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How to make ImmPort data fit for secondary use

How to make ImmPort data fit for secondary use. Barry Smith http://ontology.buffalo.edu/smith. Goals of ImmPort. Accelerate a more collaborative and coordinated research environment Create an integrated database that broadens the usefulness of scientific data

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How to make ImmPort data fit for secondary use

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  1. How to make ImmPort data fit for secondary use Barry Smith http://ontology.buffalo.edu/smith

  2. Goals of ImmPort • Accelerate a more collaborative and coordinated research environment • Create an integrated database that broadens the usefulness of scientific data • Advance the pace and quality of scientific discovery • Integrate relevant data sets from participating laboratories, public and government databases, and private data sources • Promote rapid availability of important findings • Provide analysis tools to advance immunological research

  3. Improve immunology research through enhanced • Collaboration • Coordination • Discoverability • Integration • Analyzability Hypothesis: all of these ends will be promoted by describing ImmPort data using terms from shared high quality ontologies

  4. ImmPort data is already being tagged with ontology terms For example • where data is prepared to meet FDA requirements • where data is published to meet NIH mandates for reusability • in the post-submission phase, where data is analyzed by third parties But this tagging is • partial • uncoordinated • uses ontologies and analysis tools of varying quality

  5. SDY 165: Characterization of in vitro Stimulated B Cells from Human Subjects shared to Semi-Public Workspace (SPW) Project

  6. SDY 165: Characterization of in vitro Stimulated B Cells from Human Subjects shared to Semi-Public Workspace (SPW) Project During the human B cell (Bc) recall response, rapid cell division results in multiple Bc subpopulations. RNA microarray and functional analyses showed that proliferating CD27lo cells are a transient pre-plasmablast population, expressing genes associated with Bc receptor editing. Undivided cells had an active transcriptional program of non-ASC B cell functions, including cytokine secretion and costimulation, suggesting a link between innate and adaptive Bc responses. Transcriptome analysis suggested a gene regulatory network for CD27lo and CD27hi Bc differentiation.  • In vitro stimulated B cells from human subjects • B cell receptor editing

  7. SDY 165: Characterization of in vitro Stimulated B Cells from Human Subjects shared to Semi-Public Workspace (SPW) Project

  8. Pubmed 22468229

  9. Discoverability: examples • Find [ImmPort] data pertaining to in vitro stimulated B cells from human subjects • Find studies of genes associated with B cell receptor editing in human subjects • Find all data in public and government databases relating to B cell receptor editing

  10. Discoverability through literature search Two queries: • In vitro stimulated B cells from human subjects • B cell receptor editing on • Pubmed • MeSH (Medical Subject Headings) • Google

  11. Pubmed 22468229

  12. PubMed retrieves 144 results for “In vitro stimulated B cells from human Subjects” – Zand paper not found

  13. PubMed retrieves 0 results for “Zand[Author] AND In vitro stimulated B cells from human subjects”

  14. Pubmed retrieves 179 results for “B cell receptor editing” – Zand paper not found

  15. MeSH results for “In vitro stimulated B cells from human subjects”

  16. MeSH results for “in vitro stimulated B cells from human subjects”

  17. MeSH results for “B Cell receptor editing”

  18. Google retrieves 180 results for “In vitro stimulated B cells from human subjects” – Zand paper not found

  19. Jackpot

  20. How to make this [ImmPort data] SDY 165: Characterization of in vitro Stimulated B Cells from Human Subjects shared to Semi-Public Workspace (SPW) Project During the human B cell (Bc) recall response, rapid cell division results in multiple Bc subpopulations. RNA microarray and functional analyses showed that proliferating CD27lo cells are a transient pre-plasmablast population, expressing genes associated with Bc receptor editing. Undivided cells had an active transcriptional program of non-ASC B cell functions, including cytokine secretion and costimulation, suggesting a link between innate and adaptive Bc responses. Transcriptome analysis suggested a gene regulatory network for CD27lo and CD27hi Bc differentiation.  discoverable?

  21. B cell receptor editing GO:0002452

  22. GO definition GO provides a definition

  23. and position in GO hierarchy -- hierarchy allows logical reasoning

  24. GOPubMed: 179 results for “B cell receptor editing”

  25. (B cell receptor editing Zand) AND ("Zand"[au]) why are zero documents retrieved?

  26. Proposal1. Tag ImmPort SDY abstracts with GO URIs2. Publish the results to the GO Annotation database During the human B cell recall response, rapid cell division results in multiple B cell subpopulations. RNA microarray and functional analyses showed that proliferating CD27lo cells are a transient pre-plasmablast population, expressing genes associated with B cell receptor editing. Undivided cells had an active transcriptional program of non-ASC B cell functions, including cytokine secretion and costimulation, suggesting a link between innate and adaptive Bc responses. Transcriptome analysis suggested a gene regulatory network for CD27lo and CD27hi Bc differentiation. 

  27. But GO is not enough See http://ncorwiki.buffalo.edu/index.php/ Immunology_Ontologies immune disorders infectious diseases allergies immune epitopes, etc. etc. For special case of Flow Cytometry and CyTOF: ImmPort Ontology Meeting, Stanford, September 4-5, 2013: http://x.co/1W1Om

  28. Files in SDY 165

  29. lk_race.txt American Indian or Alaska Native Asian Black or African American Native Hawaiian or Other Pacific Islander Not_Specified Other Unknown White

  30. ImmPort Templates https://immport.niaid.nih.gov/immportWeb/experimental/displaySubmitTemplates.do

  31. ImmPort Templates: Race https://immport.niaid.nih.gov/immportWeb/experimental/displaySubmitTemplates.do

  32. ImmPort Templates How specify Race if Race = ‘Other’?

  33. ImmPort Templates How specify “Subject Phenotype”?

  34. NG / BISC proposal create controlled vocabularies (ontology drop down lists) for fields currently populated by submitters with free text

  35. Files in SDY 165

  36. lk_sample_type proposal: where controlled vocabularies exist, provide definitions for all terms

  37. Two kinds of definitions • human readable definitions support consistency of data entry • logical definitions • allow logical analysis of data • support aggregation of data • allow automatic validation of consistent data entry Definitions can often be taken over from already existing public domain ontologies such as GO • use of ready-made definitions supports discoverability, and creates automatic linkage to huge bodies of public domain data

  38. ImmPort Antibody Registry (Diehl, et al) from BD Lyoplate Screening Panels Human Surface Markers

  39. Discoverability

  40. Where did this lk_sample_type list come from?

  41. CDISC • Clinical Data Interchange Standards Consortium • http://www.cdisc.org/

  42. CDISC Glossary

  43. SDTM • Study Data Tabulation Model developed by FDA as part of CDISC • for Race, Gender, Ethnicity, … • no human readable definitions • no logical definitions Jan 2013: release of CDISC SDTM Model by CDISC2RDF (Kerstin Forsberg of AstraZeneca)

  44. PHUSE (EU, Roche, AstraZeneca, FDA, …) project to incorporate ontology technology into CDISC

  45. BRIDG • http://bridgmodel.nci.nih.gov/files/BRIDG_Model_3.2_html/index.htm • Biomedical Research Integrated Domain Group (BRIDG) Project

  46. BRIDG 3.2 Domain Analysis Model

  47. Other strategies to simplify creation of structured data for submission into ImmPort • ELN: Electronic Lab Notebooks • PRIME: “Contur ELN has been automating the process of data deposition into ImmPort, making it much easier for our researchers to submit data to ImmPort” • CTMS: Clinical Trial Management Systems • EHR: Electronic Health Records • experiments to prepopulate EHR data into CTMS and from there into case report forms (and into ImmPort?) • Minimal Information Checklists

  48. MIFLOWCYT: Minimal Information for a Flow Cytometry Experiment

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