Aweb resource for exploring integrated cancer biomarker ...Dingerdissen... · •ISMB (at ITCR...
Transcript of Aweb resource for exploring integrated cancer biomarker ...Dingerdissen... · •ISMB (at ITCR...
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A web resource for exploring integrated cancer biomarker data in the context of mutation, differential
expression, evolutionarily conserved expression patterns, and automatically mined literature evidence
Presented by: Hayley Dingerdissen – GW Project Lead
Multi-PIs:Dan Crichton – NASA JPL
Raja Mazumder – GW
Sub-awardees:Frédéric Bastian – SIB; Vijay Shanker – UD
ITCR Annual Meeting | May 28 - 31, 2019 | Deer Valley, UtahSlides available as CC BY 4.0
![Page 2: Aweb resource for exploring integrated cancer biomarker ...Dingerdissen... · •ISMB (at ITCR booth) •JCO manuscript submission (planned) •AMIA (submitted) •EDRN (planning](https://reader034.fdocuments.us/reader034/viewer/2022050609/5fb09669da955b693c450ff7/html5/thumbnails/2.jpg)
A semantic web of integrated cancer
biomarker data
AUTOMATICALLY MINED LITERATURE
BIOMARKERS
PATHWAYS
MORE
MUTATION
DIFFERENTIAL EXPRESSIONIN CANCER
CANCER EXPRESSION SPECIFICITY
EVOLUTIONARYCONSERVATION
OF NORMALEXPRESSION
4.0
FDA Approved
Breast Cancer
Biomarkers
NCBI SRA
Custom
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Resulting web portal – a PCA3 case studyhttps://www.oncomx.org/(https://beta.oncomx.org/)
https://www.ncbi.nlm.nih.gov/gene/50652
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Future directionsDevelopment plans
• Refining biomarker data model
• Integrated views• Increase external linkages• Increase cancer biomarker
(and other) datasets• Explore linkages to imaging
projects/databases
Upcoming outreach•ISMB (at ITCR booth)•JCO manuscript submission (planned)•AMIA (submitted)•EDRN (planning to submit)•OncoMX user community workshop (tentatively September 16, 2019)
Collaboration• SingleCellTK• INODE (use-case for EU
grant with SIB)• IEDB• IMAT (planning to submit LOI)• Looking for additional ITCR
collaborators
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Acknowledgements
• W. Evan Johnson(ITCR Collaborator)
• Raja Mazumder (Multi-PI)• Robel Kahsay• Amanda Bell• Evan Holmes• Stephanie Singleton• Reza Mousavi• Charles Hadley King• Jonathon Keeney• Nicole Ferrer• Olga Reghay• Dacian Stremtan
• Daniel Crichton (Multi-PI)• Heather Kincaid• David Liu
• Frѐdѐric Bastian (Sub-Awardee)• Marc Robinson-Rechavi
• K. Vijay-Shanker (Sub-Awardee)• Samir Gupta
• Jeet Vora• Rahi Navelkar• Yao Ren• Janisha Patel• Naila Gulzar
Funding: NCI U01CA2015010; NCI EDRN award 156620
Previous contributions• Ashique Mahmood• Lama ElZohary• Yu Hu• Ting-Chia Chang• Prince Birring• Julien Wollbrett
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Questions?
Contact us:Hayley Dingerdissen – [email protected]
Dan Crichton – [email protected] Mazumder – [email protected]
Poster #22 Tonight
We are looking for biomarker data (preferably mapped to gene level) – please let us know if you
have data and would like to collaborate!
Join us at our next workshop!Tentatively September 16, 2019
@OncoMX_KB
![Page 7: Aweb resource for exploring integrated cancer biomarker ...Dingerdissen... · •ISMB (at ITCR booth) •JCO manuscript submission (planned) •AMIA (submitted) •EDRN (planning](https://reader034.fdocuments.us/reader034/viewer/2022050609/5fb09669da955b693c450ff7/html5/thumbnails/7.jpg)
A web resource for exploring integrated cancer biomarker data in the context of mutation, differential
expression, evolutionarily conserved expression patterns, and automatically mined literature evidence
Presented by: Hayley Dingerdissen – GW Project Lead
Multi-PIs:Dan Crichton – NASA JPL
Raja Mazumder – GW
Sub-awardees:Frédéric Bastian – SIB; Vijay Shanker - UD
ITCR Annual Meeting | May 28 - 31, 2019 | Deer Valley, UtahSlides available as CC BY 4.0
![Page 8: Aweb resource for exploring integrated cancer biomarker ...Dingerdissen... · •ISMB (at ITCR booth) •JCO manuscript submission (planned) •AMIA (submitted) •EDRN (planning](https://reader034.fdocuments.us/reader034/viewer/2022050609/5fb09669da955b693c450ff7/html5/thumbnails/8.jpg)
Resulting web portal – a PCA3 case studyhttps://www.oncomx.org/(https://beta.oncomx.org/)
8https://www.ncbi.nlm.nih.gov/gene/50652
![Page 9: Aweb resource for exploring integrated cancer biomarker ...Dingerdissen... · •ISMB (at ITCR booth) •JCO manuscript submission (planned) •AMIA (submitted) •EDRN (planning](https://reader034.fdocuments.us/reader034/viewer/2022050609/5fb09669da955b693c450ff7/html5/thumbnails/9.jpg)
Resulting web portal – a PCA3 case study
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Resulting web portal – a PCA3 case study
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Resulting web portal – a PCA3 case study
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Resulting web portal – a PCA3 case study
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Use-case driven interface development
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Major featuresIntegrated, single, accessible, harmonized, online resource, built to support extensibility of different data types over time• User community focus• Provenance standards (BCO)• Definition of a biomarker data model• Ontology-guided data integration• Leveraging existing literature• Adherence to FAIR principles
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