Open obi-bot opened 13 years ago
obi-bot
commented
13 years ago C95027 is clearly in scope of OBI. However the request is too nonspecific. Could you please prepare a list of specific NCI terms that you think relevant to be included in OBI so we can attend to those?
Original comment by: alanruttenberg
obi-bot
commented
13 years ago I agree with Alan, but because I misunderstood him at first, let me rephrase what he wrote to hopefully clarify: OBI is happy to add assays like C95027, and the definition you supplied is sufficient for us to act on it. In contrasst, 'Genetic Linkage' does not seem to be an experiemental method, but rather a biological mechanism explaining shared inheritance. That is outside of the scope of OBI. If you want to describe methodologies examining genetic linkage, that would be in the scope, but would require a different definition. I hope this explains the comment from Alan that your request to 'import many of the NCI terms' is not specific for us to act upon, but rather we need a specific list of terms and definitions.
Original comment by: bpeters42
obi-bot
commented
13 years ago Sounds good. I'll identify what part of the NCI thesaurus would be within the scope of OBI and will let you know. Thanks.
Original comment by: elodiepc
obi-bot
commented
13 years ago One last question: are you happy re-using the terms from the NCI thesaurus (in which case we would just import those you need) or are there issues with the thesaurus in the usage you want to make of the terms, which would require for us to work on their definitions (textual and/or logical)?
Original comment by: mcourtot
obi-bot
commented
13 years ago To answer your last question, yes I am happy with the terms as they are in NCI and they could be imported as is.
Regarding listing the terms I would be interested in, I think what would be best for OBI is to include as many terms as possible in order to be as complete as possible. I've identified 2 sub-parts of NCI that are relevant to OBI. There is some overlap with terms already in OBI but a lot of them are missing. These terms are in: Activity > Technique > Research Technique AND Activity >Clinical or Research Activity > Intervention or Procedure > Laboratory Procedure > Molecular Analysis
However if such a bulk import approach is not feasible, I can list the specific terms I am missing but I will probably identify more to add on a regular basis.
Original comment by: elodiepc
obi-bot
commented
12 years ago Dear elodiepc, Are you still working on the list of specific terms? Please let us know, and please submit even a partial list so that we can get started on the implementation.
Best,
Bjoern
Original comment by: bpeters42
obi-bot
commented
12 years ago Hi Bjoern, I was actually waiting for an answer to my last comment from June 16th regarding bulk import. Is that not possible? Elodie
Original comment by: elodiepc
obi-bot
commented
12 years ago Hi Bjoern, Here is a list of terms from NCI that we would like to be added to OBI. Thanks for letting me know if these are acceptable. Elodie
blood protein measurement NCI C92745 cytokine measurement NCI C74804 developmental diagnostic NCI C15796 fluorescent in situ hybridisation NCI C17563 gene mapping NCI C16438 genetic linkage analysis NCI C16797 Immunofluorescence NCI C17370 immunofluorescence NCI C17370 immunohistochemistry NCI C16722 Karyotyping NCI C16878 magnetic resonance imaging NCI C16809 meta-analysis NCI C17886 Radioimmunoassay NCI C17057 restriction fragment length polymorphism NCI C17093 two dimensional gel electrophoresis NCI C16538 ultrasound NCI C64384 Electroencephalography NCl C38054
Original comment by: elodiepc
We want to use OBI as an ontology for describing investigation methods but many widely used methods are missing. These methods can often be found in the NCI thesaurus and it would be great if OBI could integrate many of the terms from there. See a few examples below. Thanks, Elodie Portales-Casamar
Genetic Linkage (Code C94542) NCI-GLOSS Definition: The tendency for genes or segments of DNA closely positioned along a chromosome to segregate together at meiosis, and therefore be inherited together.
Colorimetric Cell Viability Assay (Code C95027) Definition: A colorimetric assay that can assess the viability of cells by quantitation of the reduction of a yellow tetrazolium salt substrate to a product that has a purple color. This assay can measure the cytotoxicity of a chemical or drug by determining the affect of treatment on cell viability.
Reported by: elodiepc
Original Ticket: obi/obi-terms/594