Text mining network2011-11-22T12:34:36+00:00/groups/432015-04-29T09:23:12+00:00Kristina Hettne shared Prioritize gene list for the Cure gameThis 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 database http://www.ncbi.nlm.nih.gov/gene/urn:uuid:09d775df-ef7d-4456-96fc-6a87e68386c2Kristina Hettne2013-08-28T12:02:59+00:00Kristina Hettne shared Concept profile analysis using Anni Web servicesConcept 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:fa9048f2-9dc7-4e0a-b38d-4b342b23db6bKristina Hettne2012-01-17T16:21:59+00:00Mdmmsrhs joined the Text mining network groupurn:uuid:d000e1c8-89ad-41ff-ad78-6fbdfb5a867fMdmmsrhs2011-12-17T22:55:39+00:00Mustafa joined the Text mining network groupurn:uuid:23279d4f-23c0-4eae-85c7-7943ec13ab3cMustafa2011-06-10T10:36:03+00:00Kristina Hettne joined the Text mining network groupurn:uuid:9717f18c-fd86-457b-8fca-e1dee55edda7Kristina Hettne2010-12-08T11:55:13+00:00Paul Fisher shared Text Mining WorkflowsThis pack contains workflows to navigate from candidate Quantitative Trait genes and pathways to a given phenotype.urn:uuid:5609d573-6ce0-4808-9c3a-184420d75a5dPaul Fisher2010-12-08T11:50:05+00:00Paul Fisher shared Extract Scientific TermsThis workflow takes in a document containg text and removes and non-ascii characters. The cleaned text is then sent to a service in dresden to extract all scientific terms. These terms represent a profile for the input document. Any null values are also removed.urn:uuid:c4800051-c0e7-4dd2-a760-571b867adaefPaul Fisher2010-12-08T11:47:14+00:00Paul Fisher shared Pathway to PubmedThis workflow takes in a list of KEGG pathway descriptions and searches the PubMed database for corresponding articles. Any matches to the pathways are then retrieved (abstracts only). These abstracts are then returned to the user.urn:uuid:1289d98a-f3a0-4e54-8679-abdb78a46976Paul Fisher2010-12-08T11:42:39+00:00Paul Fisher shared Gene to PubmedThis workflow takes in a list of gene names and searches the PubMed database for corresponding articles. Any matches to the genes are then retrieved (abstracts only). These abstracts are then returned to the user.urn:uuid:48ebd2b7-fde7-4fc8-8af1-fedc36b31682Paul Fisher2010-12-08T11:38:40+00:00Paul Fisher shared Rank Phenotype TermsThis workflow counts the number of articles in the pubmed database in which each term occurs, and identifies the total number of articles in the entire PubMed database. It also identified the total number of articles within pubmed so that a term enrichment score may be calculated. The workflow also takes in a document containing abstracts that are related to a particular phenotype. Scientiifc terms are then extracted from this text and given a weighting according to the number of terms that appear in the document. The higher the value the better the score. This is given as: X = log((a / b) / (c / d)) where: a = number of occurnaces of individual terms in phenotype corpus b = number of abstracts in entire phenotype corpus c = number of occurnaces of individual terms in entire pubmed d = numb …urn:uuid:325c1a61-9a19-458b-be39-29fe961a9bb6Paul Fisher2010-12-08T11:35:21+00:00Paul Fisher shared Cosine vector spaceThis workflow calculates the cosine vector space between two sets of corpora. The workflow then removes any null values from the output. this is some extra text vbeing addedurn:uuid:6a45ba4d-2b02-424a-bfbd-9762ef8f25eePaul Fisher2010-11-09T08:34:07+00:00Siaw Ling joined the Text mining network groupurn:uuid:71243828-a1bc-42ba-8b14-38092ad574b1Siaw Ling