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LemBix Journal Club

LemBix Journal Club. February 15 th , 2010 Robin Smith. Fun stuff?. 2000 . 2007 . “new”. High Throughput Screening Campaigns. PubChem: repository for HTS data. PubChem: description/protocol. Pubchem: data representation. Pubchem bioassays by date. @Time of grant proposal: 1500

jileen-caffrey
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LemBix Journal Club

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  1. LemBix Journal Club February 15th, 2010 Robin Smith

  2. Fun stuff? 2000  2007 

  3. “new”

  4. High Throughput Screening Campaigns

  5. PubChem: repository for HTS data

  6. PubChem: description/protocol

  7. Pubchem: data representation

  8. Pubchem bioassays by date @Time of grant proposal: 1500 @Time of Robin start: 1885 @Last Month: 2029

  9. The problems with Pubchem • Very generic data repository: Flexible to put data in, difficult to get data out • Few annotations of assay technologies and the underlying biology (e.g. no cell-based/biochemical distinction!) • No standardization of data • Difficult to search • Very compound-centric – no overexpression experiments, very few knockdown experiments

  10. Example: Targets • Only protein targets allowed • Assay can have no target or 1 target (2 targets not allowed) • Links to redundant protein GI database

  11. Example: Technologies

  12. Example: Endpoints

  13. The BioAssay Ontology Project http://www.bioassayontology.org

  14. BAO Objectives • Develop an ontology to describe high-throughput and high content bioassays • Annotate data from Pubchem and other sources using BAO concepts and store in a repository • Develop software tools to allow users to browse and visualize annotations in the repository

  15. What is an ontology? • A formal, machine-readable, description of knowledge of a domain of interest Food is a Pizza is a is a Margherita Napoletana has topping is a Tomato Topping

  16. Pizza Ontology

  17. Pizza Finder Application

  18. Gene Ontology (amigo.geneontology.org)

  19. Gene Ontology (amigo.geneontology.org)

  20. GO annotation of KLF7 on Entrez Gene

  21. Other biomedical ontologies - BioPortal http://bioportal.bioontology.org

  22. ABA Adult Mouse Brain atlas http://bioportal.bioontology.org/visualize/40133#visualization

  23. Automated annotation of an abstract http://bioportal.bioontology.org/annotator

  24. Automatic annotation of an abstract

  25. What about HTS/HCS? • Currently no public ontology available for describing the domain of HTS and HCS bioassays • Can borrow ideas from related domains (e.g. microarray experiments), the cell line ontology, etc… • Need to describe biological targets, assay technologies, types of assays, types of results, etc…

  26. Breaking down a BioAssay BioAssay Perturbagen Purpose • e.g.Primary screening, confirmatory • e.g. Counter assay, Alternate Technology e.g. Compound e.g. RNAi Measure Group Endpoint e.g. Activity linked measure For high content assays! Target 3 5 1 2 P 4 Technology e.g. Viability e.g. Binding Format e.g. Primary Cells e.g. Purified Proteins e.g. Activity at 10mM e.g. IC50

  27. BAO Components

  28. “Purpose” component • Why was this bioassay undertaken and how does it relate to other assays in the campaign? • Primary – one concentration • Confirmatory – multiple concentration response of hit series • Secondary – used to expand/subtract from hits • Counter – used to eliminate bad hits • Orthogonal – alternate technology to verify/add to results • qHTS assay – primary and confirmatory all at once • Further specifications: description, protocol, comments

  29. “Format” component • What types of biological and chemical ingredients were present in each well of the bioassay? • Live cell – living dissociated cells • Primary cell • Cell Line • Biochemical – no intact live cells • Purified protein • Lysed cell (cells lysed before treatment) • Whole organism – includes bacteria, yeast, drosophila etc. • Ex vivo – intact tissues (slices, organs, etc) • Further specifications: cell line, cell type, assay plate, chemical additives

  30. “Technology” component • What techniques and apparatus were used to measure the effect of the perturbagens on the target? • Binding reporter • Energy transfer, scintillation, luminescent proximity, etc. • Enzyme reporter • Modified substrate, coupled substrate • Protein conformation reporter • Viability reporter • ATP Luciferin, Caspase, NADH, etc. • Redistribution reporter • GFP/Calcium/cAMP/etc. • Inducible reporter • Luc, Bla, LacZ, GFP • Further specifications: detection technique, apparatus, signal direction

  31. Text-Mining for Technology Concepts Protocol Enriched Description Enriched

  32. Supervised organization of tech concepts

  33. “Perturbagen” component • What type of agent was used to perturb biological targets in the bioassay? • Chemical compounds – synthetic small molecules • Crude extracts – mixture of molecules derived from a natural source • RNA – siRNA/RNAi • DNA – cDNAs, oligos • Further specifications: database, reference, notes

  34. “Meta Target” component • The biological identity that is the presumably affected by the action of the perturbagen. “Meta” = not just protein. • Cell component • Organelles, intracellular complexes • Interaction • Protein-protein, protein-RNA, protein-DNA • Biological Process, e.g. Neurite Outgrowth • Protein • Enzyme, TF, receptor, ion channel, etc. • Signaling Pathway • Further specifications: database, reference

  35. “Endpoint” component • A measurement or parameter quantifying or qualifying a perturbation. • Pubchem Outcome • Pubchem Score • Concentration at defined response • IC50, EC80, AC50 • Response at defined concentration • E.g. Activity at 10um • Tested Concentration • Further specifications: unit, data type, attribute, attribute value, attribute unit

  36. (web-based) Software in development • BAO Annotator • Allows domain experts to view original assay data (e.g. from Pubchem) and specify each component • Uses ontology rules to generate HTML forms • BAO Repository Search • Search annotation repository for: • A set of compounds, “luciferase” assays, “cell-based” assays, “transcription factor” targets, etc. • Browse the annotation repository using a treemap • Add assays to a work set that can be further filtered/manipulated for export to Excel/Spotfire • Visualize/download the ontology structure • View compound activities across multiple assays with comparable endpoints (e.g. IC50)

  37. Spotfire annotation of assay data = slow

  38. What should I be able to ask with a BAO? • Which compounds affect members of the STAT3 signaling pathway? • What technologies could be used to test whether my hit compound is acting non-specifically? • Which compounds have similar profiles to my compound but are less toxic? • What cell lines has my kinase been targeted in? • Which compounds are active with pAC50 < -5 in a set of related bioassays?

  39. Ontology Team • Stephan Schürer • Vance Lemmon • Ubbo Visser • Robin Smith • Saminda Abeyruwan • Mitsunori Ogihara • Dusica Vidovic • Software Team • Chris Mader • Felimon Gayalino • Nakul Datar

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