1. Status Report from Relations Branch
Liju Fan
on behalf of
Relations Branch
NCORB
s/core4/core1

2. Strategies of Development
Collect horizontal relations from OBI branches
(Bottom-Up)
Define horizontal relations and model
Assist OBI branches in identification of horizontal relations
Collaborate with Relation Ontology (RO) developers

3. Use cases Relations were collected from OBI branches based on needs
Thus, exempted from repeating their use cases ?

4. One use case
Chromium Release assay by Alan and Protocol Application branch – Write inputs and outputs for each step.
This assay records the release of radioactive labeled biological chromium from cells as a result of killer cell activity.
Some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at

5. Curated relations by the Relations branch before last workshop
has_input (Inverse: is_input_for)
has_output (inverse: is_output_for)
inputs_data
outputs_data
utilizes_reagent (inverse: is_reagent_in)
utilizes_instrument
is_proxy_for (inverse: is_represented_by)
has_function

6. Curated relations by the Relations branch after last workshop
inheres_in (inverse: has_function)
has_role
has_quality
Is_realization_of
utilizes

7. Relations collected from OBI branches https://wiki. cbil. upenn
Relations collected from OBI branches before last workshop
Inter-branch relations with domain and range
Some with definitions and examples
Flow Cytometry community (6 relations with definitions)
Transcriptomics community (6 relations with definitions)
Investigation branch (5 relations)
Biomaterial branch (2 relations)
Protocol Application branch (7 relations)
Instrument branch (20 relations)
Mixed with a few datatype annotation properties

8. New relations or definitions collected from OBI branches and others since last workshop
Instrument branch (20 definitions)
KPC, IEDB (2 relations with definitions)
Data Transformation branch (3 relations with definitions)

9. Relations submitted to RO for consideration
inheres_in (inverse: has_function)
has_input (inverse: is_input_for)
has_output (inverse: is_output_for)
has_role
has_function
has_quality
Is_realization_of
utilizes
is_proxy_for

10. Development Issues
Slow process of interacting within the relations branch and with other branches and RO
Relations with incomplete definitions (without domains or ranges, examples, or use cases)
Unclear meaning of definitions (e.g., has_base)
Relations outside of OBI scope (e.g., repels) or redundant (e.g., is_manufactured_by vs. has_make)
Generalization of specific relations applicable to low-level OBI classes (e.g., last-checked)
Proposed domains or ranges do not exist in OBI and may need to be created (e.g., data_throughput_scale)

11. User Issues Unintended use of relations (e.g., has_role)
Intended for independent continuant
Also used by induction of natural process, which is a protocol application and an occurrent
Hidden relations (e.g., protocol application)
Definition (definition_source: OBI): A protocol application is a process carried out to bring about the effect defined in the protocol applied. Every protocol_application has one or more inputs and outputs
Is the effect actually defined in a protocol, or is it the process itself that gets described?

12. Other relevant relations that RO is considering
Lacks: for negation
results_in: for change

13. Next step Short and long-term
Continue to review and define relations contributed by branches and add to OBI’s Relations.owl
Continue to discuss RO II
Short and long-term
Assist branches in identifying new relations hidden in class definitions
Assist branches in making logical definitions of classes, and classify them
Promote OBI relations to Relation Ontology

14. Acknowledgements Relations Branch Editors Alan Ruttenberg
Daniel Schober
Cristian Cocos (RO)
Other ObiBranch Editors RO
Chris Mungal (RO)
Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus