http://w3id.org/ro-id/rohub/model#change_specifications/140a9ab3-c360-4ba4-ba8f-f4df6f060eb5/changes/bc474904-2d2d-410d-9aad-a0e3129f0679
type: Addition
type: Change
related resource: annotate_genes_biological_processes_xpath_cpids.t2flow

deregulate in HD
type: Expression

HD
type: Concept

participate in epigenetic processes
type: Expression

genetics
type: Domain

genes
type: Concept

have an epigenetic role
type: Expression

Explain Scores
type: Workflow
type: Object
description: Purpose of workflow: This workflow takes two concept ids as input and returns the top ranking "B" concepts according to Swanson's ABC model of discovery, where the relationships AB and BC are known and reported in the literature, and the implicit relationship AC is a putative new discovery. It might also be the case that AC is already known. In that case AC does not represent a new discovery but will still be returned (see workflow example values). The B concepts are returned sorted on the percentage of the contributions of the individual concepts to the coherence score (the average of the inner product scores of all possible concept pairs within the group).

missing link
type: Lemma
norm score: 5.304445274561076
score: 14.2

life sciences (general)
type: NASA
norm score: 35.87466373187602
score: 0.9233048558235168

have an epigenetic role
type: Phrase
norm score: 0.06863417982155112
score: 0.2

life sciences (general)
type: NASA
norm score: 35.76177208527657
score: 0.9203993678092957

chromatin
type: Concept
norm score: 4.039375424304141
score: 11.9

epigenetic process
type: Phrase
norm score: 17.84488675360329
score: 52.0

role
type: Lemma
norm score: 5.491221516623086
score: 14.7

epigenetic role
type: Phrase
norm score: 6.554564172958133
score: 19.1

testing
type: Concept
norm score: 2.545824847250509
score: 7.5

participate in epigenetic process
type: Phrase
norm score: 0.20590253946465337
score: 0.6

Genoa
type: Concept
norm score: 20.570264765784113
score: 60.6

epigenetic
type: Concept
norm score: 1.5274949083503053
score: 4.5

geology
type: FieldOfResearch
norm score: 47.691405491207696
score: 0.9814894795417786

HD
type: Lemma
norm score: 3.9596563317146063
score: 10.6

life sciences
type: NASA
norm score: 28.363564182847412
score: 0.7299919724464417

HD
type: Concept
norm score: 8.146639511201629
score: 24.0

chromatin
type: Lemma
norm score: 4.59469555472544
score: 12.3

service-account-enrichment
type: Agent

Interpretation of the results from the analysis of RO: http://sandbox.rohub.org/rodl/ROs/HD_chromatin_analysis/
type: ResearchObject
type: SnapshotRO
type: Dataset
is snapshot of: http://sandbox.rohub.org/rodl/ROs/data_interpretation/
snapshoted at time: 2014-02-11T16:28:33.504+01:00
snapshoted by: Eleni Mina
was changed by: http://w3id.org/ro-id/rohub/model#change_specifications/140a9ab3-c360-4ba4-ba8f-f4df6f060eb5
author: Eleni Mina
content size: 90137
creator: Eleni Mina
date created: 2013-08-30 16:15:52.229000+00:00
date modified: 2025-03-05 00:55:18.105872+00:00
date published: 2013-08-30 16:15:52.229000+00:00
description: This RO is an extension of the HD chromatin analysis to interpret the results and reveal missing links that can according to literature explain HD gene deregulation
encoding format: application/ld+json
license: no-permission
was revision of: http://sandbox.rohub.org/rodl/ROs/data_interpretation-snapshot/
domain: linguistics
concept: chromatin
concept: testing
concept: Genoa
concept: epigenetic
concept: HD
concept: role
concept: missing link
concept: analyzation
concept: system
concept: deregulation
concept: hard drive
concept: http
concept: Ro
concept: outcome
concept: gene
field of research: geology
field of research: earth sciences
field of research: geochemistry
IPTC: Animal
IPTC: Economic policy
IPTC: Language
lemma: missing link
lemma: role
lemma: HD
lemma: chromatin
lemma: gene
lemma: deregulation
lemma: analysis
lemma: Genoa
lemma: Ro
NASA: life sciences (general)
NASA: life sciences
phrase: have an epigenetic role
phrase: epigenetic process
phrase: epigenetic role
phrase: participate in epigenetic process
phrase: analysis of Ro
phrase: HD gene deregulation
phrase: gene deregulation
phrase: chromatin analysis
phrase: HD chromatin analysis
phrase: results from the analysis
phrase: deregulate in HD
sentence: https://w3id.org/ro-id/5c589b0d-0fd4-4e10-a949-254f733bad51

service-account-generation-service
type: Agent

Eleni Mina
type: Agent

data_interpretation
type: Folder
type: Dataset

conclusion
type: Conclusions
type: Resource
type: MediaObject
author: Eleni Mina
content size: 67
creator: Eleni Mina
date created: 2013-08-31 15:11:30.970000+00:00
date modified: 2022-03-25 09:24:40.710743+00:00
encoding format: text/plain
license: no-permission
sd date published: 2013-08-31 15:11:30.970000+00:00

workflow sketch data interpretation
type: Sketch
type: Resource
type: MediaObject
author: Eleni Mina
content size: 39476
creator: Eleni Mina
date created: 2013-08-31 15:37:06.058000+00:00
date modified: 2022-03-25 09:24:39.842471+00:00
description: Sketch of the workflows and their explanation, for data interpretation, plus the connection to the output from the RO for chromatin analysis
encoding format: image/png
license: no-permission
sd date published: 2013-08-31 15:37:06.058000+00:00

hypothesis.txt
type: Hypothesis
type: Resource
type: MediaObject
author: Eleni Mina
content size: 63
creator: Eleni Mina
date created: 2013-08-31 15:04:48.724000+00:00
date modified: 2022-03-25 09:24:28.805556+00:00
encoding format: text/plain
license: no-permission
sd date published: 2013-08-31 15:04:48.724000+00:00

Explain Scores
type: Resource
type: MediaObject
author: Eleni Mina
content size: 41573
creator: Eleni Mina
date created: 2013-11-05 13:09:46.561000+00:00
date modified: 2022-03-25 09:24:37.622734+00:00
description: Purpose of workflow: This workflow takes two concept ids as input and returns the top ranking "B" concepts according to Swanson's ABC model of discovery, where the relationships AB and BC are known and reported in the literature, and the implicit relationship AC is a putative new discovery. It might also be the case that AC is already known. In that case AC does not represent a new discovery but will still be returned (see workflow example values). The B concepts are returned sorted on the percentage of the contributions of the individual concepts to the coherence score (the average of the inner product scores of all possible concept pairs within the group).
license: no-permission
sd date published: 2013-11-05 13:09:46.561000+00:00

Prioritize gene list related to a concept /list of concepts
type: Resource
type: MediaObject
type: ComputationalWorkflow
author: Eleni Mina
content size: 188023
creator: Eleni Mina
date created: 2013-11-05 13:07:43.493000+00:00
date modified: 2022-03-25 09:24:47.224634+00:00
description: This workflow can prioritize genes that are related to a specific concept, e.g. HTT. In order to obtain the concept id of the term that is going to be matched against the gene list, the workflow Get concept suggestions from term, needs to run first. matchConceptProfileList: the gene list we want to match (order) against a particular concept queryConceptProfileList: the concept (or gene list) we want to match the query against
license: no-permission
sd date published: 2013-11-05 13:07:43.493000+00:00

Annotate a gene list with Biological processes
type: Resource
type: MediaObject
type: ComputationalWorkflow
author: Eleni Mina
content size: 214639
creator: Eleni Mina
date created: 2014-02-11 15:25:01.110000+00:00
date modified: 2022-03-25 09:24:49.007856+00:00
description: This workflow annotates a comma separated gene list with a predefined concept set as for example Biological processes or Disease/syndrome. To obtain the particular id for each concept set (e.g. "5" for Biological processes), the workflow listPredefinedConceptSets needs to run first. The workflow is using the anni web services
license: no-permission
sd date published: 2014-02-11 15:25:01.110000+00:00

ListPredefinedConceptSets
type: Resource
type: MediaObject
type: ComputationalWorkflow
author: Eleni Mina
content size: 30787
creator: Eleni Mina
date created: 2013-11-05 13:09:01.493000+00:00
date modified: 2022-03-25 09:24:44.673277+00:00
description: This workflow lists all IDs and descriptions of the predefined concept set
license: no-permission
sd date published: 2013-11-05 13:09:01.493000+00:00

Get concept suggestions from term
type: Resource
type: MediaObject
type: ComputationalWorkflow
author: Eleni Mina
content size: 41692
creator: Eleni Mina
date created: 2013-08-31 15:02:18.108000+00:00
date modified: 2022-03-25 09:24:48.176013+00:00
description: This workflow suggests concept ids that match the query term. The user can run this workflow with any term of interest as for example "human", "htt", "Transcription" etc, and will get suggestions for concept ids together with descriptions. Then can choose the concept id that matches the best to her/his needs and use it to the rest of the CPA workflows
license: no-permission
sd date published: 2013-08-31 15:02:18.108000+00:00

gene
type: Lemma
norm score: 3.399327605528577
score: 9.1

earth sciences
type: FieldOfResearch
norm score: 47.691405491207696
score: 0.9814894795417786

role
type: Concept
norm score: 5.363204344874406
score: 15.8

missing link
type: Concept
norm score: 4.514596062457569
score: 13.3

analyzation
type: Concept
norm score: 1.4596062457569585
score: 4.3

life sciences
type: NASA
norm score: 35.76177208527657
score: 0.9203993678092957

HD
type: Lemma
norm score: 4.632050803137841
score: 12.4

analysis of Ro
type: Phrase
norm score: 3.843514070006863
score: 11.2

Animal
type: IPTC
path: Human interest/Animal

system
type: Concept
norm score: 3.6320434487440596
score: 10.7

deregulation
type: Concept
norm score: 9.911744738628649
score: 29.2

https://w3id.org/ro-id/5c589b0d-0fd4-4e10-a949-254f733bad51
type: Sentence
name: Interpretation of the results from the analysis of RO: http://sandbox.rohub.org/rodl/ROs/HD_chromatin_analysis/. This RO is an extension of the HD chromatin analysis to interpret the results and reveal missing links that can according to literature explain HD gene deregulation
norm score: 33.333333333333336
score: 100.0

Economic policy
type: IPTC
path: Economy, business and finance/Economy/Economic policy

HD
type: Concept
norm score: 3.8696537678207736
score: 11.4

deregulation
type: Concept
norm score: 3.598099117447386
score: 10.6

geochemistry
type: FieldOfResearch
norm score: 27.692441186701984
score: 0.5699106454849243

hard drive
type: Concept
norm score: 4.107264086897488
score: 12.1

earth sciences
type: FieldOfResearch
norm score: 27.692441186701984
score: 0.5699106454849243

life sciences
type: NASA
norm score: 35.87466373187602
score: 0.9233048558235168

epigenetic
type: Concept
norm score: 1.357773251866938
score: 4.0

HD gene deregulation
type: Phrase
norm score: 11.358956760466711
score: 33.1

deregulation
type: Lemma
norm score: 11.31864026895779
score: 30.3

analysis
type: Lemma
norm score: 3.0257751214045574
score: 8.1

Genoa
type: Lemma
norm score: 25.476279417258127
score: 68.2

linguistics
type: Domain
norm score: 100.0
score: 7.7

Economic policy
type: IPTC
path: Economy, business and finance/Economy/Economic policy

HD
type: Lemma
norm score: 8.06873365707882
score: 21.6

genes involved in HD gene deregulation have an epigenetic role
type: Sentence
norm score: 33.333333333333336
score: 100.0

deregulation
type: Lemma
norm score: 4.333208815838626
score: 11.6

http
type: Concept
norm score: 2.0706042090970804
score: 6.1

gene
type: Lemma
norm score: 14.60590212924916
score: 39.1

gene deregulation
type: Phrase
norm score: 1.8188057652711047
score: 5.3

Ro
type: Concept
norm score: 4.989816700610998
score: 14.7

chromatin analysis
type: Phrase
norm score: 0.857927247769389
score: 2.5

HD gene deregulation
type: Phrase
norm score: 25.806451612903224
score: 75.2

geology
type: FieldOfResearch
norm score: 24.616153322090323
score: 0.5066006183624268

earth sciences
type: FieldOfResearch
norm score: 24.616153322090323
score: 0.5066006183624268

Ro
type: Lemma
norm score: 5.790063503922301
score: 15.5

outcome
type: Concept
norm score: 1.2219959266802443
score: 3.6

Language
type: IPTC
path: Arts, culture and entertainment/Culture/Language

Genes deregulated in HD, are participating in epigenetic processes
type: Sentence
norm score: 33.333333333333336
score: 100.0

HD chromatin analysis
type: Phrase
norm score: 14.13864104323953
score: 41.2

life sciences (general)
type: NASA
norm score: 28.363564182847412
score: 0.7299919724464417

gene
type: Concept
norm score: 13.06856754921928
score: 38.5

results from the analysis
type: Phrase
norm score: 1.3040494166094714
score: 3.8

deregulate in HD
type: Phrase
norm score: 16.197666437886067
score: 47.2

gene
type: Concept
norm score: 2.919212491513917
score: 8.6

Interpretation of the results from the analysis of RO: http://sandbox.rohub.org/rodl/ROs/HD_chromatin_analysis/
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