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Items tagged with "text mining" (61)

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Files (11)
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Blob Pathway Cosine Scores from Day7 and Tir1 QTL

Created: 2009-08-10 15:55:24

Credits: User 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

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Blob Gene Cosine Scores

Created: 2009-08-10 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: 2009-08-11 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: 2009-08-11 13:05:07 | Last updated: 2009-08-11 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: 2009-08-11 13:34:42 | Last updated: 2009-08-11 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: 2009-08-11 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 Pathway Abstracts for Day7 Microarray Tir1 QTL

Created: 2009-08-11 14:08:41 | Last updated: 2009-08-11 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: 2009-08-11 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: 2009-10-22 13:50:53 | Last updated: 2009-10-22 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: 2010-12-07 16:34:31 | Last updated: 2010-12-07 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 Bilateral Perisylvian Polymicrogyria

Created: 2011-03-17 10:56:15 | Last updated: 2011-03-17 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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Groups (2)
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Network-member National Centre for Text Mining (NaCTeM)

Unique name: nactem
Created: Monday 19 May 2008 16:56:09 (UTC)

A group representing researches at the National Centre for Text Mining - www.nactem.ac.uk The National Centre for Text Mining (NaCTeM) is the first publicly-funded text mining centre in the world. We provide text mining services in response to the requirements of the UK academic community. NaCTeM is operated by the University of Manchester with close collaboration with the University of Tokyo....

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Network-member BioSemantics

Unique name: biosemantics
Created: Thursday 30 June 2011 13:06:48 (UTC)

Group for members of the BioSemantics group and their close collaborators.BiosemanticsWith the explosion of information in the biomolecular field, there is a dire need for information technology that assists in retrieving, extracting, and relating information and knowledge in the biomedical literature and databases. Biosemantics researchers and developers develop, evaluate, and apply such techn...

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Packs (8)
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Pack Pathway to Phenotype using Text Mining


Created: 2009-08-10 13:01:47 | Last updated: 2009-08-11 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

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Pack Core text mining workflows


Created: 2010-02-19 10:12:33 | Last updated: 2011-12-13 16:03:17

This pack contains workflows we have created to support core text mining tasks. We currently provide workflows to do these tasks Loading documents (text or PDF) PDF to text conversion Sentence splitting Text cleaning (ASCII or XML-valid) Term recognition (using NaCTeM service TerMine)  

7 items in this pack

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Pack Text Mining Workflows


Created: 2010-12-08 11:55:03 | Last updated: 2011-02-01 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

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Pack Trichuriasis induced Colitis


Created: 2011-02-16 12:49:21 | Last updated: 2011-02-16 15:26:36

This pack contains the workflows and data relating to Trichuriasis induced colitis.

5 items in this pack

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Pack Creating a focused corpus of factual outcomes from b...


Created: 2011-06-28 11:19:04 | Last updated: 2011-12-13 16:02:16

 This pack contains resources and supplementary files for the submission to the MIND2011 workshop titled "Creating a focused corpus of factual outcomes from biomedical experiments" by James Eales, George Demetriou and Robert Stevens

1 item in this pack

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Pack Concept profile analysis using Anni Web services


Created: 2013-02-06 19:11:26 | Last updated: 2014-07-15 08:17:33

Concept profile analysis is a knowledge discovery method that proved successful in generating hypotheses about molecular mechanisms explaining the results from genotype-phenotype studies. This technology has been implemented in the Anni standalone application (http://biosemantics.org/anni). This pack contains a number of workflows that can be used together to configure and run typical user pipelines from Anni through the Anni Web services (http://www.biocatalogue.org/services/3559).

11 items in this pack

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Pack HD data interpretation


Created: 2013-09-02 13:18:22 | Last updated: 2015-04-03 21:14:41

This workflow pack, was created in order to further analyse and interpret the results from workflow pack 485 (HD chromatin analysis). The workflows in this pack are using the anni web services, implemented by the Biosemantics group. 

6 items in this pack

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Pack Genotype-phenotype knowledge discovery using the Con...


Created: 2015-04-07 18:38:40 | Last updated: 2015-04-07 18:44:49

This pack compiles workflows and workflow results for the generation of literature-generated fingerprints of human phenotypes.

5 items in this pack

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Workflows (40)

Workflow GeneIlluminator_Disambiguate (2)

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Example workflow demonstrating how to use GeneIlluminator_Disambiguate, a synchronous BioMOBY service for gene symbol disambiguation. If a gene symbol is ambiguous this service provides GI_Clusters describing which different genes, sharing the same symbol, exist in different parts of the tree of life. Provides also gene symbol aliases associated to the input gene symbol. (This is the same output as the one from the GeneIlluminator_GetClusters service.) In addition this service takes an Organi...

Created: 2008-02-27 | Last updated: 2008-03-03

Credits: User Pieter Neerincx User Alako

Workflow GeneIlluminator_GetClusters (2)

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Example workflow demonstrating how to use GeneIlluminator_GetClusters, a synchronous BioMOBY service for gene symbol disambiguation. If a gene symbol is ambiguous this service provides GI_Clusters describing which different genes, sharing the same symbol, exist in different parts of the tree of life. Provides also gene symbol aliases associated to the input gene symbol. (Use GeneIlluminator_GetGraph for a graphical representation of the clusters or GeneIlluminator_Disambiguate to get the mos...

Created: 2008-02-27 | Last updated: 2008-03-03

Credits: User Pieter Neerincx User Alako

Workflow GeneIlluminator_GetGraph (2)

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Example workflow demonstrating how to use GeneIlluminator_GetGraph, 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, a graphical overview of the clusters and gene symbols is created in SVG format and returned to ...

Created: 2008-02-27 | Last updated: 2008-03-03

Credits: User Pieter Neerincx User Alako

Workflow GeneIlluminator_GetPubMedQuery (2)

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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...

Created: 2008-02-27 | Last updated: 2008-03-03

Credits: User Pieter Neerincx User Alako

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Workflow Termine Webservice (1)

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Termine is a service provided by the National Centre for Text Mining (NaCTeM) to assist in the discovery of terms in text. More information on the Termine service can be found here. This workflow represents the simplest method of using Termine. The input represents a text string with the output being an string containing a representation of the list of terms, with their C-Value scores (representing significance in the text), in a simple xml format. Other variations of this tools will be adde...

Created: 2008-05-19 | Last updated: 2008-05-19

Credits: User Brian Rea Network-member National Centre for Text Mining (NaCTeM)

Workflow EBI_Whatizit (1)

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Perform a text-mining analysis of an input text document using the EBI's Whatizit tool (http://www.ebi.ac.uk/webservices/whatizit/info.jsf). Whatizit provides a number of text-mining pipelines which can can detect various terms of biological interest in text documents. For example finding gene names and mapping them to UniProtKB identifiers, finding chemical terms and mapping them to ChEBI, etc.

Created: 2008-07-09

Credits: User Hamish McWilliam

Workflow Cosine vector space (1)

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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.

Created: 2009-08-10 | Last updated: 2009-08-10

Credits: User Paul Fisher

Workflow Extract Scientific Terms (1)

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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.

Created: 2009-08-10 | Last updated: 2009-08-10

Credits: User Paul Fisher

Workflow Rank Phenotype Terms (1)

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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 ...

Created: 2009-08-10

Credits: User Paul Fisher

Workflow dreseden-term-extraction1 (1)

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No description

Created: 2007-11-22

Credits: User Simon Jupp

Workflow Clean plain text (ASCII) (1)

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This workflow will remove any XML-invalid and non-ASCII characters (e.g. for sending to the ASCII-only Termine service) from any text supplied to the input port. This is a workflow component, designed to be used as a nested workflow inside a larger text mining or text processing workflow.

Created: 2010-02-18 | Last updated: 2011-12-13

Credits: User James Eales

Workflow Clean plain text (1)

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This workflow will remove any XML-invalid characters (these characters often appear in the output of PDF to text software) from any text supplied to the input port. This is a workflow component, designed to be used as a nested workflow inside a larger text mining or text processing workflow.  

Created: 2010-02-18 | Last updated: 2011-12-13

Credits: User James Eales

Workflow Load plain text from directory (1)

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This workflow will automate the reading of a set of text files stored in a single directory (the path to which should be supplied as a single input value).  It will assume that the text files are saved using the default character encoding for the system that Taverna is running on.  This is a workflow component, designed to be used as a nested workflow inside a larger text mining or text processing workflow.  

Created: 2010-02-18 | Last updated: 2011-12-13

Credits: User James Eales

Workflow Load PDF from directory (1)

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This workflow will automate the reading of a set of PDF files stored in a single directory (the path to which should be supplied as a single input value). This is a workflow component, designed to be used as a nested workflow inside a larger text mining or text processing workflow.  

Created: 2010-02-19 | Last updated: 2011-12-13

Credits: User James Eales

Workflow PDF to plain text (1)

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This workflow will extract the plain text content of PDF files supplied to the input port.  You can connect the Load PDF from directory workflow to this workflows input. We recommend you send the output from this workflow to the Clean plain text workflow, because the PDF to text process can add characters into the text that are XML-invalid and therefore can not be sent to most services as plain text.  Another way round this problem is to encode the text as Base64 using the handy loc...

Created: 2010-02-19 | Last updated: 2011-12-13

Credits: User James Eales

Workflow Sentence splitting (1)

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This workflow will attempt to split up text into sentences, returning a list of sentences to the output port.  The sentence splitting service makes use of the OpenNLP sentence detector and has been trained to work on english text. This workflow can be used to provide input to the Termine with c-value threshold workflow. This is a workflow component, designed to be used as a nested workflow inside a larger text mining or text processing workflow.

Created: 2010-02-19 | Last updated: 2011-12-13

Credits: User James Eales

Workflow Termine with c-value threshold (1)

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This workflow accepts a list of sentences from a single document and returns the terms found by the TerMine web service. It also allows you to set a threshold c-value score so that only terms with a user-controlled probability (of being a real term) are returned as an output.   To get sentences to supply to this workflow you can use the sentence splitting workflow.  The TerMine service (used in this workflow) only accepts text in ASCII encoding, so you should also use the Clean p...

Created: 2010-02-19 | Last updated: 2011-12-13

Credits: User James Eales

Workflow Terms from collection of PDF files (2)

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This workflow will give you a set of candidate terms for each PDF document in a user-specified directory. You can also specify a c-value threshold that will restrict the terms to those with higher scores. This workflow was created using only nested workflows.  These workflow components work on their own and can be linked together to form more complex workflows such as this. You can view the text mining workflow components in this pack. If you receive errors when running this workflow t...

Created: 2010-02-19 | Last updated: 2011-12-13

Credits: User James Eales

Workflow Terms from collection of text files (1)

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This workflow will give you a set of candidate terms for each text file in a user-specified directory. You can also specify a c-value threshold that will restrict the terms to those with higher scores. This workflow was created using only nested workflows.  These workflow components work on their own and can be linked together to form more complex workflows such as this. You can view the text mining workflow components in this pack. If you receive errors when running this workflow then...

Created: 2010-02-22 | Last updated: 2011-12-13

Credits: User James Eales

Workflow microRNA to KEGG Pathways and Abstracts (1)

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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

Created: 2010-03-17

Credits: User Paul Fisher

Attributions: Workflow Pathways and Gene annotations for QTL region

Workflow Gene to Pubmed (3)

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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.

Created: 2010-07-05 | Last updated: 2011-01-26

Credits: User Paul Fisher

Workflow Phenotype to pubmed (3)

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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

Created: 2010-07-05 | Last updated: 2011-01-11

Credits: User Paul Fisher

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Workflow Connect to twitter and analyze the key words (1)

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Hi All, This workflow connects RapidMiner to Twitter and downloads the timeline. It then creates a wordlist from the tweets and breaks them into key words that are mentioned in the tweets. You can then visualize the key words mentioned in the tweets. This workflow can be further modified to review various key events that have been talked about in the twitterland. Do let me know your feedback and feel free to ask me any questions that you may have. Shaily web: http://advanced-analyti...

Created: 2010-07-26 | Last updated: 2010-07-26

Workflow Cosine vector space (2)

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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. this is some extra text vbeing added

Created: 2010-12-08 | Last updated: 2011-01-11

Credits: User Paul Fisher

Attributions: Workflow Cosine vector space

Workflow Rank Phenotype Terms (2)

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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 ...

Created: 2010-12-08 | Last updated: 2011-01-11

Credits: User Paul Fisher

Attributions: Workflow Rank Phenotype Terms

Workflow Pathway to Pubmed (2)

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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.

Created: 2010-12-08 | Last updated: 2011-01-11

Credits: User Paul Fisher

Workflow Rank Phenotype Terms (1)

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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 ...

Created: 2011-02-01 | Last updated: 2011-02-01

Credits: User Paul Fisher

Attributions: Workflow Cosine vector space Workflow Rank Phenotype Terms

Workflow Gene to Pubmed (4)

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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.

Created: 2011-02-08 | Last updated: 2011-02-10

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 Pathway and Gene to Pubmed (2)

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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...

Created: 2011-02-10 | Last updated: 2011-02-18

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

Workflow Content based recommender (1)

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This process is a special case of the item to item similarity matrix based recommender where the item to item similarity is calculated as cosine similarity over TF-IDF word vectors obtained from the textual analysis over all the available textual data. The inputs to the process are context defined macros: %{id} defines an item ID for which we would like to obtain recommendation and %{recommender_no} defines the required number of recommendations. The process internally uses an example set of...

Created: 2011-03-15 | Last updated: 2011-03-15

Workflow Content based recommender system template (1)

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As an input, this workflow takes two distinct example sets: a complete set of items with IDs and appropriate textual attributes (item example set) and a set of IDs of items our user had interaction with (user example set). Also, a macro %{recommendation_no} is defined in the process context, as a required number of outputted recommendations. The first steps of the workflow are to preprocess those example sets; select only textual attributes of item example set, and set ID roles on both of th...

Created: 2011-05-05 | Last updated: 2011-05-09

Credits: User Matko Bošnjak User Ninoaf

Attributions: Blob Datasets for the pack: RCOMM2011 recommender systems workflow templates

Workflow One sentence per line (1)

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This workflow accepts a plain text input and provides a single text document per input containing one sentence per line.  Newline characters are removed from the original input. The OpenNLP sentence splitter is used to split the text, this is provided by University of Manchester Web Services.

Created: 2011-05-06 | Last updated: 2011-12-13

Credits: User James Eales

Workflow Extract chemical structures from a Beilste... (1)

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 Uses the Oscar4 text mining tool to extract chemical structures from a Beilstein Journal of Organic Chemistry paper and visualizes them in the molecules table. Jericho is used to extract text from the paper's HTML page.

Created: 2011-05-12 | Last updated: 2011-05-12

Credits: User Egon Willighagen

Workflow Match concept profiles (6)

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Purpose of workflow: The workflow can be used to match a set of concept profiles with another set of concept profiles. Result: A list of concepts ordered by their match to the query concept profiles.

Created: 2011-12-02 | Last updated: 2014-07-14

Credits: User Marco Roos User Kristina Hettne User Martijn Schuemie User Reinout van Schouwen

Workflow Annotate a gene list with disease concepts (1)

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Purpose: Currently, this workflow takes a list of genes and a concept set as input, calculates the matching score between these and finds the concept that contributes the most to the match. Author comments: The workflow is in Beta stage. It runs, but needs more testing with different parameter settings. This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/368 for functional gene annotation and knowledge discovery.

Created: 2013-02-06

Credits: User Kristina Hettne User Reinout van Schouwen User Marco Roos Network-member BioSemantics

Attributions: Workflow SNPs to Concept Set through Concept Profile Matching v2

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Workflow Get concept suggestions from term (1)

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This workflow suggests concept ids that match the query term. The user can run this workflow with any term of interest as for example "human", "htt", "Transcription" etc, and will get suggestions for concept ids together with descriptions. Then can choose the concept id that matches the best to her/his needs and use it to the rest of the CPA workflows.

Created: 2013-08-31

Credits: User Eleni Network-member BioSemantics

Workflow Match concept to HPO profiles (1)

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This workflow matches a query concept to the list of Human Phenotypes. The Human Phenotypes are the subset of the Human Phenotype Ontology for which we have a mapped UMLS concept available and a concept profile. HPO-UMLS mapping: Winnenburg, R., & Bodenreider, O. (2014). Coverage of Phenotypes in Standard Terminologies. In Proceedings of the ISMB’2014 SIG meeting “BioLINK.” Retrieved from http://phenoday2014.bio-lark.org/pdf/5.pdf Concept Profile Database: July 2012

Created: 2014-10-20

Credits: User Marco Roos Network-member BioSemantics

Attributions: Workflow Match concept profiles Workflow Get concept information

Workflow Get concept suggestions from term (1)

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This workflow suggests concept ids that match the query term. The user can run this workflow with any term of interest as for example "human", "htt", "Transcription" etc, and will get suggestions for concept ids together with descriptions. Then can choose the concept id that matches the best to her/his needs and use it to the rest of the CPA workflows.

Created: 2015-02-18

Credits: User Eelke van der Horst User Kristina Hettne User Marco Roos User Eleni

Attributions: Workflow Get concept suggestions from term

Workflow Prioritize gene list for the Cure game (1)

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This workflow prioritizes a gene list according to its association with the 'concept_id'. Here we are prioritizing a gene list against breast cancer, in order to try to beat Barney in the game The Cure (http://genegames.org/cure/). Note: Before running this workflow the gene names supplied in the game first needs to be mapped to Entrez gene identifiers. This can be done using either this workflow http://www.myexperiment.org/workflows/3722 or a by performing a search in the NCBI Entrez gene d...

Created: 2015-04-29

Credits: User Kristina Hettne User Eleni

Attributions: Workflow Prioritize gene list

Workflow Author to Wordcloud (3)

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This small workflow demonstrates how to connect to and use Europe PMC (http://europepmc.org/RestfulWebService). The workflow searches the publications of an author, extracts the abstracts, counts the word frequencies and plot a wordcloud using the R package of the same name. The Rshell plot_wordcloud also applies text mining operations (transformation to lower case, removing punctuation, stripping whitespace and removing English stopwords) using the R package tm.

Created: 2015-12-02 | Last updated: 2015-12-07

Credits: User Magnus Palmblad

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Linked Data

Non-Information Resource URI: http://www.myexperiment.org/tags/498


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