identifier: METPO:1001000 label: observation definition: A data-collection or measurement context in which trait-relevant qualities of organisms, samples, or conditions are recorded. definition_source: DOI:10.1371/journal.pone.0154556 trait_category: UPPER term_kind: CLASS mapping_status: REVIEWED evidence: - reference: DOI:10.1371/journal.pone.0154556 snippet: data generated and the types of analysis performed notes: Supports observation as an investigation/data-generation context. - reference: DOI:10.1371/journal.pone.0154556 snippet: the output of an assay is typically a data item notes: Supports observations as links between assays, measurements, and data. causal_graphs: - graph_id: observation_measurement_upper_context title: Observation measurement upper-class context description: DOI-backed upper-ontology context graph for observations as assay or measurement outputs about material entities and qualities. Child observation records are deprecated relation/value carriers and are not expanded as mechanistic trait nodes here. nodes: - node_id: observation_trait label: observation node_type: EXPERIMENTAL_FACTOR grounding: METPO:1001000 description: Upper-level class for trait-relevant measurement observations. - node_id: assay_measurement label: assay or measurement process node_type: EXPERIMENTAL_FACTOR description: Investigation process that measures a quality. - node_id: data_item label: data item node_type: EXPERIMENTAL_FACTOR description: Information output generated by an assay or observation. - node_id: measured_quality label: measured quality node_type: TRAIT grounding: METPO:1000188 description: Quality such as temperature, pH, salinity, oxygen, or phenotype status captured by observation records. - node_id: material_entity label: material entity node_type: TRAIT grounding: METPO:1000186 description: Entity or sample about which an observation is made. - node_id: geographic_location label: geographic location node_type: ENVIRONMENTAL_FACTOR description: Contextual place metadata (e.g., location) attached to an observation data item. - node_id: material_entity_evaluant label: material entity with evaluant role node_type: TRAIT description: Generalized observed target/input of an assay, bearing an evaluant role. - node_id: measurement_datum label: measurement datum node_type: EXPERIMENTAL_FACTOR description: Information output of an observation/assay process, comparable to SOSA Result. - node_id: planned_process label: planned process node_type: EXPERIMENTAL_FACTOR description: OBI planned process with specified inputs and outputs; assays are planned processes. - node_id: sample label: sample node_type: TRAIT description: Collected material entity about which observations are made. - node_id: metadata label: metadata node_type: EXPERIMENTAL_FACTOR description: Contextual information about samples, procedures, and analysis. - node_id: mixs_standard label: MIxS reporting standard node_type: EXPERIMENTAL_FACTOR description: Standard providing per-sample metadata elements for genomic sample provenance. - node_id: fair_principles label: FAIR principles node_type: EXPERIMENTAL_FACTOR description: Principles tying observation reuse to rich metadata and persistent identifiers. - node_id: unique_identifier label: unique identifier node_type: EXPERIMENTAL_FACTOR description: Persistent identifier required for FAIR objects and datasets. edges: - subject: assay_measurement predicate: produces object: data_item description: Assays and measurements generate data items. evidence: - reference: DOI:10.1371/journal.pone.0154556 snippet: the output of an assay is typically a data item notes: Supports assay outputs as data items. predicate_id: METPO:2000202 - subject: data_item predicate: records object: measured_quality description: Observation data record a measured quality. evidence: - reference: DOI:10.1371/journal.pone.0154556 snippet: measuring its glucose concentration notes: Supports measurement outputs as records of qualities. - subject: observation_trait predicate: is about object: material_entity description: Observation records are about material entities or samples and their qualities. evidence: - reference: DOI:10.1371/journal.pone.0154556 snippet: can be about any material entity notes: Supports observations and study outputs as about material entities. - subject: observation_trait predicate: has context object: geographic_location description: Observation data items require contextual information about time and place of measurement. evidence: - reference: DOI:10.3233/sw-223096 notes: An observation data item requires a data structure to encompass the contextual information about the time and place etc. of a measurement. - subject: assay_measurement predicate: has specified input object: material_entity_evaluant description: An assay has a material entity with evaluant role as specified input. evidence: - reference: DOI:10.3233/sw-223096 notes: 'OBI: assay and has_specified_input some (material entity and has role some evaluant role); generalized, not microbe-specific.' - subject: assay_measurement predicate: has output object: measurement_datum description: An assay produces a measurement datum as output of the observation process. evidence: - reference: DOI:10.3233/sw-223096 notes: SOSA Result and IAO measurement datum are comparable outputs of an observation process. - subject: planned_process predicate: has specified input object: sample description: A planned process takes material entities such as samples as specified inputs. evidence: - reference: DOI:10.3233/sw-223096 notes: OBI has specified input/output pertain to planned process with material entities (for assays) as targets. - subject: metadata predicate: recorded in object: mixs_standard description: Sample/source-environment metadata is recorded using MIxS metadata elements. evidence: - reference: DOI:10.1007/978-1-0716-3838-5_20 notes: MIxS consists of a number of metadata elements that describe a particular characteristic of the sample or its source environment. - subject: fair_principles predicate: requires metadata object: unique_identifier description: FAIR requires each object or dataset to have a unique identifier and rich metadata. evidence: - reference: DOI:10.3389/fcimb.2024.1384809 notes: FAIR requires each FAIR object or dataset have a unique identifier and be described with rich metadata. curation_history: - timestamp: '2026-05-05T01:35:46.923123+00:00' curator: seed_from_metpo action: SEEDED_FROM_METPO changes: imported from data/raw/metpo.owl (CLASS) llm_assisted: false - timestamp: '2026-05-15T00:35:00-07:00' curator: codex action: CURATED_UPPER_CONTEXT changes: Added definition, DOI-backed evidence, and a measurement-context graph for observation; deprecated observation child records were reviewed as relation/value carriers rather than standalone mechanistic traits. llm_assisted: true - timestamp: '2026-05-20T03:35:32Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202×1). llm_assisted: true - timestamp: '2026-06-23T00:00:00Z' curator: claude action: ENRICH_CAUSAL_GRAPH changes: Added 6 evidence-backed generic edges (9 new nodes) from the deep-research report. llm_assisted: true