microarray-ontol-digest Monday, July 30 2001 Volume 01 : Number 009 ---------------------------------------------------------------------- Date: Mon, 9 Jul 2001 10:54:02 -0400 From: Chris Stoeckert Subject: [microarray-ontol] Treatment concepts Dear Group, Another request. I'm trying to generate an ontology to cover general (non-species dependent) aspects of sample (biomaterial) descriptions starting with treatments and growth conditions. Below is a list of concepts that I will try to define and relate. (Haven't settled on how but am investigating Description Logics - see Baker et al Bioinformatics 15:510-520, 1999, An ontology for bioinformatics applications). My request is that you let me know if you think that this is a good start and make suggestions for extending or improving the list. That is, does the list have a field for everything that is important to you for describing how the sample was prepared? Are these clear? I hope this request does better than my last one for example sample descriptions - only one response and I still haven't seen any new examples! Thanks, Chris Biomaterial: The source of the nucleic acid used to generate labelled material for the microarray experiment. Organism: The source of the biomaterial. Biomaterial preparation: A description of the state and condition of the biomaterial. Time of day when the biomaterial was generated (i.e., sampled). Pathological staging: pre or post mortem at sampling state at start of treatment (age, time of day) physio-chemical composition of the sample: amount of material, number of cells, purity protocol: method used. Environmental history: A description of the conditions the organism has been exposed to that are not one of the variables under study. culture conditions: A description of the isolated environment used to grow organisms or parts of the organism. atmosphere: The gases and their concentrations used during culture. temperature: The temperature during culture. light: The photoperiod and type (e.g., natural, restricted wavelength) of light exposure. nutrients: The food provided to the organism (e.g., chow, fertilizer, DEMM 10%FBS, etc.). medium: The physical state or matrix used to provide nutrients to the organism (e.g., liquid, agar, soil) density range: The concentration range of the organism. contaminant organisms: Organisms present that were not planned as part of the study (e.g., mycoplasma). removal of contaminants: Steps taken to eliminate contaminant organisms. host organism or organism parts: Organisms or organism parts used as a designed part of the culture (e.g., red blood cells, stromal cells). generations: The number of cell divisions if the organism or organism part that is cultured is unicellular otherwise the number of breedings. clinical history: The organism's (i.e., the patient's) medical record. family history: Relevant aspects of genetic preconditions or family members clinical history water: additives and treatments bedding barrier facility pathogen test results: both positive and negative. preservation: seed dormancy, frozen storage Treatment: The manipulation of the biomaterial for the purposes of generating one of the variables under study. surgical modification: The organism has had parts removed, added, or rearranged. genetic modification: The organism has had genes removed, added, or rearranged. starvation: The organism (or organism part) has been deprived of nutrients. infection: The organism (or organism part) has been exposed to a virus or pathogen. behavioral stimulus: The organism is forced to respond to a stimulus with some behavior (e.g., avoidance, obtaining a reward, etc.) agent-based treatment: The treatment is effected by a defined chemical, biological, or physical agent. agent type: chemical (drugs), biological (macromolecule), physical (stress from light, temperature, etc.) agent application in vivo, in vitro, in situ qualitative or quantitative treatment protocol: method of treatment treatment parameters: constant, variable treatment duration: length of treatment ------------------------------ Date: Mon, 16 Jul 2001 17:53:21 -0400 From: Chris Stoeckert Subject: [microarray-ontol] correct URL for home page Dear Group, There was a typo in the URL I included in my request for sample descriptions. It should be: http://www.cbil.upenn.edu/Ontology/MGED_ontology.html I had capitalized the second instance of ontology by mistake before. Sorry. Note that http://www.cbil.upenn.edu/Ontology/ will also work. I have gotten a few responses and am trying to go over them before the BioOntologies meeting next Thursday. I will post a summary of my talk and incorporate these new submissions when I return. I'm still open to more submissions! either for sample descriptions or for comments on treatments. see http://bfx.kribb.re.kr/microarray/ for previous mails from the ontology list as well as the other MGED working groups. Chris 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 ------------------------------ Date: Mon, 30 Jul 2001 12:14:54 -0400 From: Chris Stoeckert Subject: [microarray-ontol] Update on Bio-Ontologies meeting Dear Group, I gave a talk at the Bio-ontologies workshop following ISMB 01 last Thursday in Copenhagen and have posted the slides on our web page. I think the talk served its purpose of alerting people in the bio-ontologies community as to who we are and what we are trying to do. The workshop itself was useful in seeing what issues were on people's minds. Afterwards, we had an Ontology Working Group meeting. Attending were: Cathy Ball, Stanford Gail Binkley, Stanford Alvis Brazma, EBI Richard Bruskiewich, IRRI Graham Kemp, U Aberdeen Martin Ringwald, Jackson Labs Steffen Schulze-Kremer, RZPD Chris Stoeckert, U Penn Peter Van Heusden, Electric Genetics The discussion primarily focussed on how to take the concepts and definitions that have been gathered so far and turn them into an ontology with the goal of generating a first pass ontology of sample (biosource/biomaterial) descriptions by the upcoming MGED 4 meeting in February. We all agreed that while an ontology covering all aspects of a microarray experiment was desireable, we would continue our focus on sample descriptions. Furthermore, we would also continue to collect controlled vocabularies and ontologies for concepts such as developmental stage, organism part, and disease state which are highly species dependent. Instead, we will generate ontologies for concepts which are common to all (microarray) experiments such as environmental conditions and treatment. There are various tools with varying degrees of expressivity and error checking. These include using the Gene Ontology editor, a UML modelling tool, and GKB (generic knowledge base) editor. Description Logic and deductive database approaches are also possibilities. A common ontology language DAML-OIL is being developed by the Bio-Ontologies consortium. Rather than choose one approach, we decided to start with a common set of concepts and definitions that we would try to structure and extend in our ontology editor of choice. We will compare notes on how well and how far we each get before November 8 so that I can present our findings to the MGED steering committee and decide whether there is a clear winner or if further parallel development is warranted. This assessment will be made by seeing which support the various use cases and associated scenarios that the OWG group will be asked to generate. I will follow this mail up with the common concepts and pointers to various ontology tools and encourage others to join this effort. Several of you have sent responses to requests for example annotations using the listed MGED concepts. Thanks again as these have been useful in identifying the various types of information we need to cover. Cheers, Chris ------------------------------ End of microarray-ontol-digest V1 #9 ************************************