Group: BioSemantics Privileged Users @ Human Genetics LUMC + collaborators

Overview

Group of colleagues at the Human Genetics Department of the Leiden University Medical Centre and closely collaborating groups who are interested to be prime users of new developments in BioSemantics and e-Science, and in return are willing to provide feedback and suggestions. See http://biosemantics.org for more information about the BioSemantics collaboration in the Netherlands.

Created at: Wednesday 23 September 2009 01:10:24 (UTC)

Unique name: LeidenBioSemanticsUsers

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    Marco Roos shared BioAID_EnirchBioModelWithProteinsFromText
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    This workflow is for demonstration purposes only. Please contact the authors if you wish to try it. We will gladly collaborate with you. Summary This workflow extracts proteins and protein relations from Medline. Extracted protein names (symbols of at least 3 characters) are validated against mouse, …
    Wednesday 08 May 2013 14:51:52 (UTC)
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    Kristina Hettne shared Annotate a gene list with disease concepts
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    Purpose: Currently, this workflow takes a list of genes and a concept set as input, calculates the matching score between these and finds the concept that contributes the most to the match. Author comments: The workflow is in Beta stage. It runs, but needs more testing with different parameter settin …
    Wednesday 06 February 2013 20:02:25 (UTC)
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    Kristina Hettne shared Anni workflows
    Concept profile analysis is a knowledge discovery method that proved successful in generating hypotheses about molecular mechanisms explaining the results from genotype-phenotype studies. This technology has been implemented in the Anni standalone application ( http://biosemantics.org/anni ). This pa …
    Wednesday 06 February 2013 19:11:26 (UTC)
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    Kristina Hettne shared Match concept profiles with predefined set
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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.
    Tuesday 05 February 2013 21:13:17 (UTC)
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    Kristina Hettne shared Filter concepts with profiles
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    Purpose: Filter a list of concept id(s) by returning only those with a concept profile in the database.
    Friday 14 September 2012 10:14:13 (UTC)
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    Kristina Hettne shared Find co-occurring documents
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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.
    Friday 13 July 2012 07:45:39 (UTC)
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    Kristina Hettne shared List Concept Sets
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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.
    Friday 06 July 2012 14:25:52 (UTC)
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    Kristina Hettne shared Get concept information
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    The workflow takes a (list of) concept ID(s) as input and returns the profile, ID, definition and name of the concept.
    Friday 06 July 2012 14:20:41 (UTC)
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    Kristina Hettne shared Get Concept IDs
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    Purpose: The workflow retrieves the concepts within a concept set. The Web service/workflow currently returns no values (bug).
    Friday 06 July 2012 14:17:36 (UTC)
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    Kristina Hettne shared Functional annotation of SNPs using next-generation text mining
    This pack implements the concept profile matching pipeline in the knowledge discovery tool Anni ( http://biosemantics.org/anni ), and adapts it to interpret the top SNPs from a GWAS. The underlying literature and concept profile databases are the same as the for the current version of Anni (2.1). The …
    Tuesday 26 June 2012 10:41:39 (UTC)
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    Kristina Hettne shared SNPs to Concept Set through Concept Profile Matching v2
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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. …
    Tuesday 26 June 2012 10:27:34 (UTC)

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