microarray-ontol-digest Thursday, April 25 2002 Volume 01 : Number 023 ---------------------------------------------------------------------- Date: Sun, 14 Apr 22:51:35 2002 -0400 From: "Seetharamulu Peddaiahgari" Subject: [microarray-ontol] unsubscribe unsubscribe seetha@origenix.com on microarrays ------------------------------ Date: Mon, 15 Apr 2002 09:58:30 +0200 From: "Paola Scaruffi" Subject: [microarray-ontol] unsubscribe unsubscribe scaruffi@cba.unige.it on microarrays ------------------------------ Date: Fri, 19 Apr 2002 13:45:22 -0400 From: Chris Stoeckert Subject: [microarray-ontol] interesting article Dear Group, I learned of the "standard-upper-ontology" mail list from a posting today to the gene ontology "gofriends" list. At suo I found an interesting article (http://www.cnn.com/2002/TECH/industry/04/11/memome.project.idg/index.html) and discussion (http://suo.ieee.org/email/msg08310.html) about Cyc. Thought you might find this interesting as well. BTW. I've gotten some more resources from Helen Parkinson and Susanna Sansone and will add them to the list this weekend. Cheers, Chris ------------------------------ Date: Fri, 19 Apr 2002 13:24:52 -0500 From: "Jason S. Ellis" Subject: [microarray-ontol] unsubscribe This is a multi-part message in MIME format. - ------=_NextPart_000_0032_01C1E7A5.968FA160 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable - ------=_NextPart_000_0032_01C1E7A5.968FA160 Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable

- ------=_NextPart_000_0032_01C1E7A5.968FA160-- ------------------------------ Date: Mon, 22 Apr 2002 14:16:53 -0400 From: Chris Stoeckert Subject: [microarray-ontol] follow-up to OILed 3.4 Dear Group, In an earlier mail, I wrote about my first try at OILed 3.4: > Anyway this seems to work. I opened up a RDFS file and a DAML file made > with 2.2a. > The DAML file duplicated all the classes - one was simply the class > name and the other was the class name preceeded by a full directory > path! Only the latter had attributes (now called properties instead of > slots). The RDFS file did not duplicate the classes but also did not > have attributes. > > Will continue to play with this and let you know how it goes. Please > share your thoughts and experiences if you use it. In the accompanying README.txt, I found: > Compatability with earlier releases > =================================== > > Some DAML+OIL RDFS models produced using earlier version of OilEd may > not be read properly and may cause warning and/or error messages > during parsing. If you find this happening, one possible solution to > this is to change the rdf:ID attributes in the model to > rdf:about. This will often fix the problem. It did. Cheers, Chris ------------------------------ Date: Mon, 22 Apr 2002 17:22:40 -0400 From: Chris Stoeckert Subject: [microarray-ontol] definitions Dear Group, The subclasses to IndividualGeneticCharacteristics need definitions. Here's a first go. Allele: A variant of a gene or genetic locus that occurs at the nucleotide level. Genotype: The allelic composition of a genetic locus or set of loci for all copies of a chromosome. Haplotype: The genotype of a single chromosome (i.e. the haploid genotype). Polymorphism: A sequence variation that is found in a population. I was going to use an on-line dictionary but the terms of use put me off. Let's do our own which has no restrictions! Chris ------------------------------ Date: Tue, 23 Apr 2002 08:44:58 +0100 From: Michael Ashburner (Genetics) Subject: Re: [microarray-ontol] definitions By far the most authorative dictionary of genetics is that by Rieger, Michaelis and Green. From this, with some alterations: allele - has nothing whatsover to do with nucleotides: Allele: One of two or more alternative forms of a gene occupying the same locus. Genotype: The total sum of the genetic information of an organism. Polymorphism: The regular and simultaneous occurrence in the same population of two or more discontinuous variants or genotypes. Michael > From owner-microarray-ontol@ebi.ac.uk Mon Apr 22 22:24:16 2002 > Envelope-to: ma11@gen.cam.ac.uk > Delivery-date: Mon, 22 Apr 2002 22:24:16 +0100 > X-Authentication-Warning: alpha1.ebi.ac.uk: majordom set sender to owner-microarray-ontol@alpha1.ebi.ac.uk using -f > Date: Mon, 22 Apr 2002 17:22:40 -0400 > Mime-Version: 1.0 (Apple Message framework v481) > Subject: [microarray-ontol] definitions > From: Chris Stoeckert > To: microarray-ontol@ebi.ac.uk > Content-Transfer-Encoding: 7bit > X-Mailer: Apple Mail (2.481) > Sender: owner-microarray-ontol@ebi.ac.uk > > Dear Group, > The subclasses to IndividualGeneticCharacteristics need definitions. > > Here's a first go. > Allele: A variant of a gene or genetic locus that occurs at the > nucleotide level. > > Genotype: The allelic composition of a genetic locus or set of loci for > all copies of a chromosome. > > Haplotype: The genotype of a single chromosome (i.e. the haploid > genotype). > > Polymorphism: A sequence variation that is found in a population. > > I was going to use an on-line dictionary but the terms of use put me > off. Let's do our own which has no restrictions! > > Chris > > ------------------------------ Date: Tue, 23 Apr 2002 16:34:39 +0100 From: "andy law (RI)" Subject: RE: [microarray-ontol] definitions All, Ahaa! Semantics. My favourite! We have periodical discussions/battles/religious wars at Roslin over the definition of these and some related terms. For the record, what are we trying to capture in *these* definitions, as I'm not clear where haplotype might come in to the equation or the relevance of some of the detail of my personal interpretations of these terms? Personally, I like the Rieger,Michaelis & Green (via Ashburner) definitions up to a point. I have a problem with the word 'locus' (although that may be irrelevant in this context). In my mind, a locus is an open-ended structure. It could be a single nucleotide or it could be a whole chromosomal region. The things that have 'alleles' that can be detected by some kind of assay method I prefer to call 'markers'. A 'marker' IS a 'locus'. A 'locus' IS NOT NECESSARILY a 'marker' (it may contain zero or more 'markers'). A 'locus' need not have any 'polymorphisms' which are the basis of 'alleles'. 'Alleles' and hence 'markers' and therefore 'loci' need not be in 'genes'. 'Genotype' refers to the sum total of 'alleles' within an individual for one or more 'markers'. Thus an individual's 'genotype' is of variable size in the same way that a 'locus' can be of variable size. As always, your mileage may vary. I look forward to a useful (and probably ultimately brutal and possibly bloody) debate :o} Later, Andy Dr. Andy Law - -------------------- Head of Bioinformatics - Roslin Institute > -----Original Message----- > From: Michael Ashburner [mailto:ma11@gen.cam.ac.uk] > Sent: 23 April 2002 08:45 > To: microarray-ontol@ebi.ac.uk; stoeckrt@snowball.pcbi.upenn.edu > Subject: Re: [microarray-ontol] definitions > > > By far the most authorative dictionary of genetics is that by > Rieger, Michaelis > and Green. From this, with some alterations: > > allele - has nothing whatsover to do with nucleotides: > Allele: One of two or more alternative forms of a gene > occupying the same > locus. > > Genotype: The total sum of the genetic information of an organism. > > Polymorphism: The regular and simultaneous occurrence in the > same population > of two or more discontinuous variants or genotypes. > > Michael > > > > From owner-microarray-ontol@ebi.ac.uk Mon Apr 22 22:24:16 2002 > > Envelope-to: ma11@gen.cam.ac.uk > > Delivery-date: Mon, 22 Apr 2002 22:24:16 +0100 > > X-Authentication-Warning: alpha1.ebi.ac.uk: majordom set > sender to owner-microarray-ontol@alpha1.ebi.ac.uk using -f > > Date: Mon, 22 Apr 2002 17:22:40 -0400 > > Mime-Version: 1.0 (Apple Message framework v481) > > Subject: [microarray-ontol] definitions > > From: Chris Stoeckert > > To: microarray-ontol@ebi.ac.uk > > Content-Transfer-Encoding: 7bit > > X-Mailer: Apple Mail (2.481) > > Sender: owner-microarray-ontol@ebi.ac.uk > > > > Dear Group, > > The subclasses to IndividualGeneticCharacteristics need definitions. > > > > Here's a first go. > > Allele: A variant of a gene or genetic locus that occurs at the > > nucleotide level. > > > > Genotype: The allelic composition of a genetic locus or set > of loci for > > all copies of a chromosome. > > > > Haplotype: The genotype of a single chromosome (i.e. the haploid > > genotype). > > > > Polymorphism: A sequence variation that is found in a population. > > > > I was going to use an on-line dictionary but the terms of > use put me > > off. Let's do our own which has no restrictions! > > > > Chris > > > > > ------------------------------ Date: Tue, 23 Apr 2002 18:01:25 +0200 From: Tim Eyres Subject: [microarray-ontol] Contact class question Hi all I have a question that has been concerning me for some time. We have been looking at how to record who is the contact person for a given biomaterial. I note that within the microarray ontology we have a contact class with two sub-classes of Organization and Person. If I interpret this correctly this means that a contact can be either a company or a person, but not both. 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. Are my interpretations of the ontology correct? Is there a solution to this problem that I have missed up to now? Thanks Tim Eyres ------------------------------ Date: 23 Apr 2002 11:29:47 -0600 From: jason@openinformatics.com (Jason E. Stewart) Subject: Re: [microarray-ontol] 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. I don't know how well the ontology has kept up with the MAGE model, but in MAGE a Person has an 'affiliation' which is an Organization. Also Organizations can be hierarchical - they have a 'parentOrganization' attribute so that you can describe someone in a lab, in a department, in a college at a university. jas. ------------------------------ Date: Tue, 23 Apr 2002 15:07:49 -0400 From: Chris Stoeckert Subject: Re: [microarray-ontol] Contact class question On Tuesday, April 23, 2002, at 01:29 PM, Jason E. Stewart wrote: > "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. > > I don't know how well the ontology has kept up with the MAGE model, > but in MAGE a Person has an 'affiliation' which is an > Organization. This is true of the MGED ontology. See http://www.cbil.upenn.edu/Ontology/biomaterial13.html#Person > Also Organizations can be hierarchical - they have a > 'parentOrganization' attribute so that you can describe someone in a > lab, in a department, in a college at a university. We have not added this attribute to Organization. I can add it to the next version. Chris ------------------------------ Date: Tue, 23 Apr 2002 12:09:43 -0700 From: John Matese Subject: [microarray-ontol] Audit and Security; Re: Contact class question At 11:29 AM -0600 4/23/02, Jason E. Stewart wrote: >"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. > >I don't know how well the ontology has kept up with the MAGE model, >but in MAGE a Person has an 'affiliation' which is an >Organization. Also Organizations can be hierarchical - they have a >'parentOrganization' attribute so that you can describe someone in a >lab, in a department, in a college at a university. > >jas. Hi all, Thanks for your answers to previous questions... 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? For example, a user could be a member of 3 organizations (say, the Brown lab, the Botstein lab and the "Mouse Consortium") . Two of these are child-organizations of Stanford, and the last could be a multi-institution organization (multiple parents). These groups may share a few persons, but are for the most part distinct. What do you do with the person who has their fingers in many projects (i.e. organizations)? According to the model, a person can only be affiliated with one organization (along with its parent super-organizations). And organizations are also single parented (preventing a multi-university consortium, like the Arabidopsis Functional Genomics Consortium (AFGC)) [Note: many would argue (myself among them) that consortiums should be the top-most organization, with no direct affiliations with multiple universities and that person *can't* be affiliated with multiple institutions. I just thought I would throw it out there as an example (however bad). I do think people can be affiliated with multiple labs, however.] Along similar lines, within security, only one owner is specified. How should we handle collaborations where several people share ownership. For example, one contact provided the precious biomaterial and a different contact performed the hybridization. Shared ownership of the resulting experimental data is desired. Granted, multiple read groups and write groups might compensate for this but we've had requests here for shared ownership off arrays (something we were planning on implementing here at SMD). As always, your thoughts are valued, John Matese SMD Curator and Software Developer jcmatese@genome.stanford.edu ------------------------------ Date: 23 Apr 2002 14:04:10 -0600 From: jason@openinformatics.com (Jason E. Stewart) Subject: [microarray-ontol] Re: [Mged-mage] Audit and Security; Re: Contact class question "John Matese" writes: > 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? Yes this is correct. > For example, a user could be a member of 3 organizations (say, the > Brown lab, the Botstein lab and the "Mouse Consortium") . Two of > these are child-organizations of Stanford, and the last could be a > multi-institution organization (multiple parents). These groups may > share a few persons, but are for the most part distinct. What do > you do with the person who has their fingers in many projects > (i.e. organizations)? According to the model, a person can only be > affiliated with one organization (along with its parent > super-organizations). And organizations are also single parented > (preventing a multi-university consortium, like the Arabidopsis > Functional Genomics Consortium (AFGC)) > > [Note: many would argue (myself among them) that consortiums should be > the top-most organization, with no direct affiliations with multiple > universities and that person *can't* be affiliated with multiple > institutions. I just thought I would throw it out there as an example > (however bad). I do think people can be affiliated with multiple > labs, however.] You (the organization that supplies data) has to create a policy that defines how you will use this information. If it becomes critical that some people belong to multiple organizations, fine, make multiple Person entries for the individual. But I really don't see the point. The idea behind the concept is to enable tracking of data - who changed what and when, who has privileges with the data and who doesn't. It is not meant as a Human Resources tracking DB. > Along similar lines, within security, only one owner is > specified. How should we handle collaborations where several people > share ownership. For example, one contact provided the precious > biomaterial and a different contact performed the > hybridization. Shared ownership of the resulting experimental data > is desired. Granted, multiple read groups and write groups might > compensate for this but we've had requests here for shared ownership > off arrays (something we were planning on implementing here at SMD). The concept of ownership in MAGE merely means who has permission to change the permissions, i.e. who can modify the read group or the write group. I developed this part of the model based on the GeneX security model, and it turns out that we decided to completely eliminate the concept of the 'owner' entirely. We felt that it was redundant with the function of the write group, and so we completely eliminated the Security object as well - now each object that has security has two groups: a read group and a write group, and the readers can view the data, and the writers can modify the data. It's much simpler that way. During the FTF process I'm want to incorporate this and other issues associated with Audit to better handle these important interfaces. jas. ------------------------------ Date: Tue, 23 Apr 2002 13:16:50 -0700 From: "Miller, Michael (Rosetta)" Subject: RE: [microarray-ontol] Re: [Mged-mage] Audit and Security; Re: Co ntact class question Hi Jason, > You (the organization that supplies data) has to create a policy that > defines how you will use this information. If it becomes critical that > some people belong to multiple organizations, fine, make multiple > Person entries for the individual. If it turns out this case is common, then I think we should reconsider. Otherwise I agree with you, but to denormalize data for a common case wouldn't be good. > The concept of ownership in MAGE merely means who has permission to > change the permissions, i.e. who can modify the read group or the > write group. I developed this part of the model based on the GeneX > security model, and it turns out that we decided to completely > eliminate the concept of the 'owner' entirely. We felt that it was > redundant with the function of the write group, and so we completely > eliminated the Security object as well - now each object that has > security has two groups: a read group and a write group, and the > readers can view the data, and the writers can modify the data. Owner is absolutely necessary for us, otherwise who decides who has write/read permissions for an experiment? This can be synonymous with the write group but quite often isn't. Michael > -----Original Message----- > From: jason@openinformatics.com [mailto:jason@openinformatics.com] > Sent: Tuesday, April 23, 2002 1:04 PM > To: John Matese > Cc: mged-mage@lists.sourceforge.net; microarray-ontol@ebi.ac.uk; Gail > Binkley > Subject: [microarray-ontol] Re: [Mged-mage] Audit and Security; Re: > Contact class question > > > "John Matese" writes: > ------------------------------ Date: 23 Apr 2002 15:04:25 -0600 From: jason@openinformatics.com (Jason E. Stewart) Subject: Re: [microarray-ontol] Re: [Mged-mage] Audit and Security; Re: Co ntact class question "Miller, Michael (Rosetta)" writes: > Owner is absolutely necessary for us, otherwise who decides who has > write/read permissions for an experiment? This can be synonymous > with the write group but quite often isn't. At one point in time, I agreed with you and thought owner was critical. But it started to become a silly 'exception to the rule'. All of our security checking looked at the write group to see if an action was allowed - *except* if the attributes being modified were the read_group or write_group then you look at the owner. It simplified things a lot just to allow anyone in the write_group to modify the data in any way. After all, if you trust them to modify the data, why not trust them to modify the priveleges? And after all, if a user modifies the priveleges in an unpopular way, you've got a DBA that can reverse it. jas. ------------------------------ Date: Tue, 23 Apr 2002 22:33:50 -0400 From: Chris Stoeckert Subject: Re: [microarray-ontol] definitions Andy raises the important point of clarifying what we are trying to capture. In my view, we are trying to capture details of an individual organisms genetic characteristics that are known and relevant to the microarray experiment. The current proposed definitions adapted in part from the fifth edition (1991) of Rieger, Michaelis, and Green are: 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. Genotype: The total sum of the genetic information of an organism. Haplotype: The genotype of a single chromosome (i.e. the haploid genotype). Polymorphism: The regular and simultaneous occurrence in the same population of two or more discontinuous variants or genotypes. An example where haplotype might be relevant are studies of patients with thalassemias or sickle cell anemia. I have been involved in a study where we are trying to understand the molecular basis for hereditary persistence of fetal hemoglobin in thalassemic patients using microarrays of cultured erythroblasts. Knowing the haplotype of the beta-globin gene cluster is useful in ruling out various possible contributors to this syndrome. Knowing the genotype of the alpha-globin cluster is also relevant as are any polymorphisms in the promoters or enhancers of the fetal globin genes. Cheers, Chris On Tuesday, April 23, 2002, at 11:34 AM, andy law (RI) wrote: > All, > > Ahaa! Semantics. My favourite! > > We have periodical discussions/battles/religious wars at Roslin over the > definition of these and some related terms. For the record, what are we > trying to capture in *these* definitions, as I'm not clear where > haplotype > might come in to the equation or the relevance of some of the detail of > my > personal interpretations of these terms? > > Personally, I like the Rieger,Michaelis & Green (via Ashburner) > definitions > up to a point. > > I have a problem with the word 'locus' (although that may be irrelevant > in > this context). In my mind, a locus is an open-ended structure. It could > be a > single nucleotide or it could be a whole chromosomal region. The things > that > have 'alleles' that can be detected by some kind of assay method I > prefer to > call 'markers'. A 'marker' IS a 'locus'. A 'locus' IS NOT NECESSARILY a > 'marker' (it may contain zero or more 'markers'). A 'locus' need not > have > any 'polymorphisms' which are the basis of 'alleles'. 'Alleles' and > hence > 'markers' and therefore 'loci' need not be in 'genes'. > > 'Genotype' refers to the sum total of 'alleles' within an individual > for one > or more 'markers'. Thus an individual's 'genotype' is of variable size > in > the same way that a 'locus' can be of variable size. > > As always, your mileage may vary. I look forward to a useful (and > probably > ultimately brutal and possibly bloody) debate > > :o} > > Later, > > Andy > > Dr. Andy Law > -------------------- > Head of Bioinformatics - Roslin Institute > > >> -----Original Message----- >> From: Michael Ashburner [mailto:ma11@gen.cam.ac.uk] >> Sent: 23 April 2002 08:45 >> To: microarray-ontol@ebi.ac.uk; stoeckrt@snowball.pcbi.upenn.edu >> Subject: Re: [microarray-ontol] definitions >> >> >> By far the most authorative dictionary of genetics is that by >> Rieger, Michaelis >> and Green. From this, with some alterations: >> >> allele - has nothing whatsover to do with nucleotides: >> Allele: One of two or more alternative forms of a gene >> occupying the same >> locus. >> >> Genotype: The total sum of the genetic information of an organism. >> >> Polymorphism: The regular and simultaneous occurrence in the >> same population >> of two or more discontinuous variants or genotypes. >> >> Michael >> >> >>> From owner-microarray-ontol@ebi.ac.uk Mon Apr 22 22:24:16 2002 >>> Envelope-to: ma11@gen.cam.ac.uk >>> Delivery-date: Mon, 22 Apr 2002 22:24:16 +0100 >>> X-Authentication-Warning: alpha1.ebi.ac.uk: majordom set >> sender to owner-microarray-ontol@alpha1.ebi.ac.uk using -f >>> Date: Mon, 22 Apr 2002 17:22:40 -0400 >>> Mime-Version: 1.0 (Apple Message framework v481) >>> Subject: [microarray-ontol] definitions >>> From: Chris Stoeckert >>> To: microarray-ontol@ebi.ac.uk >>> Content-Transfer-Encoding: 7bit >>> X-Mailer: Apple Mail (2.481) >>> Sender: owner-microarray-ontol@ebi.ac.uk >>> >>> Dear Group, >>> The subclasses to IndividualGeneticCharacteristics need definitions. >>> >>> Here's a first go. >>> Allele: A variant of a gene or genetic locus that occurs at the >>> nucleotide level. >>> >>> Genotype: The allelic composition of a genetic locus or set >> of loci for >>> all copies of a chromosome. >>> >>> Haplotype: The genotype of a single chromosome (i.e. the haploid >>> genotype). >>> >>> Polymorphism: A sequence variation that is found in a population. >>> >>> I was going to use an on-line dictionary but the terms of >> use put me >>> off. Let's do our own which has no restrictions! >>> >>> Chris >>> >>> >> > ------------------------------ Date: Wed, 24 Apr 2002 08:57:02 +0200 From: Tim Eyres 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: Wed, 24 Apr 2002 15:06:04 +0100 From: "andy law (RI)" Subject: RE: [microarray-ontol] definitions Chris, (All) > Andy raises the important point of clarifying what we are trying to > capture. In my view, we are trying to capture details of an > individual > organisms genetic characteristics that are known and relevant to the > microarray experiment. OK. That was my assumption. > > The current proposed definitions adapted in part from the > fifth edition > (1991) of Rieger, Michaelis, and Green are: > > 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. > > Genotype: The total sum of the genetic information of an organism. > "Total"? Is that what we are describing? I think not. (see example below) > Haplotype: The genotype of a single chromosome (i.e. the haploid > genotype). The whole chromosome? > > Polymorphism: The regular and simultaneous occurrence in the same > population > of two or more discontinuous variants or genotypes. > How does this differ from allele? > An example where haplotype might be relevant are studies of patients > with thalassemias or sickle cell anemia. I have been involved > in a study > where we are trying to understand the molecular basis for hereditary > persistence of fetal hemoglobin in thalassemic patients using > microarrays of cultured erythroblasts. Knowing the haplotype of the > beta-globin gene cluster is useful in ruling out various possible > contributors to this syndrome. Knowing the genotype of the > alpha-globin > cluster is also relevant as are any polymorphisms in the promoters or > enhancers of the fetal globin genes. Are the polymorphisms in the promoters not also alleles? How big is a gene. Which marker in that gene is the allele derived from? Let's assume that we are looking at a well-defined locus on a chromosome in an un-named species. The locus spans 3 genes, Gene A, Gene B and Gene C. There are 4 known, well-defined markers for Gene A, 1 for Gene B and 2 for Gene C. In addition, there is a microsatellite marker that lies midway between Gene B and Gene C. It is very unlikely that I will type all of the markers for Gene A. It is also unlikely that Lab B will use the same marker for Gene A that my lab has since they developed their marker independently and each lab has the system for typing up and running in their lab. Both are markers for the same gene, but they are not directly comparable. The distance between the outermost markers for Gene A make it well within the bounds of statistical possibility that a re-combination event will occur. What is the Genotype and Haplotype in this case? Can you define Genotype, Haplotype or locus without explicit reference to the actual *markers* used in the study? I would contend that you can't do so and therefore you need a concept of marker to be central to the definition of the other terms. Later, Andy ------------------------------ Date: Wed, 24 Apr 2002 20:05:51 +0530 From: Suraj Peri Subject: Fwd: RE: [microarray-ontol] definitions Hi group, using terms orthologs and paralogs is sometimes confusing. In this connection I have a question. Is it apt to say what is the number of ortholog genes found in humans or is it better to say what is the number of paralog genes found in humans? please excuse me if this not a good question. regards suraj. =========================================== Suraj Peri Center for Experimental Bioinformatics University of Southern Denmark Campusvej Odense DENMARK Ph:+45-6550-247 =========================================== ------------------------------ Date: Wed, 24 Apr 2002 15:39:22 +0100 From: Susanna Sansone Subject: Re: Fwd: RE: [microarray-ontol] definitions Surai, depend what you are trying to say here. Orthologous refers to genes in 'different species' that are so similar that one can assume have originated from a single ancestral gene. Paralogous refers to 2 o more different genes in the 'same species' that are so similar that one can say they have originated from a single ancestral gene. Susanna Suraj Peri wrote: > Hi group, > using terms orthologs and paralogs is sometimes confusing. > In this connection I have a question. Is it apt to say what is the > number of ortholog genes found in humans or is it better to say what > is the number of paralog genes found in humans? > please excuse me if this not a good question. > regards > suraj. > > =========================================== > Suraj Peri > Center for Experimental Bioinformatics > University of Southern Denmark > Campusvej > Odense DENMARK > Ph:+45-6550-247 > =========================================== > - -- ******************************* Susanna Assunta Sansone, PhD Microarray Informatics EBI - The European Bioinformatics Institute EMBL Outstation - Hinxton, Wellcome Trust Genome Campus Cambridge CB10 1SD, UK email: sansone@ebi.ac.uk direct: +44 (0)1223 494 691 fax: +44 (0)1223 494 468 http://www.ebi.ac.uk/microarray ******************************* ------------------------------ Date: Wed, 24 Apr 2002 07:46:11 -0700 From: "Miller, Michael (Rosetta)" Subject: RE: [microarray-ontol] Audit and Security; Re: Contact class ques tion 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: 24 Apr 2002 09:16:00 -0600 From: jason@openinformatics.com (Jason E. Stewart) Subject: Re: [microarray-ontol] Audit and Security; Re: Contact class question "Tim Eyres" writes: > 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. I have no issue with enable a Person to have a list of affiliations, but I'd like to make sure that I'm doing it for the correct reason. Correct me if I'm wrong but it sounds to me that what you're describing overlaps quite heavily with our notion of SecurityGroup's. Do you want people to be in multiple organizations in order to determine their access priveleges to information? or is it because you Our notion of Contact exists to describe enough information about who did something so that you can contact that person. To define access priveleges you would need to add that individual to different SecurityGroup's. > 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. Correct. I asked for the flexibility, not because I wanted people to implement their HR division using MAGE, but simply because I didn't want to add two or three or six attributes to Person that described what sub-organizations they belonged to. Some people felt that 'department' was needed, some wanted 'division', and some wanted 'lab'. This way the model is very simple, and you may define your organization at the granularity you choose. jas. ------------------------------ Date: Thu, 25 Apr 2002 09:44:55 +0200 From: Tim Eyres Subject: Re: [microarray-ontol] Audit and Security; Re: Contact class question "Jason E. Stewart" wrote: > > I have no issue with enable a Person to have a list of affiliations, > but I'd like to make sure that I'm doing it for the correct reason. > > Correct me if I'm wrong but it sounds to me that what you're > describing overlaps quite heavily with our notion of > SecurityGroup's. Do you want people to be in multiple organizations in > order to determine their access priveleges to information? or is it > because you > > Our notion of Contact exists to describe enough information about who > did something so that you can contact that person. > > To define access priveleges you would need to add that individual to > different SecurityGroup's. The issues of privileges are a outside of my realm with regards to MAGE, so I don't want to comment to much on this, but I would say the the intention of the contact information should be, as you said, "to describe enough information about who did something so that you can contact that person." They are not for security privileges which is indeed another area. As a person can be connected to several organizations this knowledge could be important to re-establish contact if contact is lost. > Correct. I asked for the flexibility, not because I wanted people to > implement their HR division using MAGE, but simply because I didn't > want to add two or three or six attributes to Person that described > what sub-organizations they belonged to. Some people felt that > 'department' was needed, some wanted 'division', and some wanted > 'lab'. > > This way the model is very simple, and you may define your > organization at the granularity you choose. This is very good. Thanks Tim ------------------------------ End of microarray-ontol-digest V1 #23 *************************************