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Marco Roos

User: Marco Roos

Name: Marco Roos

Joined: Saturday 21 July 2007 @ 10:43:23 (BST)

Last seen: Saturday 13 March 2010 @ 15:59:16 (GMT)

Email (public): roos [at] science.uva.nl

Website: http://home.medewerker.uva.nl/m.roos1

Location: Amsterdam, Netherlands

54 Friends

14 Groups (admin)

13 Groups (member)

2 Blogs

9 Packs

3 Files

26 Workflows

0 Favourites

Marco Roos has been credited 29 times

Marco Roos has an average rating of:

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My role as a biologist and bioinformatician in e-science is to help increase the usefulness of emerging information technologies for biology, while experimenting with new ways to increase insight into mechanisms related to structure and function of DNA in the cell. I experiment with technologies such as workflow, knowledge extraction from text, semantic web and virtual research environments such as myExperiment.

More information on the blog below (originally uploaded as an example for the 'NBIC on workflows' workshop in Lunteren, the Netherlands, March 2008).

http://www.myexperiment.org/blogs/15

Other contact details:

If for some reason I am not available, please contact my colleague Scott Marshall (marshall@science.uva.nl)

Interests:

Structure/function relationship of DNA in the cell, e-science, automated support for modeling biological mechanisms by knowledge extraction and semantic web technology.

Field/Industry: Biology

Occupation/Role(s): Post-doc, e-(bio)scientist (biology 'power-user'), PAL for OMII-UK, BioAssist core group member

Organisation(s):

University of Amsterdam
NBIC
OMII-UK

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Taverna 1

Original Uploader

Marco Roos

BioAID_EnirchBioModelWithProteinsFromText (v7)

Created: 22/08/08 @ 11:00:51 | Last updated: 16/05/09 @ 01:13:19

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

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

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

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Taverna 1

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Marco Roos

BioAID_ProteinDiscovery_filterOnHumanUniprot_perDoc_html (v11)

Created: 29/02/08 @ 01:34:47 | Last updated: 28/05/09 @ 12:21:06

Credits: Marco Roos Martijn Schuemie AID AID_myGrid_collaboration

Attributions: BioAID_DiseaseDiscovery

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

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Taverna 1

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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 Unported License

This workflow finds disease relevant to the query string via the following steps: 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. Retrieve documents: finds 'maximumNumberOfHits' relevant documents (abstract+title) based on query (the AIDA service inside is based on Apache's Lucene)...

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Taverna 1

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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 Unported 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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Taverna 1

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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 Unported 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

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Taverna 1

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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 Unported License

This workflow does four things: it retrieves documents relevant for the query string it discovers entities in those documents, these are considered relevant entities it filters proteins from those entities (on the tag protein_molecule) 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 tag, ...

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Taverna 1

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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 Unported License

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Taverna 1

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Marco Roos

Flatten_and_make_unique (v1)

Created: 10/12/07 @ 22:12:01

Credits: Marco Roos AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Taverna 1

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Marco Roos

Extract_proteins (v2)

Created: 10/12/07 @ 22:10:51 | Last updated: 10/12/07 @ 22:30:53

Credits: Marco Roos

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow filters protein_molecule-labeled terms from an input string(list). The result is a tagged list of proteins (disregarding false positives in the input). Internal information: This workflow is a copy of 'filter_protein_molecule_MR3' used for the NBIC poster (now in Archive).

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Taverna 1

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Marco Roos

Discover_entities (v2)

Created: 10/12/07 @ 21:48:34 | Last updated: 10/12/07 @ 22:54:42

Credits: Marco Roos Sophia katrenko AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow contains the 'Named Entity Recognize' web service from the AIDA toolbox, created by Sophia Katrenko. It can be used to discover entities of a certain type (determined by 'learned_model') in documents provided in a lucene output format. Known issues: The output of NErecognize contains concepts with / characters, breaking the xml. For post-processing its results it is better to use string manipulation than xml manipulations. The output is per document, which means entities will ...

Rating: 5.0 / 5 (1 rating) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

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Taverna 1

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Marco Roos

TestIteratorStrategy_withCloning (v2)

Created: 29/11/07 @ 15:35:49 | Last updated: 29/11/07 @ 15:40:30

Credits: Marco Roos

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow implements a strategy for this problem: > I would like to perform an iteration including a dot product between > a list and a list of lists; example: > Input: > > [1] (1) > [A,B,C] (2) > [[a,b],[c,d],[e,f]] (3) > > Desired output: > > [1Aa, 1Ab, 1Bc, 1Bd, 1Ce, 1Cf] In this implementation a java beanshell is used to clone the items in list 2 as many times per item as there are items in the sublists of list 3. The iteration stra...

Rating: 5.0 / 5 (1 rating) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

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Taverna 1

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Marco Roos

CloneItemsInList (v1)

Created: 29/11/07 @ 15:34:53

Credits: Marco Roos

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Utility workflow that clones an item copy_number times. You can use this to work around standard iteration strategies, e.g. in combination with the CountListItems workflow. Workflow examples: TestIterationStrategy_withClones. For an alternative approach see TestIterationStrategy_withNesting. Example I/O: input: A copy_number: 3 result: [A,A,A] input: [A,B,C] copy_number: 3 result: [[A,A,A][B,B,B][C,C,C]] input: [A,B,C] copy_number: [3,2] result: [[[A,A,A],[A,A]][[B,B,B],[B,B]],[[C,C,C],...

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Taverna 1

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Marco Roos

TestIteratorStrategy_withNesting (v1)

Created: 29/11/07 @ 15:31:33

Credits: Marco Roos Tomoinn

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Implementation of the iteration workaround by Tom Oin conform the Q&A below. The nested workflow 'NestedProcessor' is called that to conform to Tom's explanation. For an alternative solution using a java beanshell to clone list items see 'TestIteratorStrategy_withCloning. This workflow implements the following Q&A: Marco Roos wrote: > Dear Taverna user, > > Issue 1: Complex iteration > > I would like to perform an iteration including a dot product between > a list and a list of li...

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Taverna 1

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TestIterator (v1)

Created: 28/11/07 @ 15:28:44

Credits: Marco Roos

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Workflow to experiment with list iteration strategies. Look at metadata of nested workflow 'Concatenate' to see the current iteration strategy.

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Taverna 1

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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 Unported 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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Taverna 1

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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 Unported 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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Taverna 1

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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 Unported 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: 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 ...

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Taverna 1

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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 Unported License

This workflow finds proteins relevant to the query string via the following steps: 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 Retrieve documents: finds relevant documents (abstract+title) based on query (edit maxHits to change the default maximum number of documents returned) Discover proteins: extract proteins discovered in the set of relevant abstracts. Services by...

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Taverna 1

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Marco Roos

BioAID_DiseaseDiscovery (v3)

Created: 12/11/07 @ 22:39:04 | Last updated: 15/12/08 @ 20:47:51

Credits: Marco Roos AID

License: Creative Commons Attribution-Share Alike 3.0 Unported 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 Apa...

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

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Taverna 1

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Marco Roos

CountListElements (v5)

Created: 17/10/07 @ 14:44:27 | Last updated: 17/10/07 @ 16:13:54

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

Very simple workflow to count the number of items in a list (top level only in case of nested lists). Does no more than count = list.size();

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Taverna 1

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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 Unported 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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Taverna 1

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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 Unported 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

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