Pack: HD data interpretation

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 output provides us with the top (cutoff) concepts that describe our gene list of interest The workflow is using the anni web services .

Description:

This ruby script creates nanopublications for the results of the prioritized gene list from pack : http://www.myexperiment.org/packs/486.html

Description:

This workflow creates nanopublications for a gene list that is associated to Huntington's Disease

Description:

Purpose of workflow: This workflow takes two 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). The example values for this workflow are tailored to describe the relationship between two entrez gene ids. The user can change that by using other ids and a database identifier for the db (in our case is EG for entrez gene ids).

Description:

Pupose:

The workflow returns a list of all Concept Set IDs currently available in the database. The Concept Sets have an hierarchical structure that can be inferred by referring to the parent Concept Set ID.

Description:

This workflow prioritizes a gene list according to its association with the 'concept_id'. In our example here we are prioritizing a gene list to obtain genes that are more closely associated to huntingtin, the cause of huntington's disease