Functional annotation of SNPs using next-generation text mining
type: Nanopublication
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: RoCrateNanopub
created: 2025-11-11T17:04:49.668+01:00

../Datasets/List Concept Sets output.xls
type: Dataset
type: Object
was output from: ../Workflows/List_Predefined_Concept_Sets.t2flow

../Datasets/output snp gene kegg.txt
type: Dataset
type: Object
was output from: ../Workflows/SNP2KEGG.t2flow

../Datasets/rs11158519 output.xls
type: Dataset
type: Object
was output from: ../Workflows/main_nested_workflow.t2flow

../Datasets/rs168622 output.xls
type: Dataset
type: Object
was output from: ../Workflows/main_nested_workflow.t2flow

../Datasets/rs174547 output.xls
type: Dataset
type: Object
was output from: ../Workflows/main_nested_workflow.t2flow

../Datasets/rs2014355 output.xls
type: Dataset
type: Object
was output from: ../Workflows/main_nested_workflow.t2flow

../Datasets/rs2046813 output.xls
type: Dataset
type: Object
was output from: ../Workflows/main_nested_workflow.t2flow

../Datasets/rs211718 output.xls
type: Dataset
type: Object
was output from: ../Workflows/main_nested_workflow.t2flow

../Datasets/rs2216405 output.xls
type: Dataset
type: Object
was output from: ../Workflows/main_nested_workflow.t2flow

../Datasets/rs2286963 output.xls
type: Dataset
type: Object
was output from: ../Workflows/main_nested_workflow.t2flow

../Datasets/rs272889 output.xls
type: Dataset
type: Object
was output from: ../Workflows/main_nested_workflow.t2flow

../Datasets/rs541503 output.xls
type: Dataset
type: Object
was output from: ../Workflows/main_nested_workflow.t2flow

../Datasets/rs603424 output.xls
type: Dataset
type: Object
was output from: ../Workflows/main_nested_workflow.t2flow

../Datasets/rs7094971 output.xls
type: Dataset
type: Object
was output from: ../Workflows/main_nested_workflow.t2flow

../Datasets/rs7156144 output.xls
type: Dataset
type: Object
was output from: ../Workflows/main_nested_workflow.t2flow

../Datasets/rs8396 output.xls
type: Dataset
type: Object
was output from: ../Workflows/main_nested_workflow.t2flow

../Datasets/rs9393903 output.xls
type: Dataset
type: Object
was output from: ../Workflows/main_nested_workflow.t2flow

../Datasets/top snps to annotate input.txt
type: Dataset
type: Object
used input: ../Workflows/SNP2KEGG.t2flow
used input: ../Workflows/main_nested_workflow.t2flow

../Documents/HOWTO.txt
type: Document
type: Object
comment: Text file describing the protocol for the experiment, including the order of workflow execution.

../Documents/README.txt
type: Document
type: Object
comment: Text file describing the background of the experiment, and the formulated hypothesis.

../Documents/kegg cp comparison results.xls
type: Document
type: Results
type: Object
comment: Excel file comparing the results from the workflows.

../Documents/workflow sketch final.jpg
type: Document
type: Object
comment: High-level overview of experiment and order of workflow execution.

../Documents/workflow sketch final.odp
type: Document
type: Object
comment: High-level overview of experiment and order of workflow execution.

../Documents/workflow sketch final.pdf
type: Document
type: Object
comment: High-level overview of experiment and order of workflow execution.

../Documents/workflow sketch final.png
type: Document
type: Object
comment: High-level overview of experiment and order of workflow execution.

../Workflow-runs/List-Concept-Sets-prov-export.zip
type: WorkflowRun
type: Object
described by workflow: ../Workflows/List_Predefined_Concept_Sets.t2flow
wprov:enactor agent: Kristina Hettne

../Workflow-runs/Main-nested-workflow-rs11158519-prov-export.zip
type: WorkflowRun
type: Object
described by workflow: ../Workflows/main_nested_workflow.t2flow
wprov:enactor agent: Kristina Hettne

../Workflow-runs/Main-nested-workflow-rs168622-prov-export.zip
type: WorkflowRun
type: Object
described by workflow: ../Workflows/main_nested_workflow.t2flow
wprov:enactor agent: Kristina Hettne

../Workflow-runs/Main-nested-workflow-rs174547-prov-export.zip
type: WorkflowRun
type: Object
described by workflow: ../Workflows/main_nested_workflow.t2flow
wprov:enactor agent: Kristina Hettne

../Workflow-runs/Main-nested-workflow-rs2014355-prov-export.zip
type: WorkflowRun
type: Object
described by workflow: ../Workflows/main_nested_workflow.t2flow
wprov:enactor agent: Kristina Hettne

../Workflow-runs/Main-nested-workflow-rs2046813-prov-export.zip
type: WorkflowRun
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described by workflow: ../Workflows/main_nested_workflow.t2flow
wprov:enactor agent: Kristina Hettne

../Workflow-runs/Main-nested-workflow-rs211718-prov-export.zip
type: WorkflowRun
type: Object
described by workflow: ../Workflows/main_nested_workflow.t2flow
wprov:enactor agent: Kristina Hettne

../Workflow-runs/Main-nested-workflow-rs2216405-prov-export.zip
type: WorkflowRun
type: Object
described by workflow: ../Workflows/main_nested_workflow.t2flow
wprov:enactor agent: Kristina Hettne

../Workflow-runs/Main-nested-workflow-rs2286963-prov-export.zip
type: WorkflowRun
type: Object
described by workflow: ../Workflows/main_nested_workflow.t2flow
wprov:enactor agent: Kristina Hettne

../Workflow-runs/Main-nested-workflow-rs272889-prov-export.zip
type: WorkflowRun
type: Object
described by workflow: ../Workflows/main_nested_workflow.t2flow
wprov:enactor agent: Kristina Hettne

../Workflow-runs/Main-nested-workflow-rs541503-prov-export.zip
type: WorkflowRun
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described by workflow: ../Workflows/main_nested_workflow.t2flow
wprov:enactor agent: Kristina Hettne

../Workflow-runs/Main-nested-workflow-rs603424-prov-export.zip
type: WorkflowRun
type: Object
described by workflow: ../Workflows/main_nested_workflow.t2flow
wprov:enactor agent: Kristina Hettne

../Workflow-runs/Main-nested-workflow-rs7094971-prov-export.zip
type: WorkflowRun
type: Object
described by workflow: ../Workflows/main_nested_workflow.t2flow
wprov:enactor agent: Kristina Hettne

../Workflow-runs/Main-nested-workflow-rs7156144-prov-export.zip
type: WorkflowRun
type: Object
described by workflow: ../Workflows/main_nested_workflow.t2flow
wprov:enactor agent: Kristina Hettne

../Workflow-runs/Main-nested-workflow-rs8396-prov-export.zip
type: WorkflowRun
type: Object
described by workflow: ../Workflows/main_nested_workflow.t2flow
wprov:enactor agent: Kristina Hettne

../Workflow-runs/Main-nested-workflow-rs9393903-prov-export.zip
type: WorkflowRun
type: Object
described by workflow: ../Workflows/main_nested_workflow.t2flow
wprov:enactor agent: Kristina Hettne

../Workflow-runs/SNP2KEGG-prov-export.zip
type: WorkflowRun
type: Object
described by workflow: ../Workflows/SNP2KEGG.t2flow
wprov:enactor agent: Kristina Hettne

../Workflows/main nested workflow.t2flow
type: Workflow
type: Object
has sub workflow: ../Workflows/DatabaseID_to_ConceptID_component.t2flow
has sub workflow: ../Workflows/Explain_concept_scores_component.t2flow
has sub workflow: ../Workflows/Filter_concepts_with_profiles_component.t2flow
has sub workflow: ../Workflows/Find_Supporting_Documents_component.t2flow
has sub workflow: ../Workflows/Find_co_occurring_documents_component.t2flow
has sub workflow: ../Workflows/Get_Concept_IDs_component.t2flow
has sub workflow: ../Workflows/Get_concept_information_component.t2flow
has sub workflow: ../Workflows/Match_concept_profiles_component.t2flow

set Match SNPs with concept profiles find
type: Expression

Madrid
type: Place

PubMed records
type: Organization

concept profile database
type: Expression

workflow
type: Concept

genetics
type: Domain

list concept
type: Expression

Gene
type: Person

KEGG pathway
type: Expression

SNPs
type: Concept

concept
type: Concept

supporting literature
type: Expression

databases
type: Concept

Palaeontology
type: IPTC
path: Science and technology/Natural science/Biology/Palaeontology

List concept sets Match SNPs with concept profiles Find supporting literature
type: Sentence
norm score: 21.102248005801304
score: 58.2

biosynthesis
type: Concept
norm score: 2.008181480104128
score: 5.4

profile
type: Concept
norm score: 2.863518036444775
score: 7.7

Sport event
type: IPTC
path: Sport/Sport event

https://w3id.org/ro-id/07e56bb7-9b00-44aa-8dde-98f06e49a1fe
type: Sentence
name: rs174547 DKFZP434K028 -1 rs174547 DAGLA path:hsa04723 Retrograde endocannabinoid signaling - Homo sapiens (human) rs174547 C11orf9 -1 rs174547 C11orf10 -1 rs174547 FEN1 path:hsa03030 DNA replication - Homo sapiens (human) rs174547 FEN1 path:hsa03410 Base excision repair - Homo sapiens (human) rs174547 FEN1 path:hsa03450 Non-homologous end-joining - Homo sapiens (human) rs174547 FADS2 path:hsa00592 alpha-Linolenic acid metabolism - Homo sapiens (human) rs174547 FADS2 path:hsa01040 Biosynthesis of unsaturated fatty acids - Homo sapiens (human) rs174547 FADS2 path:hsa03320 PPAR signaling pathway - Homo sapiens (human) rs174547 MIR1908 -1 rs174547 FADS1 path:hsa01040 Biosynthesis of unsaturated fatty acids - Homo sapiens (human) rs174547 FADS3 -1 rs174547 RAB3IL1 -1 rs174547 MIR611 -1 rs2014355 CABP1 -1 rs2014355 MLEC -1 rs2014355 UNC119B -1 rs2014355 ACADS path:hsa00071 Fatty acid metabolism - Homo sapiens (human) rs2014355 ACADS path:hsa00280 Valine rs2014355 ACADS leucine and isoleucine degradation - Homo sapiens (human) rs2014355 ACADS path:hsa00650 Butanoate metabolism - Homo sapiens (human) rs2014355 ACADS path:hsa01100 Metabolic pathways - Homo sapiens (human) rs2014355 SPPL3 -1 rs2014355 MIR4700 -1 rs211718 SLC44A5 -1 rs211718 ACADM path:hsa00071 Fatty acid metabolism - Homo sapiens (human) rs211718 ACADM path:hsa00280 Valine rs211718 ACADM leucine and isoleucine degradation - Homo sapiens (human) rs211718 ACADM path:hsa00410 beta-Alanine metabolism - Homo sapiens (human) rs211718 ACADM path:hsa00640 Propanoate metabolism - Homo sapiens (human) rs211718 ACADM path:hsa01100 Metabolic pathways - Homo sapiens (human) rs211718 ACADM path:hsa03320 PPAR signaling pathway - Homo sapiens (human) rs2286963 KANSL1L -1 rs2286963 ACADL path:hsa00071 Fatty acid metabolism - Homo sapiens (human) rs2286963 ACADL path:hsa01100 Metabolic pathways - Homo sapiens (human) rs2286963 ACADL path:hsa03320 PPAR signaling pathway - Homo sapiens (human) rs2286963 MYL1 -1 rs9393903 unchara…
norm score: 36.25815808556925
score: 100.0

FUNCTIONAL ANNOTATION OF SINGLE NUCLEOTIDE POLYMORHPISMS USING NEXT-GENERATION TEXT MINING AND CURATED METABOLIC PATHWAY DATABASES RESEARCH OBJECT
type: Sentence
norm score: 3.1182015953589555
score: 8.6

profile
type: Lemma
norm score: 2.772963604852686
score: 6.4

service-account-enrichment
type: Agent

Functional annotation of SNPs using next-generation text mining
type: ResearchObject
type: LiveRO
type: Dataset
author: Kristina Hettne
content size: 1419920
creator: Kristina Hettne
date created: 2012-12-14 11:04:18.118000+00:00
date modified: 2025-03-05 00:59:09.110748+00:00
date published: 2012-12-14 11:04:18.118000+00:00
description: This research object implements the concept profile matching pipeline in the knowledge discovery tool Anni (http://biosemantics.org/anni), and adapts it to interpret the top SNPs from a GWAS. The underlying literature and concept profile databases are the same as the for the current version of Anni (2.1). The pack consists of three main workflows (http://www.myexperiment.org/workflows/2999, http://www.myexperiment.org/workflows/2973, http://www.myexperiment.org/workflows/2972). Workflow 2999 returns a list of available concept sets to match the SNPs against. As an example, the concept set GO biological processes is used. Workflow 2973 consist of nine nested workflows (eight different components in the pack, for which one is used twice within the main workflow for different purposes). It reuses the SNP to Entrez gene identifier part of this workflow: http://www.myexperiment.org/workflows/3124, here implemented as a separate workflow (http://www.myexperiment.org/workflows/2971). Workflow 2973 takes a SNP ID and a set of GO biological processes as input together with a set of parameter settings. The outputs give the following information: 1) information about the GO biological process with the highest matching score against the SNPs, 2) if there are any co-occurring documents supporting this finding, and 3) the concepts contributing most to the match (intermediate concepts). The output parameters can be saved in Taverna as an Excel sheet together with the input parameters for interpretation. Documents supporting the relation with the intermediate concepts contributing most to the match can be retrieved with workflow http://www.myexperiment.org/workflows/2972.
encoding format: application/ld+json
license: no-permission
comment: Described in myExperiment pack number 282
domain: chemistry
domain: genetics
domain: software
domain: linguistics
domain: computer science
domain: information technology
domain: biology
domain: medicine
domain: biochemistry
place: Madrid
concept: biosynthesis
concept: profile
concept: question
concept: web service
concept: literature
concept: workflow
concept: user account
concept: footpath
concept: concept
concept: metabolism
concept: text mining
concept: single nucleotide polymorphism
concept: http
concept: gene
concept: database
concept: Homo sapiens
field of research: earth sciences
field of research: oceanography
field of research: geology
IPTC: Palaeontology
IPTC: Sport event
IPTC: IT-computer sciences
IPTC: Science and technology
IPTC: People
IPTC: Philosophy
IPTC: Non-fiction
IPTC: Anthropology
IPTC: Organic chemical
IPTC: Genetics
lemma: profile
lemma: pathway
lemma: rs603424
lemma: text mining
lemma: http
lemma: KEGG
lemma: Match SNPs
lemma: Homo sapiens
lemma: database
lemma: SNP
lemma: literature
lemma: Anni
lemma: concept
lemma: query

download
type: Hypothesis
type: Resource
type: MediaObject
author: public
content size: 803
creator: public
date created: 2013-01-29 16:21:41.780000+00:00
date modified: 2022-03-25 09:49:17.234450+00:00
license: no-permission
sd date published: 2013-01-29 16:21:41.780000+00:00

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type: Results
type: Resource
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date created: 2022-03-25 09:47:30.811987+00:00
date modified: 2022-03-25 09:49:16.032875+00:00
encoding format: application/pdf
license: no-permission
name: http://docs.example.com/file.pdf
sd date published: 2022-03-25 09:47:30.811987+00:00

literature database PubMed
type: Phrase
norm score: 1.7148014440433212
score: 3.8

profile
type: Lemma
norm score: 3.4662045060658575
score: 8.0

IT-computer sciences
type: IPTC
path: Science and technology/Technology and engineering/IT-computer sciences

space sciences (general)
type: NASA
norm score: 4.812991677298901
score: 0.05067460238933563

pathway
type: Lemma
norm score: 4.159445407279029
score: 9.6

chemistry
type: Domain
norm score: 8.571428571428571
score: 7.2

Science and technology
type: IPTC
path: Science and technology

genetics
type: Domain
norm score: 6.071428571428571
score: 5.1

question
type: Concept
norm score: 2.2313127556712535
score: 6.0

software
type: Domain
norm score: 4.523809523809524
score: 3.8

2010
type: TimeReference

https://w3id.org/ro-id/22c8c450-830f-445b-9a45-a597e7138c8d
type: Sentence
name: The pack consists of three main workflows (http://www.myexperiment.org/workflows/2999, http://www.myexperiment.org/workflows/2973, http://www.myexperiment.org/workflows/2972). Workflow 2999 returns a list of available concept sets to match the SNPs against.
norm score: 4.169688179840464
score: 11.5

web service
type: Concept
norm score: 3.830420230568985
score: 10.3

concept profile database
type: Phrase
norm score: 8.12274368231047
score: 18.0

Functional annotation of single nucleotide polymorphisms (SNPs) using next-generation text mining and curated metabolic pathway databases.
type: Sentence
norm score: 3.4082668600435095
score: 9.4

literature
type: Concept
norm score: 2.4172554853105246
score: 6.5

linguistics
type: Domain
norm score: 15.714285714285714
score: 13.2

workflow
type: Concept
norm score: 2.9378951283004837
score: 7.9

rs603424
type: Lemma
norm score: 3.4228769497400346
score: 7.9

Functional annotation of SNPs using next-generation text mining.
type: Sentence
norm score: 4.278462654097171
score: 11.8

life sciences (general)
type: NASA
norm score: 55.27437915589638
score: 0.5819680094718933

user account
type: Concept
norm score: 4.165117143919673
score: 11.2

The EntrezGene id is used to query the Anni concept database to retrieve the internal concept id, which is used to retrieve the concept profile for the concept from the concept profile database.
type: Sentence
norm score: 2.030456852791878
score: 5.6

set Match SNPs
type: Phrase
norm score: 2.075812274368231
score: 4.6

text mining
type: Lemma
norm score: 2.68630849220104
score: 6.2

genetics
type: Domain
norm score: 2.5
score: 2.1

list concept
type: Phrase
norm score: 28.249097472924188
score: 62.6

research object
type: Phrase
norm score: 2.9332129963898916
score: 6.5

http
type: Lemma
norm score: 4.9393414211438476
score: 11.4

output parameter
type: Phrase
norm score: 1.9855595667870038
score: 4.4

2009 Nov-15
type: TimeReference

earth sciences
type: FieldOfResearch
norm score: 16.173050320071866
score: 0.43228960037231445

earth sciences
type: FieldOfResearch
norm score: 32.83800326176385
score: 0.8777272701263428

People
type: IPTC
path: Human interest/People

2008
type: TimeReference

This research object implements the concept profile matching pipeline in the knowledge discovery tool Anni (http://biosemantics.org/anni), and adapts it to interpret the top SNPs from a GWAS.
type: Sentence
norm score: 14.140681653372008
score: 39.0

SCD path
type: Phrase
norm score: 2.2111913357400725
score: 4.9

ACADS leucine
type: Phrase
norm score: 1.5794223826714802
score: 3.5

Philosophy
type: IPTC
path: Science and technology/Social sciences/Philosophy

earth sciences
type: FieldOfResearch
norm score: 36.437974138474104
score: 0.9739509224891663

computer science
type: Domain
norm score: 6.190476190476191
score: 5.2

proline metabolism
type: Phrase
norm score: 1.8050541516245489
score: 4.0

user account
type: Concept
norm score: 4.3510598735589445
score: 11.7

Non-fiction
type: IPTC
path: Arts, culture and entertainment/Arts and entertainment/Literature/Non-fiction

KEGG
type: Lemma
norm score: 5.849220103986135
score: 13.5

information technology
type: Domain
norm score: 8.452380952380953
score: 7.1

mathematical and computer sciences
type: NASA
norm score: 23.10239118737426
score: 0.2432384192943573

biology
type: Domain
norm score: 6.309523809523809
score: 5.3

footpath
type: Concept
norm score: 3.3469691335068803
score: 9.0

query KEGG pathways with SNPs
type: Phrase
norm score: 7.400722021660649
score: 16.4

concept
type: Concept
norm score: 8.702119747117889
score: 23.4

mathematical and computer sciences
type: NASA
norm score: 16.810237979430458
score: 0.17699015140533447

Match SNPs
type: Lemma
norm score: 11.741767764298093
score: 27.1

space sciences
type: NASA
norm score: 4.812991677298901
score: 0.05067460238933563

Madrid
type: Place
wikidata: https://www.wikidata.org/wiki/Q2807

CURATED metabolic pathway database
type: Phrase
norm score: 1.6696750902527075
score: 3.7

Homo sapiens
type: Lemma
norm score: 7.019064124783362
score: 16.2

Query KEGG pathways with SNPs
type: Sentence
norm score: 7.686729514140682
score: 21.2

oceanography
type: FieldOfResearch
norm score: 14.550972279690173
score: 0.38893306255340576

database
type: Lemma
norm score: 2.5129982668977466
score: 5.8

fatty acid
type: Phrase
norm score: 1.7599277978339352
score: 3.9

computer science
type: Domain
norm score: 14.285714285714286
score: 12.0

life sciences
type: NASA
norm score: 55.27437915589638
score: 0.5819680094718933

Anthropology
type: IPTC
path: Science and technology/Social sciences/Anthropology

metabolism
type: Concept
norm score: 2.9378951283004837
score: 7.9

Concept sets
type: Sentence
norm score: 3.807106598984771
score: 10.5

geology
type: FieldOfResearch
norm score: 32.83800326176385
score: 0.8777272701263428

SNP
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score: 6.1

medicine
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text mining
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geology
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score: 0.9739509224891663

CHUK path
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score: 30.2

single nucleotide polymorphism
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score: 11.2

curated metabolic pathway database
type: Phrase
norm score: 1.9855595667870038
score: 4.4

concept profile database
type: Phrase
norm score: 3.068592057761733
score: 6.8

http
type: Concept
norm score: 5.169207883971737
score: 13.9

Match SNPs with concept profile
type: Phrase
norm score: 5.099277978339351
score: 11.3

database change
type: Phrase
norm score: 1.94043321299639
score: 4.3

literature
type: Lemma
norm score: 2.772963604852686
score: 6.4

Anni
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concept
type: Lemma
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score: 23.2

IT-computer sciences
type: IPTC
path: Science and technology/Technology and engineering/IT-computer sciences

query
type: Lemma
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score: 6.0

mathematical and computer sciences (general)
type: NASA
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score: 0.2432384192943573

profile
type: Lemma
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SNP
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earth sciences
type: FieldOfResearch
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score: 0.38893306255340576

database
type: Lemma
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score: 9.7

single nucleotide polymorphism
type: Concept
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score: 13.4

SNP ID
type: Phrase
norm score: 5.009025270758123
score: 11.1

2010
type: TimeReference

2007
type: TimeReference

Organic chemical
type: IPTC
path: Economy, business and finance/Economic sector/Chemicals/Organic chemical

mathematical and computer sciences (general)
type: NASA
norm score: 16.810237979430458
score: 0.17699015140533447

workflow
type: Lemma
norm score: 2.772963604852686
score: 6.4

gene
type: Concept
norm score: 2.2685013015991076
score: 6.1

database
type: Concept
norm score: 2.6031982149497956
score: 7.0

Homo sapiens
type: Concept
norm score: 8.999628114540723
score: 24.2

database
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Kristina Hettne
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