BioSemantics Privileged Users @ Human Genetics LUMC + collaborators2011-11-22T12:35:07+00:00/groups/2112014-10-22T09:20:22+00:00Christine Chichester joined the BioSemantics Privileged Users @ Human Genetics LUMC + collaborators groupurn:uuid:fe823b04-614d-4ddc-9772-4b88074eedb8Christine Chichester2014-10-19T21:02:17+00:00Rajireturn joined the BioSemantics Privileged Users @ Human Genetics LUMC + collaborators groupurn:uuid:bb542894-aee8-49fb-ab46-3abf2ee133b3Rajireturn2013-05-08T14:51:52+00:00Marco Roos shared BioAID_EnirchBioModelWithProteinsFromTextThis 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, rat, and human UniProt symbols, so the results are limited to these species. This workflow follows the following basic steps: it retrieves documents relevant for the query string it discovers proteins in those documents, that are considered relevant to the query string and related to the proteins mentioned in the query (colocation in text mining jargon) it stores the results in a semantic repository To support hypothesis formation, the results are added to a repository containing proto-ontologie …urn:uuid:371df2b4-a2d1-478c-b4fc-a753a412ad7aMarco Roos2013-02-06T20:02:25+00:00Kristina Hettne shared Annotate a gene list with disease conceptsPurpose: 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 settings. This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/368 for functional gene annotation and knowledge discovery.urn:uuid:c01cc5b6-1d81-4ef7-bac1-a9764c8344b1Kristina Hettne2013-02-06T19:11:26+00:00Kristina Hettne shared Anni workflowsConcept 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 pack contains a number of workflows that can be used together to configure and run typical user pipelines from Anni through the Anni Web services ( http://www.biocatalogue.org/services/3559 ).urn:uuid:76f67d83-0866-4c43-8a3d-1592b4954611Kristina Hettne2013-02-05T21:13:17+00:00Kristina Hettne shared Match concept profiles with predefined setPurpose 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.urn:uuid:8673ad8e-bc6b-43f3-92dd-c99aa162e1ecKristina Hettne2012-09-14T10:14:13+00:00Kristina Hettne shared Filter concepts with profilesPurpose: Filter a list of concept id(s) by returning only those with a concept profile in the database.urn:uuid:f5633aa2-0828-400e-8678-7ae7dd55726cKristina Hettne2012-07-13T07:45:39+00:00Kristina Hettne shared Find co-occurring documentsPurpose: This workflow search an indexed literature database for documents mentioning both of the input concepts. Author comments: Currently, PubMed is the underlying data source.urn:uuid:c1ed9dce-5007-4efa-889e-7a79a64254e0Kristina Hettne2012-07-06T14:25:52+00:00Kristina Hettne shared List Concept SetsPupose: 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.urn:uuid:611e5ea2-593d-4dfb-afce-c3fde0f4e60fKristina Hettne2012-07-06T14:20:41+00:00Kristina Hettne shared Get concept informationThe workflow takes a (list of) concept ID(s) as input and returns the profile, ID, definition and name of the concept.urn:uuid:1ab03f97-2ae5-4977-9404-d34b49cd4a99Kristina Hettne2012-07-06T14:17:36+00:00Kristina Hettne shared Get Concept IDsPurpose: The workflow retrieves the concepts within a concept set. The Web service/workflow currently returns no values (bug).urn:uuid:73964c81-acdf-4e1f-b610-82889c64721dKristina Hettne2012-06-26T10:41:39+00:00Kristina Hettne shared Functional annotation of SNPs using next-generation text miningThis 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 pack consists of three main workflows ( http://www.myexperiment.org/workflows/2999 , http://www.myexperiment.org/workflows/2973 , http://www.myexperiment.org/workflows/2972 ). Workflow 2999 returns a list of available concept sets to match the SNPs against. As an example, the concept set GO biological processes is used. Workflow 2973 consist of nine nested workflows (eight different components in the pack, for which one is used twice within the main workflow for different purposes). It reuses t …urn:uuid:4e49a219-589c-42c8-8e3b-a33ff0f0e808Kristina Hettne