Functional Genomics Investigation Ontology Ryan R. Brinkman, Helen C. Causton, Liju Fan, Dawn Field, Jennifer Fostel, Gilberto Fragoso, Tanya Gray, Mervi Heiskanen, Tina Hernandez-Boussard, Norman Morrison, Helen Parkinson, Philippe Rocca-Serra, Susanna-Assunta Sansone, Daniel Schober, Barry Smith, Robert Stevens, Chris Stoeckert, Chris Taylor, Trish Whetzel, Joe White, Andrew Wood An ontology for the annotation of functional genomics experiments. en the Functional Genomics Investigation Ontology (FuGO) is a collaborative, international effort which will serve as a resource for annotating functional genomics investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. FuGO will contain both terms that are common to all functional genomics investigations and those that are domain specific. 2006-06-14 0.2 study_report e.g. whole individual, mouse, human etc study_organism document mobile_phase column_chromatography_solvent environment a dependent enduring entity which is the set of ranges of conditions surrounding an independent entity LC_software_control_mode one of the variables under examination in the study study_factor an object that describes a protocol protocol_document an inherent purpose of the entity function conclusion a study in which time is not a variable e.g. an experiment that documents a particular point in time, a ‘snap shot’; experiment, such as a proteomics or microarray experiment in which the absolute time at which the samples are taken is not immediately relevant/a factor in the experiment. time-independent_study software_testing_objective The aim of the study is designed to examine the effects of using different software, software parameters, or algorithms (e.g. data processing software). as in environmental variable a location that is shaped by the space around it (a site is not made of matter). site continuant a thing which endures through time. continuant time_point a stage at which something happens. May be measured in absolute time weds 9am, or relative time e.g. phase of the moon. part of study; relevant to study outcome; to study participants; during study timeline unscheduled_process study in which time is important e.g. ‘real time’ metabonomics experiments in which measurements are taken over a time course. a study in which time is a variable study_with_timeline LC_software plan of the timeline timeline_protocol order e.g. putting into order column_chromatography_matrix stationary_phase study_object actual participant in a study dependent_continuant a continuant whose manifestation requires another entity, e.g. temperature of an organism dose_effect a set of machine instructions software the part played by an entity within the context of a process role e.g. lunar cycle, Time intervals are labeled. Includes all time (non-relativistic). time_interval event an instantaneous point in time number_designation modification_of_design assay_protocol characteristic measurable_entity a dependant enduring entity which can be measured; syn: measurable entity parameter Chris T means dose and rpm; cardinal part of protocol; Barry: not clear why we have this; do not need measurement a term that describes a protocol but which doesn’t exist in the absence of the protocol. Some parameters are set e.g. settings on an instrument, sex of an organism. Hue, saturation and brightness don’t exist without colour. LC_instrument a thing that occurs during time. occurrent occurrent hypothesis cardinal_part_of_LC_instrument cardinal_part_of_quantitative_value e.g. yeast culture, group of Icelandic fishermen. study_population a continuant which exists on it's own, e.g. an organism independent_continuant platform standalone equipment & consumables that performs protocol 'x' perturbation_role {en} starting of timeline, part of study timeline_protocol_application A part of the design specification that is cardinally relevant within the context of the entire study or investigation, e.g., a protocol, the hypothesis/hypotheses, an objective or a variable. cardinal_part_of_design_specification study_sample e.g. liver from a person (in this case the details of the individual are characteristics of the study sample) , water taken from a pond. a series of planned actions which is recorded/ a set of instructions that can be followed. It does not include unintended events e.g. earthquakes that occur while the experiment and is distinct from the protocol document which is an object that gets written down. A protocol may be used in multiple experimental designs. protocol measured_value the process of applying one or more protocols assay the plan that can be realized in a process design_specification this is an actual part of the experiment. It includes the protocol that the experimenter intends to carry out, deviations from this and unintended variables, such as the earthquake that occurred while the experiment was taking place. has an input entity and an output entity protocol_application part of study spatial_region cardinal_part_of_value study_phase process lcms_platform sex_effect A variable in an experiment that is designed to look at differences between organisms of different genders, mating types etc. investigation a set of studies that are designed to address a related question. It may include individual studies that are domain specific(?) , microarray, proteomics. reported_value characteristic or pre-set on instrument confidence_interval cardinal_part_of_qualitative_value role of data or material played by an entity at the end of a process output_role measuring? measuring chromatography_column cardinal_part_of_protocol_application unit analysis_protocol child of protocol final_transformation_of_study_data record tells you how the experiment really proceeded. Might not be the method the protocol described. datum pump_valve_switch data_set observing microarray_platform study_design_specification the plan for the execution of the study objective motivation/reason for doing experiment. input_role role of data or material played by an entity at the start of a process intensity parameter_value_setting e.g. turning the centrifuge to 4 degrees MS_instrument set_parmameter_value cardinal_part_of_protocol a part of protocol that is relevant within the context of the whole protocol a dependent continuant which is realizable through a process; example: a Study executes a Study Design. (a thing that can be executed or run) e candidate name = executable; doesn't work for all realizable_continuant consumables physical entity object dimension measurable scale; very restrictive values are subtypes of attributes quality executes the study design study cardinal_part_of_instrument instrument