be53-6193297440cd 2014-06-10 10:59:34.689 UTC f2a26852-747d-41b3-957a-6b32bd38f698 2014-06-15 17:16:56.191 UTC 39bb73a3-e51b-42da-8706-944c99ff6ef2 2014-04-25 09:31:36.342 UTC f6285fa8-00e8-4b4b-848b-4c3faecaff0c 2014-06-15 17:03:23.327 UTC 01279793-743e-42c9-879d-c89edae5620b 2014-06-15 16:41:24.510 UTC e07305cf-4d3c-4732-817c-fc8c1897b04b 2014-06-15 17:23:16.414 UTC 5747cb6c-cfd7-4461-ba4d-aaca2ff23764 2014-06-15 17:18:14.417 UTC 8cb5442b-fa0d-4ab5-a534-ad79415bdc04 2014-06-15 17:22:42.241 UTC efb2e85a-454a-43fb-a82e-8d82a29111e2 2014-05-08 15:06:01.281 UTC aaf687fd-8ecb-42e8-b118-4f865db9db69 2014-06-15 16:20:50.770 UTC b905d192-afc7-4e80-9b87-3c62568fe512 2014-06-10 16:12:44.94 UTC ee6ad738-c5f6-4af6-8e6c-feb0c97d5504 2014-05-12 13:58:30.889 UTC 15224b89-9d42-4abb-888a-cc96a03354bf 2014-06-15 17:26:06.238 UTC 0f84cc52-37eb-4728-8f78-efd8981e9770 2014-06-11 12:45:50.859 UTC d0c0ac03-d7c1-410e-ae8a-d0a3fb71cc23 2014-06-15 16:42:33.166 UTC c0782138-c8e8-4d33-a524-12e3af3d28fa 2014-05-12 11:52:51.417 UTC 9fbf74e6-c25a-47f9-9065-8aeee27a62fa 2014-06-10 09:35:20.474 UTC 1a6c0667-e77d-45e6-9f10-ea3b62ab8b32 2014-06-15 17:05:00.249 UTC 200cd498-f8d4-4ab0-bf9c-e96aa415be2e 2014-06-10 16:10:53.665 UTC 7b1e6650-564c-4d1a-9533-3e729f80f4b0 2014-06-15 17:19:26.528 UTC 6f805bc9-25de-40db-bdfc-9f02de07addc 2014-06-11 09:03:14.417 UTC 8477156c-f078-4565-b8af-5db33fada212 2014-05-12 13:43:53.377 UTC 048b9168-bc32-4af6-ba1b-96c66ea34032 2014-06-15 17:05:43.430 UTC a5ab9df6-c2f1-49bc-8788-f300d6fee7c8 2014-05-08 12:51:28.905 UTC 73b839a8-067a-4f75-9229-2657a8171883 2014-06-15 16:39:15.477 UTC e9e4a3b8-0c6a-469a-aec7-11e0dbe2514b 2014-04-25 09:08:00.69 UTC Create Tables 2014-04-25 09:03:12.547 UTC 98e5f737-bfc2-4631-9018-55ad9e650902 2014-06-15 16:26:26.955 UTC ba007108-e797-4ecd-88d9-cb675d81568b 2014-05-12 13:38:14.79 UTC 31df5173-0ae3-44b1-a101-68d3ee2b6c66 2014-06-11 12:43:52.905 UTC 4040ef45-3e66-4f71-b7cb-b56f0b0aacff 2014-05-12 13:55:09.958 UTC bd5d7656-0001-4e1e-9e00-65bda9a575b6 2014-05-12 13:51:18.129 UTC 203b885f-17e1-446a-a321-5e0b888e6004 2014-06-15 17:23:48.706 UTC 920a4ba4-90cf-4a89-a943-571ac36e7d47 2014-06-15 16:13:50.623 UTC 0a15b5d5-9ad4-4394-a44b-a773c3cfbc60 2014-04-25 09:30:39.667 UTC f8521f7a-4def-44dd-9e0c-5919119df0b5 2014-06-15 17:12:31.867 UTC 3aa918f3-ff7c-4125-8c0e-0a0251f8e67a 2014-06-15 16:28:37.25 UTC 58d2e665-ec1f-4ea3-806d-cafa02adedee 2014-05-12 13:47:58.714 UTC fe3eb75e-1e1b-4846-849e-625552e0e9cc 2014-06-11 09:07:30.689 UTC 071ca1ba-e357-4fd3-8943-c544199f9dd0 2014-04-25 09:23:33.706 UTC 1e050fa6-0e46-47cc-852a-78351e49fd4b 2014-06-15 16:21:22.366 UTC e89e40ff-8e2c-401f-96ba-c233c6bf4dbd 2014-06-15 17:20:08.149 UTC c725fae1-9407-4643-8078-208328519914 2014-06-15 17:25:46.789 UTC a0444c47-ea11-48c9-9c0c-b52d326b35ad 2014-06-11 13:09:53.254 UTC 26b21b9b-a674-4e35-b03f-807d71510259 2014-05-12 13:28:52.14 UTC 8bacc18d-de0f-4fdf-99a7-3f5bca0f03ae 2014-06-15 17:20:36.58 UTC e3e82f84-c36d-4445-9009-146e4a867dc2 2014-06-15 16:39:33.753 UTC 994307a6-939b-48c2-a874-5be73efc8731 2014-06-10 10:56:30.827 UTC a3744263-cf8d-4ce4-8a77-8d75529492e3 2014-06-11 08:50:09.675 UTC Calculate_Contingenctable_name00 Needs the correct table name given for writing the values. The tablename needs to be the same as the one that is created and is a prefix of the whole table to identify a table. This is usually a timestamp. 2014-05-05 11:38:57.164 UTC alpha 2014-06-06 14:36:34.332 UTC propertyString00 Please load a file in as seen in the example where the user, password, url (which is the database it should use), and driver is stated. 2014-06-11 12:13:53.198 UTC mysql.user=root mysql.password=amrishsql mysql.url=jdbc:mysql://localhost:3306/mydb mysql.driver=com.mysql.jdbc.Driver 2014-06-06 14:36:25.795 UTC outputlist A output port for the concept pairs. 2014-05-02 16:33:00.498 UTC corrected_contingency_values A output port for producing the contincengy table values. The first value is the co-occurence, second values only of concept a, third of only concept b and fourth is the amount neither of A or B. 2014-05-02 16:32:31.767 UTC Beanshell_SQL_generate_contingency_tableconcept_pairs0table_name0out100 A Beanshell script that generates a SQL statement to retrieve the amount two concepts co-occur, concept A only occurs and not concept B, concept B occurs and not concept A. When a concept pair is the same. As in concept pair A A or B B etc. It will use the first SQL statement. Else it will use the second SQL statement. The output of only concept A and only concept B needs to be corrected and the value to get when neither concepts occur in literature is done in the Beanshell script called: "Beanshell_correct_contincengy_table". 2014-06-11 12:20:03.523 UTC net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity concept_pairs 0 text/plain java.lang.String true table_name 0 text/plain java.lang.String true out1 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_SQL_insert_into_co_occurrence_tablecontingency_values1concept_pairs0timestamp0out100 A Beanshell script that generates SQL statement to insert into the co-occurrence table the amount two given concepts co-occur together in literature. 2014-06-11 12:21:58.73 UTC net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity contingency_values 1 text/plain java.lang.String true timestamp 0 text/plain java.lang.String true concept_pairs 0 text/plain java.lang.String true out1 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_correct_contingency_tablecontingency_values1total_nr_abtracts2corrected_contingency_values11 A Beanshell script that corrects the output SQL retrieved contingency table by subtracting the co-occurence values of the concept only A and of concept only B value. It also uses the value of the total amount of abstracts there are in the dataset for calculating the value of when neither concepts occure. 2014-06-11 12:21:25.39 UTC net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity contingency_values 1 text/plain java.lang.String true total_nr_abtracts 2 text/plain java.lang.String true corrected_contingency_values 1 1 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_generate_SQL_statement_Get_distinct_concepttable_name0out100 A Beanshell script that retrieves every concept from the Sql table TableName_occurrence. 2014-06-11 12:14:03.731 UTC net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity table_name 0 text/plain java.lang.String true out1 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Loop net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_make_concept_pairsconcept_A0concept_B0concept_pair00 A Beanshell script that gets as input a list of concepts to create concept pairs. 2014-04-14 10:55:52.228 UTC net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity concept_B 0 text/plain java.lang.String true concept_A 0 text/plain java.lang.String true concept_pair 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExecute_SQL_Querysql0propertyString0resultList22 Executes the Beanshell generated SQL statement for getting destinct concepts. 2014-05-02 15:14:36.450 UTC net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity sql 0 text/plain java.lang.String true params 1 text/plain java.lang.String true propertyString 0 text/plain java.lang.String true resultList 2 2 xmlresults 0 0 system mysql-connector-java.jar net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker UserNameHere 2014-06-04 13:27:44.254 UTC net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExecute_SQL_Query_2sql0propertyString0resultList22 Executes the SQL generated query of the Beanshell script to retrieve the values of the contingency table. 2014-05-05 11:51:02.525 UTC net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity sql 0 text/plain java.lang.String true params 1 text/plain java.lang.String true propertyString 0 text/plain java.lang.String true resultList 2 2 xmlresults 0 0 workflow net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker UserNameHere 2014-05-12 11:45:00.69 UTC net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExecute_SQL_Update_INSERT_INTO_Co_occurrence_tablesql0propertyString0net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity sql 0 text/plain java.lang.String true params 1 text/plain java.lang.String true propertyString 0 text/plain java.lang.String true resultList 0 0 workflow net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker UserNameHere 2014-05-12 11:45:40.670 UTC net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_Listinputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity inputlist 2 l(l('')) [B true outputlist 1 l('') 1 workflow org.embl.ebi.escience.scuflworkers.java.FlattenList net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_List_2inputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity inputlist 2 l(l('')) [B true outputlist 1 l('') 1 workflow org.embl.ebi.escience.scuflworkers.java.FlattenList net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_List_3inputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity inputlist 2 l(l('')) [B true outputlist 1 l('') 1 workflow org.embl.ebi.escience.scuflworkers.java.FlattenList net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_SQL_count_abstractsout100net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity out1 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExecute_SQL_Query_3sql0propertyString0resultList22net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity sql 0 text/plain java.lang.String true params 1 text/plain java.lang.String true propertyString 0 text/plain java.lang.String true resultList 2 2 xmlresults 0 0 workflow net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker UserNameHere 2014-06-06 13:26:31.104 UTC net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_SQL_generate_contingency_tableconcept_pairsFlatten_List_2outputlistBeanshell_SQL_generate_contingency_tabletable_nametable_nameBeanshell_SQL_insert_into_co_occurrence_tablecontingency_valuesFlatten_List_3outputlistBeanshell_SQL_insert_into_co_occurrence_tableconcept_pairsFlatten_List_2outputlistBeanshell_SQL_insert_into_co_occurrence_tabletimestamptable_nameBeanshell_correct_contingency_tablecontingency_valuesFlatten_List_3outputlistBeanshell_correct_contingency_tabletotal_nr_abtractsExecute_SQL_Query_3resultListBeanshell_generate_SQL_statement_Get_distinct_concepttable_nametable_nameBeanshell_make_concept_pairsconcept_AFlatten_ListoutputlistBeanshell_make_concept_pairsconcept_BFlatten_ListoutputlistExecute_SQL_QuerysqlBeanshell_generate_SQL_statement_Get_distinct_conceptout1Execute_SQL_QuerypropertyStringpropertyStringExecute_SQL_Query_2sqlBeanshell_SQL_generate_contingency_tableout1Execute_SQL_Query_2propertyStringpropertyStringExecute_SQL_Update_INSERT_INTO_Co_occurrence_tablesqlBeanshell_SQL_insert_into_co_occurrence_tableout1Execute_SQL_Update_INSERT_INTO_Co_occurrence_tablepropertyStringpropertyStringFlatten_ListinputlistExecute_SQL_QueryresultListFlatten_List_2inputlistBeanshell_make_concept_pairsconcept_pairFlatten_List_3inputlistExecute_SQL_Query_2resultListExecute_SQL_Query_3sqlBeanshell_SQL_count_abstractsout1Execute_SQL_Query_3propertyStringpropertyStringoutputlistFlatten_List_2outputlistcorrected_contingency_valuesBeanshell_correct_contingency_tablecorrected_contingency_values fe7933ae-1b38-4fab-acc1-f2637db3a9a5 2014-06-10 15:51:33.431 UTC 0a6042a5-4d83-41ea-b2ae-3cefafb4265a 2014-05-05 11:22:16.615 UTC 340235a3-2479-420b-a33d-11529380bd97 2014-06-10 13:54:52.405 UTC fe291e3b-1b6d-4c09-8cea-87a24ad2533c 2014-06-08 16:10:17.851 UTC Calculate Contingency table 2014-05-05 13:44:48.426 UTC aeeef64f-1c80-4a16-ab56-89b439bed50d 2014-06-10 14:06:24.571 UTC bb618d97-2857-4d79-84e8-e20543f38116 2014-05-05 11:54:00.498 UTC 987dfb83-6ae8-458a-8dd0-d45c2d572854 2014-06-08 16:36:47.756 UTC f4c7469a-b9b2-42e0-81c2-2c5b0fd04f0f 2014-06-06 13:10:41.936 UTC 723d1cc8-9d97-4791-9f64-94b329b4876d 2014-06-08 15:36:19.904 UTC 9b8d4323-3e99-4fa3-bfbf-812acf73d615 2014-05-02 15:40:47.612 UTC febcbc5c-3e29-4c4c-b0eb-af50a9d2a7a6 2014-06-08 16:08:37.388 UTC 46f263f0-54aa-4132-96be-d2831ac84db1 2014-05-12 11:46:08.98 UTC f38ed2d2-f8f0-41be-af6f-43cf113a8de2 2014-06-06 16:24:53.251 UTC d1b17379-8eac-4dcd-a5b6-9754f99b0c94 2014-05-05 13:44:50.330 UTC 53e2be4c-2db0-4203-9d4d-f47d9bbe5512 2014-05-05 11:37:52.424 UTC A workflow that retrieves the values of a 2x2 contingency table and puts the co-occurence of made concept pairs into the SQL table TableName_co_occurence. This contingency table consits out of a matrix where two concepts co-occur, concept A only occurs and not concept B, concept B occurs and not concept A and neither concepts occur in literature. B Not B A AB A not A B not A not B To be able to run this workflow. You need to have in the database mydb a SQL table named TableName_occurence with document URIs and concept URIs occurences as followed: concept_doc_id concept_uri doc_uri 1 <http://concept1> <http://doc1> 2 <http://concept2> <http://doc1> etc. For an example please go to myexperiment and download the file standaard output occurence. And a table named TableName_co_occurence constructed to insert the amount of concept co-occurences in documents with the following columns: concept_id concept1 concept2 concept_co_occurence Keep in mind the TableName is a part of the whole tablename. This is used to identify the table to be used. 2014-05-06 09:26:25.982 UTC 9ac9ac33-565a-4f05-9353-57e6fcd510b8 2014-05-05 11:39:00.253 UTC 2e8d40f2-125f-4d34-ae61-1d10508f1be8 2014-06-06 14:43:04.450 UTC 241acb88-15bf-4b76-a78a-2e57174073b5 2014-06-10 14:00:00.86 UTC f83a0a65-9046-4c27-8b27-30820f2b9c3e 2014-06-08 16:40:27.780 UTC cc570f9b-f9a5-494d-af4a-fcc31285755c 2014-06-05 11:16:18.854 UTC e529c545-ce7c-41a3-a337-91137d5cb2a0 2014-05-02 16:35:22.526 UTC 9db66f08-1aa9-4b76-8592-a90c3e1710c5 2014-05-05 09:41:53.767 UTC 2eae8fad-b196-4141-ad91-e4c079e4205f 2014-05-02 16:58:36.311 UTC Amrish Mahes 2014-05-02 15:42:14.33 UTC 94065ddd-d3e1-4e39-b7ee-31d8079d4553 2014-05-05 11:54:11.870 UTC 16e2c6df-f5ca-4b7c-9745-2784eddd346d 2014-06-08 15:40:29.722 UTC 1b260c16-3554-4fa6-b27b-d537f9440fb7 2014-06-06 14:54:06.793 UTC 711f5d11-bc72-4e31-8716-4dad288862f0 2014-04-25 09:08:01.83 UTC 0f7062ef-e729-49c8-9ee0-bc26eae41dbb 2014-06-06 13:27:31.365 UTC dc4b9ca5-6031-4dd0-9286-9f482177036d 2014-06-06 16:32:03.193 UTC 7d1aba2f-ef9b-4892-a3fa-cc3607cf18dd 2014-06-05 11:32:59.648 UTC 4ecbd389-493e-4068-884e-a28c56d39745 2014-06-05 11:43:31.206 UTC 228d8f2d-cdfe-486a-bf03-85a13a5a38aa 2014-06-11 08:57:45.345 UTC b2268ff9-c16a-45e3-82ea-549ecfb66d8a 2014-06-06 16:27:30.743 UTC 811704db-ff82-4ab7-9e31-dcfb7f8600a0 2014-06-04 13:27:49.995 UTC 68c46c7a-4dee-44de-8819-dc7701124973 2014-05-05 09:37:41.543 UTC 6a1ccba3-c527-47ce-9a4c-a57634881a7c 2014-05-02 15:57:55.741 UTC 918e96e6-9dcc-4cec-b541-93a529efd2a6 2014-06-06 16:17:33.159 UTC 90bde618-33be-4318-a858-580937541806 2014-06-06 16:04:34.227 UTC 3da9a958-ebc0-4193-83cd-29a45c70a1fd 2014-05-02 16:40:17.937 UTC fb10914b-9f29-4c60-a29c-fb854cb987c3 2014-06-06 14:47:16.415 UTC 95c84125-55a5-42cd-b9a6-27c68d9cf5ed 2014-06-05 12:02:34.59 UTC ce4e0e0d-369c-4896-8aca-4db7f7f33289 2014-06-06 15:00:21.670 UTC e41e4bc5-4099-4a7c-920a-95b2aa64bb7a 2014-06-06 14:25:01.771 UTC 7862fb3a-5815-4dda-ad77-80da4baef153 2014-06-06 14:42:04.585 UTC bdf80876-bf4b-46ba-a19e-25bd53bb8347 2014-06-06 16:30:07.558 UTC 9ae4cca8-d24a-4d87-a784-5809699b058e 2014-06-06 13:34:31.302 UTC 850d2eaa-ea05-4ee5-8d14-046298603152 2014-06-05 12:14:15.409 UTC 50590288-22d5-4cb0-a152-29357aab7c35 2014-05-08 12:49:18.288 UTC f722e927-3c17-42c9-a101-a9f940334ee8 2014-06-11 09:10:32.353 UTC 9f2b6abe-3efc-4dee-8b84-2e0d876278ca 2014-04-25 10:02:35.250 UTC b02057d9-6ad6-4d77-88df-e5ec60cff83f 2014-06-10 14:01:09.699 UTC 3b7ddb36-6527-4c89-a70a-8ed0e0abb81f 2014-06-10 16:04:44.704 UTC 4b47a42f-beeb-410e-a735-185f96ddc74f 2014-06-08 15:43:15.664 UTC f7c8d6a5-6521-466c-92ec-c1c8a41a7821 2014-06-06 14:52:41.206 UTC 5bb26871-542e-4b07-9fcc-710b6f71aca0 2014-06-08 16:41:13.319 UTC e71229bc-a274-4c5b-9ecc-6fb654098711 2014-06-08 16:06:16.226 UTC 9a0c161d-6467-459d-b55a-48d0026e5552 2014-06-06 14:56:33.37 UTC 33424e51-31a8-4228-90fb-86e60edac9f4 2014-06-08 16:13:45.548 UTC 3f040ee9-ec30-4c0c-b9bb-5dacc1e7af80 2014-06-10 14:02:38.260 UTC 942f3272-b926-4fe6-bf15-b4e29e44fb8f 2014-05-05 09:44:20.269 UTC a8536e59-cdaf-4188-b9a4-f5da97103756 2014-06-06 16:21:40.873 UTC f54ed762-bb43-453e-9ecf-2968a05b46f3 2014-06-08 15:52:19.127 UTC 03e63620-9e88-4a91-b89e-7de8e08c7929 2014-06-06 14:36:34.512 UTC b17158d5-fab3-4a62-88b9-57bd2d3d063d 2014-06-08 15:53:29.146 UTC 37048185-fb68-4f68-a8d8-af47d65da0d9 2014-06-11 08:53:32.981 UTC 3d9659ca-8dcd-4bee-a225-6244cd901929 2014-05-12 13:42:30.73 UTC d539393d-2c47-4958-8a22-e06cc46c2fad 2014-06-10 08:53:28.265 UTC bf203a6d-fa48-4f35-ad40-cff4913b6868 2014-05-05 11:55:10.214 UTC f052486b-3ab3-429f-af0c-9e191594decd 2014-06-06 16:26:12.958 UTC 5074fd15-046f-4536-bb9e-f540c06b26af 2014-06-08 16:39:33.787 UTC 7b99a485-c395-4f74-b829-44d6cd00ffbc 2014-06-08 16:38:10.539 UTC d3760d97-73e7-402e-a47c-421392a6246e 2014-06-06 14:40:00.102 UTC a18418ec-e800-43d9-b55a-3cd23557d717 2014-06-08 15:40:10.621 UTC e5fc58d3-008d-40e9-985e-fac63f5b396a 2014-06-08 15:47:21.197 UTC 0a099cde-b9b8-42fd-9417-7d3362d7402e 2014-06-06 16:23:15.466 UTC 7b84d7d9-225f-47ef-bd5b-484de5900fa0 2014-06-06 16:29:07.154 UTC e773d991-e7ef-48a1-9c29-a315e1540e13 2014-06-06 14:31:40.433 UTC aabaff7d-f657-4b17-84ad-457822c48f13 2014-06-10 14:01:49.804 UTC 875e8727-ce2f-43e5-9fa1-50ecce24615c 2014-05-12 13:43:58.973 UTC dede7b6f-0c01-4fa0-88ad-928280419cb2 2014-06-08 16:30:18.818 UTC b121dd0d-4518-47b1-9d05-feda0930456e 2014-06-06 14:33:40.65 UTC 472f5535-90a3-4107-ae8f-24e71c1e8fbc 2014-06-11 12:22:01.979 UTC bc99ee26-4f25-45c9-8d87-5c4c3b4c7af4 2014-06-05 11:32:22.394 UTC 7895790d-29ba-4a96-8da9-d33cecd207cb 2014-06-10 15:29:06.258 UTC 31647e87-e8a1-4409-8f3d-6802cc2596ba 2014-05-06 09:26:28.104 UTC c708232c-6b47-4fdd-b66a-ec00cdf8a9b5 2014-06-10 08:51:53.249 UTC bd93275c-7f78-4fe3-98ca-c4efd3cbdfbc 2014-04-25 10:05:58.574 UTC 1540f783-07df-4f33-9fe2-baf9a2993831 2014-06-06 14:38:24.966 UTC Calculate Inner Producttimestamp00 2014_04_30_21_24_30 2014-06-11 12:29:21.857 UTC Needs the correct table name given for writing the values. The tablename needs to be the same as the one that is created and is a prefix of the whole table to identify a table. This is usually a timestamp. 2014-06-11 12:28:58.863 UTC concept_pairs11 A list of all the concept pairs. [concept1,concept1 concept1,concept2 concept2,concept1 concept2,concept2 etc.] For a complete example please download the file input_concept_pairs_for_calculate_UC_workflow from myexperiment. 2014-06-11 12:30:37.432 UTC propertyString00 mysql.user=root mysql.password=amrishsql mysql.url=jdbc:mysql://localhost:3306/mydb mysql.driver=com.mysql.jdbc.Driver 2014-06-11 12:31:04.966 UTC Please load a file in as seen in the example where the user, password, url (which is the database it should use), and driver is stated. 2014-06-11 12:30:49.377 UTC outputBeanshell_SQL_generate_Get_Inner_Producttimestamp0concept_pairs0out100 A Beanshell script that generates a SQL statement to calculate the inner product between two concept profiles. These concept profiles only have concepts that both have in common. The concepts that are in common in the concept profiles are multiplied with each others UC value and added. This summed up value of two concept profiles is the inner product. For example: Concept profile A, has the concept A, B, C and D. Concept profile B has the concepts B, C, E. This means the common concepts for both concept profiles are B, C. These values are multiplied and added. This final value is the inner product between two concept profiles. 2014-06-11 12:33:09.498 UTC net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity concept_pairs 0 text/plain java.lang.String true timestamp 0 text/plain java.lang.String true out1 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_SQL_generate_INSERT_INTO_Inner_Product_tableinner_product_value0timestamp0concept_pairs0out100 A Beanshell script that generates a SQL statement to insert the inner product values calculated of two concept profiles into the inner product table. 2014-04-14 11:02:08.466 UTC net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity concept_pairs 0 text/plain java.lang.String true timestamp 0 text/plain java.lang.String true inner_product_value 0 text/plain java.lang.String true out1 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExecute_SQL_Query_Get_Inner_Productsql0propertyString0resultList22net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity sql 0 text/plain java.lang.String true params 1 text/plain java.lang.String true propertyString 0 text/plain java.lang.String true resultList 2 2 xmlresults 0 0 workflow net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker UserNameHere 2014-05-12 11:48:50.529 UTC net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExecute_SQL_Update_INSERT_INTO_Inner_Product_tablesql0propertyString0resultList00net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity sql 0 text/plain java.lang.String true params 1 text/plain java.lang.String true propertyString 0 text/plain java.lang.String true resultList 0 0 workflow net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker UserNameHere 2014-05-12 11:49:52.483 UTC net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_List_4inputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity inputlist 2 l(l('')) [B true outputlist 1 l('') 1 workflow org.embl.ebi.escience.scuflworkers.java.FlattenList net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_List_5inputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity inputlist 2 l(l('')) [B true outputlist 1 l('') 1 workflow org.embl.ebi.escience.scuflworkers.java.FlattenList net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_SQL_generate_Get_Inner_ProducttimestamptimestampBeanshell_SQL_generate_Get_Inner_Productconcept_pairsconcept_pairsBeanshell_SQL_generate_INSERT_INTO_Inner_Product_tableinner_product_valueFlatten_List_5outputlistBeanshell_SQL_generate_INSERT_INTO_Inner_Product_tabletimestamptimestampBeanshell_SQL_generate_INSERT_INTO_Inner_Product_tableconcept_pairsconcept_pairsExecute_SQL_Query_Get_Inner_ProductsqlBeanshell_SQL_generate_Get_Inner_Productout1Execute_SQL_Query_Get_Inner_ProductpropertyStringpropertyStringExecute_SQL_Update_INSERT_INTO_Inner_Product_tablesqlBeanshell_SQL_generate_INSERT_INTO_Inner_Product_tableout1Execute_SQL_Update_INSERT_INTO_Inner_Product_tablepropertyStringpropertyStringFlatten_List_4inputlistExecute_SQL_Query_Get_Inner_ProductresultListFlatten_List_5inputlistFlatten_List_4outputlistoutputExecute_SQL_Update_INSERT_INTO_Inner_Product_tableresultList ad11b9f4-2a6c-417c-a99a-53391e22ae59 2014-04-25 09:54:33.677 UTC be6eb3aa-d26b-4d6a-856e-bb7b6594f355 2014-06-10 15:33:40.565 UTC 348801cf-d2ad-43fc-9b91-ab63e359fdcc 2014-04-25 09:07:18.526 UTC 33db0c4f-7076-4cbd-9913-57f2bcaad402 2014-04-25 09:06:56.615 UTC 5d9a8682-9ef8-46a4-b6e7-60e0566eb18f 2014-05-12 11:50:18.963 UTC e9c85439-4022-4bf3-9d93-77f70e4cd5fa 2014-04-25 09:55:56.310 UTC bde675e9-64ec-49a0-b079-cbe4ae8e7f13 2014-05-05 14:33:52.891 UTC Calculate Inner Product 2014-04-25 09:00:49.797 UTC ab9d319b-bbd6-4012-9c18-26c62114c2a1 2014-04-25 11:11:47.249 UTC 807d1911-1342-4922-b766-69bbcab70c68 2014-05-05 14:34:36.368 UTC Amrish Mahes 2014-05-05 13:59:12.828 UTC 0c8d2279-44d5-4b7c-99df-68381065da4d 2014-06-10 11:02:18.385 UTC b87808dc-5d2c-4362-9d49-dddf3b17ce32 2014-05-12 13:51:14.794 UTC 0fc79d92-8f31-4987-bb91-f4de8f131b7f 2014-06-11 12:33:09.623 UTC Summarize Big Tabletimestamp00 2014_04_30_21_24_30 2014-06-11 12:42:12.180 UTC Needs the correct table name given for writing the values. The tablename needs to be the same as the one that is created. 2014-06-11 12:41:55.80 UTC propertyString00 Please load a file in as seen in the example where the user, password, url (which is the database it should use), and driver is stated. 2014-06-11 12:41:28.838 UTC mysql.user=root mysql.password=amrishsql mysql.url=jdbc:mysql://localhost:3306/mydb mysql.driver=com.mysql.jdbc.Driver 2014-05-12 11:33:50.205 UTC resultListBeanshell_SQL_Generate_INSERT_INTO_summary_tablein11timestamp0out100 A Beanshell script that generates SQL statements to insert two concepts and their given co-occurence, uncertainty coefficientcy and inner product values into the table. 2014-04-14 11:03:42.908 UTC net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity timestamp 0 text/plain java.lang.String true in1 1 text/plain java.lang.String true out1 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_SQL_statement_get_last_table_data_inputtimestamp0out100 A Beanshell that generates SQL statements to retrieve the inner product of two concept profiles, the co-occurence of the concepts and the uncertainty coefficient. 2014-04-14 11:04:05.263 UTC net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity timestamp 0 text/plain java.lang.String true out1 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExecute_SQL_Query_Get_data_for_summary_tablesql0propertyString0resultList22net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity sql 0 text/plain java.lang.String true params 1 text/plain java.lang.String true propertyString 0 text/plain java.lang.String true resultList 2 2 xmlresults 0 0 workflow net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker UserNameHere 2014-05-12 11:30:17.440 UTC net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExecute_SQL_Update_INSERT_INTO_summary_tablesql0propertyString0resultList00net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity sql 0 text/plain java.lang.String true params 1 text/plain java.lang.String true propertyString 0 text/plain java.lang.String true resultList 0 0 workflow net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker UserNameHere 2014-05-12 11:33:03.328 UTC net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_SQL_Generate_INSERT_INTO_summary_tablein1Execute_SQL_Query_Get_data_for_summary_tableresultListBeanshell_SQL_Generate_INSERT_INTO_summary_tabletimestamptimestampBeanshell_SQL_statement_get_last_table_data_inputtimestamptimestampExecute_SQL_Query_Get_data_for_summary_tablesqlBeanshell_SQL_statement_get_last_table_data_inputout1Execute_SQL_Query_Get_data_for_summary_tablepropertyStringpropertyStringExecute_SQL_Update_INSERT_INTO_summary_tablesqlBeanshell_SQL_Generate_INSERT_INTO_summary_tableout1Execute_SQL_Update_INSERT_INTO_summary_tablepropertyStringpropertyStringresultListExecute_SQL_Update_INSERT_INTO_summary_tableresultList 69fe9a94-2c42-4563-9f6d-e774eaec2a52 2014-05-12 13:55:06.42 UTC f347fea1-c0b9-4e9f-9963-a9ef5b9db7c5 2014-06-11 09:22:30.197 UTC a6f4b2f7-86f7-4d90-92ee-0047f4e61302 2014-05-12 13:36:33.505 UTC bc9fef0e-afbe-4e64-be84-e6e6f4fa772b 2014-06-11 12:42:19.340 UTC f7e2d77a-dd3e-4a3e-9ca2-30659d91d6ad 2014-05-12 13:31:29.564 UTC 4b65159f-b6b4-4457-b9db-59672f7c2c7d 2014-04-25 10:24:37.597 UTC Summarize Big Table 2014-04-25 09:06:31.655 UTC f6377916-ad80-4b93-a881-5e4b3a5fde97 2014-06-11 09:03:05.338 UTC 0f55befa-f320-4aad-8f28-7d47f0e40320 2014-05-12 11:33:51.663 UTC e59e5168-be6b-4bb5-8d34-cd386cbfda7d 2014-04-25 09:53:26.34 UTC 00c47db0-5469-40ed-8b74-b4a694708959 2014-05-12 11:33:22.736 UTC 6137cf86-1e2e-42ba-aef2-1a0adb9fbbd0 2014-04-25 09:07:59.8 UTC Calculate Uncertainty Coefficientcorrected_contingency_values22 The contingency values of the concept pair. For example the concept pair A,A and A,B have contincengy values of [ [ 1,0,0,8 ],[1,2,2,4] ]. 2014-06-11 12:24:34.24 UTC timestamp00 2014_04_30_21_24_30 2014-06-11 12:25:28.260 UTC Needs the correct table name given for writing the values. The tablename needs to be the same as the one that is created and is a prefix of the whole table to identify a table. This is usually a timestamp. 2014-05-05 12:49:25.823 UTC concept_pairs11 A list of all the concept pairs. [concept1,concept1 concept1,concept2 concept2,concept1 concept2,concept2 etc.] For a complete example please download the file input_concept_pairs_for_calculate_UC_workflow from myexperiment. 2014-05-05 13:29:23.249 UTC propertyString00 Please load a file in as seen in the example where the user, password, url (which is the database it should use), and driver is stated. 2014-06-11 12:26:04.211 UTC mysql.user=root mysql.password=amrishsql mysql.url=jdbc:mysql://localhost:3306/mydb mysql.driver=com.mysql.jdbc.Driver 2014-06-11 12:26:15.897 UTC outputBeanshell_SQL_INSERT_UC_values_INTO_tabletimestamp0UC_value0concept_pairs0output_SQL00 A Beanshell script that generates a SQL statement to insert the calculated values of uncertainty coefficient per concept pair into the table. 2014-04-14 11:00:40.794 UTC net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity timestamp 0 text/plain java.lang.String true concept_pairs 0 text/plain java.lang.String true UC_value 0 text/plain java.lang.String true output_SQL 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_calculate_Uncertainty_Coefficientcorrected_contingency_values1UC_value00 A Beanshell script that calculates the Uncertainty coefficient based on a script of Herman van Haagen. 2014-06-11 12:27:47.930 UTC net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity corrected_contingency_values 1 text/plain java.lang.String true UC_value 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExecute_SQL_Update_INSERT_INTO_UC_tablesql0propertyString0resultList00net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity sql 0 text/plain java.lang.String true params 1 text/plain java.lang.String true propertyString 0 text/plain java.lang.String true resultList 0 0 workflow net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker UserNameHere 2014-05-12 11:46:55.841 UTC net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_SQL_INSERT_UC_values_INTO_tabletimestamptimestampBeanshell_SQL_INSERT_UC_values_INTO_tableUC_valueBeanshell_calculate_Uncertainty_CoefficientUC_valueBeanshell_SQL_INSERT_UC_values_INTO_tableconcept_pairsconcept_pairsBeanshell_calculate_Uncertainty_Coefficientcorrected_contingency_valuescorrected_contingency_valuesExecute_SQL_Update_INSERT_INTO_UC_tablesqlBeanshell_SQL_INSERT_UC_values_INTO_tableoutput_SQLExecute_SQL_Update_INSERT_INTO_UC_tablepropertyStringpropertyStringoutputExecute_SQL_Update_INSERT_INTO_UC_tableresultList 6fae7384-536a-47de-989d-1bce376249ed 2014-06-11 12:28:09.901 UTC 7d75255a-84e6-43d3-a398-60bfae801940 2014-05-08 15:06:24.745 UTC 13548fc4-b946-4adc-b56e-d7aa856174f7 2014-06-10 13:43:49.66 UTC 1dc7cdb3-165a-4413-9adb-54081500717f 2014-06-10 14:08:27.331 UTC 6a956c52-35e9-42a0-acad-c7c17e2a45ba 2014-05-08 15:00:02.697 UTC 8f04d577-c676-46ea-b867-d849e7af0e6d 2014-05-05 12:49:30.628 UTC 46d45a69-6c44-4185-84a4-119f054a16f8 2014-05-05 13:29:23.342 UTC 4ebf7d25-6d88-4481-8109-a28a055c26c2 2014-06-10 15:32:28.918 UTC Calculate Uncertainty Coefficient 2014-04-25 08:57:47.839 UTC Amrish Mahes 2014-05-05 13:43:58.257 UTC 0cdc32e9-e9b0-4221-b53c-a65cd3db8f90 2014-05-05 13:17:31.804 UTC 8eca8dc6-84e5-4412-bb2d-5e38d591e5d4 2014-06-10 13:46:59.916 UTC 81609bfe-030c-4b35-98b7-45fe6f9a4e1c 2014-06-10 13:39:04.13 UTC 2e19c3f7-489e-4f69-a4b7-744d4f046fe4 2014-05-05 13:14:30.664 UTC 000df03c-2c75-49ee-b7e9-25dd34d507fa 2014-05-05 13:42:48.991 UTC 4137be61-327d-4d14-8066-e1d75d8f5f4e 2014-04-25 11:04:18.674 UTC 76ae35e5-bd6f-4da6-a8fc-157da2bd0ea5 2014-04-25 09:09:07.360 UTC 2ebf0b6a-071d-46f6-b793-2dde8cb9d22f 2014-05-05 13:43:59.598 UTC This workflow calculates the uncertainty coefficient for concept pairs and their 2x2 contingency values. It is necessary to have a table to insert the calculated uncertainty coefficient values into the table TableName_uc. The uncertainty coefficient table has the following columns: concept_profile_id concept_alpha concept_beta Uncertainty_coefficient concept_profile_id = PK Uncertainty_coefficient = DOUBLE 2014-05-05 13:42:27.42 UTC eb63e5b4-4ec9-4e70-932c-c22fe8ac8c3b 2014-05-05 13:43:43.341 UTC 5b89a766-6e15-4189-98ab-1b7e4640cd7b 2014-05-12 13:47:37.834 UTC 1157056b-06f9-4caf-b68f-635230a545c4 2014-04-25 09:07:59.975 UTC 34c726a4-4e83-461c-a95d-f96eaa1c0575 2014-05-08 12:49:59.727 UTC 71245a73-7b81-4bff-8ab5-6750b4866ccd 2014-05-12 11:47:24.645 UTC 8e91b850-ccce-4938-a5c4-132bf4423c61 2014-06-10 16:06:35.992 UTC 8570b4b6-c56e-4588-89ee-eab59efc547d 2014-06-10 11:13:15.21 UTC