1.5B Data Points trapped in International Repository - Daring Rescue in Progress! Simon N. Twigger 1,2 , Joey F. Geiger 2 , Jennifer R. Smith 1 , Rajni Nigam 1 , Clement Jonquet 3 , Mark Musen 3 1 Human and Molecular Genetics Center and 2 : Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, WI, USA, 3 National Center for Biomedical Ontology, Stanford University, Palo Alto, CA, USA Expression data is at the core of many critical questions asked by researchers. Project data is available at http://gminer.mcw.edu This work is funded by the National Center for Biomedical Ontology as a Driving Biological Project. The NCBO is funded as part of the NIH Roadmap Initiative. The Rat Genome Database is funded by NHLBI What tissue is this gene expressed in? What expression data is known for SD (aka SD/NHsd, Harlan Sprague Dawley, Sprague Dawley) rats? Are any of these genes associated with my phenotype? Has this gene been seen in the brain? What rat expression studies have been done on Mammary Cancer(aka breast neoplasms/breast cancer/cancer of the breast, breast carcinoma...)? Has anyone done any expression studies using congenic rats? ?? INDEX Brain 11 hits Forebrain 5 hits Hindbrain 3 hits Amygdyla 3 hits SS rats 23 hits SS/Jr 9 hits SS/NHsd 10 hits S.R(9)x3a 4 hits ... Mouse Anatomy Ontology Rat Strain Ontology http://bioontology.org Create Annotation Jobs & Queue Up Q-In Put results in to queue for save Parse Results Index text at OBA 1..n Annot. Workers Results saved to GMiner database Q-Out RabbitMQ GEO Records Gabrd Kab Probeset P/A p-value Probeset 1369048_at (Gabrd) was Present in sample GSM132484 which was from hippocampus. Can we compile all such results for Gabrd...? NCBI's Gene Expression Omnibus has a lot of data but results are very detailed, centered on experiments, not genes. Lots of valuable information is encoded in the text of the records but is not easy to access or repurpose. Can we get more information out of GEO by identifying information in the text and creating an Index of the GEO records? Can we link this index to the billions of data points stored in GEO to extract more information? National Center for Biomedical Ontology hosts a wide variety of Ontologies that provide a structure for knowledge in many critical areas We use NCBO tools and an automated pipeline to match ontology terms to GEO text (concept mapping) and manually review to create the index. Use Linked Tag Clouds to navigate the GEO data to find GEO records associated with strains or anatomical regions. Tag Clouds also provide a summary of the search results as well as an intuitive navigation aid. Using ontologies and the ontology structure allows queries not possible using other search approaches We are exploring linking our annotations and GEO expression data to derive novel gene-to- tissue relationships
The New GMIner Tool
Jul 16, 2015
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1.5B Data Points trapped in International Repository - Daring Rescue in Progress!Simon N. Twigger1,2, Joey F. Geiger2, Jennifer R. Smith1, Rajni Nigam1, Clement Jonquet3, Mark Musen31 Human and Molecular Genetics Center and 2: Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, WI, USA, 3 National Center for Biomedical Ontology, Stanford University, Palo Alto, CA, USA
Expression data is at the core of many critical questions asked by researchers.
Project data is available at http://gminer.mcw.edu
This work is funded by the National Center for Biomedical Ontology as a Driving Biological Project.The NCBO is funded as part of the NIH Roadmap Initiative. The Rat Genome Database is funded by NHLBI
What tissue is this gene expressed in?
What expression data is known for SD (aka SD/NHsd,
Harlan Sprague Dawley, Sprague Dawley) rats?
Are any of these genes associated with my
phenotype?Has this gene been seen in the brain?
What rat expression studies have been done on Mammary Cancer(aka breast neoplasms/breast
cancer/cancer of the breast, breast carcinoma...)?
Has anyone done any expression studies using congenic rats?
?? INDEX
Brain 11 hits Forebrain 5 hits Hindbrain 3 hits Amygdyla 3 hits
SS rats 23 hits SS/Jr 9 hits SS/NHsd 10 hits S.R(9)x3a 4 hits
...
Mouse AnatomyOntology
Rat StrainOntology
http://bioontology.org
Create AnnotationJobs & Queue Up
Q-In
Put results in toqueue for save
ParseResults
Index textat OBA
1..n Annot. Workers
Results saved toGMiner database
Q-Out
RabbitMQ
GEO Records
GabrdKab
Probeset P/A p-value
Probeset 1369048_at (Gabrd) was Present in sample GSM132484 which was from hippocampus. Can we compile all such results for Gabrd...?
NCBI's Gene Expression Omnibus has a lot of data but results are very detailed, centered on experiments, not genes.
Lots of valuable information is encoded in the text of the records but is not easy to access or repurpose.
Can we get more information out of GEO by identifying information in the text and creating an Index of the GEO records? Can we link this index to the billions of data points stored in GEO to extract more information?
National Center for Biomedical Ontology hosts a wide variety of Ontologies that provide a structure for knowledge in many critical areas
We use NCBO tools and an automated pipeline to match ontology terms to GEO text (concept mapping) and manually review to create the index.
Use Linked Tag Clouds to navigate the GEO data to find GEO records associated with strains or anatomical regions. Tag Clouds also provide a summary of the search results as well as an intuitive navigation aid.
Using ontologies and the ontology structure allows queries not possible using other search approaches
We are exploring linking our annotations and GEO expression data to derive novel gene-to-tissue relationships
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