The Drosophila anatomy ontology (DAO) defines the broad anatomy of the fruitfly Drosophila melanogaster, a genetic model organism. It contains over 8700 classes, with close to half of these corresponding to neuroanatomical terms. We are systematically reviewing the DAO classes, improving the textual information and classification. This includes adding definitions, comments and synonyms, as well as formal definitions, which results in a full classification in some cases. Classes belonging to each of the defined organ systems are reviewed together to improve consistency of free text and formalisation. So far we have reviewed 7 of the 11 organs system classes, resulting in 83% of classes having a definition.
The Drosophila anatomy ontology (DAO)
When the DAO was first developed over 20 years ago, it did
not include textual information or significant formalisation.
A large effort has been undertaken in the last 9 years to
improve this situation
The neuroanatomy field has grown massively in the last few years thanks to technical advances, enabling researchers to identify and characterize the function of individual neurons and several projects are currently underway to map all neurons in a variety of model organisms. We, in collaboration with the Virtual Fly Brain project, have focused on capturing this information in Drosophila. Currently, 46% of the DAO comprises terms that are part of the nervous system, including close to 2300 distinct neuron classes, over 220 neuroblast lineage clones and neuropils.
Here, we present our most recent work in improving the textual information and formalisation patterns of DAO classes. 2
In order to maintain consistency between related terms, we are reviewing existing classes by making use of their current classification into 11 different organ systems, such as the tracheal, muscle, adipose, etc. Around 80% of classes in the DAO had previously been classified as part of an organ system previously, thus making it easy to retrieve a list of classes to review. Work has proceeded class by class, improving both the textual information and formalisation. When necessary, we have sought advice from expert researchers. The systematic review of classes uncovered several cases of redundancy and duplication, which were resolved by obsoleting one of the terms. For example, the classes Malpighian tubule Type II cell (see section 2.1) and excretory star cell were found to refer to same entity. In this case, the latter was obsoleted, and the name added as a synonym to the former.
We have concluded this review for 7 of the 11 organ systems (muscle, tracheal, reproductive, digestive, circulatory, excretory and adipose), corresponding to 570 classes. Work is ongoing to complete the remaining (muscle, nervous, endocrine and sensory).
We have added textual definitions to 83% of DAO classes, an improvement of 10% since October 2013. The definition describes the general classification of the anatomical entity, its properties, and when appropriate, any distinguishing traits. These statements are supported by references, either cited in the text, or listed at the end with a publication identifier (mostly a FlyBase one: prefix FBrf followed by 7 digits).
Comments are added when appropriate, for one of two reasons. The first is to provide relevant information relating to the experimental setup when, for example, investigating the function of a neuron. The second is to clarify the relationship between competing nomenclatures.
Synonyms from the published literature are added to each class, together with references. The addition of synonyms has particular relevance to anatomy ontologies, for which competing nomenclatures often exist.
An example of the textual information for a class is below: name: Malpighian tubule Type II cell definition: "Morphologically distinct cell type found only in the initial, transitional and main segments of the Malpighian tubules interspersed with Type I cells. Type II cells are smaller and flatter than Type I cells, with shorter (main segment) or no (initial region) apical microvilli. Type II cells originate from a subset of caudal visceral mesoderm cells that overlie the tubule primordia as they evert from the hindgut. By stage 15, Type II cells have been incorporated in the tubules and adopt epithelial characteristics. In the mature tubules there are on average 110 Type II cells." [FlyBase:FBrf0064792, FlyBase:FBrf0102373, FlyBase:FBrf0160477, FlyBase:FBrf0222532] comment: These cells are involved in primary urine production via the presence of ion channels that allow chloride and water to enter the tubule lumen (O'Donnell et al., 1998). synonyms: "excretory star cell" EXACT; "Malpighian tubule stellate cell" EXACT [FlyBase:FBrf0030988]
In systems such as the tracheal, in which certain structures are repeated in each metameric unit, adding a formal definition to each of these terms significantly increases the robustness of error checking procedures. An example of some of the relationships that are added is below: name: adult abdominal spiracular branch intersection_of: FBbt:00003071 ! adult spiracular branch intersection_of: connected_to FBbt:00003040 ! adult lateral trunk intersection_of: connected_to FBbt:00004814 ! adult abdominal spiracle intersection_of: part_of FBbt:00003024 ! adult abdominal segment In other instances, adding a formal definition allows for full classification of terms. This becomes particularly relevant for neuroanatomy, a field in which new neuron types are being frequently described. Having a formal definition for a class ensures that new terms are correctly classified, provided that enough information is available, such as developmental origin.
An example of a neuron class that can be fully classified based on expression (which identifies this subset of very well studied neurons) and developmental origin is below. This formalisation pattern, or a similar one (excluding only the neuroblast information), was used to define the 104 classes of adult fruitless neurons.
name: adult fruitless aDT-b (female) neuron intersection_of: FBbt:00005106 ! neuron intersection_of: develops_from FBbt:00050148 ! neuroblast CREa1 (female) intersection_of: expresses FlyBase:FBgn0004652 ! fruitless intersection_of: part_of FBbt:00110416 ! adult fruitless aDT-b (female) lineage clone
We have reviewed terms that belong to 7 of the 11 organ systems in the DAO, improving the textual information essential for casual users, and the formalisation necessary to easily maintain a correct classification and to prevent the introduction of errors. Reviewing related classes as a group helps to maintain consistency in the ontology, both in terms of free text and the formalisation patterns used.
Future work will focus on completing the systematic review of the DAO by revising the classes in the remaining 4 organ systems.