Annotation hierarchy

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For describing spatial and temporal gene expression patterns in embryogenesis, we use only two types of relationships between CV terms; “part of” to cover spatial relations and “develops from” to cover temporal relationships among structures. Importantly, we link terms to 6 developmental stage-ranges and used “develops from” relationships exclusively to link terms that belong to consecutive stage-ranges. Our anatomical terms were organized into a hierarchical tree, starting with stage-range 1-3, which has only two CV terms (maternal, pole plasm), and progressively branching through the 6 stage ranges to reach the stage-range 13-16 with 126 anatomical terms (Figure 1). Anatomical structures that are contained within a larger structure are linked to the larger structure by the “part of” relationships (e.g. 13-16 midline glia is “part of” 13-16 midline). Anatomical structures that develop from one another across time are linked by “develops from “ relationship (for example 13-16 midline develops from 11-12 midline primordium (PR)). CV terms can have simultaneously part of and develops from relationship  (e.g. midline glioblast is part of midline PR and midline glia develops from the midline glioblast). Every term occurs in the hierarchy only once. When two terms develop into a single later structure (for example anterior and posterior midgut primordium forming midgut), the strictly hierarchical nature of the tree is broken, and both are linked to the child term (midgut) by “develops from” relationship. This fits within the directed acyclic graph (DAG) format which is used to capture many biological ontologies.

Many specific structures representing small subsets of tissues have very few or no associated genes. Throughout this article, we summarize the obtained data by focusing on subset of 131 structures that make up the most common and readily distinguishable structures in our in situ data. Genes annotated with more specific structures are collapsed into more general parent structures. For example, the terms dorsal epidermis, dorsal apodeme, dorsal histoblast nest abdominal, dorsal ridge and leading edge cell are collapsed into dorsal ectoderm. We distinguish two levels of collapsing. First, we collapse within a stage all “part of” relationships up to the parent term that the curators used frequently and therefore are readily distinguishable. The resulting blocks of terms represent the most relevant units of embryo anatomy for describing the RNA in situ results. Several such blocks may be defined within a single organ system for example trunk and head somatic and visceral musculature (TrunkSomMusc, HeadSomMusc, TrunkViscMusc, HeadViscMusc) in the muscle system.  Second, we collapse terms referring to the same organ system across a range of stages: structures from stage 4-6 are collapsed into early organ systems anlagen; structures from stages 7-8 and 9-10 into mid organ systems (suppl. Table 1); and structures from stages 11-12 and 13-16 into late organ systems (suppl. Table 2). For example, Endocrine_heart refers to the combined anatomical terms for all components of circulatory and endocrine related structures at stages 11-16 (combining blocks 11-12 CardioVAsc, 11-12 RingGland, 13-16 CardMeso, 13-16 RingGland).

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