Concepts:
Listed are concepts to be structured in an ontology. Most are defined and I will continue to add to and define the rest. Usage of terms such as "biomaterial" and "biosource" comes from the OMG MAGE-OM submission. I see our goal as to extend the standard that they have made and only modify it when absolutely necessary. I have changed "cell source and type" to "biosource provider" because of confusion about the term. MAGE (the combination of MAML and GEML) is guided by MIAME. (see MAGE and MIAME figures at the end of this section). Some of these concepts such as "organism", "organism part" , and "disease state" are references to external controlled vocabularies/ ontologies. Established ontologies such as the NCBI taxonomy should be used whenever possible. Links to the NCBI taxonomy browser and to model organism databases such as FlyBase, MGD, SGD, TAIR, and WormBase are available in the ontology resources (on the main OWG page). Thanks to B. Aronow, U. Cincinnati, and M. Ashburner, Cambridge U. for suggestions.
Biomaterial: The source of the nucleic acid used to generate labelled material for the microarray experiment.
Biosource: The primary source of the nucleic acid used to generate labelled material for the microarray experiment.
Biosample: The biosource after any treatment.
Labeled Extract: The biosample after labeling for detection of the nucleic acids.
Organism: The genus and species (and subspecies) of the organism from which the biomaterial is derived from.
Biosource provider: The resource (e.g, company, hospital, geographical location) used to obtain or purchase the biomaterial.
Sex: The gender of the organism or the reproductive organs present on the organism (prior to any modification) that the biomaterial is derived from.
| Term | Definition |
|---|---|
| male | The organism contains only the reproductive organ that produces male gametes (spermatozoa). |
| female | The organism contains only the reproductive organs that produces female gametes (oocytes). |
| both | The organism contains both male and female reproductive organs. |
| none | The organism does not have reproductive organs. |
| unknown | The reproductive organs of the organism are unknown. |
Age: The time period elapsed since an identifiable point in the life cycle of an organism. If a developmental stage is specified, the identifiable point would be the beginning of that stage. Otherwise, the identifiable point must be specified such as planting.
| Initial time point | Definition |
|---|---|
| birth | The time point at the end of parturition. |
| fertilization | The time point at which gametes are joined. May also be used for post-coital measurements. |
| hatching | The time point at which the organism leaves the egg. |
| planting | The time point at which a seed is planted. |
Developmental stage: The developmental stage of the organism's life cycle during which the biomaterial was extracted.
Organism part: The part of the organism's anatomy from which the biomaterial was derived.
Strain or line: Animals or plants that have a single ancestral breeding pair or parent as a result of brother x sister or parent x offspring matings.
Genetic Variation: The genetic modification introduced into the organism from which the biomaterial was derived. Examples of genetic variation include specification of a transgene or the gene knocked-out.
Individual: Identifier or name of the individual organism from which the biomaterial was derived.
Individual genetic characteristics: The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes.
Disease state: The name of the pathology diagnosed in the organism from which the biomaterial was derived. The disease state is normal if no disease has been diagnosed.
Targeted cell type: The target cell type is the cell of primary interest. The biomaterial may be derived from a mixed population of cells although only one cell type is of interest.
Cell line: The identifier for the immortalized cell line if one was used to derive the biomaterial.
Biomaterial preparation: A description of the state and condition of the biomaterial.
Environmental or experimental history: A description of the conditions the organism has been exposed to that are not one of the variables under study.
Treatment: The manipulation of the biomaterial for the purposes of generating one of the variables under study.
Ontology tools:
The ontology editors are either open source or licensed for free (at least for academics, let me know if I misrepresented anything). Thanks to Robert Stevens, U. Manchester, for info on Protege and OILed.
Products such as those from Rational Rose and Embarcadero can also be used to generate UML models (class diagrams). These are not free.