pattaran - User contributions [en]

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==COLLABORATIVE: ABI Development: Methodology for Pattern Creation, Imprint Validation, and Discovery from the Annotated Biological Web (PattArAn)==

===Acknowledgement===

This project is funded by the National Science Foundation Biological Infrastructure [http://www.nsf.gov/div/index.jsp?div=DBI NSF DBI] program.

[http://nsf.gov/awardsearch/showAward.do?AwardNumber=1147144 UMD award] [http://nsf.gov/awardsearch/showAward.do?AwardNumber=1146256 U. Iowa award] [http://nsf.gov/awardsearch/showAward.do?AwardNumber=1146300 St. Bonaventure U award]

===Intellectual Merit===

The project will develop a methodology that exploits the wealth of annotation knowledge,
notably Gene Ontology (GO) and Plant Ontology (PO) annotations of Arabidopsis genes.

Motivated by the availability of rich and as yet insufficiently tapped collections of gene annotations,
the project aims to facilitate the discovery of hidden knowledge that could be the basis of further
scientific research. The methodology will extract patterns of interest from annotation graphs (pattern
discovery). Literature-based methods will extract sentences that validate the biological meaning
underlying these patterns (pattern validation).

To demonstrate the methodology, the PattArAn tool (Patterns in Arabidopsis Annotations) will be
customized for Arabidopsis. PattArAn will provide the user with a graphical presentation of patterns
of Arabidopsis genes and associated GO and PO CV terms. Graph data mining techniques and
efficient algorithmic solutions to identify dense subgraphs (DSG) and to perform graph
summarization (GS) will be developed. Algorithms to mine the literature for relevant sentences for
an extracted pattern (referred to as the imprint) will be developed. PattArAn will enable iterative
exploration and will incorporate allied steps such as consulting gene function prediction.
The project will involve collaboration with biologists for building and refining annotation graphs, and
validating patterns to ensure relevance to their research.

===Broader Impact===

This project brings broad contributions to the Arabidopsis thaliana community;
PattArAn may assist Arabidopsis curators to manage GO-PO annotations. It can
also be used to bootstrap an annotation database for other plant species. The
project will offer significant research and educational experiences for graduate
students (University of Maryland and Iowa) and undergraduate students (St.
Bonaventure University). Team members will continue to mentor women and students
from under-represented communities, participate in outreach activities, lead a
Journal Club, etc. The outcomes from this research project will be disseminated
via biology and bioinformatics venues.

==Publications==

An Evaluation of Metrics to Compute Concept Similarity Based on Evidence from Ontologies
Guillermo Palma, Eric Haag, Louiqa Raschid, Andreas Thor, Maria Esther Vidal
Email louiqa@umiacs.umd.edu for a copy.

PAnG - Finding Patterns in Annotation Graphs
P. Anderson, J. Benik, L. Raschid, A. Thor and M. E. Vidal
Proceedings of the ACM SIGMOD International Conference (Demonstration Paper), 2012. [http://www.informatik.uni-trier.de/~ley/db/conf/sigmod/sigmod2012.html#AndersonTBRV12]

MeSH: a window into full text for document summarization.
Sanmitra Bhattacharya, Viet Ha-Thuc, Padmini Srinivasan
Journal of Bioinformatics [ISMB/ECCB] 27(13): 120-128 (2011) [http://www.informatik.uni-trier.de/~ley/db/journals/bioinformatics/bioinformatics27.html#BhattacharyaHS11]

Link Prediction for Annotation Graphs using Graph Summarization
Andreas Thor, Philip Anderson, Louiqa Raschid,
Saket Navlakha, Barna Saha, Samir Khuller, Xiao-Ning Zhang
Proceedings of the International Semantic Web Conference 2011. [http://www.informatik.uni-trier.de/~ley/db/conf/semweb/iswc2011-1.html#ThorARNSKZ11]

Dense Subgraphs with Restrictions and Applications to Gene Annotation Graphs
Barna Saha and Allison Hoch and Samir Khuller and Louiqa Raschid and Xiao-Ning Zhang
In Research in Computational Molecular Biology.
Lecture Notes in Computer Science 6044 Springer ISBN 978-3-642-12682-6.
Also Proceedings of RECOMB 2010. Bonnie Berger, editor. Pages 456-472, 2010. [http://www.informatik.uni-trier.de/~ley/db/conf/recomb/recomb2010.html#SahaHKRZ10]

==Tools and Datasets==

===PattArAn portal for Arabidopsis===

Arabidopsis genes, GO and PO annotations as of xxx 2012 [http://pattaran.umiacs.umd.edu/]
This site will let you search for genes based on GO or PO terms and visualize their annotations
as well as graph summaries.

===PAnG portal for LinkedCT===

Clinical trials and Condition and Interventions from LinkedCT.org as of xxx 2012 [http://pang.umiacs.umd.edu/linkedct.html]
This site will let you search for clinical trials based on conditions and interventions and
let you visualize the graphs and graph summaries.

== Summer 2012 Imprint Experiment ==

Mahmuda Khan's experience with finding the imprints for sentences is described here.
[[File:Mahmuda_Summer2001.pptx]]

Overview of the project and instructions to the supervisors are available here.
[[File:Overview.docx]]

Annotation flowchart.
[[File:FlowchartAnnotation.pdf]]

Padmini's worksheet [https://docs.google.com/document/d/19ISt8qu4RRnpnCOJOg5H-_u6SWLRHU6RNVHlqo_9bxk/edit]

DILS poster [http://homepage.cs.uiowa.edu/~psriniva/UMD-UI/DILS_Poster_Final.pptx]

== Getting started ==
* [//www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [//www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]

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Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

==COLLABORATIVE: ABI Development: Methodology for Pattern Creation, Imprint Validation, and Discovery from the Annotated Biological Web (PattArAn)==

===Acknowledgement===

This project is funded by the National Science Foundation Biological Infrastructure [http://www.nsf.gov/div/index.jsp?div=DBI NSF DBI] program.

[http://nsf.gov/awardsearch/showAward.do?AwardNumber=1147144 UMD award] [http://nsf.gov/awardsearch/showAward.do?AwardNumber=1146256 U. Iowa award] [http://nsf.gov/awardsearch/showAward.do?AwardNumber=1146300 St. Bonaventure U award]

===Intellectual Merit===

The project will develop a methodology that exploits the wealth of annotation knowledge,
notably Gene Ontology (GO) and Plant Ontology (PO) annotations of Arabidopsis genes.

Motivated by the availability of rich and as yet insufficiently tapped collections of gene annotations,
the project aims to facilitate the discovery of hidden knowledge that could be the basis of further
scientific research. The methodology will extract patterns of interest from annotation graphs (pattern
discovery). Literature-based methods will extract sentences that validate the biological meaning
underlying these patterns (pattern validation).

To demonstrate the methodology, the PattArAn tool (Patterns in Arabidopsis Annotations) will be
customized for Arabidopsis. PattArAn will provide the user with a graphical presentation of patterns
of Arabidopsis genes and associated GO and PO CV terms. Graph data mining techniques and
efficient algorithmic solutions to identify dense subgraphs (DSG) and to perform graph
summarization (GS) will be developed. Algorithms to mine the literature for relevant sentences for
an extracted pattern (referred to as the imprint) will be developed. PattArAn will enable iterative
exploration and will incorporate allied steps such as consulting gene function prediction.
The project will involve collaboration with biologists for building and refining annotation graphs, and
validating patterns to ensure relevance to their research.

===Broader Impact===

This project brings broad contributions to the Arabidopsis thaliana community;
PattArAn may assist Arabidopsis curators to manage GO-PO annotations. It can
also be used to bootstrap an annotation database for other plant species. The
project will offer significant research and educational experiences for graduate
students (University of Maryland and Iowa) and undergraduate students (St.
Bonaventure University). Team members will continue to mentor women and students
from under-represented communities, participate in outreach activities, lead a
Journal Club, etc. The outcomes from this research project will be disseminated
via biology and bioinformatics venues.

==Publications==

An Evaluation of Metrics to Compute Concept Similarity Based on Evidence from Ontologies
Guillermo Palma, Eric Haag, Louiqa Raschid, Andreas Thor, Maria Esther Vidal
Email louiqa@umiacs.umd.edu for a copy.

PAnG - Finding Patterns in Annotation Graphs
P. Anderson, J. Benik, L. Raschid, A. Thor and M. E. Vidal
Proceedings of the ACM SIGMOD International Conference (Demonstration Paper), 2012. [http://www.informatik.uni-trier.de/~ley/db/conf/sigmod/sigmod2012.html#AndersonTBRV12]

MeSH: a window into full text for document summarization.
Sanmitra Bhattacharya, Viet Ha-Thuc, Padmini Srinivasan
Journal of Bioinformatics [ISMB/ECCB] 27(13): 120-128 (2011) [http://www.informatik.uni-trier.de/~ley/db/journals/bioinformatics/bioinformatics27.html#BhattacharyaHS11]

Link Prediction for Annotation Graphs using Graph Summarization
Andreas Thor, Philip Anderson, Louiqa Raschid,
Saket Navlakha, Barna Saha, Samir Khuller, Xiao-Ning Zhang
Proceedings of the International Semantic Web Conference 2011. [http://www.informatik.uni-trier.de/~ley/db/conf/semweb/iswc2011-1.html#ThorARNSKZ11]

Dense Subgraphs with Restrictions and Applications to Gene Annotation Graphs
Barna Saha and Allison Hoch and Samir Khuller and Louiqa Raschid and Xiao-Ning Zhang
In Research in Computational Molecular Biology.
Lecture Notes in Computer Science 6044 Springer ISBN 978-3-642-12682-6.
Also Proceedings of RECOMB 2010. Bonnie Berger, editor. Pages 456-472, 2010. [http://www.informatik.uni-trier.de/~ley/db/conf/recomb/recomb2010.html#SahaHKRZ10]

==Tools and Datasets==

===PattArAn portal for Arabidopsis===

Arabidopsis genes, GO and PO annotations as of xxx 2012 [http://pattaran.umiacs.umd.edu/]
This site will let you search for genes based on GO or PO terms and visualize their annotations
as well as graph summaries.

===PAnG portal for LinkedCT===

Clinical trials and Condition and Interventions from LinkedCT.org as of xxx 2012 [http://pang.umiacs.umd.edu/linkedct.html]
This site will let you search for clinical trials based on conditions and interventions and
let you visualize the graphs and graph summaries.

== Summer 2012 Imprint Experiment ==

Mahmuda Khan's experience with finding the imprints for sentences is described here.
[[File:Mahmuda_Summer2001.pptx]]

Overview of the project and instructions to the supervisors are available here.
[[File:Overview.docx]]

Annotation flowchart.
[[File:FlowchartAnnotation.pdf]]

Padmini's worksheet [https://docs.google.com/document/d/19ISt8qu4RRnpnCOJOg5H-_u6SWLRHU6RNVHlqo_9bxk/edit]

DILS poster [http://homepage.cs.uiowa.edu/~psriniva/UMD-UI/DILS_Poster_Final.pptx]

== Getting started ==
* [//www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [//www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]