User: Martijn Schuemie

Name: Martijn Schuemie

Joined: Thursday 10 September 2009 14:34:02 (UTC)

Email (public): Not specified

Website: http://biosemantics.org

Location: Rotterdam, Netherlands

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Martijn Schuemie has been credited 8 times

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Field/Industry: Text mining

Occupation/Role(s): Assistant professor

Organisation(s):

Erasmus University Medical Center

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Workflow

Taverna 2

Uploader

Kristina Hettne

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

Workflow

Taverna 2

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Kristina Hettne

SNPs to Concept Set through Concept Profil... (6)

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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. Author comments: The workflow is in Beta stage. It runs, but needs more testing with different parameter settings. This workflow can be used together with other workflows in this pack: http://www...

Created: 2012-06-26 | Last updated: 2013-02-05

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

Attributions: Find Supporting Documents SNP_ID2EntrezGene_ID DatabaseID to ConceptID Match gene lists based on information in literature Match concept profiles Explain concept scores

Workflow

Taverna 2

Uploader

Kristina Hettne

Get Concept IDs (5)

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Purpose: The workflow retrieves the concepts within a concept set. The Web service/workflow currently returns no values (bug).

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

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

Workflow

Taverna 2

Uploader

Kristina Hettne

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

Workflow

Taverna 2

Uploader

Kristina Hettne

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

Workflow

Taverna 2

Uploader

Kristina Hettne

List Concept Sets (3)

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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.

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

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

Workflow

Taverna 2

Uploader

Marco Roos

Match concept profiles (6)

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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.