PRO and the NIF / ImmPort Antibody Registries Alexander Diehl Protein Ontology Workshop 6/18/14

ImmPort Immunology Database and Analysis Portal NIAID-funded (via BISC mechanism) data and tool repository for immunology data produced by NIAID funded investigators Current PI: Atul Butte (Stanford) IT Support: Northrup-Grummen Ontology Support: Barry Smith (UB)

ImmPort Immunology Database and Analysis Portal Accelerate a more collaborative and coordinated research environment Create an integrated database that broadens the usefulness of scientific data and advances hypothesis-driven and hypothesis-generating research Advance the pace and quality of scientific discovery while extending the value of scientific data in all areas of immunological research Integrate relevant data sets from participating laboratories, public and government databases, and private data sources Promote rapid availability of important findings, making new discoveries available to the research community for further analysis and interpretation Provide analysis tools to advance immunological research

Monoclonal Antibodies Used extensively in biological and medical research, diagnostics, and therapy. Can be made to target specific proteins or forms of proteins, as well as other antigens. Produced in mice, rats, rabbits, and through genetic engineering techniques. Typically identified via clone names, derived from the name of the clonal population of hybridoma cells used to produce antibodies.

Monoclonal Antibodies 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)

ImmPort Antibody Registry 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 PRO 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

ImmPort Antibody Registry BD Lyoplate provided initial list of antibodies, primarily against human cell surface markers. 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.

ImmPort Antibody Registry Roughly 400 unique markers identified (CD2, CD45, CD45RA, CD45 RO, BTK/ITK, etc) Roughly 1,600 entries representing a unique combination of marker, clone, species reactivity, vendor 52 terms are currently in the PRO request document; mostly for phosphorylated forms not currently represented Around PubMed papers checked for antibodies in the last three months, some linked to ImmPort studies Data recorded: Marker, species reactivity, name, HGNC ID/link, UniProt ID/link, PR ID/link, clone, species of origin, isotype, vendor, vendor catalog #

NIF Antibody Registry Public-funded registry of antibody reagents 2.2 million entries Cooperation with over 300 vendors Flexible search interface

Difference between IAR and NIF-AR IAR is manually curated; NIF-AR is built largely computationally. IAR has direct mappings to PR entities as targets; NIF-AR searches Entrez Gene, although appears to have hidden PR mappings. IAR has a limited focus to commonly used monoclonal antibodies in immunology; NIF-AR focuses on the full universe of (mostly) commercially available monoclonal and polyclonal antibodies. IAR focuses on the clone; NIF-AR on the vendor product.

ImmPort Antibody Ontology Next step: transformation of ImmPort Antibody Registry into an ontology format. Will facilitate incorporation in to ImmPort templates, and querying and reuse of antibody knowledge. Using Reagent Ontology developed by Matthew Brush and Melissa Haendel as a model. Will incorporate NIF-AR entries into ontology.

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 ImmPort Antibody Ontology.

Antibody Panels

Useful for flow cytometry and CyTOF standardization for HIPC and more. Standardized panels for tumor typing can be generated and queried in a variety of ways.

Acknowledgments Travis Allen Olivia Helfer Barry Smith Alan Ruttenberg Members of ImmPort and HIPC projects Anita Bandrowski/NIF NIAID for support

End