Checklist for Rearrangement Class

[schristley]

• [x] Is the class an entity or a process? Is it an information entity about a material entity/process, or a pure information entity/process?

• [x] Specify the ontology URI for class. Is there a hierarchy of ontology terms that are relevant?

• [x] Define the slots for the class. Every slot should have an URI either to an ontology term or schema.org term for its semantics. Is there a hierarchy of terms that are relevant for its semantics?

• [x] Define the attributes of each slot. Identifier? Required? Data type? Controlled vocabulary or ontology for the values?

• [x] Define the direct relations to other objects. What is the cardinality of the relation? Is there an ontology URI for the relation?

• [x] If the class is a process, there should be slots for the inputs/outputs of the process. They may be directly defined in the class or are relations.

• [x] Should any slots be potential made into a class? Is the class a composite of other classes?

• [x] Review and approval by each group (ADC, IEDB, IRAD, OGRDB)

[schristley]

• [ ] Is the class an entity or a process? Is it an information entity about a material entity/process, or a pure information entity/process?

Material entity. Represents both T and B cell receptor chains. Many of the slots are observations of receptor chains using an assay (AIRR-seq is sequencing assay and generates sequencing data), and those observations are further annotated by computation analysis.

There is a subtlety here in that the observation is not of the receptor chain protein. It is an observation of a precursor material entity, either RNA or genomic DNA, with the inference that it translates to the receptor chain protein. The subtlety is that there are unproductive rearrangements, they are valid observations of DNA or RNA, but are not translatable to protein.

[schristley]

• [ ] Define the slots for the class. Every slot should have an URI either to an ontology term or schema.org term for its semantics. Is there a hierarchy of terms that are relevant for its semantics?
• [ ] Define the attributes of each slot. Identifier? Required? Data type? Controlled vocabulary or ontology for the values?
• [ ] Define the direct relations to other objects. What is the cardinality of the relation? Is there an ontology URI for the relation?

We will rely upon #28 to import the slots from AIRR Rearrangement. The slot_uri might be a challenge to automatically assign depending if we want to attach more meaning beyond primitive types. In particular, we might wish to relate various slots to gene features in the IMGT ontology.

[schristley]

This now corresponds to the AKC Chain class and slots. We defined an initial set of slots from AIRR Rearrangement. We don't expect to incorporate 100% of the data elements in AIRR Rearrangement into AKC Chain as many are annotations currently not needed by the AKC use cases, at least for this milestone. We might incorporate more later.