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From: Chris S. <stoeckrt@SNOWBALL.pcbi.upenn.edu> - 2002-09-23 20:38:50
|
Hi Everyone, Below are proposals of new classes, subclasses and individuals to add=20 to the MGED Ontology. Note that some of these such as "element type",=20 "platform type" and "substrate type" represent aspects of microarrays=20 and move the ontology toward complete coverage of a microarray=20 experiment. The list was generated by Trish Whetzel and myself from a combination=20 of what we have in RAD, what we saw on the MIAMExpress forms, and=20 feedback from Helen Parkinson, Helen Causton, and their colleagues.=20 There are some outstanding questions and issues that are noted in=20 parenthesis and listed at the end. If accepted by this group, we will add these to the ontology and=20 advocate their use in our respective databases and forms. Clearly, the=20= list is limited by what we are familiar with so please suggest new=20 things to add on an ongoing basis. Thanks, Chris New classes (class-definition): element type - The physical nature of the reporter (1). platform type - The technology type used to place the reporters on the=20= array. substrate type - The physical surface of the array (2). New subclasses of protocol (class, subclass - definition): protocol , image quantification - The process of obtaining quantifiable=20= values from the scanned image of the array. protocol , image acquisition - The process of generating an image from=20= the array. protocol , array manufacture - The process of printing the array. protocol , treatment - The manipulation of the biomaterial for the=20 purposes of generating one of the variables under study. protocol , hybridization - The process of incubating one or more=20 labeled extracts with an array. protocol , labeling =96 The process of attaching a label to the nucleic=20= acid. New individuals within classes (class, value - definition): biomaterial preparation , microdissection =96 A procedure involving=20 cutting apart or separating the biomaterial under a microscope, camera=20= or magnifying glass. (3) biomaterial preparation , trimming =96 A procedure involving separating=20= the biomaterial by gross dissection. biomaterial preparation , FACS - Flow activated cell sorting. A=20 procedure for separating cells based on the presence or absence of a=20 cell surface marker. biomaterial preparation , embryo sorting =96 A procedure for sorting=20 embryos based on fluorescence (e.g., GFP expression in Drosophila). biosource , blood - A biosource obtained as fluid consisting of plasma,=20= blood cells and platelets. biosource , frozen section =96 A biosource obtained as frozen material. biosource , feces - A biosource obtained as fecal matter. biosource , paraffin section - A biosource obtained embedded in=20 paraffin (wax). element type , long oligo =96 An element that is an oligonucleotide of = at=20 least 50 nucleotides in length. element type , PCR =96 Polymerase chain reaction. An element generated=20= using this procedure. element type , short oligo =96 An element that is an oligonucleotide of=20= less than 50 nucleotides in length (usually 20 to 25 nt as in=20 Affymentrix probes). genetic variation , mutation =96 The modification of the genetic = material=20 (either coding or non-coding) of an organism. genetic variation , gene knock out =96 The modification of an organism=20= that renders a gene non-functional e.g. due to the removal of all, or=20 part of, the gene. genetic variation , gene knock in =96 The modification of an organism=20 that inserts a functional gene at the site of a nonfunctional locus for=20= that gene. genetic variation , transgenic variation =96 The modification of an=20 organism due to the presence of DNA from another individual, e.g. of a=20= different strain, species or breed. (4) platform type , spotted cDNA array =96 An array platform in which the=20= arrays are manufactured by spotting PCR fragments from cDNA clones on=20 the substrate. (5) platform type , photolithographic oligo array =96 An array platform in=20= which the arrays are manufactured using photolithography (e.g.=20 Affymetrix). platform type, spotted oligo array =96 An array platform in which the=20 arrays are manufactured by spotting oligonucleotides (of any length) on=20= the substrate. study design , dose response design - Groups of assays that are related=20= as part of a dose response series. study design , time series design - Groups of assays that are related=20 as part of a time series. study factor , biological factor (this is the parent of the following): study factor , disease state - The name of the pathology diagnosed in=20 the organism from which the biomaterial was derived. The disease state=20= is normal if no disease has been diagnosed. study factor , organism part - The part of the organism's anatomy from=20= which the biomaterial was derived. study factor , developmental stage =96 The developmental stage of the=20 organism from which the biomaterial was derived. study factor , genetic variation =96 The genetic variation of the=20 organism from which the biomaterial was derived. study factor, sex - substrate type , glass =96 The array is made on a glass slide. substrate type , nylon =96 The array is made on a nylon membrane. substrate type, nitrocellulose =96 The array is made on a nitrocellulose=20= filter. treatment type , pooling - The procedure of combining two or more=20 biomaterials. treatment type , splitting =96 The procedure of separating of a=20 biomaterial into two or more biomaterials. The biomaterial may be a=20 biousource (e.g., a tissue) or a biosample (e.g, RNA extracted from a=20 biosource). treatment type , RNA extraction - The procedure of extracting the RNA=20 from the biomaterial. treatment type , labeling =96 The procedure of labeling a biosample. Notes: 1. An alternative term for =93reporter=94 is =93biological sequence=94 = [Helen=20 P. Reporters have the biosequence assn but they aren't physically on=20 the array, they're a grouping of features, MAGE terms are often best=20 avoided when they are abstractions.] 2. May also need surface type to describe coating. 3. Specify that this includes robotic microdissection? 4. Queston as to whether inserting DNA from another organism of the=20 same strain constitutes transgenic in organisms like yeast. 5. Spotted arrays could refer to both inkjet and standard pin=20 (non-contact and contact deposition). Do we want to make this=20 distinction and if so how? Also since element type specifies what is=20 attached to the array, do we want to restate that here in platform?=20 I.e., use platform to just specify how the biosequence is attached or=20 generated. Chris Stoeckert, Ph.D. Research Associate Professor, Dept. of Genetics 1415 Blockley Hall, Center for Bioinformatics 423 Guardian Dr., University of Pennsylvania Philadelphia, PA 19104 Ph: 215-573-4409 FAX: 215-573-3111= |
From: Chris S. <stoeckrt@SNOWBALL.pcbi.upenn.edu> - 2002-09-20 22:22:19
|
Dear Group, The mailing list is moving to Sourceforge. The reason is to provide better mail management tools for me as administrator but also you will be able to set options like digest and delivery modes. We will also have a web-browseable archive that is automatically generated. Many thanks to Jason Stewart for suggesting this and then setting this up. What you have to do: 1. Go to https://lists.sourceforge.net/lists/listinfo/mged-ontologies. Enter your email address and a password. That's it to be part of the new list. 2. To post a message to all the list members, send email to mge...@li.... I will not be posting to the other list other than to send occasional reminders like this one to switch. Please switch soon as I would like to send out a proposal for a number of new additions for the ontology. These terms come from our usage in RAD, but also usage in MIAMExpress, and the Clinical Sciences Centre/ Imperial College Microarray Centre. Thanks and see you on the new list! Cheers, Chris Chris Stoeckert, Ph.D. Research Associate Professor, Dept. of Genetics 1415 Blockley Hall, Center for Bioinformatics 423 Guardian Dr., University of Pennsylvania Philadelphia, PA 19104 Ph: 215-573-4409 FAX: 215-573-3111 |