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Development and Use of Controlled Vocabularies at the Arabidopsis Information Resource (TAIR)

Development and Use of Controlled Vocabularies at the Arabidopsis Information Resource (TAIR). Sue Rhee Carnegie Institution Dept. Plant Biology rhee@acoma.stanford.edu. TAIR http://arabidopsis.org. A model organism database for Arabidopsis thaliana Current major data types:

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Development and Use of Controlled Vocabularies at the Arabidopsis Information Resource (TAIR)

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  1. Development and Use of Controlled Vocabularies at the Arabidopsis Information Resource (TAIR) Sue Rhee Carnegie Institution Dept. Plant Biology rhee@acoma.stanford.edu

  2. TAIRhttp://arabidopsis.org • A model organism database for Arabidopsis thaliana • Current major data types: • community (~11,000 people, ~4,000 labs) • literature (~12,000 articles, ~450 reviews) • genes and proteins (~29,000 genes, ~28000 proteins) • alleles and polymorphisms (~150,000) • germplasms (~150,000, ~1000 mutant, ~800 ecotypes ) • ‘expert’ gene families (~450 containing ~4000 genes) • microarray data (~130 experiments, ~600 hybridizations) • metabolic pathways (~170 pathways, ~1000 reactions)

  3. Controlled Vocabularies Existing: • GO function, process, component • Arabidopsis anatomy, developmental stages Under development: • experimental methods • environmental factors • PO anatomy, developmental stages Planned: • PO trait Needed: • chemical • values? (qualitative and quantitative)

  4. Developing controlled vocabs • Anatomy • Developmental Stages • Methodology Using controlled vocabs • Gene and gene product functional annotation • Community • Microarray experiments and array elements • Alleles • Germplasm

  5. Purpose for Anatomy and Developmental Stages Ontologies To describe things like: • where is a gene expressed in the plant • at what stage of development was the plant when the RNA sample taken • from what tissues was the protein sample derived • what part(s) of the plant are affected in a mutant line

  6. Leonore Reiser (TAIR), Jonathan Clarke (JIC) Anatomy and Developmental Stages • anatomical parts (295) • developmental stages (69) • Sources • Katherine Esau (1960) The Anatomy of Seed Plants • John Bowman (1994) Arabidopsis An Atlas of Morphology and Development • Meyerowitz & Somerville ed. (1994) Arabidopsis An Atlas of Morphology and Development • Numerous primary articles and websites on development/anatomy • Stanley Letovsky, Cereon Genomics • Doug Boyes, Paradigm Genetics

  7. Rules for Anatomy and Developmental Stages Ontology Development • Terms from literature and text books that describe anatomy and development (364 terms; 221 defs). • For anatomy- the terms must describe parts that are found in Arabidopsis (limited scope). • Developmental stages should be based on morphological features- regardless of a time component as different accessions reach the same stage at different times. An example is the floral developmental stages defined by John Bowman.

  8. Methods for Anatomy and Developmental Stages Ontology Development • Created separate anatomy and developmental stages as directed acyclic graphs. • Tried to make the graphs orthogonal in order to generate cross products easily. • Creating cross products between stages and anatomy (what parts exist at what stage?) • Creating cross products with developmental process terms. • Used DAGEditor (BDGP) for ontologies and eventually making cross products.

  9. Ontologies for Anatomy and Development

  10. Crossing Anatomy and Developmental Stsages etc.etc.etc…

  11. Current Status • 221/364 terms are defined. • Terms (definitions and relationships) are checked for accuracy (external review and literature). • Being used to annotate genes and products • Files available on GOBO and TAIR ftp sites • In collaboration with MaizeDB and Gramene on sharing the ontologies to build a common plant ontology (probably flowering plant…)

  12. Developing Methods Ontology(An ontology of experimental techniques) Leonore Reiser, Margarita Garcia-Hernandez, Gabe Lander • Sources: • short, semi-controlled description of experimental information during annotation (102) • protocols from the research community (152) • microarray experiments (129) • Current status: • DAG structure • 195 terms and 3 definitions • more structure revision needed

  13. Developing controlled vocabs • Anatomy • Developmental Stages • Methodology Using controlled vocabs • Gene and gene product functional annotation • Community • Microarray experiments and array elements • Alleles • Germplasm

  14. Currently Annotated Data Types • Genes and gene products (2931) • molecular function (2599 genes to 296 terms) • biological process (536 genes to 269 terms) • subcellular location (695 genes to 104 terms) • Anatomy & devel. Stages (117 genes to 50 terms) • spatial and temporal expression pattern (110 genes to 52 terms) • Community (2415 comm. to 2892 terms) • research interest (2737 terms) • organism of interest (192 terms)

  15. Binds to Involved in Functions as Expressed in Is subunit of Related to Required for Located in Interacts with Regulates More… Basic Process of Literature Curation Currently 20 types controlled vocabulary data object data object (e.g. gene) Subject term Object term manual automatic automatic Paper

  16. Data typesunique matched (unique papers) Genes 3182 (7485), 8.9% GO process terms 653 (8439), 9.5% GO function terms 830 (6537), 15.2% GO component terms 266 (5686), 23.1% Anatomy/develop terms 213 (5583), 58.5% Pubsearch Statistics (10/02) TOP TEN LISTS | development | 2531 | | growth | 1900 | | transcription | 1114 | | biosynthesis | 865 | | flowering | 697 | | transduction | 684 | | transport | 659 | | signal transduction | 625 | | germination | 455 | | metabolism | 425 | | binding | 1494 | | enzyme | 1184 | | kinase | 637 | | receptor | 433 | | beta-glucuronidase | 413 | | protein kinase | 309 | | hormone | 302 | | DNA binding | 299 | | transcription factor | 269 | | transporter | 230 | | cell | 2487 | | membrane | 1031 | | chromosome | 842 | | chloroplast | 604 | | plasma membrane | 408 | | cell wall | 291 | | plastid | 270 | | nucleus | 258 | | intracellular | 236 | | host | 230 |

  17. PubSearch Annotation User Interface

  18. Expanding Data Objects to Annotate • microarray experiments • RNA samples • array elements (ESTs, oligos, PCR products) • alleles (natural variant & mutant forms) • germplasm (ecotypes & mutant lines)

  19. Experiments • goals (e.g. GO process) • variables (e.g. anatomy, environment, chemical) • need a qualifier (e.g. values ontology?) • type/category (e.g. methods) • RNA Samples • germplasm • biomaterial (e.g. anatomy, devel. stages) • external conditions (e.g. methods, envirnoment, chemical) • Array elements • affected by/in XXX (e.g. GO process, anat, dev) • induced during/in XXX • reduced during/in XXX Microarray Data Annotation

  20. Condition environment chemical ConditionValue Phenotype Annotation absence light Germplasm TraitValue Trait height hy4-1 mutant line long Methodology Anatomy Biol. Process etc… measure with ruler hypocotyl

  21. Expanding Types of Annotations By using more relationship types rather than more terms in an ontology. For example: • Gene to gene family • Relationship type: is a member of • Molecular interactions • Relationship types: represses, activates, binds to • Genetic interactions • Relationship types: suppresses, enhances

  22. A model of control of flowering in Arabidopsis From “Molecular Genetics of Plant Development”

  23. Represses = Activates = ELF3 GA1 ELF3 GA1, SPY ELF3 GA1, SPY EMF1 Generating the image from the database

  24. Genetic Interaction / Transcriptional Regulation Pathways

  25. Leonore Reiser • Tanya Berardini • Suparna Mundodi • Margarita Garcia-Hernandez • Eva Huala • Lukas Mueller • Peifen Zhang • Aisling Doyle, J. Yoon, Gabe Lander • Danny Yoo, Iris Xu • Jonathan Clarke (John Innes Institute) • GO, TIGR, Monsanto, MaizeDB, Gramene, • SRI International Acknowledgements

  26. Where to get our stuff • ontologies and annotations (ftp site) • ftp://ftp.arabidopsis.org/home/tair/Ontologies/ • annotations (search & download ) • http://www.arabidopsis.org/info/ontologies/ • literature curation software-pubsearch (download) • http://www.gmod.org/

  27. Sources of Vocabularies • Literature • primary research articles (~12000) • textbooks (~10) • protocols (~150) • web sites and databases (~50) • Community • individual database submission (e.g. research interest) • collaboration (e.g. JIC, MaizeDB, Gramene) • bulk contribution (e.g. Monsanto)

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