_CPGP_Peregrine_Get_Ontology_input00 A Skos formated dictionary/thesaurus of predefined concepts. 2014-04-11 13:48:01.261 UTC @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . @prefix skos: <http://www.w3.org/2004/02/skos/core#> . @prefix dct: <http://purl.org/dc/terms/> . @prefix emco: <http://rdf.biosemantics.org/emco/> . @prefix emco15: <http://rdf.biosemantics.org/emco/v1.5/> . @prefix concepts: <http://rdf.biosemantics.org/emco/v1.5/concepts/> . @prefix prop: <http://rdf.biosemantics.org/emco/properties/> . @prefix datatype: <http://rdf.biosemantics.org/emco/datatypes/> . @prefix semtype: <http://rdf.biosemantics.org/emco/semtypes/> . @prefix vocab: <http://rdf.biosemantics.org/emco/v1.5/vocabularies/> . prop:prefLabel_CI rdfs:subPropertyOf skos:prefLabel . prop:prefLabel_NO rdfs:subPropertyOf skos:prefLabel . prop:prefLabel_CI_NO rdfs:subPropertyOf skos:prefLabel . prop:altLabel_CI rdfs:subPropertyOf skos:altLabel . prop:altLabel_NO rdfs:subPropertyOf skos:altLabel . prop:altLabel_CI_NO rdfs:subPropertyOf skos:altLabel . vocab:default rdfs:comment "ErasmusMC ontology file" ; dct:title "Anni2_1_June2009" ; a skos:ConceptScheme . vocab:MSH dct:title "MeSH" ; a skos:ConceptScheme . vocab:SNOMEDCT dct:title "SNOMED Clinical Terms" ; a skos:ConceptScheme . semtype:T47 skos:topConceptOf vocab:default ; rdfs:label "Disease or Syndrome" ; skos:definition "A condition which alters or interferes with a normal process, state, or activity of an organism. It is usually characterized by the abnormal functioning of one or more of the host's systems, parts, or organs. Included here is a complex of symptoms descriptive of a disorder." ; a skos:Concept . concepts:C9187 skos:inScheme vocab:default ; prop:altLabel_CI_NO "Coccidiosis"@es ; prop:prefLabel_CI_NO "Coccidiosis" ; skos:notation "C0009187"^^datatype:umls-notation-datatype ; rdfs:label "Coccidiosis" ; skos:definition "Protozoan infection found in animals and man. It is caused by several different genera of COCCIDIA." ; skos:broader semtype:T47 ; a skos:Concept ; skos:inScheme vocab:MSH , vocab:SNOMEDCT . concepts:C24530 skos:inScheme vocab:default ; prop:altLabel_CI_NO "Malaria NOS" , "Plasmodium Infections" , "Remittent Fever" , "Paludism" , "Plasmodiosis" , "Malarial fever" , "Malaria (disorder)" , "Marsh Fever" , "Malaria"@es ; prop:prefLabel_CI "Malaria" ; skos:notation "C0024530"^^datatype:umls-notation-datatype ; rdfs:label "test" ; skos:broader concepts:C9187 , semtype:T47 ; a skos:Concept ; skos:inScheme vocab:MSH , vocab:SNOMEDCT . concepts:C3031092 skos:inScheme vocab:default ; prop:altLabel_NO "myelocytomatosis viral oncogene homolog (avian)" , "myelocytomatosis oncogene" , "Transcription factor p64" , "Myc proto-oncogene protein" , "v-myc myelocytomatosis viral oncogene homolog (avian)" , "Myc2" , "myc proto-oncogene protein" , "Transcription factor p-64" , "Myc-2" ; skos:notation "120208"^^datatype:gd-notation-datatype , "3130"^^datatype:gd-notation-datatype , "31092"^^datatype:ho-notation-datatype , "NM"^^datatype:rq-notation-datatype , "17869"^^datatype:eg-notation-datatype , "24577"^^datatype:eg-notation-datatype , "4609"^^datatype:eg-notation-datatype , "3130"^^datatype:rgd-notation-datatype , "190080"^^datatype:om-notation-datatype , "7553"^^datatype:hg-notation-datatype , "P01106"^^datatype:sp-notation-datatype , "P01108"^^datatype:sp-notation-datatype , "P09416"^^datatype:sp-notation-datatype , "Q6WDF7"^^datatype:sp-notation-datatype , "Hs.202453"^^datatype:ug-notation-datatype , "97250"^^datatype:mgi-notation-datatype , "1368308"^^datatype:af-notation-datatype , "1424942"^^datatype:af-notation-datatype , "202431"^^datatype:af-notation-datatype , "239931"^^datatype:af-notation-datatype ; rdfs:label "MYC" ; skos:prefLabel "MYC" , "C-MYC" , "Myc" , "Niard" , "Nird" , "c-Myc" , "c-myc" , "Myc-II" ; skos:broader semtype:T116 ; a skos:Concept ; skos:inScheme vocab:GENE , vocab:HOMOLOGENE . concepts:C3003921 skos:inScheme vocab:default ; prop:altLabel_NO "v-myc myelocytomatosis viral oncogene homolog 1, lung carcinoma derived (avian)" , "oncogene lmyc" , "l-myc-1 proto-oncogene" , "Lmyc1" , "myc-related gene from lung cancer" , "Oncogene MYC, lung carcinoma-derived" , "l-myc protein" , "Lmyc-1" , "Mycl1" , "L-myc-1 proto-oncogene protein" , "v-myc myelocytomatosis viral oncogene homolog 1, lung carcinoma derived (avian) (mapped)" , "v-myc avian myelocytomatosis viral oncogene homolog 1, lung carcinoma derived" , "MYCL-1" , "Mycl-1" ; prop:prefLabel_NO "MYCL1" ; skos:notation "120706"^^datatype:gd-notation-datatype , "1588591"^^datatype:gd-notation-datatype , "3921"^^datatype:ho-notation-datatype , "NM"^^datatype:rq-notation-datatype , "16918"^^datatype:eg-notation-datatype , "298506"^^datatype:eg-notation-datatype , "4610"^^datatype:eg-notation-datatype , "1588591"^^datatype:rgd-notation-datatype , "164850"^^datatype:om-notation-datatype , "7555"^^datatype:hg-notation-datatype , "P10166"^^datatype:sp-notation-datatype , "P12524"^^datatype:sp-notation-datatype , "Q6TLI1"^^datatype:sp-notation-datatype , "Hs.437922"^^datatype:ug-notation-datatype , "96799"^^datatype:mgi-notation-datatype , "1422087"^^datatype:af-notation-datatype , "1422088"^^datatype:af-notation-datatype , "214058"^^datatype:af-notation-datatype ; rdfs:label "MYCL1" ; skos:prefLabel "LMYC" , "MYCL" , "MYCL" , "MYCL-I" , "Lmyc-I" , "Mycl-I" ; skos:broader semtype:T116 ; a skos:Concept ; skos:inScheme vocab:GENE , vocab:HOMOLOGENE . concepts:C3003922 skos:inScheme vocab:default ; prop:altLabel_NO "v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian) (mapped)" , "v-myc myelocytomatosis viral related oncogene, neuroblastoma derived" , "v-myc avian myelocytomatosis viral related oncogene, neuroblastoma derived" , "Nmyc-1" , "neuroblastoma-derived v-myc avian myelocytomatosis viral related oncogene" , "v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)" , "N-MYC PROTO-ONCOGENE PROTEIN" , "Nmyc1" , "neuroblastoma MYC oncogene" , "pp65/67" , "oncogene NMYC" , "Oncogene NMYC" , "N-myc proto-oncogene protein" ; skos:notation "120527"^^datatype:gd-notation-datatype , "1584995"^^datatype:gd-notation-datatype , "3922"^^datatype:ho-notation-datatype , "NM"^^datatype:rq-notation-datatype , "18109"^^datatype:eg-notation-datatype , "298894"^^datatype:eg-notation-datatype , "4613"^^datatype:eg-notation-datatype , "1584995"^^datatype:rgd-notation-datatype , "164840"^^datatype:om-notation-datatype , "7559"^^datatype:hg-notation-datatype , "P03966"^^datatype:sp-notation-datatype , "Q53XS5"^^datatype:sp-notation-datatype , "Q63379"^^datatype:sp-notation-datatype , "Hs.25960"^^datatype:ug-notation-datatype , "97357"^^datatype:mgi-notation-datatype , "1417155"^^datatype:af-notation-datatype , "1425922"^^datatype:af-notation-datatype , "1425923"^^datatype:af-notation-datatype , "209756"^^datatype:af-notation-datatype , "209757"^^datatype:af-notation-datatype , "211377"^^datatype:af-notation-datatype , "234376"^^datatype:af-notation-datatype ; rdfs:label "MYCN" ; skos:prefLabel "MYCN" , "Mycn" , "N-myc" , "ODED" , "MODED" , "Nmyc" , "NMYC" , "Nmyc-I" ; skos:broader semtype:T116 ; a skos:Concept ; skos:inScheme vocab:GENE , vocab:HOMOLOGENE . concepts:C3020128 skos:inScheme vocab:default ; prop:altLabel_NO "neural cell adhesion molecule L1" , "NEURAL CELL ADHESION MOLECULE L1" , "Neural cell adhesion molecule L1" , "N-CAML1" , "L1cam" , "MIC5" , "antigen identified by monoclonal antibody R1" , "L1 cell adhesion molecule (hydrocephalus, stenosis of aqueduct of Sylvius 1, MASA (mental retardation, aphasia, shuffling gait and adducted thumbs) syndrome, spastic paraplegia 1)" , "CD171 antigen" , "HSAS1" , "S10" , "CAML1" , "NCAM-L1" , "MIC5" , "L1 cell adhesion molecule" , "SPG1" , "CD171" , "N-CAM L1" , "neural cell adhesion molecule L-I" , "neural cell adhesion molecule L-1" , "NEURAL CELL ADHESION MOLECULE L-I" , "NEURAL CELL ADHESION MOLECULE L-1" , "Neural cell adhesion molecule L-I" , "Neural cell adhesion molecule L-1" , "N-CAML-1" , "MIC-5" , "antigen identified by monoclonal antibody R-I" , "antigen identified by monoclonal antibody R-1" , "HSAS-1" , "CAML-1" , "NCAM-L-1" , "MIC-5" , "SPG-1" , "CD-171" , "N-CAM L-I" , "N-CAM L-1" ; prop:prefLabel_NO "L1CAM" ; skos:notation "120133"^^datatype:gd-notation-datatype , "120526"^^datatype:gd-notation-datatype , "619777"^^datatype:gd-notation-datatype , "20128"^^datatype:ho-notation-datatype , "NM"^^datatype:rq-notation-datatype , "16728"^^datatype:eg-notation-datatype , "3897"^^datatype:eg-notation-datatype , "50687"^^datatype:eg-notation-datatype , "619777"^^datatype:rgd-notation-datatype , "308840"^^datatype:om-notation-datatype , "6470"^^datatype:hg-notation-datatype , "P11627"^^datatype:sp-notation-datatype , "P32004"^^datatype:sp-notation-datatype , "Q05695"^^datatype:sp-notation-datatype , "Hs.522818"^^datatype:ug-notation-datatype , "96721"^^datatype:mgi-notation-datatype , "1369213"^^datatype:af-notation-datatype , "1421958"^^datatype:af-notation-datatype , "1450435"^^datatype:af-notation-datatype , "204584"^^datatype:af-notation-datatype , "204585"^^datatype:af-notation-datatype ; rdfs:label "L1CAM" ; skos:prefLabel "HSAS" , "MASA" , "N-CAML-I" , "MIC-V" , "HSAS-I" , "CAML-I" , "NCAM-L-I" , "MIC-V" , "SPG-I" ; skos:broader semtype:T116 ; a skos:Concept ; skos:inScheme vocab:GENE , vocab:HOMOLOGENE . concepts:C3000168 skos:inScheme vocab:default ; prop:altLabel_NO "CD54 antigen" , "intercellular adhesion molecule I" , "intercellular adhesion molecule1" , "Icam-1" , "CD-54" , "BB-2" , "Intercellular adhesion molecule I" , "Intercellular adhesion molecule1" , "Intercellular adhesion molecule-I" ; prop:prefLabel_NO "ICAM-1" ; skos:notation "120076"^^datatype:gd-notation-datatype , "2857"^^datatype:gd-notation-datatype , "168"^^datatype:ho-notation-datatype , "NM"^^datatype:rq-notation-datatype , "15894"^^datatype:eg-notation-datatype , "25464"^^datatype:eg-notation-datatype , "3383"^^datatype:eg-notation-datatype , "2857"^^datatype:rgd-notation-datatype , "147840"^^datatype:om-notation-datatype , "5344"^^datatype:hg-notation-datatype , "Q00238"^^datatype:sp-notation-datatype , "Q15463"^^datatype:sp-notation-datatype , "Hs.643447"^^datatype:ug-notation-datatype , "1387202"^^datatype:af-notation-datatype , "1424067"^^datatype:af-notation-datatype , "1427805"^^datatype:af-notation-datatype , "1427806"^^datatype:af-notation-datatype , "202637"^^datatype:af-notation-datatype , "202638"^^datatype:af-notation-datatype , "215485"^^datatype:af-notation-datatype ; rdfs:label "ICAM1" ; skos:prefLabel "ICAM-I" , "Icam-I" , "BB-II" ; skos:broader semtype:T116 ; a skos:Concept ; skos:inScheme vocab:GENE , vocab:HOMOLOGENE . 2014-03-21 13:04:42.508 UTC db_properties00 Please load a file in as seen in the example where the user, password, url (which is the database it should use), and driver is stated. 2014-05-12 14:03:22.531 UTC mysql.user=root mysql.password=amrishsql mysql.url=jdbc:mysql://localhost:3306/mydb mysql.driver=com.mysql.jdbc.Driver 2014-05-12 09:23:12.452 UTC Path_Peregrine_Indexer00 Give the full path where the production.properties and peregrine-skos-cli.jar files are located of the Peregrine Indexer Tool. Which are supposed to be in the same path/Directory. path/to/ production.properties path/to/ peregrine-skos-cli.jar 2014-06-15 17:48:37.4 UTC F:/School/Stage2/peregrine/ 2014-06-15 17:31:44.152 UTC endPeregrine_Indexertable_name0ontology0Input2propertyString0Path0output11 The nested workflow Peregrine Indexer uses a java peregrine skos cli.jar file to index the occurrence of concepts in documents. The Peregrine indexer program can be downloaded from trac.nbic.nl/biosemantics/downloads. Install LVG2013Lite. See: https://trac.nbic.nl/biosemantics/wiki/Peregrine%20SKOS%20CLI Copy properties file from production.properties which can be downloaded from: https://trac.nbic.nl/biosemantics/wiki/Peregrine%20SKOS%20CLI Change lvg.properties LVG_DIR=/home/path/to/lvg2013lite/ This file can be found in: /home/path/to/lvg2013lite/data/config/lvg.properties Change the normalizer.lvg.properties and normalizer.lvg.binaryCache properties to point to the LVG installation path. normalizer.lvg.properties =/home/path/to/lvg2013lite/data/config/config/lvg.properties normalizer.lvg.binaryCahce=/home/path/to/lvg2013lite/standartNormCache2013.bin Have MySQL installed with a database called mydb or please create one. Have mysql-connector-java-5.1.28-bin.jar or better placed in the local JAR files. 2014-06-11 11:57:41.849 UTC net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeCreate_Tablesdb_properties0timeStamp00 This nested workflows creates the necessary tables for inserting the generated values. The following tables are created: - Co-occurrence table - Occurrence table - Uncertainty coefficient table - Inner product table - Summary table 2014-06-11 11:53:41.270 UTC net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGet_abstractspropertyString0db_results22 A nested workflow to retrieve abstracts from a sql table. This table is assumed to have atleast two columns consisting out of pmid and abstract text. 2014-06-11 11:04:59.773 UTC net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokePeregrine_Indexertable_nameCreate_TablestimeStampPeregrine_IndexerontologyOntology_inputPeregrine_IndexerInputGet_abstractsdb_resultsPeregrine_IndexerpropertyStringdb_propertiesPeregrine_IndexerPathPath_Peregrine_IndexerCreate_Tablesdb_propertiesdb_propertiesGet_abstractspropertyStringdb_propertiesendPeregrine_Indexeroutput 79e34035-259d-4a70-be8d-4835b07d7c81 2014-03-19 13:21:15.504 UTC a8b056e3-6be4-4928-ade6-5f6a0c92fc4d 2014-03-10 13:47:55.727 UTC 2ad0a457-b237-4118-87b0-e9bf3a828044 2014-03-27 09:50:52.100 UTC 0ad567dd-bec4-4ae1-ae7a-664edd5f5cfd 2014-03-18 11:59:51.577 UTC fa089d0e-6e15-4aa7-b6d6-248c28d5a8c3 2014-03-11 15:16:30.693 UTC 99a327c3-9639-4330-a42b-38211e0a6fb1 2014-05-08 15:06:29.540 UTC 90a54608-c2d9-407e-99cb-0e7d6a2f884f 2014-03-12 15:28:58.480 UTC 0d4e9666-c21d-4ec7-9f6f-365c94b95d4c 2014-03-17 12:33:48.483 UTC 071af52e-3b78-40b0-8b4a-618fd3f8347c 2014-04-01 09:12:24.41 UTC b4aad310-ecdd-4c8b-8919-99817ecaa9cc 2014-02-26 13:07:54.522 UTC 034e2cfa-4acb-40db-91df-6e6a4a23521d 2014-03-19 12:32:40.153 UTC fdbd6cba-b2bc-4d2a-9c7c-8bc50001962b 2014-05-08 12:51:33.5 UTC 7f6d900b-1832-4b86-b7f4-08c039b9edd2 2014-03-03 15:06:51.165 UTC ee5d3fc0-9b1c-4a12-b200-11b0e081fc9b 2014-03-19 12:27:37.255 UTC 90225384-5852-4768-ba1d-cb7671b920da 2014-03-19 09:49:54.0 UTC e3f89d60-193f-4c1d-a512-babb81d7f2b7 2014-03-20 13:17:02.613 UTC 36893096-771e-4ccb-9ab0-02255dc8586c 2014-03-18 15:03:15.901 UTC c2951694-2c06-486d-a711-a3c4beb6f633 2014-03-11 15:23:08.145 UTC 780b5e58-5a7a-4592-b867-9bb2ac080e20 2014-04-01 09:07:20.694 UTC 2a1025ec-1df7-4647-96a3-63cb6de64448 2014-03-26 17:25:27.527 UTC 03051fe8-32a0-4e06-8db7-e9c6f48683eb 2014-04-08 09:23:51.472 UTC f466d95f-500a-43f5-8dc4-f33327ecc230 2014-04-10 12:43:15.28 UTC 2cab688c-e221-43b1-bd26-897e2ec25da1 2014-06-10 08:53:41.117 UTC c15bb5b6-e40b-420a-a025-540945e52250 2014-06-11 13:09:58.188 UTC 752fa5eb-11f0-440d-932a-9baf1837d14b 2014-05-05 13:44:57.506 UTC 8ee54bdd-2a85-4d00-9d44-6f76716c30ab 2014-04-11 12:11:42.696 UTC 21293efa-08e5-4f9b-8476-69542bd4ed30 2014-02-26 17:25:02.958 UTC 37b9ec60-f32e-41d2-a794-00268b5676d1 2014-03-03 14:50:17.274 UTC 583ce5b9-1b7e-4727-b578-99a9446d6c24 2014-04-10 14:21:17.895 UTC 32a10a11-25c7-49c8-9faf-f4fe5bdb429c 2014-04-07 08:35:40.279 UTC e0738573-74ec-4a05-9768-5f6228713e7e 2014-04-11 11:35:15.599 UTC 3c13d0f5-4bd2-4a91-a604-d37ffe95325b 2014-02-26 17:50:57.277 UTC a6467614-66ae-4e21-bc79-5a933557e105 2014-04-07 09:13:03.21 UTC beac6462-fcc9-4f61-a2a5-04d33abf9655 2014-03-18 10:21:54.817 UTC eae2daff-664b-403c-a280-fd0bf608c07e 2014-03-04 17:02:50.721 UTC f852ed2b-c5f1-45e3-b14b-c9d70363b8bf 2014-03-18 11:46:51.868 UTC 639bdbdd-79b8-43ff-a3e8-4cdf9bd10d3b 2014-04-10 08:49:54.608 UTC a44e14ee-29aa-42ae-ab74-89e4b62867f7 2014-05-01 14:07:48.100 UTC 1f2880c0-39cb-453f-86a1-e0988e1193e3 2014-04-10 12:11:23.86 UTC 4062840e-f51a-4b93-82e2-ff09d290113c 2014-06-15 17:24:03.411 UTC ac19e98b-d3ef-416a-b3ed-f15bf0d38dd3 2014-03-19 12:59:20.910 UTC ec776175-b47a-4675-93c3-4894d06d0a1d 2014-03-13 13:44:07.901 UTC d90ba032-33eb-417e-b1e8-020c076dca6a 2014-03-19 12:40:54.240 UTC 4f495cae-fb6b-4bea-9807-88c1313e8d99 2014-03-19 16:19:31.627 UTC CPGP Peregrine Get Abstracts Create tables 2014-06-30 09:14:49.77 UTC 117a64ff-4752-44a2-be39-2abb80498151 2014-04-15 14:51:48.399 UTC 1309e27f-34a7-4d52-8d1a-2fb43dfe4821 2014-03-31 14:51:11.904 UTC 5c8c8c5f-3cf7-4086-8801-a26d875a7a8d 2014-03-03 14:09:27.240 UTC 602a8686-3cef-41a9-81e1-7b5cc0835686 2014-05-01 14:56:53.206 UTC 2bcb2e8f-1db6-4c3d-82be-f67dd9dbf27f 2014-04-07 08:37:00.748 UTC 4b5a4cac-0ae8-4bac-9c09-3eb1d87dcfa8 2014-04-15 15:01:08.423 UTC 24fecb95-af50-4286-96ce-a71b19c86a52 2014-03-31 14:01:48.127 UTC 5efeac9e-af11-4b80-b35d-a3bfbf0c23db 2014-03-19 13:12:22.521 UTC 04b2105f-5028-4142-9cd1-205c458908af 2014-06-11 12:37:58.807 UTC a140a8e2-40da-4572-85c6-8657f51e0be2 2014-03-27 09:22:56.548 UTC dd2a167b-7fdb-422c-b7b8-2df915bdb8f0 2014-04-09 08:26:57.666 UTC 2eb0f038-4ecd-440b-b39e-f188243e37c0 2014-03-26 17:23:46.827 UTC ef76bf9a-9917-4e3e-b87d-53ad76171c49 2014-03-20 13:39:38.887 UTC 2c5ea41b-97b9-4abc-91ff-4f2484a8e4da 2014-04-02 08:21:59.626 UTC a15a8f83-fb3a-4539-8fec-b6f9cfbff092 2014-02-26 12:50:45.406 UTC 4c2d5bca-4745-4dcc-b5c4-1dec5989c1d5 2014-03-21 13:50:11.428 UTC 558f78ee-316b-45d1-b74d-08d613b59f81 2014-06-10 15:32:38.405 UTC b04f1761-c23c-4c94-96fe-9f5952836a36 2014-06-15 17:43:07.239 UTC c3af8057-fe35-4f34-bb39-0e2f13d5bc9b 2014-04-08 09:36:56.270 UTC c616d7b9-797b-47d0-936a-1a8485b38d5d 2014-03-21 13:20:55.583 UTC 440d354f-0961-4fc0-930b-5cf65114671b 2014-04-10 09:50:21.474 UTC f07d191d-1fc4-4eb9-b4c4-6d28c7825d52 2014-04-15 14:47:07.705 UTC db191651-73cb-49cc-95c5-22ec9300e026 2014-03-31 13:57:44.101 UTC 6d0a32e3-1bad-4917-82e8-8a7969a74325 2014-02-26 13:31:53.24 UTC eeaf9724-ad78-471c-9d76-bd14822bf8bc 2014-04-11 12:06:04.868 UTC 474781e2-4053-4460-9062-2c102596efdf 2014-05-12 13:04:27.927 UTC 750e214e-95e5-47d7-8a16-b5215fa651f5 2014-03-21 10:18:23.575 UTC 308a57a4-127d-4ce1-a1d1-5bec7884c40f 2014-04-09 08:45:28.176 UTC 172f16de-913f-4c36-9dd9-8f1976082e02 2014-03-27 15:00:44.396 UTC ee306759-1dd0-4677-bba9-96e3b79caec5 2014-03-03 14:57:11.282 UTC 6bf66067-e2f9-41f4-bb67-afd72869d8fa 2014-03-20 14:09:31.707 UTC 6f7b6d14-3b41-4cb7-a937-0004943c3fc3 2014-03-27 15:02:23.494 UTC 9ff8f0a5-94b7-4f91-9d43-0393c8f57412 2014-06-10 13:39:46.26 UTC 1821fee1-4517-4b40-8b16-329b5a715fcf 2014-04-09 08:31:52.587 UTC d733cb03-4b3a-4a90-8ba8-ce9141a40c59 2014-03-18 14:47:05.491 UTC f6d7a038-81e9-4342-b1d8-a06784a052df 2014-03-12 10:35:09.457 UTC 5c742679-0199-4a84-b0d5-fa3671ca2328 2014-03-17 12:34:38.631 UTC d16225e3-4e03-4ca7-a7b3-f442287ec941 2014-03-13 13:18:06.888 UTC 09abbd60-7a95-497f-ba88-65327905e6df 2014-03-31 11:28:18.774 UTC 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1c3b0a2e-afdb-4df9-bafc-6a4e91a09bd6 2014-06-15 16:13:59.352 UTC 07485e5a-d4a0-48f8-b8db-370e51ff1627 2014-05-08 09:38:44.679 UTC 45f73324-89b9-4983-a2f8-e64d4923bc12 2014-04-14 08:48:25.831 UTC 771080e5-fee1-477c-afc7-48eb021eeef0 2014-03-13 13:01:18.912 UTC b9d0d7ca-fce7-4395-b539-3f6e37bab3b9 2014-04-11 12:07:23.118 UTC 95fb6bdb-5a34-40dd-8427-d19f6c73d4a7 2014-03-04 16:36:46.845 UTC 1d00ea19-4378-44fe-9096-03de5bfc0a27 2014-03-19 12:05:45.996 UTC 2b5434b8-306f-4c49-be67-e6eb3ddaf69f 2014-04-15 13:49:23.596 UTC b1c7c740-d9ff-4bf5-90b1-70bef408b035 2014-06-10 08:29:01.358 UTC 76c6dd4c-f320-4201-8332-f66dfae8e588 2014-04-01 13:54:38.259 UTC 2277faa5-f908-403a-9974-71989c2e9620 2014-06-11 11:01:54.926 UTC b3225a8b-74d2-4e9b-9577-585b73e3b076 2014-04-09 08:34:09.963 UTC cf0e0e58-2e01-4b6b-b690-abdcf02c5e29 2014-03-31 13:03:01.42 UTC c4a0c388-2f5b-4fcb-9d03-438319509d2f 2014-03-18 12:21:22.938 UTC d38184f1-fafd-43b2-a12e-4ac7e6dfc387 2014-04-10 09:16:18.992 UTC 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d2ede6ca-e2a5-472c-89e1-46c1f89bad4a 2014-06-15 17:48:38.372 UTC d71c37ab-c786-40ee-8618-55907c9f3c6a 2014-03-11 11:41:18.224 UTC fa94530d-37fc-4b21-bb1f-1a78507d8eed 2014-06-30 09:15:19.409 UTC 344da505-68bc-47c1-ba68-afd6a55ebf7e 2014-03-21 10:16:16.121 UTC 8ad24b39-e9fe-4556-a335-c0368c8761c1 2014-03-03 15:22:06.680 UTC 812d5229-115b-47d5-bc40-7c25fa72ef52 2014-03-19 16:10:15.870 UTC e10307c2-3b72-4116-bb8c-f749e5c5d4f4 2014-05-12 13:48:04.765 UTC f7b5641b-c9a4-4a6b-9f0e-f76b56fcbe41 2014-04-10 09:19:31.47 UTC 05687d54-4107-43c2-aa91-0b7b706756db 2014-06-11 09:03:42.795 UTC ee149ce2-e3ba-465e-9c63-04b297aa5059 2014-03-04 16:18:24.468 UTC dd37c9d5-0cfd-4087-9023-c0490efb9b96 2014-06-26 14:06:03.685 UTC 45bbc83c-373f-4d38-bd1e-e64484df169a 2014-03-27 15:06:36.53 UTC 93512370-e9f6-49b6-ba46-4482dae8c38e 2014-05-02 16:40:23.354 UTC 0f253965-1e8b-469b-96a0-0f1e6e7d483d 2014-05-05 09:41:59.8 UTC 6b5b0fe0-7ad4-41fd-9f0c-759f9cf3443f 2014-04-11 11:28:29.860 UTC 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1b106332-9480-492d-98b0-5b23b305ae79 2014-04-08 15:43:34.927 UTC 7d900bd5-5bad-43de-b753-3b85f88eb42b 2014-04-03 14:21:51.228 UTC cd268e72-7ac2-4916-966b-82af1cebc502 2014-04-15 13:37:03.488 UTC 6bd83cca-7051-4d40-b247-e4e00416f07f 2014-03-04 09:34:11.615 UTC 924fb17b-6881-4e2f-b131-0305cd8f6dc4 2014-02-26 17:32:58.624 UTC 1aa12185-de42-4a9c-8170-ab9df6ac378c 2014-02-26 12:45:33.366 UTC 0d50bbee-3571-4315-b7d7-44342273a8b9 2014-04-10 08:33:00.501 UTC f1ee128e-cedc-46a9-8300-f0813cbd40b1 2014-03-12 09:49:26.849 UTC 1d0651fa-abaa-4003-b87a-017ec740796c 2014-04-01 09:05:15.570 UTC 6877eac7-feb3-4b6f-a96c-64feb10050e8 2014-05-12 11:50:23.695 UTC 4f53517b-d092-4c7e-af69-58cc424051d1 2014-03-12 09:58:16.101 UTC 787df02e-4aa1-4712-9ae0-0682c900f43f 2014-05-12 13:55:14.171 UTC 2d213aed-77c4-40d7-a3f9-b06ce1f93960 2014-04-09 08:37:09.195 UTC a2aa9e83-b14b-4160-8607-d06228a5a210 2014-04-25 09:30:45.977 UTC 67c536e3-dc8a-4f21-9bf3-80c503131a63 2014-03-31 14:21:15.949 UTC 6a0bf53c-6cc9-485b-96c5-c9e8fe2e3c0e 2014-03-13 13:32:22.428 UTC bbc1a00b-a48b-44f5-a291-597d30838c76 2014-05-12 13:36:37.252 UTC 3a11d4bf-efb7-4d2e-9ba2-31e237da4053 2014-03-21 10:39:12.836 UTC b73de25f-87f0-4b09-a0d3-c339d340f8c0 2014-06-10 11:16:06.229 UTC 8e5f70fe-027f-462b-bceb-baa02da36313 2014-03-11 13:45:06.542 UTC 1407f28f-2b20-4a4b-987f-0e8a978fd069 2014-04-14 12:19:58.355 UTC d98af7c3-005b-4c4c-be87-3cedc55890d3 2014-03-19 16:15:51.545 UTC 37d0c11f-4290-441b-b2a6-892031d0fccf 2014-03-20 14:14:32.853 UTC 9b4b3216-062a-4e63-8031-a38217d8888c 2014-03-12 10:34:47.363 UTC 9ad3210e-5f72-4ad4-b178-3078dc331f88 2014-03-19 16:07:41.590 UTC fc62010b-c26e-43b3-a420-8e8d8ea6c2cf 2014-03-20 14:18:42.422 UTC 706b149b-29b6-4996-9da7-177b4fc1cae3 2014-02-26 17:19:09.154 UTC db32d696-f69e-44d3-9472-82883b50e3de 2014-05-01 14:29:35.815 UTC a5dc39ce-b9a2-42b9-80b8-ebbe26c16c34 2014-06-11 08:57:50.961 UTC 4c60a50a-bde4-47e3-b2de-54422aafd320 2014-04-02 08:37:52.284 UTC dbdc039a-a221-43bc-a79a-b24724697451 2014-04-11 11:20:16.786 UTC 657b97ed-bf89-4242-9e1d-508cc5d1f388 2014-05-12 12:02:02.203 UTC 86664bb4-700b-4f06-a9bc-e1c93746e79d 2014-05-12 08:26:16.935 UTC 65061b5e-4240-4e5d-bea5-395adf42981f 2014-03-20 10:20:03.284 UTC 5744d0eb-9aa6-4f42-9ba1-e5130128eca7 2014-06-10 08:43:19.41 UTC 677a87f1-b930-466a-a20b-fe5461419926 2014-03-03 15:05:37.100 UTC 6011272e-139a-4102-b7a1-f8ee7164acdf 2014-04-11 12:10:20.841 UTC Amrish Mahes 2014-03-21 13:44:24.679 UTC 4262b74b-76fd-4461-b272-65c92e28bbc6 2014-03-03 14:14:19.365 UTC 936c0da5-18d3-4670-842e-b6de7827f6be 2014-04-10 14:22:40.555 UTC 71665e19-759b-423c-83b4-6c937dcd3739 2014-03-27 14:42:20.647 UTC e05d8961-a33e-4646-be69-3c64a2b675df 2014-03-03 12:55:48.706 UTC 0cabfae5-a1b5-4bfd-a39e-635a28acf414 2014-02-26 17:15:32.909 UTC 3e2684d1-5518-413a-83c4-656511321e7c 2014-03-18 12:15:32.494 UTC 71c0ae47-08a2-42e7-8b61-368228badc87 2014-04-09 11:38:19.412 UTC 34035ec0-5395-4c6e-b313-33420000b5eb 2014-03-19 13:06:21.871 UTC 308af5ff-dc7e-48cc-a8f5-2ff1040a0513 2014-03-03 14:11:42.281 UTC 2a53ea5f-84d9-4a68-b53b-93d78a31af54 2014-04-11 12:03:01.35 UTC ec5570e9-72eb-4bc9-9026-4bca5d5fd204 2014-03-03 14:58:47.797 UTC 8b8967de-7f97-44fe-aae2-1cbcb82f8c17 2014-03-18 10:23:30.253 UTC b4a7f556-a9d0-49a0-9979-ecfee03c27cb 2014-03-26 16:49:56.104 UTC f35c4f25-28fc-4dd2-9e2c-9bfb96d34a10 2014-03-27 14:40:58.914 UTC c59ee9c4-e463-48c7-a0f2-c9b65cdfb83b 2014-06-10 15:53:56.13 UTC b095475b-dfdc-4b2a-95c3-96598f58d286 2014-04-25 11:04:25.359 UTC 4b062ff7-3737-457c-9079-3e0e7a9c45f9 2014-05-21 16:11:02.255 UTC db468038-5e51-4adf-88f9-1c2073d8d2d0 2014-04-14 08:57:21.101 UTC 04e81e51-4243-4c7d-bedf-52e110d75941 2014-03-26 17:21:42.891 UTC ea0d3514-021d-4416-a92c-e847e8cb3b05 2014-04-14 12:34:34.807 UTC a76a2189-7906-4a4c-998f-c4ddf2125891 2014-06-15 17:30:02.969 UTC 0ee66d3a-3174-4e42-a06e-a238013fb17a 2014-04-25 10:02:43.752 UTC 1ffc7cc7-bd8c-49e0-92ff-0ca02090bca3 2014-03-31 13:45:49.982 UTC Requirements: Have MySQL installed with a database called mydb or please create one. Have a mysql connector file. This can be downloaded from mysql.com. Rename the downloaded file to mysql-connector-java.jar and place it in the the local lib file of Taverna as written on the dependencies tab. Choose this dependency by rightclicking a beanshell script and selecting it for the whole workflow as system classloader. Download the Peregrine SKOS CLI from: https://trac.nbic.nl/biosemantics/downloads Install LVG2013Lite. See: https://trac.nbic.nl/biosemantics/wiki/Peregrine%20SKOS%20CLI Change lvg.properties LVG_DIR=/home/path/to/lvg2013lite/ This file can be found in: /home/path/to/lvg2013lite/data/config/lvg.properties Copy properties file from production.properties which can be found on: https://trac.nbic.nl/biosemantics/wiki/Peregrine%20SKOS%20CLI Change the normalizer.lvg.properties and normalizer.lvg.binaryCache properties to point to the LVG installation path. This file can be obtained from https://trac.nbic.nl/biosemantics/wiki/Peregrine%20SKOS%20CLI Have Peregrine indexer installed locally and give it the correct path in the component named "Indexer_tool". Which can be found in the nested workflow named Peregrine indexer. Optional: If using a Windows machine please install cygwin. Set cygwin in the $PATH of the environment variabale. Go to taverna File --> preferences --> Tool invocation --> set modify on explicit locations --> edit a default local to Shell: C:\Windows\system32\cmd.exe /c and save that. -->Set Modify on: symbolic locations --> edit --> choose default local and save. When using a unix environment make sure the default local is set Shell into /bin/sh -c. Please make sure this is also set into the indexer tool part. Have JAVA_HOME C:\Program Files\jdk 1.7.0 in environment variabale when using Windows. The nested workflow Get_abstract uses a sql command to retrieve abstracts which assumes are located in the database mydb. If this is not the case, please change the database in the SQL value. 2014-06-30 09:15:19.183 UTC c54c7bf6-0749-40b1-9c4f-85647486ef12 2014-03-03 15:34:41.175 UTC 232adcb2-22e3-4169-ad4c-40f057cf4a1a 2014-03-13 13:12:29.15 UTC 92f7d5bb-9ea0-4379-adb1-89e477fb84b7 2014-04-14 12:24:39.293 UTC 4fe9e39b-66cb-4c52-ae54-6ef679bdf8db 2014-03-20 13:32:59.530 UTC 05fc1170-1530-4218-b74c-7f19168686bf 2014-06-11 10:55:52.360 UTC 4b901027-fa5c-4b28-8d85-66c3277f3f1a 2014-03-19 10:37:36.546 UTC 2f539e4b-879e-4d36-a60c-791a4e31e27e 2014-03-20 09:42:42.306 UTC 40381d4e-1806-42c8-a9e5-fab64c0ff659 2014-05-12 11:53:14.551 UTC 29b5941c-7c3e-4797-87fd-e28de347ac65 2014-05-12 09:20:19.540 UTC a813966c-f68b-42a2-ad7d-07244e4c93e5 2014-03-21 10:27:16.965 UTC 3bf9710d-fbff-4111-9da4-e08881c792e7 2014-05-01 13:38:15.975 UTC eba3b574-0664-4825-983c-d8fa440e058a 2014-02-26 13:11:53.323 UTC 24579545-55ab-4f48-8c51-ece59bf52d2a 2014-04-02 11:29:44.386 UTC 682d73e2-12c4-411c-90fa-dc99abf44a47 2014-03-12 15:19:24.565 UTC 62cadf7c-0be2-4a5c-9116-19c5508d2262 2014-04-02 11:34:26.859 UTC b5665198-250c-49ee-953a-43fa6d0e478c 2014-03-11 10:37:17.931 UTC 9515f2ec-5584-49ca-b5f1-2d4296246b16 2014-05-12 11:42:13.548 UTC fe78f1e4-aac0-4eab-977d-3e8e55cb0128 2014-06-10 16:05:03.331 UTC bc0d0dd7-0034-4627-a9bb-1f83b679df6e 2014-04-07 08:33:13.704 UTC df44c443-621a-4b10-956e-a290c7295010 2014-05-01 13:29:47.45 UTC c846e819-1279-4011-9cc4-713087a79bb7 2014-03-19 12:46:50.121 UTC db315bb8-4ed8-4a0a-b138-e516ea69d662 2014-03-21 09:14:35.264 UTC b59275ba-3d95-4001-afb4-03b40cf5ac78 2014-03-20 13:21:01.681 UTC fda95fdc-2ca7-4156-a8d9-42a2a05f40af 2014-03-19 13:16:29.792 UTC d92b5894-75ef-48e1-b233-2144d51fcd9a 2014-03-18 11:53:02.58 UTC b391da2e-fc44-4714-b15e-168690266ec1 2014-06-15 17:48:27.145 UTC 0a9fc708-f04c-4b3b-9c2b-3077d360a004 2014-03-26 16:58:01.18 UTC c75a45b3-f266-4a39-85d9-90cdfbedbe4f 2014-04-08 09:34:45.207 UTC 7729c962-481a-439a-9792-fea74acd1ccc 2014-03-20 15:19:54.660 UTC 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c67330f8-d0d2-466d-878d-e496fa03f54a 2014-06-15 17:32:08.363 UTC 3fcee352-9a66-4edd-a4d1-5791b5ec67a8 2014-06-11 08:53:49.813 UTC d09e054e-8c6d-440b-8c53-4359677d9812 2014-03-20 15:57:06.707 UTC 60360c09-c322-4219-aef4-05e39c550194 2014-04-08 09:49:57.235 UTC 224d82d5-73dd-4dce-baea-8ad1341e9152 2014-04-11 12:18:58.687 UTC 528650c7-af4e-4106-9e93-32ff0d747139 2014-03-03 16:01:16.452 UTC b8e2805c-da5f-4ed9-bafd-d5fd3b452727 2014-06-15 17:32:44.897 UTC c988fac0-98e3-43db-befb-77dca1246b26 2014-03-31 13:47:32.764 UTC 956fb694-89be-42e6-abd0-b250502afecd 2014-04-10 09:25:11.725 UTC ff2b9545-a710-422c-b6da-89868e82c43d 2014-03-11 15:15:45.746 UTC 3972a234-06e9-47be-a797-a53d11735f29 2014-05-12 11:46:14.236 UTC 32035473-cbac-46fb-8f01-232d9c3e9c60 2014-03-03 12:43:17.878 UTC 513c4d46-b511-4a6d-9b9f-9f046720c2b7 2014-03-27 14:40:34.469 UTC 46682a5f-c527-4cc3-953f-119b95ab410b 2014-03-20 13:31:32.320 UTC 0fdf5cdf-e9cd-4a15-a314-44e0123dcb97 2014-03-20 10:30:41.570 UTC db4e0e6d-92c5-4213-bfba-045445a269aa 2014-03-31 14:07:11.673 UTC 9093978f-8c71-42e7-b121-a2ad8df96bbc 2014-06-11 12:13:20.342 UTC 7287d9e7-e561-46b3-a85e-fbec3c55f295 2014-04-16 14:32:15.351 UTC 5af50851-3fd4-4f60-93c4-37dd7e4d2a38 2014-03-18 12:18:13.691 UTC 392cb15c-a3dd-490e-93d2-ac28fd03b6a5 2014-03-19 13:03:01.757 UTC f4ebe843-a6a9-4381-b58d-598f0b7cc5c7 2014-03-11 14:52:39.601 UTC 4c4cec6d-8632-4576-a6e9-571c6b0c6236 2014-03-11 14:45:15.59 UTC 86887b54-0c4b-485a-9110-f6257cbde1d7 2014-03-11 14:57:05.945 UTC de62503f-e5e2-4bb8-b179-32403d5ecaa9 2014-04-15 14:10:59.793 UTC 678d7e43-6ee9-4751-b194-ff8640bfe6bb 2014-03-13 17:11:35.775 UTC 1c51b3f3-9137-47a7-85ac-8bf8f1d86dde 2014-04-14 11:04:37.235 UTC 3dee3c3f-9568-4261-8f49-e84aaff43613 2014-04-14 08:47:36.378 UTC Create Tablesdb_properties00 Please load a file in as seen in the example where the user, password, url (which is the database it should use), and driver is stated. 2014-06-11 12:42:39.196 UTC mysql.user=root mysql.password=amrishsql mysql.url=jdbc:mysql://localhost:3306/mydb mysql.driver=com.mysql.jdbc.Driver 2014-06-11 12:42:50.723 UTC timeStampBeanshell_get_timestamptimeStamp00 A Beanshell script which retreives the time the program started. As in year, month, day, hour, minutes and seconds in military time. 2014-04-11 13:57:49.999 UTC net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity timeStamp 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_SQL_Create_TablestimeStamp0Table_sql00 A Beanshell script for creating the tables. 2014-06-15 17:25:33.10 UTC net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity timeStamp 0 text/plain java.lang.String true Table_sql 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExecute_SQL_UpdatepropertyString0sql0net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity sql 0 text/plain java.lang.String true params 1 text/plain java.lang.String true propertyString 0 text/plain java.lang.String true resultList 0 0 workflow net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker UserNameHere 2014-06-15 16:25:51.599 UTC net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSplit_string_into_string_list_by_regular_expressionregex0string0split11net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity string 0 'text/plain' java.lang.String true regex 0 'text/plain' java.lang.String true split 1 l('text/plain') 1 workflow org.embl.ebi.escience.scuflworkers.java.SplitByRegex net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeregex_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity [\n] net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_SQL_Create_TablestimeStampBeanshell_get_timestamptimeStampExecute_SQL_UpdatepropertyStringdb_propertiesExecute_SQL_UpdatesqlSplit_string_into_string_list_by_regular_expressionsplitSplit_string_into_string_list_by_regular_expressionregexregex_valuevalueSplit_string_into_string_list_by_regular_expressionstringBeanshell_SQL_Create_TablesTable_sqltimeStampBeanshell_get_timestamptimeStamp 26b21b9b-a674-4e35-b03f-807d71510259 2014-05-12 13:28:52.14 UTC 048b9168-bc32-4af6-ba1b-96c66ea34032 2014-06-15 17:05:43.430 UTC 8477156c-f078-4565-b8af-5db33fada212 2014-05-12 13:43:53.377 UTC 4040ef45-3e66-4f71-b7cb-b56f0b0aacff 2014-05-12 13:55:09.958 UTC e3e82f84-c36d-4445-9009-146e4a867dc2 2014-06-15 16:39:33.753 UTC 203b885f-17e1-446a-a321-5e0b888e6004 2014-06-15 17:23:48.706 UTC 9635824a-e4f1-4881-97e5-929978878075 2014-06-11 08:57:20.555 UTC 39bb73a3-e51b-42da-8706-944c99ff6ef2 2014-04-25 09:31:36.342 UTC 1582f59b-8bd9-43ce-9f83-644f97d954c7 2014-05-12 12:01:29.197 UTC 920a4ba4-90cf-4a89-a943-571ac36e7d47 2014-06-15 16:13:50.623 UTC 98e5f737-bfc2-4631-9018-55ad9e650902 2014-06-15 16:26:26.955 UTC Create Tables 2014-04-25 09:03:12.547 UTC 3aa918f3-ff7c-4125-8c0e-0a0251f8e67a 2014-06-15 16:28:37.25 UTC b8b7e9df-ad2f-4d94-98ed-240cc4740e10 2014-06-26 21:33:59.252 UTC 7b1e6650-564c-4d1a-9533-3e729f80f4b0 2014-06-15 17:19:26.528 UTC 0a15b5d5-9ad4-4394-a44b-a773c3cfbc60 2014-04-25 09:30:39.667 UTC 73b839a8-067a-4f75-9229-2657a8171883 2014-06-15 16:39:15.477 UTC aaf687fd-8ecb-42e8-b118-4f865db9db69 2014-06-15 16:20:50.770 UTC e07305cf-4d3c-4732-817c-fc8c1897b04b 2014-06-15 17:23:16.414 UTC c725fae1-9407-4643-8078-208328519914 2014-06-15 17:25:46.789 UTC 071ca1ba-e357-4fd3-8943-c544199f9dd0 2014-04-25 09:23:33.706 UTC 31df5173-0ae3-44b1-a101-68d3ee2b6c66 2014-06-11 12:43:52.905 UTC 86079042-0398-4522-b766-79a51a2061b6 2014-04-25 09:34:08.496 UTC 50075aae-f1e4-44c2-9c80-ab5c8bd3f4e3 2014-06-15 16:33:07.624 UTC bd5d7656-0001-4e1e-9e00-65bda9a575b6 2014-05-12 13:51:18.129 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 994307a6-939b-48c2-a874-5be73efc8731 2014-06-10 10:56:30.827 UTC 6f805bc9-25de-40db-bdfc-9f02de07addc 2014-06-11 09:03:14.417 UTC f0837d2f-5152-4031-9f5c-d25c661c9168 2014-06-26 14:06:00.145 UTC e89e40ff-8e2c-401f-96ba-c233c6bf4dbd 2014-06-15 17:20:08.149 UTC ee6ad738-c5f6-4af6-8e6c-feb0c97d5504 2014-05-12 13:58:30.889 UTC f2a26852-747d-41b3-957a-6b32bd38f698 2014-06-15 17:16:56.191 UTC b905d192-afc7-4e80-9b87-3c62568fe512 2014-06-10 16:12:44.94 UTC 01279793-743e-42c9-879d-c89edae5620b 2014-06-15 16:41:24.510 UTC 1a6c0667-e77d-45e6-9f10-ea3b62ab8b32 2014-06-15 17:05:00.249 UTC a3744263-cf8d-4ce4-8a77-8d75529492e3 2014-06-11 08:50:09.675 UTC 1e050fa6-0e46-47cc-852a-78351e49fd4b 2014-06-15 16:21:22.366 UTC d0c0ac03-d7c1-410e-ae8a-d0a3fb71cc23 2014-06-15 16:42:33.166 UTC 15224b89-9d42-4abb-888a-cc96a03354bf 2014-06-15 17:26:06.238 UTC c0782138-c8e8-4d33-a524-12e3af3d28fa 2014-05-12 11:52:51.417 UTC f70ead12-638d-4210-be53-6193297440cd 2014-06-10 10:59:34.689 UTC 200cd498-f8d4-4ab0-bf9c-e96aa415be2e 2014-06-10 16:10:53.665 UTC 5747cb6c-cfd7-4461-ba4d-aaca2ff23764 2014-06-15 17:18:14.417 UTC 58d2e665-ec1f-4ea3-806d-cafa02adedee 2014-05-12 13:47:58.714 UTC 8cb5442b-fa0d-4ab5-a534-ad79415bdc04 2014-06-15 17:22:42.241 UTC 9fbf74e6-c25a-47f9-9065-8aeee27a62fa 2014-06-10 09:35:20.474 UTC 8bacc18d-de0f-4fdf-99a7-3f5bca0f03ae 2014-06-15 17:20:36.58 UTC efb2e85a-454a-43fb-a82e-8d82a29111e2 2014-05-08 15:06:01.281 UTC a5ab9df6-c2f1-49bc-8788-f300d6fee7c8 2014-05-08 12:51:28.905 UTC f8521f7a-4def-44dd-9e0c-5919119df0b5 2014-06-15 17:12:31.867 UTC fe3eb75e-1e1b-4846-849e-625552e0e9cc 2014-06-11 09:07:30.689 UTC 567b503f-7be0-411b-a1ec-8904190704ef 2014-06-26 14:19:00.919 UTC 0f84cc52-37eb-4728-8f78-efd8981e9770 2014-06-11 12:45:50.859 UTC ba007108-e797-4ecd-88d9-cb675d81568b 2014-05-12 13:38:14.79 UTC a0444c47-ea11-48c9-9c0c-b52d326b35ad 2014-06-11 13:09:53.254 UTC f6285fa8-00e8-4b4b-848b-4c3faecaff0c 2014-06-15 17:03:23.327 UTC 1c464dba-d276-4ea4-8e3d-e37f4893e7d0 2014-06-15 16:54:44.837 UTC Peregrine indexerontology00 A Skos formated dictionary/thesaurus of predefined concepts. 2014-05-01 14:22:40.779 UTC @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . @prefix skos: <http://www.w3.org/2004/02/skos/core#> . @prefix dct: <http://purl.org/dc/terms/> . @prefix emco: <http://rdf.biosemantics.org/emco/> . @prefix emco15: <http://rdf.biosemantics.org/emco/v1.5/> . @prefix concepts: <http://rdf.biosemantics.org/emco/v1.5/concepts/> . @prefix prop: <http://rdf.biosemantics.org/emco/properties/> . @prefix datatype: <http://rdf.biosemantics.org/emco/datatypes/> . @prefix semtype: <http://rdf.biosemantics.org/emco/semtypes/> . @prefix vocab: <http://rdf.biosemantics.org/emco/v1.5/vocabularies/> . prop:prefLabel_CI rdfs:subPropertyOf skos:prefLabel . prop:prefLabel_NO rdfs:subPropertyOf skos:prefLabel . prop:prefLabel_CI_NO rdfs:subPropertyOf skos:prefLabel . prop:altLabel_CI rdfs:subPropertyOf skos:altLabel . prop:altLabel_NO rdfs:subPropertyOf skos:altLabel . prop:altLabel_CI_NO rdfs:subPropertyOf skos:altLabel . vocab:default rdfs:comment "ErasmusMC ontology file" ; dct:title "Anni2_1_June2009" ; a skos:ConceptScheme . vocab:MSH dct:title "MeSH" ; a skos:ConceptScheme . vocab:SNOMEDCT dct:title "SNOMED Clinical Terms" ; a skos:ConceptScheme . semtype:T47 skos:topConceptOf vocab:default ; rdfs:label "Disease or Syndrome" ; skos:definition "A condition which alters or interferes with a normal process, state, or activity of an organism. It is usually characterized by the abnormal functioning of one or more of the host's systems, parts, or organs. Included here is a complex of symptoms descriptive of a disorder." ; a skos:Concept . concepts:C9187 skos:inScheme vocab:default ; prop:altLabel_CI_NO "Coccidiosis"@es ; prop:prefLabel_CI_NO "Coccidiosis" ; skos:notation "C0009187"^^datatype:umls-notation-datatype ; rdfs:label "Coccidiosis" ; skos:definition "Protozoan infection found in animals and man. It is caused by several different genera of COCCIDIA." ; skos:broader semtype:T47 ; a skos:Concept ; skos:inScheme vocab:MSH , vocab:SNOMEDCT . concepts:C24530 skos:inScheme vocab:default ; prop:altLabel_CI_NO "Malaria NOS" , "Plasmodium Infections" , "Remittent Fever" , "Paludism" , "Plasmodiosis" , "Malarial fever" , "Malaria (disorder)" , "Marsh Fever" , "Malaria"@es ; prop:prefLabel_CI "Malaria" ; skos:notation "C0024530"^^datatype:umls-notation-datatype ; rdfs:label "test" ; skos:broader concepts:C9187 , semtype:T47 ; a skos:Concept ; skos:inScheme vocab:MSH , vocab:SNOMEDCT . concepts:C3031092 skos:inScheme vocab:default ; prop:altLabel_NO "myelocytomatosis viral oncogene homolog (avian)" , "myelocytomatosis oncogene" , "Transcription factor p64" , "Myc proto-oncogene protein" , "v-myc myelocytomatosis viral oncogene homolog (avian)" , "Myc2" , "myc proto-oncogene protein" , "Transcription factor p-64" , "Myc-2" ; skos:notation "120208"^^datatype:gd-notation-datatype , "3130"^^datatype:gd-notation-datatype , "31092"^^datatype:ho-notation-datatype , "NM"^^datatype:rq-notation-datatype , "17869"^^datatype:eg-notation-datatype , "24577"^^datatype:eg-notation-datatype , "4609"^^datatype:eg-notation-datatype , "3130"^^datatype:rgd-notation-datatype , "190080"^^datatype:om-notation-datatype , "7553"^^datatype:hg-notation-datatype , "P01106"^^datatype:sp-notation-datatype , "P01108"^^datatype:sp-notation-datatype , "P09416"^^datatype:sp-notation-datatype , "Q6WDF7"^^datatype:sp-notation-datatype , "Hs.202453"^^datatype:ug-notation-datatype , "97250"^^datatype:mgi-notation-datatype , "1368308"^^datatype:af-notation-datatype , "1424942"^^datatype:af-notation-datatype , "202431"^^datatype:af-notation-datatype , "239931"^^datatype:af-notation-datatype ; rdfs:label "MYC" ; skos:prefLabel "MYC" , "C-MYC" , "Myc" , "Niard" , "Nird" , "c-Myc" , "c-myc" , "Myc-II" ; skos:broader semtype:T116 ; a skos:Concept ; skos:inScheme vocab:GENE , vocab:HOMOLOGENE . concepts:C3003921 skos:inScheme vocab:default ; prop:altLabel_NO "v-myc myelocytomatosis viral oncogene homolog 1, lung carcinoma derived (avian)" , "oncogene lmyc" , "l-myc-1 proto-oncogene" , "Lmyc1" , "myc-related gene from lung cancer" , "Oncogene MYC, lung carcinoma-derived" , "l-myc protein" , "Lmyc-1" , "Mycl1" , "L-myc-1 proto-oncogene protein" , "v-myc myelocytomatosis viral oncogene homolog 1, lung carcinoma derived (avian) (mapped)" , "v-myc avian myelocytomatosis viral oncogene homolog 1, lung carcinoma derived" , "MYCL-1" , "Mycl-1" ; prop:prefLabel_NO "MYCL1" ; skos:notation "120706"^^datatype:gd-notation-datatype , "1588591"^^datatype:gd-notation-datatype , "3921"^^datatype:ho-notation-datatype , "NM"^^datatype:rq-notation-datatype , "16918"^^datatype:eg-notation-datatype , "298506"^^datatype:eg-notation-datatype , "4610"^^datatype:eg-notation-datatype , "1588591"^^datatype:rgd-notation-datatype , "164850"^^datatype:om-notation-datatype , "7555"^^datatype:hg-notation-datatype , "P10166"^^datatype:sp-notation-datatype , "P12524"^^datatype:sp-notation-datatype , "Q6TLI1"^^datatype:sp-notation-datatype , "Hs.437922"^^datatype:ug-notation-datatype , "96799"^^datatype:mgi-notation-datatype , "1422087"^^datatype:af-notation-datatype , "1422088"^^datatype:af-notation-datatype , "214058"^^datatype:af-notation-datatype ; rdfs:label "MYCL1" ; skos:prefLabel "LMYC" , "MYCL" , "MYCL" , "MYCL-I" , "Lmyc-I" , "Mycl-I" ; skos:broader semtype:T116 ; a skos:Concept ; skos:inScheme vocab:GENE , vocab:HOMOLOGENE . concepts:C3003922 skos:inScheme vocab:default ; prop:altLabel_NO "v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian) (mapped)" , "v-myc myelocytomatosis viral related oncogene, neuroblastoma derived" , "v-myc avian myelocytomatosis viral related oncogene, neuroblastoma derived" , "Nmyc-1" , "neuroblastoma-derived v-myc avian myelocytomatosis viral related oncogene" , "v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)" , "N-MYC PROTO-ONCOGENE PROTEIN" , "Nmyc1" , "neuroblastoma MYC oncogene" , "pp65/67" , "oncogene NMYC" , "Oncogene NMYC" , "N-myc proto-oncogene protein" ; skos:notation "120527"^^datatype:gd-notation-datatype , "1584995"^^datatype:gd-notation-datatype , "3922"^^datatype:ho-notation-datatype , "NM"^^datatype:rq-notation-datatype , "18109"^^datatype:eg-notation-datatype , "298894"^^datatype:eg-notation-datatype , "4613"^^datatype:eg-notation-datatype , "1584995"^^datatype:rgd-notation-datatype , "164840"^^datatype:om-notation-datatype , "7559"^^datatype:hg-notation-datatype , "P03966"^^datatype:sp-notation-datatype , "Q53XS5"^^datatype:sp-notation-datatype , "Q63379"^^datatype:sp-notation-datatype , "Hs.25960"^^datatype:ug-notation-datatype , "97357"^^datatype:mgi-notation-datatype , "1417155"^^datatype:af-notation-datatype , "1425922"^^datatype:af-notation-datatype , "1425923"^^datatype:af-notation-datatype , "209756"^^datatype:af-notation-datatype , "209757"^^datatype:af-notation-datatype , "211377"^^datatype:af-notation-datatype , "234376"^^datatype:af-notation-datatype ; rdfs:label "MYCN" ; skos:prefLabel "MYCN" , "Mycn" , "N-myc" , "ODED" , "MODED" , "Nmyc" , "NMYC" , "Nmyc-I" ; skos:broader semtype:T116 ; a skos:Concept ; skos:inScheme vocab:GENE , vocab:HOMOLOGENE . concepts:C3020128 skos:inScheme vocab:default ; prop:altLabel_NO "neural cell adhesion molecule L1" , "NEURAL CELL ADHESION MOLECULE L1" , "Neural cell adhesion molecule L1" , "N-CAML1" , "L1cam" , "MIC5" , "antigen identified by monoclonal antibody R1" , "L1 cell adhesion molecule (hydrocephalus, stenosis of aqueduct of Sylvius 1, MASA (mental retardation, aphasia, shuffling gait and adducted thumbs) syndrome, spastic paraplegia 1)" , "CD171 antigen" , "HSAS1" , "S10" , "CAML1" , "NCAM-L1" , "MIC5" , "L1 cell adhesion molecule" , "SPG1" , "CD171" , "N-CAM L1" , "neural cell adhesion molecule L-I" , "neural cell adhesion molecule L-1" , "NEURAL CELL ADHESION MOLECULE L-I" , "NEURAL CELL ADHESION MOLECULE L-1" , "Neural cell adhesion molecule L-I" , "Neural cell adhesion molecule L-1" , "N-CAML-1" , "MIC-5" , "antigen identified by monoclonal antibody R-I" , "antigen identified by monoclonal antibody R-1" , "HSAS-1" , "CAML-1" , "NCAM-L-1" , "MIC-5" , "SPG-1" , "CD-171" , "N-CAM L-I" , "N-CAM L-1" ; prop:prefLabel_NO "L1CAM" ; skos:notation "120133"^^datatype:gd-notation-datatype , "120526"^^datatype:gd-notation-datatype , "619777"^^datatype:gd-notation-datatype , "20128"^^datatype:ho-notation-datatype , "NM"^^datatype:rq-notation-datatype , "16728"^^datatype:eg-notation-datatype , "3897"^^datatype:eg-notation-datatype , "50687"^^datatype:eg-notation-datatype , "619777"^^datatype:rgd-notation-datatype , "308840"^^datatype:om-notation-datatype , "6470"^^datatype:hg-notation-datatype , "P11627"^^datatype:sp-notation-datatype , "P32004"^^datatype:sp-notation-datatype , "Q05695"^^datatype:sp-notation-datatype , "Hs.522818"^^datatype:ug-notation-datatype , "96721"^^datatype:mgi-notation-datatype , "1369213"^^datatype:af-notation-datatype , "1421958"^^datatype:af-notation-datatype , "1450435"^^datatype:af-notation-datatype , "204584"^^datatype:af-notation-datatype , "204585"^^datatype:af-notation-datatype ; rdfs:label "L1CAM" ; skos:prefLabel "HSAS" , "MASA" , "N-CAML-I" , "MIC-V" , "HSAS-I" , "CAML-I" , "NCAM-L-I" , "MIC-V" , "SPG-I" ; skos:broader semtype:T116 ; a skos:Concept ; skos:inScheme vocab:GENE , vocab:HOMOLOGENE . concepts:C3000168 skos:inScheme vocab:default ; prop:altLabel_NO "CD54 antigen" , "intercellular adhesion molecule I" , "intercellular adhesion molecule1" , "Icam-1" , "CD-54" , "BB-2" , "Intercellular adhesion molecule I" , "Intercellular adhesion molecule1" , "Intercellular adhesion molecule-I" ; prop:prefLabel_NO "ICAM-1" ; skos:notation "120076"^^datatype:gd-notation-datatype , "2857"^^datatype:gd-notation-datatype , "168"^^datatype:ho-notation-datatype , "NM"^^datatype:rq-notation-datatype , "15894"^^datatype:eg-notation-datatype , "25464"^^datatype:eg-notation-datatype , "3383"^^datatype:eg-notation-datatype , "2857"^^datatype:rgd-notation-datatype , "147840"^^datatype:om-notation-datatype , "5344"^^datatype:hg-notation-datatype , "Q00238"^^datatype:sp-notation-datatype , "Q15463"^^datatype:sp-notation-datatype , "Hs.643447"^^datatype:ug-notation-datatype , "1387202"^^datatype:af-notation-datatype , "1424067"^^datatype:af-notation-datatype , "1427805"^^datatype:af-notation-datatype , "1427806"^^datatype:af-notation-datatype , "202637"^^datatype:af-notation-datatype , "202638"^^datatype:af-notation-datatype , "215485"^^datatype:af-notation-datatype ; rdfs:label "ICAM1" ; skos:prefLabel "ICAM-I" , "Icam-I" , "BB-II" ; skos:broader semtype:T116 ; a skos:Concept ; skos:inScheme vocab:GENE , vocab:HOMOLOGENE . 2014-05-01 13:27:51.940 UTC Input22 Give a list with sublist. Each sublist consist out of two elements. Such as [ [ Document_URI, Abstract_URI] ]. For an example please load in the file named: input value for full CPGP. Which can be found under the files tab on MyExperiment. 2014-05-01 14:22:24.867 UTC 2014-05-01 14:21:52.278 UTC table_name00 2014_04_30_21_24_30 2014-05-01 13:33:43.886 UTC Needs the correct table name given for writing the values. The tablename needs to be the same as the one that is created. 2014-05-02 15:02:59.945 UTC propertyString00 Please load a file in as seen in the example where the user, password, url (which is the database it should use), and driver is stated. 2014-06-11 12:01:06.826 UTC mysql.user=root mysql.password=amrishsql mysql.url=jdbc:mysql://localhost:3306/mydb mysql.driver=com.mysql.jdbc.Driver 2014-06-11 12:00:51.795 UTC Path00 Give the full path where the production.properties and peregrine-skos-cli.jar files are located of the Peregrine Indexer Tool. Which are supposed to be in the same path/Directory. path/to/ production.properties path/to/ peregrine-skos-cli.jar 2014-06-15 17:49:12.785 UTC F:/School/Stage2/peregrine/ 2014-06-15 17:40:54.119 UTC outputBeanshell_SQL_query_generator_Concept_Doc_occurrencetable_name0concept_occurence_document0out100 A Beanshell script that generates a Sql statement to INSERT the concept URI and document URI in the table named after the timestamp/tablename the workflow started. It uses a database called mydb. If there is not a database/schema named mydb, please create one. 2014-05-01 14:28:50.45 UTC net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity table_name 0 text/plain java.lang.String true concept_occurence_document 0 text/plain java.lang.String true out1 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_extract_uri_doc_and_abstractInput1abstracts00doc_uri00 A Beanshell script which loops through the input to seperate the Document URIs and Abstract URIs. 2014-03-21 13:07:52.147 UTC net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity Input 1 text/plain java.lang.String true doc_uri 0 0 abstracts 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_remove_dot_and_correct_doc_uri_in_con_docdoc_uri1concept_occurence_document0out100 A Beanshell script that replaces the temp created Taverna file with the correct Document URI. 2014-04-11 13:53:30.291 UTC net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity concept_occurence_document 0 text/plain java.lang.String true doc_uri 1 text/plain java.lang.String true out1 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExecute_SQL_Update_INSERT_INTO_occurrence_tablesql0propertyString0resultList00 Executes the SQL statement generated by the Beanshell script: "Sql_beanshell_query_generator_Concept_occ_Doc" which insert the concept and document URI into the table named 'timestamp'_occurence. 2014-05-01 14:29:19.326 UTC net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity sql 0 text/plain java.lang.String true params 1 text/plain java.lang.String true propertyString 0 text/plain java.lang.String true resultList 0 0 workflow net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker UserNameHere 2014-05-12 11:39:07.643 UTC net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokePeregrine_Indexer_toolontology0abstract_content1path0concept_per_document00 Uses a jar peregrine program to index which concept occurs in what document. Change the commands to : java -Dperegrine.config.location=your/path/to/peregrine/production.properties -jar path/to/peregrine-skos-cli.jar ontology abstract_content out1 When using a Windows machine please install cygwin. Set cygwin in the $PATH of the environment variabale. Go to Location tab select radiobutton "Select an symbolic location" and default . Press Manage locations and go to explicit locations --> edit a default local to Shell: C:\Windows\system32\cmd.exe /c and save that. -->Set Modify on: symbolic locations --> pick default --> edit and choose default local and save. When using a unix environment make sure the default local is set Shell into /bin/sh -c and link command to: /bin/ln -s %%PATH_TO_ORIGINAL%% %%TARGET_NAME%%. Save settings by clicking apply . 2014-06-11 12:11:02.104 UTC net.sf.taverna.t2.activitiesexternal-tool-activity1.4net.sf.taverna.t2.activities.externaltool.ExternalToolActivity default 789663B8-DA91-428A-9F7D-B3F3DA185FD4 default local <?xml version="1.0" encoding="UTF-8"?> <localInvocation /> 6c76743e-a600-4f7e-832f-6d0e284a1a29 java -Xmx20g -Xms20g -Dperegrine.config.location=%%pwd%%production.properties -jar %%pwd%%peregrine-skos-cli.jar ontology abstract_content concept_per_document 1200 1800 pwd abstract_content abstract_content true false false windows-1252 false true false path pwd false false false windows-1252 false false false ontology ontology true false false windows-1252 false false false concept_per_document concept_per_document false false false false 0 false net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSplit_string_into_string_list_by_regular_expressionstring0regex0split11 Uses Regex to split string into string list. 2014-03-21 13:10:43.967 UTC net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity string 0 'text/plain' java.lang.String true regex 0 'text/plain' java.lang.String true split 1 1 workflow org.embl.ebi.escience.scuflworkers.java.SplitByRegex UserNameHere 2014-03-11 10:44:03.209 UTC net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeregex_valuevalue00 Regex value of enter. 2014-05-01 14:27:23.340 UTC net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity [\n] net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_SQL_query_generator_Concept_Doc_occurrencetable_nametable_nameBeanshell_SQL_query_generator_Concept_Doc_occurrenceconcept_occurence_documentBeanshell_remove_dot_and_correct_doc_uri_in_con_docout1Beanshell_extract_uri_doc_and_abstractInputInputBeanshell_remove_dot_and_correct_doc_uri_in_con_docdoc_uriBeanshell_extract_uri_doc_and_abstractdoc_uriBeanshell_remove_dot_and_correct_doc_uri_in_con_docconcept_occurence_documentSplit_string_into_string_list_by_regular_expressionsplitExecute_SQL_Update_INSERT_INTO_occurrence_tablesqlBeanshell_SQL_query_generator_Concept_Doc_occurrenceout1Execute_SQL_Update_INSERT_INTO_occurrence_tablepropertyStringpropertyStringPeregrine_Indexer_toolontologyontologyPeregrine_Indexer_toolabstract_contentBeanshell_extract_uri_doc_and_abstractabstractsPeregrine_Indexer_toolpathPathSplit_string_into_string_list_by_regular_expressionstringPeregrine_Indexer_toolconcept_per_documentSplit_string_into_string_list_by_regular_expressionregexregex_valuevalueoutputExecute_SQL_Update_INSERT_INTO_occurrence_tableresultList 3674dfd2-59e3-4a0b-9355-9c89beb5d437 2014-05-12 08:26:10.414 UTC 21d0d9ac-38df-4c79-a6a3-95e6abd02e8f 2014-05-21 16:04:24.164 UTC 28b58762-e9a5-4336-ae8c-0de8bbde97cf 2014-05-08 13:28:53.205 UTC a6d65617-4186-4283-9a7a-7970d1a58331 2014-06-27 08:28:06.202 UTC eb47dba0-b920-4535-b634-e4db661210b5 2014-06-15 17:29:43.252 UTC 8054095d-ff1d-434d-8db7-73e0d92521ab 2014-05-01 14:56:49.352 UTC 7013adf6-1cff-4da4-a4f4-1dc8348cdefb 2014-05-08 12:48:10.297 UTC 68476bab-0e32-4f6a-8e9d-f50804088938 2014-06-10 08:28:55.760 UTC Peregrine indexer 2014-04-25 08:41:57.947 UTC ea1540f5-3320-4fd4-aae0-1a7233b7f828 2014-06-10 16:00:54.719 UTC 1ff46360-e709-4c6b-a1ed-1fec7a20532b 2014-06-15 17:49:14.94 UTC 10819a0d-58bf-4f76-86ee-9acc1332edde 2014-06-27 09:20:14.55 UTC 64734dc3-1155-4296-aefe-58117c4e2e63 2014-05-12 13:39:42.471 UTC 68bfb5a4-5361-40f7-b1e8-e9d2285f985d 2014-05-01 13:36:50.25 UTC ddac8804-8407-4785-beae-b2d5ce0a80e3 2014-05-08 15:23:53.460 UTC fe4de177-331a-46bc-919c-0b60de007289 2014-05-01 13:29:11.726 UTC 65c07cb7-552e-414e-b0d9-d691dee366dc 2014-06-10 08:32:43.599 UTC f746b38a-fa7c-4188-b916-8b157d2cbfd3 2014-05-21 16:13:01.500 UTC 417fb3f9-90d0-4da1-9b1b-71687090d140 2014-06-11 12:11:48.558 UTC 87fe3bfb-dcd3-4cf3-bca5-a4ddcf8d3b32 2014-05-05 09:43:02.878 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 c54ca59d-de52-4b86-8f4d-6f34db8e1cda 2014-06-15 17:43:35.549 UTC ef75149c-93d4-4a53-938d-598b34c547c0 2014-04-25 08:43:19.286 UTC 7a8e521a-ce70-464f-b5be-b38496ea9a7a 2014-05-02 15:03:12.106 UTC 7a8efe41-e6c8-4b99-8e20-d005bd0db003 2014-06-11 12:01:06.934 UTC e13584ce-2e64-4486-8ae5-e6e2c08f20d5 2014-05-01 14:22:50.934 UTC 2c3c56e4-87ff-48c8-a895-54c7eabeca9f 2014-05-01 14:29:30.621 UTC Amrish Mahes 2014-05-01 14:47:30.600 UTC 7d302e8e-e49f-46c2-9620-cbc9a8acd7c3 2014-05-01 13:38:12.169 UTC c45a8012-d1be-44b9-b9f1-5d547075682c 2014-05-12 11:39:52.208 UTC 899b13f9-9169-42a4-8c8f-c6c8437c9b72 2014-06-15 17:42:28.355 UTC 685e7713-6183-4320-a76a-f4bfd8d87b60 2014-06-10 16:00:27.639 UTC 58b4fc1a-33f4-45d0-8a33-f87356cc96e1 2014-04-25 08:42:29.100 UTC 5fae11dd-f324-4db1-a120-a04debed40f6 2014-06-11 08:50:56.448 UTC nestedpropertyString00 Please load a file in as seen in the example where the user, password, url (which is the database it should use), and driver is stated. 2014-06-11 11:59:30.901 UTC mysql.user=root mysql.password=amrishsql mysql.url=jdbc:mysql://localhost:3306/mydb mysql.driver=com.mysql.jdbc.Driver 2014-05-12 09:36:25.325 UTC db_resultsExecute_SQL_Querysql0propertyString0resultList22net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity sql 0 text/plain java.lang.String true params 1 text/plain java.lang.String true propertyString 0 text/plain java.lang.String true resultList 2 2 xmlresults 0 0 system mysql-connector-java.jar net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker UserNameHere 2014-05-12 09:40:09.625 UTC net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokesql_valuevalue00 SQL code for using the abstracts with their corresponding pubmed id. 2014-06-11 11:58:55.226 UTC net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity SELECT pmid, abstract_text FROM mydb.abstracts; net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExecute_SQL_Querysqlsql_valuevalueExecute_SQL_QuerypropertyStringpropertyStringdb_resultsExecute_SQL_QueryresultList nested 2014-05-08 17:44:28.277 UTC 75949b8c-bb4b-4ae7-8924-5c1fb95f5fa3 2014-06-15 17:52:50.74 UTC c614eadc-67ae-45d9-9f65-96ced3bb0c45 2014-05-12 11:36:32.316 UTC 1a3144fd-9bb3-474a-8760-ced1e79cbf60 2014-06-10 08:34:23.241 UTC 29a8b7aa-9837-4483-8e93-896c111c3780 2014-05-08 17:54:18.980 UTC 48169015-d279-400c-9a11-e0e9748f312b 2014-05-12 09:45:01.638 UTC 1bf0a549-ef7b-4c62-b298-fbcac4792269 2014-06-11 11:59:30.999 UTC 1607252e-3503-4b77-9617-ed429023613a 2014-05-12 09:26:40.211 UTC 39c6af3b-223f-4ff5-bd6f-aa2e6899ad80 2014-05-12 09:39:42.53 UTC c7bbc90c-8116-494b-ba64-8769830aff55 2014-05-12 09:36:58.375 UTC 67c5c3e5-fa09-4524-931f-b09f47abad5f 2014-05-12 08:36:52.574 UTC dd77b156-bebc-4183-952c-2e2fe4f1cc96 2014-05-12 09:38:33.591 UTC 6830ad2e-b9bd-4907-8a40-dd10863cd570 2014-05-21 16:10:52.487 UTC 00987503-eb35-484e-a701-05958e3fb254 2014-05-12 09:40:51.404 UTC 8aa3f84f-3b34-4860-b383-4e023cbf1c66 2014-05-12 09:39:08.438 UTC 08396e51-5a76-4ec0-be54-fecd90bf6e0d 2014-06-10 08:43:12.865 UTC