Use Cases

From Program on Ontologies of Neural Structures

Contents 1 Use cases of Biologists 1.1 Giorgio: 1.2 David OS: 1.3 Query needs 1.4 Anatomist with a new atlas 1.5 New data collection efforts 2 Use cases of tool needs for Ontology Services 2.1 Data Collection 2.1.1 Labeling the data with the appropriate information 2.1.2 Locating data similar to yours 2.1.3 Naming something new 2.2 Data Discovery

Use cases of Biologists

Giorgio:

• Expert curators populating a knowledge base specific to hippocampus (?)
• Queries: what neurons have connections to what hippocampal regions

David OS:

• Expert curators populating a knowledge base specific to drosophila
• Queries: What neurons have connections to what nuclei/glomeruli (?)

Query needs

• Scientist looking for data, e.g. genes in cerebral cortex

Anatomist with a new atlas

• • receive unique IDs for each structure
  • create NeuroLex Page for each structure

New data collection efforts

• molecular biologist with 12 million to create a mouse brain protein expression atlas

Use cases of tool needs for Ontology Services

Data Collection

Labeling the data with the appropriate information

There is a project focused on collecting large amounts of similar data (e.g. MRI). They are creating metadata files and database entries associated with each dataset. They would like to access ontology services with a tool that writes the metadata to a file. This would help ensure the data collectors input appropriate information for both the metadata titles as well as the entries.

An example:

• Species (id-xxx): c57bl6J mouse (id-yyy)
• Data type (or collection method) (id-ddd) : MRI-T2 (id-mmm)
• Age (or developmental stage) (id-aaa) : P0 represented as unit=day (id-ddd) and value=0 (handled differently if age or stage)

Locating data similar to yours

An investigator has just discovered a cell type they have never seen before. How do they use a simple tool to see if anything has been reported that has the same characteristics of this cell?

Naming something new

In the previous example, the investigator cannot find anything similar in the literature or with their ontology resources to their new cell type. They would like to use a tool that uses the accepted rules of describing and subsequently naming this new cell type.

Data Discovery

An investigator is viewing an atlas in a visualization tool. This tool is tied to ontologies and their services to describe their atlases and the information tied to locations in the atlas. The investigator has identified a region of interest (ROI) in an atlas and want to find the following information:

• The name of the structure they are in and from what nomenclature it is derived
• What other nomenclatures call this location
• What cell types are found in this region (or in the structure)
• What other structures cells in this region connect to
• What genes are expressed in this area
• What genes expressed here are related to disease states
• What genes expressed here are found to have a similar expression in other species