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 User_password00 Input your sql password to acces as root. 2014-03-27 10:09:15.466 UTC abstract_input_depth222 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 13:36:08.810 UTC Driver_value00 com.mysql.jdbc.Driver 2014-04-10 09:16:05.435 UTC The driver needed for all SQL query to run. 2014-04-11 13:47:39.250 UTC usr_id00 root 2014-04-11 12:10:39.499 UTC The user ID which is in this case root. 2014-04-11 13:48:20.13 UTC url_value00 jdbc:mysql://localhost:3306/mydb 2014-04-14 09:03:49.901 UTC The url value Sql connects to. 2014-05-01 14:21:40.281 UTC endPeregrine indexertable_name0url0password0ontology0Input2userid0driver0 The nested workflow Peregrine Indexer uses a java peregrine skos cli.jar file to index the occurence 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. 2014-05-02 15:58:43.549 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 Coefficientuserid0password0concept_pairs1corrected_contingency_values2url0driver0timestamp0 A nested workflow to calculate the Uncertainty coefficient with the contingency values of the concept pairs. The calculated values are afterwards inserted into a SQL table. 2014-05-05 12:45:20.473 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 Contincengy tableurl0driver0password0table_name0userid0outputlist11corrected_contingency_values22 A nested 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 is done by creating concept pairs which is retrieved from the Sql table TableName_occurence. This contincengy 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 This is calculated for every possible concept pair. 2014-05-05 11:56:04.847 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 Productuserid0password0concept_pairs1driver0timestamp0url0 A nested workflow to calculate the inner product of a concept profile. 2014-05-05 14:01:15.774 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 Tablesuserid0url0driver0password0timeStamp00 This nested workflows create the necessary tables for inserting the generated values. The following tables are created: - Co-occurence table This table will consist out of - Occurence table - Uncertainty coefficient table - Inner product table - Big table 2014-05-01 14:34:44.380 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.InvokeSummarize Big Tabletimestamp0userid0url0password0driver0resultList11net.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 indexerurlurl_valuePeregrine indexerpasswordUser_passwordPeregrine indexerontologyOntology_inputPeregrine indexerInputabstract_input_depth2Peregrine indexeruseridusr_idPeregrine indexerdriverDriver_valueCalculate Uncertainty Coefficientuseridusr_idCalculate Uncertainty CoefficientpasswordUser_passwordCalculate Uncertainty Coefficientconcept_pairsCalculate Contincengy tableoutputlistCalculate Uncertainty Coefficientcorrected_contingency_valuesCalculate Contincengy tablecorrected_contingency_valuesCalculate Uncertainty Coefficienturlurl_valueCalculate Uncertainty CoefficientdriverDriver_valueCalculate Uncertainty CoefficienttimestampCreate TablestimeStampCalculate Contincengy tableurlurl_valueCalculate Contincengy tabledriverDriver_valueCalculate Contincengy tablepasswordUser_passwordCalculate Contincengy tabletable_nameCreate TablestimeStampCalculate Contincengy tableuseridusr_idCalculate Inner Productuseridusr_idCalculate Inner ProductpasswordUser_passwordCalculate Inner Productconcept_pairsCalculate Contincengy tableoutputlistCalculate Inner ProductdriverDriver_valueCalculate Inner ProducttimestampCreate TablestimeStampCalculate Inner Producturlurl_valueCreate Tablesuseridusr_idCreate Tablesurlurl_valueCreate TablesdriverDriver_valueCreate TablespasswordUser_passwordSummarize Big TabletimestampCreate TablestimeStampSummarize Big Tableuseridusr_idSummarize Big Tableurlurl_valueSummarize Big TablepasswordUser_passwordSummarize Big TabledriverDriver_valueendSummarize Big TableresultList 8da2ffdd-f0a7-47e7-88a0-facfa734e653 2014-03-03 14:01:20.166 UTC 90a54608-c2d9-407e-99cb-0e7d6a2f884f 2014-03-12 15:28:58.480 UTC d92b5894-75ef-48e1-b233-2144d51fcd9a 2014-03-18 11:53:02.58 UTC 71f14995-6503-40d5-8948-2d64864e36d2 2014-03-12 15:28:10.329 UTC 899ddd42-c5bb-4b8c-ada0-14b2ec4f2108 2014-02-26 13:46:59.936 UTC 62cadf7c-0be2-4a5c-9116-19c5508d2262 2014-04-02 11:34:26.859 UTC 0fdf5cdf-e9cd-4a15-a314-44e0123dcb97 2014-03-20 10:30:41.570 UTC bb263958-6955-44d3-b785-8b8cb552ca4e 2014-04-09 11:48:16.918 UTC ba78f25c-5d59-4fe1-a362-7c3739ef7245 2014-03-18 10:51:14.675 UTC b4aad310-ecdd-4c8b-8919-99817ecaa9cc 2014-02-26 13:07:54.522 UTC ee149ce2-e3ba-465e-9c63-04b297aa5059 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571302b5-dfde-4840-be63-1be297253e9e 2014-04-10 12:07:08.106 UTC 85eb7ca4-2261-4b6b-8dbc-e983dfffad06 2014-04-25 08:42:27.977 UTC b4a7f556-a9d0-49a0-9979-ecfee03c27cb 2014-03-26 16:49:56.104 UTC 583ce5b9-1b7e-4727-b578-99a9446d6c24 2014-04-10 14:21:17.895 UTC a6467614-66ae-4e21-bc79-5a933557e105 2014-04-07 09:13:03.21 UTC db32d696-f69e-44d3-9472-82883b50e3de 2014-05-01 14:29:35.815 UTC f8fe3791-3d20-4ab8-bc33-af4bc6f36a01 2014-03-12 09:33:32.129 UTC 780b5e58-5a7a-4592-b867-9bb2ac080e20 2014-04-01 09:07:20.694 UTC 60360c09-c322-4219-aef4-05e39c550194 2014-04-08 09:49:57.235 UTC 8c483773-b44f-4ff1-91e4-308faf79f86f 2014-03-19 12:32:54.364 UTC 7f687e62-ab7d-4c23-9183-1f0576b5b87e 2014-03-19 13:02:15.478 UTC 93512370-e9f6-49b6-ba46-4482dae8c38e 2014-05-02 16:40:23.354 UTC 1e32cd62-6709-4253-8812-b7f7823f323f 2014-03-19 12:39:25.755 UTC de9360d0-050d-46d1-917c-c126ba6aee9d 2014-03-18 14:46:45.702 UTC d386f854-8273-43e6-980b-11dc034eaaf2 2014-03-12 10:23:18.366 UTC 11372cda-aea4-44fd-ae2c-e0b0b4692bc1 2014-03-13 14:16:41.274 UTC Requirements: 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. Choose this dependency by rightclicking a beanshell script and selecting it for the whole workflow. 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 --> Edit defaul local --> write in Shell: C:\Windows\system32\cmd.exe /c and save that. Have JAVA_HOME C:\Program Files\jdk 1.7.0 in environment variabale when using Windows. 2014-05-02 15:09:50.696 UTC 24fecb95-af50-4286-96ce-a71b19c86a52 2014-03-31 14:01:48.127 UTC 0a9fc708-f04c-4b3b-9c2b-3077d360a004 2014-03-26 16:58:01.18 UTC 2eb0f038-4ecd-440b-b39e-f188243e37c0 2014-03-26 17:23:46.827 UTC 0ad567dd-bec4-4ae1-ae7a-664edd5f5cfd 2014-03-18 11:59:51.577 UTC 4d97f9f1-73f8-43d2-a469-7d2eb25fbb50 2014-04-15 14:25:53.521 UTC 12a8dbd6-f54e-496a-ab44-44c16adb4fc1 2014-03-11 15:24:33.988 UTC a813d261-a464-409a-a69d-b1db65087f9a 2014-03-19 10:28:56.598 UTC 60fc7d82-094b-4402-b701-1286eebd4d5a 2014-04-11 12:13:11.476 UTC 812d5229-115b-47d5-bc40-7c25fa72ef52 2014-03-19 16:10:15.870 UTC 4190d231-a8d9-4d5d-ad58-db36295f4e7d 2014-04-02 11:23:57.647 UTC 9565794d-e2b6-469c-abbb-70d5d05ede32 2014-04-10 09:13:39.325 UTC 15f01c42-3708-46b7-b489-9d0915964073 2014-04-11 11:54:34.890 UTC 7651968d-2f43-4d3c-99f2-be208404bb19 2014-03-11 14:43:35.34 UTC d38184f1-fafd-43b2-a12e-4ac7e6dfc387 2014-04-10 09:16:18.992 UTC 9330fd5a-7583-4a1d-bee0-762a6896c11e 2014-03-03 14:12:44.325 UTC f292ef28-a3ba-4153-adda-835d97af251a 2014-03-19 13:12:54.250 UTC a2aa9e83-b14b-4160-8607-d06228a5a210 2014-04-25 09:30:45.977 UTC 2c5ea41b-97b9-4abc-91ff-4f2484a8e4da 2014-04-02 08:21:59.626 UTC e7da0c52-301c-4412-8c0d-d9224a0aaa2e 2014-03-03 16:42:26.53 UTC b845dbf5-d131-4fa3-a030-09e1c43eea1c 2014-03-17 13:04:39.719 UTC 8b3262d0-4df3-4545-bef0-49d1f237a235 2014-04-03 14:00:43.527 UTC c1c39cdd-ae80-47b1-838d-e9ac8377e564 2014-03-18 10:22:36.564 UTC 469f1513-2711-47e9-8616-3981f756cba9 2014-03-11 09:47:24.758 UTC 771080e5-fee1-477c-afc7-48eb021eeef0 2014-03-13 13:01:18.912 UTC 32035473-cbac-46fb-8f01-232d9c3e9c60 2014-03-03 12:43:17.878 UTC 056aa17d-7616-412a-bc85-9e060860084a 2014-03-04 17:39:10.43 UTC b960c713-c531-4151-ab14-c2cc808f9f23 2014-03-20 10:31:39.457 UTC 641b1f1d-bc00-4316-980c-ffde8c56b985 2014-03-13 13:22:43.253 UTC 3bf9710d-fbff-4111-9da4-e08881c792e7 2014-05-01 13:38:15.975 UTC 3e195092-0304-43c9-8f85-14d5c433e071 2014-02-26 12:53:28.622 UTC 529b0a59-d5b5-4a86-9f68-176441054011 2014-03-21 10:47:02.223 UTC 5d4f93fb-bc93-4153-94cb-30db318b3202 2014-03-27 09:25:29.554 UTC cfe3aeea-2e13-43bb-b760-a1d3a30333c7 2014-03-11 14:48:11.937 UTC 04e81e51-4243-4c7d-bedf-52e110d75941 2014-03-26 17:21:42.891 UTC b22dd61f-0163-4907-910f-1039f97dbeb0 2014-04-25 09:53:37.142 UTC 7729c962-481a-439a-9792-fea74acd1ccc 2014-03-20 15:19:54.660 UTC c9f48caa-ab69-465b-a144-56845094a227 2014-04-25 09:07:55.498 UTC d83c0e81-10ac-461a-8c4f-eb767050ef48 2014-03-13 09:43:57.550 UTC cffa6413-a93c-4ffd-82cf-32195410de09 2014-03-12 15:32:56.814 UTC a119641e-5206-4690-af10-c138a1f751c9 2014-02-26 13:33:07.439 UTC d733cb03-4b3a-4a90-8ba8-ce9141a40c59 2014-03-18 14:47:05.491 UTC 74142a02-82df-4805-acf3-1533774ee460 2014-04-10 14:46:06.976 UTC 36f648dc-0bcc-46a1-a637-d635b7f452e4 2014-04-11 11:51:48.200 UTC 7df13f1f-4b0d-471c-a7a3-f2ef2401d44b 2014-03-03 15:03:01.436 UTC 9da3c9c2-1c84-4fe7-acc9-60d0cff316e7 2014-03-12 10:37:54.386 UTC bad5ca35-5e6d-4a04-b6c8-99088d249c7b 2014-05-05 09:43:08.41 UTC e132ba8c-d158-4fd7-b392-735c5313998b 2014-04-09 11:47:31.757 UTC 6a0bf53c-6cc9-485b-96c5-c9e8fe2e3c0e 2014-03-13 13:32:22.428 UTC 393c3128-043d-4598-aeab-8d8a7ff26f25 2014-04-25 09:09:37.203 UTC 5f59b925-7143-452b-83c2-8b6e5aafb805 2014-05-02 16:58:43.434 UTC 86887b54-0c4b-485a-9110-f6257cbde1d7 2014-03-11 14:57:05.945 UTC 4fe9e39b-66cb-4c52-ae54-6ef679bdf8db 2014-03-20 13:32:59.530 UTC 7fa1d021-c166-4f12-abe3-eae08e6e8c38 2014-04-02 11:21:12.430 UTC 59dfee9a-e1a0-41f7-9773-76963f5e908d 2014-03-13 09:22:15.930 UTC 7ddc8203-6893-4a71-ba03-1a1946ef28e9 2014-03-03 14:35:41.955 UTC 1b106332-9480-492d-98b0-5b23b305ae79 2014-04-08 15:43:34.927 UTC ac6c0fcd-bc4f-43b1-9959-01b8d230a96b 2014-03-21 10:49:15.411 UTC ec5570e9-72eb-4bc9-9026-4bca5d5fd204 2014-03-03 14:58:47.797 UTC a6e6761f-003e-40e4-ab83-ffd1b28c2e54 2014-04-02 10:56:47.418 UTC 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b7956990-8189-4f16-bf37-da3363361e3e 2014-05-05 12:45:22.875 UTC 1407f28f-2b20-4a4b-987f-0e8a978fd069 2014-04-14 12:19:58.355 UTC 46682a5f-c527-4cc3-953f-119b95ab410b 2014-03-20 13:31:32.320 UTC 3cc77fb5-0a47-41f9-a05e-23928200198b 2014-05-05 09:23:41.703 UTC f1684085-3cd9-49b4-9aaa-b847711347d1 2014-03-11 14:26:16.783 UTC dd2a167b-7fdb-422c-b7b8-2df915bdb8f0 2014-04-09 08:26:57.666 UTC 117a64ff-4752-44a2-be39-2abb80498151 2014-04-15 14:51:48.399 UTC 4ba46cc2-bff3-489c-b7ef-bba9d59fde5b 2014-03-27 09:47:24.51 UTC 4c60a50a-bde4-47e3-b2de-54422aafd320 2014-04-02 08:37:52.284 UTC c75a45b3-f266-4a39-85d9-90cdfbedbe4f 2014-04-08 09:34:45.207 UTC 0ee66d3a-3174-4e42-a06e-a238013fb17a 2014-04-25 10:02:43.752 UTC eb045764-68c6-4da1-b138-769f29f1f807 2014-03-19 12:18:51.439 UTC 5b411999-5685-47eb-b8cd-49837b0d4621 2014-03-27 09:19:58.748 UTC ecf63282-d832-4834-8a96-37ea8ac8ee17 2014-02-25 13:46:14.324 UTC 80fa4879-53f3-4e2e-9fb6-54933f6d5fe9 2014-03-11 14:29:24.267 UTC 22186289-ff1c-40cb-a5ce-a70c27195d55 2014-03-12 10:32:56.6 UTC f5da0401-6671-4f45-8f65-539f0ad139d7 2014-03-18 11:42:45.964 UTC 706b149b-29b6-4996-9da7-177b4fc1cae3 2014-02-26 17:19:09.154 UTC 0d4e9666-c21d-4ec7-9f6f-365c94b95d4c 2014-03-17 12:33:48.483 UTC 79e34035-259d-4a70-be8d-4835b07d7c81 2014-03-19 13:21:15.504 UTC dbdc039a-a221-43bc-a79a-b24724697451 2014-04-11 11:20:16.786 UTC b1e747b9-ee6a-40df-976b-889971b45bc2 2014-03-13 13:53:42.245 UTC 4262b74b-76fd-4461-b272-65c92e28bbc6 2014-03-03 14:14:19.365 UTC 0e2f1dd1-2855-4bc4-8b5d-dd508515ed0e 2014-03-03 14:34:04.832 UTC 5d52eecf-5985-4d2f-8525-fa42dbfd5298 2014-04-09 08:30:05.398 UTC 512913cf-8077-4451-aeb4-4a60fe4e612a 2014-03-19 13:05:01.467 UTC 752fa5eb-11f0-440d-932a-9baf1837d14b 2014-05-05 13:44:57.506 UTC Concept Profile Generation Pipeline 2014-05-01 14:08:56.475 UTC ee306759-1dd0-4677-bba9-96e3b79caec5 2014-03-03 14:57:11.282 UTC f4ebe843-a6a9-4381-b58d-598f0b7cc5c7 2014-03-11 14:52:39.601 UTC 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e23ec56f-c04b-4b4d-b430-268bedd87c2b 2014-04-08 09:35:47.724 UTC 38d964d0-ea84-4a48-9ed1-1cf110296f70 2014-03-27 10:03:22.360 UTC 30d3b703-18a7-4ce5-86fc-f38688bed4ed 2014-04-14 09:04:55.429 UTC a499c334-d6c5-49da-a937-135c297dfd25 2014-04-10 08:40:12.395 UTC 95fb6bdb-5a34-40dd-8427-d19f6c73d4a7 2014-03-04 16:36:46.845 UTC 1ffc7cc7-bd8c-49e0-92ff-0ca02090bca3 2014-03-31 13:45:49.982 UTC 4792a9cb-3d7e-4327-8c8e-4e499b8f4f28 2014-03-11 15:47:23.615 UTC 7f57bf70-4232-4af9-82bd-c524120cf7fe 2014-03-20 10:27:13.607 UTC b4976a71-5ec3-4040-895b-bf43fc0f638b 2014-04-08 09:38:22.895 UTC 35a691e7-674a-4b89-9013-057c3234215d 2014-03-19 12:54:00.816 UTC 45bbc83c-373f-4d38-bd1e-e64484df169a 2014-03-27 15:06:36.53 UTC d09e054e-8c6d-440b-8c53-4359677d9812 2014-03-20 15:57:06.707 UTC 4f495cae-fb6b-4bea-9807-88c1313e8d99 2014-03-19 16:19:31.627 UTC 2297254e-6aa3-4a26-9de9-413ed0d2aedf 2014-04-02 08:28:40.49 UTC bdf4e519-633f-411f-a269-1ce906fd414a 2014-03-18 14:57:00.738 UTC b9d0d7ca-fce7-4395-b539-3f6e37bab3b9 2014-04-11 12:07:23.118 UTC d98af7c3-005b-4c4c-be87-3cedc55890d3 2014-03-19 16:15:51.545 UTC 4f2c074d-9996-401e-85a0-fc8b1dcae1de 2014-04-09 08:20:42.56 UTC f5cc091e-2cdc-4159-b1c1-5c739cd41729 2014-02-26 17:17:41.423 UTC f07d191d-1fc4-4eb9-b4c4-6d28c7825d52 2014-04-15 14:47:07.705 UTC 79a230ce-31d1-4ede-a0ff-7ac5d486a0b7 2014-04-16 12:36:13.922 UTC 8519bed0-083a-420b-a11d-ef125a3e5ce1 2014-03-18 12:19:43.782 UTC eed395e4-da87-432e-9a6f-1db669dd1c0c 2014-03-27 10:27:04.552 UTC e2a7cbd9-e97a-4502-bf56-8943ecb45c8d 2014-03-18 12:04:41.795 UTC f6d7a038-81e9-4342-b1d8-a06784a052df 2014-03-12 10:35:09.457 UTC db468038-5e51-4adf-88f9-1c2073d8d2d0 2014-04-14 08:57:21.101 UTC a15a8f83-fb3a-4539-8fec-b6f9cfbff092 2014-02-26 12:50:45.406 UTC 3e2684d1-5518-413a-83c4-656511321e7c 2014-03-18 12:15:32.494 UTC eae2daff-664b-403c-a280-fd0bf608c07e 2014-03-04 17:02:50.721 UTC c2951694-2c06-486d-a711-a3c4beb6f633 2014-03-11 15:23:08.145 UTC Amrish Mahes 2014-03-21 13:44:24.679 UTC 4e8f9e85-5679-43e6-a10e-aa7d94605033 2014-02-26 17:34:58.520 UTC 6f7b6d14-3b41-4cb7-a937-0004943c3fc3 2014-03-27 15:02:23.494 UTC 224d82d5-73dd-4dce-baea-8ad1341e9152 2014-04-11 12:18:58.687 UTC 23e95981-3e7f-4edb-b4a9-aa00b02970b3 2014-04-15 14:34:38.478 UTC 1aa12185-de42-4a9c-8170-ab9df6ac378c 2014-02-26 12:45:33.366 UTC cbe0804d-d7de-48c7-a6af-9ddb0eb53893 2014-03-21 09:12:56.192 UTC c1502973-37dc-4638-91af-273ffdbfe437 2014-03-18 10:53:53.672 UTC 25f25fb0-1bc1-4232-8e54-d8bf50c7090d 2014-05-05 11:55:23.646 UTC 4b83d89b-697d-441d-b7f3-7f78bdd220c7 2014-03-18 14:50:05.432 UTC e68175ef-8d96-4443-974b-2881c906cf8b 2014-02-26 17:22:17.505 UTC f99cff70-f2d7-490f-b750-1f2d137b22f9 2014-03-20 13:25:48.957 UTC ebf0578c-3add-4bb9-bf38-f34bba0f2934 2014-04-14 08:37:17.965 UTC 590c3455-9bfb-42e3-8c12-4852221d876a 2014-03-31 13:10:04.43 UTC 2f539e4b-879e-4d36-a60c-791a4e31e27e 2014-03-20 09:42:42.306 UTC eeaf9724-ad78-471c-9d76-bd14822bf8bc 2014-04-11 12:06:04.868 UTC 2b413fa4-b58e-4524-a6ce-ffbfee8f7f5f 2014-03-20 15:24:38.247 UTC 6011272e-139a-4102-b7a1-f8ee7164acdf 2014-04-11 12:10:20.841 UTC 5fddb0b2-585d-466c-a72a-00031f0cceef 2014-03-18 10:47:26.114 UTC a3ab3e68-d9ce-4f45-b180-2fd2351245fa 2014-04-10 09:02:19.105 UTC 308a57a4-127d-4ce1-a1d1-5bec7884c40f 2014-04-09 08:45:28.176 UTC 528650c7-af4e-4106-9e93-32ff0d747139 2014-03-03 16:01:16.452 UTC 2c47d2ca-e8e9-4772-814d-419a9692b619 2014-04-02 08:25:11.411 UTC cc2f757d-0765-4739-a73c-cb3725aade3b 2014-04-11 12:45:37.710 UTC 7b12bd1c-3cc5-45d9-af65-faaceeb2aa2b 2014-04-11 12:22:19.316 UTC 21293efa-08e5-4f9b-8476-69542bd4ed30 2014-02-26 17:25:02.958 UTC e13b5664-6be1-4bec-80b7-7b02c07aa434 2014-04-10 09:36:43.319 UTC 36893096-771e-4ccb-9ab0-02255dc8586c 2014-03-18 15:03:15.901 UTC 6b5b0fe0-7ad4-41fd-9f0c-759f9cf3443f 2014-04-11 11:28:29.860 UTC d90ba032-33eb-417e-b1e8-020c076dca6a 2014-03-19 12:40:54.240 UTC 1c33ffe7-d851-4dca-abf4-09dd5e77319d 2014-03-31 13:09:14.90 UTC ac19e98b-d3ef-416a-b3ed-f15bf0d38dd3 2014-03-19 12:59:20.910 UTC f7b5641b-c9a4-4a6b-9f0e-f76b56fcbe41 2014-04-10 09:19:31.47 UTC f9aec2a9-f5e0-4156-a71e-2bd418c35ce5 2014-04-25 11:11:59.636 UTC f2df5997-0b15-4f5c-a013-3a69d54a32d2 2014-02-26 15:55:33.594 UTC 4f53517b-d092-4c7e-af69-58cc424051d1 2014-03-12 09:58:16.101 UTC 6fd2842f-7586-4bf5-92fe-9ce66ecca5e8 2014-04-25 09:23:40.718 UTC 82892b23-b8fb-4a2b-a970-a42628155bba 2014-03-11 14:53:43.627 UTC 1ac80c1f-52ec-4482-8c55-9ea3d405258d 2014-03-27 09:55:03.583 UTC ef76bf9a-9917-4e3e-b87d-53ad76171c49 2014-03-20 13:39:38.887 UTC 0d04b4b8-261d-4c2a-8502-0000d540fe4d 2014-03-04 16:47:24.293 UTC b9041ca9-82f1-423e-8647-2f7fa6c5bc2c 2014-04-02 11:43:46.373 UTC ffeffe1d-e0d0-4c76-b83c-f10547b08cfc 2014-04-02 10:58:20.995 UTC 1a0b60bc-7790-4ab6-b952-560b357644d9 2014-03-04 16:08:15.186 UTC 98ebda84-158b-436c-9954-5adf6b6ee465 2014-03-20 14:03:04.635 UTC ed6dfbde-62dd-41fe-91d3-4166e154fc24 2014-03-17 13:07:25.393 UTC 639bdbdd-79b8-43ff-a3e8-4cdf9bd10d3b 2014-04-10 08:49:54.608 UTC 39de7cd9-af94-4837-b402-8ca5c0f8ec62 2014-03-03 16:32:49.300 UTC 6e3bd1f4-ce2e-4eab-987c-aff2b7df20be 2014-04-11 11:15:47.240 UTC e05d8961-a33e-4646-be69-3c64a2b675df 2014-03-03 12:55:48.706 UTC a8b056e3-6be4-4928-ade6-5f6a0c92fc4d 2014-03-10 13:47:55.727 UTC bc510c1b-3918-4a2e-ad6b-83fd94a3fdcd 2014-04-10 12:48:04.773 UTC 387103d2-fa7f-47d6-82b4-52901824cd9d 2014-03-03 15:04:24.531 UTC 172f16de-913f-4c36-9dd9-8f1976082e02 2014-03-27 15:00:44.396 UTC fa1a9637-8c02-41ec-a11f-dd3d324cd8ce 2014-03-21 12:24:04.746 UTC 44e24804-6ea6-4042-ab9a-c1107670580b 2014-04-09 12:05:18.51 UTC 37d0c11f-4290-441b-b2a6-892031d0fccf 2014-03-20 14:14:32.853 UTC e7c699d6-7dad-41a2-94f2-2d4e900467eb 2014-03-20 15:55:08.972 UTC 2d0294ee-3f2e-4e51-9851-75cf0a3fe1dc 2014-04-15 14:49:57.646 UTC 9caf9793-397e-413f-9a8e-e495428a9e74 2014-03-13 09:20:53.598 UTC daf54378-2467-490e-864a-dc9be079888e 2014-03-11 15:53:22.214 UTC aeb3b8fc-439c-4951-9232-aa96373e89c1 2014-04-10 08:53:00.1 UTC 3bb62ed0-53b6-409f-b20d-8076f6c6b652 2014-04-10 12:05:55.745 UTC c4946899-d88b-4915-8508-81bac2383c97 2014-02-26 12:57:51.737 UTC a8c98f38-e76b-480b-b905-be19c1533bc2 2014-04-14 12:46:02.401 UTC 286b188a-0da9-4555-a97d-73ab48014519 2014-04-10 12:09:41.147 UTC 9ea56195-696a-4806-99e8-3b04681039e0 2014-03-11 10:42:41.730 UTC 8cbbae64-7fff-4d96-aca0-f37c13057cca 2014-04-10 10:59:19.754 UTC b59275ba-3d95-4001-afb4-03b40cf5ac78 2014-03-20 13:21:01.681 UTC e3f89d60-193f-4c1d-a512-babb81d7f2b7 2014-03-20 13:17:02.613 UTC b5665198-250c-49ee-953a-43fa6d0e478c 2014-03-11 10:37:17.931 UTC 1f45e8aa-5a6f-4946-81cb-9ecb061bae3d 2014-03-11 15:26:57.870 UTC 4887afd4-b47f-4da9-923b-91e273d07551 2014-05-06 10:53:19.170 UTC 34035ec0-5395-4c6e-b313-33420000b5eb 2014-03-19 13:06:21.871 UTC 6bf66067-e2f9-41f4-bb67-afd72869d8fa 2014-03-20 14:09:31.707 UTC 5efeac9e-af11-4b80-b35d-a3bfbf0c23db 2014-03-19 13:12:22.521 UTC 71665e19-759b-423c-83b4-6c937dcd3739 2014-03-27 14:42:20.647 UTC 5ed05d10-6606-4eb6-a549-f0acd558a5e1 2014-03-12 16:27:46.614 UTC c06f69e2-0869-404e-af72-28e934d6d962 2014-03-18 15:20:03.706 UTC 034e2cfa-4acb-40db-91df-6e6a4a23521d 2014-03-19 12:32:40.153 UTC 8615d7dc-3eef-4f20-8b96-d335e0bed8aa 2014-05-01 14:08:56.741 UTC 249c0e7a-36c9-4465-987f-aafc55f748d2 2014-04-14 12:44:51.310 UTC b3225a8b-74d2-4e9b-9577-585b73e3b076 2014-04-09 08:34:09.963 UTC e40f76e8-4c2c-4aa5-a73b-2ef8ccafbc47 2014-04-15 14:11:27.302 UTC 64e699b4-3457-40a6-8f8e-6868c7685b12 2014-02-25 17:00:16.327 UTC 92551418-3894-4f7c-994d-6da5dc5993a4 2014-03-17 12:53:11.620 UTC 425a399d-2c99-4a8f-9d9e-4359af241dc5 2014-03-17 11:07:45.361 UTC c4a0c388-2f5b-4fcb-9d03-438319509d2f 2014-03-18 12:21:22.938 UTC 58d7b869-f24f-4b54-97cf-7857c67050d3 2014-05-01 14:35:03.444 UTC 53713f1b-e31d-412f-8cd5-d5b16c7ad8f3 2014-02-26 13:25:52.272 UTC 750e214e-95e5-47d7-8a16-b5215fa651f5 2014-03-21 10:18:23.575 UTC 2ad0a457-b237-4118-87b0-e9bf3a828044 2014-03-27 09:50:52.100 UTC 168c50b9-63fa-4fcd-87cb-a578cbc40aaa 2014-04-10 08:45:06.341 UTC 2b2697b5-c1b9-4e7a-96c3-21bcc936ce38 2014-03-03 15:12:59.225 UTC cc2b43bd-3940-469b-853c-25be708c5f29 2014-03-20 15:26:40.631 UTC cdbaad4b-972d-4356-9fe6-233ccc65d6ff 2014-03-18 15:00:23.263 UTC CREATE Inner Product Tabletimestamp00password00driver00userid00url00Beanshell_generate_SQL_table_inner_producttimestamp0out100net.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_Update_CREATE_TABLE_Inner_Productsql0password0driver0userid0url0net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity driver 0 text/plain java.lang.String true password 0 text/plain java.lang.String true userid 0 text/plain java.lang.String true url 0 text/plain java.lang.String true sql 0 text/plain java.lang.String true params 1 text/plain java.lang.String true resultList 0 text/plain 0 workflow net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker 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_table_inner_producttimestamptimestampExecute_SQL_Update_CREATE_TABLE_Inner_ProductsqlBeanshell_generate_SQL_table_inner_productout1Execute_SQL_Update_CREATE_TABLE_Inner_ProductpasswordpasswordExecute_SQL_Update_CREATE_TABLE_Inner_ProductdriverdriverExecute_SQL_Update_CREATE_TABLE_Inner_ProductuseriduseridExecute_SQL_Update_CREATE_TABLE_Inner_Producturlurl df98b1a9-ac72-4798-a461-b8bd7862075b 2014-04-25 09:23:33.878 UTC CREATE Inner Product Table 2014-04-25 09:23:28.207 UTC Calculate Inner Producttimestamp00concept_pairs11password00 Input your sql password to acces as root. 2014-05-05 13:48:54.350 UTC driver00 The driver needed for all SQL query to run. 2014-05-05 13:48:07.235 UTC com.mysql.jdbc.Driver 2014-05-05 13:48:16.486 UTC userid00 The user ID which is in this case root. 2014-05-05 13:48:29.480 UTC root 2014-05-05 13:48:33.85 UTC url00 jdbc:mysql://localhost:3306/mydb 2014-05-05 13:47:51.276 UTC The url value Sql connects to. 2014-05-05 13:47:38.422 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. Deze waardes worden gemultipliceerd en opgeteld. 2014-05-05 14:34:34.745 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_Productsql0password0driver0userid0url0resultList22net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity driver 0 text/plain java.lang.String true password 0 text/plain java.lang.String true userid 0 text/plain java.lang.String true url 0 text/plain java.lang.String true provideXml 0 text/plain java.lang.String true sql 0 text/plain java.lang.String true params 1 text/plain java.lang.String true resultList 2 text/plain 2 xmlresults 0 text/plain 0 workflow net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker 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_tablesql0driver0url0userid0password0resultList00net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity driver 0 text/plain java.lang.String true password 0 text/plain java.lang.String true userid 0 text/plain java.lang.String true url 0 text/plain java.lang.String true sql 0 text/plain java.lang.String true params 1 text/plain java.lang.String true resultList 0 text/plain 0 workflow net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker 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_ProductpasswordpasswordExecute_SQL_Query_Get_Inner_ProductdriverdriverExecute_SQL_Query_Get_Inner_ProductuseriduseridExecute_SQL_Query_Get_Inner_ProducturlurlExecute_SQL_Update_INSERT_INTO_Inner_Product_tablesqlBeanshell_SQL_generate_INSERT_INTO_Inner_Product_tableout1Execute_SQL_Update_INSERT_INTO_Inner_Product_tabledriverdriverExecute_SQL_Update_INSERT_INTO_Inner_Product_tableurlurlExecute_SQL_Update_INSERT_INTO_Inner_Product_tableuseriduseridExecute_SQL_Update_INSERT_INTO_Inner_Product_tablepasswordpasswordFlatten_List_4inputlistExecute_SQL_Query_Get_Inner_ProductresultListFlatten_List_5inputlistFlatten_List_4outputlistoutputExecute_SQL_Update_INSERT_INTO_Inner_Product_tableresultList 33db0c4f-7076-4cbd-9913-57f2bcaad402 2014-04-25 09:06:56.615 UTC Calculate Inner Product 2014-04-25 09:00:49.797 UTC bde675e9-64ec-49a0-b079-cbe4ae8e7f13 2014-05-05 14:33:52.891 UTC 348801cf-d2ad-43fc-9b91-ab63e359fdcc 2014-04-25 09:07:18.526 UTC Amrish Mahes 2014-05-05 13:59:12.828 UTC ad11b9f4-2a6c-417c-a99a-53391e22ae59 2014-04-25 09:54:33.677 UTC ab9d319b-bbd6-4012-9c18-26c62114c2a1 2014-04-25 11:11:47.249 UTC e9c85439-4022-4bf3-9d93-77f70e4cd5fa 2014-04-25 09:55:56.310 UTC 807d1911-1342-4922-b766-69bbcab70c68 2014-05-05 14:34:36.368 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 password00 Input your sql password to acces as root. 2014-05-01 14:19:59.349 UTC driver00 com.mysql.jdbc.Driver 2014-05-01 13:26:43.363 UTC The driver needed for all SQL query to run. 2014-05-01 14:20:14.715 UTC userid00 root 2014-05-01 13:26:48.667 UTC The user ID which is in this case root. 2014-05-01 14:20:31.500 UTC url00 jdbc:mysql://localhost:3306/mydb 2014-05-01 13:27:16.279 UTC The url value Sql connects to. 2014-05-01 14:21:45.710 UTC Input22 2014-05-01 14:21:52.278 UTC 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 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 outputBeanshell_SQL_query_generator_Concept_Doc_occurencetable_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_put_correct_doc_uri_in_con_occ_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_occurence_tablepassword0driver0userid0url0sql0resultList00 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 driver 0 text/plain java.lang.String true password 0 text/plain java.lang.String true userid 0 text/plain java.lang.String true url 0 text/plain java.lang.String true sql 0 text/plain java.lang.String true params 1 text/plain java.lang.String true resultList 0 0 workflow mysql-connector-java-5.1.28-bin.jar net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker UserNameHere 2014-03-18 10:21:46.580 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.InvokeIndexer_toolontology0abstract_content1concept_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: Go to Location tab select radiobutton "Select an explicit location" and default local then save settings by clicking apply. 2014-04-11 13:51:08.181 UTC net.sf.taverna.t2.activitiesexternal-tool-activity1.4net.sf.taverna.t2.activities.externaltool.ExternalToolActivity 789663B8-DA91-428A-9F7D-B3F3DA185FD4 default local_12 <?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=F:/School/Stage2/peregrine/production.properties -jar F:/School/Stage2/peregrine/peregrine-skos-cli.jar ontology abstract_content concept_per_document 1200 1800 abstract_content abstract_content true false false windows-1252 false true 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_occurencetable_nametable_nameBeanshell_SQL_query_generator_Concept_Doc_occurenceconcept_occurence_documentBeanshell_remove_dot_and_put_correct_doc_uri_in_con_occ_docout1Beanshell_extract_uri_doc_and_abstractInputInputBeanshell_remove_dot_and_put_correct_doc_uri_in_con_occ_docdoc_uriBeanshell_extract_uri_doc_and_abstractdoc_uriBeanshell_remove_dot_and_put_correct_doc_uri_in_con_occ_docconcept_occurence_documentSplit_string_into_string_list_by_regular_expressionsplitExecute_SQL_Update_INSERT_INTO_occurence_tablepasswordpasswordExecute_SQL_Update_INSERT_INTO_occurence_tabledriverdriverExecute_SQL_Update_INSERT_INTO_occurence_tableuseriduseridExecute_SQL_Update_INSERT_INTO_occurence_tableurlurlExecute_SQL_Update_INSERT_INTO_occurence_tablesqlBeanshell_SQL_query_generator_Concept_Doc_occurenceout1Indexer_toolontologyontologyIndexer_toolabstract_contentBeanshell_extract_uri_doc_and_abstractabstractsSplit_string_into_string_list_by_regular_expressionstringIndexer_toolconcept_per_documentSplit_string_into_string_list_by_regular_expressionregexregex_valuevalueoutputExecute_SQL_Update_INSERT_INTO_occurence_tableresultList Peregrine indexer 2014-04-25 08:41:57.947 UTC 87fe3bfb-dcd3-4cf3-bca5-a4ddcf8d3b32 2014-05-05 09:43:02.878 UTC 7d302e8e-e49f-46c2-9620-cbc9a8acd7c3 2014-05-01 13:38:12.169 UTC 2c3c56e4-87ff-48c8-a895-54c7eabeca9f 2014-05-01 14:29:30.621 UTC ef75149c-93d4-4a53-938d-598b34c547c0 2014-04-25 08:43:19.286 UTC 8054095d-ff1d-434d-8db7-73e0d92521ab 2014-05-01 14:56:49.352 UTC 58b4fc1a-33f4-45d0-8a33-f87356cc96e1 2014-04-25 08:42:29.100 UTC Amrish Mahes 2014-05-01 14:47:30.600 UTC 68bfb5a4-5361-40f7-b1e8-e9d2285f985d 2014-05-01 13:36:50.25 UTC fe4de177-331a-46bc-919c-0b60de007289 2014-05-01 13:29:11.726 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 7a8e521a-ce70-464f-b5be-b38496ea9a7a 2014-05-02 15:03:12.106 UTC e13584ce-2e64-4486-8ae5-e6e2c08f20d5 2014-05-01 14:22:50.934 UTC CREATE UC Tabletime_stamp00password00driver00userid00url00Beanshell_SQL_generate_table_UCtime_stamp0output00 A Beanshell script that generates a table for the uncertainty coefficient values. 2014-04-11 13:58:36.737 UTC net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity time_stamp 0 text/plain java.lang.String true output 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_CREATE_TABLE_UCsql0password0driver0userid0url0net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity driver 0 text/plain java.lang.String true password 0 text/plain java.lang.String true userid 0 text/plain java.lang.String true url 0 text/plain java.lang.String true sql 0 text/plain java.lang.String true params 1 text/plain java.lang.String true resultList 0 0 workflow mysql-connector-java-5.1.28-bin.jar net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker UserNameHere 2014-04-02 10:56:24.103 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_table_UCtime_stamptime_stampExecute_SQL_Update_CREATE_TABLE_UCsqlBeanshell_SQL_generate_table_UCoutputExecute_SQL_Update_CREATE_TABLE_UCpasswordpasswordExecute_SQL_Update_CREATE_TABLE_UCdriverdriverExecute_SQL_Update_CREATE_TABLE_UCuseriduseridExecute_SQL_Update_CREATE_TABLE_UCurlurl c0014817-f92d-4042-ad3a-590bfa66298c 2014-04-25 09:23:33.815 UTC CREATE UC Table 2014-04-25 09:22:42.93 UTC CREATE Co-occurence Tabletimestamp00password00driver00userid00url00Beanshell_SQL_create_table_co_occurencetimestamp0out100net.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_Update_CREATE_TABLE_Co_Occurencesql0password0driver0userid0url0net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity driver 0 text/plain java.lang.String true password 0 text/plain java.lang.String true userid 0 text/plain java.lang.String true url 0 text/plain java.lang.String true sql 0 text/plain java.lang.String true params 1 text/plain java.lang.String true resultList 0 text/plain 0 workflow net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker 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_table_co_occurencetimestamptimestampExecute_SQL_Update_CREATE_TABLE_Co_OccurencesqlBeanshell_SQL_create_table_co_occurenceout1Execute_SQL_Update_CREATE_TABLE_Co_OccurencepasswordpasswordExecute_SQL_Update_CREATE_TABLE_Co_OccurencedriverdriverExecute_SQL_Update_CREATE_TABLE_Co_OccurenceuseriduseridExecute_SQL_Update_CREATE_TABLE_Co_Occurenceurlurl 23363d61-3e85-4adb-83e6-28ded507e083 2014-04-25 09:23:33.831 UTC CREATE Co-occurence Table 2014-04-25 09:22:23.124 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 [ [ 0,3,3,7 ],[1,2,2,4] ]. For a complete example please download the file input_contingency_values_for_calculate_UC_workflow from myexperiment. 2014-05-05 13:43:11.517 UTC timestamp00 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 password00 Input your sql password to acces as root. 2014-05-05 12:48:23.634 UTC driver00 com.mysql.jdbc.Driver 2014-05-05 12:47:57.473 UTC The driver needed for all SQL query to run. 2014-05-05 12:48:08.627 UTC userid00 The user ID which is in this case root. 2014-05-05 12:47:43.418 UTC root 2014-05-05 12:47:30.173 UTC url00 The url value Sql connects to. 2014-05-05 12:47:27.381 UTC jdbc:mysql://localhost:3306/mydb 2014-05-05 12:47:13.403 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 the script of Herman van Haagen. 2014-05-05 12:53:25.613 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_tablepassword0sql0driver0userid0url0resultList00net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity driver 0 text/plain java.lang.String true password 0 text/plain java.lang.String true userid 0 text/plain java.lang.String true url 0 text/plain java.lang.String true sql 0 text/plain java.lang.String true params 1 text/plain java.lang.String true resultList 0 0 workflow mysql-connector-java-5.1.28-bin.jar net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker UserNameHere 2014-04-02 11:18:53.21 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_tablepasswordpasswordExecute_SQL_Update_INSERT_INTO_UC_tablesqlBeanshell_SQL_INSERT_UC_values_INTO_tableoutput_SQLExecute_SQL_Update_INSERT_INTO_UC_tabledriverdriverExecute_SQL_Update_INSERT_INTO_UC_tableuseriduseridExecute_SQL_Update_INSERT_INTO_UC_tableurlurloutputExecute_SQL_Update_INSERT_INTO_UC_tableresultList Amrish Mahes 2014-05-05 13:43:58.257 UTC 2e19c3f7-489e-4f69-a4b7-744d4f046fe4 2014-05-05 13:14:30.664 UTC 46d45a69-6c44-4185-84a4-119f054a16f8 2014-05-05 13:29:23.342 UTC Calculate Uncertainty Coefficient 2014-04-25 08:57:47.839 UTC 2ebf0b6a-071d-46f6-b793-2dde8cb9d22f 2014-05-05 13:43:59.598 UTC 1157056b-06f9-4caf-b68f-635230a545c4 2014-04-25 09:07:59.975 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 0cdc32e9-e9b0-4221-b53c-a65cd3db8f90 2014-05-05 13:17:31.804 UTC eb63e5b4-4ec9-4e70-932c-c22fe8ac8c3b 2014-05-05 13:43:43.341 UTC 8f04d577-c676-46ea-b867-d849e7af0e6d 2014-05-05 12:49:30.628 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 000df03c-2c75-49ee-b7e9-25dd34d507fa 2014-05-05 13:42:48.991 UTC Calculate_Contingencpassword00 Input your sql password to acces as root. 2014-05-02 16:33:41.921 UTC driver00 The driver needed for all SQL query to run. 2014-05-02 16:34:02.498 UTC com.mysql.jdbc.Driver 2014-05-02 16:28:36.675 UTC userid00 root 2014-05-02 16:28:44.89 UTC The user ID which is in this case root. 2014-05-02 16:34:26.972 UTC url00 The url value Sql connects to. 2014-05-05 09:27:15.843 UTC jdbc:mysql://localhost:3306/mydb 2014-05-02 16:28:19.761 UTC table_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 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 and neither concepts occur in literature. The output of only concept A and only concept B needs to be corrected. This is done in the Beanshell script called: "Beanshell_correct_contincengy_table". Because the output of those two values were with the co-occurence. This needed to be subtracted. 2014-05-05 11:54:02.11 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_occurence_tablecontingency_values1concept_pairs0timestamp0out100 A Beanshell script that generates SQL statement to insert into the co-occurence table the amount two given concepts co-occur together in literature. 2014-04-14 10:59:59.235 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_contincengy_tablecontingency_values1corrected_contingency_values11 A Beanshell script that corrects the output SQL retrieved contincengy table by subtracting the co-occurence values of the concept only a and of concept only b value. 2014-05-05 11:55:07.905 UTC net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity contingency_values 1 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_destinct_concepttable_name0out100 A Beanshell script that retrieves every concept from the Sql table TableName_occurence. 2014-05-02 15:13:56.544 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_Querysql0password0driver0url0userid0resultList22 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 driver 0 text/plain java.lang.String true password 0 text/plain java.lang.String true userid 0 text/plain java.lang.String true url 0 text/plain java.lang.String true provideXml 0 text/plain java.lang.String true sql 0 text/plain java.lang.String true params 1 text/plain java.lang.String true resultList 2 2 xmlresults 0 0 workflow mysql-connector-java-5.1.28-bin.jar net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker UserNameHere 2014-03-27 15:02:07.658 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_2sql0password0driver0url0userid0resultList22 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 driver 0 text/plain java.lang.String true password 0 text/plain java.lang.String true userid 0 text/plain java.lang.String true url 0 text/plain java.lang.String true provideXml 0 text/plain java.lang.String true sql 0 text/plain java.lang.String true params 1 text/plain java.lang.String true resultList 2 2 xmlresults 0 0 workflow mysql-connector-java-5.1.28-bin.jar net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker UserNameHere 2014-04-02 11:05:14.242 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_occurence_tablesql0password0driver0userid0url0net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity driver 0 text/plain java.lang.String true password 0 text/plain java.lang.String true userid 0 text/plain java.lang.String true url 0 text/plain java.lang.String true sql 0 text/plain java.lang.String true params 1 text/plain java.lang.String true resultList 0 text/plain 0 workflow net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker 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_generate_contingency_tableconcept_pairsFlatten_List_2outputlistBeanshell_SQL_generate_contingency_tabletable_nametable_nameBeanshell_SQL_insert_into_co_occurence_tablecontingency_valuesFlatten_List_3outputlistBeanshell_SQL_insert_into_co_occurence_tableconcept_pairsFlatten_List_2outputlistBeanshell_SQL_insert_into_co_occurence_tabletimestamptable_nameBeanshell_correct_contincengy_tablecontingency_valuesFlatten_List_3outputlistBeanshell_generate_SQL_statement_Get_destinct_concepttable_nametable_nameBeanshell_make_concept_pairsconcept_AFlatten_ListoutputlistBeanshell_make_concept_pairsconcept_BFlatten_ListoutputlistExecute_SQL_QuerysqlBeanshell_generate_SQL_statement_Get_destinct_conceptout1Execute_SQL_QuerypasswordpasswordExecute_SQL_QuerydriverdriverExecute_SQL_QueryurlurlExecute_SQL_QueryuseriduseridExecute_SQL_Query_2sqlBeanshell_SQL_generate_contingency_tableout1Execute_SQL_Query_2passwordpasswordExecute_SQL_Query_2driverdriverExecute_SQL_Query_2urlurlExecute_SQL_Query_2useriduseridExecute_SQL_Update_INSERT_INTO_Co_occurence_tablesqlBeanshell_SQL_insert_into_co_occurence_tableout1Execute_SQL_Update_INSERT_INTO_Co_occurence_tablepasswordpasswordExecute_SQL_Update_INSERT_INTO_Co_occurence_tabledriverdriverExecute_SQL_Update_INSERT_INTO_Co_occurence_tableuseriduseridExecute_SQL_Update_INSERT_INTO_Co_occurence_tableurlurlFlatten_ListinputlistExecute_SQL_QueryresultListFlatten_List_2inputlistBeanshell_make_concept_pairsconcept_pairFlatten_List_3inputlistExecute_SQL_Query_2resultListoutputlistFlatten_List_2outputlistcorrected_contingency_valuesBeanshell_correct_contincengy_tablecorrected_contingency_values 9db66f08-1aa9-4b76-8592-a90c3e1710c5 2014-05-05 09:41:53.767 UTC 6a1ccba3-c527-47ce-9a4c-a57634881a7c 2014-05-02 15:57:55.741 UTC 31647e87-e8a1-4409-8f3d-6802cc2596ba 2014-05-06 09:26:28.104 UTC 94065ddd-d3e1-4e39-b7ee-31d8079d4553 2014-05-05 11:54:11.870 UTC bf203a6d-fa48-4f35-ad40-cff4913b6868 2014-05-05 11:55:10.214 UTC 3da9a958-ebc0-4193-83cd-29a45c70a1fd 2014-05-02 16:40:17.937 UTC 9ac9ac33-565a-4f05-9353-57e6fcd510b8 2014-05-05 11:39:00.253 UTC 2eae8fad-b196-4141-ad91-e4c079e4205f 2014-05-02 16:58:36.311 UTC 68c46c7a-4dee-44de-8819-dc7701124973 2014-05-05 09:37:41.543 UTC bd93275c-7f78-4fe3-98ca-c4efd3cbdfbc 2014-04-25 10:05:58.574 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 711f5d11-bc72-4e31-8716-4dad288862f0 2014-04-25 09:08:01.83 UTC Calculate Contingency table 2014-05-05 13:44:48.426 UTC 9b8d4323-3e99-4fa3-bfbf-812acf73d615 2014-05-02 15:40:47.612 UTC bb618d97-2857-4d79-84e8-e20543f38116 2014-05-05 11:54:00.498 UTC e529c545-ce7c-41a3-a337-91137d5cb2a0 2014-05-02 16:35:22.526 UTC Amrish Mahes 2014-05-02 15:42:14.33 UTC 942f3272-b926-4fe6-bf15-b4e29e44fb8f 2014-05-05 09:44:20.269 UTC 0a6042a5-4d83-41ea-b2ae-3cefafb4265a 2014-05-05 11:22:16.615 UTC d1b17379-8eac-4dcd-a5b6-9754f99b0c94 2014-05-05 13:44:50.330 UTC 9f2b6abe-3efc-4dee-8b84-2e0d876278ca 2014-04-25 10:02:35.250 UTC CREATE Occurence TabletimeStamp00password00driver00userid00url00Beanshell_generate_SQL_occurence_concept_doc_tabletimeStamp0Table_sql00 A Beanshell script which generates a sql statement to CREATE a TABLE. TABLE name is the input of the timestamp. The table consists out of 4 columns: concept_occ_doc_id, concept_uri, occurence_uri and doc_uri. Where as concept_occ_doc_id is the PRIMARY KEY and AUTOINCREMENTED. Every other column has a VARCHAR(200) 2014-03-21 13:29:30.395 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_Update_CREATE_TABLE_Occurencepassword0driver0userid0url0sql0net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity driver 0 text/plain java.lang.String true password 0 text/plain java.lang.String true userid 0 text/plain java.lang.String true url 0 text/plain java.lang.String true sql 0 text/plain java.lang.String true params 1 text/plain java.lang.String true resultList 0 0 workflow mysql-connector-java-5.1.28-bin.jar net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker UserNameHere 2014-03-18 14:43:00.534 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_generate_SQL_occurence_concept_doc_tabletimeStamptimeStampExecute_SQL_Update_CREATE_TABLE_OccurencepasswordpasswordExecute_SQL_Update_CREATE_TABLE_OccurencedriverdriverExecute_SQL_Update_CREATE_TABLE_OccurenceuseriduseridExecute_SQL_Update_CREATE_TABLE_OccurenceurlurlExecute_SQL_Update_CREATE_TABLE_OccurencesqlBeanshell_generate_SQL_occurence_concept_doc_tableTable_sql CREATE Occurence Table 2014-04-25 09:23:04.230 UTC 0a2d11bc-f65f-4eab-ab63-73ab7988a148 2014-04-25 09:23:33.862 UTC Create Tablespassword00driver00userid00url00timeStampBeanshell_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.InvokeCREATE Big Tabletimestamp0password0driver0userid0url0net.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 Co-occurence Tabletimestamp0password0driver0userid0url0net.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 UC Tableurl0userid0driver0password0time_stamp0net.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 Occurence TabletimeStamp0password0driver0userid0url0net.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 Inner Product Tabletimestamp0password0driver0userid0url0net.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 Big TabletimestampBeanshell_get_timestamptimeStampCREATE Big TablepasswordpasswordCREATE Big TabledriverdriverCREATE Big TableuseriduseridCREATE Big TableurlurlCREATE Co-occurence TabletimestampBeanshell_get_timestamptimeStampCREATE Co-occurence TablepasswordpasswordCREATE Co-occurence TabledriverdriverCREATE Co-occurence TableuseriduseridCREATE Co-occurence TableurlurlCREATE UC TableurlurlCREATE UC TableuseriduseridCREATE UC TabledriverdriverCREATE UC TablepasswordpasswordCREATE UC Tabletime_stampBeanshell_get_timestamptimeStampCREATE Occurence TabletimeStampBeanshell_get_timestamptimeStampCREATE Occurence TablepasswordpasswordCREATE Occurence TabledriverdriverCREATE Occurence TableuseriduseridCREATE Occurence TableurlurlCREATE Inner Product TabletimestampBeanshell_get_timestamptimeStampCREATE Inner Product TablepasswordpasswordCREATE Inner Product TabledriverdriverCREATE Inner Product TableuseriduseridCREATE Inner Product TableurlurltimeStampBeanshell_get_timestamptimeStamp 86079042-0398-4522-b766-79a51a2061b6 2014-04-25 09:34:08.496 UTC 071ca1ba-e357-4fd3-8943-c544199f9dd0 2014-04-25 09:23:33.706 UTC 0a15b5d5-9ad4-4394-a44b-a773c3cfbc60 2014-04-25 09:30:39.667 UTC e9e4a3b8-0c6a-469a-aec7-11e0dbe2514b 2014-04-25 09:08:00.69 UTC f3183def-03f7-46b5-a971-9b5ca2eb1ad3 2014-04-25 09:32:55.418 UTC 39bb73a3-e51b-42da-8706-944c99ff6ef2 2014-04-25 09:31:36.342 UTC Create Tables 2014-04-25 09:03:12.547 UTC CREATE Big Tabletimestamp00driver00password00userid00url00Beanshell_SQL_CREATE_last_big_tabletimestamp0out100net.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_Update_CREATE_TABLE_big_datasql0driver0password0userid0url0net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity driver 0 text/plain java.lang.String true password 0 text/plain java.lang.String true userid 0 text/plain java.lang.String true url 0 text/plain java.lang.String true sql 0 text/plain java.lang.String true params 1 text/plain java.lang.String true resultList 0 text/plain 0 workflow net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker 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_last_big_tabletimestamptimestampExecute_SQL_Update_CREATE_TABLE_big_datasqlBeanshell_SQL_CREATE_last_big_tableout1Execute_SQL_Update_CREATE_TABLE_big_datadriverdriverExecute_SQL_Update_CREATE_TABLE_big_datapasswordpasswordExecute_SQL_Update_CREATE_TABLE_big_datauseriduseridExecute_SQL_Update_CREATE_TABLE_big_dataurlurl CREATE Big Table 2014-04-25 09:21:46.261 UTC d1a4f89b-a497-4f54-8ab1-a5075aeeb403 2014-04-25 09:23:33.784 UTC Summarize Big Tabletimestamp00password00driver00userid00url00resultListBeanshell_SQL_Generate_INSERT_INTO_big_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_big_tablesql0password0driver0userid0url0resultList22net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity driver 0 text/plain java.lang.String true password 0 text/plain java.lang.String true userid 0 text/plain java.lang.String true url 0 text/plain java.lang.String true provideXml 0 text/plain java.lang.String true sql 0 text/plain java.lang.String true params 1 text/plain java.lang.String true resultList 2 text/plain 2 xmlresults 0 text/plain 0 workflow net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker 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_big_tablesql0driver0password0userid0url0resultList00net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity driver 0 text/plain java.lang.String true password 0 text/plain java.lang.String true userid 0 text/plain java.lang.String true url 0 text/plain java.lang.String true sql 0 text/plain java.lang.String true params 1 text/plain java.lang.String true resultList 0 text/plain 0 workflow net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker 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_big_tablein1Execute_SQL_Query_Get_data_for_big_tableresultListBeanshell_SQL_Generate_INSERT_INTO_big_tabletimestamptimestampBeanshell_SQL_statement_get_last_table_data_inputtimestamptimestampExecute_SQL_Query_Get_data_for_big_tablesqlBeanshell_SQL_statement_get_last_table_data_inputout1Execute_SQL_Query_Get_data_for_big_tablepasswordpasswordExecute_SQL_Query_Get_data_for_big_tabledriverdriverExecute_SQL_Query_Get_data_for_big_tableuseriduseridExecute_SQL_Query_Get_data_for_big_tableurlurlExecute_SQL_Update_INSERT_INTO_big_tablesqlBeanshell_SQL_Generate_INSERT_INTO_big_tableout1Execute_SQL_Update_INSERT_INTO_big_tabledriverdriverExecute_SQL_Update_INSERT_INTO_big_tablepasswordpasswordExecute_SQL_Update_INSERT_INTO_big_tableuseriduseridExecute_SQL_Update_INSERT_INTO_big_tableurlurlresultListExecute_SQL_Update_INSERT_INTO_big_tableresultList 4b65159f-b6b4-4457-b9db-59672f7c2c7d 2014-04-25 10:24:37.597 UTC e59e5168-be6b-4bb5-8d34-cd386cbfda7d 2014-04-25 09:53:26.34 UTC 6137cf86-1e2e-42ba-aef2-1a0adb9fbbd0 2014-04-25 09:07:59.8 UTC Summarize Big Table 2014-04-25 09:06:31.655 UTC