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Items tagged with "pubmed" (46)

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Files (13)
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Blob Gene Cosine Scores

Created: 10/08/09 @ 16:00:45

Credits: User 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

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Blob Phenotype Abstracts for Trypanosomiasis Resistance

Created: 11/08/09 @ 12:45:24

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a list of published abstracts from MEDLINE, that are related to the African Trypanosomiasis resistance phentoype in the mouse. The term used in the PubMed search was: trypanosom* AND (tolerance OR resistance) . The workflow limited the date of the search using PubMed between 31/12/2005 to 01/01/2009, and was restricted to 500 abstracts.

File type: Plain text

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Blob Phenotype Concept Profile - Terms

Created: 11/08/09 @ 13:05:07 | Last updated: 11/08/09 @ 13:06:51

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a list of all terms extracted from the phenotype corpus, relating to African trypanosomiasis resistance in the mouse model. These terms were extracted using the following service: http://gopubmed4.biotec.tu-dresden.de/GoPubMedTermGenerationService/services/GoPubMedTermGeneration?wsdl These terms represent the concept profile for the phenotype.

File type: Plain text

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Blob Phenotype Term Counts (in Phenotype Corpus)

Created: 11/08/09 @ 13:34:42 | Last updated: 11/08/09 @ 13:58:28

Credits: User 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

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Blob PubMed Abstract Number

Created: 11/08/09 @ 13:54:45

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains the number of articles available in MEDLINE, through PubMed, at the time of performing these data analyses. The date of identifying these publications was 25/02/2009.

File type: Plain text

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Blob PubMed Term Counts

Created: 11/08/09 @ 13:59:35

Credits: User 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 MEDLINE 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

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Blob Pathway Abstracts for Day7 Microarray Tir1 QTL

Created: 11/08/09 @ 14:08:41 | Last updated: 11/08/09 @ 14:15:58

Credits: User 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

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Blob Pathway Term Enrichment Scores

Created: 11/08/09 @ 14:23:49

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains a list of each pathway identified from day 7 post infection and linked to the Tir1 QTL. With each pathway is a list of terms that are common to both pathway and phenotype corpora. These terms were ranked accoring to their enrichement scores. The higher the score, the more significant the term is in relation to correlating the pathway with the African trypanosomiasis resistance phenotype.

File type: Plain text

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Blob Ondex and Taverna Tutorial

Created: 22/10/09 @ 13:50:53 | Last updated: 22/10/09 @ 13:51:51

Credits: User George

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Biological Data Integration Using Ondex and Taverna: A Tutorial 25/26th November 2009 The University of Manchester The Ondex SABR project (http://ondex.org/sabr.html) invite you to a two-day tutorial that aims to show participants how to use Ondex and Taverna to perform common biological data collection, integration and visualisation tasks.

File type: Word document

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Blob Bilateral Perisylvian Polymicrogyria (Epilepsy)

Created: 07/12/10 @ 16:34:31 | Last updated: 07/12/10 @ 16:34:37

Credits: User 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

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Blob Trichuriasis Induced Colitis

Created: 16/02/11 @ 15:16:17 | Last updated: 16/02/11 @ 15:16:24

Credits: User Paul Fisher

Attributions: Workflow Pathways and Gene annotations for RefSeq ids Workflow KEGG pathways common to both QTL and microarray based investigations Workflow Pathways and Gene annotations for QTL region Workflow 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)

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Blob Bilateral Perisylvian Polymicrogyria

Created: 17/03/11 @ 10:56:15 | Last updated: 17/03/11 @ 11:16:53

Credits: User Paul Fisher

Attributions: Workflow Pathway and Gene to Pubmed Workflow 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

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Blob Ondex Workflows

Created: 01/09/11 @ 17:17:57 | Last updated: 01/09/11 @ 17:18:05

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This zip file contains a large number of Taverna 2 workflows that utilise the Ondex Web Service, for manipulating Ondex graphs.

File type: ZIP archive

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Workflows (30)
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Workflow Perform a search through NCBI eUtils eSearch (3)

Created: 27/11/09 @ 14:44:11 | Last updated: 03/12/09 @ 16:32:26

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

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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

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 8 | Citations: 0

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Workflow GeneIlluminator_GetPubMedQuery (2)

Created: 27/02/08 @ 00:49:44 | Last updated: 03/03/08 @ 22:08:39

Credits: User Pieter Neerincx User Alako

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Example workflow demonstrating how to use GeneIlluminator_GetPubMedQuery, a synchronous BioMOBY service for gene symbol disambiguation. If a gene symbol is ambiguous this service uses GeneIlluminator to create clusters describing which different genes, sharing the same symbol, exist in different parts of the tree of life. GeneIlluminator provides also aliases associated to the input gene symbol. Finally, using the cluster characteristics it creates a boolean PubMed query that could be used to...

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow Escherichia coli : From cDNA Microarray Ra... (1)

Created: 08/05/08 @ 15:25:29 | Last updated: 12/05/08 @ 09:01:37

Credits: User Saeedeh User Paul Fisher

Attributions: Workflow HUMAN Microarray CEL file to candidate pathways

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow takes in a CDNA raw file and a normalisation method then returns a series of images/graphs which represent the same output obtained using the R and bioconductor. 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 changes in the microarray data. By identifying the candidate pathways, more detailed...

Rating: 5.0 / 5 (1 rating) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 336 times | Downloaded: 109 times

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Workflow EBI_CiteXplore (1)

Created: 09/07/08 @ 04:53:56

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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Perform a literature search using the EBI's CiteXplore service (http://www.ebi.ac.uk/citexplore/), and get the results in a minimal XML format containing the citation information (i.e. title, author, journal, etc.), the identifier of the citation in the source database (PubMed/Medline, Agricola, Patent Abstracts, CBA, CiteSeer, etc.) and information about abstract and full article availablity including URLs.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow Retrieve_abstract_from_Medline (1)

Created: 17/09/08 @ 15:22:56 | Last updated: 17/09/08 @ 15:24:22

Credits: User Franck Tanoh

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow retrieves Medline Abstracts given PMIDs (PubMed id) You can use: 9879 as input example to test this workflow

Rating: 5.0 / 5 (1 rating) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 180 times | Downloaded: 74 times

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Workflow Author's collaborators according to pubmed (1)

Created: 20/01/09 @ 02:22:32 | Last updated: 20/01/09 @ 03:41:26

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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SELECT distinct ?s2 FROM <http://atlas.bio2rdf.org/sparql> WHERE {   ?s1 ?p1 ?o1 .   ?o1 bif:contains "author" .   ?s2 ?p2 ?s1 .   FILTER( regex(?s1, "pubmed") ) } followed by SELECT ?creator, count() FROM <http://localhost:8890/sparql> WHERE {   ?s1 ?p1 .   ?s1 ?p2 ?o2 .   FILTER( regex(?o2, "author"))   ?s1 ?creator . } ORDER BY DESC(count())

Rating: 3.0 / 5 (1 rating) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 170 times | Downloaded: 76 times

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Workflow What is Paget's disease sparql query example (3)

Created: 20/01/09 @ 03:34:08

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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SELECT distinct ?s1 FROM <http://atlas.bio2rdf.org/sparql> WHERE {   ?s1 ?p1 ?o1 .   ?o1 bif:contains "paget" .   FILTER( regex(?s1, "omim")   OR regex(?s1, "geneid") OR regex(?s1, "uniprot")) }   followed by SELECT ?type1, count(*) FROM <http://localhost:8890/sparql> WHERE {   ?s1 ?p1 ?o1 .   ?o1 bif:contains "paget" .   ?s1  

Rating: 3.0 / 5 (1 rating) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow What is known about HIV using Bio2RDF's SP... (2)

Created: 05/02/09 @ 06:13:53 | Last updated: 05/02/09 @ 06:15:22

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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To answer this question Bio2RDF Atlas about mouse and human genome sparql endpoint available at http://atlas.bio2rdf.org/sparql is searched.  The selected URIs are then loaded into your local Virtuoso triplestore at http://localhost:8890/sparql. You must enable insert mode into the graph. Once the mashup is built, two SPARQL queries analyze the obtained graph.  Finally you can submit queries to the RDF mashup about HIV as you like.  Enjoy. This is the queries present in t...

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Workflow Cosine vector space (1)

Created: 10/08/09 @ 13:19:36 | Last updated: 10/08/09 @ 13:24:28

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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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Workflow Rank Phenotype Terms (1)

Created: 10/08/09 @ 15:43:48

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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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Viewed: 139 times | Downloaded: 0 times

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Workflow Search for BMURI in PubMed [myexperiment:p... (1)

Created: 17/11/09 @ 06:59:06

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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test values: subkecttest values: query = bio2rdf graph = http://bio2rdf query = nur77 AND Rouillard,C graph = http://nur77 test values: query = bio2rdf graph = http://bio2rdf query = nur77 AND Rouillard,C graph = http://nur77 query = labrie graph = http://labrie

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Workflow Search for citations and related article i... (1)

Created: 17/11/09 @ 07:02:11

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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graph = http://nur77 bmuri = http://bio2rdf.org/pubmed:18843482 http://bio2rdf.org/pubmed:18466322 http://bio2rdf.org/pubmed:17201484 http://bio2rdf.org/pubmed:14603264 http://bio2rdf.org/pubmed:12629527

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Viewed: 73 times | Downloaded: 14 times

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Workflow Sponge into Virtuoso triplestore the neede... (2)

Created: 17/11/09 @ 07:09:01 | Last updated: 27/11/09 @ 03:32:15

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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query = labrie,f query = labrie query = labrie,f query = labrie query = h1n1 query = morissette,j query = labrie,f query = labrie query = h1n1 Get a list of paper from pubmed.

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Workflow microRNA to KEGG Pathways and Abstracts (1)

Created: 17/03/10 @ 10:53:02

Credits: User Paul Fisher

Attributions: Workflow Pathways and Gene annotations for QTL region

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Workflow takes in a text file of microRNAs from microCOSM (at the EBI) and outputs a list of KEGG pathway information, including genes in pathways and pathway abstracts from PubMed. The results can then be used in various text mining applications/workflows to rank the results against a given disease.Workflow takes in a file of microRNAs

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Workflow Nucleotide frequency workflow (2)

Created: 13/05/10 @ 01:51:22 | Last updated: 12/11/10 @ 10:30:15

Credits: User wabi

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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No description

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Workflow Perfrom a text based search through PubMed (1)

Created: 05/07/10 @ 13:03:35 | Last updated: 05/07/10 @ 13:03:37

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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

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Viewed: 42 times | Downloaded: 21 times

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Workflow Gene to Pubmed (3)

Created: 05/07/10 @ 13:14:36 | Last updated: 26/01/11 @ 16:57:39

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 3 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 55 times | Downloaded: 32 times

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Workflow Phenotype to pubmed (3)

Created: 05/07/10 @ 14:07:33 | Last updated: 11/01/11 @ 12:07:22

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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

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Workflow Who is Dr Labrie according to Pubmed publi... (2)

Created: 08/07/10 @ 07:18:09 | Last updated: 08/07/10 @ 07:32:26

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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To use this wokflow you need to import services from To use this wokflow you need to import services from http://proxy.bio2rdf.org/bio2rdf/services.txt you can explore the loaded data at http://proxy.bio2rdf.org/fct

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 23 times | Downloaded: 10 times

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Original Uploader

Workflow Rank Phenotype Terms (2)

Created: 08/12/10 @ 11:38:37 | Last updated: 11/01/11 @ 12:02:30

Credits: User Paul Fisher

Attributions: Workflow Rank Phenotype Terms

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 32 times | Downloaded: 15 times

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Original Uploader

Workflow Rank Phenotype Terms (1)

Created: 01/02/11 @ 11:22:14 | Last updated: 01/02/11 @ 11:24:42

Credits: User Paul Fisher

Attributions: Workflow Cosine vector space Workflow Rank Phenotype Terms

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 34 times | Downloaded: 15 times

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Original Uploader

Workflow PubMed Search (1)

Created: 03/02/11 @ 15:24:57 | Last updated: 03/02/11 @ 15:25:32

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow takes in a search term, are passed to the eSearch function and searched for in PubMed. Those abstracts found are returned to the user

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Viewed: 43 times | Downloaded: 27 times

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Workflow Gene to Pubmed (4)

Created: 08/02/11 @ 13:04:06 | Last updated: 10/02/11 @ 16:01:41

Credits: User Paul Fisher

Attributions: Workflow Cosine vector space Workflow Extract Scientific Terms Workflow Rank Phenotype Terms Workflow Cosine vector space Workflow Rank Phenotype Terms Workflow Pathway to Pubmed Workflow Extract Scientific Terms

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 51 times | Downloaded: 25 times

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Workflow Pathway and Gene to Pubmed (2)

Created: 10/02/11 @ 16:10:52 | Last updated: 18/02/11 @ 13:47:08

Credits: User Paul Fisher

Attributions: Workflow Cosine vector space Workflow Extract Scientific Terms Workflow Rank Phenotype Terms Workflow Cosine vector space Workflow Rank Phenotype Terms Workflow Pathway to Pubmed Workflow Extract Scientific Terms Workflow Gene to Pubmed

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 75 times | Downloaded: 20 times

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Workflow XPath Pubmed Ids (1)

Created: 23/03/11 @ 11:24:23 | Last updated: 23/03/11 @ 11:24:58

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow takes in a search term (as used in the normal PubMed interface) and retrieves a list of PubMed ids in xml

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Workflow XPath Pubmed Ids (2)

Created: 23/03/11 @ 16:19:10 | Last updated: 30/03/11 @ 09:28:13

Credits: User Paul Fisher

Attributions: Workflow XPath Pubmed Ids

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow takes in a search term (as used in the normal PubMed interface) and retrieves a list of PubMed ids in xml. The xml is then parsed to retrieve a list of PubMed ids

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow EUADR Relationship Extraction Workflow (1)

Created: 27/07/11 @ 16:16:16 | Last updated: 07/09/12 @ 18:14:57

Credits: User Bharat Singh

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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The workflow offers the ability to automatically determine if an ADR and a Drug are co-mentioned in any of the indexed resources. However the actual relationship between a Drug and an ADR can only be determined by referring to the actual resource The co-occurance relationship workflow seeks to automate the search for resources (publications, drug labels) related to ADRs corresponding to a given drug/ adverse event association. To enable this concept profiles for drugs and adverse effects wer...

Rating: 5.0 / 5 (1 rating) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow BioAID_ProteinDiscovery (7)

Created: 10/05/10 @ 16:21:09 | Last updated: 20/03/12 @ 17:16:11

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This protein discovery workflow extracts protein names from documents retrieved from MedLine based on a user Query (cf Apache Lucene syntax). The protein names are filtered by checking if there exists a valid UniProt ID for the given protein name.

Rating: 0.0 / 5 (0 ratings) | Versions: 7 | Reviews: 0 | Comments: 1 | Citations: 0

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Workflow Retrieve_Pubmed_Publication_by_kegg_pathwa... (1)

Created: 18/10/12 @ 15:06:12

Credits: User Massimo La Rosa User Antonino Fiannaca

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow shows in your browser pubmed articles related to input pathway

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

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Packs (3)
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Pack 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.

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Pack 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.

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Pack 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.

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