Pack: Concept profile analysis using Anni Web services

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:

Purpose:

This workflow maps input Identifiers, common database identifiers, to the Concept Identifiers from the EMC ontology.

Result:

Concept Identifiers from the EMC ontology.

Comments:

Database: one of CAS, DRUG, etc. The supported databases are listed below (database, description, example).

CAS, Chemical Abstracts Service registry number, 64-17-5. DRUG, Drug Bank, DB00316. AF, Affymetrix, 200007_at. CHEB, ChEBI, 16236. CHID, ChemIDplus, 0000050000. EG, Entrez-Gene, 3064. GO, Gene Ontology, GO:0008219. HG, HGNC, 4851. HMBD, Human Metabolome Database, HMDB01859. KEGD, KEGD, D00217. KEGG, KEGG, C12345. MESH, Medical Subject Headings, D000082. MGI, Mouse Genome Database, 96067. OM, OMIM, 143100. PUBC, PubChem Compound, 1983. PUBS, PubChem Substance, 7847284. RGD, Rat Genome Database, 68337. UG, UniGene, Mm.281700. UMLS, Unified Medical Language System, C0027439. UP, UniProt, P42858.

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).

Description:

Purpose: Filter a list of concept id(s) by returning only those with a concept profile in the database.

Description:

Purpose: This workflow search an indexed literature database for documents mentioning both of the input concepts.

Author comments:

Currently, PubMed is the underlying data source.

Description:

The workflow takes a (list of) concept ID(s) as input and returns the profile, ID, definition and name of the concept.

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.

Description:

Genome-Wide Association studies (GWAS) with metabolomic phenotypes yield several statistically significant SNP-metabolite associations. To understand the biological basis of the association, scientists typically dwell on identifying genes in the vicinity of the SNP and the possible pathways that the gene participates in. The information needed to arrive at an understanding of the mechanistic basis of the association requires integration of disparate data sources. The purpose of this workflow is to take the GWAS output consisting of SNP-metabolite associations and return genes present in the vicinity of the SNP ( for example, ± 100 kb of the snp), and the ranked biomedical concepts mined from the PubMed database relevant to these genes. The user is provided with the choice of setting the flanking width to interrogate around the SNP, the biomedical concept set to rank against the genes, the number of ranked concepts to return, the number of explaining concepts to return, the number of co-occurring documents to return, the type of gene database identifier, and the SNP identifier.

Purpose:

Currently, this workflow takes one SNP and a concept set as input, calculates the matching score between these, finds co-occuring documents between the query concept and the match concept, finds the concept that contributes the most to the match, and the documents that support this finding.

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:

Purpose of workflow: The workflow can be used to match a set of concept profiles with another set of concept profiles.

Result: A list of concepts ordered by their match to the query concept profiles.

Description:

Purpose of workflow: The workflow can be used to match a set of concept profiles with predefined set of concept profiles.

Result: A list of concepts ordered by their match to the query concept profiles.