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Items tagged with "text_mining" (19)

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Groups (2)
Owner

Network-member Semantic_BioAID_collaboration


Created: Friday 22 August 2008 @ 10:49:27 (GMT)

Group for collaboration of Andy, Scott, and Marco.

5 shared items   |   1 announcements

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Owner

Network-member BioSemantics Privileged Users @ Human Gene...

Unique name: LeidenBioSemanticsUsers
Created: Wednesday 23 September 2009 @ 01:10:24 (GMT)

Group of colleagues at the Human Genetics Department of the Leiden University Medical Centre and closely collaborating groups who are interested to be prime users of new developments in BioSemantics and e-Science, and in return are willing to provide feedback and suggestions. See http://biosemantics.org for more information about the BioSemantics collaboration in the Netherlands.

12 shared items   |   1 announcements

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Workflows (14)
Original Uploader

Workflow DiscoverProteinLink (2)

Created: 03/10/07 @ 18:36:12 | Last updated: 15/11/07 @ 09:02:44

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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COMPETITION: For friends only: If you find any two topics that return true positives with this workflow I will buy you a bottle of wine (or equivalent). Terms: if we confirm that the protein was indeed never mentioned together with both input topics in one article, we will publish this together. ---- This workflow implements Swanson's prinicple with services from the AIDA toolbox. It tries to find proteins that link two topics, while they never mentioned together with both topics in ...

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

Viewed: 303 times | Downloaded: 65 times

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Original Uploader

Workflow BioAID_DiseaseDiscovery_RatHumanMouseUnipr... (4)

Created: 15/12/08 @ 20:46:09 | Last updated: 11/08/11 @ 09:22:23

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow finds disease relevant to the query string via the following steps: 1. A user query: a list of terms or boolean query - look at the Apache Lucene project for all details. E.g.: (EZH2 OR "Enhancer of Zeste" +(mutation chromatin) -clinical); consider adding 'ProteinSynonymsToQuery' in front of the input if your query is a protein. 2. Retrieve documents: finds 'maximumNumberOfHits' relevant documents (abstract+title) based on query (the AIDA service inside is based on Apa...

Rating: 4.0 / 5 (2 ratings) | Versions: 4 | Reviews: 0 | Comments: 3 | Citations: 0

Viewed: 4266 times | Downloaded: 664 times

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Original Uploader

Workflow ProteinSynonymsToQuery (2)

Created: 03/10/07 @ 18:36:10 | Last updated: 13/11/07 @ 23:47:41

Credits: User Marco Roos User Martijn Schuemie Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow uses Martijn Schuemie's protein synonym service to produce synonyms and a new query string from the input query term. The service is limited to proteins, enzymes and genes. An input query that is a boolean string will be split and processed, but the boolean logic of the input query will be lost. Workflow URL: http://rdf.adaptivedisclosure.org/~marco/BioAID/Public/Workflows/BioAID/ProteinSynonymsToQuery.xml

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

Viewed: 175 times | Downloaded: 72 times

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Original Uploader

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

Viewed: 389 times | Downloaded: 144 times

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Original Uploader

Workflow BioAID_ProteinToDiseases (1)

Created: 14/11/07 @ 12:47:57 | Last updated: 15/11/07 @ 09:00:44

Credits: User Marco Roos User Martijn Schuemie Network-member AID

Attributions: Workflow BioAID_DiseaseDiscovery_RatHumanMouseUniprotFilter

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow was based on BioAID_DiseaseDiscovery, changes: expects only one protein name, adds protein synonyms). This workflow finds diseases relevant to the query string via the following steps: A user query: a single protein name Add synonyms (service courtesy of Martijn Scheumie, Erasmus University Rotterdam) Retrieve documents: finds relevant documents (abstract+title) based on query Discover proteins: extract proteins discovered in the set of relevant abstracts 5. Link proteins ...

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

Viewed: 197 times | Downloaded: 94 times

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Original Uploader

Workflow Discover_proteins_from_text (2)

Created: 15/11/07 @ 08:58:00 | Last updated: 15/11/07 @ 09:12:34

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow discovers proteins from plain text. It is built around the AIDA 'Named Entity Recognize' web service by Sophia Katrenko (service based on LingPipe), from which output it filters out proteins. The Named Recognizer services uses the pre-learned genomics model, named 'MedLine', to find genomics concepts in plain text.

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

Viewed: 194 times | Downloaded: 71 times

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Original Uploader

Workflow BioAID_Discover_proteins_from_text_plus_sy... (1)

Created: 15/11/07 @ 09:40:24

Credits: User Marco Roos User Martijn Schuemie Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow discovers proteins from plain text and adds synonyms using Martijn Schuemie's proteins synonym service. Proteins are discovered with the AIDA 'Named Entity Recognize' web service by Sophia Katrenko (service based on LingPipe), from which output it filters out proteins. The Named Recognizer services uses the pre-learned genomics model, named 'MedLine', to find genomics concepts in plain text.

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

Viewed: 97 times | Downloaded: 2 times

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Original Uploader

Workflow BioAID_ProteinDiscovery_filterOnHumanUnipr... (11)

Created: 28/05/09 @ 12:21:05

Credits: User Marco Roos User Martijn Schuemie Network-member AID Network-member AID_myGrid_collaboration

Attributions: Workflow BioAID_DiseaseDiscovery_RatHumanMouseUniprotFilter

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow finds proteins relevant to the query string via the following steps: A user query: a single gene/protein name. E.g.: (EZH2 OR "Enhancer of Zeste"). Retrieve documents: finds 'maximumNumberOfHits' relevant documents (abstract+title) based on query (the AIDA service inside is based on Apache's Lucene) Discover proteins: extract proteins discovered in the set of relevant abstracts with a 'named entity recognizer' trained on genomic terms using a Bayesian approach; the AIDA serv...

Rating: 0.0 / 5 (0 ratings) | Versions: 11 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 471 times | Downloaded: 173 times

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Original Uploader

Workflow EBI_Whatizit (1)

Created: 09/07/08 @ 05:14:28

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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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.

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

Viewed: 185 times | Downloaded: 63 times

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Original Uploader

Workflow BioAID_EnirchBioModelWithProteinsFromText (7)

Created: 16/05/09 @ 01:06:26 | Last updated: 16/05/09 @ 01:13:18

Credits: User Marco Roos User Sophia katrenko User Andrew Gibson User M. Scott Marshall User Willem van Hage User Edgar User Martijn Schuemie Network-member AID

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

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This workflow is for demonstration purposes only. Please contact the authors if you wish to try it. We will gladly collaborate with you. Summary This workflow extracts proteins and protein relations from Medline. Extracted protein names (symbols of at least 3 characters) are validated against mouse, rat, and human UniProt symbols, so the results are limited to these species. This workflow follows the following basic steps: it retrieves documents relevant for the query string i...

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

Viewed: 163 times | Downloaded: 38 times

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Original Uploader

Workflow Text search within sparql point (1)

Created: 19/01/09 @ 16:37:53

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow make possible full text search within different sparql point made available by the Bio2RDF project.

Rating: 1.0 / 5 (1 rating) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 111 times | Downloaded: 49 times

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Original Uploader

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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Original Uploader

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

Viewed: 320 times | Downloaded: 80 times

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Original Uploader

Workflow Gene expression interpretation by the Glob... (1)

Created: 26/04/11 @ 08:31:51 | Last updated: 26/04/11 @ 08:31:52

Credits: User Marco Roos

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 42 times | Downloaded: 0 times

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Packs (3)
Creator

Pack AIDA toolbox


Created: 01/08/08 @ 11:33:03 | Last updated: 14/02/10 @ 16:04:25

Adaptive Information Disclosure Application toolbox: AIDA web services for automated knowledge extraction and knowledge management Documentation    

9 items in this pack

Comments: 0 | Viewed: 182 times | Downloaded: 23 times

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Creator

Pack AIDA demo pack


Created: 14/12/08 @ 21:35:43 | Last updated: 01/05/09 @ 17:35:26

 Pack with AIDA demo material

2 items in this pack

Comments: 0 | Viewed: 123 times | Downloaded: 0 times

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Pack Supporting material for Roos et al., BMC Bioinformat...


Created: 15/05/09 @ 15:45:32 | Last updated: 11/08/11 @ 10:01:23

Supporting material for BMC Bioinformatics, supplement for Semantic Web Applications and Tools for Life Science (2009) Structuring and extracting knowledge for the support of hypothesis generation in molecular biology Marco Roos, M. Scott Marshall, Andrew P. Gibson, Martijn Schuemie, Edgar Meij, Sophia Katrenko, Willem Robert van Hage, Konstantinos Krommydas, Pieter W. Adriaans Acknowledgements We thank the myGrid team and OMII-UK for their support in applying their e-Science tools, and M...

2 items in this pack

Comments: 0 | Viewed: 42 times | Downloaded: 18 times

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