chromatin data interpretation
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type: Nanopublication
created: 2025-11-11T16:44:41.685+01:00
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Genes deregulated in HD, are participating in epigenetic processes
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https://w3id.org/ro-id/enrichment/f90033c2-8c63-44c3-926a-af18526d1f1b
name: This research object, was created in order to further analyse and interpret the results from the research object http://sandbox.rohub.org/rodl/ROs/HD_chromatin_analysis/ (HD chromatin analysis). The workflows in this research object are using the anni web services, implemented by the Biosemantics group.
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data
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Economic policy
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chromatin data interpretation
is snapshot of: data interpretation-2
snapshoted at time: 2014-02-26T14:16:20.355+01:00
snapshoted by: Eleni Mina
author: Eleni Mina
content size: 81201
creator: Eleni Mina
date created: 2014-02-21 13:36:32.163000+00:00
date modified: 2025-10-18 11:54:49.104646+00:00
date published: 2014-02-21 13:36:32.163000+00:00
description: This research object, was created in order to further analyse and interpret the results from the research object http://sandbox.rohub.org/rodl/ROs/HD_chromatin_analysis/ (HD chromatin analysis). The workflows in this research object are using the anni web services, implemented by the Biosemantics group.
encoding format: application/ld+json
license: no-permission
type: ResearchObject
type: SnapshotRO
type: Dataset
cite-as: Eleni Mina. "chromatin data interpretation." ROHub. Feb 21 ,2014. https://w3id.org/ro-id/f84d00ef-47b2-40b3-af26-099ed7e82f5b.

data_interpretation
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type: Dataset

List Predefined Concept Sets
author: Eleni Mina
content size: 30787
creator: Eleni Mina
date created: 2014-02-25 16:10:46.463000+00:00
date modified: 2022-03-25 16:50:57.659485+00:00
description: This workflow lists all IDs and descriptions of the predefined concept set
license: no-permission
sd date published: 2014-02-25 16:10:46.463000+00:00
type: Resource
type: MediaObject
type: ComputationalWorkflow

Explain concept scores
author: Eleni Mina
content size: 69369
creator: Eleni Mina
date created: 2014-02-26 13:14:06.663000+00:00
date modified: 2022-03-25 16:51:01.271983+00:00
description: 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). This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/282 for functional gene and SNP annotation and knowledge discovery.
license: no-permission
sd date published: 2014-02-26 13:14:06.663000+00:00
type: Resource
type: MediaObject
type: ComputationalWorkflow

hypothesis.txt
author: Eleni Mina
content size: 63
creator: Eleni Mina
date created: 2014-02-25 16:03:44.993000+00:00
date modified: 2022-03-25 16:50:58.525827+00:00
encoding format: text/plain
license: no-permission
sd date published: 2014-02-25 16:03:44.993000+00:00
type: Hypothesis
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Annotate a gene list with Biological processes
author: Eleni Mina
content size: 203555
creator: Eleni Mina
date created: 2014-02-25 16:06:54.756000+00:00
date modified: 2022-03-25 16:51:00.400167+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: 2014-02-25 16:06:54.756000+00:00
type: Resource
type: MediaObject
type: ComputationalWorkflow

Prioritize gene list related to a concept /list of concepts
author: Eleni Mina
content size: 188023
creator: Eleni Mina
date created: 2014-02-25 16:12:14.228000+00:00
date modified: 2022-03-25 16:50:56.779303+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: 2014-02-25 16:12:14.228000+00:00
type: Resource
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workflow sketch data interpretation
author: Eleni Mina
content size: 39476
creator: Eleni Mina
date created: 2014-02-25 16:04:13.823000+00:00
date modified: 2022-03-25 16:50:55.921582+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: 2014-02-25 16:04:13.823000+00:00
type: Sketch
type: Resource
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Get concept suggestions from term
author: Eleni Mina
content size: 41692
creator: Eleni Mina
date created: 2014-02-25 16:09:23.429000+00:00
date modified: 2022-03-25 16:50:59.349734+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: 2014-02-25 16:09:23.429000+00:00
type: Resource
type: MediaObject
type: ComputationalWorkflow

conclusions.txt
author: Eleni Mina
content size: 67
creator: Eleni Mina
date created: 2014-02-25 16:03:12.283000+00:00
date modified: 2022-03-25 16:50:54.643219+00:00
encoding format: text/plain
license: no-permission
sd date published: 2014-02-25 16:03:12.283000+00:00
type: Conclusions
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Eleni Mina
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Eleni Mina
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service-account-enrichment
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service-account-generation-service
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