_CPGP_Peregrine_Get_Ontology_input00
A Skos formated dictionary/thesaurus of predefined concepts.
2014-04-11 13:48:01.261 UTC
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix dct: <http://purl.org/dc/terms/> .
@prefix emco: <http://rdf.biosemantics.org/emco/> .
@prefix emco15: <http://rdf.biosemantics.org/emco/v1.5/> .
@prefix concepts: <http://rdf.biosemantics.org/emco/v1.5/concepts/> .
@prefix prop: <http://rdf.biosemantics.org/emco/properties/> .
@prefix datatype: <http://rdf.biosemantics.org/emco/datatypes/> .
@prefix semtype: <http://rdf.biosemantics.org/emco/semtypes/> .
@prefix vocab: <http://rdf.biosemantics.org/emco/v1.5/vocabularies/> .
prop:prefLabel_CI rdfs:subPropertyOf skos:prefLabel .
prop:prefLabel_NO rdfs:subPropertyOf skos:prefLabel .
prop:prefLabel_CI_NO rdfs:subPropertyOf skos:prefLabel .
prop:altLabel_CI rdfs:subPropertyOf skos:altLabel .
prop:altLabel_NO rdfs:subPropertyOf skos:altLabel .
prop:altLabel_CI_NO rdfs:subPropertyOf skos:altLabel .
vocab:default rdfs:comment "ErasmusMC ontology file" ;
dct:title "Anni2_1_June2009" ;
a skos:ConceptScheme .
vocab:MSH dct:title "MeSH" ;
a skos:ConceptScheme .
vocab:SNOMEDCT dct:title "SNOMED Clinical Terms" ;
a skos:ConceptScheme .
semtype:T47 skos:topConceptOf vocab:default ;
rdfs:label "Disease or Syndrome" ;
skos:definition "A condition which alters or interferes with a normal process, state, or activity of an organism. It is usually characterized by the abnormal functioning of one or more of the host's systems, parts, or organs. Included here is a complex of symptoms descriptive of a disorder." ;
a skos:Concept .
concepts:C9187 skos:inScheme vocab:default ;
prop:altLabel_CI_NO "Coccidiosis"@es ;
prop:prefLabel_CI_NO "Coccidiosis" ;
skos:notation "C0009187"^^datatype:umls-notation-datatype ;
rdfs:label "Coccidiosis" ;
skos:definition "Protozoan infection found in animals and man. It is caused by several different genera of COCCIDIA." ;
skos:broader semtype:T47 ;
a skos:Concept ;
skos:inScheme vocab:MSH , vocab:SNOMEDCT .
concepts:C24530 skos:inScheme vocab:default ;
prop:altLabel_CI_NO "Malaria NOS" , "Plasmodium Infections" , "Remittent Fever" , "Paludism" , "Plasmodiosis" , "Malarial fever" , "Malaria (disorder)" , "Marsh Fever" , "Malaria"@es ;
prop:prefLabel_CI "Malaria" ;
skos:notation "C0024530"^^datatype:umls-notation-datatype ;
rdfs:label "test" ;
skos:broader concepts:C9187 , semtype:T47 ;
a skos:Concept ;
skos:inScheme vocab:MSH , vocab:SNOMEDCT .
concepts:C3031092 skos:inScheme vocab:default ;
prop:altLabel_NO "myelocytomatosis viral oncogene homolog (avian)" , "myelocytomatosis oncogene" , "Transcription factor p64" , "Myc proto-oncogene protein" , "v-myc myelocytomatosis viral oncogene homolog (avian)" , "Myc2" , "myc proto-oncogene protein" , "Transcription factor p-64" , "Myc-2" ;
skos:notation "120208"^^datatype:gd-notation-datatype , "3130"^^datatype:gd-notation-datatype , "31092"^^datatype:ho-notation-datatype , "NM"^^datatype:rq-notation-datatype , "17869"^^datatype:eg-notation-datatype , "24577"^^datatype:eg-notation-datatype , "4609"^^datatype:eg-notation-datatype , "3130"^^datatype:rgd-notation-datatype , "190080"^^datatype:om-notation-datatype , "7553"^^datatype:hg-notation-datatype , "P01106"^^datatype:sp-notation-datatype , "P01108"^^datatype:sp-notation-datatype , "P09416"^^datatype:sp-notation-datatype , "Q6WDF7"^^datatype:sp-notation-datatype , "Hs.202453"^^datatype:ug-notation-datatype , "97250"^^datatype:mgi-notation-datatype , "1368308"^^datatype:af-notation-datatype , "1424942"^^datatype:af-notation-datatype , "202431"^^datatype:af-notation-datatype , "239931"^^datatype:af-notation-datatype ;
rdfs:label "MYC" ;
skos:prefLabel "MYC" , "C-MYC" , "Myc" , "Niard" , "Nird" , "c-Myc" , "c-myc" , "Myc-II" ;
skos:broader semtype:T116 ;
a skos:Concept ;
skos:inScheme vocab:GENE , vocab:HOMOLOGENE .
concepts:C3003921 skos:inScheme vocab:default ;
prop:altLabel_NO "v-myc myelocytomatosis viral oncogene homolog 1, lung carcinoma derived (avian)" , "oncogene lmyc" , "l-myc-1 proto-oncogene" , "Lmyc1" , "myc-related gene from lung cancer" , "Oncogene MYC, lung carcinoma-derived" , "l-myc protein" , "Lmyc-1" , "Mycl1" , "L-myc-1 proto-oncogene protein" , "v-myc myelocytomatosis viral oncogene homolog 1, lung carcinoma derived (avian) (mapped)" , "v-myc avian myelocytomatosis viral oncogene homolog 1, lung carcinoma derived" , "MYCL-1" , "Mycl-1" ;
prop:prefLabel_NO "MYCL1" ;
skos:notation "120706"^^datatype:gd-notation-datatype , "1588591"^^datatype:gd-notation-datatype , "3921"^^datatype:ho-notation-datatype , "NM"^^datatype:rq-notation-datatype , "16918"^^datatype:eg-notation-datatype , "298506"^^datatype:eg-notation-datatype , "4610"^^datatype:eg-notation-datatype , "1588591"^^datatype:rgd-notation-datatype , "164850"^^datatype:om-notation-datatype , "7555"^^datatype:hg-notation-datatype , "P10166"^^datatype:sp-notation-datatype , "P12524"^^datatype:sp-notation-datatype , "Q6TLI1"^^datatype:sp-notation-datatype , "Hs.437922"^^datatype:ug-notation-datatype , "96799"^^datatype:mgi-notation-datatype , "1422087"^^datatype:af-notation-datatype , "1422088"^^datatype:af-notation-datatype , "214058"^^datatype:af-notation-datatype ;
rdfs:label "MYCL1" ;
skos:prefLabel "LMYC" , "MYCL" , "MYCL" , "MYCL-I" , "Lmyc-I" , "Mycl-I" ;
skos:broader semtype:T116 ;
a skos:Concept ;
skos:inScheme vocab:GENE , vocab:HOMOLOGENE .
concepts:C3003922 skos:inScheme vocab:default ;
prop:altLabel_NO "v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian) (mapped)" , "v-myc myelocytomatosis viral related oncogene, neuroblastoma derived" , "v-myc avian myelocytomatosis viral related oncogene, neuroblastoma derived" , "Nmyc-1" , "neuroblastoma-derived v-myc avian myelocytomatosis viral related oncogene" , "v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)" , "N-MYC PROTO-ONCOGENE PROTEIN" , "Nmyc1" , "neuroblastoma MYC oncogene" , "pp65/67" , "oncogene NMYC" , "Oncogene NMYC" , "N-myc proto-oncogene protein" ;
skos:notation "120527"^^datatype:gd-notation-datatype , "1584995"^^datatype:gd-notation-datatype , "3922"^^datatype:ho-notation-datatype , "NM"^^datatype:rq-notation-datatype , "18109"^^datatype:eg-notation-datatype , "298894"^^datatype:eg-notation-datatype , "4613"^^datatype:eg-notation-datatype , "1584995"^^datatype:rgd-notation-datatype , "164840"^^datatype:om-notation-datatype , "7559"^^datatype:hg-notation-datatype , "P03966"^^datatype:sp-notation-datatype , "Q53XS5"^^datatype:sp-notation-datatype , "Q63379"^^datatype:sp-notation-datatype , "Hs.25960"^^datatype:ug-notation-datatype , "97357"^^datatype:mgi-notation-datatype , "1417155"^^datatype:af-notation-datatype , "1425922"^^datatype:af-notation-datatype , "1425923"^^datatype:af-notation-datatype , "209756"^^datatype:af-notation-datatype , "209757"^^datatype:af-notation-datatype , "211377"^^datatype:af-notation-datatype , "234376"^^datatype:af-notation-datatype ;
rdfs:label "MYCN" ;
skos:prefLabel "MYCN" , "Mycn" , "N-myc" , "ODED" , "MODED" , "Nmyc" , "NMYC" , "Nmyc-I" ;
skos:broader semtype:T116 ;
a skos:Concept ;
skos:inScheme vocab:GENE , vocab:HOMOLOGENE .
concepts:C3020128 skos:inScheme vocab:default ;
prop:altLabel_NO "neural cell adhesion molecule L1" , "NEURAL CELL ADHESION MOLECULE L1" , "Neural cell adhesion molecule L1" , "N-CAML1" , "L1cam" , "MIC5" , "antigen identified by monoclonal antibody R1" , "L1 cell adhesion molecule (hydrocephalus, stenosis of aqueduct of Sylvius 1, MASA (mental retardation, aphasia, shuffling gait and adducted thumbs) syndrome, spastic paraplegia 1)" , "CD171 antigen" , "HSAS1" , "S10" , "CAML1" , "NCAM-L1" , "MIC5" , "L1 cell adhesion molecule" , "SPG1" , "CD171" , "N-CAM L1" , "neural cell adhesion molecule L-I" , "neural cell adhesion molecule L-1" , "NEURAL CELL ADHESION MOLECULE L-I" , "NEURAL CELL ADHESION MOLECULE L-1" , "Neural cell adhesion molecule L-I" , "Neural cell adhesion molecule L-1" , "N-CAML-1" , "MIC-5" , "antigen identified by monoclonal antibody R-I" , "antigen identified by monoclonal antibody R-1" , "HSAS-1" , "CAML-1" , "NCAM-L-1" , "MIC-5" , "SPG-1" , "CD-171" , "N-CAM L-I" , "N-CAM L-1" ;
prop:prefLabel_NO "L1CAM" ;
skos:notation "120133"^^datatype:gd-notation-datatype , "120526"^^datatype:gd-notation-datatype , "619777"^^datatype:gd-notation-datatype , "20128"^^datatype:ho-notation-datatype , "NM"^^datatype:rq-notation-datatype , "16728"^^datatype:eg-notation-datatype , "3897"^^datatype:eg-notation-datatype , "50687"^^datatype:eg-notation-datatype , "619777"^^datatype:rgd-notation-datatype , "308840"^^datatype:om-notation-datatype , "6470"^^datatype:hg-notation-datatype , "P11627"^^datatype:sp-notation-datatype , "P32004"^^datatype:sp-notation-datatype , "Q05695"^^datatype:sp-notation-datatype , "Hs.522818"^^datatype:ug-notation-datatype , "96721"^^datatype:mgi-notation-datatype , "1369213"^^datatype:af-notation-datatype , "1421958"^^datatype:af-notation-datatype , "1450435"^^datatype:af-notation-datatype , "204584"^^datatype:af-notation-datatype , "204585"^^datatype:af-notation-datatype ;
rdfs:label "L1CAM" ;
skos:prefLabel "HSAS" , "MASA" , "N-CAML-I" , "MIC-V" , "HSAS-I" , "CAML-I" , "NCAM-L-I" , "MIC-V" , "SPG-I" ;
skos:broader semtype:T116 ;
a skos:Concept ;
skos:inScheme vocab:GENE , vocab:HOMOLOGENE .
concepts:C3000168 skos:inScheme vocab:default ;
prop:altLabel_NO "CD54 antigen" , "intercellular adhesion molecule I" , "intercellular adhesion molecule1" , "Icam-1" , "CD-54" , "BB-2" , "Intercellular adhesion molecule I" , "Intercellular adhesion molecule1" , "Intercellular adhesion molecule-I" ;
prop:prefLabel_NO "ICAM-1" ;
skos:notation "120076"^^datatype:gd-notation-datatype , "2857"^^datatype:gd-notation-datatype , "168"^^datatype:ho-notation-datatype , "NM"^^datatype:rq-notation-datatype , "15894"^^datatype:eg-notation-datatype , "25464"^^datatype:eg-notation-datatype , "3383"^^datatype:eg-notation-datatype , "2857"^^datatype:rgd-notation-datatype , "147840"^^datatype:om-notation-datatype , "5344"^^datatype:hg-notation-datatype , "Q00238"^^datatype:sp-notation-datatype , "Q15463"^^datatype:sp-notation-datatype , "Hs.643447"^^datatype:ug-notation-datatype , "1387202"^^datatype:af-notation-datatype , "1424067"^^datatype:af-notation-datatype , "1427805"^^datatype:af-notation-datatype , "1427806"^^datatype:af-notation-datatype , "202637"^^datatype:af-notation-datatype , "202638"^^datatype:af-notation-datatype , "215485"^^datatype:af-notation-datatype ;
rdfs:label "ICAM1" ;
skos:prefLabel "ICAM-I" , "Icam-I" , "BB-II" ;
skos:broader semtype:T116 ;
a skos:Concept ;
skos:inScheme vocab:GENE , vocab:HOMOLOGENE .
2014-03-21 13:04:42.508 UTC
db_properties00
Please load a file in as seen in the example where the user, password, url (which is the database it should use), and driver is stated.
2014-05-12 14:03:22.531 UTC
mysql.user=root
mysql.password=amrishsql
mysql.url=jdbc:mysql://localhost:3306/mydb
mysql.driver=com.mysql.jdbc.Driver
2014-05-12 09:23:12.452 UTC
Path_Peregrine_Indexer00
Give the full path where the production.properties and peregrine-skos-cli.jar files are located of the Peregrine Indexer Tool. Which are supposed to be in the same path/Directory.
path/to/ production.properties
path/to/ peregrine-skos-cli.jar
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F:/School/Stage2/peregrine/
2014-06-15 17:31:44.152 UTC
endPeregrine_Indexertable_name0ontology0Input2propertyString0Path0output11
The nested workflow Peregrine Indexer uses a java peregrine skos cli.jar file to index the occurrence of concepts in documents.
The Peregrine indexer program can be downloaded from trac.nbic.nl/biosemantics/downloads.
Install LVG2013Lite. See: https://trac.nbic.nl/biosemantics/wiki/Peregrine%20SKOS%20CLI
Copy properties file from production.properties which can be downloaded from: https://trac.nbic.nl/biosemantics/wiki/Peregrine%20SKOS%20CLI
Change lvg.properties
LVG_DIR=/home/path/to/lvg2013lite/
This file can be found in:
/home/path/to/lvg2013lite/data/config/lvg.properties
Change the normalizer.lvg.properties and normalizer.lvg.binaryCache properties to point to the LVG installation path.
normalizer.lvg.properties =/home/path/to/lvg2013lite/data/config/config/lvg.properties normalizer.lvg.binaryCahce=/home/path/to/lvg2013lite/standartNormCache2013.bin
Have MySQL installed with a database called mydb or please create one.
Have mysql-connector-java-5.1.28-bin.jar or better placed in the local JAR files.
2014-06-11 11:57:41.849 UTC
net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeCreate_Tablesdb_properties0timeStamp00
This nested workflows creates the necessary tables for inserting the generated values. The following tables are created:
- Co-occurrence table
- Occurrence table
- Uncertainty coefficient table
- Inner product table
- Summary table
2014-06-11 11:53:41.270 UTC
net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGet_abstractspropertyString0db_results22
A nested workflow to retrieve abstracts from a sql table. This table is assumed to have atleast two columns consisting out of pmid and abstract text.
2014-06-11 11:04:59.773 UTC
net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokePeregrine_Indexertable_namePeregrine_IndexerontologyPeregrine_IndexerInputPeregrine_IndexerpropertyStringPeregrine_IndexerPathCreate_Tablesdb_propertiesGet_abstractspropertyStringend
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CPGP Peregrine Get Abstracts Create tables
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Amrish Mahes
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Requirements:
Have MySQL installed with a database called mydb or please create one.
Have a mysql connector file. This can be downloaded from mysql.com.
Rename the downloaded file to mysql-connector-java.jar and place it in the the local lib file of Taverna as written on the dependencies tab.
Choose this dependency by rightclicking a beanshell script and selecting it for the whole workflow as system classloader.
Download the Peregrine SKOS CLI from: https://trac.nbic.nl/biosemantics/downloads
Install LVG2013Lite. See: https://trac.nbic.nl/biosemantics/wiki/Peregrine%20SKOS%20CLI
Change lvg.properties
LVG_DIR=/home/path/to/lvg2013lite/
This file can be found in:
/home/path/to/lvg2013lite/data/config/lvg.properties
Copy properties file from production.properties which can be found on: https://trac.nbic.nl/biosemantics/wiki/Peregrine%20SKOS%20CLI
Change the normalizer.lvg.properties and normalizer.lvg.binaryCache properties to point to the LVG installation path.
This file can be obtained from https://trac.nbic.nl/biosemantics/wiki/Peregrine%20SKOS%20CLI
Have Peregrine indexer installed locally and give it the correct path in the component named "Indexer_tool". Which can be found in the nested workflow named Peregrine indexer.
Optional:
If using a Windows machine please install cygwin. Set cygwin in the $PATH of the environment variabale.
Go to taverna File --> preferences --> Tool invocation --> set modify on explicit locations --> edit a default local to Shell: C:\Windows\system32\cmd.exe /c and save that. -->Set Modify on: symbolic locations --> edit --> choose default local and save. When using a unix environment make sure the default local is set Shell into /bin/sh -c.
Please make sure this is also set into the indexer tool part.
Have JAVA_HOME C:\Program Files\jdk 1.7.0 in environment variabale when using Windows.
The nested workflow Get_abstract uses a sql command to retrieve abstracts which assumes are located in the database mydb. If this is not the case, please change the database in the SQL value.
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2014-03-18 12:18:13.691 UTC
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2014-03-13 17:11:35.775 UTC
1c51b3f3-9137-47a7-85ac-8bf8f1d86dde
2014-04-14 11:04:37.235 UTC
3dee3c3f-9568-4261-8f49-e84aaff43613
2014-04-14 08:47:36.378 UTC
Create Tablesdb_properties00
Please load a file in as seen in the example where the user, password, url (which is the database it should use), and driver is stated.
2014-06-11 12:42:39.196 UTC
mysql.user=root
mysql.password=amrishsql
mysql.url=jdbc:mysql://localhost:3306/mydb
mysql.driver=com.mysql.jdbc.Driver
2014-06-11 12:42:50.723 UTC
timeStampBeanshell_get_timestamptimeStamp00
A Beanshell script which retreives the time the program started.
As in year, month, day, hour, minutes and seconds in military time.
2014-04-11 13:57:49.999 UTC
net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity
timeStamp
0
0
workflow
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_SQL_Create_TablestimeStamp0Table_sql00
A Beanshell script for creating the tables.
2014-06-15 17:25:33.10 UTC
net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity
timeStamp
0
text/plain
java.lang.String
true
Table_sql
0
0
workflow
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExecute_SQL_UpdatepropertyString0sql0net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity
sql
0
text/plain
java.lang.String
true
params
1
text/plain
java.lang.String
true
propertyString
0
text/plain
java.lang.String
true
resultList
0
0
workflow
net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker
UserNameHere
2014-06-15 16:25:51.599 UTC
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
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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
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSplit_string_into_string_list_by_regular_expressionregex0string0split11net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity
string
0
'text/plain'
java.lang.String
true
regex
0
'text/plain'
java.lang.String
true
split
1
l('text/plain')
1
workflow
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
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net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeregex_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity
[\n]
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
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net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_SQL_Create_TablestimeStampExecute_SQL_UpdatepropertyStringExecute_SQL_UpdatesqlSplit_string_into_string_list_by_regular_expressionregexSplit_string_into_string_list_by_regular_expressionstringtimeStamp
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2014-06-15 16:13:50.623 UTC
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Create Tables
2014-04-25 09:03:12.547 UTC
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2014-04-25 09:08:00.69 UTC
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2014-06-10 10:56:30.827 UTC
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1c464dba-d276-4ea4-8e3d-e37f4893e7d0
2014-06-15 16:54:44.837 UTC
Peregrine indexerontology00
A Skos formated dictionary/thesaurus of predefined concepts.
2014-05-01 14:22:40.779 UTC
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix dct: <http://purl.org/dc/terms/> .
@prefix emco: <http://rdf.biosemantics.org/emco/> .
@prefix emco15: <http://rdf.biosemantics.org/emco/v1.5/> .
@prefix concepts: <http://rdf.biosemantics.org/emco/v1.5/concepts/> .
@prefix prop: <http://rdf.biosemantics.org/emco/properties/> .
@prefix datatype: <http://rdf.biosemantics.org/emco/datatypes/> .
@prefix semtype: <http://rdf.biosemantics.org/emco/semtypes/> .
@prefix vocab: <http://rdf.biosemantics.org/emco/v1.5/vocabularies/> .
prop:prefLabel_CI rdfs:subPropertyOf skos:prefLabel .
prop:prefLabel_NO rdfs:subPropertyOf skos:prefLabel .
prop:prefLabel_CI_NO rdfs:subPropertyOf skos:prefLabel .
prop:altLabel_CI rdfs:subPropertyOf skos:altLabel .
prop:altLabel_NO rdfs:subPropertyOf skos:altLabel .
prop:altLabel_CI_NO rdfs:subPropertyOf skos:altLabel .
vocab:default rdfs:comment "ErasmusMC ontology file" ;
dct:title "Anni2_1_June2009" ;
a skos:ConceptScheme .
vocab:MSH dct:title "MeSH" ;
a skos:ConceptScheme .
vocab:SNOMEDCT dct:title "SNOMED Clinical Terms" ;
a skos:ConceptScheme .
semtype:T47 skos:topConceptOf vocab:default ;
rdfs:label "Disease or Syndrome" ;
skos:definition "A condition which alters or interferes with a normal process, state, or activity of an organism. It is usually characterized by the abnormal functioning of one or more of the host's systems, parts, or organs. Included here is a complex of symptoms descriptive of a disorder." ;
a skos:Concept .
concepts:C9187 skos:inScheme vocab:default ;
prop:altLabel_CI_NO "Coccidiosis"@es ;
prop:prefLabel_CI_NO "Coccidiosis" ;
skos:notation "C0009187"^^datatype:umls-notation-datatype ;
rdfs:label "Coccidiosis" ;
skos:definition "Protozoan infection found in animals and man. It is caused by several different genera of COCCIDIA." ;
skos:broader semtype:T47 ;
a skos:Concept ;
skos:inScheme vocab:MSH , vocab:SNOMEDCT .
concepts:C24530 skos:inScheme vocab:default ;
prop:altLabel_CI_NO "Malaria NOS" , "Plasmodium Infections" , "Remittent Fever" , "Paludism" , "Plasmodiosis" , "Malarial fever" , "Malaria (disorder)" , "Marsh Fever" , "Malaria"@es ;
prop:prefLabel_CI "Malaria" ;
skos:notation "C0024530"^^datatype:umls-notation-datatype ;
rdfs:label "test" ;
skos:broader concepts:C9187 , semtype:T47 ;
a skos:Concept ;
skos:inScheme vocab:MSH , vocab:SNOMEDCT .
concepts:C3031092 skos:inScheme vocab:default ;
prop:altLabel_NO "myelocytomatosis viral oncogene homolog (avian)" , "myelocytomatosis oncogene" , "Transcription factor p64" , "Myc proto-oncogene protein" , "v-myc myelocytomatosis viral oncogene homolog (avian)" , "Myc2" , "myc proto-oncogene protein" , "Transcription factor p-64" , "Myc-2" ;
skos:notation "120208"^^datatype:gd-notation-datatype , "3130"^^datatype:gd-notation-datatype , "31092"^^datatype:ho-notation-datatype , "NM"^^datatype:rq-notation-datatype , "17869"^^datatype:eg-notation-datatype , "24577"^^datatype:eg-notation-datatype , "4609"^^datatype:eg-notation-datatype , "3130"^^datatype:rgd-notation-datatype , "190080"^^datatype:om-notation-datatype , "7553"^^datatype:hg-notation-datatype , "P01106"^^datatype:sp-notation-datatype , "P01108"^^datatype:sp-notation-datatype , "P09416"^^datatype:sp-notation-datatype , "Q6WDF7"^^datatype:sp-notation-datatype , "Hs.202453"^^datatype:ug-notation-datatype , "97250"^^datatype:mgi-notation-datatype , "1368308"^^datatype:af-notation-datatype , "1424942"^^datatype:af-notation-datatype , "202431"^^datatype:af-notation-datatype , "239931"^^datatype:af-notation-datatype ;
rdfs:label "MYC" ;
skos:prefLabel "MYC" , "C-MYC" , "Myc" , "Niard" , "Nird" , "c-Myc" , "c-myc" , "Myc-II" ;
skos:broader semtype:T116 ;
a skos:Concept ;
skos:inScheme vocab:GENE , vocab:HOMOLOGENE .
concepts:C3003921 skos:inScheme vocab:default ;
prop:altLabel_NO "v-myc myelocytomatosis viral oncogene homolog 1, lung carcinoma derived (avian)" , "oncogene lmyc" , "l-myc-1 proto-oncogene" , "Lmyc1" , "myc-related gene from lung cancer" , "Oncogene MYC, lung carcinoma-derived" , "l-myc protein" , "Lmyc-1" , "Mycl1" , "L-myc-1 proto-oncogene protein" , "v-myc myelocytomatosis viral oncogene homolog 1, lung carcinoma derived (avian) (mapped)" , "v-myc avian myelocytomatosis viral oncogene homolog 1, lung carcinoma derived" , "MYCL-1" , "Mycl-1" ;
prop:prefLabel_NO "MYCL1" ;
skos:notation "120706"^^datatype:gd-notation-datatype , "1588591"^^datatype:gd-notation-datatype , "3921"^^datatype:ho-notation-datatype , "NM"^^datatype:rq-notation-datatype , "16918"^^datatype:eg-notation-datatype , "298506"^^datatype:eg-notation-datatype , "4610"^^datatype:eg-notation-datatype , "1588591"^^datatype:rgd-notation-datatype , "164850"^^datatype:om-notation-datatype , "7555"^^datatype:hg-notation-datatype , "P10166"^^datatype:sp-notation-datatype , "P12524"^^datatype:sp-notation-datatype , "Q6TLI1"^^datatype:sp-notation-datatype , "Hs.437922"^^datatype:ug-notation-datatype , "96799"^^datatype:mgi-notation-datatype , "1422087"^^datatype:af-notation-datatype , "1422088"^^datatype:af-notation-datatype , "214058"^^datatype:af-notation-datatype ;
rdfs:label "MYCL1" ;
skos:prefLabel "LMYC" , "MYCL" , "MYCL" , "MYCL-I" , "Lmyc-I" , "Mycl-I" ;
skos:broader semtype:T116 ;
a skos:Concept ;
skos:inScheme vocab:GENE , vocab:HOMOLOGENE .
concepts:C3003922 skos:inScheme vocab:default ;
prop:altLabel_NO "v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian) (mapped)" , "v-myc myelocytomatosis viral related oncogene, neuroblastoma derived" , "v-myc avian myelocytomatosis viral related oncogene, neuroblastoma derived" , "Nmyc-1" , "neuroblastoma-derived v-myc avian myelocytomatosis viral related oncogene" , "v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)" , "N-MYC PROTO-ONCOGENE PROTEIN" , "Nmyc1" , "neuroblastoma MYC oncogene" , "pp65/67" , "oncogene NMYC" , "Oncogene NMYC" , "N-myc proto-oncogene protein" ;
skos:notation "120527"^^datatype:gd-notation-datatype , "1584995"^^datatype:gd-notation-datatype , "3922"^^datatype:ho-notation-datatype , "NM"^^datatype:rq-notation-datatype , "18109"^^datatype:eg-notation-datatype , "298894"^^datatype:eg-notation-datatype , "4613"^^datatype:eg-notation-datatype , "1584995"^^datatype:rgd-notation-datatype , "164840"^^datatype:om-notation-datatype , "7559"^^datatype:hg-notation-datatype , "P03966"^^datatype:sp-notation-datatype , "Q53XS5"^^datatype:sp-notation-datatype , "Q63379"^^datatype:sp-notation-datatype , "Hs.25960"^^datatype:ug-notation-datatype , "97357"^^datatype:mgi-notation-datatype , "1417155"^^datatype:af-notation-datatype , "1425922"^^datatype:af-notation-datatype , "1425923"^^datatype:af-notation-datatype , "209756"^^datatype:af-notation-datatype , "209757"^^datatype:af-notation-datatype , "211377"^^datatype:af-notation-datatype , "234376"^^datatype:af-notation-datatype ;
rdfs:label "MYCN" ;
skos:prefLabel "MYCN" , "Mycn" , "N-myc" , "ODED" , "MODED" , "Nmyc" , "NMYC" , "Nmyc-I" ;
skos:broader semtype:T116 ;
a skos:Concept ;
skos:inScheme vocab:GENE , vocab:HOMOLOGENE .
concepts:C3020128 skos:inScheme vocab:default ;
prop:altLabel_NO "neural cell adhesion molecule L1" , "NEURAL CELL ADHESION MOLECULE L1" , "Neural cell adhesion molecule L1" , "N-CAML1" , "L1cam" , "MIC5" , "antigen identified by monoclonal antibody R1" , "L1 cell adhesion molecule (hydrocephalus, stenosis of aqueduct of Sylvius 1, MASA (mental retardation, aphasia, shuffling gait and adducted thumbs) syndrome, spastic paraplegia 1)" , "CD171 antigen" , "HSAS1" , "S10" , "CAML1" , "NCAM-L1" , "MIC5" , "L1 cell adhesion molecule" , "SPG1" , "CD171" , "N-CAM L1" , "neural cell adhesion molecule L-I" , "neural cell adhesion molecule L-1" , "NEURAL CELL ADHESION MOLECULE L-I" , "NEURAL CELL ADHESION MOLECULE L-1" , "Neural cell adhesion molecule L-I" , "Neural cell adhesion molecule L-1" , "N-CAML-1" , "MIC-5" , "antigen identified by monoclonal antibody R-I" , "antigen identified by monoclonal antibody R-1" , "HSAS-1" , "CAML-1" , "NCAM-L-1" , "MIC-5" , "SPG-1" , "CD-171" , "N-CAM L-I" , "N-CAM L-1" ;
prop:prefLabel_NO "L1CAM" ;
skos:notation "120133"^^datatype:gd-notation-datatype , "120526"^^datatype:gd-notation-datatype , "619777"^^datatype:gd-notation-datatype , "20128"^^datatype:ho-notation-datatype , "NM"^^datatype:rq-notation-datatype , "16728"^^datatype:eg-notation-datatype , "3897"^^datatype:eg-notation-datatype , "50687"^^datatype:eg-notation-datatype , "619777"^^datatype:rgd-notation-datatype , "308840"^^datatype:om-notation-datatype , "6470"^^datatype:hg-notation-datatype , "P11627"^^datatype:sp-notation-datatype , "P32004"^^datatype:sp-notation-datatype , "Q05695"^^datatype:sp-notation-datatype , "Hs.522818"^^datatype:ug-notation-datatype , "96721"^^datatype:mgi-notation-datatype , "1369213"^^datatype:af-notation-datatype , "1421958"^^datatype:af-notation-datatype , "1450435"^^datatype:af-notation-datatype , "204584"^^datatype:af-notation-datatype , "204585"^^datatype:af-notation-datatype ;
rdfs:label "L1CAM" ;
skos:prefLabel "HSAS" , "MASA" , "N-CAML-I" , "MIC-V" , "HSAS-I" , "CAML-I" , "NCAM-L-I" , "MIC-V" , "SPG-I" ;
skos:broader semtype:T116 ;
a skos:Concept ;
skos:inScheme vocab:GENE , vocab:HOMOLOGENE .
concepts:C3000168 skos:inScheme vocab:default ;
prop:altLabel_NO "CD54 antigen" , "intercellular adhesion molecule I" , "intercellular adhesion molecule1" , "Icam-1" , "CD-54" , "BB-2" , "Intercellular adhesion molecule I" , "Intercellular adhesion molecule1" , "Intercellular adhesion molecule-I" ;
prop:prefLabel_NO "ICAM-1" ;
skos:notation "120076"^^datatype:gd-notation-datatype , "2857"^^datatype:gd-notation-datatype , "168"^^datatype:ho-notation-datatype , "NM"^^datatype:rq-notation-datatype , "15894"^^datatype:eg-notation-datatype , "25464"^^datatype:eg-notation-datatype , "3383"^^datatype:eg-notation-datatype , "2857"^^datatype:rgd-notation-datatype , "147840"^^datatype:om-notation-datatype , "5344"^^datatype:hg-notation-datatype , "Q00238"^^datatype:sp-notation-datatype , "Q15463"^^datatype:sp-notation-datatype , "Hs.643447"^^datatype:ug-notation-datatype , "1387202"^^datatype:af-notation-datatype , "1424067"^^datatype:af-notation-datatype , "1427805"^^datatype:af-notation-datatype , "1427806"^^datatype:af-notation-datatype , "202637"^^datatype:af-notation-datatype , "202638"^^datatype:af-notation-datatype , "215485"^^datatype:af-notation-datatype ;
rdfs:label "ICAM1" ;
skos:prefLabel "ICAM-I" , "Icam-I" , "BB-II" ;
skos:broader semtype:T116 ;
a skos:Concept ;
skos:inScheme vocab:GENE , vocab:HOMOLOGENE .
2014-05-01 13:27:51.940 UTC
Input22
Give a list with sublist. Each sublist consist out of two elements.
Such as [ [ Document_URI, Abstract_URI] ].
For an example please load in the file named: input value for full CPGP.
Which can be found under the files tab on MyExperiment.
2014-05-01 14:22:24.867 UTC
2014-05-01 14:21:52.278 UTC
table_name00
2014_04_30_21_24_30
2014-05-01 13:33:43.886 UTC
Needs the correct table name given for writing the values.
The tablename needs to be the same as the one that is created.
2014-05-02 15:02:59.945 UTC
propertyString00
Please load a file in as seen in the example where the user, password, url (which is the database it should use), and driver is stated.
2014-06-11 12:01:06.826 UTC
mysql.user=root
mysql.password=amrishsql
mysql.url=jdbc:mysql://localhost:3306/mydb
mysql.driver=com.mysql.jdbc.Driver
2014-06-11 12:00:51.795 UTC
Path00
Give the full path where the production.properties and peregrine-skos-cli.jar files are located of the Peregrine Indexer Tool. Which are supposed to be in the same path/Directory.
path/to/ production.properties
path/to/ peregrine-skos-cli.jar
2014-06-15 17:49:12.785 UTC
F:/School/Stage2/peregrine/
2014-06-15 17:40:54.119 UTC
outputBeanshell_SQL_query_generator_Concept_Doc_occurrencetable_name0concept_occurence_document0out100
A Beanshell script that generates a Sql statement to INSERT
the concept URI and document URI in the table named after the timestamp/tablename the workflow started.
It uses a database called mydb. If there is not a database/schema named mydb, please create one.
2014-05-01 14:28:50.45 UTC
net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity
table_name
0
text/plain
java.lang.String
true
concept_occurence_document
0
text/plain
java.lang.String
true
out1
0
0
workflow
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_extract_uri_doc_and_abstractInput1abstracts00doc_uri00
A Beanshell script which loops through the input to seperate the Document URIs and Abstract URIs.
2014-03-21 13:07:52.147 UTC
net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity
Input
1
text/plain
java.lang.String
true
doc_uri
0
0
abstracts
0
0
workflow
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_remove_dot_and_correct_doc_uri_in_con_docdoc_uri1concept_occurence_document0out100
A Beanshell script that replaces the temp created Taverna file with the correct Document URI.
2014-04-11 13:53:30.291 UTC
net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity
concept_occurence_document
0
text/plain
java.lang.String
true
doc_uri
1
text/plain
java.lang.String
true
out1
0
0
workflow
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExecute_SQL_Update_INSERT_INTO_occurrence_tablesql0propertyString0resultList00
Executes the SQL statement generated by the Beanshell script: "Sql_beanshell_query_generator_Concept_occ_Doc" which insert the concept and document URI into the table named 'timestamp'_occurence.
2014-05-01 14:29:19.326 UTC
net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity
sql
0
text/plain
java.lang.String
true
params
1
text/plain
java.lang.String
true
propertyString
0
text/plain
java.lang.String
true
resultList
0
0
workflow
net.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorker
UserNameHere
2014-05-12 11:39:07.643 UTC
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokePeregrine_Indexer_toolontology0abstract_content1path0concept_per_document00
Uses a jar peregrine program to index which concept occurs in what document.
Change the commands to :
java -Dperegrine.config.location=your/path/to/peregrine/production.properties -jar path/to/peregrine-skos-cli.jar ontology abstract_content out1
When using a Windows machine please install cygwin. Set cygwin in the $PATH of the environment variabale.
Go to Location tab select radiobutton "Select an symbolic location" and default .
Press Manage locations and go to explicit locations --> edit a default local to Shell: C:\Windows\system32\cmd.exe /c and save that. -->Set Modify on: symbolic locations --> pick default --> edit and choose default local and save. When using a unix environment make sure the default local is set Shell into /bin/sh -c
and link command to: /bin/ln -s %%PATH_TO_ORIGINAL%% %%TARGET_NAME%%.
Save settings by clicking apply .
2014-06-11 12:11:02.104 UTC
net.sf.taverna.t2.activitiesexternal-tool-activity1.4net.sf.taverna.t2.activities.externaltool.ExternalToolActivity
default
789663B8-DA91-428A-9F7D-B3F3DA185FD4
default local
<?xml version="1.0" encoding="UTF-8"?>
<localInvocation />
6c76743e-a600-4f7e-832f-6d0e284a1a29
java -Xmx20g -Xms20g -Dperegrine.config.location=%%pwd%%production.properties -jar %%pwd%%peregrine-skos-cli.jar ontology abstract_content concept_per_document
1200
1800
pwd
abstract_content
abstract_content
true
false
false
windows-1252
false
true
false
path
pwd
false
false
false
windows-1252
false
false
false
ontology
ontology
true
false
false
windows-1252
false
false
false
concept_per_document
concept_per_document
false
false
false
false
0
false
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSplit_string_into_string_list_by_regular_expressionstring0regex0split11
Uses Regex to split string into string list.
2014-03-21 13:10:43.967 UTC
net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity
string
0
'text/plain'
java.lang.String
true
regex
0
'text/plain'
java.lang.String
true
split
1
1
workflow
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
UserNameHere
2014-03-11 10:44:03.209 UTC
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeregex_valuevalue00
Regex value of enter.
2014-05-01 14:27:23.340 UTC
net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity
[\n]
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_SQL_query_generator_Concept_Doc_occurrencetable_nameBeanshell_SQL_query_generator_Concept_Doc_occurrenceconcept_occurence_documentBeanshell_extract_uri_doc_and_abstractInputBeanshell_remove_dot_and_correct_doc_uri_in_con_docdoc_uriBeanshell_remove_dot_and_correct_doc_uri_in_con_docconcept_occurence_documentExecute_SQL_Update_INSERT_INTO_occurrence_tablesqlExecute_SQL_Update_INSERT_INTO_occurrence_tablepropertyStringPeregrine_Indexer_toolontologyPeregrine_Indexer_toolabstract_contentPeregrine_Indexer_toolpathSplit_string_into_string_list_by_regular_expressionstringSplit_string_into_string_list_by_regular_expressionregexoutput
3674dfd2-59e3-4a0b-9355-9c89beb5d437
2014-05-12 08:26:10.414 UTC
21d0d9ac-38df-4c79-a6a3-95e6abd02e8f
2014-05-21 16:04:24.164 UTC
28b58762-e9a5-4336-ae8c-0de8bbde97cf
2014-05-08 13:28:53.205 UTC
a6d65617-4186-4283-9a7a-7970d1a58331
2014-06-27 08:28:06.202 UTC
eb47dba0-b920-4535-b634-e4db661210b5
2014-06-15 17:29:43.252 UTC
8054095d-ff1d-434d-8db7-73e0d92521ab
2014-05-01 14:56:49.352 UTC
7013adf6-1cff-4da4-a4f4-1dc8348cdefb
2014-05-08 12:48:10.297 UTC
68476bab-0e32-4f6a-8e9d-f50804088938
2014-06-10 08:28:55.760 UTC
Peregrine indexer
2014-04-25 08:41:57.947 UTC
ea1540f5-3320-4fd4-aae0-1a7233b7f828
2014-06-10 16:00:54.719 UTC
1ff46360-e709-4c6b-a1ed-1fec7a20532b
2014-06-15 17:49:14.94 UTC
10819a0d-58bf-4f76-86ee-9acc1332edde
2014-06-27 09:20:14.55 UTC
64734dc3-1155-4296-aefe-58117c4e2e63
2014-05-12 13:39:42.471 UTC
68bfb5a4-5361-40f7-b1e8-e9d2285f985d
2014-05-01 13:36:50.25 UTC
ddac8804-8407-4785-beae-b2d5ce0a80e3
2014-05-08 15:23:53.460 UTC
fe4de177-331a-46bc-919c-0b60de007289
2014-05-01 13:29:11.726 UTC
65c07cb7-552e-414e-b0d9-d691dee366dc
2014-06-10 08:32:43.599 UTC
f746b38a-fa7c-4188-b916-8b157d2cbfd3
2014-05-21 16:13:01.500 UTC
417fb3f9-90d0-4da1-9b1b-71687090d140
2014-06-11 12:11:48.558 UTC
87fe3bfb-dcd3-4cf3-bca5-a4ddcf8d3b32
2014-05-05 09:43:02.878 UTC
To be able to run this workflow it is necessary to have the following ready.
The Peregrine indexer program which can be downloaded from: trac.nbic.nl/biosemantics/downloads.
Install LVG2013Lite. See: https://trac.nbic.nl/biosemantics/wiki/Peregrine%20SKOS%20CLI
Copy properties file from production.properties which can be downloaded from: https://trac.nbic.nl/biosemantics/wiki/Peregrine%20SKOS%20CLI
Change lvg.properties
LVG_DIR=/home/path/to/lvg2013lite/
This file can be found in:
/home/path/to/lvg2013lite/data/config/lvg.properties
Change the normalizer.lvg.properties and normalizer.lvg.binaryCache properties to point to the LVG installation path.
normalizer.lvg.properties =/home/path/to/lvg2013lite/data/config/config/lvg.properties normalizer.lvg.binaryCahce=/home/path/to/lvg2013lite/standartNormCache2013.bin
Have MySQL installed with a database called mydb or please create one.
Have mysql-connector-java-5.1.28-bin.jar or better placed in the local JAR files.
Have a table created with the following sql statement:
CREATE TABLE mydb.YourTableName_occurence(
concept_doc_id INT NOT NULL AUTO_INCREMENT,
concept_uri VARCHAR(255) NULL,
doc_uri VARCHAR(255) NULL,
PRIMARY KEY (concept_doc_id));
2014-05-05 09:43:00.319 UTC
c54ca59d-de52-4b86-8f4d-6f34db8e1cda
2014-06-15 17:43:35.549 UTC
ef75149c-93d4-4a53-938d-598b34c547c0
2014-04-25 08:43:19.286 UTC
7a8e521a-ce70-464f-b5be-b38496ea9a7a
2014-05-02 15:03:12.106 UTC
7a8efe41-e6c8-4b99-8e20-d005bd0db003
2014-06-11 12:01:06.934 UTC
e13584ce-2e64-4486-8ae5-e6e2c08f20d5
2014-05-01 14:22:50.934 UTC
2c3c56e4-87ff-48c8-a895-54c7eabeca9f
2014-05-01 14:29:30.621 UTC
Amrish Mahes
2014-05-01 14:47:30.600 UTC
7d302e8e-e49f-46c2-9620-cbc9a8acd7c3
2014-05-01 13:38:12.169 UTC
c45a8012-d1be-44b9-b9f1-5d547075682c
2014-05-12 11:39:52.208 UTC
899b13f9-9169-42a4-8c8f-c6c8437c9b72
2014-06-15 17:42:28.355 UTC
685e7713-6183-4320-a76a-f4bfd8d87b60
2014-06-10 16:00:27.639 UTC
58b4fc1a-33f4-45d0-8a33-f87356cc96e1
2014-04-25 08:42:29.100 UTC
5fae11dd-f324-4db1-a120-a04debed40f6
2014-06-11 08:50:56.448 UTC
nestedpropertyString00
Please load a file in as seen in the example where the user, password, url (which is the database it should use), and driver is stated.
2014-06-11 11:59:30.901 UTC
mysql.user=root
mysql.password=amrishsql
mysql.url=jdbc:mysql://localhost:3306/mydb
mysql.driver=com.mysql.jdbc.Driver
2014-05-12 09:36:25.325 UTC
db_resultsExecute_SQL_Querysql0propertyString0resultList22net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity
sql
0
text/plain
java.lang.String
true
params
1
text/plain
java.lang.String
true
propertyString
0
text/plain
java.lang.String
true
resultList
2
2
xmlresults
0
0
system
mysql-connector-java.jar
net.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorker
UserNameHere
2014-05-12 09:40:09.625 UTC
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokesql_valuevalue00
SQL code for using the abstracts with their corresponding pubmed id.
2014-06-11 11:58:55.226 UTC
net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity
SELECT pmid, abstract_text
FROM mydb.abstracts;
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExecute_SQL_QuerysqlExecute_SQL_QuerypropertyStringdb_results
nested
2014-05-08 17:44:28.277 UTC
75949b8c-bb4b-4ae7-8924-5c1fb95f5fa3
2014-06-15 17:52:50.74 UTC
c614eadc-67ae-45d9-9f65-96ced3bb0c45
2014-05-12 11:36:32.316 UTC
1a3144fd-9bb3-474a-8760-ced1e79cbf60
2014-06-10 08:34:23.241 UTC
29a8b7aa-9837-4483-8e93-896c111c3780
2014-05-08 17:54:18.980 UTC
48169015-d279-400c-9a11-e0e9748f312b
2014-05-12 09:45:01.638 UTC
1bf0a549-ef7b-4c62-b298-fbcac4792269
2014-06-11 11:59:30.999 UTC
1607252e-3503-4b77-9617-ed429023613a
2014-05-12 09:26:40.211 UTC
39c6af3b-223f-4ff5-bd6f-aa2e6899ad80
2014-05-12 09:39:42.53 UTC
c7bbc90c-8116-494b-ba64-8769830aff55
2014-05-12 09:36:58.375 UTC
67c5c3e5-fa09-4524-931f-b09f47abad5f
2014-05-12 08:36:52.574 UTC
dd77b156-bebc-4183-952c-2e2fe4f1cc96
2014-05-12 09:38:33.591 UTC
6830ad2e-b9bd-4907-8a40-dd10863cd570
2014-05-21 16:10:52.487 UTC
00987503-eb35-484e-a701-05958e3fb254
2014-05-12 09:40:51.404 UTC
8aa3f84f-3b34-4860-b383-4e023cbf1c66
2014-05-12 09:39:08.438 UTC
08396e51-5a76-4ec0-be54-fecd90bf6e0d
2014-06-10 08:43:12.865 UTC