myExperiment - Tags

Workflows (25)

Taverna 2 Original Uploader Paul Fisher	Pathways and Gene annotations for QTL region (v7) Created: 19/11/09 @ 18:18:52 \| Last updated: 02/09/11 @ 11:44:57 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the mouse, Mus musculus. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG path... Rating: 4.9 / 5 (8 ratings) \| Versions: 7 \| Reviews: 1 \| Comments: 6 \| Citations: 1 Viewed: 4944 times \| Downloaded: 839 times Tags (22): adasd \| chromosome \| data-driven \| disease \| ensembl \| entrez \| gene \| genes \| genotype \| kegg \| mouse \| nbiconworkflows \| pathway \| pathway-driven \| pathways \| phenotype \| qtl \| shim \| subworkflow \| uniprot	View Download (v7)
Taverna 1 Original Uploader Paul Fisher	HUMAN Microarray CEL file to candidate pathways (v4) Created: 03/10/07 @ 18:35:55 \| Last updated: 26/11/09 @ 17:34:24 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License This workflow takes in a CEL file and a normalisation method then returns a series of images/graphs which represent the same output obtained using the MADAT software package (MicroArray Data Analysis Tool) [http://www.bioinf.manchester.ac.uk/MADAT/index.html]. Also returned by this workflow are a list of the top differentialy expressed genes (size dependant on the number specified as input - geneNumber), which are then used to find the candidate pathways which may be influencing the observed ... Rating: 5.0 / 5 (2 ratings) \| Versions: 4 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 1314 times \| Downloaded: 372 times Tags (12): affymetrix \| cel \| file \| genotype \| kegg \| microarray \| nbiconworkflows \| pathway-driven \| pathways \| phenotype \| shim	View Download (v4)
Taverna 1 Original Uploader Paul Fisher	Entrez Gene to KEGG Pathway (v5) Created: 04/12/09 @ 16:04:38 \| Last updated: 30/11/10 @ 12:18:53 Credits: Paul Fisher License: Creative Commons Attribution 3.0 Unported License This workflow takes in Entrez gene ids then adds the string "ncbi-geneid:" to the start of each gene id. These gene ids are then cross-referenced to KEGG gene ids. Each KEGG gene id is then sent to the KEGG pathway database and its relevant pathways returned. Rating: 4.8 / 5 (4 ratings) \| Versions: 5 \| Reviews: 0 \| Comments: 2 \| Citations: 0 Viewed: 1162 times \| Downloaded: 463 times Tags (9): entrez \| genotype \| kegg \| ncbi \| pathway \| pathway-driven \| pathways \| phenotype \| shim	View Download (v5)
Taverna 1 Original Uploader Paul Fisher	KEGG pathways common to both QTL and microarray based investigations (v3) Created: 24/11/09 @ 17:14:43 \| Last updated: 03/12/09 @ 15:28:49 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License This workflow takes in two lists of KEGG pathway ids. These are designed to come from pathways found from genes in a QTL (Quantitative Trait Loci) region, and from pathways found from genes differentially expressed in a microarray study. By identifying the intersecting pathways from both studies, a more informative picture is obtained of the candidate processes involved in the expression of a phenotype. Example input for this workflow is given below (as newline separated values). qt... Rating: 0.0 / 5 (0 ratings) \| Versions: 3 \| Reviews: 0 \| Comments: 0 \| Citations: 1 Viewed: 286 times \| Downloaded: 129 times Tags (11): common \| data-driven \| disease \| genotype \| kegg \| microarray \| pathway \| pathway-driven \| pathways \| phenotype \| similarity	View Download (v3)
Taverna 1 Original Uploader Paul Fisher	Mouse Microarray Analysis (v3) Created: 03/10/07 @ 18:36:05 \| Last updated: 03/12/09 @ 16:20:33 License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow takes in probesets from and AffyMetrix micorarray experiment and returns: the genes ; gene start and end positions; chromosome where genes reside; ensembl trasncripts; SwissProt ids; affy probeset identifiers for chips Mouse430_2 and Mouse430a_2. Example ids from the Mouse430_2 affymetrix array are as follows (newline separated): 1447227_at 1440624_at 1436240_at 1454904_at 1435665_at 1418148_at 1429831_at Rating: 5.0 / 5 (1 rating) \| Versions: 3 \| Reviews: 0 \| Comments: 1 \| Citations: 1 Viewed: 517 times \| Downloaded: 135 times Tags (18): affmetrix \| cel \| data-driven \| disease \| expression \| file \| gene \| genotype \| kegg \| microarray \| mouse \| nbiconworkflows \| pathway-driven \| phenotype \| RNA \| shim \| uniprot	View Download (v3)
Taverna 1 Original Uploader Paul Fisher	Arabidopsis thaliana Microarray Analysis (v1) Created: 08/07/09 @ 16:28:34 Credits: Paul Fisher License: Creative Commons Attribution-No Derivative Works 3.0 Unported License This workflow searches for genes which are found to be differentially expressed in a microarray study using Arabidopsis thaliana. The workflow requires an input of a list of differentially expressed AffyMetrix Probeset identifiers. Data is then extracted from BioMart to annotate each of the genes. The UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway database. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 145 times \| Downloaded: 30 times Tags (19): affmetrix \| affymetrix \| arabidopsis \| bconv \| data-driven \| ensembl \| gene \| gene expression \| geneid \| genes \| genotype \| kegg \| Kegg Pathways \| microarray \| pathway \| pathways \| phenotype \| thaliana \| uniprot	View Download (v1)
Taverna 1 Original Uploader Paul Fisher	Cosine vector space (v1) Created: 10/08/09 @ 13:19:36 \| Last updated: 10/08/09 @ 13:24:28 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow calculates the cosine vector space between two sets of corpora. The workflow then removes any null values from the output. The result is a cosine vector score between 0 and 1, showing the significance of any links between one concept (e.g. pathway) to another (e.g. phenotype). A score of 0 means there is no or an undetermined correlation between the two concepts. A score approaching 1 represents positive correlation. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 54 times \| Downloaded: 0 times Tags (14): abstracts \| cosine vector space \| gene \| information \| Kegg Pathways \| pathway \| phenotype \| pubmed \| qtl \| terms \| text \| text mining \| text mining; term extraction; entity recognition \| vector	View
Taverna 1 Original Uploader Paul Fisher	Extract Scientific Terms (v1) Created: 10/08/09 @ 13:31:07 \| Last updated: 10/08/09 @ 13:32:21 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow takes in a document containg text and removes any non-ascii characters. The cleaned text is then sent to a service in Dresden, to extract all scientific terms. These terms represent a concept profile for the input concpet. Any null values are also removed. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 125 times \| Downloaded: 0 times Tags (18): abstracts \| authors \| data-driven \| entity recognition \| gene \| getconcepts \| kegg \| Kegg Pathways \| mining \| mouse \| pathway-driven \| pathways \| phenotype \| sleeping sickness \| term extraction \| text \| text mining \| text mining; term extraction; entity recognition	View
Taverna 1 Original Uploader Paul Fisher	Rank Phenotype Terms (v1) Created: 10/08/09 @ 15:43:48 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This 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 ... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 124 times \| Downloaded: 0 times Tags (24): abstracts \| append term \| authors \| concept \| cosine vector space \| data-driven \| enrichment \| gene identifier \| geneid \| genes \| genotype \| information \| mining \| ncbi \| pathways \| phenotype \| pubmed \| ranking \| term \| term extraction \| terms \| text \| text mining \| text mining; term extraction; entity recognition	View
Taverna 2 Original Uploader Paul Fisher	Phenotype to pubmed (v3) Created: 05/07/10 @ 14:07:33 \| Last updated: 11/01/11 @ 12:07:22 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow takes in a phenotype search term, and searches for abstracts in the PubMed database. These are passed to the eSearch function and searched for in PubMed. Those abstracts found are returned to the user Rating: 0.0 / 5 (0 ratings) \| Versions: 3 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 109 times \| Downloaded: 28 times Tags (18): abstracts \| african trypanosomiasis \| disease \| efetch \| entrez \| esearch \| loci \| ncbi \| phenotype \| pubmed \| qtl \| quanitative \| sleeping sickness \| term \| text \| text mining \| text mining; term extraction; entity recognition \| trait	View Download (v3)
Taverna 2 Original Uploader Paul Fisher	Pathways and Gene annotations for QTL region (v1) Created: 15/11/10 @ 12:08:18 \| Last updated: 16/11/10 @ 16:07:49 Credits: Paul Fisher Attributions: Pathways and Gene annotations for QTL region License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the mouse, Mus musculus. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG path... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 33 times \| Downloaded: 10 times Tags (33): african trypanosomiasis \| binfo \| chromosome \| common \| data-driven \| database \| disease \| ensembl \| entrez \| gene \| gene identifier \| geneid \| genes \| genomic \| genotype \| kegg \| Kegg Pathways \| KeggID \| loci \| locus \| mouse \| pathway \| pathway-driven \| pathways \| phenotype \| qtl \| quanitative \| region \| sleeping sickness \| species \| trait \| trichuris muris \| uniprot	View Download (v1)
Taverna 2 Original Uploader Paul Fisher	Pathways and Gene annotations for RefSeq ids (v1) Created: 15/11/10 @ 12:25:01 \| Last updated: 15/11/10 @ 12:28:12 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow searches for genes which were found to be differentially expressed from a microarray study in the mouse, Mus musculus. The workflow requires an input of gene ref_seq identifiers. Data is then extracted from BioMart to annotate each of the genes found for each ref_seq id. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to search for pathways in the KEGG pathway database. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 72 times \| Downloaded: 35 times Tags (34): affmetrix \| affymetrix \| bconv \| binfo \| chromosome \| common \| data-driven \| database \| disease \| ensembl \| entrez \| expression \| gene \| gene expression \| gene identifier \| geneid \| genes \| genomic \| kegg \| Kegg Pathways \| KeggID \| microarray \| mouse \| pathway \| pathway-driven \| pathways \| phenotype \| species \| swissprot \| trait \| transcribe \| transcription \| trichuris muris \| uniprot	View Download (v1)
Taverna 2 Original Uploader Paul Fisher	KEGG pathways common to both QTL and microarray based investigations (v1) Created: 15/11/10 @ 12:30:21 \| Last updated: 15/11/10 @ 12:30:59 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow takes in two lists of KEGG pathway ids. These are designed to come from pathways found from genes in a QTL (Quantitative Trait Loci) region, and from pathways found from genes differentially expressed in a microarray study. By identifying the intersecting pathways from both studies, a more informative picture is obtained of the candidate processes involved in the expression of a phenotype Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 21 times \| Downloaded: 15 times Tags (21): affmetrix \| affymetrix \| binfo \| chromosome \| common \| data-driven \| gene expression \| gene identifier \| geneid \| genotype \| kegg \| Kegg Pathways \| KeggID \| microarray \| pathway \| pathway-driven \| pathways \| phenotype \| qtl \| quanitative \| trait	View Download (v1)
Taverna 2 Original Uploader Paul Fisher	Cosine vector space (v2) Created: 08/12/10 @ 11:35:18 \| Last updated: 11/01/11 @ 12:05:41 Credits: Paul Fisher Attributions: Cosine vector space License: Creative Commons Attribution-Share Alike 3.0 Unported License This 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 added Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 19 times \| Downloaded: 12 times Tags (14): abstracts \| concept \| concept profile \| cosine vector space \| genotype \| pathway \| phenotype \| space \| term \| terms \| text \| text mining \| text mining; term extraction; entity recognition \| vector	View Download (v2)
Taverna 2 Original Uploader Paul Fisher	Rank Phenotype Terms (v2) Created: 08/12/10 @ 11:38:37 \| Last updated: 11/01/11 @ 12:02:30 Credits: Paul Fisher Attributions: Rank Phenotype Terms License: Creative Commons Attribution-Share Alike 3.0 Unported License This 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 ... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 26 times \| Downloaded: 14 times Tags (12): abstracts \| concept \| concept profile \| enrichment \| genotype \| phenotype \| pubmed \| ranking \| term \| text \| text mining \| text mining; term extraction; entity recognition	View Download (v2)
Taverna 2 Original Uploader Paul Fisher	Pathway to Pubmed (v2) Created: 08/12/10 @ 11:47:10 \| Last updated: 11/01/11 @ 12:00:16 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 36 times \| Downloaded: 19 times Tags (13): abstracts \| concept \| data-driven \| genotype \| Kegg Pathways \| KeggID \| pathway \| pathway-driven \| pathways \| phenotype \| text \| text mining \| text mining; term extraction; entity recognition	View Download (v2)
Taverna 2 Original Uploader Paul Fisher	Extract Scientific Terms (v2) Created: 08/12/10 @ 11:50:01 \| Last updated: 11/01/11 @ 11:58:09 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 55 times \| Downloaded: 17 times Tags (13): abstracts \| ascii \| concept \| concept profile \| dresden \| entity recognition \| genotype \| phenotype \| term \| term extraction \| terms \| text \| text mining; term extraction; entity recognition	View Download (v2)
Taverna 2 Original Uploader Paul Fisher	Pathways and Gene annotations forQTL region (v1) Created: 21/01/11 @ 16:56:47 \| Last updated: 21/01/11 @ 16:58:50 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in Cow, Bos taurus. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway data... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 19 times \| Downloaded: 13 times Tags (22): african trypanosomiasis \| bos taurus \| cattle \| chromosome \| cow \| ensembl \| entrez \| gene \| genes \| genotype \| kegg \| Kegg Pathways \| KeggID \| pathway \| pathways \| phenotype \| qtl \| quanitative \| re-use \| region \| sleeping sickness \| uniprot	View Download (v1)
Taverna 2 Original Uploader Paul Fisher	Rank Phenotype Terms (v1) Created: 01/02/11 @ 11:22:14 \| Last updated: 01/02/11 @ 11:24:42 Credits: Paul Fisher Attributions: Cosine vector space Rank Phenotype Terms License: Creative Commons Attribution-Share Alike 3.0 Unported License This 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 ... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 25 times \| Downloaded: 14 times Tags (26): concept \| concept profile \| cosine vector space \| data-driven \| enrichment \| entity recognition \| eutils \| evidence \| getconcepts \| literature \| mining \| pathway \| pathway-driven \| pathways \| phenotype \| pubmed \| qtl \| quanitative \| ranking \| significance \| term \| term extraction \| terms \| text \| text mining \| text mining; term extraction; entity recognition	View Download (v1)
Taverna 2 Original Uploader Paul Fisher	Gene to Pubmed (v4) Created: 08/02/11 @ 13:04:06 \| Last updated: 10/02/11 @ 16:01:41 Credits: Paul Fisher Attributions: Cosine vector space Extract Scientific Terms Rank Phenotype Terms Cosine vector space Rank Phenotype Terms Pathway to Pubmed Extract Scientific Terms License: Creative Commons Attribution-Share Alike 3.0 Unported License This 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 4 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 43 times \| Downloaded: 23 times Tags (30): abstracts \| cosine vector space \| data-driven \| disease \| enrichment \| entity recognition \| evidence \| kegg \| Kegg Pathways \| literature \| loci \| locus \| medline \| microarray \| mining \| pathway \| pathway-driven \| pathways \| phenotype \| pubmed \| qtl \| ranking \| re-use \| term \| term extraction \| terms \| text \| text mining \| text mining; term extraction; entity recognition \| trichuris muris	View Download (v4)
Taverna 2 Original Uploader Paul Fisher	Pathway and Gene to Pubmed (v2) Created: 10/02/11 @ 16:10:52 \| Last updated: 18/02/11 @ 13:47:08 Credits: Paul Fisher Attributions: Cosine vector space Extract Scientific Terms Rank Phenotype Terms Cosine vector space Rank Phenotype Terms Pathway to Pubmed Extract Scientific Terms Gene to Pubmed License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow takes in a list of gene names and KEGG pathway descriptions, and searches the PubMed database for corresponding articles. Any matches to the genes are then retrieved (abstracts only). These abstracts are then used to calculate a cosine vector space between two sets of corpora (gene and phenotype, or pathway and phenotype). The 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 PubMe... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 64 times \| Downloaded: 19 times Tags (36): annotation \| concept \| concept profile \| controlled vocabulary \| cosine vector space \| data integration \| data-driven \| dresden \| efetch \| enrichment \| entity recognition \| esearch \| eutils \| gene \| gene identifier \| geneid \| genotype \| kegg \| Kegg Pathways \| KeggID \| literature \| loci \| locus \| medline \| mesh \| pathway \| pathway-driven \| pathways \| phenotype \| pubmed \| qtl \| quanitative \| text mining \| text mining; term extraction; entity recognition \| trait \| triat	View Download (v2)
Taverna 2 Original Uploader Paul Fisher	Pathways and Gene annotations forQTL region (v2) Created: 17/03/11 @ 11:10:28 \| Last updated: 30/08/11 @ 10:40:14 Credits: Paul Fisher Attributions: Pathways and Gene annotations for QTL region License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in Human, Homo sapiens. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway ... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 25 times \| Downloaded: 14 times Tags (26): bilateral perisylvian polymicrogyria \| chromosome \| data integration \| data-driven \| database \| disease \| ensembl \| entrez \| epilepsy \| gene \| gene identifier \| geneid \| genes \| genomic \| genotype \| homo sapiens \| human \| Kegg Pathways \| KeggID \| pathway \| pathway-driven \| pathways \| phenotype \| qtl \| quanitative \| uniprot	View Download (v2)
Taverna 2 Original Uploader Marco Roos	Gene expression interpretation by the Global Test (v1) Created: 26/04/11 @ 08:31:51 \| Last updated: 26/04/11 @ 08:31:52 Credits: Marco Roos License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow adds meaning to gene expresion values by performing a standard and a literature weighted Global Test. Gene expression is expected to be from Affymetrix microarrays, for which an RMA normalization and entrez Gene ID mapping/summation is performed. Original workflow is by Dennis Leenheer, edits by Marco Roos. Scripts by Kristina Hettne, acknowledging Rob Jellier, Jelle Goeman, and Peter-Bram 't Hoen. The workflow was created for the LUMC BioSemantics group, part of the Human Gen... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 29 times \| Downloaded: 0 times Tags (8): biosemantics \| e-science \| entrez \| gene expression \| GO \| normalization \| phenotype \| text_mining	View
Taverna 2 Original Uploader Tim Beck	get human and mouse phenotypes for a gene (v2) Created: 20/05/11 @ 15:18:50 \| Last updated: 29/03/12 @ 09:01:06 Credits: Tim Beck License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow gets phenotype annotations associated with human genes and the mouse orthologs from human (GWAS Central) and mouse (EuroPhenome and MGI) databases. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 52 times \| Downloaded: 13 times Tags (4): gwas \| human \| mouse \| phenotype	View Download (v2)
Taverna 2 Original Uploader Paul Fisher	Pathways and Gene annotations for QTL region (v1) Created: 27/05/11 @ 11:06:11 \| Last updated: 27/05/11 @ 11:06:52 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in rice, Oryza sativa. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniGene identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway d... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 30 times \| Downloaded: 9 times Tags (15): chromosome \| entrez \| genes \| genotype \| kegg \| Kegg Pathways \| loci \| locus \| pathway \| pathways \| phenotype \| qtl \| quanitative \| rice \| trait	View Download (v1)

Packs (5)

Creator: Paul Fisher	Towards Genotype-Phenotype Correlations Created: 08/04/09 @ 13:14:54 \| Last updated: 11/08/09 @ 14:50:01 It is increasingly common to combine Microarray and Quantitative Trait Loci data to aid the search for candidate genes responsible for phenotypic variation. Workflows provide a means of systematically processing large datasets, and represent a framework for the re-use and the explicit declaration of experimental methods. In this pack is a paper which describes the issues facing the manual analysis of microarray and QTL data for the discovery of candidate genes underlying complex phenotypes.&n... 20 items in this pack Comments: 0 \| Viewed: 159 times \| Downloaded: 34 times Tags: affymetrix \| african trypanosomiasis \| cattle \| data-driven \| disease \| entrez \| genotype \| Kegg Pathways \| KeggID \| link-integration \| microarray \| mouse \| pathway \| pathway-driven \| phenotype \| sleeping sickness \| swissprot \| uniprot \| web services	View Download
Creator: Paul Fisher	Pathway to Phenotype using Text Mining Created: 10/08/09 @ 13:01:47 \| Last updated: 11/08/09 @ 14:51:31 This pack contains a list of workflows and result files obtained from the analysis of candidate pathways believed to play a role in resistance to African Trypanosomiasis in the mouse model organism. 12 items in this pack Comments: 0 \| Viewed: 190 times \| Downloaded: 34 times Tags: abstracts \| african trypanosomiasis \| authors \| beanshell \| data-driven \| daxx \| eutils \| information \| kegg \| Kegg Pathways \| mining \| mouse \| pathway \| pathway-driven \| pathways \| phenotype \| pubmed \| qtl \| sleeping sickness \| terms \| text \| text mining \| trait \| workflow	View Download
Creator: Paul Fisher	Open Data: Bilateral Perisylvian Polymicrogyria Created: 16/11/10 @ 16:20:43 \| Last updated: 23/09/11 @ 10:55:08 This pack contains freely accessible data for scientific researchers to try and identify key genes linked to Bilateral Perisylvian Polymicrogyria. For those who want more information about this condition before they download the data, please see this link, which describes the condition and traits: http://omim.org/entry/300388?search=bilateral%20perisylvian%20polymicrogyria The results conatined within this pack are the output from running a scientific workflow that identifies candidate genes... 7 items in this pack Comments: 0 \| Viewed: 124 times \| Downloaded: 21 times Tags: bilateral perisylvian polymicrogyria \| bioinformatics \| chromosome \| cosine vector space \| data-driven \| epilepsy \| genotype \| homo sapiens \| human \| Kegg Pathways \| phenotype \| text mining; term extraction; entity recognition \| trait	View Download
Creator: Paul Fisher	Text Mining Workflows Created: 08/12/10 @ 11:55:03 \| Last updated: 01/02/11 @ 11:33:11 This pack contains workflows to navigate from candidate Quantitative Trait genes and pathways to a given phenotype. 5 items in this pack Comments: 0 \| Viewed: 77 times \| Downloaded: 12 times Tags: concept profile \| cosine vector space \| data-driven \| efetch \| entity recognition \| esearch \| gene \| gene identifier \| geneid \| genes \| genotype \| kegg \| Kegg Pathways \| KeggID \| literature \| loci \| locus \| ncbi \| pathway \| pathway-driven \| pathways \| phenotype \| pubmed \| qtl \| quanitative \| ranking \| space \| term \| term extraction \| terms \| text \| text mining \| text mining; term extraction; entity recognition \| trait \| vector	View Download
Creator: Paul Fisher	Trichuriasis induced Colitis Created: 16/02/11 @ 12:49:21 \| Last updated: 16/02/11 @ 15:26:36 This pack contains the workflows and data relating to Trichuriasis induced colitis. 5 items in this pack Comments: 0 \| Viewed: 16 times \| Downloaded: 2 times Tags: annotation \| chromosome \| controlled vocabulary \| cosine vector space \| data integration \| data-driven \| dresden \| efetch \| enrichment \| ensembl \| entity recognition \| esearch \| evidence \| gene expression \| gene identifier \| genotype \| kegg \| Kegg Pathways \| KeggID \| literature \| loci \| locus \| medline \| microarray \| mining \| pathway \| pathway-driven \| phenotype \| pubmed \| qtl \| quanitative \| ranking \| re-use \| significance \| term \| term extraction \| terms \| text \| text mining \| text mining; term extraction; entity recognition \| trait \| trichuris muris	View Download

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Mariebrown

metabolomics

Created: Thursday 29 November 2007 @ 11:50:47 (GMT)

Data analysis and bioinformatics of metabolomic studies

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Uploader: Paul Fisher	A Systematic Strategy for Large-Scale Analysis of Genotype-Phenotype Correlations: Identification of candidate genes involved in African Trypanosomiasis Created: 08/04/09 @ 13:23:03 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This PDF is my personal copy of the NAR publication. File type: Adobe PDF Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 31 times \| Downloaded: 30 times Tags: african trypanosomiasis \| genotype \| pathway-driven \| phenotype \| sleeping sickness	View Download
Uploader: Paul Fisher	Candidate Gene protocol Created: 08/04/09 @ 13:27:20 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This protocol provides details on how to identify candidate genes from the returned workflow results. File type: Word document Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 37 times \| Downloaded: 39 times Tags: affymetrix \| african trypanosomiasis \| gene \| gene identifier \| geneid \| Kegg Pathways \| KeggID \| pathway \| pathway-driven \| pathways \| phenotype \| sleeping sickness	View Download
Uploader: Paul Fisher	Table of SNP sequenceing results Created: 08/04/09 @ 13:29:32 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This file contains the results of re-sequencing the Daxx gene File type: Word document Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 347 times \| Downloaded: 24 times Tags: african trypanosomiasis \| daxx \| genotype \| mouse \| phenotype \| sleeping sickness \| snp \| snps	View Download
Uploader: Paul Fisher	Pathway Cosine Scores from Day7 and Tir1 QTL Created: 10/08/09 @ 15:55:24 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This excel file contains a list of all pathways found to be differentially expressed at day 7 post infection in the trypanosomiasis resistance phenotype, which contain genes in the Tir1 QTL. The pathways in this file have been ranked according to the scores obtained after calculating a cosine vector value against the trypanosomiasis resistance phenotype. The higher the score, the more closely linked to a phentype a given pathway is. This allows each pathway to be ranked giving biologists a ... File type: Excel workbook Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 14 times \| Downloaded: 0 times Tags: abstracts \| african trypanosomiasis \| cosine vector space \| data-driven \| kegg \| Kegg Pathways \| pathway \| pathway-driven \| pathways \| phenotype \| sleeping sickness \| term \| term extraction \| terms \| text \| text mining \| text mining; term extraction; entity recognition \| trait	View
Uploader: Paul Fisher	Gene Cosine Scores Created: 10/08/09 @ 16:00:45 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This excel file contains a list of genes linked to the resistance to African trypanosomiasis in the mouse. Genes from the Tir1 QTL were used in a search through PubMed. The results were then correlated to the trypanosomiasis resistance phenotype. The higher the score (and ranking) the more related to the phenotype the gene is likely to be. This is based on the co-occurrence of terms within the gene and phentoype corpora. File type: Excel workbook Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 14 times \| Downloaded: 0 times Tags: abstracts \| african trypanosomiasis \| authors \| cosine vector space \| data-driven \| enrichment \| entity recognition \| gene \| geneid \| genes \| mouse \| ncbi \| phenotype \| pubmed \| ranking \| sleeping sickness \| term \| term extraction \| terms \| text \| text mining \| text mining; term extraction; entity recognition	View
Uploader: Paul Fisher	Phenotype Term Counts (in Phenotype Corpus) Created: 11/08/09 @ 13:34:42 \| Last updated: 11/08/09 @ 13:58:28 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This file contains a count of each phenotype term extracted from corpus of phenotype abstracts. Each value represents the number of articles in the phenotype corpus the term appears. The use of this file is to calculate a cosine vector score for correlating a given concept (e.g. pathway or gene) with a phenotype. File type: Plain text Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 16 times \| Downloaded: 0 times Tags: abstracts \| african trypanosomiasis \| append term \| authors \| phenotype \| pubmed \| ranking \| sleeping sickness \| term \| term extraction \| terms \| text \| text mining \| text mining; term extraction; entity recognition	View
Uploader: Paul Fisher	Pathway Abstracts for Day7 Microarray Tir1 QTL Created: 11/08/09 @ 14:08:41 \| Last updated: 11/08/09 @ 14:15:58 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This file contains all the abstracts for pathways found to be differentially expressed at day 7 post infection and intersect the Tir1 QTL region, from the African Trypanosomiasis project. Each pathway is listed as ">> [Pathway Name]", together with a PubMed identifier, date, and abstract for each article. Each pathway has been restricted to 500 abstracts, and is given in the date range 31/12/2007 to 01/01/2009. Note, some pathways do not have any abstracts available due to th... File type: Plain text Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 16 times \| Downloaded: 0 times Tags: abstracts \| african trypanosomiasis \| authors \| cosine vector space \| data-driven \| enrichment \| esearch \| eutils \| genotype \| kegg \| Kegg Pathways \| pathway \| pathway-driven \| pathways \| phenotype \| pubmed \| term \| term extraction \| terms \| text \| text mining \| text mining; term extraction; entity recognition	View
Uploader: M. Kirsh	Uniqueness , Self Belonging and Intercourse in Nature Created: 23/08/09 @ 07:53:40 \| Last updated: 23/08/09 @ 08:06:11 Credits: M. Kirsh License: Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License The world is discussed and framed so that it does not evolve divisions alike the conceptual division between Special and General Relativity in which emerged divides are suggested to be parallel to and emerged from paradoxes of mind-matter, the self and nature. Of all of the potential properties of the unique Universe, emergence, affinity, self avoidance , etc., self belonging is never a characteristic of unique and energy metabolizing spaces/entities. ... File type: Adobe PDF Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 16 times \| Downloaded: 6 times Tags: affinity \| chromatin folding and shape \| concept of vacuum \| correspondances in nature \| einstein \| energy \| entity \| evolution \| force \| intercourse \| mass \| numbers and kinds \| phenotype \| RNA \| role of dna \| self avoidance \| self belonging \| set theory \| social science \| theory of nature \| theory of relativity \| time \| uniqueness \| universal form \| universal shape \| volume and space	View Download
Uploader: M. Kirsh	Uniqueness, Self Belonging and Intercourse in Nature-New Version(rev) Created: 09/01/10 @ 04:42:06 Credits: M. Kirsh License: Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License Abstract Biological organization is discussed within a holistic framework . A new orientation is presented of natural processes with an approach in model construction that is focused strictly on physical form and centered away from abstractions that escape the perceptual senses, lead towards the postulation of non-verifiable and non-witnessible entities. A universal construction composed of first perspective representations of path, witness as unique loci in volumes o... File type: Adobe PDF Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 10 times \| Downloaded: 13 times Tags: affinity \| correspondences in nature \| descriptiontimeforceuniversaluracilvelocity \| einstein \| energy \| entity \| evolution \| force \| intercourse \| inversion \| mass \| mobius strip \| numbers and kinds \| origin of life \| phenotype \| representation of nature \| RNA \| role of dna \| self avoidance \| self belonging \| set theory \| social science \| theory of nature \| theory of relativity \| time \| unified theory of nature \| uniqueness \| universal form \| universal shape \| volume and space	View Download
Uploader: Paul Fisher	Bilateral Perisylvian Polymicrogyria (Epilepsy) Created: 07/12/10 @ 16:34:31 \| Last updated: 07/12/10 @ 16:34:37 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This zip file contains the results of running a QTL workflow for Bilateral Perisylvian Polymicrogyria in human (homo sapiens). Provided are a list of candidate QTL genes (QTg) and their corresponding KEGG pathways. Each gene and pathway have been subsequently run through a series of text mining workflows to determine the significance of each may play in relation to Bilateral Perisylvian Polymicrogyria AND/OR Epilepsy. Further to this, I have also collected the SNPs (single nucleotide... File type: application/x-zip-compressed Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 12 times \| Downloaded: 0 times Tags: bilateral perisylvian polymicrogyria \| cosine vector space \| data-driven \| epilepsy \| gene identifier \| geneid \| genotype \| homo sapiens \| human \| literature \| pathway \| pathway-driven \| pathways \| phenotype \| pubmed \| re-use \| region \| snp \| snps \| text \| text mining \| text mining; term extraction; entity recognition	View
Uploader: Paul Fisher	Trichuriasis Induced Colitis Created: 16/02/11 @ 15:16:17 \| Last updated: 16/02/11 @ 15:16:24 Credits: Paul Fisher Attributions: Pathways and Gene annotations for RefSeq ids KEGG pathways common to both QTL and microarray based investigations Pathways and Gene annotations for QTL region Pathway and Gene to Pubmed License: Creative Commons Attribution-Share Alike 3.0 Unported License This zip file contains the results of workflow runs for: identifying genes in each of the 7 QTL regions for Trichuris muris infection; identifying genes differentially expressed in mice challenged with Trichuris muris; and Text mining results (including cosine vector scores and Term Enrichment values). File type: Trident (Package) Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 8 times \| Downloaded: 6 times Tags: gene expression \| genotype \| Kegg Pathways \| microarray \| pathway-driven \| phenotype \| pubmed \| qtl \| trait \| trichuris muris	View Download
Uploader: Paul Fisher	Bilateral Perisylvian Polymicrogyria Created: 17/03/11 @ 10:56:15 \| Last updated: 17/03/11 @ 11:16:53 Credits: Paul Fisher Attributions: Pathway and Gene to Pubmed Pathways and Gene annotations forQTL region License: Creative Commons Attribution-Share Alike 3.0 Unported License This zip file contains the results of running a QTL workflow for Bilateral Perisylvian Polymicrogyria in human (homo sapiens). Provided are a list of candidate QTL genes (QTg) and their corresponding KEGG pathways. Each gene and pathway have been subsequently run through a series of text mining workflows to determine the significance each may play in relation to Bilateral Perisylvian Polymicrogyria. If you want to help me identify candidate genes for this disorder, please get i... File type: ZIP archive Rating: 0.0 / 5 (0 ratings) \| Comments: 0 \| Viewed: 12 times \| Downloaded: 7 times Tags: bilateral perisylvian polymicrogyria \| cosine vector space \| data integration \| data-driven \| enrichment \| entity recognition \| epilepsy \| gene \| homo sapiens \| human \| Kegg Pathways \| pathways \| phenotype \| pubmed \| qtl \| quanitative \| region \| text mining \| text mining; term extraction; entity recognition	View Download

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Items tagged with "phenotype" (43)