microarray-ontol-digest Monday, July 2 2001 Volume 01 : Number 008 ---------------------------------------------------------------------- Date: Wed, 13 Jun 2001 17:47:29 +0100 From: Alvis Brazma Subject: [microarray-ontol] an EMBO course on microarray informatics for information see http://www.ebi.ac.uk/microarray/EMBO/index.html - - Alvis Brazma ------------------------------ Date: Mon, 2 Jul 2001 10:43:14 -0400 From: Chris Stoeckert Subject: [microarray-ontol] Call for sample descriptions - --Apple-Mail-594816237-3 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; format=flowed; charset=windows-1252 Dear group, We will have a brief Ontologies Working Group mmeeting after the=20 Bio-Ontologies Worskshop at ISMB on July 27th (2001) in Copenhagen,=20 Denmark. I will be presenting a status report of our working group=20 during the Bioontologies working group and I would like to say that we=20= are sharing efforts to annotate sample desciptions in an effort to=20 identify current resources and needs for semantic standards. To do that,=20= I need microarray experiment sample descriptions from you! There were a=20= number of promises at MGED3 and I need you folks to come through now. At=20= the very least, take one representative microarray experiment and fill=20= out the list below (a definition is provided with each term). Please=20 supply any other annotations (e.g., protocols for hybridization extract=20= preparation or labelling) you have or think is important. Use the=20 resources listed on our home page=20 (http://www.cbil.upenn.edu/Ontology/MGED_Ontology.html) when=20 appropriate. Otherwise indicate where you came up with the terms you=20 used. What I will do is compile the submissions in terms of which fields=20= are well covered and which are not. I will post your submissions only if=20= you give me permission. Thanks in advance! Chris Sample (biomaterial) annotations list. Organism: The genus and species (and subspecies) of the organism from=20 which the biomaterial is derived from. Cell source: The resource (e.g, company, hospital, geographical=20 location) used to obtain or purchase the biomaterial. The mailing=20 address can be used for resources that can be contacted. For resources=20= that cannot be contacted such as geographical areas, recommendations for=20= information to be provided are longitude and latitude or map locations=20= and the identity of the map. Cell type: The procurement type of the biomaterial. This concept is a candidate for a MGED ontology/ controlled vocabulary.=20= It would include terms such as tumor biopsy, paraffin section, and stool=20= sample that should be defined and relationships between terms specified. Sex: The gender of the organism or the reproductive organs present on=20 the organism (prior to any modification) that the biomaterial is derived=20= from. This concept is a candidate for a MGED ontology/ controlled vocabulary.=20= Sex is organism dependent. A first draft is provided for organisms with=20= reproductive organs. The draft does not cover unicellular organisms. Term Definition male The organism contains only the reproductive organ that produces=20= male gametes (spermatozoa). female The organism contains only the reproductive organs that=20 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 early in the=20 life of an organism. Examples of the identifiable point include=20 conception, birth, or planting. This concept is a candidate for a MGED ontology/ controlled vocabulary.=20= The value for age has three parts: a real number, a unit of time, and=20 the time point from which measurement starts. A first draft is provided=20= for terms that can be used for the point in time from which measurement=20= starts. 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=20= 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. Growth conditions: The parameters critical to reproduction of the=20 experiment relating to nutrients provided to the organism as well as the=20= environmental conditions the organism was exposed to. This may also be=20= regarded as a =93treatment=94 (see below). Developmental stage: The developmental stage of the organism's life=20 cycle during which the biomaterial was extracted. Organism part: The part of the organism's anatomy from which the=20 biomaterial was derived. Strain or line: Animals or plants that have a single ancestral breeding=20= pair or parent as a result of brother x sister or parent x offspring=20 matings. Genetic Variation: The genetic modification introduced into the organism=20= from which the biomaterial was derived. Examples of genetic variation=20 include specification of a transgene or the gene knocked-out. Individual: Identifier or name of the individual organism from which the=20= biomaterial was derived. Individual genetic characteristics: The genotype of the individual=20 organism from which the biomaterial was derived. Individual genetic=20 characteristics include polymorphisms, disease alleles, and haplotypes. Disease state: The name of the pathology diagnosed in the organism from=20= which the biomaterial was derived. The disease state is normal if no=20 disease has been diagnosed. Targeted cell type: The target cell type is the cell of primary=20 interest. The biomaterial may be derived from a mixed population of=20 cells although only one cell type is of interest. Cell line: The identifier for the immortalized cell line if one was used=20= to derive the biomaterial. Treatment: Action taken on sample, order in which it was taken, and=20 object (if any) added to (or taken away) from sample. The object may be=20= a compound (see below). The treatment is considered =93in vivo=94 if it=20= occurs within the (living) organism. The treatment is considered =93in=20= vitro=94 if applied to a part of the organism that has been removed. Compound: The (bio)chemical object added to the sample during treatment.=20= The compound may be a drug, metabolite, or toxin. Clinical Information: Clinical records available in a separate file that=20= can be accessed to obtain details of a patient=92s history. Separation technique: The protocol used to isolate (enrich for) the=20 targeted cell type of the organism. Separation is considered a treatment=20= (see above). Chris Stoeckert, Ph.D. Research Associate Professor, Dept. of Genetics Center for Bioinformatics, University of Pennsylvania 418 Guardian Dr., Philadelphia, PA 19104 Ph:215-573-4409 FAX:215-573-3111 - --Apple-Mail-594816237-3 Content-Transfer-Encoding: quoted-printable Content-Type: text/enriched; charset=windows-1252 Dear group, We will have a brief Ontologies Working Group mmeeting after the Bio-Ontologies Worskshop at ISMB on July 27th (2001) in Copenhagen, Denmark. I will be presenting a status report of our working group during the Bioontologies working group and I would like to say that we are sharing efforts to annotate sample desciptions in an effort to identify current resources and needs for semantic standards. To do that, I need microarray experiment sample descriptions from you! There were a number of promises at MGED3 and I need you folks to come through now. At the very least, take one representative microarray experiment and fill out the list below (a definition is provided with each term). Please supply any other annotations (e.g., protocols for hybridization extract preparation or labelling) you have or think is important. Use the resources listed on our home page (http://www.cbil.upenn.edu/Ontology/MGED_Ontology.html) when appropriate. Otherwise indicate where you came up with the terms you used. What I will do is compile the submissions in terms of which fields are well covered and which are not. I will post your submissions only if you give me permission. Thanks in advance! Chris Sample (biomaterial) annotations list. TimesOrganism: The genus and species (and subspecies) of the organism from which the biomaterial is derived from. =20 Cell source: The resource (e.g, company, hospital, geographical location) used to obtain or purchase the biomaterial. The mailing address can be used for resources that can be contacted. For resources that cannot be contacted such as geographical areas, recommendations for information to be provided are longitude and latitude or map locations and the identity of the map.=20 Cell type: The procurement type of the biomaterial.=20 This concept is a candidate for a MGED ontology/ controlled vocabulary. It would include terms such as tumor biopsy, paraffin section, and stool sample that should be defined and relationships between terms specified.=20 Sex: The gender of the organism or the reproductive organs present on the organism (prior to any modification) that the biomaterial is derived from.=20 This concept is a candidate for a MGED ontology/ controlled vocabulary. Sex is organism dependent. A first draft is provided for organisms with reproductive organs. The draft does not cover unicellular organisms. 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.=20= none The organism does not have reproductive organs.=20 unknown The reproductive organs of the organism are unknown. Age: The time period elapsed since an identifiable point early in the life of an organism. Examples of the identifiable point include conception, birth, or planting.=20 This concept is a candidate for a MGED ontology/ controlled vocabulary. The value for age has three parts: a real number, a unit of time, and the time point from which measurement starts. A first draft is provided for terms that can be used for the point in time from which measurement starts. 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. Growth conditions: The parameters critical to reproduction of the experiment relating to nutrients provided to the organism as well as the environmental conditions the organism was exposed to. This may also be regarded as a =93treatment=94 (see below). Developmental stage: The developmental stage of the organism's life cycle during which the biomaterial was extracted.=20 Organism part: The part of the organism's anatomy from which the biomaterial was derived.=20 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.=20 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.=20 Individual: Identifier or name of the individual organism from which the biomaterial was derived.=20 Individual genetic characteristics: The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes.=20 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.=20 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.=20 Cell line: The identifier for the immortalized cell line if one was used to derive the biomaterial.=20 Treatment: Action taken on sample, order in which it was taken, and object (if any) added to (or taken away) from sample. The object may be a compound (see below). The treatment is considered =93in vivo=94 if = it occurs within the (living) organism. The treatment is considered =93in vitro=94 if applied to a part of the organism that has been removed. Compound: The (bio)chemical object added to the sample during treatment. The compound may be a drug, metabolite, or toxin. Clinical Information: Clinical records available in a separate file that can be accessed to obtain details of a patient=92s history.=20 Separation technique: The protocol used to isolate (enrich for) the targeted cell type of the organism. Separation is considered a treatment (see above). Chris Stoeckert, Ph.D. Research Associate Professor, Dept. of Genetics Center for Bioinformatics, University of Pennsylvania 418 Guardian Dr., Philadelphia, PA 19104 Ph:215-573-4409 FAX:215-573-3111 - --Apple-Mail-594816237-3-- ------------------------------ End of microarray-ontol-digest V1 #8 ************************************