New Terminologies for OBI (Yale Med School)

[obi-bot]

Hi,

We are using BioPortal’s ontology recommender, linked open vocabularies and aber-owl services to map the ImmPort’s tempaltes to OBI and other relevant ontologies. Based on our observation, most of the terms (listed below) are not available in any available bio-ontology and according to our understanding these should be part of OBI. Therefore, we request to add tye following terms into OBI updated version.

Do contact us, if you have any question.

Thanks

CyTOF: currently in ERO, also add to OBI if not exist Cytometry Time Of Flight CyTOF (DVS Sciences) or Mass cytometry, or , is a variation of flow cytometry in which antibodies are labeled with heavy metal ion tags rather than fluorochromes. Readout is by time-of-flight mass spectrometry.

HPLC: currently in ERO, also add to OBI if not exist High Performace Liquid Chromotography is used to separate components of a mixture by using a variety of chemical interactions between the substance being analyzed (analyte) and the chromatography column.

Immunoblot: western bolt analysis in OBI a western blot analysis is an assay which allows detection of protein present in a extract resolved on polyacrylamide gel by electrophoresis, transfered to a membrane made of nitrocellulose or polyvinylidene difluoride and immobilized using formaldehyde based cross linking.

In situ hybridization: currently in ERO, also add to OBI if not exist Uses a labelled complementary DNA or RNA strand (i.e., probe) to localize a specific DNA or RNA sequence in a portion or section of tissue (in situ), or the entire tissue (whole mount ISH), in cells and in circulating tumor cells (CTCs).

KIR typing: add to OBI if not exist Killer cell immunoglobulin-like receptors. Microscopy: currently in ERO, also add to OBI if not exist Visualization of very small entities from cellular to sub-cellular and molecular resolution depending on technique.

Mixed lymphocyte reaction: add to OBI if not exist each other to proliferate significantly (e.g. measured by tritiated thymidine uptake) whereas those from compatible individuals will not; in the one-way MLC test, the lymphocytes from one of the individuals are inactivated thereby allowing only the untreated remaining population of cells to proliferate in response to foreign histocompatibility antigens.

Nanostring: add to OBI if not exist Nanostring technology uses molecular "barcodes" and single molecule imaging to detect and count hundreds of unique transcripts in a single reaction.

NMR: add as a synonym to OBI_0000623 Nuclear Magnetic Resonance spectroscopy is a technique for determining the structure of organic compounds.

Optical Density: currently in CHMO, also add to OBI if not exist Optical Density is a class of techniques to measure the amount of light absorbed/transmitted by a sample. The sample O.D. is compared to a standard curve to interpolate the sample's concentration of an analyte.

Sequencing: add as a synonym to OBI_0600047 Sequencing Sequencing is used to discover new sequence variants and to genotype a sample for known variants.

TCID50: currently in FLU, also add to OBI if not exist

50 percent Tissue Culture Infective Dose, (TCID50) is the measure of infectious virus titer. This endpoint dilution assay quantifies the amount of virus required to kill 50% of infected hosts or to produce a cytopathic effect in 50% of inoculated tissue culture cells. Western blot: add as a synonym to OBI_0000854 Western blot is a method in molecular biology/biochemistry/immunogenetics to detect protein in a given sample of tissue homogenate or extract. It uses gel electrophoresis to separate denatured proteins by mass. The proteins are then transferred out of the gel and onto a membrane (typically nitrocellulose), where they are probed using antibodies specific to the protein. As a result, researchers can examine the amount of protein in a given sample and compare levels between several groups. Other techniques also using antibodies allow detection of proteins in tissues (immunohistochemistry) and cells (immunocytochemistry). The confirmatory HIV test employs a western blot to detect anti-HIV antibody in a human serum sample. A Western blot is also used as the definitive test for Bovine spongiform encephalopathy (BSE, commonly referred to as 'mad cow disease'). Some forms of Lyme disease testing employ Western blotting.

Whole genome sequencing: currently in ERO, also add to OBI if not exist Laboratory process that determines the complete DNA sequence of an organism's genome at a single time. Sequencing process which uses deoxyribonucleic acid as input and results in a the creation of DNA sequence information artifact Yeast two hybrid: add as a synonym to OBI_0001679

Two-hybrid screening is a molecular biology technique used to discover protein-protein interactions by testing for physical interactions (such as binding) between two proteins.

Thanks

Regards,

Syed Ahmad Chan Bukhari syedahmadchan.bukhari@yale.edu Postdoc, Kleinstein Lab, Yale School of Medicine

Reported by: bukharig8

Original Ticket: obi/obi-terms/800

[obi-bot]

Quick update: The IEDB team is going to coordinate with the Kleinstein group on this.

Original comment by: jamesaoverton

[obi-bot]

• assigned_to: James A. Overton

Original comment by: jamesaoverton

[obi-bot]

• status: open --> closed

Original comment by: bpeters42