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 .
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User_password00
Input your sql password to acces as root.
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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.
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Driver_value00
com.mysql.jdbc.Driver
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The driver needed for all SQL query to run.
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usr_id00
root
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The user ID which is in this case root.
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url_value00
jdbc:mysql://localhost:3306/mydb
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The url value Sql connects to.
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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
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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
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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
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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
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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.
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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
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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
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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
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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
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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
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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
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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
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net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokePeregrine indexertable_namePeregrine indexerurlPeregrine indexerpasswordPeregrine indexerontologyPeregrine indexerInputPeregrine indexeruseridPeregrine indexerdriverCalculate Uncertainty CoefficientuseridCalculate Uncertainty CoefficientpasswordCalculate Uncertainty Coefficientconcept_pairsCalculate Uncertainty Coefficientcorrected_contingency_valuesCalculate Uncertainty CoefficienturlCalculate Uncertainty CoefficientdriverCalculate Uncertainty CoefficienttimestampCalculate Contincengy tableurlCalculate Contincengy tabledriverCalculate Contincengy tablepasswordCalculate Contincengy tabletable_nameCalculate Contincengy tableuseridCalculate Inner ProductuseridCalculate Inner ProductpasswordCalculate Inner Productconcept_pairsCalculate Inner ProductdriverCalculate Inner ProducttimestampCalculate Inner ProducturlCreate TablesuseridCreate TablesurlCreate TablesdriverCreate TablespasswordSummarize Big TabletimestampSummarize Big TableuseridSummarize Big TableurlSummarize Big TablepasswordSummarize Big Tabledriverend
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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
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Concept Profile Generation Pipeline
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2014-03-11 15:23:08.145 UTC
Amrish Mahes
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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_producttimestampExecute_SQL_Update_CREATE_TABLE_Inner_ProductsqlExecute_SQL_Update_CREATE_TABLE_Inner_ProductpasswordExecute_SQL_Update_CREATE_TABLE_Inner_ProductdriverExecute_SQL_Update_CREATE_TABLE_Inner_ProductuseridExecute_SQL_Update_CREATE_TABLE_Inner_Producturl
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_ProducttimestampBeanshell_SQL_generate_Get_Inner_Productconcept_pairsBeanshell_SQL_generate_INSERT_INTO_Inner_Product_tableinner_product_valueBeanshell_SQL_generate_INSERT_INTO_Inner_Product_tabletimestampBeanshell_SQL_generate_INSERT_INTO_Inner_Product_tableconcept_pairsExecute_SQL_Query_Get_Inner_ProductsqlExecute_SQL_Query_Get_Inner_ProductpasswordExecute_SQL_Query_Get_Inner_ProductdriverExecute_SQL_Query_Get_Inner_ProductuseridExecute_SQL_Query_Get_Inner_ProducturlExecute_SQL_Update_INSERT_INTO_Inner_Product_tablesqlExecute_SQL_Update_INSERT_INTO_Inner_Product_tabledriverExecute_SQL_Update_INSERT_INTO_Inner_Product_tableurlExecute_SQL_Update_INSERT_INTO_Inner_Product_tableuseridExecute_SQL_Update_INSERT_INTO_Inner_Product_tablepasswordFlatten_List_4inputlistFlatten_List_5inputlistoutput
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_nameBeanshell_SQL_query_generator_Concept_Doc_occurenceconcept_occurence_documentBeanshell_extract_uri_doc_and_abstractInputBeanshell_remove_dot_and_put_correct_doc_uri_in_con_occ_docdoc_uriBeanshell_remove_dot_and_put_correct_doc_uri_in_con_occ_docconcept_occurence_documentExecute_SQL_Update_INSERT_INTO_occurence_tablepasswordExecute_SQL_Update_INSERT_INTO_occurence_tabledriverExecute_SQL_Update_INSERT_INTO_occurence_tableuseridExecute_SQL_Update_INSERT_INTO_occurence_tableurlExecute_SQL_Update_INSERT_INTO_occurence_tablesqlIndexer_toolontologyIndexer_toolabstract_contentSplit_string_into_string_list_by_regular_expressionstringSplit_string_into_string_list_by_regular_expressionregexoutput
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_stampExecute_SQL_Update_CREATE_TABLE_UCsqlExecute_SQL_Update_CREATE_TABLE_UCpasswordExecute_SQL_Update_CREATE_TABLE_UCdriverExecute_SQL_Update_CREATE_TABLE_UCuseridExecute_SQL_Update_CREATE_TABLE_UCurl
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_occurencetimestampExecute_SQL_Update_CREATE_TABLE_Co_OccurencesqlExecute_SQL_Update_CREATE_TABLE_Co_OccurencepasswordExecute_SQL_Update_CREATE_TABLE_Co_OccurencedriverExecute_SQL_Update_CREATE_TABLE_Co_OccurenceuseridExecute_SQL_Update_CREATE_TABLE_Co_Occurenceurl
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_tabletimestampBeanshell_SQL_INSERT_UC_values_INTO_tableUC_valueBeanshell_SQL_INSERT_UC_values_INTO_tableconcept_pairsBeanshell_calculate_Uncertainty_Coefficientcorrected_contingency_valuesExecute_SQL_Update_INSERT_INTO_UC_tablepasswordExecute_SQL_Update_INSERT_INTO_UC_tablesqlExecute_SQL_Update_INSERT_INTO_UC_tabledriverExecute_SQL_Update_INSERT_INTO_UC_tableuseridExecute_SQL_Update_INSERT_INTO_UC_tableurloutput
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_pairsBeanshell_SQL_generate_contingency_tabletable_nameBeanshell_SQL_insert_into_co_occurence_tablecontingency_valuesBeanshell_SQL_insert_into_co_occurence_tableconcept_pairsBeanshell_SQL_insert_into_co_occurence_tabletimestampBeanshell_correct_contincengy_tablecontingency_valuesBeanshell_generate_SQL_statement_Get_destinct_concepttable_nameBeanshell_make_concept_pairsconcept_ABeanshell_make_concept_pairsconcept_BExecute_SQL_QuerysqlExecute_SQL_QuerypasswordExecute_SQL_QuerydriverExecute_SQL_QueryurlExecute_SQL_QueryuseridExecute_SQL_Query_2sqlExecute_SQL_Query_2passwordExecute_SQL_Query_2driverExecute_SQL_Query_2urlExecute_SQL_Query_2useridExecute_SQL_Update_INSERT_INTO_Co_occurence_tablesqlExecute_SQL_Update_INSERT_INTO_Co_occurence_tablepasswordExecute_SQL_Update_INSERT_INTO_Co_occurence_tabledriverExecute_SQL_Update_INSERT_INTO_Co_occurence_tableuseridExecute_SQL_Update_INSERT_INTO_Co_occurence_tableurlFlatten_ListinputlistFlatten_List_2inputlistFlatten_List_3inputlistoutputlistcorrected_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_tabletimeStampExecute_SQL_Update_CREATE_TABLE_OccurencepasswordExecute_SQL_Update_CREATE_TABLE_OccurencedriverExecute_SQL_Update_CREATE_TABLE_OccurenceuseridExecute_SQL_Update_CREATE_TABLE_OccurenceurlExecute_SQL_Update_CREATE_TABLE_Occurencesql
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 TabletimestampCREATE Big TablepasswordCREATE Big TabledriverCREATE Big TableuseridCREATE Big TableurlCREATE Co-occurence TabletimestampCREATE Co-occurence TablepasswordCREATE Co-occurence TabledriverCREATE Co-occurence TableuseridCREATE Co-occurence TableurlCREATE UC TableurlCREATE UC TableuseridCREATE UC TabledriverCREATE UC TablepasswordCREATE UC Tabletime_stampCREATE Occurence TabletimeStampCREATE Occurence TablepasswordCREATE Occurence TabledriverCREATE Occurence TableuseridCREATE Occurence TableurlCREATE Inner Product TabletimestampCREATE Inner Product TablepasswordCREATE Inner Product TabledriverCREATE Inner Product TableuseridCREATE Inner Product TableurltimeStamp
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_tabletimestampExecute_SQL_Update_CREATE_TABLE_big_datasqlExecute_SQL_Update_CREATE_TABLE_big_datadriverExecute_SQL_Update_CREATE_TABLE_big_datapasswordExecute_SQL_Update_CREATE_TABLE_big_datauseridExecute_SQL_Update_CREATE_TABLE_big_dataurl
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
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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
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4b65159f-b6b4-4457-b9db-59672f7c2c7d
2014-04-25 10:24:37.597 UTC
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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