diff --git a/obi.owl b/obi.owl index 945e655a..5495774f 100755 --- a/obi.owl +++ b/obi.owl @@ -13,7 +13,7 @@ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + en Ontology for Biomedical Investigations Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester @@ -80,7 +80,7 @@ http://creativecommons.org/licenses/by/4.0/ Ontology for Biomedical Investigations Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. - 2023-07-25 + 2023-09-20 @@ -9317,6 +9317,7 @@ JAR: A data item is an approximately justified approximately true approximate be PERSON: Chris Stoeckert PERSON: Jonathan Rees data + data item @@ -9375,6 +9376,7 @@ JAR: A data item is an approximately justified approximately true approximate be Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. PERSON: Chris Stoeckert OBI_0000142 + information content entity @@ -19111,7 +19113,8 @@ that has_part some material entity is a material entity. If we add as equivalent manufacturing - Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process + A planned process with the objective to produce a processed material which will have a function for future use. + A person or organization (having manufacturer role) is a participant in this process Manufacturing implies reproducibility and responsibility AR This includes a single scientist making a processed material for personal use. PERSON: Bjoern Peters @@ -24402,9 +24405,9 @@ http://sourceforge.net/p/obi/obi-terms/716/ vaccine preparation The production of B. pertussis vaccine. - vaccine preparation is a planned process with specified output a vaccine + A planned process with the objective to create a vaccine. OBI - vaccine preparation + vaccine production @@ -25907,8 +25910,9 @@ http://en.wikipedia.org/wiki/Survival_rate informing investigator of subject study arm + Informing the investigator whether a patient is receiving a placebo or a treatment with an investigational compound. - A process in which an investigator is made aware of which study arm that a patient is participating in, for example whether they are receiving a placebo or a treatment with an investigational compound. + A planned process with the objective to make the investigator aware of which study arm a patient is participating in. 09/28/2009 Alan Ruttenberg. This and the class informing-subject-of-study-arm are defined in order to solve the question of how to represent single and double blind experiments. To represent the aspect of double blinding pertaining to investigators, we say that the study execution doesn't include any processes of this sort Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case @@ -25986,7 +25990,7 @@ http://en.wikipedia.org/wiki/Survival_rate presentation of stimulus The presentation of a flashing light to a monkey during reward training - a planned process in which an organism is exposed to some stimulus with the intent to invoke an action + A planned process with the objective to expose an organism to a stimulus. Helen Parkinson, Jessica Turner, Dirk Derom stimulation of organism Helen Parkinson, Jessica Turner, Dirk Derom @@ -26077,7 +26081,7 @@ http://en.wikipedia.org/wiki/Survival_rate informed consent process - A planned process in which a person or their legal representative is informed about key facts about potential risks and benefits of a process and makes a documented decision as to whether the person in question will participate. + A planned process with the objective to inform a person or their legal representative of legally and ethically relevant facts about a process that the person in question is asked to participate in, and which results in a documented decision as to whether the person in question will participate. 09/28/2009 Alan Ruttenberg: This is made a subclass of the higher level processual entity in BFO because I don't want to take a stand on whether it is a process aggregate. Analogous to the situation with Material entity. Person:Alan Ruttenberg http://clinicaltrials.gov/ct2/info/glossary#informed @@ -26699,7 +26703,7 @@ http://en.wikipedia.org/wiki/Survival_rate material maintenance - a process with that achieves the objective to maintain some or all of the characteristics of an input material over time + A planned process with the objective to maintain some or all of the characteristics of an input material over time. material maintenance @@ -26753,7 +26757,7 @@ placeholder unblinding process - The part of the study execution in which the subjects are told what study arm they are in and in which the investigators are told which subjects are in which trials + A planned process that is the part of the study execution in which the subjects are told what study arm they are in and in which the investigators are told which subjects are in which trials. Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case unblinding process @@ -26773,7 +26777,7 @@ placeholder subject agrees they understand informed consent document - A process in which a subject receives an informed consent document and agrees that they have understood it + A planned process in which a subject receives an informed consent document and agrees that they have understood it. 09/28/2009 Alan Ruttenberg. There's a need for a general process like this in IAO - document and person in, signed document (and associated obligations, rights, out Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case @@ -26806,8 +26810,9 @@ placeholder informing subject of study arm + Informing participants whether they are receiving a placebo or a treatment with an investigational compound. - A process in which the subject is made aware of which study arm they are participating in, for example whether they are receiving a placebo or a treatment with an investigational compound. + A planned process with the objective to make the subject aware of which study arm they are participating in. 09/28/2009 Alan Ruttenberg. This and the class informing-investigator-of-study-arm are defined in order to solve the question of how to represent single and double blind experiments. To represent the aspect of blinding pertaining to subjects (happens in single and double blinding) we say that that the study execution doesn't include any processes of this sort Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case @@ -28217,6 +28222,7 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. + in vitro cell killing assay Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to tissue culture plates, and 1:2 serial dilutions of effectors were made. After a 4-h incubation of the effector cells with the target cells, supernatants were collected and counted with the LKB 1272 Clinigamma counter. Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100. @@ -28232,6 +28238,7 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. + @@ -28325,8 +28332,7 @@ Dev call Nov 22, 2010: To reflect this, the term's label has been updated t supplying Jackson Labs supplies mouse strains. - The planned process of providing material entities -to be used in an investigation. + A planned process with the objective to provide material entities to be used in an investigation. Jennifer Fostel Jennifer Fostel 5/31/2012: A supplying process implies that there is an acquisition process. These may need to be tied together, so that modeling either way is reciprocal. @@ -29180,7 +29186,7 @@ Added duirng Mar 1, 2010 dev call study intervention - the part of the execution of an intervention design study which is varied between two or more subjects in the study + A planned process that is the part of the execution of an intervention design study which is varied between two or more subjects in the study. PERSON: Bjoern Peters GROUP: OBI study intervention @@ -53213,7 +53219,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + @@ -64122,7 +64128,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ selection 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. - A planned process which results in the creation of group of entity from a larger group by the application of predefined criteria. + A planned process with the objective to create a group of entities by applying a predefined criteria to a larger group of entities. 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) Person: Philippe Rocca-Serra selection process @@ -64731,7 +64737,7 @@ PMID: 23587118. freezing - A planned process in which a material entity has it's temperature lowered to below the freezing point in order to bring it to a state in which it can be maintained at this lower temperature in order to preserve some of its qualities. + A planned process with the objective to bring some material entity to a temperature below its freezing point. Person: Mathias Brochhausen, Jie Zheng Mathias Brochhausen freezing @@ -78840,7 +78846,7 @@ https://www.doi.org/ machine learning - A planned process in which statistical techniques are used to give computers the ability to learn about patterns in data, without being explicitly programmed. Learning is defined in this case as progressively improving performance on a specific task. + A planned process with the objective to give a computer the ability to use patterns in data to progressively improve its performance on a specific task, achieved by using statistical techniques instead of explicitly programming the ability. Mark A. Miller https://en.wikipedia.org/wiki/Machine_learning https://github.com/TrisSN @@ -87990,6 +87996,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre A sequencing assay that determines the sequences of DNA or RNA molecules that encode the repertoire of T cell receptors within an input sample. Rebecca Jackson TCR repertoire sequencing assay + bulk TCR assay doi:10.1186/s12896-017-0379-9 https://github.com/obi-ontology/obi/issues/1307 T cell receptor repertoire sequencing assay @@ -88007,6 +88014,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre Rebecca Jackson Antibody repertoire sequencing assay BCR repertoire sequencing assay + bulk BCR assay doi:10.1186/s12896-017-0379-9 https://github.com/obi-ontology/obi/issues/1307 B cell receptor repertoire sequencing assay @@ -100522,7 +100530,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre functional assessment of individual - A physical examination of an individual's ability to perform functional activities. + A physical examination of an organism's ability to perform functional activities. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -101608,7 +101616,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre observational assessment of individual - A physical examination of an individual through visual assesment. + A physical examination of an organism through visual assesment. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -102649,6 +102657,531 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + + + + + + + + + + + + + + + + cell culture assay + + An assay that has cell culture as an input. + Randi Vita + Sebastian Duesing + cell culture assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + serum anti-Epstein-Barr virus antibody level assay + + An antigen specific antibodies assay that is meant to detect antibodies that bind to Epstein-Barr virus (EBV) antigens in a serum sample. + Randi Vita + Sebastian Duesing + EBV + serum anti-Epstein-Barr virus antibody level assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + serum anti-cytomegalovirus antibody level assay + + A CMV antibody assay that has serum as an input. + Randi Vita + Sebastian Duesing + CMV + serum anti-cytomegalovirus antibody level assay + + + + + + + + + + + + + + + chronic allograft damage index score + + A clinical data item that quantifies the degree of tissue damage in biopsies taken from transplanted kidneys. + Sebastian Duesing + CADI + chronic allograft damage index score + + + + + + + + + sequential organ failure assessment score + + A clinical data item that quantifies the degree of function of a critically ill patient's organs. + Sebastian Duesing + SOFA score + https://en.wikipedia.org/wiki/SOFA_score + sequential organ failure assessment score + + + + + + + + + + + + + + + physician's global assessment of disease activity + + A clinical data item that quantifies a physician's judgement of the overall activity of some specific disease in a patient. + Sebastian Duesing + MD global, PGA + physician's global assessment of disease activity + + + + + + + + + human leukocyte antigen mismatch count + + A genetic characteristics information that is about the number of dissimilarities in the human leukocyte antigen gene complexes of two humans. + Sebastian Duesing + HLA mismatch count, HLA mismatch + human leukocyte antigen mismatch count + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + nasal lavage fluid + + A specimen collected through nasal cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the nasal cavity space. + Randi Vita + Sebastian Duesing + nasal lavage fluid + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + single cell B cell receptor repertoire sequencing assay + + A B cell receptor repertoire sequencing assay that determines the sequence of DNA or RNA molecules that encode the repertoire of B cell receptors that can be traced to a single cell of origin. + Randi Vita + Sebastian Duesing + single-cell BCR assay + single cell B cell receptor repertoire sequencing assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + single cell T cell receptor repertoire sequencing assay + + A T cell receptor repertoire sequencing assay that determines the sequence of DNA or RNA molecules that encode the repertoire of T cell receptors that can be traced to a single cell of origin. + Randi Vita + Sebastian Duesing + single-cell TCR assay + single cell T cell receptor repertoire sequencing assay + + + + + + + + + hypertension grade + + A categorical value specification that indicates the severity of hypertension. + Bjoern Peters + Randi Vita + Sebastian Duesing + hypertension grade + + + + + + + + + quartz crystal microbalance assay + + An assay that measures the change in frequency of a quartz crystal resonator resulting from the addition or removal of a small mass of a ligand specifically binding at the surface of the resonator. + Bjoern Peters + Randi Vita + Sebastian Duesing + QCM + http://www.ncbi.nlm.nih.gov/pubmed/23504432 + https://en.wikipedia.org/wiki/Quartz_crystal_microbalance + quartz crystal microbalance assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + quartz crystal microbalance measuring the dissociation constant [KD] of a B cell epitope:antibody complex + + A quartz crystal microbalance assay that measures the dissociation constant [KD] of an antigen binding with an antibody. + Bjoern Peters + Randi Vita + Sebastian Duesing + QCM measuring KD + IEDB + dissociation constant KD|quartz crystal microbalance|nM + quartz crystal microbalance assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex + + + + + + + + + multiplexed error-robust fluorescence in situ hybridization assay + + A fluorescence in-situ hybridization assay that uses combinatorial FISH labeling with error resistant encoding schemes for highly multiplexed single-molecule imaging. + Sebastian Duesing + MERFISH + https://en.wikipedia.org/wiki/Fluorescence_in_situ_hybridization#MERFISH + https://github.com/obi-ontology/obi/issues/1724 + Brain Image Library + multiplexed error-robust fluorescence in situ hybridization assay + + + + + + + + + single molecule fluorescence in situ hybridization + + A fluorescence in-situ hybridization assay that detects single RNA molecules in fixed cells, allowing for both the quantification and localization at the single-cell level and single-molecule resolution. + Sebastian Duesing + smFISH + https://doi.org/10.21769/BioProtoc.3070 + https://github.com/obi-ontology/obi/issues/1725 + Brain Image Library + single molecule fluorescence in situ hybridization + + + + + + + + + + + + + + + Illumina NextSeq 1000 + + A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells. + Sebastian Duesing + NextSeq 1000 + https://www.illumina.com/systems/sequencing-platforms/nextseq-1000-2000.html + https://github.com/obi-ontology/obi/issues/1711 + GENEPIO + Illumina NextSeq 1000 + + + + @@ -103096,7 +103629,7 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from - + primary cultured cell population Spleen cells put directly into culture; Cold storage of biopsies from wild endangered native Chilean species in field conditions and subsequent isolation of primary culture cell lines. In Vitro Cell Dev Biol Anim. 2008 Jul 2. PMID: 18594934 cells that have been isolated from some organismal source, expanded in culture, but not undergone a complete passaging (ie are still in culture, or have been lifted from culture and frozen in aliquots for future use) @@ -103109,7 +103642,7 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from PERSON:Matthew Brush primary cultured cell population - + 0 @@ -103117,7 +103650,7 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from - + consider if we really want to be so strict here . . . ie maybe we we say that they have not been output from an 'establishing cell line' process, but in some cases a passage or two may be allowed for a primary culture. the establishing of a line requires some procedss that attains a degree of homogeneity in the culture. @@ -105564,7 +106097,7 @@ In this equation b0 is the regression coefficient for the intercept and the bi v data visualization Generation of a heatmap from a microarray dataset - An planned process that creates images, diagrams or animations from the input data. + A planned process with the objective to graphically represent some data by inputing the data and outputting images, diagrams or animations. Elisabetta Manduchi James Malone Melanie Courtot @@ -108280,7 +108813,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 storage PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10. - A maintenance process by which material entities that are not actively metabolizing are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability + A planned process with the objective to preserve and protect material entities by placing them in an identified location which may have a controlled environment. Philippe Rocca-Serra OBI-Branch storage @@ -111990,7 +112523,7 @@ https://sourceforge.net/p/obi/obi-terms/738/ acquisition Downloading a 3D structure from the PDB. Purchasing antibodies from sigma. - the planned process of gaining possession of a continuant. + A planned process with the objective of gaining possession of an entity. 5/31/2012 - OBI workshop: This process is not implying ownership of the material / information. Following OBI call November 2012,5th: addition of a restriction to acquisition class to capture the need of having selection criteria @@ -112489,7 +113022,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ maintaining cell culture When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture - a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing + A planned process with the objective to keep cells alive in a defined environment outside of an organism. PlanAndPlannedProcess Branch OBI branch derived maintaining cell culture @@ -112690,6 +113223,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ + @@ -114484,7 +115018,7 @@ Possible ecological risks of transgenic organism release when transgenes affect Immunization in vitro - Process of administering an object playing the role of immunogen to a cell culture + A planned process with the objective to administer an object playing the role of immunogen to a cell culture. IEDB IEDB Immunization in vitro @@ -145448,6 +145982,18 @@ realizes some 'host of immune response role' + + + + + clinical data item + A data item that is about a patient and is the specified output of a health care process assay or diagnostic process + + clinical data item + + + + @@ -147255,7 +147801,7 @@ realizes some 'host of immune response role' anatomical cluster - Anatomical group that has its parts adjacent to one another. + Anatomical group whose component anatomical structures lie in close proximity to each other. anatomical cluster diff --git a/views/NIAID-GSC-BRC.owl b/views/NIAID-GSC-BRC.owl index a6522054..6eba5cc0 100644 --- a/views/NIAID-GSC-BRC.owl +++ b/views/NIAID-GSC-BRC.owl @@ -11,7 +11,7 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"> - + en Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester Alan Ruttenberg @@ -77,7 +77,7 @@ http://creativecommons.org/licenses/by/4.0/ Ontology for Biomedical Investigations Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. - 2023-07-25 + 2023-09-20 @@ -2003,6 +2003,7 @@ JAR: A data item is an approximately justified approximately true approximate be PERSON: Chris Stoeckert PERSON: Jonathan Rees data + data item @@ -2048,6 +2049,7 @@ JAR: A data item is an approximately justified approximately true approximate be Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. PERSON: Chris Stoeckert OBI_0000142 + information content entity @@ -3837,7 +3839,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ material maintenance - a process with that achieves the objective to maintain some or all of the characteristics of an input material over time + A planned process with the objective to maintain some or all of the characteristics of an input material over time. material maintenance @@ -6136,6 +6138,31 @@ http://vivoweb.org/ontology/core#FundingOrganization + + + + + + + + + + + + + + + + cell culture assay + + An assay that has cell culture as an input. + Randi Vita + Sebastian Duesing + cell culture assay + + + + @@ -6420,7 +6447,7 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from storage PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10. - A maintenance process by which material entities that are not actively metabolizing are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability + A planned process with the objective to preserve and protect material entities by placing them in an identified location which may have a controlled environment. Philippe Rocca-Serra OBI-Branch storage @@ -6578,7 +6605,7 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from maintaining cell culture When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture - a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing + A planned process with the objective to keep cells alive in a defined environment outside of an organism. PlanAndPlannedProcess Branch OBI branch derived maintaining cell culture @@ -7042,7 +7069,7 @@ realizes some 'host of immune response role' anatomical cluster - Anatomical group that has its parts adjacent to one another. + Anatomical group whose component anatomical structures lie in close proximity to each other. anatomical cluster diff --git a/views/obi-base.owl b/views/obi-base.owl index cb301e74..c52c9b00 100644 --- a/views/obi-base.owl +++ b/views/obi-base.owl @@ -13,7 +13,7 @@ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + en Ontology for Biomedical Investigations Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester @@ -80,7 +80,7 @@ http://creativecommons.org/licenses/by/4.0/ Ontology for Biomedical Investigations Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. - 2023-07-25 + 2023-09-20 @@ -9704,7 +9704,8 @@ that has_part some material entity is a material entity. If we add as equivalent manufacturing - Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process + A planned process with the objective to produce a processed material which will have a function for future use. + A person or organization (having manufacturer role) is a participant in this process Manufacturing implies reproducibility and responsibility AR This includes a single scientist making a processed material for personal use. PERSON: Bjoern Peters @@ -14954,9 +14955,9 @@ http://sourceforge.net/p/obi/obi-terms/716/ vaccine preparation The production of B. pertussis vaccine. - vaccine preparation is a planned process with specified output a vaccine + A planned process with the objective to create a vaccine. OBI - vaccine preparation + vaccine production @@ -16435,8 +16436,9 @@ http://en.wikipedia.org/wiki/Survival_rate informing investigator of subject study arm + Informing the investigator whether a patient is receiving a placebo or a treatment with an investigational compound. - A process in which an investigator is made aware of which study arm that a patient is participating in, for example whether they are receiving a placebo or a treatment with an investigational compound. + A planned process with the objective to make the investigator aware of which study arm a patient is participating in. 09/28/2009 Alan Ruttenberg. This and the class informing-subject-of-study-arm are defined in order to solve the question of how to represent single and double blind experiments. To represent the aspect of double blinding pertaining to investigators, we say that the study execution doesn't include any processes of this sort Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case @@ -16513,7 +16515,7 @@ http://en.wikipedia.org/wiki/Survival_rate presentation of stimulus The presentation of a flashing light to a monkey during reward training - a planned process in which an organism is exposed to some stimulus with the intent to invoke an action + A planned process with the objective to expose an organism to a stimulus. Helen Parkinson, Jessica Turner, Dirk Derom stimulation of organism Helen Parkinson, Jessica Turner, Dirk Derom @@ -16602,7 +16604,7 @@ http://en.wikipedia.org/wiki/Survival_rate informed consent process - A planned process in which a person or their legal representative is informed about key facts about potential risks and benefits of a process and makes a documented decision as to whether the person in question will participate. + A planned process with the objective to inform a person or their legal representative of legally and ethically relevant facts about a process that the person in question is asked to participate in, and which results in a documented decision as to whether the person in question will participate. 09/28/2009 Alan Ruttenberg: This is made a subclass of the higher level processual entity in BFO because I don't want to take a stand on whether it is a process aggregate. Analogous to the situation with Material entity. Person:Alan Ruttenberg http://clinicaltrials.gov/ct2/info/glossary#informed @@ -17217,7 +17219,7 @@ http://en.wikipedia.org/wiki/Survival_rate material maintenance - a process with that achieves the objective to maintain some or all of the characteristics of an input material over time + A planned process with the objective to maintain some or all of the characteristics of an input material over time. material maintenance @@ -17271,7 +17273,7 @@ placeholder unblinding process - The part of the study execution in which the subjects are told what study arm they are in and in which the investigators are told which subjects are in which trials + A planned process that is the part of the study execution in which the subjects are told what study arm they are in and in which the investigators are told which subjects are in which trials. Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case unblinding process @@ -17291,7 +17293,7 @@ placeholder subject agrees they understand informed consent document - A process in which a subject receives an informed consent document and agrees that they have understood it + A planned process in which a subject receives an informed consent document and agrees that they have understood it. 09/28/2009 Alan Ruttenberg. There's a need for a general process like this in IAO - document and person in, signed document (and associated obligations, rights, out Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case @@ -17324,8 +17326,9 @@ placeholder informing subject of study arm + Informing participants whether they are receiving a placebo or a treatment with an investigational compound. - A process in which the subject is made aware of which study arm they are participating in, for example whether they are receiving a placebo or a treatment with an investigational compound. + A planned process with the objective to make the subject aware of which study arm they are participating in. 09/28/2009 Alan Ruttenberg. This and the class informing-investigator-of-study-arm are defined in order to solve the question of how to represent single and double blind experiments. To represent the aspect of blinding pertaining to subjects (happens in single and double blinding) we say that that the study execution doesn't include any processes of this sort Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case @@ -18809,8 +18812,7 @@ Dev call Nov 22, 2010: To reflect this, the term's label has been updated t supplying Jackson Labs supplies mouse strains. - The planned process of providing material entities -to be used in an investigation. + A planned process with the objective to provide material entities to be used in an investigation. Jennifer Fostel Jennifer Fostel 5/31/2012: A supplying process implies that there is an acquisition process. These may need to be tied together, so that modeling either way is reciprocal. @@ -19644,7 +19646,7 @@ Added duirng Mar 1, 2010 dev call study intervention - the part of the execution of an intervention design study which is varied between two or more subjects in the study + A planned process that is the part of the execution of an intervention design study which is varied between two or more subjects in the study. PERSON: Bjoern Peters GROUP: OBI study intervention @@ -52790,7 +52792,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ 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. - A planned process which results in the creation of group of entity from a larger group by the application of predefined criteria. + A planned process with the objective to create a group of entities by applying a predefined criteria to a larger group of entities. 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) Person: Philippe Rocca-Serra selection process @@ -53369,7 +53371,7 @@ PMID: 23587118. - A planned process in which a material entity has it's temperature lowered to below the freezing point in order to bring it to a state in which it can be maintained at this lower temperature in order to preserve some of its qualities. + A planned process with the objective to bring some material entity to a temperature below its freezing point. Person: Mathias Brochhausen, Jie Zheng Mathias Brochhausen freezing @@ -66559,7 +66561,7 @@ https://www.doi.org/ machine learning - A planned process in which statistical techniques are used to give computers the ability to learn about patterns in data, without being explicitly programmed. Learning is defined in this case as progressively improving performance on a specific task. + A planned process with the objective to give a computer the ability to use patterns in data to progressively improve its performance on a specific task, achieved by using statistical techniques instead of explicitly programming the ability. Mark A. Miller https://en.wikipedia.org/wiki/Machine_learning https://github.com/TrisSN @@ -75203,6 +75205,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre A sequencing assay that determines the sequences of DNA or RNA molecules that encode the repertoire of T cell receptors within an input sample. Rebecca Jackson TCR repertoire sequencing assay + bulk TCR assay doi:10.1186/s12896-017-0379-9 https://github.com/obi-ontology/obi/issues/1307 T cell receptor repertoire sequencing assay @@ -75218,6 +75221,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre Rebecca Jackson Antibody repertoire sequencing assay BCR repertoire sequencing assay + bulk BCR assay doi:10.1186/s12896-017-0379-9 https://github.com/obi-ontology/obi/issues/1307 B cell receptor repertoire sequencing assay @@ -86705,7 +86709,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A physical examination of an individual's ability to perform functional activities. + A physical examination of an organism's ability to perform functional activities. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -87721,7 +87725,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A physical examination of an individual through visual assesment. + A physical examination of an organism through visual assesment. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 @@ -88700,6 +88704,499 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + + + + + + + + + + + + + + + An assay that has cell culture as an input. + Randi Vita + Sebastian Duesing + cell culture assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An antigen specific antibodies assay that is meant to detect antibodies that bind to Epstein-Barr virus (EBV) antigens in a serum sample. + Randi Vita + Sebastian Duesing + EBV + serum anti-Epstein-Barr virus antibody level assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A CMV antibody assay that has serum as an input. + Randi Vita + Sebastian Duesing + CMV + serum anti-cytomegalovirus antibody level assay + + + + + + + + + + + + + + + A clinical data item that quantifies the degree of tissue damage in biopsies taken from transplanted kidneys. + Sebastian Duesing + CADI + chronic allograft damage index score + + + + + + + + + A clinical data item that quantifies the degree of function of a critically ill patient's organs. + Sebastian Duesing + SOFA score + https://en.wikipedia.org/wiki/SOFA_score + sequential organ failure assessment score + + + + + + + + + + + + + + + A clinical data item that quantifies a physician's judgement of the overall activity of some specific disease in a patient. + Sebastian Duesing + MD global, PGA + physician's global assessment of disease activity + + + + + + + + + A genetic characteristics information that is about the number of dissimilarities in the human leukocyte antigen gene complexes of two humans. + Sebastian Duesing + HLA mismatch count, HLA mismatch + human leukocyte antigen mismatch count + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A specimen collected through nasal cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the nasal cavity space. + Randi Vita + Sebastian Duesing + nasal lavage fluid + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + single cell B cell receptor repertoire sequencing assay + A B cell receptor repertoire sequencing assay that determines the sequence of DNA or RNA molecules that encode the repertoire of B cell receptors that can be traced to a single cell of origin. + Randi Vita + Sebastian Duesing + single-cell BCR assay + single cell B cell receptor repertoire sequencing assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + single cell T cell receptor repertoire sequencing assay + A T cell receptor repertoire sequencing assay that determines the sequence of DNA or RNA molecules that encode the repertoire of T cell receptors that can be traced to a single cell of origin. + Randi Vita + Sebastian Duesing + single-cell TCR assay + single cell T cell receptor repertoire sequencing assay + + + + + + + + + hypertension grade + A categorical value specification that indicates the severity of hypertension. + Bjoern Peters + Randi Vita + Sebastian Duesing + hypertension grade + + + + + + + + + quartz crystal microbalance assay + An assay that measures the change in frequency of a quartz crystal resonator resulting from the addition or removal of a small mass of a ligand specifically binding at the surface of the resonator. + Bjoern Peters + Randi Vita + Sebastian Duesing + QCM + http://www.ncbi.nlm.nih.gov/pubmed/23504432 + https://en.wikipedia.org/wiki/Quartz_crystal_microbalance + quartz crystal microbalance assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + quartz crystal microbalance measuring the dissociation constant [KD] of a B cell epitope:antibody complex + A quartz crystal microbalance assay that measures the dissociation constant [KD] of an antigen binding with an antibody. + Bjoern Peters + Randi Vita + Sebastian Duesing + QCM measuring KD + IEDB + dissociation constant KD|quartz crystal microbalance|nM + quartz crystal microbalance assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex + + + + + + + + + A fluorescence in-situ hybridization assay that uses combinatorial FISH labeling with error resistant encoding schemes for highly multiplexed single-molecule imaging. + Sebastian Duesing + MERFISH + https://en.wikipedia.org/wiki/Fluorescence_in_situ_hybridization#MERFISH + https://github.com/obi-ontology/obi/issues/1724 + Brain Image Library + multiplexed error-robust fluorescence in situ hybridization assay + + + + + + + + + A fluorescence in-situ hybridization assay that detects single RNA molecules in fixed cells, allowing for both the quantification and localization at the single-cell level and single-molecule resolution. + Sebastian Duesing + smFISH + https://doi.org/10.21769/BioProtoc.3070 + https://github.com/obi-ontology/obi/issues/1725 + Brain Image Library + single molecule fluorescence in situ hybridization + + + + + + + + + + + + + + + A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells. + Sebastian Duesing + NextSeq 1000 + https://www.illumina.com/systems/sequencing-platforms/nextseq-1000-2000.html + https://github.com/obi-ontology/obi/issues/1711 + GENEPIO + Illumina NextSeq 1000 + + + + @@ -89141,7 +89638,7 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from - + primary cultured cell population Spleen cells put directly into culture; Cold storage of biopsies from wild endangered native Chilean species in field conditions and subsequent isolation of primary culture cell lines. In Vitro Cell Dev Biol Anim. 2008 Jul 2. PMID: 18594934 cells that have been isolated from some organismal source, expanded in culture, but not undergone a complete passaging (ie are still in culture, or have been lifted from culture and frozen in aliquots for future use) @@ -89154,7 +89651,7 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from PERSON:Matthew Brush primary cultured cell population - + 0 @@ -89162,7 +89659,7 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from - + consider if we really want to be so strict here . . . ie maybe we we say that they have not been output from an 'establishing cell line' process, but in some cases a passage or two may be allowed for a primary culture. the establishing of a line requires some procedss that attains a degree of homogeneity in the culture. @@ -91578,7 +92075,7 @@ In this equation b0 is the regression coefficient for the intercept and the bi v data visualization Generation of a heatmap from a microarray dataset - An planned process that creates images, diagrams or animations from the input data. + A planned process with the objective to graphically represent some data by inputing the data and outputting images, diagrams or animations. Elisabetta Manduchi James Malone Melanie Courtot @@ -94261,7 +94758,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 storage PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10. - A maintenance process by which material entities that are not actively metabolizing are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability + A planned process with the objective to preserve and protect material entities by placing them in an identified location which may have a controlled environment. Philippe Rocca-Serra OBI-Branch storage @@ -97960,7 +98457,7 @@ https://sourceforge.net/p/obi/obi-terms/738/ acquisition Downloading a 3D structure from the PDB. Purchasing antibodies from sigma. - the planned process of gaining possession of a continuant. + A planned process with the objective of gaining possession of an entity. 5/31/2012 - OBI workshop: This process is not implying ownership of the material / information. Following OBI call November 2012,5th: addition of a restriction to acquisition class to capture the need of having selection criteria @@ -98457,7 +98954,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ maintaining cell culture When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture - a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing + A planned process with the objective to keep cells alive in a defined environment outside of an organism. PlanAndPlannedProcess Branch OBI branch derived maintaining cell culture @@ -100434,7 +100931,7 @@ Possible ecological risks of transgenic organism release when transgenes affect Immunization in vitro - Process of administering an object playing the role of immunogen to a cell culture + A planned process with the objective to administer an object playing the role of immunogen to a cell culture. IEDB IEDB Immunization in vitro @@ -130240,6 +130737,12 @@ realizes some 'host of immune response role' + + + + + + diff --git a/views/obi.obo b/views/obi.obo index 9e98bdbb..7dd459a5 100644 --- a/views/obi.obo +++ b/views/obi.obo @@ -1,6 +1,6 @@ format-version: 1.2 -data-version: 2023-07-25 -date: 25:07:2023 11:02 +data-version: 2023-09-20 +date: 20:09:2023 10:45 remark: Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. ontology: obi property_value: defaultLanguage "en" xsd:string @@ -67,7 +67,7 @@ property_value: http://purl.org/dc/elements/1.1/subject "An ontology for the ann property_value: http://purl.org/dc/terms/license "http://creativecommons.org/licenses/by/4.0/" xsd:string property_value: http://purl.org/dc/terms/title "Ontology for Biomedical Investigations" xsd:string property_value: IAO:0000589 "Ontology for Biomedical Investigations" xsd:string -property_value: owl:versionInfo "2023-07-25" xsd:string +property_value: owl:versionInfo "2023-09-20" xsd:string [Term] id: APOLLO_SV:00000008 @@ -5690,7 +5690,7 @@ is_a: IAO:0000005 ! objective specification [Term] id: OBI:0000457 name: manufacturing -def: "Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process" [] +def: "A planned process with the objective to produce a processed material which will have a function for future use." [] is_a: OBI:0000094 ! material processing [Term] @@ -7219,8 +7219,8 @@ is_a: BFO:0000023 ! role [Term] id: OBI:0000719 -name: vaccine preparation -def: "vaccine preparation is a planned process with specified output a vaccine" [] +name: vaccine production +def: "A planned process with the objective to create a vaccine." [] is_a: OBI:0000094 ! material processing [Term] @@ -7542,7 +7542,7 @@ is_a: OBI:0000094 ! material processing [Term] id: OBI:0000804 name: informing investigator of subject study arm -def: "A process in which an investigator is made aware of which study arm that a patient is participating in, for example whether they are receiving a placebo or a treatment with an investigational compound." [] +def: "A planned process with the objective to make the investigator aware of which study arm a patient is participating in." [] is_a: OBI:0000011 ! planned process [Term] @@ -7561,7 +7561,7 @@ is_a: IAO:0000005 ! objective specification [Term] id: OBI:0000807 name: presentation of stimulus -def: "a planned process in which an organism is exposed to some stimulus with the intent to invoke an action" [] +def: "A planned process with the objective to expose an organism to a stimulus." [] synonym: "stimulation of organism" EXACT [] is_a: OBI:0000011 ! planned process @@ -7581,7 +7581,7 @@ is_a: OBI:0000047 ! processed material [Term] id: OBI:0000810 name: informed consent process -def: "A planned process in which a person or their legal representative is informed about key facts about potential risks and benefits of a process and makes a documented decision as to whether the person in question will participate." [] +def: "A planned process with the objective to inform a person or their legal representative of legally and ethically relevant facts about a process that the person in question is asked to participate in, and which results in a documented decision as to whether the person in question will participate." [] is_a: OBI:0000011 ! planned process [Term] @@ -7742,7 +7742,7 @@ is_a: OBI:0000952 ! oral administration [Term] id: OBI:0000838 name: material maintenance -def: "a process with that achieves the objective to maintain some or all of the characteristics of an input material over time" [] +def: "A planned process with the objective to maintain some or all of the characteristics of an input material over time." [] is_a: OBI:0000011 ! planned process [Term] @@ -7754,19 +7754,19 @@ is_a: OBI:0001936 ! molecular-labeled material [Term] id: OBI:0000840 name: unblinding process -def: "The part of the study execution in which the subjects are told what study arm they are in and in which the investigators are told which subjects are in which trials" [] +def: "A planned process that is the part of the study execution in which the subjects are told what study arm they are in and in which the investigators are told which subjects are in which trials." [] is_a: OBI:0000011 ! planned process [Term] id: OBI:0000841 name: subject agrees they understand informed consent document -def: "A process in which a subject receives an informed consent document and agrees that they have understood it" [] +def: "A planned process in which a subject receives an informed consent document and agrees that they have understood it." [] is_a: OBI:0000011 ! planned process [Term] id: OBI:0000842 name: informing subject of study arm -def: "A process in which the subject is made aware of which study arm they are participating in, for example whether they are receiving a placebo or a treatment with an investigational compound." [] +def: "A planned process with the objective to make the subject aware of which study arm they are participating in." [] is_a: OBI:0000011 ! planned process [Term] @@ -8068,12 +8068,14 @@ id: OBI:0000903 name: in vitro cell killing assay def: "A cell killing assay that measures if and how many target cells are actively killed by other cells in a cell culture." [] is_a: OBI:0000882 ! cell-cell killing assay +is_a: OBI:0003587 ! cell culture assay [Term] id: OBI:0000904 name: reporter cell line analyte detection bioassay def: "An analyte assay in which a cell line whose growth is known to be affected by the presence of a specific type of material (the anlyte) is cultured in the presence of an input material (the evaluant) in order to detect presence of the analyte in the evaluant." [] is_a: OBI:0000443 ! analyte assay +is_a: OBI:0003587 ! cell culture assay [Term] id: OBI:0000905 @@ -8092,7 +8094,7 @@ is_a: OBI:0000094 ! material processing [Term] id: OBI:0000907 name: supplying -def: "The planned process of providing material entities\nto be used in an investigation." [] +def: "A planned process with the objective to provide material entities to be used in an investigation." [] is_a: OBI:0000011 ! planned process [Term] @@ -8253,7 +8255,7 @@ is_a: OBI:0000832 ! measurement device [Term] id: OBI:0000931 name: study intervention -def: "the part of the execution of an intervention design study which is varied between two or more subjects in the study" [] +def: "A planned process that is the part of the execution of an intervention design study which is varied between two or more subjects in the study." [] is_a: OBI:0000011 ! planned process [Term] @@ -13157,7 +13159,7 @@ is_a: OBI:0001146 ! binding assay id: OBI:0001672 name: gene knock-down assay def: "An assay which transiently disrupts gene transcripts by expressing antisense RNA constructs or delivering RNA interfering molecules in cells." [] -is_a: OBI:0000070 ! assay +is_a: OBI:0003587 ! cell culture assay [Term] id: OBI:0001673 @@ -15016,7 +15018,7 @@ is_a: OBI:0000424 ! transcription profiling assay [Term] id: OBI:0001928 name: selection -def: "A planned process which results in the creation of group of entity from a larger group by the application of predefined criteria." [] +def: "A planned process with the objective to create a group of entities by applying a predefined criteria to a larger group of entities." [] synonym: "selection process" EXACT [] is_a: OBI:0000011 ! planned process @@ -15161,7 +15163,7 @@ is_a: OBI:0001953 ! freezing [Term] id: OBI:0001953 name: freezing -def: "A planned process in which a material entity has it's temperature lowered to below the freezing point in order to bring it to a state in which it can be maintained at this lower temperature in order to preserve some of its qualities." [] +def: "A planned process with the objective to bring some material entity to a temperature below its freezing point." [] is_a: OBI:0000011 ! planned process [Term] @@ -18385,7 +18387,7 @@ is_a: OBI:0000968 ! device [Term] id: OBI:0002587 name: machine learning -def: "A planned process in which statistical techniques are used to give computers the ability to learn about patterns in data, without being explicitly programmed. Learning is defined in this case as progressively improving performance on a specific task." [] +def: "A planned process with the objective to give a computer the ability to use patterns in data to progressively improve its performance on a specific task, achieved by using statistical techniques instead of explicitly programming the ability." [] is_a: OBI:0000011 ! planned process [Term] @@ -20601,6 +20603,7 @@ is_a: BFO:0000040 ! material entity id: OBI:0002990 name: T cell receptor repertoire sequencing assay def: "A sequencing assay that determines the sequences of DNA or RNA molecules that encode the repertoire of T cell receptors within an input sample." [] +synonym: "bulk TCR assay" EXACT [] synonym: "TCR repertoire sequencing assay" EXACT [] is_a: OBI:0600047 ! sequencing assay @@ -20610,6 +20613,7 @@ name: B cell receptor repertoire sequencing assay def: "A sequencing assay that determines the sequence of a DNA or RNA molecules that encode the repertoire of B cell receptors within an input sample." [] synonym: "Antibody repertoire sequencing assay" EXACT [] synonym: "BCR repertoire sequencing assay" EXACT [] +synonym: "bulk BCR assay" EXACT [] is_a: OBI:0600047 ! sequencing assay [Term] @@ -23371,7 +23375,7 @@ is_a: OBI:0000070 ! assay [Term] id: OBI:0003501 name: functional assessment of individual -def: "A physical examination of an individual's ability to perform functional activities." [] +def: "A physical examination of an organism's ability to perform functional activities." [] is_a: OBI:0002441 ! physical examination of an organism [Term] @@ -23581,7 +23585,7 @@ is_a: OBI:0003517 ! deep tendon reflex assessment [Term] id: OBI:0003536 name: observational assessment of individual -def: "A physical examination of an individual through visual assesment." [] +def: "A physical examination of an organism through visual assesment." [] is_a: OBI:0002441 ! physical examination of an organism [Term] @@ -23751,6 +23755,117 @@ name: Annexin V staining def: "Staining using Annexin V to detect apoptotic cells." [] is_a: OBI:0302887 ! staining +[Term] +id: OBI:0003587 +name: cell culture assay +def: "An assay that has cell culture as an input." [] +is_a: OBI:0000070 ! assay + +[Term] +id: OBI:0003589 +name: serum anti-Epstein-Barr virus antibody level assay +def: "An antigen specific antibodies assay that is meant to detect antibodies that bind to Epstein-Barr virus (EBV) antigens in a serum sample." [] +synonym: "EBV" EXACT [] +is_a: OBI:0002145 ! antigen specific antibodies assay + +[Term] +id: OBI:0003590 +name: serum anti-cytomegalovirus antibody level assay +def: "A CMV antibody assay that has serum as an input." [] +synonym: "CMV" EXACT [] +is_a: OBI:0002154 ! CMV antibody assay + +[Term] +id: OBI:0003591 +name: chronic allograft damage index score +def: "A clinical data item that quantifies the degree of tissue damage in biopsies taken from transplanted kidneys." [] +synonym: "CADI" EXACT [] +is_a: OGMS:0000123 ! clinical data item + +[Term] +id: OBI:0003592 +name: sequential organ failure assessment score +def: "A clinical data item that quantifies the degree of function of a critically ill patient's organs." [] +synonym: "SOFA score" EXACT [] +is_a: OGMS:0000123 ! clinical data item + +[Term] +id: OBI:0003593 +name: physician's global assessment of disease activity +def: "A clinical data item that quantifies a physician's judgement of the overall activity of some specific disease in a patient." [] +synonym: "MD global, PGA" EXACT [] +is_a: OGMS:0000123 ! clinical data item + +[Term] +id: OBI:0003594 +name: human leukocyte antigen mismatch count +def: "A genetic characteristics information that is about the number of dissimilarities in the human leukocyte antigen gene complexes of two humans." [] +synonym: "HLA mismatch count, HLA mismatch" EXACT [] +is_a: OBI:0001404 ! genetic characteristics information + +[Term] +id: OBI:0003595 +name: nasal lavage fluid +def: "A specimen collected through nasal cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the nasal cavity space." [] +is_a: OBI:0100051 ! specimen + +[Term] +id: OBI:0003598 +name: single cell B cell receptor repertoire sequencing assay +def: "A B cell receptor repertoire sequencing assay that determines the sequence of DNA or RNA molecules that encode the repertoire of B cell receptors that can be traced to a single cell of origin." [] +synonym: "single-cell BCR assay" EXACT [] +is_a: OBI:0002991 ! B cell receptor repertoire sequencing assay + +[Term] +id: OBI:0003599 +name: single cell T cell receptor repertoire sequencing assay +def: "A T cell receptor repertoire sequencing assay that determines the sequence of DNA or RNA molecules that encode the repertoire of T cell receptors that can be traced to a single cell of origin." [] +synonym: "single-cell TCR assay" EXACT [] +is_a: OBI:0002990 ! T cell receptor repertoire sequencing assay + +[Term] +id: OBI:0003600 +name: hypertension grade +def: "A categorical value specification that indicates the severity of hypertension." [] +is_a: OBI:0001930 ! categorical value specification + +[Term] +id: OBI:0003601 +name: quartz crystal microbalance assay +def: "An assay that measures the change in frequency of a quartz crystal resonator resulting from the addition or removal of a small mass of a ligand specifically binding at the surface of the resonator." [] +synonym: "QCM" EXACT [] +is_a: OBI:0000070 ! assay + +[Term] +id: OBI:0003602 +name: quartz crystal microbalance assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex +def: "A quartz crystal microbalance assay that measures the dissociation constant [KD] of an antigen binding with an antibody." [] +synonym: "dissociation constant KD|quartz crystal microbalance|nM" EXACT [] +synonym: "QCM measuring KD" EXACT [] +is_a: OBI:0001708 ! assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex +is_a: OBI:0003601 ! quartz crystal microbalance assay + +[Term] +id: OBI:0003604 +name: multiplexed error-robust fluorescence in situ hybridization assay +def: "A fluorescence in-situ hybridization assay that uses combinatorial FISH labeling with error resistant encoding schemes for highly multiplexed single-molecule imaging." [] +synonym: "MERFISH" EXACT [] +is_a: OBI:0003094 ! fluorescence in-situ hybridization assay + +[Term] +id: OBI:0003605 +name: single molecule fluorescence in situ hybridization +def: "A fluorescence in-situ hybridization assay that detects single RNA molecules in fixed cells, allowing for both the quantification and localization at the single-cell level and single-molecule resolution." [] +synonym: "smFISH" EXACT [] +is_a: OBI:0003094 ! fluorescence in-situ hybridization assay + +[Term] +id: OBI:0003606 +name: Illumina NextSeq 1000 +def: "A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells." [] +synonym: "NextSeq 1000" EXACT [] +is_a: OBI:0400103 ! DNA sequencer + [Term] id: OBI:0005246 name: injection function @@ -24552,7 +24667,7 @@ is_a: OBI:0200169 ! normalization data transformation [Term] id: OBI:0200111 name: data visualization -def: "An planned process that creates images, diagrams or animations from the input data." [] +def: "A planned process with the objective to graphically represent some data by inputing the data and outputting images, diagrams or animations." [] synonym: "data encoding as image" EXACT [] synonym: "visualization" EXACT [] is_a: OBI:0000011 ! planned process @@ -25319,7 +25434,7 @@ is_a: OBI:0000094 ! material processing [Term] id: OBI:0302893 name: storage -def: "A maintenance process by which material entities that are not actively metabolizing are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability" [] +def: "A planned process with the objective to preserve and protect material entities by placing them in an identified location which may have a controlled environment." [] is_a: OBI:0000838 ! material maintenance [Term] @@ -26431,7 +26546,7 @@ is_a: OBI:0000274 ! adding a material entity into a target [Term] id: OBI:0600008 name: acquisition -def: "the planned process of gaining possession of a continuant." [] +def: "A planned process with the objective of gaining possession of an entity." [] is_a: OBI:0001928 ! selection [Term] @@ -26537,7 +26652,7 @@ disjoint_from: OBI:0600050 ! specific enzymatic cleavage [Term] id: OBI:0600024 name: maintaining cell culture -def: "a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing" [] +def: "A planned process with the objective to keep cells alive in a defined environment outside of an organism." [] is_a: OBI:0000838 ! material maintenance [Term] @@ -26582,6 +26697,7 @@ name: enzyme-linked immunospot assay def: "A cytometry assay in which cells are cultured on a surface coated with a capture antibody binding a secretory material of interest which subsequently gets stained resulting in a spot for each cell producing the secretory material of interest." [] synonym: "ELISPOT assay" EXACT [] is_a: OBI:0001977 ! cytometry assay +is_a: OBI:0003587 ! cell culture assay [Term] id: OBI:0600032 @@ -26949,7 +27065,7 @@ is_a: OBI:1110111 ! environmental proximity to infectious agent [Term] id: OBI:1110020 name: Immunization in vitro -def: "Process of administering an object playing the role of immunogen to a cell culture" [] +def: "A planned process with the objective to administer an object playing the role of immunogen to a cell culture." [] is_a: OBI:0000094 ! material processing [Term] @@ -30317,6 +30433,12 @@ name: treatment def: "A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process" [] is_a: OBI:0000011 ! planned process +[Term] +id: OGMS:0000123 +name: clinical data item +def: "A data item that is about a patient and is the specified output of a health care process assay or diagnostic process" [] +is_a: IAO:0000027 ! data item + [Term] id: OMIABIS:0000050 name: fixed tissue specimen @@ -31221,7 +31343,7 @@ is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0000477 name: anatomical cluster -def: "Anatomical group that has its parts adjacent to one another." [] +def: "Anatomical group whose component anatomical structures lie in close proximity to each other." [] is_a: BFO:0000040 ! material entity [Term] diff --git a/views/obi_core.owl b/views/obi_core.owl index 1a9f5803..840c80b0 100644 --- a/views/obi_core.owl +++ b/views/obi_core.owl @@ -11,7 +11,7 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"> - + en Ontology for Biomedical Investigations Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester @@ -78,7 +78,7 @@ http://creativecommons.org/licenses/by/4.0/ Ontology for Biomedical Investigations Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. - 2023-07-25 + 2023-09-20 @@ -2002,6 +2002,7 @@ JAR: A data item is an approximately justified approximately true approximate be PERSON: Chris Stoeckert PERSON: Jonathan Rees data + data item @@ -2047,6 +2048,7 @@ JAR: A data item is an approximately justified approximately true approximate be Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. PERSON: Chris Stoeckert OBI_0000142 + information content entity @@ -3450,7 +3452,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ informed consent process - A planned process in which a person or their legal representative is informed about key facts about potential risks and benefits of a process and makes a documented decision as to whether the person in question will participate. + A planned process with the objective to inform a person or their legal representative of legally and ethically relevant facts about a process that the person in question is asked to participate in, and which results in a documented decision as to whether the person in question will participate. 09/28/2009 Alan Ruttenberg: This is made a subclass of the higher level processual entity in BFO because I don't want to take a stand on whether it is a process aggregate. Analogous to the situation with Material entity. Person:Alan Ruttenberg http://clinicaltrials.gov/ct2/info/glossary#informed @@ -3703,7 +3705,7 @@ The following are NOT conclusions based on data: data themselves; results from p selection 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. - A planned process which results in the creation of group of entity from a larger group by the application of predefined criteria. + A planned process with the objective to create a group of entities by applying a predefined criteria to a larger group of entities. 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) Person: Philippe Rocca-Serra selection process @@ -4092,7 +4094,7 @@ defines and states the requirements (positive or negative) for an entity to be c acquisition Downloading a 3D structure from the PDB. Purchasing antibodies from sigma. - the planned process of gaining possession of a continuant. + A planned process with the objective of gaining possession of an entity. 5/31/2012 - OBI workshop: This process is not implying ownership of the material / information. Following OBI call November 2012,5th: addition of a restriction to acquisition class to capture the need of having selection criteria