Group: AID

Original Uploader

Marco Roos

ProteinSynonymsToQuery (v2)

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

Credits: Marco Roos Martijn Schuemie AID

License: Creative Commons Attribution-Share Alike 3.0 License

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: 851 times | Downloaded: 765 times

Original Uploader

Marco Roos

BioAID_ProteinToDiseases (v1)

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

Credits: Marco Roos Martijn Schuemie AID

Attributions: BioAID_DiseaseDiscovery

License: Creative Commons Attribution-Share Alike 3.0 License

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: 1. A user query: a single protein name 2. Add synonyms (service courtesy of Martijn Scheumie, Erasmus University Rotterdam) 3. Retrieve documents: finds relevant documents (abstract+title) based on query 4. Discover proteins: extract proteins discovered in the set of relevant abstracts 5. Link pr...

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Viewed: 728 times | Downloaded: 804 times

Original Uploader

Marco Roos

BioAID_protein_discovery (v1)

Created: 14/11/07 @ 12:46:33 | Last updated: 15/11/07 @ 09:01:13

Credits: Marco Roos AID

License: Creative Commons Attribution-Share Alike 3.0 License

This workflow finds proteins 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 2. Retrieve documents: finds relevant documents (abstract+title) based on query (edit maxHits to change the default maximum number of documents returned) 3. Discover proteins: extract proteins discovered in the set of relevant abstracts. Servic...

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Viewed: 629 times | Downloaded: 686 times

Original Uploader

Marco Roos

BioAID_DiseaseDiscovery (v1)

Created: 12/11/07 @ 22:39:04 | Last updated: 21/10/08 @ 10:44:19

Credits: Marco Roos AID

License: Creative Commons Attribution-Share Alike 3.0 License

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) 2. Retrieve documents: finds relevant documents (abstract+title) based on query (edit maxHits to change the default maximum number of documents returned; the AIDA service inside is based on Apache Lucene) 3. Discover proteins: extract...

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

Viewed: 3360 times | Downloaded: 1301 times

Original Uploader

Marco Roos

DiscoverProteinLink (v2)

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

Credits: Marco Roos AID

License: Creative Commons Attribution-Share Alike 3.0 License

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 ...

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Viewed: 929 times | Downloaded: 812 times

Original Uploader

Marco Roos

Discover_proteins_from_text (v2)

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

Credits: Marco Roos AID

License: Creative Commons Attribution-Share Alike 3.0 License

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.

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Viewed: 858 times | Downloaded: 758 times

Original Uploader

Marco Roos

BioAID_Discover_proteins_from_text_plus_synonyms (v1)

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

Credits: Marco Roos Martijn Schuemie AID

License: Creative Commons Attribution-Share Alike 3.0 License

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.

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Original Uploader

Marco Roos

BioAID_DiseaseDiscovery_count (v3)

Created: 22/11/07 @ 12:09:20 | Last updated: 05/12/07 @ 23:09:13

Credits: Marco Roos AID

Attributions: BioAID_DiseaseDiscovery

License: Creative Commons Attribution-Share Alike 3.0 License

This adds counting to BioAID_DiseaseDiscovery, which allows you to check the results more properly. A major issue is that some false positives among the discovered proteins may have a disproportionate effect on the number of diseases found. We therefore advice to use 'BioAID_DiseaseDiscovery_byHumanUniprot' if you main interest is human proteins and diseases. This workflow finds disease relevant to the query string via the following steps: 1. A user query: a list of terms or boolean query - ...

Rating: 5.0 / 5 (1 rating) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 1117 times | Downloaded: 885 times

Original Uploader

Marco Roos

BioAID_DiseaseDiscovery_byHumanUniprot (v3)

Created: 05/12/07 @ 23:11:44 | Last updated: 15/05/08 @ 21:10:32

Credits: Marco Roos Martijn Schuemie AID

License: Creative Commons Attribution-Share Alike 3.0 License

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 Apache's Luce...

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

Viewed: 1001 times | Downloaded: 932 times

Original Uploader

Marco Roos

BioAID_ProteinDiscovery_filterOnHumanUniprot_perDoc_html (v8)

Created: 29/02/08 @ 01:34:47 | Last updated: 29/10/08 @ 09:29:36

Credits: Marco Roos Martijn Schuemie AID AID_myGrid_collaboration

Attributions: BioAID_DiseaseDiscovery

License: Creative Commons Attribution-Share Alike 3.0 License

This workflow finds proteins relevant to the query string via the following steps: 1. A user query: a single gene/protein name. E.g.: (EZH2 OR "Enhancer of Zeste"). 2. Retrieve documents: finds 'maximumNumberOfHits' relevant documents (abstract+title) based on query (the AIDA service inside is based on Apache's Lucene) 3. Discover proteins: extract proteins discovered in the set of relevant abstracts with a 'named entity recognizer' trained on genomic terms using a Bayesian approach...

Rating: 0.0 / 5 (0 ratings) | Versions: 8 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 1129 times | Downloaded: 878 times

Uploader:

Marco Roos

From biologist to web service to Taverna to myExperiment to biologist

Created: 21/03/08 @ 19:00:24 | Last updated: 23/03/08 @ 10:39:27

Credits: Marco Roos Martijn Schuemie AID myGrid

Attributions: BioAID_DiseaseDiscovery_byHumanUniprot

License: Creative Commons Attribution-Share Alike 3.0 License

File type: video/x-msvideo

Rating: 1.0 / 5 (1 rating) | Comments: 0 | Viewed: 480 times | Downloaded: 393 times

Creator:

Marco Roos

AIDA toolbox

Created: 01/08/08 @ 11:33:03 | Last updated: 01/08/08 @ 11:54:45

8 items in this pack

Comments: 0 | Viewed: 248 times |

Uploader:

Marco Roos

From biologist to web service to Taverna to myExperiment to biologist

Created: 21/03/08 @ 19:00:24 | Last updated: 23/03/08 @ 10:39:27

Credits: Marco Roos Martijn Schuemie AID myGrid

Attributions: BioAID_DiseaseDiscovery_byHumanUniprot

License: Creative Commons Attribution-Share Alike 3.0 License

File type: video/x-msvideo

Rating: 1.0 / 5 (1 rating) | Comments: 0 | Viewed: 480 times | Downloaded: 393 times

Original Uploader

Marco Roos

BioAID_ProteinDiscovery_filterOnHumanUniprot_perDoc_html (v8)

Created: 29/02/08 @ 01:34:47 | Last updated: 29/10/08 @ 09:29:36

Credits: Marco Roos Martijn Schuemie AID AID_myGrid_collaboration

Attributions: BioAID_DiseaseDiscovery

License: Creative Commons Attribution-Share Alike 3.0 License

This workflow finds proteins relevant to the query string via the following steps: 1. A user query: a single gene/protein name. E.g.: (EZH2 OR "Enhancer of Zeste"). 2. Retrieve documents: finds 'maximumNumberOfHits' relevant documents (abstract+title) based on query (the AIDA service inside is based on Apache's Lucene) 3. Discover proteins: extract proteins discovered in the set of relevant abstracts with a 'named entity recognizer' trained on genomic terms using a Bayesian approach...

Rating: 0.0 / 5 (0 ratings) | Versions: 8 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 1129 times | Downloaded: 878 times

Original Uploader

Marco Roos

BioAID_DiseaseDiscovery_byHumanUniprot (v3)

Created: 05/12/07 @ 23:11:44 | Last updated: 15/05/08 @ 21:10:32

Credits: Marco Roos Martijn Schuemie AID

License: Creative Commons Attribution-Share Alike 3.0 License

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 Apache's Luce...

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

Viewed: 1001 times | Downloaded: 932 times

Original Uploader

Marco Roos

Demo_DiseaseDiscovery_byHumanUniprot_scaffold (v1)

Created: 10/12/07 @ 23:10:00

Credits: Marco Roos AID

License: Creative Commons Attribution-Share Alike 3.0 License

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 Apache's Luce...

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

Viewed: 555 times | Downloaded: 491 times

Original Uploader

Marco Roos

Retrieve_documents_MR1 (v1)

Created: 10/12/07 @ 22:17:00

Credits: Marco Roos Edgar AID

License: Creative Commons Attribution-Share Alike 3.0 License

This workflow applies the search web service from the AIDA toolbox. Comments: This search service is based on lucene defaults; it may be necessary to optimize the querystring to adopt the behaviour to what is most relevant in a particular domain (e.g. for medline prioritizing based on publication date is useful). Lucene favours shorter sentences, which may be bad for subsequent information extraction.

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Viewed: 536 times | Downloaded: 497 times

Original Uploader

Marco Roos

Retrieve_bio_documents (v2)

Created: 10/12/07 @ 22:15:54 | Last updated: 10/12/07 @ 22:45:49

Credits: Marco Roos Edgar AID

License: Creative Commons Attribution-Share Alike 3.0 License

This workflow retrieves relevant documents, based on a query optimized by adding a string to the original query that will rank the search output according to the most recent years. The added string adds years with priorities (most recent is highest); it starts at 2007.

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

Viewed: 733 times | Downloaded: 599 times

Original Uploader

Marco Roos

Lucene_bioquery_optimizer_MR1 (v1)

Created: 10/12/07 @ 22:14:26

Credits: Marco Roos AID

License: Creative Commons Attribution-Share Alike 3.0 License

This workflow does four things: 1. it retrieves documents relevant for the query string 2. it discovers entities in those documents, these are considered relevant entities 3. it filters proteins from those entities (on the tag protein_molecule) 4. it removes all terms from the list produced by 3 (query terms temporarily considered proteins) ToDo * Replace step 4 by the following procedure: 1. remove the query terms from the output of NER (probably by a regexp matching on what is inside the...

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Viewed: 580 times | Downloaded: 474 times

Original Uploader

Marco Roos

Link_protein_to_OMIM_disease (v1)

Created: 10/12/07 @ 22:13:35

Credits: Marco Roos AID

License: Creative Commons Attribution-Share Alike 3.0 License

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

Viewed: 623 times | Downloaded: 536 times

Original Uploader

Marco Roos