http://www.ebi.ac.uk/efo/EFO_0001442

protocol

OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)

study protocol

true

a protocol is a plan specification which has sufficient level of detail and quantitative information to communicate it between domain experts, so that different domain experts will reliably be able to independently reproduce the process., A protocol is an information entity which is a set of instructions that describe an how an experiment is done., A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.

PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.

http://purl.obolibrary.org/obo/IAO_0000122

plan specification, method, method used in an experiment

PlanAndPlannedProcess Branch, James Malone, Tomasz Adamusiak, Jie Zheng