Concept_Profile_GeneOntology_input00A 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 UTCdb_properties00mysql.user=root
mysql.password=amrishsql
mysql.url=jdbc:mysql://localhost:3306/mydb
mysql.driver=com.mysql.jdbc.Driver2014-05-12 09:23:12.452 UTCPlease 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 UTCPath_Peregrine_Indexer00F:/School/Stage2/peregrine/2014-06-15 17:31:44.152 UTCGive the full path where the production.properties and peregrine-skos-cli.jar files are located of the Peregrine Indexer Tool.
path/to/ production.properties
path/to/ peregrine-skos-cli.jar2014-06-15 17:43:06.759 UTCendPeregrine_Indexertable_name0ontology0Input2propertyString0Path0The 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 UTCnet.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.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeCalculate_Uncertainty_Coefficientconcept_pairs1corrected_contingency_values2timestamp0propertyString0A nested workflow to calculate the Uncertainty coefficient with the contingency table values of the concept pairs.
The calculated values are afterwards inserted into the uncertainty coefficient SQL table.
The row with the same concepts in column name concept_uri_1 is the concept profile. The values in the columns name concept_uri_2 are the concepts that are used for calculating the uncertainty coefficient (similarity measure).
Example of the constructed SQL table:
1 A A UC value of concept pair AA
2 A B UC value of concept pair AB
3 A C UC value of concept pair AC
Example of a concept profile made of concept A:
A
|
|__UC value__A
|__UC value__B
|__UC value__C
2014-06-11 12:23:10.770 UTCnet.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.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeCalculate_Contingency_Tabletable_name0propertyString0outputlist11corrected_contingency_values22A nested workflow that retrieves the values of a 2x2 contingency table and puts the co-occurrence of made concept pairs into the SQL table TableName_co_occurrence.
This is done by creating concept pairs which is retrieved from the Sql table TableName_occurrence.
This contingency table consits out of a matrix where two concepts co-occur, concept A only occurs
and not concept B, concept B occurs and not concept A and neither concepts occur in literature.
Example of a 2x2 contingency table of concept pair A B:
B Not B
A AB A
not A B not A not B
This is calculated for every possible concept pair.2014-06-11 12:13:17.153 UTCnet.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.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeCalculate_Inner_Productconcept_pairs1timestamp0propertyString0A nested workflow to calculate the inner product between concept profile pairs for concept profile matching. The calculated values are afterwards inserted into the inner product SQL table.
Example of calculating the inner product between two concept profiles:
A B
| |
|__UC value__A x A__UC value__|
| + |
|__UC value__B x B__UC value__|
| |
|__UC value__C D__UC value__|
The inner product of the two concept profile A and B is the common concept multplied between each other and added:
(UC value AA x UC value BA) + (UC value AB x UC value BB) = inner product
2014-06-11 12:37:47.216 UTCnet.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.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeCreate_Tablesdb_properties0timeStamp00This 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 UTCnet.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.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGet_Summary_Tabletimestamp0propertyString0resultList11A nested workflow to retrieve the calculated co-occurrence, occurrence, uncertainty coefficient and inner product values. These values are inserted into one table to summarize and quick access.2014-06-11 10:55:51.663 UTCnet.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.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGet_abstractspropertyString0db_results22A 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 UTCnet.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.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokePeregrine_Indexertable_namePeregrine_IndexerontologyPeregrine_IndexerInputPeregrine_IndexerpropertyStringPeregrine_IndexerPathCalculate_Uncertainty_Coefficientconcept_pairsCalculate_Uncertainty_Coefficientcorrected_contingency_valuesCalculate_Uncertainty_CoefficienttimestampCalculate_Uncertainty_CoefficientpropertyStringCalculate_Contingency_Tabletable_nameCalculate_Contingency_TablepropertyStringCalculate_Inner_Productconcept_pairsCalculate_Inner_ProducttimestampCalculate_Inner_ProductpropertyStringCreate_Tablesdb_propertiesGet_Summary_TabletimestampGet_Summary_TablepropertyStringGet_abstractspropertyStringend6e3bd1f4-ce2e-4eab-987c-aff2b7df20be2014-04-11 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10:59:19.754 UTC0fa5ae93-fe58-4958-a86a-4118f2b82cb82014-06-11 11:57:44.520 UTC7f5909ba-e457-4017-827e-28756be2a2db2014-05-12 11:34:18.819 UTC85eb7ca4-2261-4b6b-8dbc-e983dfffad062014-04-25 08:42:27.977 UTC1407f28f-2b20-4a4b-987f-0e8a978fd0692014-04-14 12:19:58.355 UTC71c0ae47-08a2-42e7-8b61-368228badc872014-04-09 11:38:19.412 UTC393c3128-043d-4598-aeab-8d8a7ff26f252014-04-25 09:09:37.203 UTC2eb0f038-4ecd-440b-b39e-f188243e37c02014-03-26 17:23:46.827 UTC65061b5e-4240-4e5d-bea5-395adf42981f2014-03-20 10:20:03.284 UTC921d4091-ab1d-4a97-ae19-f89b54d5d6f12014-06-11 11:53:44.5 UTC7fa1d021-c166-4f12-abe3-eae08e6e8c382014-04-02 11:21:12.430 UTCf2fcd097-92b8-4fdc-a7d4-b2577d4ac7f82014-03-11 10:22:44.507 UTC7a09384c-cf1e-4b6c-856b-36abc5e2981f2014-04-11 11:26:47.475 UTC4b062ff7-3737-457c-9079-3e0e7a9c45f92014-05-21 16:11:02.255 UTC5404ca4a-6824-47f0-b99d-3bac2972d3b32014-04-09 08:25:23.468 UTC529b0a59-d5b5-4a86-9f68-1764410540112014-03-21 10:47:02.223 UTCbb263958-6955-44d3-b785-8b8cb552ca4e2014-04-09 11:48:16.918 UTCdbdc039a-a221-43bc-a79a-b247246974512014-04-11 11:20:16.786 UTC7309ae74-fe52-47cb-8faa-0255373b31bb2014-05-12 09:26:43.227 UTC392cb15c-a3dd-490e-93d2-ac28fd03b6a52014-03-19 13:03:01.757 UTCc59ee9c4-e463-48c7-a0f2-c9b65cdfb83b2014-06-10 15:53:56.13 UTC2140fe4d-db70-420e-9ca2-595da9e5f8cf2014-04-10 14:40:42.779 UTC45dd4291-684e-43c3-bfa6-ae2a37ee87ce2014-05-02 15:40:52.743 UTCRequirements:
Have MySQL installed with a database called mydb or please create one.
Have a mysql connector file. This can be downloaded from mysql.com.
Rename the downloaded file to mysql-connector-java.jar and place it in the the local lib file of Taverna as written on the dependencies tab.
Choose this dependency by rightclicking a beanshell script and selecting it for the whole workflow as system classloader.
Download the Peregrine SKOS CLI from: https://trac.nbic.nl/biosemantics/downloads
Install LVG2013Lite. See: https://trac.nbic.nl/biosemantics/wiki/Peregrine%20SKOS%20CLI
Change lvg.properties
LVG_DIR=/home/path/to/lvg2013lite/
This file can be found in:
/home/path/to/lvg2013lite/data/config/lvg.properties
Copy properties file from production.properties which can be found on: https://trac.nbic.nl/biosemantics/wiki/Peregrine%20SKOS%20CLI
Change the normalizer.lvg.properties and normalizer.lvg.binaryCache properties to point to the LVG installation path.
This file can be obtained from https://trac.nbic.nl/biosemantics/wiki/Peregrine%20SKOS%20CLI
Have Peregrine indexer installed locally and give it the correct path in the component named "Indexer_tool". Which can be found in the nested workflow named Peregrine indexer.
If using a Windows machine please install cygwin. Set cygwin in the $PATH of the environment variabale.
Go to taverna File --> preferences --> Tool invocation --> set modify on explicit locations --> edit a default local to Shell: C:\Windows\system32\cmd.exe /c and save that. -->Set Modify on: symbolic locations --> edit --> choose default local and save. When using a unix environment make sure the default local is set Shell into /bin/sh -c.
Please make sure this is also set into the indexer tool part.
Have JAVA_HOME C:\Program Files\jdk 1.7.0 in environment variabale when using Windows.
The nested workflow Get_abstract uses a sql command to retrieve abstracts which assumes are located in the database mydb. If this is not the case, please change the database in the SQL value.2014-06-11 11:56:14.761 UTCd0997741-9889-48a1-af06-9b4601e6876d2014-05-01 13:36:53.145 UTC1e32cd62-6709-4253-8812-b7f7823f323f2014-03-19 12:39:25.755 UTC513c4d46-b511-4a6d-9b9f-9f046720c2b72014-03-27 14:40:34.469 UTC0a9fc708-f04c-4b3b-9c2b-3077d360a0042014-03-26 16:58:01.18 UTCeed395e4-da87-432e-9a6f-1db669dd1c0c2014-03-27 10:27:04.552 UTC74f97370-a9b5-40a6-98ae-e263c8f9debe2014-03-27 16:59:33.565 UTC5ed05d10-6606-4eb6-a549-f0acd558a5e12014-03-12 16:27:46.614 UTCa116a99e-7b24-4fcb-949c-434c185de7c42014-06-10 09:39:52.374 UTCbc510c1b-3918-4a2e-ad6b-83fd94a3fdcd2014-04-10 12:48:04.773 UTC867e8a5a-c59f-4c68-8e3b-11e1f3d811d42014-04-09 08:32:47.874 UTC448d9b98-3eb9-4ead-921c-3baef48a0efe2014-03-21 13:36:17.856 UTC936c0da5-18d3-4670-842e-b6de7827f6be2014-04-10 14:22:40.555 UTCc912b1cf-361c-4414-8d15-535730449e202014-05-02 15:09:58.330 UTC7f57bf70-4232-4af9-82bd-c524120cf7fe2014-03-20 10:27:13.607 UTCb73de25f-87f0-4b09-a0d3-c339d340f8c02014-06-10 11:16:06.229 UTC93512370-e9f6-49b6-ba46-4482dae8c38e2014-05-02 16:40:23.354 UTC474781e2-4053-4460-9062-2c102596efdf2014-05-12 13:04:27.927 UTC558f78ee-316b-45d1-b74d-08d613b59f812014-06-10 15:32:38.405 UTC05fc1170-1530-4218-b74c-7f19168686bf2014-06-11 10:55:52.360 UTCecc3b293-9ddf-4063-8645-7215221ef3422014-03-04 17:15:26.661 UTCee149ce2-e3ba-465e-9c63-04b297aa50592014-03-04 16:18:24.468 UTC90225384-5852-4768-ba1d-cb7671b920da2014-03-19 09:49:54.0 UTC4792a9cb-3d7e-4327-8c8e-4e499b8f4f282014-03-11 15:47:23.615 UTC5110b42a-7d69-4212-82a9-7adefe6d3c212014-06-15 16:21:38.370 UTC224d82d5-73dd-4dce-baea-8ad1341e91522014-04-11 12:18:58.687 UTCad0d25ec-2b96-4307-bf18-4b95f1c7740c2014-04-11 11:31:27.283 UTC8e44e788-4fc5-447f-bde6-9bdf3be24bd02014-03-18 12:02:18.860 UTC5fddb0b2-585d-466c-a72a-00031f0cceef2014-03-18 10:47:26.114 UTC0fa803bd-3469-415e-89a7-039489d3480c2014-03-17 10:45:38.163 UTCb7956990-8189-4f16-bf37-da3363361e3e2014-05-05 12:45:22.875 UTC05687d54-4107-43c2-aa91-0b7b706756db2014-06-11 09:03:42.795 UTC0d50bbee-3571-4315-b7d7-44342273a8b92014-04-10 08:33:00.501 UTC71f14995-6503-40d5-8948-2d64864e36d22014-03-12 15:28:10.329 UTC344da505-68bc-47c1-ba68-afd6a55ebf7e2014-03-21 10:16:16.121 UTC53b52fe4-2b10-4717-b7c6-5bbcef46b2062014-04-15 14:29:31.643 UTCbbc1a00b-a48b-44f5-a291-597d30838c762014-05-12 13:36:37.252 UTC4a392f2b-0aab-4721-94f6-f7b73d5dbc962014-03-27 09:49:33.460 UTC2d213aed-77c4-40d7-a3f9-b06ce1f939602014-04-09 08:37:09.195 UTC7f6d900b-1832-4b86-b7f4-08c039b9edd22014-03-03 15:06:51.165 UTCb04f1761-c23c-4c94-96fe-9f5952836a362014-06-15 17:43:07.239 UTC1ffc7cc7-bd8c-49e0-92ff-0ca02090bca32014-03-31 13:45:49.982 UTCd98af7c3-005b-4c4c-be87-3cedc55890d32014-03-19 16:15:51.545 UTC5b411999-5685-47eb-b8cd-49837b0d46212014-03-27 09:19:58.748 UTC4c4cec6d-8632-4576-a6e9-571c6b0c62362014-03-11 14:45:15.59 UTCnestedpropertyString00Please 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 UTCmysql.user=root
mysql.password=amrishsql
mysql.url=jdbc:mysql://localhost:3306/mydb
mysql.driver=com.mysql.jdbc.Driver2014-05-12 09:36:25.325 UTCdb_resultsExecute_SQL_Querysql0propertyString0resultList22net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivitysql0text/plainjava.lang.Stringtrueparams1text/plainjava.lang.StringtruepropertyString0text/plainjava.lang.StringtrueresultList22xmlresults00systemmysql-connector-java.jarnet.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorkerUserNameHere2014-05-12 09:40:09.625 UTCnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokesql_valuevalue00SQL code for using the abstracts with their corresponding pubmed id.2014-06-11 11:58:55.226 UTCnet.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivitySELECT pmid, abstract_text
FROM mydb.abstracts
LIMIT 50 ;net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExecute_SQL_QuerysqlExecute_SQL_QuerypropertyStringdb_resultsnested2014-05-08 17:44:28.277 UTC6830ad2e-b9bd-4907-8a40-dd10863cd5702014-05-21 16:10:52.487 UTCdd77b156-bebc-4183-952c-2e2fe4f1cc962014-05-12 09:38:33.591 UTC00987503-eb35-484e-a701-05958e3fb2542014-05-12 09:40:51.404 UTC8aa3f84f-3b34-4860-b383-4e023cbf1c662014-05-12 09:39:08.438 UTC39c6af3b-223f-4ff5-bd6f-aa2e6899ad802014-05-12 09:39:42.53 UTC29a8b7aa-9837-4483-8e93-896c111c37802014-05-08 17:54:18.980 UTC48169015-d279-400c-9a11-e0e9748f312b2014-05-12 09:45:01.638 UTCc614eadc-67ae-45d9-9f65-96ced3bb0c452014-05-12 11:36:32.316 UTC1bf0a549-ef7b-4c62-b298-fbcac47922692014-06-11 11:59:30.999 UTC08396e51-5a76-4ec0-be54-fecd90bf6e0d2014-06-10 08:43:12.865 UTC1607252e-3503-4b77-9617-ed429023613a2014-05-12 09:26:40.211 UTCc7bbc90c-8116-494b-ba64-8769830aff552014-05-12 09:36:58.375 UTC67c5c3e5-fa09-4524-931f-b09f47abad5f2014-05-12 08:36:52.574 UTC1a3144fd-9bb3-474a-8760-ced1e79cbf602014-06-10 08:34:23.241 UTCPeregrine indexerontology00A 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 UTCInput22Give 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 UTC2014-05-01 14:21:52.278 UTCtable_name002014_04_30_21_24_302014-05-01 13:33:43.886 UTCNeeds 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 UTCpropertyString00Please 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 UTCmysql.user=root
mysql.password=amrishsql
mysql.url=jdbc:mysql://localhost:3306/mydb
mysql.driver=com.mysql.jdbc.Driver2014-06-11 12:00:51.795 UTCPath00Give the full path where the production.properties and peregrine-skos-cli.jar files are located.
path/to/ production.properties
path/to/ peregrine-skos-cli.jar2014-06-15 17:42:28.228 UTCF:/School/Stage2/peregrine/2014-06-15 17:40:54.119 UTCoutputBeanshell_SQL_query_generator_Concept_Doc_occurrencetable_name0concept_occurence_document0out100A 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 UTCnet.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivitytable_name0text/plainjava.lang.Stringtrueconcept_occurence_document0text/plainjava.lang.Stringtrueout100workflownet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_extract_uri_doc_and_abstractInput1abstracts00doc_uri00A Beanshell script which loops through the input to seperate the Document URIs and Abstract URIs.2014-03-21 13:07:52.147 UTCnet.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivityInput1text/plainjava.lang.Stringtruedoc_uri00abstracts00workflownet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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_document0out100A Beanshell script that replaces the temp created Taverna file with the correct Document URI.2014-04-11 13:53:30.291 UTCnet.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivityconcept_occurence_document0text/plainjava.lang.Stringtruedoc_uri1text/plainjava.lang.Stringtrueout100workflownet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExecute_SQL_Update_INSERT_INTO_occurrence_tablesql0propertyString0resultList00Executes 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 UTCnet.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivitysql0text/plainjava.lang.Stringtrueparams1text/plainjava.lang.StringtruepropertyString0text/plainjava.lang.StringtrueresultList00workflownet.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorkerUserNameHere2014-05-12 11:39:07.643 UTCnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokePeregrine_Indexer_toolontology0abstract_content1path0concept_per_document00Uses 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 UTCnet.sf.taverna.t2.activitiesexternal-tool-activity1.4net.sf.taverna.t2.activities.externaltool.ExternalToolActivitydefault789663B8-DA91-428A-9F7D-B3F3DA185FD4default local<?xml version="1.0" encoding="UTF-8"?>
<localInvocation><shellPrefix>C:\Windows\system32\cmd.exe /c</shellPrefix></localInvocation>
6c76743e-a600-4f7e-832f-6d0e284a1a29java -Dperegrine.config.location=%%pwd%%production.properties -jar %%pwd%%peregrine-skos-cli.jar ontology abstract_content concept_per_document12001800pwdabstract_contentabstract_contenttruefalsefalsewindows-1252falsetruefalsepathpwdfalsefalsefalsewindows-1252falsefalsefalseontologyontologytruefalsefalsewindows-1252falsefalsefalseconcept_per_documentconcept_per_documentfalsefalsefalsefalse0falsenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSplit_string_into_string_list_by_regular_expressionstring0regex0split11Uses Regex to split string into string list.2014-03-21 13:10:43.967 UTCnet.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivitystring0'text/plain'java.lang.Stringtrueregex0'text/plain'java.lang.Stringtruesplit11workfloworg.embl.ebi.escience.scuflworkers.java.SplitByRegexUserNameHere2014-03-11 10:44:03.209 UTCnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeregex_valuevalue00Regex value of enter. 2014-05-01 14:27:23.340 UTCnet.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.Parallelize1net.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.Retry1.0100050000net.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_expressionregexoutput3674dfd2-59e3-4a0b-9355-9c89beb5d4372014-05-12 08:26:10.414 UTC7a8efe41-e6c8-4b99-8e20-d005bd0db0032014-06-11 12:01:06.934 UTCea1540f5-3320-4fd4-aae0-1a7233b7f8282014-06-10 16:00:54.719 UTCPeregrine indexer2014-04-25 08:41:57.947 UTC68476bab-0e32-4f6a-8e9d-f508040889382014-06-10 08:28:55.760 UTC8054095d-ff1d-434d-8db7-73e0d92521ab2014-05-01 14:56:49.352 UTCc54ca59d-de52-4b86-8f4d-6f34db8e1cda2014-06-15 17:43:35.549 UTC5fae11dd-f324-4db1-a120-a04debed40f62014-06-11 08:50:56.448 UTCc45a8012-d1be-44b9-b9f1-5d547075682c2014-05-12 11:39:52.208 UTC7a8e521a-ce70-464f-b5be-b38496ea9a7a2014-05-02 15:03:12.106 UTC899b13f9-9169-42a4-8c8f-c6c8437c9b722014-06-15 17:42:28.355 UTC87fe3bfb-dcd3-4cf3-bca5-a4ddcf8d3b322014-05-05 09:43:02.878 UTC28b58762-e9a5-4336-ae8c-0de8bbde97cf2014-05-08 13:28:53.205 UTCef75149c-93d4-4a53-938d-598b34c547c02014-04-25 08:43:19.286 UTC7013adf6-1cff-4da4-a4f4-1dc8348cdefb2014-05-08 12:48:10.297 UTC2c3c56e4-87ff-48c8-a895-54c7eabeca9f2014-05-01 14:29:30.621 UTC65c07cb7-552e-414e-b0d9-d691dee366dc2014-06-10 08:32:43.599 UTCTo 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 UTC68bfb5a4-5361-40f7-b1e8-e9d2285f985d2014-05-01 13:36:50.25 UTC7d302e8e-e49f-46c2-9620-cbc9a8acd7c32014-05-01 13:38:12.169 UTCddac8804-8407-4785-beae-b2d5ce0a80e32014-05-08 15:23:53.460 UTCe13584ce-2e64-4486-8ae5-e6e2c08f20d52014-05-01 14:22:50.934 UTCAmrish Mahes2014-05-01 14:47:30.600 UTCf746b38a-fa7c-4188-b916-8b157d2cbfd32014-05-21 16:13:01.500 UTCfe4de177-331a-46bc-919c-0b60de0072892014-05-01 13:29:11.726 UTC58b4fc1a-33f4-45d0-8a33-f87356cc96e12014-04-25 08:42:29.100 UTC21d0d9ac-38df-4c79-a6a3-95e6abd02e8f2014-05-21 16:04:24.164 UTC685e7713-6183-4320-a76a-f4bfd8d87b602014-06-10 16:00:27.639 UTC417fb3f9-90d0-4da1-9b1b-71687090d1402014-06-11 12:11:48.558 UTCeb47dba0-b920-4535-b634-e4db661210b52014-06-15 17:29:43.252 UTC64734dc3-1155-4296-aefe-58117c4e2e632014-05-12 13:39:42.471 UTCCreate Tablesdb_properties00mysql.user=root
mysql.password=amrishsql
mysql.url=jdbc:mysql://localhost:3306/mydb
mysql.driver=com.mysql.jdbc.Driver2014-06-11 12:42:50.723 UTCPlease 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 UTCtimeStampBeanshell_get_timestamptimeStamp00A 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 UTCnet.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivitytimeStamp00workflownet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_SQL_Create_TablestimeStamp0Table_sql00A Beanshell script for creating the tables.2014-06-15 17:25:33.10 UTCnet.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivitytimeStamp0text/plainjava.lang.StringtrueTable_sql00workflownet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.LocalworkerActivitysql0text/plainjava.lang.Stringtrueparams1text/plainjava.lang.StringtruepropertyString0text/plainjava.lang.StringtrueresultList00workflownet.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorkerUserNameHere2014-06-15 16:25:51.599 UTCnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.LocalworkerActivitystring0'text/plain'java.lang.Stringtrueregex0'text/plain'java.lang.Stringtruesplit1l('text/plain')1workfloworg.embl.ebi.escience.scuflworkers.java.SplitByRegexnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.Parallelize1net.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.Retry1.0100050000net.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_expressionstringtimeStamp1c464dba-d276-4ea4-8e3d-e37f4893e7d02014-06-15 16:54:44.837 UTCf3183def-03f7-46b5-a971-9b5ca2eb1ad32014-04-25 09:32:55.418 UTC1582f59b-8bd9-43ce-9f83-644f97d954c72014-05-12 12:01:29.197 UTC50075aae-f1e4-44c2-9c80-ab5c8bd3f4e32014-06-15 16:33:07.624 UTC9635824a-e4f1-4881-97e5-9299788780752014-06-11 08:57:20.555 UTC86079042-0398-4522-b766-79a51a2061b62014-04-25 09:34:08.496 UTCf70ead12-638d-4210-be53-6193297440cd2014-06-10 10:59:34.689 UTCf2a26852-747d-41b3-957a-6b32bd38f6982014-06-15 17:16:56.191 UTC39bb73a3-e51b-42da-8706-944c99ff6ef22014-04-25 09:31:36.342 UTCf6285fa8-00e8-4b4b-848b-4c3faecaff0c2014-06-15 17:03:23.327 UTC01279793-743e-42c9-879d-c89edae5620b2014-06-15 16:41:24.510 UTCe07305cf-4d3c-4732-817c-fc8c1897b04b2014-06-15 17:23:16.414 UTC5747cb6c-cfd7-4461-ba4d-aaca2ff237642014-06-15 17:18:14.417 UTC8cb5442b-fa0d-4ab5-a534-ad79415bdc042014-06-15 17:22:42.241 UTCefb2e85a-454a-43fb-a82e-8d82a29111e22014-05-08 15:06:01.281 UTCaaf687fd-8ecb-42e8-b118-4f865db9db692014-06-15 16:20:50.770 UTCb905d192-afc7-4e80-9b87-3c62568fe5122014-06-10 16:12:44.94 UTCee6ad738-c5f6-4af6-8e6c-feb0c97d55042014-05-12 13:58:30.889 UTC15224b89-9d42-4abb-888a-cc96a03354bf2014-06-15 17:26:06.238 UTC0f84cc52-37eb-4728-8f78-efd8981e97702014-06-11 12:45:50.859 UTCd0c0ac03-d7c1-410e-ae8a-d0a3fb71cc232014-06-15 16:42:33.166 UTCc0782138-c8e8-4d33-a524-12e3af3d28fa2014-05-12 11:52:51.417 UTC9fbf74e6-c25a-47f9-9065-8aeee27a62fa2014-06-10 09:35:20.474 UTC1a6c0667-e77d-45e6-9f10-ea3b62ab8b322014-06-15 17:05:00.249 UTC200cd498-f8d4-4ab0-bf9c-e96aa415be2e2014-06-10 16:10:53.665 UTC7b1e6650-564c-4d1a-9533-3e729f80f4b02014-06-15 17:19:26.528 UTC6f805bc9-25de-40db-bdfc-9f02de07addc2014-06-11 09:03:14.417 UTC8477156c-f078-4565-b8af-5db33fada2122014-05-12 13:43:53.377 UTC048b9168-bc32-4af6-ba1b-96c66ea340322014-06-15 17:05:43.430 UTCa5ab9df6-c2f1-49bc-8788-f300d6fee7c82014-05-08 12:51:28.905 UTC73b839a8-067a-4f75-9229-2657a81718832014-06-15 16:39:15.477 UTCe9e4a3b8-0c6a-469a-aec7-11e0dbe2514b2014-04-25 09:08:00.69 UTCCreate Tables2014-04-25 09:03:12.547 UTC98e5f737-bfc2-4631-9018-55ad9e6509022014-06-15 16:26:26.955 UTCba007108-e797-4ecd-88d9-cb675d81568b2014-05-12 13:38:14.79 UTC31df5173-0ae3-44b1-a101-68d3ee2b6c662014-06-11 12:43:52.905 UTC4040ef45-3e66-4f71-b7cb-b56f0b0aacff2014-05-12 13:55:09.958 UTCbd5d7656-0001-4e1e-9e00-65bda9a575b62014-05-12 13:51:18.129 UTC203b885f-17e1-446a-a321-5e0b888e60042014-06-15 17:23:48.706 UTC920a4ba4-90cf-4a89-a943-571ac36e7d472014-06-15 16:13:50.623 UTC0a15b5d5-9ad4-4394-a44b-a773c3cfbc602014-04-25 09:30:39.667 UTCf8521f7a-4def-44dd-9e0c-5919119df0b52014-06-15 17:12:31.867 UTC3aa918f3-ff7c-4125-8c0e-0a0251f8e67a2014-06-15 16:28:37.25 UTC58d2e665-ec1f-4ea3-806d-cafa02adedee2014-05-12 13:47:58.714 UTCfe3eb75e-1e1b-4846-849e-625552e0e9cc2014-06-11 09:07:30.689 UTC071ca1ba-e357-4fd3-8943-c544199f9dd02014-04-25 09:23:33.706 UTC1e050fa6-0e46-47cc-852a-78351e49fd4b2014-06-15 16:21:22.366 UTCe89e40ff-8e2c-401f-96ba-c233c6bf4dbd2014-06-15 17:20:08.149 UTCc725fae1-9407-4643-8078-2083285199142014-06-15 17:25:46.789 UTCa0444c47-ea11-48c9-9c0c-b52d326b35ad2014-06-11 13:09:53.254 UTC26b21b9b-a674-4e35-b03f-807d715102592014-05-12 13:28:52.14 UTC8bacc18d-de0f-4fdf-99a7-3f5bca0f03ae2014-06-15 17:20:36.58 UTCe3e82f84-c36d-4445-9009-146e4a867dc22014-06-15 16:39:33.753 UTC994307a6-939b-48c2-a874-5be73efc87312014-06-10 10:56:30.827 UTCa3744263-cf8d-4ce4-8a77-8d75529492e32014-06-11 08:50:09.675 UTCCalculate_Contingenctable_name00Needs 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 UTCalpha2014-06-06 14:36:34.332 UTCpropertyString00Please load a file in as seen in the example where the user, password, url (which is the database it should use), and driver is stated.2014-06-11 12:13:53.198 UTCmysql.user=root
mysql.password=amrishsql
mysql.url=jdbc:mysql://localhost:3306/mydb
mysql.driver=com.mysql.jdbc.Driver2014-06-06 14:36:25.795 UTCoutputlistA output port for the concept pairs.2014-05-02 16:33:00.498 UTCcorrected_contingency_valuesA 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 UTCBeanshell_SQL_generate_contingency_tableconcept_pairs0table_name0out100A Beanshell script that generates a SQL statement to retrieve the amount two concepts co-occur, concept A only occurs
and not concept B, concept B occurs and not concept A.
When a concept pair is the same. As in concept pair A A or B B etc. It will use the first SQL statement. Else it will use the second SQL statement.
The output of only concept A and only concept B needs to be corrected and the value to get when neither concepts occur in literature is done in the Beanshell script called: "Beanshell_correct_contincengy_table".
2014-06-11 12:20:03.523 UTCnet.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivityconcept_pairs0text/plainjava.lang.Stringtruetable_name0text/plainjava.lang.Stringtrueout100workflownet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_SQL_insert_into_co_occurrence_tablecontingency_values1concept_pairs0timestamp0out100A Beanshell script that generates SQL statement to insert into the co-occurrence table the amount two given concepts co-occur together in literature.2014-06-11 12:21:58.73 UTCnet.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivitycontingency_values1text/plainjava.lang.Stringtruetimestamp0text/plainjava.lang.Stringtrueconcept_pairs0text/plainjava.lang.Stringtrueout100workflownet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_correct_contingency_tablecontingency_values1total_nr_abtracts2corrected_contingency_values11A Beanshell script that corrects the output SQL retrieved contingency table by subtracting the co-occurence values of the concept only A and of concept only B value. It also uses the value of the total amount of abstracts there are in the dataset for calculating the value of when neither concepts occure.2014-06-11 12:21:25.39 UTCnet.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivitycontingency_values1text/plainjava.lang.Stringtruetotal_nr_abtracts2text/plainjava.lang.Stringtruecorrected_contingency_values11workflownet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_generate_SQL_statement_Get_distinct_concepttable_name0out100A Beanshell script that retrieves every concept from the Sql table TableName_occurrence.2014-06-11 12:14:03.731 UTCnet.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivitytable_name0text/plainjava.lang.Stringtrueout100workflownet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Loopnet.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_make_concept_pairsconcept_A0concept_B0concept_pair00A Beanshell script that gets as input a list of concepts to create concept pairs.2014-04-14 10:55:52.228 UTCnet.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivityconcept_B0text/plainjava.lang.Stringtrueconcept_A0text/plainjava.lang.Stringtrueconcept_pair00workflownet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExecute_SQL_Querysql0propertyString0resultList22Executes the Beanshell generated SQL statement for getting destinct concepts.2014-05-02 15:14:36.450 UTCnet.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivitysql0text/plainjava.lang.Stringtrueparams1text/plainjava.lang.StringtruepropertyString0text/plainjava.lang.StringtrueresultList22xmlresults00systemmysql-connector-java.jarnet.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorkerUserNameHere2014-06-04 13:27:44.254 UTCnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExecute_SQL_Query_2sql0propertyString0resultList22Executes the SQL generated query of the Beanshell script to retrieve the values of the contingency table.2014-05-05 11:51:02.525 UTCnet.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivitysql0text/plainjava.lang.Stringtrueparams1text/plainjava.lang.StringtruepropertyString0text/plainjava.lang.StringtrueresultList22xmlresults00workflownet.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorkerUserNameHere2014-05-12 11:45:00.69 UTCnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExecute_SQL_Update_INSERT_INTO_Co_occurrence_tablesql0propertyString0net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivitysql0text/plainjava.lang.Stringtrueparams1text/plainjava.lang.StringtruepropertyString0text/plainjava.lang.StringtrueresultList00workflownet.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorkerUserNameHere2014-05-12 11:45:40.670 UTCnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.LocalworkerActivityinputlist2l(l(''))[Btrueoutputlist1l('')1workfloworg.embl.ebi.escience.scuflworkers.java.FlattenListnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.LocalworkerActivityinputlist2l(l(''))[Btrueoutputlist1l('')1workfloworg.embl.ebi.escience.scuflworkers.java.FlattenListnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.LocalworkerActivityinputlist2l(l(''))[Btrueoutputlist1l('')1workfloworg.embl.ebi.escience.scuflworkers.java.FlattenListnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_SQL_count_abstractsout100net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivityout100workflownet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExecute_SQL_Query_3sql0propertyString0resultList22net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivitysql0text/plainjava.lang.Stringtrueparams1text/plainjava.lang.StringtruepropertyString0text/plainjava.lang.StringtrueresultList22xmlresults00workflownet.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorkerUserNameHere2014-06-06 13:26:31.104 UTCnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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_occurrence_tablecontingency_valuesBeanshell_SQL_insert_into_co_occurrence_tableconcept_pairsBeanshell_SQL_insert_into_co_occurrence_tabletimestampBeanshell_correct_contingency_tablecontingency_valuesBeanshell_correct_contingency_tabletotal_nr_abtractsBeanshell_generate_SQL_statement_Get_distinct_concepttable_nameBeanshell_make_concept_pairsconcept_ABeanshell_make_concept_pairsconcept_BExecute_SQL_QuerysqlExecute_SQL_QuerypropertyStringExecute_SQL_Query_2sqlExecute_SQL_Query_2propertyStringExecute_SQL_Update_INSERT_INTO_Co_occurrence_tablesqlExecute_SQL_Update_INSERT_INTO_Co_occurrence_tablepropertyStringFlatten_ListinputlistFlatten_List_2inputlistFlatten_List_3inputlistExecute_SQL_Query_3sqlExecute_SQL_Query_3propertyStringoutputlistcorrected_contingency_valuesfe7933ae-1b38-4fab-acc1-f2637db3a9a52014-06-10 15:51:33.431 UTC0a6042a5-4d83-41ea-b2ae-3cefafb4265a2014-05-05 11:22:16.615 UTC340235a3-2479-420b-a33d-11529380bd972014-06-10 13:54:52.405 UTCfe291e3b-1b6d-4c09-8cea-87a24ad2533c2014-06-08 16:10:17.851 UTCCalculate Contingency table2014-05-05 13:44:48.426 UTCaeeef64f-1c80-4a16-ab56-89b439bed50d2014-06-10 14:06:24.571 UTCbb618d97-2857-4d79-84e8-e20543f381162014-05-05 11:54:00.498 UTC987dfb83-6ae8-458a-8dd0-d45c2d5728542014-06-08 16:36:47.756 UTCf4c7469a-b9b2-42e0-81c2-2c5b0fd04f0f2014-06-06 13:10:41.936 UTC723d1cc8-9d97-4791-9f64-94b329b4876d2014-06-08 15:36:19.904 UTC9b8d4323-3e99-4fa3-bfbf-812acf73d6152014-05-02 15:40:47.612 UTCfebcbc5c-3e29-4c4c-b0eb-af50a9d2a7a62014-06-08 16:08:37.388 UTC46f263f0-54aa-4132-96be-d2831ac84db12014-05-12 11:46:08.98 UTCf38ed2d2-f8f0-41be-af6f-43cf113a8de22014-06-06 16:24:53.251 UTCd1b17379-8eac-4dcd-a5b6-9754f99b0c942014-05-05 13:44:50.330 UTC53e2be4c-2db0-4203-9d4d-f47d9bbe55122014-05-05 11:37:52.424 UTCA 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 UTC9ac9ac33-565a-4f05-9353-57e6fcd510b82014-05-05 11:39:00.253 UTC2e8d40f2-125f-4d34-ae61-1d10508f1be82014-06-06 14:43:04.450 UTC241acb88-15bf-4b76-a78a-2e57174073b52014-06-10 14:00:00.86 UTCf83a0a65-9046-4c27-8b27-30820f2b9c3e2014-06-08 16:40:27.780 UTCcc570f9b-f9a5-494d-af4a-fcc31285755c2014-06-05 11:16:18.854 UTCe529c545-ce7c-41a3-a337-91137d5cb2a02014-05-02 16:35:22.526 UTC9db66f08-1aa9-4b76-8592-a90c3e1710c52014-05-05 09:41:53.767 UTC2eae8fad-b196-4141-ad91-e4c079e4205f2014-05-02 16:58:36.311 UTCAmrish Mahes2014-05-02 15:42:14.33 UTC94065ddd-d3e1-4e39-b7ee-31d8079d45532014-05-05 11:54:11.870 UTC16e2c6df-f5ca-4b7c-9745-2784eddd346d2014-06-08 15:40:29.722 UTC1b260c16-3554-4fa6-b27b-d537f9440fb72014-06-06 14:54:06.793 UTC711f5d11-bc72-4e31-8716-4dad288862f02014-04-25 09:08:01.83 UTC0f7062ef-e729-49c8-9ee0-bc26eae41dbb2014-06-06 13:27:31.365 UTCdc4b9ca5-6031-4dd0-9286-9f482177036d2014-06-06 16:32:03.193 UTC7d1aba2f-ef9b-4892-a3fa-cc3607cf18dd2014-06-05 11:32:59.648 UTC4ecbd389-493e-4068-884e-a28c56d397452014-06-05 11:43:31.206 UTC228d8f2d-cdfe-486a-bf03-85a13a5a38aa2014-06-11 08:57:45.345 UTCb2268ff9-c16a-45e3-82ea-549ecfb66d8a2014-06-06 16:27:30.743 UTC811704db-ff82-4ab7-9e31-dcfb7f8600a02014-06-04 13:27:49.995 UTC68c46c7a-4dee-44de-8819-dc77011249732014-05-05 09:37:41.543 UTC6a1ccba3-c527-47ce-9a4c-a57634881a7c2014-05-02 15:57:55.741 UTC918e96e6-9dcc-4cec-b541-93a529efd2a62014-06-06 16:17:33.159 UTC90bde618-33be-4318-a858-5809375418062014-06-06 16:04:34.227 UTC3da9a958-ebc0-4193-83cd-29a45c70a1fd2014-05-02 16:40:17.937 UTCfb10914b-9f29-4c60-a29c-fb854cb987c32014-06-06 14:47:16.415 UTC95c84125-55a5-42cd-b9a6-27c68d9cf5ed2014-06-05 12:02:34.59 UTCce4e0e0d-369c-4896-8aca-4db7f7f332892014-06-06 15:00:21.670 UTCe41e4bc5-4099-4a7c-920a-95b2aa64bb7a2014-06-06 14:25:01.771 UTC7862fb3a-5815-4dda-ad77-80da4baef1532014-06-06 14:42:04.585 UTCbdf80876-bf4b-46ba-a19e-25bd53bb83472014-06-06 16:30:07.558 UTC9ae4cca8-d24a-4d87-a784-5809699b058e2014-06-06 13:34:31.302 UTC850d2eaa-ea05-4ee5-8d14-0462986031522014-06-05 12:14:15.409 UTC50590288-22d5-4cb0-a152-29357aab7c352014-05-08 12:49:18.288 UTCf722e927-3c17-42c9-a101-a9f940334ee82014-06-11 09:10:32.353 UTC9f2b6abe-3efc-4dee-8b84-2e0d876278ca2014-04-25 10:02:35.250 UTCb02057d9-6ad6-4d77-88df-e5ec60cff83f2014-06-10 14:01:09.699 UTC3b7ddb36-6527-4c89-a70a-8ed0e0abb81f2014-06-10 16:04:44.704 UTC4b47a42f-beeb-410e-a735-185f96ddc74f2014-06-08 15:43:15.664 UTCf7c8d6a5-6521-466c-92ec-c1c8a41a78212014-06-06 14:52:41.206 UTC5bb26871-542e-4b07-9fcc-710b6f71aca02014-06-08 16:41:13.319 UTCe71229bc-a274-4c5b-9ecc-6fb6540987112014-06-08 16:06:16.226 UTC9a0c161d-6467-459d-b55a-48d0026e55522014-06-06 14:56:33.37 UTC33424e51-31a8-4228-90fb-86e60edac9f42014-06-08 16:13:45.548 UTC3f040ee9-ec30-4c0c-b9bb-5dacc1e7af802014-06-10 14:02:38.260 UTC942f3272-b926-4fe6-bf15-b4e29e44fb8f2014-05-05 09:44:20.269 UTCa8536e59-cdaf-4188-b9a4-f5da971037562014-06-06 16:21:40.873 UTCf54ed762-bb43-453e-9ecf-2968a05b46f32014-06-08 15:52:19.127 UTC03e63620-9e88-4a91-b89e-7de8e08c79292014-06-06 14:36:34.512 UTCb17158d5-fab3-4a62-88b9-57bd2d3d063d2014-06-08 15:53:29.146 UTC37048185-fb68-4f68-a8d8-af47d65da0d92014-06-11 08:53:32.981 UTC3d9659ca-8dcd-4bee-a225-6244cd9019292014-05-12 13:42:30.73 UTCd539393d-2c47-4958-8a22-e06cc46c2fad2014-06-10 08:53:28.265 UTCbf203a6d-fa48-4f35-ad40-cff4913b68682014-05-05 11:55:10.214 UTCf052486b-3ab3-429f-af0c-9e191594decd2014-06-06 16:26:12.958 UTC5074fd15-046f-4536-bb9e-f540c06b26af2014-06-08 16:39:33.787 UTC7b99a485-c395-4f74-b829-44d6cd00ffbc2014-06-08 16:38:10.539 UTCd3760d97-73e7-402e-a47c-421392a6246e2014-06-06 14:40:00.102 UTCa18418ec-e800-43d9-b55a-3cd23557d7172014-06-08 15:40:10.621 UTCe5fc58d3-008d-40e9-985e-fac63f5b396a2014-06-08 15:47:21.197 UTC0a099cde-b9b8-42fd-9417-7d3362d7402e2014-06-06 16:23:15.466 UTC7b84d7d9-225f-47ef-bd5b-484de5900fa02014-06-06 16:29:07.154 UTCe773d991-e7ef-48a1-9c29-a315e1540e132014-06-06 14:31:40.433 UTCaabaff7d-f657-4b17-84ad-457822c48f132014-06-10 14:01:49.804 UTC875e8727-ce2f-43e5-9fa1-50ecce24615c2014-05-12 13:43:58.973 UTCdede7b6f-0c01-4fa0-88ad-928280419cb22014-06-08 16:30:18.818 UTCb121dd0d-4518-47b1-9d05-feda0930456e2014-06-06 14:33:40.65 UTC472f5535-90a3-4107-ae8f-24e71c1e8fbc2014-06-11 12:22:01.979 UTCbc99ee26-4f25-45c9-8d87-5c4c3b4c7af42014-06-05 11:32:22.394 UTC7895790d-29ba-4a96-8da9-d33cecd207cb2014-06-10 15:29:06.258 UTC31647e87-e8a1-4409-8f3d-6802cc2596ba2014-05-06 09:26:28.104 UTCc708232c-6b47-4fdd-b66a-ec00cdf8a9b52014-06-10 08:51:53.249 UTCbd93275c-7f78-4fe3-98ca-c4efd3cbdfbc2014-04-25 10:05:58.574 UTC1540f783-07df-4f33-9fe2-baf9a29938312014-06-06 14:38:24.966 UTCCalculate Inner Producttimestamp002014_04_30_21_24_302014-06-11 12:29:21.857 UTCNeeds the correct table name given for writing the values.
The tablename needs to be the same as the one that is created and is a prefix of the whole table to identify a table.
This is usually a timestamp.2014-06-11 12:28:58.863 UTCconcept_pairs11A list of all the concept pairs.
[concept1,concept1
concept1,concept2
concept2,concept1
concept2,concept2
etc.]
For a complete example please download the file input_concept_pairs_for_calculate_UC_workflow from myexperiment.2014-06-11 12:30:37.432 UTCpropertyString00mysql.user=root
mysql.password=amrishsql
mysql.url=jdbc:mysql://localhost:3306/mydb
mysql.driver=com.mysql.jdbc.Driver2014-06-11 12:31:04.966 UTCPlease load a file in as seen in the example where the user, password, url (which is the database it should use), and driver is stated.2014-06-11 12:30:49.377 UTCoutputBeanshell_SQL_generate_Get_Inner_Producttimestamp0concept_pairs0out100A Beanshell script that generates a SQL statement to calculate the inner product between two concept profiles.
These concept profiles only have concepts that both have in common. The concepts that are in common in the concept profiles are multiplied with each others UC value and added. This summed up value of two concept profiles is the inner product.
For example:
Concept profile A, has the concept A, B, C and D. Concept profile B has the concepts B, C, E. This means the common concepts for both concept profiles are B, C. These values are multiplied and added. This final value is the inner product between two concept profiles. 2014-06-11 12:33:09.498 UTCnet.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivityconcept_pairs0text/plainjava.lang.Stringtruetimestamp0text/plainjava.lang.Stringtrueout100workflownet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_SQL_generate_INSERT_INTO_Inner_Product_tableinner_product_value0timestamp0concept_pairs0out100A 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 UTCnet.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivityconcept_pairs0text/plainjava.lang.Stringtruetimestamp0text/plainjava.lang.Stringtrueinner_product_value0text/plainjava.lang.Stringtrueout100workflownet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExecute_SQL_Query_Get_Inner_Productsql0propertyString0resultList22net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivitysql0text/plainjava.lang.Stringtrueparams1text/plainjava.lang.StringtruepropertyString0text/plainjava.lang.StringtrueresultList22xmlresults00workflownet.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorkerUserNameHere2014-05-12 11:48:50.529 UTCnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExecute_SQL_Update_INSERT_INTO_Inner_Product_tablesql0propertyString0resultList00net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivitysql0text/plainjava.lang.Stringtrueparams1text/plainjava.lang.StringtruepropertyString0text/plainjava.lang.StringtrueresultList00workflownet.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorkerUserNameHere2014-05-12 11:49:52.483 UTCnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.LocalworkerActivityinputlist2l(l(''))[Btrueoutputlist1l('')1workfloworg.embl.ebi.escience.scuflworkers.java.FlattenListnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.LocalworkerActivityinputlist2l(l(''))[Btrueoutputlist1l('')1workfloworg.embl.ebi.escience.scuflworkers.java.FlattenListnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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_ProductpropertyStringExecute_SQL_Update_INSERT_INTO_Inner_Product_tablesqlExecute_SQL_Update_INSERT_INTO_Inner_Product_tablepropertyStringFlatten_List_4inputlistFlatten_List_5inputlistoutputad11b9f4-2a6c-417c-a99a-53391e22ae592014-04-25 09:54:33.677 UTCbe6eb3aa-d26b-4d6a-856e-bb7b6594f3552014-06-10 15:33:40.565 UTC348801cf-d2ad-43fc-9b91-ab63e359fdcc2014-04-25 09:07:18.526 UTC33db0c4f-7076-4cbd-9913-57f2bcaad4022014-04-25 09:06:56.615 UTC5d9a8682-9ef8-46a4-b6e7-60e0566eb18f2014-05-12 11:50:18.963 UTCe9c85439-4022-4bf3-9d93-77f70e4cd5fa2014-04-25 09:55:56.310 UTCbde675e9-64ec-49a0-b079-cbe4ae8e7f132014-05-05 14:33:52.891 UTCCalculate Inner Product2014-04-25 09:00:49.797 UTCab9d319b-bbd6-4012-9c18-26c62114c2a12014-04-25 11:11:47.249 UTC807d1911-1342-4922-b766-69bbcab70c682014-05-05 14:34:36.368 UTCAmrish Mahes2014-05-05 13:59:12.828 UTC0c8d2279-44d5-4b7c-99df-68381065da4d2014-06-10 11:02:18.385 UTCb87808dc-5d2c-4362-9d49-dddf3b17ce322014-05-12 13:51:14.794 UTC0fc79d92-8f31-4987-bb91-f4de8f131b7f2014-06-11 12:33:09.623 UTCSummarize Big Tabletimestamp002014_04_30_21_24_302014-06-11 12:42:12.180 UTCNeeds the correct table name given for writing the values.
The tablename needs to be the same as the one that is created.2014-06-11 12:41:55.80 UTCpropertyString00Please load a file in as seen in the example where the user, password, url (which is the database it should use), and driver is stated.2014-06-11 12:41:28.838 UTCmysql.user=root
mysql.password=amrishsql
mysql.url=jdbc:mysql://localhost:3306/mydb
mysql.driver=com.mysql.jdbc.Driver2014-05-12 11:33:50.205 UTCresultListBeanshell_SQL_Generate_INSERT_INTO_summary_tablein11timestamp0out100A 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 UTCnet.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivitytimestamp0text/plainjava.lang.Stringtruein11text/plainjava.lang.Stringtrueout100workflownet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_SQL_statement_get_last_table_data_inputtimestamp0out100A 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 UTCnet.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivitytimestamp0text/plainjava.lang.Stringtrueout100workflownet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExecute_SQL_Query_Get_data_for_summary_tablesql0propertyString0resultList22net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivitysql0text/plainjava.lang.Stringtrueparams1text/plainjava.lang.StringtruepropertyString0text/plainjava.lang.StringtrueresultList22xmlresults00workflownet.sourceforge.taverna.scuflworkers.jdbc.SQLQueryWorkerUserNameHere2014-05-12 11:30:17.440 UTCnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExecute_SQL_Update_INSERT_INTO_summary_tablesql0propertyString0resultList00net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivitysql0text/plainjava.lang.Stringtrueparams1text/plainjava.lang.StringtruepropertyString0text/plainjava.lang.StringtrueresultList00workflownet.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorkerUserNameHere2014-05-12 11:33:03.328 UTCnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_SQL_Generate_INSERT_INTO_summary_tablein1Beanshell_SQL_Generate_INSERT_INTO_summary_tabletimestampBeanshell_SQL_statement_get_last_table_data_inputtimestampExecute_SQL_Query_Get_data_for_summary_tablesqlExecute_SQL_Query_Get_data_for_summary_tablepropertyStringExecute_SQL_Update_INSERT_INTO_summary_tablesqlExecute_SQL_Update_INSERT_INTO_summary_tablepropertyStringresultList69fe9a94-2c42-4563-9f6d-e774eaec2a522014-05-12 13:55:06.42 UTCf347fea1-c0b9-4e9f-9963-a9ef5b9db7c52014-06-11 09:22:30.197 UTCa6f4b2f7-86f7-4d90-92ee-0047f4e613022014-05-12 13:36:33.505 UTCbc9fef0e-afbe-4e64-be84-e6e6f4fa772b2014-06-11 12:42:19.340 UTCf7e2d77a-dd3e-4a3e-9ca2-30659d91d6ad2014-05-12 13:31:29.564 UTC4b65159f-b6b4-4457-b9db-59672f7c2c7d2014-04-25 10:24:37.597 UTCSummarize Big Table2014-04-25 09:06:31.655 UTCf6377916-ad80-4b93-a881-5e4b3a5fde972014-06-11 09:03:05.338 UTC0f55befa-f320-4aad-8f28-7d47f0e403202014-05-12 11:33:51.663 UTCe59e5168-be6b-4bb5-8d34-cd386cbfda7d2014-04-25 09:53:26.34 UTC00c47db0-5469-40ed-8b74-b4a6947089592014-05-12 11:33:22.736 UTC6137cf86-1e2e-42ba-aef2-1a0adb9fbbd02014-04-25 09:07:59.8 UTCCalculate Uncertainty Coefficientcorrected_contingency_values22The contingency values of the concept pair. For example the concept pair A,A and A,B have contincengy values of [ [ 1,0,0,8 ],[1,2,2,4] ].
2014-06-11 12:24:34.24 UTCtimestamp002014_04_30_21_24_302014-06-11 12:25:28.260 UTCNeeds 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 UTCconcept_pairs11A 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 UTCpropertyString00Please load a file in as seen in the example where the user, password, url (which is the database it should use), and driver is stated.2014-06-11 12:26:04.211 UTCmysql.user=root
mysql.password=amrishsql
mysql.url=jdbc:mysql://localhost:3306/mydb
mysql.driver=com.mysql.jdbc.Driver2014-06-11 12:26:15.897 UTCoutputBeanshell_SQL_INSERT_UC_values_INTO_tabletimestamp0UC_value0concept_pairs0output_SQL00A 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 UTCnet.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivitytimestamp0text/plainjava.lang.Stringtrueconcept_pairs0text/plainjava.lang.StringtrueUC_value0text/plainjava.lang.Stringtrueoutput_SQL00workflownet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_calculate_Uncertainty_Coefficientcorrected_contingency_values1UC_value00A Beanshell script that calculates the Uncertainty coefficient based on a script of Herman van Haagen.2014-06-11 12:27:47.930 UTCnet.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivitycorrected_contingency_values1text/plainjava.lang.StringtrueUC_value00workflownet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExecute_SQL_Update_INSERT_INTO_UC_tablesql0propertyString0resultList00net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivitysql0text/plainjava.lang.Stringtrueparams1text/plainjava.lang.StringtruepropertyString0text/plainjava.lang.StringtrueresultList00workflownet.sourceforge.taverna.scuflworkers.jdbc.SQLUpdateWorkerUserNameHere2014-05-12 11:46:55.841 UTCnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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_tablesqlExecute_SQL_Update_INSERT_INTO_UC_tablepropertyStringoutput6fae7384-536a-47de-989d-1bce376249ed2014-06-11 12:28:09.901 UTC7d75255a-84e6-43d3-a398-60bfae8019402014-05-08 15:06:24.745 UTC13548fc4-b946-4adc-b56e-d7aa856174f72014-06-10 13:43:49.66 UTC1dc7cdb3-165a-4413-9adb-54081500717f2014-06-10 14:08:27.331 UTC6a956c52-35e9-42a0-acad-c7c17e2a45ba2014-05-08 15:00:02.697 UTC8f04d577-c676-46ea-b867-d849e7af0e6d2014-05-05 12:49:30.628 UTC46d45a69-6c44-4185-84a4-119f054a16f82014-05-05 13:29:23.342 UTC4ebf7d25-6d88-4481-8109-a28a055c26c22014-06-10 15:32:28.918 UTCCalculate Uncertainty Coefficient2014-04-25 08:57:47.839 UTCAmrish Mahes2014-05-05 13:43:58.257 UTC0cdc32e9-e9b0-4221-b53c-a65cd3db8f902014-05-05 13:17:31.804 UTC8eca8dc6-84e5-4412-bb2d-5e38d591e5d42014-06-10 13:46:59.916 UTC81609bfe-030c-4b35-98b7-45fe6f9a4e1c2014-06-10 13:39:04.13 UTC2e19c3f7-489e-4f69-a4b7-744d4f046fe42014-05-05 13:14:30.664 UTC000df03c-2c75-49ee-b7e9-25dd34d507fa2014-05-05 13:42:48.991 UTC4137be61-327d-4d14-8066-e1d75d8f5f4e2014-04-25 11:04:18.674 UTC76ae35e5-bd6f-4da6-a8fc-157da2bd0ea52014-04-25 09:09:07.360 UTC2ebf0b6a-071d-46f6-b793-2dde8cb9d22f2014-05-05 13:43:59.598 UTCThis 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 = DOUBLE2014-05-05 13:42:27.42 UTCeb63e5b4-4ec9-4e70-932c-c22fe8ac8c3b2014-05-05 13:43:43.341 UTC5b89a766-6e15-4189-98ab-1b7e4640cd7b2014-05-12 13:47:37.834 UTC1157056b-06f9-4caf-b68f-635230a545c42014-04-25 09:07:59.975 UTC34c726a4-4e83-461c-a95d-f96eaa1c05752014-05-08 12:49:59.727 UTC71245a73-7b81-4bff-8ab5-6750b4866ccd2014-05-12 11:47:24.645 UTC8e91b850-ccce-4938-a5c4-132bf4423c612014-06-10 16:06:35.992 UTC8570b4b6-c56e-4588-89ee-eab59efc547d2014-06-10 11:13:15.21 UTC