[Mged-ontologies] Proposed new classes and instances

[Chris S. <stoeckrt@SNOWBALL.pcbi.upenn.edu>]

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=