Post on 18-Jan-2016
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Development and Use of Controlled Vocabularies at the
Arabidopsis Information Resource (TAIR)
Sue RheeCarnegie InstitutionDept. Plant Biology
rhee@acoma.stanford.edu
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)
Controlled VocabulariesExisting:• GO function, process, component• Arabidopsis anatomy, developmental stagesUnder development:• experimental methods• environmental factors • PO anatomy, developmental stagesPlanned:• PO traitNeeded:• chemical• values? (qualitative and quantitative)
Developing controlled vocabs• Anatomy
• Developmental Stages
• Methodology
Using controlled vocabs• Gene and gene product functional annotation
• Community
• Microarray experiments and array elements
• Alleles
• Germplasm
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
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
Leonore Reiser (TAIR), Jonathan Clarke (JIC)
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.
• 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.
Methods for Anatomy and Developmental Stages Ontology Development
Ontologies for Anatomy and Development
Crossing Anatomy and Developmental Stsages
etc.etc.etc…
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…)
Developing Methods Ontology(An ontology of experimental techniques)
• 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
Leonore Reiser, Margarita Garcia-Hernandez, Gabe Lander
Developing controlled vocabs• Anatomy
• Developmental Stages
• Methodology
Using controlled vocabs• Gene and gene product functional annotation
• Community
• Microarray experiments and array elements
• Alleles
• Germplasm
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)
Basic Process of Literature Curation
Subject term Object term
Paper
Binds toInvolved inFunctions asExpressed inIs subunit ofRelated to
Required forLocated in
Interacts withRegulatesMore…
data object (e.g. gene)controlled vocabulary
data object
automatic automatic
manual
Currently 20 types
Pubsearch Statistics (10/02)
Data types unique 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%
| 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 |
TOP TEN LISTS
PubSearch Annotation User Interface
Expanding Data Objects to Annotate
• microarray experiments
• RNA samples
• array elements (ESTs, oligos, PCR products)
• alleles (natural variant & mutant forms)
• germplasm (ecotypes & mutant lines)
Microarray Data Annotation• 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
Phenotype Annotation
Trait
Conditionenvironmentchemical
Methodology
TraitValueGermplasm
hy4-1 mutant line long height
measure with ruler
light
ConditionValue
absence
AnatomyBiol. Process
etc…hypocotyl
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
A model of control of flowering in Arabidopsis
From “Molecular Genetics of Plant Development”
Generating the image from the database
Gene1 Relationship Gene2
ELF3 Represses GA1
ELF3 Represses SPY
ELF3 Activates EMF1
Represses =
Activates =
ELF3 GA1
ELF3 GA1, SPY
ELF3 GA1, SPY
EMF1
Genetic Interaction / Transcriptional Regulation Pathways
Acknowledgements• 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
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/
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)