“The New York Stem Cell Foundation (NYSCF) Research Institute has a history of generating and distributing all forms of stem cell lines in an effort to accelerate research. In February of 2014, the eagle-i network, a Harvard Medical School informatics project aiming to make research resources more discoverable, started a collaboration with the NYSCF Research Institute to improve the mechanisms for organizing and distributing information about iPS cells. We began by developing an ontology that organizes information about iPS cells in a way that is consistent with the traditional stem cell development pipeline. iPS cell line information is digitally linked to information describing related records such as human subjects, iPS cell lines, human health studies, protocols, and biospecimens to name a few. This data organization allows a researcher to filter a large data set based, not just on the properties of the resource type (e.g. iPS cells) they’re seeking, but also on the properties of resources described in the digitally linked records (e.g. human subject, clinical, demographic, and genotype information). For this project we’ve organized data describing 587 iPSC lines and 1025 primary cell lines developed by NYSCF. This data is published, linked to de-identified human subject information, and is openly accessible.
To take advantage of this semantic organization, we’ve recently developed an advanced query form that gives researchers a graphical interface to the advanced back-end SPARQL query system. The advanced query tool allows a user to specify a disease, age of diagnosis, ethnicity, and gender of the human subject from whom the iPS cell line was derived. The tool allows the user to further filter the results by the method used for inducing pluripotency (episomal vs. integrative ectopic gene expression), and/or by the quality testing done to verify “stemcell-ness” (teratoma , embryoid body, marker, or morphological analysis). Users are able, after their query, to view data in an online table, or to optionally download data for offline manipulation or referral. We hope this advanced query interface will allow researchers to rapidly filter through very large iPS cell line data sets to zero in on the specific lines that are the most relevant to their research. Please visit www.nyscf.org/repository to access the NYSCF Stem Cell Repository and learn more about this collaboration. Regarding eagle-i, the project is now entirely sustained under Harvard Medical School’s CTSA grant; has grown nationally to over 35 Universities and is rapidly expanding.”