Midori A. Harris1, Antonia Lock2, Kim Rutherford1, Mark Mcdowall3, And

Double the Mutants, Double the Fun: Curating Multi-Allele Phenotypes in PomBase

Midori A. Harris1, Antonia Lock2, Kim Rutherford1, Mark McDowall3, and Valerie Wood1 1Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK; 2Department of Genetics, Evolution & Environment and UCL Genetics Institute, University College London, London WC1E 6BT, UK; 3EMBL—European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK

Summary The comprehensive and detailed representation of phenotypes is key feature in PomBase, the model organism database for fission yeast. We develop and maintain the Fission Yeast Phenotype Ontology, FYPO, for logical phenotype definitions, and we have made extensive progress in curating and displaying phenotype data for single mutants. We are now extending the PomBase phenotype annotation resources to annotate phenotypes observed in double mutants, triple mutants, etc. The Chado database underlying PomBase supports annotation of specific alleles, singly or in combinations, by associating phenotypes with genotypes which in turn link to their constituent alleles. Current work focuses on adapting the Canto phenotype annotation interface to capture multi-allele phenotype data and metadata, and on extending the PomBase gene page display and search options to accommodate the new data.

FYPO: Fission Yeast Phenotype Ontology Alleles, genotypes & phenotypes in Chado

Phenotype Annotation All phenotype annotation in Gene Allele PomBase uses terms from FYPO paths — example the Fission Yeast Phenotype (OBO-Edit graph viewer) Ontology (FYPO). FYPO For a single mutant, a phenotype annotation can be connected to an allele entry. terms have entity–quality (EQ) logical definitions that refer to terms from external Allele Genotype ontologies (e.g. ChEBI, GO, Allele–Genotype ID ID allele ID SO, PATO) for qualities. The gene name genotype ID ontology structure supports name description annotation and querying at description ... etc. synonyms any level. I = is_a link between more and less specific terms

Gene Phenotype Annotation Term Name Allele Expression Evidence Conditions Reference Count FYPO ID one ID many abolished protein localization tea1-1(unknown) Not specified Microscopy High temperature Bähler J et al. (1998) 6 name ECO ID to cell cortex Single mutant phenotype display * mandatory affecting pom1 coordinates reference on PomBase gene page ... etc. T-shaped cell tea1∆ (deletion) Null Cell growth assay Verde F et al. (1995) 7 ... etc. penetrance low Some details omitted for clarity, including annotation extensions

Phenotype annotations include details for alleles and expression, extensions for penetrance, To capture phenotypes for multiple mutants, alleles form parts of genotypes, expressivity, or affected genes (where available), and evidence and reference metadata. and a phenotype annotation is connected to a genotype entry.

Curating Multi-allele Phenotypes in Canto

manage genotypes for this paper

build genotypes by adding successive allele details

add genes

annotate a phenotype for this genotype

ontology term search + evidence, extensions, etc. as for single mutants Additions to the Canto interface allow a user to see existing genotypes, enter new genotype details, and associate phenotype annotations with a genotype.

PomBase gene page Querying in PomBase

Currently available: query FYPO terms by name or ID to retrieve a list of annotated genes

Expand display compact “Find mutants with defects Term Name Genotype Count in cytokinesis” abolished protein localization to cell tip sec3-2(C577R), exo70∆, marker ura4-D18 4 affecting SPAC6F12.08 affecting SPCC622.10c sensitive to methyl methanesulfonate chk1-D155A, ast1+(overexpression) 61

“Show me anything that affects the actin cytoskeleton” Collapse display

Term Name Genotype Evidence Conditions Reference Count

Genes Alleles Expression abolished protein sec3 sec3-2 (C577R) Endogenous Microscopy Bendezú FO et al. 4 localization to cell tip exo70 exo70∆ (deletion) Null (2012) affecting SPAC6F12.08 ura4 ura4-D18 (deletion) Null expanded affecting SPCC622.10c (marker)

sensitive to methyl meth- ast1 ast1+ (wild type) Overexpression Cell growth assay High temperature Kuntz K et al. (2013) 61 anesulfonate chk1 chk1-D155A (D155A) Not specified Planned: query genes, alleles or genotypes for associated phenotype terms and vice versa

“Find the phenotypes for non-deletion Multi-allele phenotype annotations will be displayed on PomBase gene pages. A compact “Which deletion mutants mutations in my favorite genes” affect cytokinesis?” view will provide a summary, and full details will be available in an expanded display. “Find any single or multiple mutations that affect the actin cytoskeleton”

Acknowledgements PomBase is funded by the Wellcome Trust, and is run by a consortium comprising the University of Cambridge, the European Bioinformatics Institute and University College London. PomBase consortium members: Steve Oliver (Cambridge); Jürg Bähler (UCL); Dan Staines, Paul Kersey (EBI). We thank Heiko Dietze, George Gkoutos, Jacky Hayles, Robert Hohendorf, and Chris Mungall for helpful discussions on various topics.