Ontology Update: Antibodies, Proteins, Cells Alexander Diehl ImmPort Science Meeting 10/3/13.

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Presentation transcript:

Ontology Update: Antibodies, Proteins, Cells Alexander Diehl ImmPort Science Meeting 10/3/13

Antibody Registry/Ontology Problem: Experimental methods typically report antibody clones or target markers using non-standardized terminology. CD3 vs. CD3e (protein names) HIT3e vs. UCHT1 (antibody clones for CD3e) vs (catalog numbers for anti- CD3e antibody reagents)

Antibody Registry/Ontology Needed for standardization and cross-referencing of antibody related information. Curation of information related to monoclonal antibody and polyclonal antibody reagents – Clone name – Protein target (identified by PR ID and UniProt ID) – Gene encoding the protein target – Species and isotype of antibody – Alternative names for protein target – Catalog numbers for antibody for multiple vendors – Link to NIF antibody registry – References to articles using a particular antibody

Antibody Registry/Ontology BD Lyoplate provided initial list of antibodies, primarily against human cell surfase marker. Additional antibodies are being curated based on usage in HIPC, CyTOF, and other datasets of interest to ImmPort. Multiple antibody clones being curated per marker.

Antibody Ontology Uses the Reagent Ontology of Matthew Brush and Melissa Haendel as a template for modeling antibodies. The Antibody Ontology is an extension of ReO and is known preliminarily as AntiO. AntiO will eventually be loaded into a triple store to support querying by users.

HIT3a

UCHT1

SK7

Querying

CD45 CD45RA CD45RO CD45RB

Antibody Panels Collections of antibody reagents labeled with unique fluorochromes or isotypes used to simultaneously ‘stain’ a population of cells to identify subpopulations via flow cytometry or CyTOF. Standardized panels can modeled ontologically using the Antibody Ontology.

Antibody Panels

Useful for flow cytometry and CyTOF standardization for HIPC and more. Problem: I don’t actually know all the antibody clones that are used in the HIPC panels, nor their conjugated fluorochromes. – Also need to know definition of lin(-) in terms of markers.

Acknowledgments Olivia Helfer Barry Smith Alan Ruttenberg

End