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

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

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

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 https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay

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

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

Relations collected from OBI branches https://wiki. cbil. upenn Relations collected from OBI branches https://wiki.cbil.upenn.edu/obiwiki/index.php/ListOfRelationships 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

New relations or definitions collected from OBI branches and others https://spreadsheets.google.com/ccc?key=p4ViR8BgYUWaAG1b5IaxcJw&hl=en since last workshop Instrument branch (20 definitions) KPC, IEDB (2 relations with definitions) Data Transformation branch (3 relations with definitions)

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

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)

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?

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

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

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