User: Paul Fisher

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Paul Fisher

Get Kegg Pathway information (v1)

Created: 10/03/10 @ 17:15:47 | Last updated: 10/03/10 @ 17:18:47

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow gets a series of information relating to a list of KEGG pathways supplied to it. It also removes any null values from a list of strings. Example input: path:mmu04010 path:mmu05014

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Paul Fisher

Pathways and Gene annotations for QTL region (v2)

Created: 19/10/09 @ 12:39:05 | Last updated: 20/11/09 @ 14:04:41

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 Pig, Sus scrofa. 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 ...

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Paul Fisher

Unconnected Filter (v1)

Created: 19/08/09 @ 16:35:09 | Last updated: 19/08/09 @ 16:35:11

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow removes any unconnected nodes from a given Ondex graph through filtering, and returns a new Ondex Graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph. RemoveContextDependencies - Set true to remove context dependencies, otherwise unconnected concepts will still remain in the ...

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Paul Fisher

SubGraph Filter (v2)

Created: 19/08/09 @ 16:32:41 | Last updated: 19/08/09 @ 16:38:18

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow filters a given Ondex graph to return a new ondex sub-graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph. ConceptID - The root concept to start at. Valid value range is 1 to 2147483647. FirstRelationType - RelationType limitation for depth 1 (Optional). FirstConceptClass - C...

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Paul Fisher

Shortest Path (v1)

Created: 19/08/09 @ 16:30:36 | Last updated: 19/08/09 @ 16:30:38

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow filters a given Ondex graph according to the shortest path (graph) algorithm. The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph. StartConceptID - The Concept ID that starts the path. Valid value range is 1 to 2147483647. UseWeights - Use gds values as edge ...

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Paul Fisher

Relation Neighbours Filter (v1)

Created: 19/08/09 @ 16:28:10 | Last updated: 19/08/09 @ 16:28:12

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow filters a given Ondex graph based on some neighbour parameters supplied by the user. The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph. Depth - The Depth (distance from seed in relations) to apply the filter to ConceptID - The Concept ID to seed th...

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Paul Fisher

Optimal Paths Filter (v1)

Created: 19/08/09 @ 16:25:51 | Last updated: 19/08/09 @ 16:25:53

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow filters a given Ondex graph based on the optimal path between one or more concepts. The result is a new Ondex graph. The parameters that can be used with service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph. PathwayDefinition - pathway definition file. StatisticsOutputDir - The directory to output statistics (Optional). Incl...

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Paul Fisher

Isolate Clusters Filter (v1)

Created: 19/08/09 @ 16:23:46 | Last updated: 19/08/09 @ 16:23:48

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow filters a given Ondex graph, isolating clusters within the graph and returning only those clusters as a new graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph. TargetConceptClass - Target Concept Class to be contained in clusters.

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Paul Fisher

Genomic Filter (v1)

Created: 19/08/09 @ 16:19:02 | Last updated: 19/08/09 @ 16:19:05

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow filters a given Ondex graph according to a chromosomal region, or QTL region. The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph. ContextID - The Concept ID of the Context (Chromosome). From - The start position on the chromosome, e.g. 100. To - The stop pos...

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Paul Fisher

Evidence Type Filter (v1)

Created: 19/08/09 @ 16:16:16 | Last updated: 19/08/09 @ 16:16:18

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow filters a given Ondex graph according to some user defined evidence values. The result is a new Ondex graph. The parameters that can be used with this web service are given below: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph. EvidenceType - EvidenceType to be taken into consideration. RefactorTrinaries - Where the qualifier of a trinary rel...

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Paul Fisher

Context Filter (v1)

Created: 19/08/09 @ 16:14:14 | Last updated: 19/08/09 @ 16:14:16

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow filters an Ondex graph according to a given context. The result is a new Ondex graph with only selected contexts. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph. ContextID - The Concept ID of the Context that starts the path. ContextBoolean - Defines two ContextIDs and a boolean operati...

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Paul Fisher

Concept Class Neighbours Filter (v1)

Created: 19/08/09 @ 16:11:57 | Last updated: 19/08/09 @ 16:11:59

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow filters a given Ondex graph based on a user defined concept class. The neighbours of the concept class are returned as a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph. Depth - The Depth (distance from seed in relations) to apply the filter to. ConceptClass - The Conce...

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Paul Fisher

Clean UniProt Filter (v1)

Created: 19/08/09 @ 16:08:49 | Last updated: 19/08/09 @ 16:08:50

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow filters a given Ondex graph, removing any erroneous UniProt data. The result is a new Ondex graph that conatains only connected UniProt data. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph.

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Paul Fisher

All Pairs Filter (v1)

Created: 19/08/09 @ 16:06:31 | Last updated: 19/08/09 @ 16:06:32

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow filters a given Ondex graph based on the occurrence of directed edges within the graph. Only those concepts that have directional edges are returned to the user, in the form of a new graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph. GdsWeight - The name of the GDS type to ...

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Paul Fisher

Table Parser (v1)

Created: 19/08/09 @ 16:04:14 | Last updated: 19/08/09 @ 16:04:15

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow parsers a table (specified by the user), into an Ondex Graph on the web server.

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Paul Fisher

Rank Phenotype Terms (v1)

Created: 10/08/09 @ 15:43:50 | Last updated: 10/08/09 @ 15:43:54

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 ...

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Paul Fisher

Gene to Pubmed (v2)

Created: 10/08/09 @ 15:31:15 | Last updated: 10/08/09 @ 15:38:32

Credits: Paul Fisher

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.

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Paul Fisher

Cosine vector space (v1)

Created: 10/08/09 @ 13:19:36 | Last updated: 10/08/09 @ 13:24:29

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.

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Paul Fisher

Arabidopsis thaliana QTL Analysis (v1)

Created: 08/07/09 @ 16:26:13 | Last updated: 14/12/09 @ 11:59:16

Credits: Paul Fisher

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in Arabidopsis thaliana. 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 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. ...

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Paul Fisher

inchi to Chebi (v1)

Created: 22/05/09 @ 16:07:51 | Last updated: 22/05/09 @ 16:07:52

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow converts an inchi string to a chebi id.

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Paul Fisher

Get relations (v1)

Created: 27/02/09 @ 16:45:40 | Last updated: 27/02/09 @ 16:45:41

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow gets all the realtions from a given Ondex graph

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Paul Fisher

Get graphs (v2)

Created: 27/02/09 @ 16:41:49 | Last updated: 05/11/09 @ 12:38:23

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Thiw workflow simply returns all the Ondex graphs that are present on a given server (where the web service is)

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Paul Fisher

Get CVs (v1)

Created: 27/02/09 @ 16:38:40

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow lets users retrive all controlled vocabularies for a given Ondex graph

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Paul Fisher

Get Kegg Gene information (v2)

Created: 05/01/09 @ 13:20:34 | Last updated: 14/12/09 @ 12:05:23

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow gets a series of information relating to a list of KEGG genes supplied to it. It also removes any null values from a list of strings.   Example input for this workflow is given below (new line separated): mmu:13163 hsa:1616

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Paul Fisher

KEGG Pathway to Pubmed (v2)

Created: 09/03/08 @ 15:03:12 | Last updated: 03/12/09 @ 16:52:10

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.   Example input for this workflow is as follows (new line separated): path:mmu04530    Tight junction - Mus musculus (mouse) path:mmu04540    Gap junction - Mus musculus (mouse) path:mmu04730    Long-term depre...

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Paul Fisher

Microarray CEL file to candidate pathways (v2)

Created: 08/02/08 @ 14:17:23 | Last updated: 13/02/09 @ 11:29:54

Credits: Paul Fisher Saeedeh

License: Creative Commons Attribution-Share Alike 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 retruned 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 ch...

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Paul Fisher

Perform a text based search through PubMed (v3)

Created: 03/10/07 @ 18:36:08 | Last updated: 03/12/09 @ 16:39:20

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

This workflow takes in a number of search terms in which to perform a search over the PubMed literature database. These search terms may be input as if entered in the web based version of PubMed. The output from this workflow is a list of PubMed identifiers in xml based format. Example input for this workflow is given as: 9215629

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Paul Fisher

Perform a search through NCBI eUtils eSearch (v3)

Created: 03/10/07 @ 18:36:07 | Last updated: 03/12/09 @ 16:32:27

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

This workflow takes in a search term and a database (e.g. snp, gene, protein) in which to perfom the search over. The result is an xml file containing summary information about the search term. Example input for this workflow are given below: database: pubmed terms: cancer AND diabetes

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Paul Fisher

Simplify a BLAST text file (v2)

Created: 03/10/07 @ 18:36:06 | Last updated: 28/07/09 @ 13:01:46

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

This workflow simplifies a BLAST text file into identifiers, descriptions and values (P, E-values). In order to extract the relevant ids etc. you need to pass the relevant string into the corresponding port, e.g. the default port being used is gi. This has been passed "gi". For any other ports simply pass in the string the SAME as the port name, e.g. seq_id, p, per etc.

Rating: 4.0 / 5 (1 rating) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

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Paul Fisher

Mouse Microarray Analysis (v3)

Created: 03/10/07 @ 18:36:05 | Last updated: 03/12/09 @ 16:20:34

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

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Paul Fisher

Back translate a protein sequence into a dna sequence (v2)

Created: 03/10/07 @ 18:36:03 | Last updated: 03/12/09 @ 16:18:44

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

This workflow back translates a protein sequence into a DNA sequence. Example input for this workflow is: MATDDSIIVLDDDDEDEAAAQPGPSNLPPNPASTGPGPGLSQQATGLSEPRVDGGSSNSG SRKCYKLDNEKLFEEFLELCKTETSDHPEVVPFLHKLQQRAQSVFLASAEFCNILSRVLA RSRKRPAKIYVYINELCTVLKAHSIKKKLNLAPAASTTSEASGPNPPTEPPSDLTNTENT ASEASRTRGSRRQIQRLEQLLALYVAEIRRLQEKELDLSELDDPDSSYLQEARLKRKLIR LFGRLCELKDCSSLTGRVIEQRIPYRGTRYPEVNRRIERLINKPGLDTFPDYGDVLRAVE KAATRHSLGLPRQQLQLLAQDAFRDVGVRLQERRHLDLIYNFGCHLTDDYRPGVDPALSD PTLARRLRENRTLAM...

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Original Uploader

Paul Fisher

Pathways and Gene annotations for QTL region (v5)

Created: 03/10/07 @ 18:36:02 | Last updated: 20/11/09 @ 10:33:28

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: 4.5 / 5 (2 ratings) | Versions: 5 | Reviews: 0 | Comments: 2 | Citations: 1

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Paul Fisher

Cow-Human Ortholog Pathways and Gene annotations for QTL Phenotype (v2)

Created: 03/10/07 @ 18:36:00 | Last updated: 03/12/09 @ 16:16:33

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the 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. As the Cow genome is currently unfinished, the workflow subsequently maps the cow ensembl gene ids to human orthologues. Entrez and UniProt identifiers are then identified...

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Paul Fisher

Transcribe a DNA sequence into an RNA sequence (v2)

Created: 03/10/07 @ 18:35:58 | Last updated: 13/11/07 @ 16:16:54

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

This workflow transcribes a DNA sequence into an RNA sequence

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