ONTOFORCE - DISQOVER - Blog Article - isscr 2015 - stockholm

ISSCR2015 Focus Session in Stockholm on hiPSC Biobanking, Characterization and Distribution

Overall challenges addressed by international initiatives for large scale production of collections of iPSC lines include the establishment of reference lines, standards for quality control and the logistic and legal challenges faced in distributing iPSCs across borders.

Overall challenges addressed by international initiatives for large scale production of collections of iPSC lines include the establishment of reference lines, standards for quality control and the logistic and legal challenges faced in distributing iPSCs across borders.

The first session addressed the quality control and characterization and **Michael Sheldon **of RUCDR Infinite Biologics called for quality and standards so adoption and use can speed up.
Other speakers confirmed this need and confirmed the traction and potential the field of stem cell research has.

 

“To get to high quality research, we need to have global standards”
Michael Sheldon – RUCDR –

 

The second session focused on the informatics and global coordination of stem cell research.

Where and how to store and find stem cell biobank data is a key question asked. Andreas Kurtz from the Human Embryonic Stem Cell Registry (hESCReg) dug deeper in the registration and access to pluripotent stem cell registries for data comprehension and comparison.

The data required to evaluate a PSC-line by a user are:

  • Where does it come from?
  • Is it pluripotent?
  • Has the data been obtained with informed consent?
  • How much genotype/phenotype data is available (from donor, cell line, relationships between them)?
  • What are the generation and cultivation conditions?
  • Is there feedback on the performance of the line?

Then Richard Pearse form the Harvard Catalyst Group started his session on developing a single point of truth for iPSC information in an open-sourced, semantic web approach using the eagle-i technology. He explained how difficult it is to find the right data and even more to get back to these findings later on … and data is piling up. The use of ontologies to extract the right data and make it interoperable using linked data is the key. Nice example of NYSCF (New York Stem Cell Foundation) mentioned as well as the recent WiCell collaboration. At the end of his talk we thank Richard for the kudo’s towards our DISQOVER app with its “beautiful visualizing linked data” and reference to our joint webinar in July on “The Semantic Web – the future of search.” We look very much forward to that.

 

“Data is piling up and re-searching it is getting more difficult every day. Making data sharable and consistent is key to help solve that problem.”
Richard Pearse – Harvard Catalyst Group –

 

Ian Streeter **from EBiSC (European Molecular Biology Laboratory – European Bioinformatics Institute) dived into some real life examples of data and how messy that gets. The EGA (European Genome/Phenome Archive) is one of the example initiatives to link out to the data and make data accessible, definitely something to follow. He also called to have less data access restrictions and more open data.

 

“The use of ontologies to clean up messy data will lead to much more powerful search capabilities.”
Ian Streeter – EBiSC / EGA –

 

David Panchision closed the session with the challenges and opportunities in resource and data integration from an NIH perspective. General recommendations are:

  • Resources: centralized sharing of patient and reference lines for wide sharing.
  • **QC/Standards: **validate re-programming and differentiated cell types; validate against other model systems.
  • Reproducibility: use same protocols and samples across labs.
  • Collaboration and Training: emphasize rapid dissemination of best practices and model after other disciplines such as genetics.

Again, the need to aggregate massive amounts of data and being able to mine this, is emphasized together with the use of the eagle-i technology. On top of that there is low hanging fruit leveraging existing resources like the 150K subject samples repository mentioned. And yes, scalable data integration is again key to success.

 

“Harmonize accumulated data so we really get return from the investments in biobanking and clinical studies.”
David Panchision – NIMH –

 

**Federating biobanks and stem cell lines **was mentioned many times and NIMH focuses on federation of studies also linking biospecimens and experimental data with existing patient records. Great vision and plans harmonizing all that data to end this interesting ISSCR 2015 session.

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