POC workshop presentations Introduction Katica Ilic POC project

POC workshop presentations • Introduction Katica Ilic, POC project coordinator • Process of developing anatomy ontology Pankaj Jaiswal (Gramene) • Annotation methods and example queries Leonore Reiser (TAIR)…and Pankaj (Annotations and query examples from Gramene). www. plantontology. org POC Workshop, Plant Biology 2004

Using ontologies for annotation of gene expression and phenotypes • • • Methods and tools for annotation used at TAIR Annotation of gene expression Annotation of phenotypes (proposed) Tools and example queries Annotation of phenotypes at Gramene (P. Jaiswal) www. plantontology. org POC Workshop, Plant Biology 2004

Why do we annotate with controlled vocabularies? Use controlled vocabularies to facilitate database mining (ie. extraction of information, making correlations and predictions in order to generate a testable hypothesis) What mutations with similar phenotypes in rice and maize map to syntenic regions? What genes are expressed in plants with compound leaves and not in plants with simple leaves? and so on… www. plantontology. org POC Workshop, Plant Biology 2004

What do we mean by annotation • “Functional annotation is defined as the process of collecting information about and describing a gene’s biological identity –its various aliases, molecular function, biological role(s), subcellular localization, and its expression domains within the plant” from Berardini et. al. (2004) Plant Phys 135: 745 -755 These assertions/ annotations are based upon some form of reproducible experimental evidence. www. plantontology. org POC Workshop, Plant Biology 2004

Evidence Codes www. plantontology. org POC Workshop, Plant Biology 2004

What an annotation looks like in TAIR www. plantontology. org POC Workshop, Plant Biology 2004

Components of an annotation A controlled vocabulary term www. plantontology. org POC Workshop, Plant Biology 2004

Components of an annotation The annotated gene (or germplasm) www. plantontology. org POC Workshop, Plant Biology 2004

Components of an annotation The relationship between the gene and controlled vocabulary term. www. plantontology. org POC Workshop, Plant Biology 2004

Components of an annotation The evidence code (elaborated from the three letter code), gives information about the strength of evidence supporting the annotation. www. plantontology. org POC Workshop, Plant Biology 2004

Components of an annotation The evidence description gives more detailed information about the method supporting the annotation www. plantontology. org POC Workshop, Plant Biology 2004

Components of an annotation The primary source for the evidence detailing how the data was generated. www. plantontology. org POC Workshop, Plant Biology 2004

Components of an annotation Date of the annotation and attribution. Tells you when the annotation was made and by whom. www. plantontology. org POC Workshop, Plant Biology 2004

TAIR: Annotation of gene expression users Expression data from literature Large scale functional genomics www. plantontology. org POC Workshop, Plant Biology 2004

Article details in Pub. Search www. plantontology. org POC Workshop, Plant Biology 2004

Pub. Search Annotation Interface www. plantontology. org POC Workshop, Plant Biology 2004

TAIR: Annotation detail view www. plantontology. org POC Workshop, Plant Biology 2004

TAIR will replace its terms with Plant Ontology terms PO: 0009009 www. plantontology. org POC Workshop, Plant Biology 2004

Annotation of phenotypes Mutants Transgenics Natural Variations www. plantontology. org POC Workshop, Plant Biology 2004

TAIR: Plan for Phenotype Annotation • EAV model § Entity: the thing you are looking at (controlled vocabulary term for the aspect being annotated such as leaf, flower). § Attribute: What is it about entity you are measuring (e. g. height, length, fertility) § Value: Quantitative or qualitative (increased, decreased, greater, fewer, yellow-green). Based on PATO-phenotype, aspect, value To view PATO, go to: http: //obo. sourceforge. net/cgi-bin/detail. cgi? poav www. plantontology. org POC Workshop, Plant Biology 2004

Example: Ag-3 mutant plant Description: Stamens and carpels converted to sepals and petals. Floral meristem is indeterminate. relationship has phenotype Entity stamen (PO: 0009029) has phenotype gynoecium (PO: 0009062) has phenotype floral meristem (PO: 0000229) Attribute number identity Value absent abnormal POC Workshop, Plant Biology 2004 www. plantontology. org

Example: Ag-3 mutant plant Only thetobasic info is Description: Stamens and carpels converted sepals and sent to POC (termpetals. Floral meristem is indeterminate. germplasm-evidence code-reference and attribution. The rest is database dependant. relationship has phenotype Entity stamen (PO: 0009029) has phenotype gynoecium (PO: 0009062) has phenotype floral meristem (PO: 0000229) Attribute number identity Value absent abnormal POC Workshop, Plant Biology 2004 www. plantontology. org

Searching Annotations www. plantontology. org POC Workshop, Plant Biology 2004

and now for pankaj… www. plantontology. org POC Workshop, Plant Biology 2004

Gramene : Comparative grass genomics resource www. gramene. org In Gramene the Cereal Plant Ontologies (GRO) are used to annotate phenotypically identified classical genes from rice • Plant anatomy : In which plant part the phenotype was expressed or the trait was assayed • Growth stage: At what growth stage the phenotype was expressed or the trait was assayed • These ontologies are used in parallel to • Trait Ontology: a vocabulary to describe the observable • Gene Ontology: a vocabulary of molecular concepts of function, biological process and cellular component By the end of 2004, the POC plant anatomy ontology will www. plantontology. org supersede cereal plant anatomy. POC Workshop, Plant Biology 2004

www. gramene. org Search the ontology terms Browse the ontology terms www. plantontology. org POC Workshop, Plant Biology 2004

Alternatively search for the mutants associated to the query term from Anatomy or growth stage www. plantontology. org POC Workshop, Plant Biology 2004

The mutant page • • • POC Workshop, Plant Biology 2004 Names/aliases Alleles Germplasm from where the it was reported Sequences if any Genetic/genomic location Associations to Traits Anatomy/growth stage www. plantontology. org References

The genetic / genomic location of sd 1 gene and search for homeologous regions in other grasses www. plantontology. org POC Workshop, Plant Biology 2004

The phenotype expression profile of sd 1 gene www. plantontology. org POC Workshop, Plant Biology 2004

Annotation process Molecular function gibberellin 20 -oxidase activity (GO: 0045544) / ISS, IEP, IMP Anatomy: stem (GRO: 0005301) / IEP, IMP Growth stage: 04 -stem elongation stage (GRO: 0007048) / IMP, IEP 06 -heading stage (GRO: 0007044) / IMP, IEP Biological process: gibberellic acid biosynthesis (GO: 0009686) / ISS, IEP, IMP response to gibberellic acid stimulus (GO: 0009739)/ ISS, IEP, IMP Trait: plant height (TO: 0000207) [phenotype: dwarf] response to gibberellic acid (TO: 0000166) [phenotype: sensitive] POC Workshop, Plant Biology 2004 www. plantontology. org

Curation tool www. plantontology. org POC Workshop, Plant Biology 2004

www. plantontology. org POC Workshop, Plant Biology 2004

Term display page www. plantontology. org POC Workshop, Plant Biology 2004

Expanding the tree www. plantontology. org POC Workshop, Plant Biology 2004

http: //arabidopsis. org/servlets/Search? action=new_search&type=keyword www. plantontology. org POC Workshop, Plant Biology 2004