The Ontology for Newborn Screening Follow-up and Translational Research

The Ontology for Newborn Screening Follow-up and Translational Research is the core component of the NBSDC, being designed to support computational reasoning and inferencing over the data collected during the everyday LTFU practice and research studies and stored in NBSDCdb.

ONSTR domain covers the data entities, agents and processes involved in newborn screening long-term follow-up clinical practice and translational research pertainig to the patients diagnosed with inherited or congenital diseases screened for by state managed Newborn Screening Programs nationwide. It lies the crossroads of medical nutrition, medicine, biochemistry, genetics, public health, pharmacology and related translational research and reflects the complexity and multidisciplinary nature of the practice of newborn screening follow-up. ONSTR domain includes the follow-up of all inherited and congenital diseases listed in SACHDNC-recommended uniformed screening panel (57 diseases as of Dec 2011) and will adapt/expand its domain in accordance with the updates in national level screening policies and practices.

ONSTR is an application ontology, built by following:

1) top-down bottom-up ontology development methodology;

2) OBO Foundry principles

3) ontological realism.

ONSTR uses the Basic Formal Ontology v2 (BFO2) as the top-level ontology and MIREOTs terms and relations from a number of OBO Foundry ontologies and candidate ontologies (e.g., OBI, IAO, GO, PR, ChEBI, OGMS etc.) It is encoded as RDF/XML serialization of OWL2 as ONSTR.owl file.

Current ontology developments are focused on the modeling of the follow-up of the patients diagnosed with one of the inherited metabolic diseases (IMDs) also known as inborn errors of metabolism (IEMs). Inherited metabolic diseases constitute the majority of all screened diseases (46 out of 57) as well as the majority of disease screened by the dried blood spot (DBS) method (46 out of 52). For this reason, our ontology development efforts are and will primarily be focused on modeling the follow-up of and translational research relayed to the inherited metabolic diseases. The first inherited metabolic disease the follow-up of which is chosen as a pilot is the hyperphenylalaninemia (also known and phenylketonuria or PKU) one of the diseases triggered by the disruption of pathways involving amino acid catabolism (amino acidemias). The next inherited metabolic disease the follow-up of which is planned to be modeled in the ONSTR is the maple sirup urine disease (MSUD).

In parallel to modeling the the follow-up of hyperphenylalaninemia, we are providing the ontological representations of those sections of the ONSTR domain that are common to the follow-up of all IMDs, such as, data entities pertaining to dietary intakes, blood metabolite levels, anthropomorphic measurements, lab assays, genetic basis etc.

ONSTR is an open source ontology.

Content license: Creative Commons Attribution 3.0 License

The latest ONSTR release is available for browsing and downloading at the NCBO BioPortal website:

http://bioportal.bioontology.org/ontologies/3137

Development version of ONSTR.owl is available for download at:

http://onstr.googlecode.com/svn/trunk/

Older versions of ONSTR are available for download at:

http://onstr.googlecode.com/svn/tags/allReleases/

ONSTR documentation (to be updated) is available at:

http://onstr.googlecode.com/svn/docs/

To cite the ontology, please use:

Nikolic, S., Shankar, P., Arabandi, S., Dhawan, A., Sunderraman, R., Navathe, S., Malhotra, K., Singh, H. R. (2013) ONSTR: The Ontology for Newborn Screening Follow-up and Translational Research. To appear in the Proceedings of Semantic Trilogy, International Conference of Biomedical Ontology 2013, (ICBO 2013), Montreal, QC.

For all ontology questions and requests, please contact Snezana Nikolic at snez.sn@gmail.com or Rani Singh at rsingh@emory.edu.

(Last updated by Adrya Stembridge, March 18, 2014)