]> The Ontology for Biomedical Investigations (OBI) OBI subset applied to OntONeo ontology. PERSON: Fernanda Farinelli This owl file represents the necessary entities of OBI that are reused in OntONeo Ontology. This file was created using Ontofox and some intermediary entities were not imported. Source Source label provides_service_consumer_with is_supported_by_data has_specified_input is_specified_input_of has_specified_output is_manufactured_by is_specified_output_of is_proxy_for achieves_planned_objective has grain supplies has_supplier objective_achieved_by is member of organization 2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population Person:Alan Ruttenberg Person:Alan Ruttenberg Person:Helen Parkinson Person:Helen Parkinson is member of organization Relating a legal person to an organization in the case where the legal person has a role as member of the organization has organization member specifies value of process is result of bound_to has_feature_value has specified value Viruses vírus Viruses virus Hepatitis B virus Hepatitis C virus Hepatitis A virus Bacteria Bacteria eubacteria Archaea Archaea Zika virus Homo sapiens Homo sapiens human human being man planned process 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) 6/11/9: Edited at workshop. Used to include: is initiated by an agent Bjoern Peters Injecting mice with a vaccine in order to test its efficacy We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. branch derived A processual entity that realizes a plan which is the concretization of a plan specification. This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) planned process drug role drug http://www.answers.com/topic/drug 1. A substance used in the diagnosis, treatment, or prevention of a disease or as a component of a medication. 2. Such a substance as recognized or defined by the U.S. Food, Drug, and Cosmetic Act. OBI, CDISC Role Branch a role borne by a molecular entity and is realized in a process of absorption by an organism alters, or effects (or is assumed to effect) a function(s) which inhere in an organism drug role processed material Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples Is a material entity that is created or changed during material processing. PERSON: Alan Ruttenberg processed material material processing A cell lysis, production of a cloning vector, creating a buffer. PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca Serra A planned process which results in physical changes in a specified input material OBI branch derived PERSON: Bjoern Peters material processing material transformation organization GROUP: OBI PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now. PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods. organization host role 30 Mar09 submitted by vaccine community 30Mar09 virus reproducing inside a cell; bacteria causing a disease, host can be harmed or not. we want to avoid a cat sitting on my lap and an animal care technician; these are not examples or hosts; dental cares = on tooth, but part of outer layer of tooth, so covered by "within" in the definition GROUP: Role Branch In biology, a host is an organism that harbors a virus or parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. http://en.wikipedia.org/wiki/Host_(biology) 30 March 09 OBI host role http://en.wikipedia.org/wiki/Host_(biology) host role is a role played by an organism and realized by providing nourishment, shelter or a means of reproduction to another organism within the organism playing the host role age measurement datum In MageTab file, we use initialTimePoint (a process) + age (a number expected) + TimeUnit (definied in UO, such as year, hour, day, etc.) Now we use the term label indicating the start time point of measuring the age, (number + TimeUnit) are expected instances of the class MO_178 Age PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng discussed on Nov 15, dev call All subtype will be defined by textual definition now. note that we are currently defining subtypes of age measurement datum that specify when the age is relative to, e.g. planting, as we don't have adequate temporal predicates yet. life of bearer doesn't imply organism this assay measures time not developmental stage. we recognize that development can take different time periods under different conditions such as media / temperature age as a quality is dubious; we plan to revisit stages in development are currently handled with controlled vocabulary, such as 2-somite stage A time measurement datum that is the result of measurement of age of an organism age measurement datum age since fertilization measurement datum Definition of fertilization comes from GO. MO_701 fertilization PERSON:Chris Stoeckert, Jie Zheng An age measurement datum that is the result of the measurement of the age of an organism since fertilization, the process of the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. age since fertilization measurement datum age since birth measurement datum MO_710 birth PERSON:Chris Stoeckert, Jie Zheng An age measurement datum that is the result of the measurement of the age of an organism since birth, the process of emergence and separation of offspring from the mother. age since birth measurement datum selection criterion A directive information entity which defines and states a principle of standard by which selection process may take place. OBI discussion summarized under the following tracker item : http://sourceforge.net/p/obi/obi-terms/678/ Person: Philippe Rocca-Serra rats should be aged between 6 and 8 weeks and weight between 180-250grams selection criterion selection rule selection A planned process which results in the creation of group of entity from a larger group by the application of predefined criteria. OBI PMID: 24023800. In this study, a set of eleven genes (VATP16, 60 S, UQCC, SMD3, EF1α, UBQ, SAND, GAPDH, ACT, PsaB, PTB2) was evaluated to identify reference genes during the first hours of interaction (6, 12, 18 and 24 hpi) between two V. vinifera genotypes and P. viticola. Two analyses were used for the selection of reference genes: direct comparison of susceptible, Trincadeira, and resistant, Regent, V. vinifera cultivars at 0 h, 6, 12, 18 and 24 hours post inoculation with P. viticola (genotype effect); and comparison of each genotype with mock inoculated samples during inoculation time-course (biotic stress effect). Three statistical methods were used, GeNorm, NormFinder, and BestKeeper, allowing to identify UBQ, EF1α and GAPDH as the most stable genes for the genotype effect. Person: Philippe Rocca-Serra selection selection process this term refers to a planned process and therefore is distinct from the notion of 'natural selection', a process covering the operation of natural causes by which those individuals of a species that are best adapted to the environment tend to be preserved and to transmit their characters, while those less adapted die out, so that in the course of generations the degree of adaptation to the environment tends progressively to increase. (as defined by Oxford English Dictionary) organism 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') GROUP: OBI Biomaterial Branch NCIT:C14250 SNOMEDID:R-005B2 ns2:SIO_010000 A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. WEB: http://en.wikipedia.org/wiki/Organism animal fungus organism plant virus acquisition 5/31/2012 - OBI workshop: This process is not implying ownership of the material / information. Downloading a 3D structure from the PDB. Purchasing antibodies from sigma. Bjoern Peters Following OBI call November 2012,5th: addition of a restriction to acquisition class to capture the need of having selection criteria Relates to the creation of a class 'selection rule' IEDB This needs to be fleshed out and logical definitions added that will allow to place the children terms automatically under acquisition acquisition the planned process of gaining possession of a continuant material acquisition The assumption is that the object already exists in its current state, e.g, an available mouse strain purchased from the Jackson Lab, this is the differentia from specimen creation material procurement This excludes processes that create or change materials, such as material transformations. Acquiring 50 C57BL/6 mice bred in the animal facility of the institute as a service to investigators. Purchasing 1 mg of peptides synthesized by Mimotopes at 80% purity. Getting a gift of purified CD4+ specific antibodies presented by Stephen Schoenberger at LIAI. An acquisition in which possession of a material entity is gained. Bjoern Peters, Alan Ruttenberg, Helen Parkinson IEDB material acquisition immunization Infection with influenza (the immunogen) leading to B cells producing antibodies (the effector function) against surface regions of the HA protein (the epitope). IEDB IEDB The process of an epitope that is part of or derived from an immunogen coming into contact with adaptive immune cells resulting in these cells acquiring immune effector functions specific for the epitope. immunization