Workflows

Explain concept scores (7)

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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 pe...

Created: 2012-02-07 | Last updated: 2014-07-14

Credits: Reinout van Schouwen

Find co-occurring documents (6)

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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.

Created: 2012-07-13 | Last updated: 2014-07-14

Credits: Kristina Hettne Reinout van Schouwen Marco Roos Martijn Schuemie BioSemantics

Find Supporting Documents (6)

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This workflow finds documents that serve as evidence for the association between two concepts. Results: Document titles Document identifiers There seems to be a bug at the moment, since it returns empty values.

Created: 2012-06-26 | Last updated: 2014-07-14

Credits: Kristina Hettne Marco Roos Reinout van Schouwen Martijn Schuemie BioSemantics

DatabaseID to ConceptID (7)

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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 Ontol...

Created: 2012-06-25 | Last updated: 2014-07-14

Credits: Marco Roos Martijn Schuemie Reinout van Schouwen BioSemantics

Prioritize gene list for the Cure game (1)

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This workflow prioritizes a gene list according to its association with the 'concept_id'. Here we are prioritizing a gene list against breast cancer, in order to try to beat Barney in the game The Cure (http://genegames.org/cure/). Note: Before running this workflow the gene names supplied in the game first needs to be mapped to Entrez gene identifiers. This can be done using either this workflow http://www.myexperiment.org/workflows/3722 or a by performing a search in the NCBI Entrez gene d...

Created: 2015-04-29

Credits: Kristina Hettne Eleni

Attributions: Prioritize gene list

Get concept suggestions from term (1)

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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.

Created: 2015-02-18

Credits: Eelke van der Horst Kristina Hettne Marco Roos Eleni

Attributions: Get concept suggestions from term

HPO-UMLS-ConceptID mapping (1)

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Generate HPO-Concept profiles via HPO-UMLS mappings. The result is a list of Concept IDs corresponding to Concept profiles for UMLS concepts that approximate HPO concepts. The output is a table of UMLS-ID, HPO- ID, COncept-ID rows.

Created: 2014-10-20

Credits: Marco Roos BioSemantics

Match concept to HPO profiles (1)

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This workflow matches a query concept to the list of Human Phenotypes. The Human Phenotypes are the subset of the Human Phenotype Ontology for which we have a mapped UMLS concept available and a concept profile. HPO-UMLS mapping: Winnenburg, R., & Bodenreider, O. (2014). Coverage of Phenotypes in Standard Terminologies. In Proceedings of the ISMB’2014 SIG meeting “BioLINK.” Retrieved from http://phenoday2014.bio-lark.org/pdf/5.pdf Concept Profile Database: July 2012

Created: 2014-10-20

Credits: Marco Roos BioSemantics

Attributions: Match concept profiles Get concept information

Match concept profiles with predefined set (2)

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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.

Created: 2013-02-05 | Last updated: 2014-07-14

Credits: Kristina Hettne Marco Roos Reinout van Schouwen BioSemantics

Filter concepts with profiles (4)

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

Created: 2012-09-14 | Last updated: 2014-07-14

Credits: Kristina Hettne Reinout van Schouwen Martijn Schuemie BioSemantics