Excerpts from a Sample Descriptioncourtesy of M. Hoffman, S. Schmidtke, Lion BioSciences

Organism: mus musculus [ NCBI taxonomy browser ]Cell source: in-house bred mice (contact: person@somewhere.ac.uk) Sex: female [ MGED ]Age: 3 - 4 weeks after birth [ MGED ]Growth conditions: normal

controlled environment20 - 22 oC average temperaturehoused in cages according to EU legislationspecified pathogen free conditions (SPF)14 hours light cycle10 hours dark cycle

Developmental stage: stage 28 (juvenile (young) mice)) [ GXD "Mouse Anatomical Dictionary" ]Organism part: thymus [ GXD "Mouse Anatomical Dictionary" ]Strain or line: C57BL/6 [International Committee on Standardized Genetic Nomenclature for Mice]Genetic Variation: Inbr (J) 150. Origin: substrains 6 and 10 were separated prior to 1937. This substrain is now probably the most widely used of all inbred strains. Substrain 6 and 10 differ at the H9, Igh2 and Lv loci. Maint. by J,N, Ola. [International Committee on Standardized Genetic Nomenclature for Mice ]Treatment: in vivo [MGED] intraperitoneal injection of Dexamethasone into mice, 10 microgram per 25 g bodyweight of the mouseCompound: drug [MGED] synthetic glucocorticoid Dexamethasone, dissolved in PBS

Use case scenarioOWG Use Cases

• Return a summary of all experiments that use a specified type of biosource.– Group the experiments according to treatment.

• Return a summary of all experiments done examining effects of a specified treatment– Group the experiments according to biosource.

• Return a summary of all experiments measuring the expression of a specified gene.– Indicate when experiments confirm results, provide new

information, or conflict.

• Generate a distance metric for experiment types• Generate an error estimation for experimental

descriptions

Ontology Example

• Concept=Age def=in standard units referenced to an identifiable time point from (class) developmental stage

• Age=6 {units=days},

• {dev_stage}=dauer

• Hierarchy=Dev_stage->larva->dauer

EMBL Outstation EMBL Outstation ——The European Bioinformatics InstituteThe European Bioinformatics Institute

Excerpts from a Sample Descriptioncourtesy of M. Hoffman, S. Schmidtke, Lion BioSciences

Organism: mus musculus[ NCBI taxonomy browser ]Cell source: in-house bred mice (contact: person@somewhere.ac.uk) Sex: female [ MGED ]Age: 3 -4 weeks after birth [ MGED ]Growth conditions: normal

controlled environment20 -22 oCaverage temperaturehoused in cages according to EU legislationspecified pathogen free conditions (SPF)14 hours light cycle10 hours dark cycle

Developmental stage: stage 28 (juvenile (young) mice)) [ GXD "Mouse Anatomical Dictionary" ]Organism part: thymus [ GXD "Mouse Anatomical Dictionary" ]Strain or line: C57BL/6 [International Committee on Standardized Genetic Nomenclature for Mice]Genetic Variation: Inbr(J) 150. Origin: substrains6 and 10 were separated prior to 1937. This substrainis now probably the most widely used of all inbred strains. Substrain6 and 10 differ at the H9, Igh2 and Lvloci. Maint. by J,N, Ola. [International Committee on Standardized Genetic Nomenclature for Mice ]Treatment: in vivo [MGED] intraperitonealinjection of Dexamethasoneinto mice, 10 microgram per 25 g bodyweight of the mouseCompound: drug [MGED]synthetic glucocorticoid Dexamethasone, dissolved in PBS