microarray-ontol-digest Sunday, May 19 2002 Volume 01 : Number 024 ---------------------------------------------------------------------- Date: Thu, 25 Apr 2002 06:48:28 -0400 From: Bruce Aronow Subject: Re: [microarray-ontol] Audit and Security; Re: Contact classques tion Hi gang I feel in agreement with everybody including Jas.. must be one of those days. As Jason described--the upload, annotation, analyze, and download functions-- all seem like read/write control and group membership functions. Let me lay out an amusing use case.. I belong to two multi-institute consortiums Both groups have overlapping and distinct array series in multiple experiment series that differing groups of us are analyzing for some overlapping and some distinct purposes. Some of the arrays are on one platform made in one place, some on another made elsewhere, but they have been normalized quantitatively and at the level of gene annotations to work with each other. Biomaterials from multiple labs are spread over the different multicenter experiments. Seems to me that if each packageable object has sufficiently granular group affiliations with parent child histories and read/write privileges, we could accommodate all sorts of over-committed investigators. An individual should be able to be listed as a member of any number of variously permissioned groups. Does this fit? best, Bruce Aronow "Miller, Michael (Rosetta)" wrote: > > Tim, > > Thanks again for your input. > > In thinking about this a little more, I think I'm in agreement that a person > should be able to belong to more than one organization. The reason is that > in thinking about Jason's solution, having multiple entries for a person, > how would you form a meaningful identifier for the same person multiple > times? One could include the organization's identifier to the person's > identifier but that begs the question, I think that is just making the > association n:n without creating the association table. > > Michael > > > -----Original Message----- > > From: Tim Eyres [mailto:Tim.Eyres@genedata.com] > > Sent: Tuesday, April 23, 2002 11:57 PM > > Cc: mged-mage@lists.sourceforge.net; microarray-ontol@ebi.ac.uk > > Subject: Re: [microarray-ontol] Audit and Security; Re: Contact class > > question > > > > > > "Tim Eyres" writes: > > > > > My question is how does one record the organisation to which a > > > person is connected? This can be important if the contact person is > > > no longer available for some reason. For example if the person > > > leaves the organisation and the contact information is not updated > > > then when trying to track down a new contact person could be > > > difficult if one does not know the department/organisation to which > > > the person belonged. > > > > Thanks a lot for the feedback on my question. It's good to > > know that this has > > been thought about and that we are not going down the wrong track. > > > > John Matese wrote: > > > > > > From the model's suggested AuditAndSecurity package(pg30 > > of RFP), it > > > appears that any one individual can affiliate with only one > > > organization. The self-describing nature of organization allows a > > > person to belong to a lab, within a department, within a university. > > > But this doesn't seem to allow a person to be associated with two > > > separate labs or institutions. Is this accurate? > > > > I think this the ability to associate a person with one or > > more organizations is > > quite an important thing to have, but not critical. In our > > model we state that a > > person can be a member of one or more organizations, and an > > organization can > > have one or more members. I think this is quite important to > > be future proof. > > > > When it comes to implementing an organizational model in a > > real application I > > feel a fully extendable hierarchical organization structure > > may be overkill. One > > only needs a contact information, not to have a full > > organagram. Keeping a full > > description up to date could be tricky, especially for > > external contacts. A > > couple of reference points, person, department and > > organization could be > > sufficient. What ever you like I guess. > > > > Tim > > ------------------------------ Date: Thu, 25 Apr 2002 08:24:52 -0700 From: "Miller, Michael (Rosetta)" Subject: [microarray-ontol] Re: Contact class question Hi Willy, Who has read and/or write permissions is entirely up to the organization/consortium or a designated contact to decide. A MAGE document only records the information, it doesn't enforce it. Michael > -----Original Message----- > From: willy.valdivia@ndsu.nodak.edu > [mailto:willy.valdivia@ndsu.nodak.edu] > Sent: Thursday, April 25, 2002 6:31 AM > To: mged-mage@lists.sourceforge.net; microarray-ontol@ebi.ac.uk > Subject: [Mged-mage] Re: [microarray-ontol] Audit and Security; Re: > Contact classques tion > > > Hello > > I been following the discussion about this issue, although I might > missed something. Is everyone belonging to a consortium capable to > read/write? If that case is affirmative how we ensure that > the data is > properly annotated? What happen in case of errors and > modifications? I > have an example: Do you think that would be necessary curators which > receive the data, verify it and write? > > Thanks > > Willy Valdivia > > > ------------------------------ Date: Thu, 25 Apr 2002 15:20:05 -0400 From: Chris Stoeckert Subject: Re: [microarray-ontol] definitions Andy, >> allele: One of two or more alternative forms of a gene and differing >> from other alleles of the gene at one or more mutational sites. A >> mutational site is any position (nucleotide) along a gene (or >> chromosome) at which mutations can occur. > > Don't like the word gene. Alleles occur at all sorts of locations in the > genome. In many species markers with recorded alleles exist and no-one > has > any idea if they sit within exons, introns or inter-genic regions. The > word > 'gene' carries all sorts of baggage that I don't think will help in > interpreting the kind of data that you want to capture. It's easy to say > that people will "know" what is meant, but I don't like to make that > assumption. I agree that I erred in omitting markers used to follow recombination. Classically alleles were distinguished by phenotype but now it's mostly by molecular probes. This definition differs from polymorphism because the underlying distinguishing mutation may not be known in alleles. Indeed the gene itself may not be known at the sequence level. However, in modern usage, allelic variants includes microsatellites not associated with any gene. Thus, I propose that we use allele to cover both the classic genetic definition as well as the molecular genetic definition. allele: One of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on phenotype or sequence. Polymorphisms are included in this definition of allele. >> Genotype: The total sum of the genetic information of an organism. >> > > "Total"? Is that what we are describing? I think not. (see example > below) How is this? Genotype: The total sum of the genetic information of an organism that is known and relevant to the experiment being performed. >> Haplotype: The genotype of a single chromosome (i.e. the haploid >> genotype). > > The whole chromosome? Likewise: Haplotype: The genotype of a single chromosome (i.e. the haploid genotype) that is known and relevant to the experiment being performed. > >> >> Polymorphism: The regular and simultaneous occurrence in the same >> population >> of two or more discontinuous variants or genotypes. Polymorphism information should be put in alleles. I propose eliminating the polymorphism subclass. Thoughts? Cheers, Chris ------------------------------ Date: Sun, 28 Apr 2002 15:18:22 -0400 From: Chris Stoeckert Subject: [microarray-ontol] new version of MGED ontology Dear Group, I have posted a new version (1.4) of the MGED ontology (http://www.cbil.upenn.edu/Ontology/biomaterial14.html). As indicated on our home page, the new version was made using the OILed v3.4 and so it looks a little different (more color!). Also note that the DAML and RDFS files are available from the namespace links. The files at MGED.sourceforge.net are from version 1.2. Maybe one day Jason will help me figure out how to log on to the CVS site and I'll update those ;-) The changes include: 1. adding instances for DiseaseState (GALEN, ICD-9-CM, MESH, MouseTumorBiology, NTPCodeTables, RENI, SNOMED, UMLS) and ClinicalInformation (LOINC). 2. changing CultureCondition to GrowthCondition and making it a subclass of Treatment. This is because protocols are used (as mentioned in previous mails) and these conditions are part of the experimental treatment. 3. adding definitions for allele, genotype, and haplotype (making polymorphism part of allele). Didn't get any negative response to my last proposal so put them in. As with any part of the ontology, these can be changed if needed. 4. adding a top class, MGEDontology, that has the property of ID. This is to give identifiers to objects in our ontology. Cheers, Chris ------------------------------ Date: Sun, 28 Apr 2002 15:26:40 -0400 From: Chris Stoeckert Subject: [microarray-ontol] another change to the MGED ontology that I forgot to mention. Organization now has the property "has_parent_organization" which points back to itself. This is in response to Tim's inquiry and matching MAGE. Chris ------------------------------ Date: Mon, 29 Apr 08:55:40 2002 -0400 From: "Seetharamulu Peddaiahgari" Subject: [microarray-ontol] unsubscibe seetha@origenix.com unsubscibe seetha@origenix.com ------------------------------ Date: Sun, 19 May 2002 09:02:27 -0400 From: Chris Stoeckert Subject: [microarray-ontol] proposed ontology classes Dear Group, Below is a proposal for classes to add to the ontology addressing experimental design. These represent an important type of annotation typically entered through forms as with biomaterial descriptions. These classes are based on: 1. MIAME 1.1 and MAGE Jan 2002 Gene Expression RFP document by Michael Miller (see pages 72-75). 2. Helen Parkinson's initial expfactor ontology 3. comments from John Potter (Fred Hutchinson Cancer Research Center) at Oncogenomics 2002 regarding the distinction between factors that are controlled during an experiment and factors which are observed or measured during a survey. Please note that this is just a start. I will add these to the ontology next weekend following any discussion. Cheers, Chris New proposed classes for describing the experiment/study (subclasses are indented): Study StudyDesign ReplicateDesign NormalizationDesign QualityControlDesign StudyFactor HistoryFactor BiologicalFactor GeneticVariationFactor StressFactor TemperatureFactor TimeCourseFactor MethodologicalFactor HardwareVariation SoftwareVariation ProtocolVariation ### Study Definition: The complete set of assays and their descriptions performed as a study for a common purpose. In general, a study will be equivalent to a publication and have a single submitter. (associations to analysis results, assays, and data will be added later). Properties: has_submitter (Contact) has_publication (BibliographicReference) has_URI (URI) has_study_design(StudyDesign) number_of_assays ### StudyDesign Definition: The organizing principles of the study including the relationships between assays and steps taken to interpret the data. Used to organize the assays into groups. Subclasses: ReplicateDesign, NormalizationDesign, QualityControlDesign Properties: study_group_id has_study_factor(StudyFactor) has_description has_study_type(one of: normal vs diseased, treated vs unstreated, time course, tiling) ### ReplicateDesign Definition: Groups of assays that represent replicates Properties: replicate_type (one_of: technical, biological) ### NormalizationDesign Definition: Groups of assays whose data have been processed to be directly comparable Properties: normalization_type (one-of: global lowess, print-tip global lowess, linrear regression) ### QualityControlDesign Definition: Groups of assays that are related as part of quality control. Properties: control_type (one-of: dye-swap, common reference) ### StudyFactor Definition: The factors in the study that are experimental parameters or regarded as influencing the study results. Factor group ID will be used to link assays to the factors associated with them. Sublcasses: BiologicalFactor, MethodologicalFactor Properties: has_factor_value (Measurement) factor_group_id ### HistoryFactor Definition: Factors that are measured or observed parts of the study but not induced or under the control of the experiment. Properties: has_environmental_history(EnvironmentalHistory) ### BiologicalFactor Definition: Factors that are varied that are not methodological, so things that relate to the biomaterial and its treatment and growth. Subclasses: GeneticVariationFactor, StressFactor, TemperatureFactor, TimeCourseFactor Properties: has_treatment(Treatment) ### MethodologicalFactor Definition: Methodological variations. Not things that relate to the biomaterial but things that are expressed as protocols for example. Only needed if relevant for experimental design. So if the point of the experiment was to compare data across two different scanners, array designs, or between teo (or more) different hybridization chambers then these should be expressed as experimental factors (MAGE terms) and can be given factor values. These should be expressed as instances in this ontology so the name of a hybridization chamber could be an instance here. Subclasses: HardwareVariation, SoftwareVariation, ProtocolVariation ### GeneticVariationFactor Definition: Describes genetically modified organisms. Does not refer to natural genetic variation ### StressFactor Definition: Degree of stress induced. ### TemperatureFactor Definition: Temperature is varied. ### TimeCourseFactor Definition: Time course refers to an experiment which has multiple time points. Cell cycle is an instance of time course. ### HardwareVariation Definition: Hardware variations that are part of experiment design. Properties: has_hardware(Hardware) ### SoftwareVariation Definition: Software variations that are part of experiment design. Properties: has_software(Software) ### ProtocolVariation Definition: Protocol variations that are part of experiment design. Properties: has_protocol(Protocol) ------------------------------ End of microarray-ontol-digest V1 #24 *************************************