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).
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
genes involved in HD gene deregulation have an epigenetic role
Economy, business and finance/Economy/Economic policy
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
Interpretation of the results from the analysis of RO: http://sandbox.rohub.org/rodl/ROs/HD_chromatin_analysis/
Eleni Mina. "Interpretation of the results from the analysis of RO: http://sandbox.rohub.org/rodl/ROs/HD_chromatin_analysis/." ROHub. Aug 30 ,2013. https://w3id.org/ro-id/95a9036b-bee9-48fb-81eb-7e9a90014293.
Sketch of the workflows and their explanation, for data interpretation, plus the connection to the output from the RO for chromatin analysis
This workflow lists all IDs and descriptions of the predefined concept set
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
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
Annotate a gene list with Biological processes
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
Prioritize gene list related to a concept /list of concepts
Arts, culture and entertainment/Culture/Language
Genes deregulated in HD, are participating in epigenetic processes